View source for Infection

{{Short description|Invasion of an organism's body by pathogenic agents}}
{{Other uses}}
{{Redirect|Infectious disease|the medical specialty|Infectious diseases (medical specialty)|the journal|Infectious Diseases (journal){{!}}''Infectious Disease'' (journal)}}
{{cs1 config|name-list-style=vanc}}
{{Infobox medical condition
 | name = Infection
 | image = Cutaneous abscess MRSA staphylococcus aureus 7826 lores.jpg
 | caption = [[Pus]] oozing from an [[abscess]] caused by [[bacteria]]
 | field = [[Infectious diseases (medical specialty)|Infectious diseases]]
| symptoms        =
| complications   =
| onset           =
| duration        =
| types           =
| causes          = [[pathogenic bacteria|Bacterial]], [[viral disease|viral]], [[parasitic disease|parasitic]], [[mycosis|fungal]], [[prion]]
| risks           =
| diagnosis       =
| differential    =
| prevention      =
| treatment       =
| medication      =
| prognosis       =
| frequency       =
| deaths          =
}}

<span lang="ml" dir="ltr">An</span> '''infection''' is the invasion of [[tissue (biology)|tissues]] by [[pathogen]]s, their multiplication, and the reaction of [[host (biology)|host]] tissues to the infectious agent and the [[toxin]]s they produce.<ref>{{Citation |title=infection |url=https://medical-dictionary.thefreedictionary.com/infection |work=The Free Dictionary |access-date=2023-11-17 |archive-date=2018-07-19 |archive-url=https://web.archive.org/web/20180719174225/https://medical-dictionary.thefreedictionary.com/infection |url-status=live }}</ref> An '''infectious disease''', also known as a '''transmissible disease''' or '''communicable disease''', is an [[Disease#Terminology|illness]] resulting from an infection.

Infections can be caused by a wide range of [[pathogen]]s, most prominently [[pathogenic bacteria|bacteria]] and [[virus]]es.<ref>{{Cite journal|last1=Sehgal|first1=Mukul|last2=Ladd|first2=Hugh J.|last3=Totapally|first3=Balagangadhar|date=2020-12-01|title=Trends in Epidemiology and Microbiology of Severe Sepsis and Septic Shock in Children|url=https://hosppeds.aappublications.org/content/10/12/1021|journal=Hospital Pediatrics|language=en|volume=10|issue=12|pages=1021–1030|doi=10.1542/hpeds.2020-0174|issn=2154-1663|pmid=33208389|s2cid=227067133|doi-access=free|access-date=2021-03-26|archive-date=2021-04-13|archive-url=https://web.archive.org/web/20210413210453/https://hosppeds.aappublications.org/content/10/12/1021|url-status=live|url-access=subscription}}</ref> Hosts can fight infections using their [[immune system]]s. [[Mammal]]ian hosts react to infections with an [[Innate immune system|innate]] response, often involving [[inflammation]], followed by an [[Adaptive immune system|adaptive]] response.

Treatment for infections depends on the type of pathogen involved. Common medications include:

* Antibiotics for bacterial infections.
* Antivirals for viral infections.
* Antifungals for fungal infections.
* Antiprotozoals for protozoan infections.
* Antihelminthics for infections caused by parasitic worms.

Infectious diseases remain a significant global health concern, causing approximately 9.2 million deaths in 2013 (17% of all deaths).<ref>{{Cite web |title=Antiprotozoal Drugs |url=https://medical-dictionary.thefreedictionary.com/Antiprotozoal+Drugs |access-date=2022-04-22 |website=The Free Dictionary |archive-date=2022-01-22 |archive-url=https://web.archive.org/web/20220122142518/https://medical-dictionary.thefreedictionary.com/Antiprotozoal+Drugs |url-status=live }}</ref> The branch of [[medicine]] that focuses on infections is referred to as [[infectious diseases (medical specialty)|infectious diseases]].<ref>{{cite web |url=https://www.aamc.org/cim/specialty/list/us/339608/infectious_disease_-internal_medicine.html |title=Infectious Disease, Internal Medicine |publisher=Association of American Medical Colleges |access-date=2015-08-20 |quote=Infectious disease is the subspecialty of internal medicine dealing with the diagnosis and treatment of communicable diseases of all types, in all organs, and in all ages of patients. |archive-url=https://web.archive.org/web/20150206201010/https://www.aamc.org/cim/specialty/list/us/339608/infectious_disease_-internal_medicine.html |archive-date=2015-02-06 }}</ref>
{{TOC limit|3}}

==Types==
Infections are caused by infectious agents ([[pathogen]]s) including:
* [[Pathogenic bacteria|Bacteria]] (e.g. ''[[Mycobacterium tuberculosis]]'', ''[[Staphylococcus aureus]]'', ''[[Escherichia coli]]'', ''[[Clostridium botulinum]]'', and ''[[Salmonella]]'' spp.)
* [[Viral infection|Virus]]es and [[subviral agent]]s such as [[viroid]]s and [[prion]]s.  (E.g. ''[[HIV]]'', ''[[Rhinovirus]]'', ''[[Lyssavirus]]es'' such as ''[[Rabies virus]]'', ''[[Ebolavirus]]'' and ''[[Severe acute respiratory syndrome coronavirus 2]]'')
* [[Fungal infection|Fungi]], further subclassified into:
** [[Ascomycota]], including yeasts such as [[Candida (fungus)|''Candida'']] (the most common [[fungal infection]]); filamentous fungi such as ''[[Aspergillus]];'' ''[[Pneumocystis]]'' species; and [[Dermatophytosis|dermatophytes]], a group of organisms causing infection of skin and other superficial structures in humans.<ref>{{Cite web|url=https://www.cdc.gov/fungal/diseases/index.html|title=Types of Fungal Diseases|date=2019-06-27|website=Centers for Disease Control and Prevention|language=en-us|access-date=2019-12-09|archive-date=2020-04-01|archive-url=https://web.archive.org/web/20200401195307/https://www.cdc.gov/fungal/diseases/index.html|url-status=live}}</ref>
** [[Basidiomycota]], including the human-pathogenic genus ''[[Cryptococcus]].''<ref>{{Citation|last1=Mada|first1=Pradeep Kumar|title=Cryptococcus (Cryptococcosis)|date=2019|url=https://www.ncbi.nlm.nih.gov/books/NBK431060/|work=StatPearls|publisher=StatPearls Publishing|pmid=28613714|access-date=2019-12-09|last2=Jamil|first2=Radia T.|last3=Alam|first3=Mohammed U.|archive-date=2020-06-19|archive-url=https://web.archive.org/web/20200619195643/https://www.ncbi.nlm.nih.gov/books/NBK431060/|url-status=live}}</ref>
* [[Parasitic disease|Parasite]]s, which are usually divided into:<ref>{{Cite web|url=https://www.cdc.gov/parasites/about.html|title=About Parasites|date=2019-02-25|website=Centers for Disease Control and Prevention|language=en-us|access-date=2019-12-09|archive-date=2019-12-25|archive-url=https://web.archive.org/web/20191225043311/https://www.cdc.gov/parasites/about.html|url-status=live}}</ref>
** Unicellular organisms (e.g. [[Plasmodium|malaria]], ''[[Toxoplasma gondii|Toxoplasma]]'', ''[[Babesia]]'')
** Macroparasites<ref>{{Cite journal |jstor = 656401|title = Microparasites and Macroparasites|journal = Cultural Anthropology|volume = 2|issue = 1|pages = 155–71|last1 = Brown|first1 = Peter J.|year = 1987|doi = 10.1525/can.1987.2.1.02a00120|doi-access = free}}</ref> ([[Parasitic worm|worms or helminths]]) including [[nematode]]s such as [[parasitic]] [[roundworm]]s and [[pinworm (parasite)|pinworms]],  [[tapeworm]]s (cestodes), and flukes ([[trematodes]], such as [[schistosomes]]).  Diseases caused by [[Parasitic worm|helminths]] are sometimes termed infestations, but are sometimes called infections.
** [[Arthropod]]s such as [[tick]]s, [[mite]]s, [[flea]]s, and [[lice]], can also cause human disease, which conceptually are similar to infections, but invasion of a human or animal body by these macroparasites is usually termed [[infestation]].

==Signs and symptoms==
The [[signs and symptoms]] of an infection depend on the type of disease. Some signs of infection affect the whole body generally, such as [[fatigue]], loss of appetite, weight loss, [[fever]]s, night sweats, chills, aches and pains. Others are specific to individual body parts, such as skin [[rash]]es, [[cough]]ing, or a [[Rhinorrhea|runny nose]].<ref>{{Cite web |title=Runny Nose: Symptoms, Causes & Treatment |url=https://my.clevelandclinic.org/health/symptoms/17660-runny-nose |access-date=2022-04-22 |website=Cleveland Clinic |archive-date=2022-05-10 |archive-url=https://web.archive.org/web/20220510130201/https://my.clevelandclinic.org/health/symptoms/17660-runny-nose |url-status=live }}</ref>

In certain cases, infectious diseases may be [[asymptomatic]] for much or even all of their course in a given host. In the latter case, the disease may only be defined as a "disease" (which by definition means an illness) in hosts who secondarily become ill after contact with an [[asymptomatic carrier]]. An infection is not synonymous with an infectious disease, as some infections do not cause illness in a host.<ref name=Sherris/>

===Bacterial or viral===
As bacterial and viral infections can both cause the same kinds of symptoms, it can be difficult to distinguish which is the cause of a specific infection.<ref name="nipa">{{Cite web |title=NIPA - Bacteria - Bacterial vs. Viral infections |url=http://www.antibiotics-info.org/bact02.html |access-date=2023-11-10 |website=www.antibiotics-info.org |archive-date=2023-11-10 |archive-url=https://web.archive.org/web/20231110111321/http://www.antibiotics-info.org/bact02.html |url-status=live }}</ref> Distinguishing the two is important, since viral infections cannot be cured by [[antibiotic]]s whereas bacterial infections can.<ref>{{cite book| title =The Truth About Illness and Disease|author1=Robert N. Golden |author2=Fred Peterson |publisher= Infobase Publishing|page=181|isbn= 978-1-4381-2637-1|year=2009 }}</ref>

{|class="wikitable"
|+Comparison of viral and bacterial infection
|-
! Characteristic
! [[Viral disease|Viral infection]]
! [[Pathogenic bacteria|Bacterial infection]]
|-
|| Typical symptoms
| In general, viral infections are systemic. This means they involve many different parts of the body or more than one body system at the same time; i.e. a runny nose, sinus congestion, cough, body aches etc. They can be local at times as in viral [[conjunctivitis]] or "pink eye" and herpes. Only a few viral infections are painful, like [[Herpes simplex virus|herpes]]. The pain of viral infections is often described as itchy or burning.<ref name="nipa"/>
| The classic symptoms of a bacterial infection are localized redness, heat, swelling and pain. One of the hallmarks of a bacterial infection is local pain, pain that is in a specific part of the body. For example, if a cut occurs and is infected with bacteria, pain occurs at the site of the infection. Bacterial throat pain is often characterized by more pain on one side of the throat. An [[ear infection]] is more likely to be diagnosed as bacterial if the pain occurs in only one ear.<ref name=nipa/> A cut that produces pus and milky-colored liquid is most likely infected.<ref>{{cite web|publisher=Rencare |url=http://www.rencareltd.com/conditions/infections/ |title=Infection |access-date=4 July 2013 |archive-url=https://web.archive.org/web/20120305023556/http://www.rencareltd.com/conditions/infections/ |archive-date=March 5, 2012 }}</ref>
|-
| Cause || [[Pathogenic viruses]] || [[Pathogenic bacteria]]
|}

==Pathophysiology==
[[File:Chain of Infection.png|thumb|Chain of infection; the chain of events that lead to infection]]
There is a general chain of events that applies to infections, sometimes called the '''chain of infection'''<ref>{{Cite web |title=Infection Cycle Symptoms and Treatment |url=https://infectioncycle.com/ |access-date=2023-11-10 |website=Infection Cycle |language=en-US |archive-date=2023-11-10 |archive-url=https://web.archive.org/web/20231110111321/https://infectioncycle.com/ |url-status=live }}</ref> or '''transmission chain'''. The chain of events involves several steps{{snd}}which include the infectious agent, reservoir, entering a susceptible host, exit and transmission to new hosts. Each of the links must be present in a chronological order for an infection to develop. Understanding these steps helps health care workers target the infection and prevent it from occurring in the first place.<ref>{{Citation |author1=((National Institutes of Health (US)))|title=Understanding Emerging and Re-emerging Infectious Diseases |date=2007 |url=https://www.ncbi.nlm.nih.gov/books/NBK20370/ |work=NIH Curriculum Supplement Series [Internet] |access-date=2023-11-17 |publisher=National Institutes of Health (US) |language=en |last2=Study |first2=Biological Sciences Curriculum |archive-date=2023-06-26 |archive-url=https://web.archive.org/web/20230626004621/https://ncbi.nlm.nih.gov/books/NBK20370/ |url-status=live }}</ref>

===Colonization===
[[File:Dit del peu gros infectat.jpg|thumb|Infection of an [[ingrown nail|ingrown toenail]]; there is pus (yellow) and resultant inflammation (redness and swelling around the nail).]]
Infection begins when an organism successfully enters the body, grows and multiplies. This is referred to as colonization. Most humans are not easily infected. Those with compromised or weakened immune systems have an increased susceptibility to chronic or persistent infections. Individuals who have a suppressed [[immune system]] are particularly susceptible to [[opportunistic infection]]s. Entrance to the host at [[host–pathogen interface]], generally occurs through the [[Mucous membrane|mucosa]] in orifices like the [[oral cavity]], nose, eyes, genitalia, anus, or the microbe can enter through open wounds. While a few organisms can grow at the initial site of entry, many migrate and cause systemic infection in different organs. Some pathogens grow within the host cells (intracellular) whereas others grow freely in bodily fluids.<ref>{{Cite book |last=Peterson |first=Johnny W. |url=https://www.ncbi.nlm.nih.gov/books/NBK8526/ |title=Bacterial Pathogenesis |date=1996 |publisher=University of Texas Medical Branch at Galveston |language=en |pmid=21413346 |isbn=978-0-9631172-1-2 |access-date=2022-10-20 |archive-date=2016-04-25 |archive-url=https://web.archive.org/web/20160425080845/http://www.ncbi.nlm.nih.gov/books/NBK8526/ |url-status=live }}</ref>

[[Wound]] colonization refers to non-replicating microorganisms within the wound, while in infected wounds, replicating organisms exist and tissue is injured.<ref>{{Cite journal|last1=Negut|first1=Irina|last2=Grumezescu|first2=Valentina|last3=Grumezescu|first3=Alexandru Mihai|date=2018-09-18|title=Treatment Strategies for Infected Wounds|journal=Molecules |volume=23|issue=9|doi=10.3390/molecules23092392|issn=1420-3049|pmc=6225154|pmid=30231567|page=2392|doi-access=free}}</ref> All [[multicellular organism]]s are colonized to some degree by extrinsic organisms, and the vast majority of these exist in either a [[Mutualism (biology)|mutualistic]] or [[commensal]] relationship with the host. An example of the former is the [[Anaerobic organism|anaerobic bacteria]] species, which colonizes the [[mammal]]ian [[colon (anatomy)|colon]], and an example of the latter are the various species of [[staphylococcus]] that exist on [[human skin]]. Neither of these colonizations are considered infections. The difference between an infection and a colonization is often only a matter of circumstance. Non-pathogenic organisms can become pathogenic given specific conditions, and even the most [[virulent]] organism requires certain circumstances to cause a compromising infection. Some colonizing bacteria, such as ''[[Corynebacteria]] sp.'' and ''[[Viridans streptococci]]'', prevent the adhesion and colonization of pathogenic bacteria and thus have a symbiotic relationship with the host, preventing infection and speeding [[wound healing]].
[[File:Pathogenic Infection.png|thumb|This image depicts the steps of pathogenic infection.<ref>{{Cite journal |last1=Duerkop |first1=Breck A |last2=Hooper |first2=Lora V |date=2013-07-01 |title=Resident viruses and their interactions with the immune system |journal=Nature Immunology |language=en |volume=14 |issue=7 |pages=654–59 |doi=10.1038/ni.2614 |pmc=3760236 |pmid=23778792}}</ref><ref>{{Cite web |title=Bacterial Pathogenesis at Washington University |url=https://www.studyblue.com/notes/note/n/bacterial-pathogenesis/deck/11094651 |access-date=2016-12-02 |website=StudyBlue |location=St. Louis |archive-date=2016-12-03 |archive-url=https://web.archive.org/web/20161203060624/https://www.studyblue.com/notes/note/n/bacterial-pathogenesis/deck/11094651 |url-status=live }}</ref><ref>{{Cite web |title=Print Friendly |url=http://www.lifeextension.com/magazine/2014/6/the-dangers-of-using-antibiotics-to-prevent-urinary-tract-infections/page-01?p=1 |archive-url=https://web.archive.org/web/20161202235200/http://www.lifeextension.com/magazine/2014/6/the-dangers-of-using-antibiotics-to-prevent-urinary-tract-infections/page-01?p=1 |archive-date=2016-12-02 |access-date=2016-12-02 |website=www.lifeextension.com}}</ref>]]
The variables involved in the outcome of a host becoming inoculated by a pathogen and the ultimate outcome include:
* the route of entry of the [[pathogen]] and the access to host regions that it gains
* the intrinsic [[virulence]] of the particular organism
* the quantity or load of the initial inoculant
* the [[immune system|immune]] status of the host being colonized

As an example, several [[staphylococcus|staphylococcal]] species remain harmless on the skin, but, when present in a normally [[sterile technique|sterile]] space, such as in the capsule of a [[joint]] or the [[peritoneum]], multiply without resistance and cause harm.<ref>{{Cite journal |last1=Tong |first1=Steven Y. C. |last2=Davis |first2=Joshua S. |last3=Eichenberger |first3=Emily |last4=Holland |first4=Thomas L. |last5=Fowler |first5=Vance G. |date=2015 |title=Staphylococcus aureus Infections: Epidemiology, Pathophysiology, Clinical Manifestations, and Management |journal=Clinical Microbiology Reviews |volume=28 |issue=3 |pages=603–661 |doi=10.1128/CMR.00134-14 |issn=0893-8512 |pmc=4451395 |pmid=26016486}}</ref>

An interesting fact that [[gas chromatography–mass spectrometry]], [[16S ribosomal RNA]] analysis, [[omics]], and other advanced technologies have made more apparent to humans in recent decades is that microbial colonization is very common even in environments that humans think of as being nearly [[asepsis|sterile]]. Because it is normal to have bacterial colonization, it is difficult to know which chronic wounds can be classified as infected and how much risk of progression exists. Despite the huge number of wounds seen in clinical practice, there are limited quality data for evaluated symptoms and signs. A review of chronic wounds in the [[JAMA|Journal of the American Medical Association]]'s "Rational Clinical Examination Series" quantified the importance of increased pain as an indicator of infection.<ref>{{cite journal |vauthors=Reddy M, Gill SS, Wu W | date = Feb 2012 | title = Does this patient have an infection of a chronic wound? | journal = JAMA | volume = 307 | issue = 6| pages = 605–11 | doi = 10.1001/jama.2012.98 | pmid = 22318282 |display-authors=etal}}</ref> The review showed that the most useful finding is an increase in the level of pain [likelihood ratio (LR) range, 11–20] makes infection much more likely, but the absence of pain (negative likelihood ratio range, 0.64–0.88) does not rule out infection (summary LR 0.64–0.88).

{{anchor|Persistent infection}}
===Disease===
[[Disease]] can arise if the host's protective immune mechanisms are compromised and the organism inflicts damage on the host. [[Microorganism]]s can cause tissue damage by releasing a variety of toxins or destructive enzymes. For example, ''[[Clostridium tetani]]'' releases a toxin that paralyzes muscles, and [[staphylococcus]] releases toxins that produce shock and [[sepsis]]. Not all infectious agents cause disease in all hosts. For example, less than 5% of individuals infected with [[polio]] develop disease.<ref>{{cite web |url=http://www.immunize.org/catg.d/p4215.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.immunize.org/catg.d/p4215.pdf |archive-date=2022-10-09 |title=Polio: Questions and Answers |website=immunize.org |access-date=9 July 2021 |url-status=live}}</ref> On the other hand, some infectious agents are highly virulent. The [[prion]] causing [[Bovine spongiform encephalopathy|mad cow disease]] and [[Creutzfeldt–Jakob disease]] invariably kills all animals and people that are infected.<ref>{{Cite journal |last=Trent |first=Ronald J |title=Infectious Diseases |date=2005 |journal=Molecular Medicine |pages=193–220 |doi=10.1016/B978-012699057-7/50008-4 |pmc=7149788|isbn=978-0-12-699057-7 }}</ref>

Persistent infections occur because the body is unable to clear the organism after the initial infection. Persistent infections are characterized by the continual presence of the infectious organism, often as latent infection with occasional recurrent relapses of active infection. There are some viruses that can maintain a persistent infection by infecting different cells of the body. Some viruses once acquired never leave the body. A typical example is the herpes virus, which tends to hide in nerves and become reactivated when specific circumstances arise.<ref>{{Cite journal |last1=Rouse |first1=Barry T. |last2=Sehrawat |first2=Sharvan |date=2010 |title=Immunity and immunopathology to viruses: what decides the outcome? |journal=Nature Reviews Immunology |language=en |volume=10 |issue=7 |pages=514–526 |doi=10.1038/nri2802 |pmid=20577268 |pmc=3899649 |issn=1474-1741}}</ref>

Persistent infections cause millions of deaths globally each year.<ref>{{cite web |url=http://www.persistentinfection.net/ |title=Chronic Infection Information |website=persistentinfection.net |access-date=2010-01-14 |archive-url=https://web.archive.org/web/20150722065612/http://www.persistentinfection.net/ |archive-date=July 22, 2015}}</ref> Chronic infections by parasites account for a high morbidity and mortality in many underdeveloped countries.<ref>{{Cite journal|last1=Torgerson|first1=Paul R.|last2=Devleesschauwer|first2=Brecht|last3=Praet|first3=Nicolas|last4=Speybroeck|first4=Niko|last5=Willingham|first5=Arve Lee|last6=Kasuga|first6=Fumiko|last7=Rokni|first7=Mohammad B.|last8=Zhou|first8=Xiao-Nong|last9=Fèvre|first9=Eric M.|last10=Sripa|first10=Banchob|last11=Gargouri|first11=Neyla|date=2015-12-03|title=World Health Organization Estimates of the Global and Regional Disease Burden of 11 Foodborne Parasitic Diseases, 2010: A Data Synthesis|journal=PLOS Medicine|volume=12|issue=12|article-number=e1001920|doi=10.1371/journal.pmed.1001920|issn=1549-1277|pmc=4668834|pmid=26633705 |doi-access=free }}</ref><ref>{{Citation|last1=Hotez|first1=Peter J.|title=Helminth Infections: Soil-transmitted Helminth Infections and Schistosomiasis|date=2006|url=https://www.ncbi.nlm.nih.gov/books/NBK11748/|work=Disease Control Priorities in Developing Countries|editor-last=Jamison|editor-first=Dean T.|edition=2nd|place=Washington (DC)|publisher=World Bank|isbn=978-0-8213-6179-5|pmid=21250326|access-date=2021-08-13|last2=Bundy|first2=Donald A. P.|last3=Beegle|first3=Kathleen|last4=Brooker|first4=Simon|last5=Drake|first5=Lesley|last6=de Silva|first6=Nilanthi|last7=Montresor|first7=Antonio|last8=Engels|first8=Dirk|last9=Jukes|first9=Matthew|editor2-last=Breman|editor2-first=Joel G.|editor3-last=Measham|editor3-first=Anthony R.|editor4-last=Alleyne|editor4-first=George|archive-date=2016-10-10|archive-url=https://web.archive.org/web/20161010040542/http://www.ncbi.nlm.nih.gov/books/NBK11748/|url-status=live}}</ref>

===Transmission<!--linked from 'Transmission (medicine)'-->===
{{Main|Transmission (medicine)}}
[[File:CulexNil.jpg|thumb|220px|A southern house mosquito (''[[Culex quinquefasciatus]]'') is a [[disease vector|vector]] that transmits the pathogens that cause [[West Nile fever]] and [[avian malaria]] among others.]]For infecting organisms to survive and repeat the infection cycle in other hosts, they (or their progeny) must leave an existing reservoir and cause infection elsewhere. Infection transmission can take place via many potential routes:<ref>{{cite web | title = How Infections Spread | url = https://www.cdc.gov/infectioncontrol/spread/index.html | website = Centers for Disease Control and Prevention | date = 1 January 2016 | access-date = 17 October 2021 | archive-date = 2 June 2023 | archive-url = https://web.archive.org/web/20230602112416/https://www.cdc.gov/infectioncontrol/spread/index.html | url-status = live }}</ref>
* '''Droplet contact''', also known as the ''respiratory route'', and the resultant infection can be termed [[airborne disease]]. If an infected person coughs or sneezes on another person the microorganisms, suspended in warm, moist droplets, may enter the body through the nose, mouth or eye surfaces.
* '''Fecal-oral transmission''', wherein foodstuffs or water become contaminated (by people not washing their hands before preparing food, or untreated sewage being released into a drinking water supply) and the people who eat and drink them become infected. Common [[Fecal–oral route|fecal-oral]] transmitted pathogens include ''[[Vibrio cholerae]]'', ''[[Giardia]]'' species, [[rotavirus]]es, ''[[Entamoeba histolytica]]'', ''[[Escherichia coli]]'', and [[tape worm]]s.<ref>[http://www.fungusfocus.com/html/flukes.htm Intestinal Parasites and Infection] {{Webarchive|url=https://web.archive.org/web/20101028013944/http://fungusfocus.com/html/flukes.htm |date=2010-10-28 }} fungusfocus.com – Retrieved on 2010-01-21</ref> Most of these pathogens cause [[gastroenteritis]].
* '''Sexual transmission''', with the result being called [[sexually transmitted infection]].
* '''Oral transmission''', diseases that are transmitted primarily by oral means may be caught through direct oral contact such as [[kiss]]ing, or by indirect contact such as by sharing a drinking glass or a cigarette.
* '''Transmission by direct contact''', Some diseases that are transmissible by direct contact include [[athlete's foot]], [[impetigo]] and [[wart]]s.
* '''Vehicle transmission''', transmission by an inanimate reservoir (food, water, soil).<ref>{{Cite web|url=http://www.microbiologybook.org/Infectious%20Disease/Infectious%20Disease%20Introduction.htm|title=Clinical Infectious Disease – Introduction|website=microbiologybook.org|access-date=2017-04-19|archive-date=2017-04-20|archive-url=https://web.archive.org/web/20170420143405/http://www.microbiologybook.org/Infectious%20Disease/Infectious%20Disease%20Introduction.htm|url-status=live}}</ref>
* '''[[Vertically transmitted infection|Vertical transmission]]''', directly from the mother to an [[embryo]], [[fetus]] or baby during [[pregnancy]] or [[childbirth]]. It can occur as a result of a [[pre-existing disease in pregnancy|pre-existing infection]] or one acquired during pregnancy.
* '''[[Iatrogenic]] transmission''', due to medical procedures such as [[Injection (medicine)|injection]] or [[organ transplant|transplantation]] of infected material.
* '''Vector-borne transmission''', transmitted by a [[Vector (epidemiology)|vector]], which is an [[organism]] that does not cause [[disease]] itself but that transmits infection by conveying [[pathogen]]s from one [[Host (biology)|host]] to another.<ref>[http://www.metapathogen.com/ Pathogens and vectors] {{Webarchive|url=https://web.archive.org/web/20171005150918/http://www.metapathogen.com/ |date=2017-10-05 }}. ''MetaPathogen.com''.</ref>

The relationship between ''[[optimal virulence|virulence versus transmissibility]]'' is complex; with studies have shown that there were no clear relationship between the two.<ref>{{cite journal |last1=Hector |first1=Tobias E. |last2=Booksmythe |first2=Isobel |title=Digest: Little evidence exists for a virulence-transmission trade-off* |journal=Evolution |date=April 2019 |volume=73 |issue=4 |pages=858–859 |doi=10.1111/evo.13724 |pmid=30900249 |s2cid=85448255 |doi-access=free }}</ref><ref>{{cite journal |last1=Acevedo |first1=Miguel A. |last2=Dillemuth |first2=Forrest P. |last3=Flick |first3=Andrew J. |last4=Faldyn |first4=Matthew J. |last5=Elderd |first5=Bret D. |title=Virulence-driven trade-offs in disease transmission: A meta-analysis* |journal=Evolution |date=April 2019 |volume=73 |issue=4 |pages=636–647 |doi=10.1111/evo.13692 |pmid=30734920 |s2cid=73418339 |url=https://digitalcommons.lsu.edu/biosci_pubs/1193 |access-date=2022-06-28 |archive-date=2022-12-04 |archive-url=https://web.archive.org/web/20221204210544/https://digitalcommons.lsu.edu/biosci_pubs/1193/ |url-status=live |url-access=subscription }}</ref> There is still a small number of evidence that partially suggests a link between virulence and transmissibility.<ref>{{cite journal |last1=Ericson |first1=L. |last2=Burdon |first2=J. J. |last3=Müller |first3=W. J. |title=Spatial and temporal dynamics of epidemics of the rust fungus Uromyces valerianae on populations of its host Valeriana salina |journal=Journal of Ecology |date=August 1999 |volume=87 |issue=4 |pages=649–658 |doi=10.1046/j.1365-2745.1999.00384.x |s2cid=86478171 |doi-access=free |bibcode=1999JEcol..87..649E }}</ref><ref>{{cite journal |last1=Mideo |first1=N |last2=Alizon |first2=S |last3=Day |first3=T |title=Linking within- and between-host dynamics in the evolutionary epidemiology of infectious diseases |journal=Trends in Ecology & Evolution |date=September 2008 |volume=23 |issue=9 |pages=511–517 |doi=10.1016/j.tree.2008.05.009|pmid=18657880 |bibcode=2008TEcoE..23..511M }}</ref><ref>{{cite journal |last1=Mordecai |first1=Erin A. |last2=Cohen |first2=Jeremy M. |last3=Evans |first3=Michelle V. |last4=Gudapati |first4=Prithvi |last5=Johnson |first5=Leah R. |last6=Lippi |first6=Catherine A. |last7=Miazgowicz |first7=Kerri |last8=Murdock |first8=Courtney C. |last9=Rohr |first9=Jason R. |last10=Ryan |first10=Sadie J. |last11=Savage |first11=Van |last12=Shocket |first12=Marta S. |last13=Stewart Ibarra |first13=Anna |last14=Thomas |first14=Matthew B. |last15=Weikel |first15=Daniel P. |title=Detecting the impact of temperature on transmission of Zika, dengue, and chikungunya using mechanistic models |journal=PLOS Neglected Tropical Diseases |date=27 April 2017 |volume=11 |issue=4 |article-number=e0005568 |doi=10.1371/journal.pntd.0005568|pmid=28448507 |pmc=5423694 |doi-access=free }}</ref>

==Diagnosis==
Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly.<ref>{{cite book | vauthors = Seventer JM, Hochberg NS | chapter = Principles of Infectious Diseases: Transmission, Diagnosis, Prevention, and Control | title = International Encyclopedia of Public Health | date=October 2016 | pages = 22–39 | doi= 10.1016/B978-0-12-803678-5.00516-6 | pmc = 7150340 | isbn = 978-0-12-803708-9 }}</ref> In practice most minor infectious diseases such as [[wart]]s, [[cutaneous]] [[abscesses]], [[respiratory system]] infections and [[diarrheal diseases]] are diagnosed by their clinical presentation and treated without knowledge of the specific causative agent. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified.<ref name=":1">{{Cite web |last=Vazquez-Pertejo |first=Maria T. |date=October 2022 |title=Diagnosis of Infectious Disease - Infections |url=https://www.merckmanuals.com/home/infections/diagnosis-of-infectious-disease/diagnosis-of-infectious-disease |archive-url=https://web.archive.org/web/20240102154139/https://www.merckmanuals.com/home/infections/diagnosis-of-infectious-disease/diagnosis-of-infectious-disease |archive-date=2024-01-02 |access-date=2024-01-02 |website=Merck Manuals Consumer Version |language=English}}</ref>

Diagnosis of infectious disease is nearly always initiated by [[medical history]] and physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.<ref name=":1" />

Many infectious organisms are identified without culture and microscopy. This is especially true for viruses, which cannot grow in culture. For some suspected pathogens, doctors may conduct tests that examine a patient's blood or other body fluids for [[antigen]]s or [[Antibody|antibodies]] that indicate presence of a specific pathogen that the doctor suspects.<ref name=":1" />

Other techniques (such as [[X-ray]]s, [[CAT scans]], [[PET scan]]s or [[NMR]]) are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone [[abscess]] or a [[spongiform encephalopathy]] produced by a [[prion]].<ref>{{Cite journal |last1=Weaver |first1=Jennifer S. |last2=Omar |first2=Imran M. |last3=Mar |first3=Winnie A. |last4=Klauser |first4=Andrea S. |last5=Winegar |first5=Blair A. |last6=Mlady |first6=Gary W. |last7=McCurdy |first7=Wendy E. |last8=Taljanovic |first8=Mihra S. |date=2022-03-05 |title=Magnetic resonance imaging of musculoskeletal infections |journal=Polish Journal of Radiology |volume=87 |pages=e141–e162 |doi=10.5114/pjr.2022.113825 |issn=1733-134X |pmc=9047866 |pmid=35505859}}</ref>

The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is likely to be [[benign]].<ref>{{Cite journal |last1=Pinsky |first1=B. A. |last2=Hayden |first2=R. T. |date=2019-08-26 |title=Cost-Effective Respiratory Virus Testing |journal=Journal of Clinical Microbiology |volume=57 |issue=9 |pages=e00373–19 |doi=10.1128/JCM.00373-19 |issn=0095-1137 |pmc=6711893 |pmid=31142607}}</ref>

===Symptomatic diagnostics===
The diagnosis is aided by the presenting symptoms in any individual with an infectious disease, yet it usually needs additional diagnostic techniques to confirm the suspicion. Some signs are specifically characteristic and indicative of a disease and are called [[pathognomonic]] signs; but these are rare. Not all infections are symptomatic.<ref name=Sternak>{{cite journal|last1=Ljubin-Sternak|first1=Suncanica|last2=Mestrovic|first2=Tomislav|title=Review: Chlamydia trachonmatis and Genital Mycoplasmias: Pathogens with an Impact on Human Reproductive Health|journal=Journal of Pathogens|page=3 |date=2014|volume=2014|issue=183167|doi=10.1155/2014/183167|pmid=25614838|pmc=4295611|doi-access=free}}</ref>

In children the presence of [[cyanosis]], rapid breathing, poor peripheral perfusion, or a [[petechial rash]] increases the risk of a serious infection by greater than 5 fold.<ref name=Lancet10>{{cite journal |vauthors=Van den Bruel A, Haj-Hassan T, Thompson M, Buntinx F, Mant D | title = Diagnostic value of clinical features at presentation to identify serious infection in children in developed countries: a systematic review | journal = Lancet | volume = 375 | issue = 9717 | pages = 834–45 | date = March 2010 | pmid = 20132979 | doi = 10.1016/S0140-6736(09)62000-6 | s2cid = 28014329 }}</ref> Other important indicators include parental concern, clinical instinct, and temperature greater than 40&nbsp;°C.<ref name=Lancet10/>

===Microbial culture===
[[File:K pneumoniae M morganii providencia styphimuriuma.JPG|thumb|200px|Four [[nutrient agar]] plates growing colonies of common [[Gram negative]] bacteria]]
Many diagnostic approaches depend on [[microbiological culture]] to isolate a pathogen from the appropriate clinical specimen.<ref>{{cite book |last1=Murray |first1=Patrick R. |title=Medical Microbiology |date=2021 |publisher=Elsevier |location=Philadelphia |isbn=978-0-323-67450-8 |edition=9th |chapter=Laboratory Diagnosis of Bacterial Diseases}}</ref> In a microbial culture, a [[growth medium]] is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium. Many pathogenic [[bacteria]] are easily grown on nutrient [[Agar#Microbiology|agar]], a form of solid medium that supplies carbohydrates and proteins necessary for growth, along with copious amounts of water. A single bacterium will grow into a visible mound on the surface of the plate called a [[Colony (biology)|colony]], which may be separated from other colonies or melded together into a "lawn". The size, color, shape and form of a colony is characteristic of the bacterial species, its specific genetic makeup (its [[Strain (biology)|strain]]), and the environment that supports its growth. Other ingredients are often added to the plate to aid in identification. Plates may contain substances that permit the growth of some bacteria and not others, or that change color in response to certain bacteria and not others. Bacteriological plates such as these are commonly used in the clinical identification of infectious bacterium. Microbial culture may also be used in the identification of [[virus]]es: the medium, in this case, being cells grown in culture that the virus can infect, and then alter or kill. In the case of viral identification, a region of dead cells results from viral growth, and is called a "plaque". [[Eukaryotic]] [[parasites]] may also be grown in culture as a means of identifying a particular agent.<ref>{{Cite journal |last1=Joyce |first1=Bradley R. |last2=Queener |first2=Sherry F. |last3=Wek |first3=Ronald C. |last4=Sullivan |first4=William J. |date=2010-10-05 |title=Phosphorylation of eukaryotic initiation factor-2α promotes the extracellular survival of obligate intracellular parasite Toxoplasma gondii |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=107 |issue=40 |pages=17200–17205 |doi=10.1073/pnas.1007610107 |issn=0027-8424 |pmc=2951449 |pmid=20855600|bibcode=2010PNAS..10717200J |doi-access=free }}</ref>

In the absence of suitable plate culture techniques, some microbes require culture within live animals. Bacteria such as ''[[Mycobacterium leprae]]'' and ''[[Treponema pallidum]]'' can be grown in animals, although serological and microscopic techniques make the use of live animals unnecessary. Viruses are also usually identified using alternatives to growth in culture or animals. Some viruses may be grown in [[embryo]]nated eggs. Another useful identification method is Xenodiagnosis, or the use of a vector to support the growth of an infectious agent. [[Chagas disease]] is the most significant example, because it is difficult to directly demonstrate the presence of the causative agent, ''[[Trypanosoma cruzi]]'' in a patient, which therefore makes it difficult to definitively make a diagnosis. In this case, [[xenodiagnosis]] involves the use of the [[Vector (epidemiology)|vector]] of the Chagas agent ''T. cruzi'', an uninfected [[Triatominae|triatomine]] bug, which takes a blood meal from a person suspected of having been infected. The bug is later inspected for growth of ''T. cruzi'' within its gut.<ref>{{Cite journal |last1=Elliot |first1=Simon L. |last2=Rodrigues |first2=Juliana de O. |last3=Lorenzo |first3=Marcelo G. |last4=Martins-Filho |first4=Olindo A. |last5=Guarneri |first5=Alessandra A. |date=2015 |title=Trypanosoma cruzi, etiological agent of Chagas disease, is virulent to its triatomine vector Rhodnius prolixus in a temperature-dependent manner |journal=PLOS Neglected Tropical Diseases |volume=9 |issue=3 |article-number=e0003646 |doi=10.1371/journal.pntd.0003646 |issn=1935-2735 |pmc=4368190 |pmid=25793495 |doi-access=free }}</ref>

===Microscopy===
Another principal tool in the diagnosis of infectious disease is [[microscopy]].<ref>{{cite book |last1=Murray |first1=Patrick R. |title=Medical Microbiology |date=2021 |publisher=Elsevier |location=Philadelphia |isbn=978-0-323-67450-8 |edition=9th |chapter=Microscopy and In Vitro Culture}}</ref> Virtually all of the culture techniques discussed above rely, at some point, on microscopic examination for definitive identification of the infectious agent. Microscopy may be carried out with simple instruments, such as the compound [[light microscope]], or with instruments as complex as an [[electron microscope]]. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with [[biochemical]] [[staining]] techniques, and can be made exquisitely specific when used in combination with [[antibody]] based techniques. For example, the use of antibodies made artificially [[fluorescent]] (fluorescently labeled antibodies) can be directed to bind to and identify a specific [[antigen]]s present on a pathogen. A [[fluorescence microscope]] is then used to detect fluorescently labeled antibodies bound to internalized antigens within clinical samples or cultured cells. This technique is especially useful in the diagnosis of viral diseases, where the light microscope is incapable of identifying a virus directly.<ref>{{Cite journal |last1=Parveen |first1=Nagma |last2=Borrenberghs |first2=Doortje |last3=Rocha |first3=Susana |last4=Hendrix |first4=Jelle |date=2018-05-10 |title=Single Viruses on the Fluorescence Microscope: Imaging Molecular Mobility, Interactions and Structure Sheds New Light on Viral Replication |journal=Viruses |volume=10 |issue=5 |page=250 |doi=10.3390/v10050250 |issn=1999-4915 |pmc=5977243 |pmid=29748498|doi-access=free }}</ref>

Other microscopic procedures may also aid in identifying infectious agents. Almost all cells readily stain with a number of basic [[dye]]s due to the [[electrostatic]] attraction between negatively charged cellular molecules and the positive charge on the dye. A cell is normally transparent under a microscope, and using a stain increases the contrast of a cell with its background. Staining a cell with a dye such as [[Giemsa]] stain or [[crystal violet]] allows a microscopist to describe its size, shape, internal and external components and its associations with other cells. The response of bacteria to different staining procedures is used in the [[taxonomic classification]] of microbes as well. Two methods, the [[Gram stain]] and the [[acid-fast]] stain, are the standard approaches used to classify bacteria and to diagnosis of disease. The Gram stain identifies the bacterial groups [[Bacillota]] and [[Actinomycetota]], both of which contain many significant human pathogens. The acid-fast staining procedure identifies the Actinomycetota genera ''[[Mycobacterium]]'' and ''[[Nocardia]]''.<ref>{{Cite journal |last1=Saubolle |first1=Michael A. |last2=Sussland |first2=Den |date=2003 |title=Nocardiosis |journal=Journal of Clinical Microbiology |volume=41 |issue=10 |pages=4497–4501 |doi=10.1128/JCM.41.10.4497-4501.2003 |issn=0095-1137 |pmid=14532173|pmc=254378 }}</ref>

===Biochemical tests===
Biochemical tests used in the identification of infectious agents include the detection of [[metabolic]] or [[enzymatic]] products characteristic of a particular infectious agent. Since bacteria ferment [[carbohydrate]]s in patterns characteristic of their [[genus]] and [[species]], the detection of [[Fermentation (biochemistry)|fermentation]] products is commonly used in bacterial identification. [[Acids]], [[alcohols]] and [[gases]] are usually detected in these tests when bacteria are grown in [[Growth medium#Selective media|selective]] liquid or solid media.<ref>{{Cite journal |last1=Flint |first1=Harry J. |last2=Scott |first2=Karen P. |last3=Duncan |first3=Sylvia H. |last4=Louis |first4=Petra |last5=Forano |first5=Evelyne |date=2012-07-01 |title=Microbial degradation of complex carbohydrates in the gut |journal=Gut Microbes |volume=3 |issue=4 |pages=289–306 |doi=10.4161/gmic.19897 |issn=1949-0976 |pmc=3463488 |pmid=22572875}}</ref>

The isolation of [[enzymes]] from infected tissue can also provide the basis of a biochemical diagnosis of an infectious disease. For example, humans can make neither [[RNA replicase]]s nor [[reverse transcriptase]], and the presence of these enzymes are characteristic., of specific types of viral infections. The ability of the viral protein [[hemagglutinin]] to bind [[red blood cells]] together into a detectable matrix may also be characterized as a biochemical test for viral infection, although strictly speaking hemagglutinin is not an ''enzyme'' and has no metabolic function.<ref>{{Cite journal |last1=Makkoch |first1=Jarika |last2=Prachayangprecha |first2=Slinporn |last3=Payungporn |first3=Sunchai |last4=Chieochansin |first4=Thaweesak |last5=Songserm |first5=Thaweesak |last6=Amonsin |first6=Alongkorn |last7=Poovorawan |first7=Yong |date=2012 |title=Erythrocyte Binding Preference of Human Pandemic Influenza Virus A and Its Effect on Antibody Response Detection |journal=Annals of Laboratory Medicine |volume=32 |issue=4 |pages=276–282 |doi=10.3343/alm.2012.32.4.276 |issn=2234-3806 |pmc=3384809 |pmid=22779069}}</ref>

[[Serological]] methods are highly sensitive, specific and often extremely rapid tests used to identify microorganisms. These tests are based upon the ability of an antibody to bind specifically to an antigen. The antigen, usually a protein or carbohydrate made by an infectious agent, is bound by the antibody. This binding then sets off a chain of events that can be visibly obvious in various ways, dependent upon the test. For example, "[[Strep throat]]" is often diagnosed within minutes, and is based on the appearance of antigens made by the causative agent, ''[[S. pyogenes]]'', that is retrieved from a patient's throat with a cotton swab. Serological tests, if available, are usually the preferred route of identification, however the tests are costly to develop and the reagents used in the test often require [[refrigeration]]. Some serological methods are extremely costly, although when commonly used, such as with the "strep test", they can be inexpensive.<ref name=Sherris/>

Complex serological techniques have been developed into what are known as [[immunoassays]]. Immunoassays can use the basic antibody – antigen binding as the basis to produce an electro-magnetic or particle radiation signal, which can be detected by some form of instrumentation. Signal of unknowns can be compared to that of standards allowing quantitation of the target antigen. To aid in the diagnosis of infectious diseases, immunoassays can detect or measure antigens from either infectious agents or proteins generated by an infected organism in response to a foreign agent. For example, immunoassay A may detect the presence of a surface protein from a virus particle. Immunoassay B on the other hand may detect or measure antibodies produced by an organism's immune system that are made to neutralize and allow the destruction of the virus.

Instrumentation can be used to read extremely small signals created by secondary reactions linked to the antibody – antigen binding. Instrumentation can control sampling, reagent use, reaction times, signal detection, calculation of results, and data management to yield a cost-effective automated process for diagnosis of infectious disease.

===PCR-based diagnostics===
[[File:ID Now testing (51038387158).jpg|thumb|Nucleic acid testing conducted using an Abbott Laboratories ID Now device]]
Technologies based upon the [[polymerase chain reaction]] (PCR) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, [[Primer (molecular biology)|primers]], are derived from the [[genomes]] of infectious agents, and with time those genomes will be known if they are not already.<ref name="auto">{{Cite journal |last1=Kozera |first1=Bartłomiej |last2=Rapacz |first2=Marcin |date=2013 |title=Reference genes in real-time PCR |journal=Journal of Applied Genetics |volume=54 |issue=4 |pages=391–406 |doi=10.1007/s13353-013-0173-x |issn=1234-1983 |pmc=3825189 |pmid=24078518}}</ref>

Thus, the technological ability to detect any infectious agent rapidly and specifically is currently available. The only remaining blockades to the use of PCR as a standard tool of diagnosis are in its cost and application, neither of which is insurmountable. The diagnosis of a few diseases will not benefit from the development of PCR methods, such as some of the [[clostridia]]l diseases ([[tetanus]] and [[botulism]]). These diseases are fundamentally biological poisonings by relatively small numbers of infectious bacteria that produce extremely potent [[neurotoxin]]s. A significant proliferation of the infectious agent does not occur, this limits the ability of PCR to detect the presence of any bacteria.<ref name="auto"/>

===Metagenomic sequencing===
{{More citations needed|date=September 2024}}
Given the wide range of bacterial, viral, fungal, protozoal, and helminthic pathogens that cause debilitating and life-threatening illnesses, the ability to quickly identify the cause of infection is important yet often challenging. For example, more than half of cases of [[encephalitis]], a severe illness affecting the brain, remain undiagnosed, despite extensive testing using the standard of care ([[microbiological culture]]) and state-of-the-art clinical laboratory methods. [[Metagenomic]] sequencing-based diagnostic tests are currently being developed for clinical use and show promise as a sensitive, specific, and rapid way to diagnose infection using a single all-encompassing test.<ref>{{cite web |last1=Lee |first1=Rose |title=Metagenomic Next Generation Sequencing: How Does It Work and Is It Coming to Your Clinical Microbiology Lab? |url=https://asm.org/articles/2019/november/metagenomic-next-generation-sequencing-how-does-it |website=American Society for Microbiology |access-date=17 September 2024}}</ref> This test is similar to current PCR tests; however, an untargeted whole genome amplification is used rather than [[Primer (molecular biology)|primers]] for a specific infectious agent. This amplification step is followed by [[next-generation sequencing]] or [[third-generation sequencing]], [[Sequence alignment|alignment comparisons]], and [[taxonomic classification]] using large databases of thousands of pathogen and commensal [[reference genome]]s. Simultaneously, [[antimicrobial resistance]] genes within pathogen and [[plasmid]] genomes are sequenced and aligned to the taxonomically classified pathogen genomes to generate an antimicrobial resistance profile – analogous to [[antibiotic sensitivity testing]] – to facilitate [[antimicrobial stewardship]] and allow for the optimization of treatment using the most effective drugs for a patient's infection.

Metagenomic sequencing could prove especially useful for diagnosis when the patient is [[immunocompromised]]. An ever-wider array of infectious agents can cause serious harm to individuals with immunosuppression, so clinical screening must often be broader. Additionally, the expression of symptoms is often atypical, making a clinical diagnosis based on presentation more difficult. Thirdly, diagnostic methods that rely on the detection of antibodies are more likely to fail. A rapid, sensitive, specific, and untargeted test for all known human pathogens that detects the presence of the organism's DNA rather than antibodies is therefore highly desirable.

===Indication of tests===
[[File:BGSU COVID-19 Drive-Thru Testing Site Close Up.jpg|thumb|A temporary drive-in testing site for COVID-19 set up with tents in a parking lot]]
There is usually an [[indication (medicine)|indication]] for a specific identification of an infectious agent only when such identification can aid in the treatment or prevention of the disease, or to advance knowledge of the course of an illness prior to the development of effective therapeutic or preventative measures. For example, in the early 1980s, prior to the appearance of [[Zidovudine|AZT]] for the treatment of [[AIDS]], the course of the disease was closely followed by monitoring the composition of patient blood samples, even though the outcome would not offer the patient any further treatment options. In part, these studies on the appearance of [[HIV]] in specific communities permitted the advancement of [[hypotheses]] as to the route of transmission of the virus. By understanding how the disease was transmitted, resources could be targeted to the communities at greatest risk in campaigns aimed at reducing the number of new infections. The specific [[serological]] diagnostic identification, and later [[genotypic]] or molecular identification, of HIV also enabled the development of hypotheses as to the [[Time|temporal]] and [[geographic]]al origins of the virus, as well as a myriad of other hypothesis.<ref name=Sherris/> The development of molecular diagnostic tools have enabled physicians and researchers to monitor the efficacy of treatment with [[anti-retroviral drugs]]. Molecular diagnostics are now commonly used to identify HIV in healthy people long before the onset of illness and have been used to demonstrate the existence of people who are genetically resistant to HIV infection. Thus, while there still is no cure for AIDS, there is great therapeutic and predictive benefit to identifying the virus and monitoring the virus levels within the blood of infected individuals, both for the patient and for the community at large.

===Classification===
====Subclinical versus clinical (latent versus apparent)====
Symptomatic infections are ''apparent'' and ''clinical'', whereas an infection that is active but does not produce noticeable symptoms may be called ''inapparent,'' ''silent,'' ''[[subclinical infection|subclinical]]'', or [[wikt:occult#Adj1|occult]]. An infection that is inactive or dormant is called a ''latent infection''.<ref>{{cite book |author1=Kayser, Fritz H |author2=Kurt A Bienz |author3=Johannes Eckert |author4=Rolf M Zinkernagel | title = Medical microbiology | publisher = Georg Thieme Verlag | location = Stuttgart | year = 2005 | page = 398 | isbn = 978-3-13-131991-3 }}</ref> An example of a latent bacterial infection is [[latent tuberculosis]]. Some viral infections can also be latent, examples of [[virus latency|latent viral infections]] are any of those from the ''[[Herpesviridae]]'' family.<ref>{{Cite journal|last=Grinde|first=Bjørn|date=2013-10-25|title=Herpesviruses: latency and reactivation – viral strategies and host response|journal=Journal of Oral Microbiology|volume=5|article-number=22766|doi=10.3402/jom.v5i0.22766|issn=0901-8328|pmc=3809354|pmid=24167660}}</ref>

The word ''infection'' can [[denotation|denote]] any presence of a particular pathogen at all (no matter how little) but also is often used in a [[word sense|sense]] implying a ''clinically apparent'' infection (in other words, a case of infectious disease). This fact occasionally creates some [[ambiguity]] or prompts some [[usage]] discussion; to get around this it is common for [[health professional]]s to speak of ''[[#Colonization|colonization]]'' (rather than ''infection'') when they mean that some of the pathogens are present but that no clinically apparent infection (no disease) is present.<ref>{{Cite journal |last=Dani |first=Arpad |date=2014 |title=Colonization and infection |journal=Central European Journal of Urology |volume=67 |issue=1 |pages=86–87 |doi=10.5173/ceju.2014.01.art19 |issn=2080-4806 |pmc=4074726 |pmid=24982790}}</ref>

====Course of infection====
Different terms are used to describe how and where infections present over time. In an ''acute'' infection, symptoms develop rapidly; its course can either be rapid or protracted. In ''chronic'' infection, symptoms usually develop gradually over weeks or months and are slow to resolve.<ref>{{Citation|last1=Boldogh|first1=Istvan|title=Persistent Viral Infections|date=1996|url=https://www.ncbi.nlm.nih.gov/books/NBK8538/|work=Medical Microbiology|editor-last=Baron|editor-first=Samuel|edition=4th|publisher=University of Texas Medical Branch at Galveston|isbn=978-0-9631172-1-2|pmid=21413348|access-date=2020-01-23|last2=Albrecht|first2=Thomas|last3=Porter|first3=David D.|archive-date=2020-04-14|archive-url=https://web.archive.org/web/20200414121324/https://www.ncbi.nlm.nih.gov/books/NBK8538/|url-status=live}}</ref> In ''subacute'' infections, symptoms take longer to develop than in acute infections but arise more quickly than those of chronic infections. A ''focal'' infection is an initial site of infection from which organisms travel [[bloodborne pathogen|via the bloodstream]] to another area of the body.<ref name=":0">{{Cite book|title= Microbiology|last=Foster|first=John|publisher=Norton|year=2018|isbn=978-0-393-60257-9|location=New York|page=39}}</ref>

====Primary versus opportunistic====

{{See also|Coinfection}}
{{anchor|Primary versus secondary}}<!-- This section is linked from Primary infection, Secondary infection and Acute infection-->
Among the many varieties of [[microorganisms]], relatively few cause disease in otherwise healthy individuals.<ref name=Baron>This section incorporates [https://www.ncbi.nlm.nih.gov/books/NBK7627/ public domain]  materials included in the text: [https://www.ncbi.nlm.nih.gov/books/NBK7627/?depth=10 Medical Microbiology]  Fourth Edition: [https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.chapter.594 Chapter 8] {{Webarchive|url=https://web.archive.org/web/20090219005050/https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.chapter.594 |date=2009-02-19 }} (1996). Baron, Samuel MD. The University of Texas Medical Branch at Galveston. {{cite book |url=https://www.ncbi.nlm.nih.gov/books/NBK7627/ |title=Medical Microbiology |access-date=2013-11-27 |url-status=live |archive-url=https://web.archive.org/web/20090629132331/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed |archive-date=June 29, 2009 |isbn=978-0-9631172-1-2 |publisher=University of Texas Medical Branch at Galveston |year=1996 |pmid=21413252 |last1=Baron |first1=S. }}</ref> Infectious disease results from the interplay between those few [[pathogen]]s and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depend upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. However, a host's immune system can also cause damage to the host itself in an attempt to control the infection. Clinicians, therefore, classify infectious microorganisms or microbes according to the status of host defenses – either as ''primary pathogens'' or as ''[[opportunistic infection|opportunistic pathogens]]''.<ref name="pmid29135922">{{cite journal |vauthors=Patil NK, Guo Y, Luan L, Sherwood ER |title=Targeting Immune Cell Checkpoints during Sepsis |journal=International Journal of Molecular Sciences |volume=18 |issue=11 |date=November 2017 |page=2413 |pmid=29135922 |pmc=5713381 |doi=10.3390/ijms18112413 |url=|doi-access=free }}</ref>

===== Primary pathogens =====
Primary pathogens cause disease as a result of their presence or activity within the normal, healthy host, and their intrinsic [[virulence]] (the severity of the disease they cause) is, in part, a necessary consequence of their need to reproduce and spread. Many of the most common primary pathogens of humans only infect humans, however, many serious diseases are caused by organisms acquired from the environment or that infect non-human hosts.<ref name="pmid31027668">{{cite journal |vauthors=McArthur DB |title=Emerging Infectious Diseases |journal=The Nursing Clinics of North America |volume=54 |issue=2 |pages=297–311 |date=June 2019 |pmid=31027668 |pmc=7096727 |doi=10.1016/j.cnur.2019.02.006 |url=}}</ref>

===== Opportunistic pathogens =====

{{main|Opportunistic infection}}
Opportunistic pathogens can cause an infectious disease in a host with depressed resistance ([[immunodeficiency]]) or if they have unusual access to the inside of the body (for example, via [[Major trauma|trauma]]). [[Opportunistic infection]] may be caused by microbes ordinarily in contact with the host, such as [[pathogenic bacteria]] or fungi in the [[gastrointestinal]] or the [[upper respiratory tract]], and they may also result from (otherwise innocuous) microbes acquired from other hosts (as in ''[[Clostridioides difficile]]'' [[colitis]]) or from the environment as a result of [[Physical trauma|traumatic]] introduction (as in [[surgical]] wound infections or [[compound fracture]]s). An opportunistic disease requires impairment of host defenses, which may occur as a result of [[genetic defect]]s (such as [[chronic granulomatous disease]]), exposure to [[antimicrobial]] drugs or [[immunosuppressive]] chemicals (as might occur following [[poison]]ing or [[cancer]] [[chemotherapy]]), exposure to [[ionizing radiation]], or as a result of an infectious disease with immunosuppressive activity (such as with [[measles]], [[malaria]] or [[HIV disease]]). Primary pathogens may also cause more severe disease in a host with depressed resistance than would normally occur in an immunosufficient host.<ref name=Sherris/>

===== Secondary infection =====
While a primary infection can practically be viewed as the [[root cause analysis|root cause]] of an individual's current health problem, a secondary infection is a [[sequela]] or [[complication (medicine)|complication]] of that root cause. For example, an infection due to a [[burn]] or [[penetrating trauma]] (the root cause) is a secondary infection. Primary pathogens often cause primary infection and often cause secondary infection. Usually, opportunistic infections are viewed as secondary infections (because immunodeficiency or [[injury]] was the predisposing factor).<ref name="pmid29135922"/>

===== Other types of infection =====
Other types of infection consist of mixed, [[Iatrogenic infections|iatrogenic]], [[Hospital-acquired infection|nosocomial]], and community-acquired infection. A mixed infection is an infection that is caused by two or more pathogens. An example of this is [[appendicitis]], which is caused by ''[[Bacteroides fragilis]]'' and ''[[Escherichia coli]]''. The second is an iatrogenic infection. This type of infection is one that is transmitted from a health care worker to a patient. A nosocomial infection is also one that occurs in a health care setting. Nosocomial infections are those that are acquired during a hospital stay. Lastly, a community-acquired infection is one in which the infection is acquired from a whole community.<ref name=":0" />

====Infectious or not====
One manner of proving that a given disease is infectious, is to satisfy [[Koch's postulates]] (first proposed by [[Robert Koch]]), which require that first, the [[infectious agent]] be identifiable only in patients who have the disease, and not in healthy controls, and second, that patients who contract the infectious agent also develop the disease. These postulates were first used in the discovery that [[Mycobacteria]] species cause [[tuberculosis]].<ref name="pmid28515626">{{cite journal |vauthors=Barberis I, Bragazzi NL, Galluzzo L, Martini M |title=The history of tuberculosis: from the first historical records to the isolation of Koch's bacillus |journal=Journal of Preventive Medicine and Hygiene |volume=58 |issue=1 |pages=E9–E12 |date=March 2017 |pmid=28515626 |pmc=5432783 |doi= |url=}}</ref>

However, Koch's postulates cannot usually be tested in modern practice for ethical reasons. Proving them would require experimental infection of a healthy individual with a [[pathogen]] produced as a pure culture. Conversely, even clearly infectious diseases do not always meet the infectious criteria; for example, ''[[Treponema pallidum]]'', the causative [[spirochete]] of [[syphilis]], cannot be [[microbiological culture|cultured]] ''in vitro'' – however the organism can be cultured in rabbit [[testes]]. It is less clear that a pure culture comes from an animal source serving as host than it is when derived from microbes derived from plate culture.<ref name="pmid31440916">{{cite journal |vauthors=Hosainzadegan H, Khalilov R, Gholizadeh P |title=The necessity to revise Koch's postulates and its application to infectious and non-infectious diseases: a mini-review |journal=European Journal of Clinical Microbiology & Infectious Diseases|volume=39 |issue=2 |pages=215–218 |date=February 2020 |pmid=31440916 |doi=10.1007/s10096-019-03681-1 |s2cid=201283277 |url=}}</ref>

[[Epidemiology]], or the study and analysis of who, why and where disease occurs, and what determines whether various populations have a disease, is another important tool used to understand infectious disease. Epidemiologists may determine differences among groups within a population, such as whether certain age groups have a greater or lesser rate of infection; whether groups living in different neighborhoods are more likely to be infected; and by other factors, such as gender and race. Researchers also may assess whether a disease [[outbreak]] is sporadic, or just an occasional occurrence; [[endemic (epidemiology)|endemic]], with a steady level of regular cases occurring in a region; [[epidemic]], with a fast arising, and unusually high number of cases in a region; or [[pandemic]], which is a global epidemic. If the cause of the infectious disease is unknown, epidemiology can be used to assist with tracking down the sources of infection.<ref name="pmid31325286">{{cite journal |vauthors=Riley LW |title=Differentiating Epidemic from Endemic or Sporadic Infectious Disease Occurrence |doi-access=free |s2cid-access=free |journal=Microbiology Spectrum |volume=7 |issue=4 |pages= |date=July 2019 |pmid=31325286 |doi=10.1128/microbiolspec.AME-0007-2019 |s2cid=198135563 |url=|pmc=10957193 }}</ref>

====Contagiousness====
Infectious diseases are sometimes called [[contagious disease]]s when they are easily transmitted by contact with an ill person or their secretions (e.g., [[influenza]]). Thus, a contagious disease is a subset of infectious disease that is especially infective or easily transmitted. All contagious diseases are infectious, but not vice versa.<ref>{{cite web|url=https://equine.ca.uky.edu/content/science-sleuths-science-shapes-diagnostic-tests-infectious-or-contagious-%E2%80%93-which-it|title=Science Sleuths: the Science that Shapes Diagnostic Tests: Infectious or Contagious – Which Is It?|publisher=Ag Equine Programs|access-date=2025-01-03}}</ref><ref>{{cite web|url=https://www.britannica.com/dictionary/eb/qa/The-Difference-between-Contagious-and-Infectious-|title=The Difference between 'Contagious' and 'Infectious'|publisher=Britannica}}</ref> Other types of infectious, transmissible, or communicable diseases with more specialized routes of infection, such as vector transmission or sexual transmission, are usually not regarded as "contagious", and often do not require medical isolation (sometimes loosely called [[quarantine]]) of those affected. However, this specialized connotation of the word "contagious" and "contagious disease" (easy transmissibility) is not always respected in popular use.

Infectious diseases are commonly transmitted from person to person through direct contact. The types of direct contact are through person to person and [[respiratory droplet|droplet spread]]. Indirect contact such as airborne transmission, contaminated objects, food and drinking water, animal person contact, animal reservoirs, insect bites, and environmental reservoirs are another way infectious diseases are transmitted. The [[basic reproduction number]] of an infectious disease measures how easily it spreads through direct or indirect contact.<ref>Higurea & Pietrangelo 2016 {{page needed|date=August 2020}}</ref><ref>{{cite web|url=https://globalhealth.harvard.edu/understanding-predictions-what-is-r-naught/|title=Understanding Predictions: What is R-Naught?|publisher=Harvard|date=February 7, 2020}}</ref>

====By anatomic location====
Infections can be classified by the [[Anatomy|anatomic]] location or [[organ system]] infected, including:<ref>{{Cite web |last=Dahal |first=Prashant |date=2023-04-16 |title=Common Human Infections and Causative Agents |url=https://microbenotes.com/human-infections/ |access-date=2025-02-25 |website=microbenotes.com |language=en-US}}</ref>{{citation needed|date=July 2021}}
* [[Urinary tract infection]]
* [[Skin infection]]
* [[Respiratory tract infection]]
* [[Odontogenic infection]] (an infection that originates within a [[tooth]] or in the closely surrounding tissues)
* [[Vaginal infections]]
* [[Intra-amniotic infection]]
In addition, locations of [[inflammation]] where infection is the most common cause include [[pneumonia]], [[meningitis]] and [[salpingitis]].<ref>{{Cite web |last=CDC |date=2024-12-09 |title=Chapter 17: Pneumococcal Disease |url=https://www.cdc.gov/pinkbook/hcp/table-of-contents/chapter-17-pneumococcal-disease.html |access-date=2025-02-25 |website=Epidemiology and Prevention of Vaccine-Preventable Diseases |language=en-us}}</ref>

==Prevention==
{{main|Public health|Infection control}}
[[File:OCD handwash.jpg|thumb|right|Washing one's hands, a form of [[hygiene]], is an effective way to prevent the spread of infectious disease.<ref name=handhygiene>{{cite journal|vauthors=Bloomfield SF, Aiello AE, Cookson B, O'Boyle C, Larson EL|url=http://www.ajicjournal.org/article/S0196-6553(07)00595-0/fulltext|title=The effectiveness of hand hygiene procedures including hand-washing and alcohol-based hand sanitizers in reducing the risks of infections in home and community settings|journal=American Journal of Infection Control|year=2007|volume=35|issue=10|pages=S27–S64|doi=10.1016/j.ajic.2007.07.001|pmc=7115270|access-date=2017-03-26|archive-date=2020-06-19|archive-url=https://web.archive.org/web/20200619195845/https://www.ajicjournal.org/article/S0196-6553(07)00595-0/fulltext|url-status=live}}</ref>]]
Techniques like hand washing, wearing gowns, and wearing face masks can help prevent infections from being passed from one person to another. [[Asepsis|Aseptic technique]] was introduced in medicine and surgery in the late 19th century and greatly reduced the incidence of infections caused by surgery. Frequent [[hand washing]] remains the most important defense against the spread of unwanted organisms.<ref>{{cite web|url=http://science.education.nih.gov/supplements/nih1/diseases/guide/fig4-longdesc.htm|title="Generalized Infectious Cycle" Diagram Illustration|website=science.education.nih.gov|access-date=2010-01-21|archive-url=https://web.archive.org/web/20090924155114/https://science.education.nih.gov/supplements/nih1/diseases/guide/fig4-longdesc.htm|archive-date=2009-09-24}}</ref> There are other forms of prevention such as avoiding the use of illicit drugs, using a [[condom]], wearing gloves, and having a healthy lifestyle with a balanced diet and regular exercise. Cooking foods well and avoiding foods that have been left outside for a long time is also important.{{citation needed|date=April 2023}}

[[Antimicrobials|Antimicrobial substances]] used to prevent transmission of infections include:{{citation needed|date=April 2023}}
* [[antiseptics]], which are applied to living [[biological tissue|tissue]]/[[skin]]
* [[disinfectant]]s, which destroy microorganisms found on non-living objects.
* [[antibiotic]]s, called [[prophylactic]] when given as prevention rather as treatment of infection. However, long term use of antibiotics leads to resistance of bacteria. While humans do not become immune to antibiotics, the bacteria does. Thus, avoiding using antibiotics longer than necessary helps preventing bacteria from forming mutations that aide in antibiotic resistance.

One of the ways to prevent or slow down the transmission of infectious diseases is to recognize the different characteristics of various diseases.<ref name=Watts>{{cite book |author=Watts, Duncan |title=Six degrees: the science of a connected age |publisher=William Heinemann |location=London |year=2003 |isbn=978-0-393-04142-2 |url-access=registration |url=https://archive.org/details/sixdegrees00dunc }}</ref> Some critical disease characteristics that should be evaluated include [[virulence]], distance traveled by those affected, and level of contagiousness. The human strains of [[Ebola]] virus, for example, incapacitate those infected extremely quickly and kill them soon after. As a result, those affected by this disease do not have the opportunity to travel very far from the initial infection zone.<ref>{{cite book |author=Preston, Richard |title=The hot zone |publisher=Anchor Books |location=Garden City, N.Y. |year=1995 |isbn=978-0-385-49522-6 }}</ref> Also, this virus must spread through skin lesions or permeable membranes such as the eye. Thus, the initial stage of [[Ebola]] is not very contagious since its victims experience only internal hemorrhaging. As a result of the above features, the spread of Ebola is very rapid and usually stays within a relatively confined geographical area. In contrast, the [[human immunodeficiency virus]] ([[HIV]]) kills its victims very slowly by attacking their immune system.<ref name=Sherris>{{cite book |veditors=Ryan KJ, Ray CG | title = Sherris Medical Microbiology | edition = 4th | publisher = McGraw Hill | year = 2004 | isbn = 978-0-8385-8529-0 }}</ref> As a result, many of its victims transmit the virus to other individuals before even realizing that they are carrying the disease. Also, the relatively low virulence allows its victims to travel long distances, increasing the likelihood of an [[epidemic]].{{citation needed|date=April 2023}}

Another effective way to decrease the transmission rate of infectious diseases is to recognize the effects of [[small-world networks]].<ref name=Watts/> In epidemics, there are often extensive interactions within hubs or groups of infected individuals and other interactions within discrete hubs of susceptible individuals. Despite the low interaction between discrete hubs, the disease can jump and spread in a susceptible hub via a single or few interactions with an infected hub. Thus, infection rates in small-world networks can be reduced somewhat if interactions between individuals within infected hubs are eliminated (Figure 1). However, infection rates can be drastically reduced if the main focus is on the prevention of transmission jumps between hubs. The use of needle exchange programs in areas with a high density of drug users with HIV is an example of the successful implementation of this treatment method.<ref>{{Cite book |last1=Programs |first1=National Research Council (US) and Institute of Medicine (US) Panel on Needle Exchange and Bleach Distribution |url=https://www.ncbi.nlm.nih.gov/books/NBK232343/ |title=The Effects of Needle Exchange Programs |last2=Normand |first2=Jacques |last3=Vlahov |first3=David |last4=Moses |first4=Lincoln E. |date=1995 |publisher=National Academies Press (US) |language=en |access-date=2022-10-20 |archive-date=2021-03-10 |archive-url=https://web.archive.org/web/20210310033308/https://www.ncbi.nlm.nih.gov/books/NBK232343/ |url-status=live }}</ref> Another example is the use of ring culling or vaccination of potentially susceptible livestock in adjacent farms to prevent the spread of the [[foot-and-mouth]] virus in 2001.<ref>{{cite journal | vauthors = Ferguson NM, Donnelly CA, Anderson RM | title = The foot-and-mouth epidemic in Great Britain: pattern of spread and impact of interventions | journal = Science | volume = 292 | issue = 5519 | pages = 1155–60 | date = May 2001 | pmid = 11303090 | doi = 10.1126/science.1061020 | bibcode = 2001Sci...292.1155F | s2cid = 16914744 | doi-access = free }}</ref>

A general method to prevent transmission of [[vector (epidemiology)|vector]]-borne pathogens is [[pest control]].

In cases where infection is merely suspected, individuals may be [[quarantined]] until the incubation period has passed and the disease manifests itself or the person remains healthy. Groups may undergo quarantine, or in the case of communities, a [[Cordon sanitaire (medicine)|cordon sanitaire]] may be imposed to prevent infection from spreading beyond the community, or in the case of [[protective sequestration]], into a community. Public health authorities may implement other forms of [[social distancing]], such as school closings, [[lockdown]]s or temporary restrictions (e.g. [[2020–21 Singapore circuit breaker measures|circuit breakers]])<ref>{{Citation |last=von Csefalvay |first=Chris |title=Modeling the control of infectious disease |date=2023 |url=https://linkinghub.elsevier.com/retrieve/pii/B9780323953894000153 |work=Computational Modeling of Infectious Disease |pages=173–215 |publisher=Elsevier |language=en |doi=10.1016/b978-0-32-395389-4.00015-3 |isbn=978-0-323-95389-4 |access-date=2023-03-02 |archive-date=2023-03-05 |archive-url=https://web.archive.org/web/20230305033759/https://linkinghub.elsevier.com/retrieve/pii/B9780323953894000153 |url-status=live |url-access=subscription }}</ref> to control an epidemic.

===Immunity===
[[File:Mallon-Mary 01.jpg|thumb|[[Mary Mallon]] (a.k.a. Typhoid Mary) was an asymptomatic carrier of [[typhoid fever]]. Over the course of her career as a cook, she infected 53 people, three of whom died.]]
Infection with most pathogens does not result in death of the host and the offending organism is ultimately cleared after the symptoms of the disease have waned.<ref name= Baron/> This process requires [[immune system|immune mechanisms]] to kill or inactivate the [[Inoculation|inoculum]] of the pathogen. Specific acquired [[immunity (medical)|immunity]] against infectious diseases may be mediated by [[Antibody|antibodies]] and/or [[T lymphocyte]]s. Immunity mediated by these two factors may be manifested by:
* a direct effect upon a pathogen, such as antibody-initiated [[complement system|complement]]-dependent bacteriolysis, [[Opsonin|opsonoization]], [[phagocytosis]] and killing, as occurs for some bacteria,
* neutralization of viruses so that these organisms cannot enter cells,
* or by T lymphocytes, which will kill a cell parasitized by a microorganism.

The immune system response to a microorganism often causes symptoms such as a high [[fever]] and [[inflammation]], and has the potential to be more devastating than direct damage caused by a microbe.<ref name=Sherris/>

Resistance to infection ([[immunity (medical)|immunity]]) may be acquired following a disease, by [[asymptomatic carrier|asymptomatic carriage]] of the pathogen, by harboring an organism with a similar structure (crossreacting), or by [[vaccination]]. Knowledge of the protective antigens and specific acquired host immune factors is more complete for primary pathogens than for [[opportunistic pathogen]]s. There is also the phenomenon of [[herd immunity]] which offers a measure of protection to those otherwise vulnerable people when a large enough proportion of the population has acquired immunity from certain infections.<ref name="ofg">{{cite web |title=Herd Immunity |url=http://vk.ovg.ox.ac.uk/herd-immunity |url-status=live |archive-url=https://web.archive.org/web/20190802220355/http://vk.ovg.ox.ac.uk/herd-immunity |archive-date=2 August 2019 |access-date=11 August 2023 |publisher=Oxford Vaccine Group, University of Oxford}}</ref>

Immune resistance to an infectious disease requires a critical level of either antigen-specific antibodies and/or T cells when the host encounters the pathogen. Some individuals develop natural [[blood plasma|serum]] antibodies to the surface [[polysaccharide]]s of some agents although they have had little or no contact with the agent, these natural antibodies confer specific protection to adults and are [[passive immunization|passively transmitted]] to newborns.

====Host genetic factors====
The organism that is the target of an infecting action of a specific infectious agent is called the host. The host harbouring an agent that is in a mature or sexually active stage phase is called the definitive host. The intermediate host comes in contact during the larvae stage. A host can be anything living and can attain to asexual and sexual reproduction.<ref>{{cite journal|vauthors=Barreto ML, Teixeira MG, Carmo EH|year=2006|title=Infectious diseases epidemiology|journal=Journal of Epidemiology and Community Health|volume=60|issue=3|pages=192–95|doi=10.1136/jech.2003.011593|pmc=2465549|pmid=16476746}}</ref>
The clearance of the pathogens, either treatment-induced or spontaneous, it can be influenced by the genetic variants carried by the individual patients. For instance, for genotype 1 [[hepatitis C]] treated with [[Pegylated interferon-alpha-2a]] or [[Pegylated interferon-alpha-2b]] (brand names Pegasys or PEG-Intron) combined with [[ribavirin]], it has been shown that genetic polymorphisms near the human IL28B gene, encoding interferon lambda 3, are associated with significant differences in the treatment-induced clearance of the virus. This finding, originally reported in ''[[Nature (journal)|Nature]]'',<ref>{{cite journal |vauthors=Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, Sulkowski M, McHutchison JG, Goldstein DB | title = Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance | journal = Nature | volume = 461 | issue = 7262 | pages = 399–401 | year = 2009 | pmid = 19684573 | doi = 10.1038/nature08309 | bibcode = 2009Natur.461..399G | s2cid = 1707096 }}</ref> showed that genotype 1 hepatitis C patients carrying certain genetic variant alleles near the IL28B gene are more possibly to achieve sustained virological response after the treatment than others. Later report from ''Nature''<ref>{{cite journal |vauthors=Thomas DL, Thio CL, Martin MP, Qi Y, Ge D, O'Huigin C, Kidd J, Kidd K, Khakoo SI, Alexander G, Goedert JJ, Kirk GD, Donfield SM, Rosen HR, Tobler LH, Busch MP, McHutchison JG, Goldstein DB, Carrington M | title = Genetic variation in IL28B and spontaneous clearance of hepatitis C virus | journal = Nature | volume = 461 | issue = 7265 | pages = 798–801 | year = 2009 | pmid = 19759533 | pmc = 3172006 | doi = 10.1038/nature08463 | bibcode = 2009Natur.461..798T }}</ref> demonstrated that the same genetic variants are also associated with the natural clearance of the genotype 1 hepatitis C virus.

==Treatments==
When infection attacks the body, [[Infection prevention and control|''anti-infective'' drugs]] can suppress the infection. Several broad types of anti-infective drugs exist, depending on the type of organism targeted; they include antibacterial ([[antibiotic]]; including [[Mycobacterium#Pathogenicity|antitubercular]]), [[Antiviral drug|antiviral]], [[Antifungal medication|antifungal]] and [[antiparasitic]] (including [[antiprotozoal]] and [[antihelminthic]]) agents. Depending on the severity and the type of infection, the antibiotic may be given by mouth or by injection, or may be applied [[topical]]ly. Severe infections of the [[Human brain|brain]] are usually treated with [[Intravenous therapy|intravenous]] antibiotics. Sometimes, multiple antibiotics are used in case there is [[Antibiotic resistance|resistance]] to one antibiotic. Antibiotics only work for bacteria and do not affect viruses. Antibiotics work by slowing down the multiplication of bacteria or killing the bacteria. The most common classes of antibiotics used in medicine include [[penicillin]], [[cephalosporin]]s, [[aminoglycoside]]s, [[macrolide]]s, [[Quinolone antibiotic|quinolones]] and [[Tetracycline antibiotics|tetracyclines]].<ref>{{cite journal | vauthors = Fair RJ, Tor Y | title = Antibiotics and Bacterial Resistance in the 21st Century | journal = Perspectives in Medicinal Chemistry | year=2014 | volume = 6 | pages = 25–64 | doi=10.4137/PMC.S14459 | pmid = 25232278| pmc = 4159373 }}</ref><ref>{{Cite web|title=Antibiotics: List of Common Antibiotics & Types|url=https://www.drugs.com/article/antibiotics.html|access-date=2020-11-10|website=Drugs.com|language=en|archive-date=2021-03-10|archive-url=https://web.archive.org/web/20210310033311/https://www.drugs.com/article/antibiotics.html|url-status=live}}</ref>

Not all infections require treatment, and for many [[self-limiting (biology)|self-limiting]] infections the treatment may cause more side-effects than benefits. [[Antimicrobial stewardship]] is the concept that healthcare providers should treat an infection with an antimicrobial that specifically works well for the target pathogen for the shortest amount of time and to only treat when there is a known or highly suspected pathogen that will respond to the medication.<ref>{{cite journal|last1=O'Brien|first1=Deirdre J.|last2=Gould|first2=Ian M.|title=Maximizing the impact of antimicrobial stewardship|journal=Current Opinion in Infectious Diseases|date=August 2013|volume=26|issue=4|pages=352–58|doi=10.1097/QCO.0b013e3283631046|pmid=23806898|s2cid=5487584}}</ref>

== Susceptibility to infection ==
Pandemics such as [[COVID-19]] show that people dramatically differ in their susceptibility to infection. This may be because of general health, age, or their immune status, e.g. when they have been infected previously. However, it also has become clear that there are genetic factor which determine susceptibility to infection. For instance, up to 40% of [[SARS-CoV-2]] infections may be asymptomatic, suggesting that many people are naturally protected from disease.<ref>{{Cite journal |last1=Oran |first1=Daniel P. |last2=Topol |first2=Eric J. |date=2020-09-01 |title=Prevalence of Asymptomatic SARS-CoV-2 Infection: A Narrative Review |journal=Annals of Internal Medicine |volume=173 |issue=5 |pages=362–367 |doi=10.7326/M20-3012 |issn=1539-3704 |pmc=7281624 |pmid=32491919}}</ref> Large genetic studies have defined risk factors for severe SARS-CoV-2 infections, and [[Genome|genome sequences]] from 659 patients with severe COVID-19 revealed genetic variants that appear to be associated with life-threatening disease. One gene identified in these studies is type I [[Interferon type I|interferon]] (IFN). Autoantibodies against type I IFNs were found in up to 13.7% of patients with life-threatening COVID-19, indicating that a complex interaction between genetics and the [[immune system]] is important for natural resistance to Covid.<ref>{{Cite journal |last1=Beck |first1=David B. |last2=Aksentijevich |first2=Ivona |date=2020-10-23 |title=Susceptibility to severe COVID-19 |journal=Science |language=en |volume=370 |issue=6515 |pages=404–405 |doi=10.1126/science.abe7591 |pmid=33093097 |s2cid=225041500 |issn=0036-8075|doi-access=free }}</ref>

Similarly, mutations in the [[ERAP2]] gene, encoding endoplasmic reticulum aminopeptidase 2, seem to increase the susceptibility to the [[Plague (disease)|plague]], the disease caused by an infection with the bacteria ''[[Yersinia pestis]]''. People who inherited two copies of a complete variant of the gene were twice as likely to have survived the plague as those who inherited two copies of a truncated variant.<ref>{{Cite journal |last1=Klunk |first1=Jennifer |last2=Vilgalys |first2=Tauras P. |last3=Demeure |first3=Christian E. |last4=Cheng |first4=Xiaoheng |last5=Shiratori |first5=Mari |last6=Madej |first6=Julien |last7=Beau |first7=Rémi |last8=Elli |first8=Derek |last9=Patino |first9=Maria I. |last10=Redfern |first10=Rebecca |last11=DeWitte |first11=Sharon N. |last12=Gamble |first12=Julia A. |last13=Boldsen |first13=Jesper L. |last14=Carmichael |first14=Ann |last15=Varlik |first15=Nükhet |date=November 2022 |title=Evolution of immune genes is associated with the Black Death |journal=Nature |volume=611 |issue=7935 |pages=312–319 |doi=10.1038/s41586-022-05349-x |issn=1476-4687 |pmc=9580435 |pmid=36261521|bibcode=2022Natur.611..312K }}</ref>

Susceptibility also determined the epidemiology of infection, given that different populations have different genetic and environmental conditions that affect infections.

==Epidemiology==
{{See also|Epidemic|Pandemic}}
{{owidslider
|start        = 2021
|list         = Template:OWID/infectious disease death rates#gallery
|location      = commons
|caption      =
|title        =
|language     =
|file         = [[File:infectious disease death rates, World, 2021.svg|link=|thumb|upright=1.6|Death rates from infectious disease]]
|startingView = World
}}
[[File:Infectious and parasitic diseases world map - DALY - WHO2004.svg|thumb|upright=1.3|[[Disability-adjusted life year]] for infectious and parasitic diseases per 100,000 inhabitants in 2004:<ref>{{cite web |url=https://www.who.int/entity/healthinfo/global_burden_disease/gbddeathdalycountryestimates2004.xls |title=Age-standardized DALYs per 100,000 by cause, and Member State, 2004 |author=World Health Organization |author-link=World Health Organization |date=February 2009 |access-date=2020-10-05 |archive-date=2021-08-28 |archive-url=https://web.archive.org/web/20210828123901/https://www.who.int/healthinfo/global_burden_disease/gbddeathdalycountryestimates2004.xls |url-status=live }}</ref>{{image key
|{{legend|#b3b3b3|no data}}
|{{legend|#ffff65|≤250}}
|{{legend|#fff200|250–500}}
|{{legend|#ffdc00|500–1000}}
|{{legend|#ffc600|1000–2000}}
|{{legend|#ffb000|2000–3000}}
|{{legend|#ff9a00|3000–4000}}
|{{legend|#ff8400|4000–5000}}
|{{legend|#ff6e00|5000–6250}}
|{{legend|#ff5800|6250–12,500}}
|{{legend|#ff4200|12,500–25,000}}
|{{legend|#ff2c00|25,000–50,000}}
|{{legend|#cb0000|≥50,000}}
}}]]

An estimated 1,680 million people died of infectious diseases in the 20th century<ref>David McCandless, [http://www.informationisbeautiful.net/visualizations/20th-century-death '20th Century Death'] {{Webarchive|url=https://web.archive.org/web/20210917222211/http://www.informationisbeautiful.net/visualizations/20th-century-death |date=17 September 2021 }}</ref> and about 10 million in 2010.<ref>{{cite news |url=http://www.cbc.ca/news/1.2802071 |title=Could Ebola rank among the deadliest communicable diseases? |publisher=CBC News |date=20 October 2014 |access-date=21 October 2014 |archive-date=27 August 2021 |archive-url=https://web.archive.org/web/20210827185958/https://www.cbc.ca/news/1.2802071 |url-status=live }}</ref>

The [[World Health Organization]] collects information on global deaths by [[ICD|International Classification of Disease (ICD) code categories]]. The following table lists the top infectious disease by number of deaths in 2002. 1993 data is included for comparison.

{| class="wikitable sortable"
|+ '''Worldwide mortality due to infectious diseases'''<ref>{{cite web | title=The World Health Report (Annex Table 2) | url=https://www.who.int/whr/2004/annex/topic/en/annex_2_en.pdf |archive-url=https://ghostarchive.org/archive/20221009/https://www.who.int/whr/2004/annex/topic/en/annex_2_en.pdf |archive-date=2022-10-09 |url-status=live | year=2004}}</ref><ref>{{cite web | url=https://www.who.int/whr/1995/en/whr95_ch1_en.pdf |archive-url=https://ghostarchive.org/archive/20221009/https://www.who.int/whr/1995/en/whr95_ch1_en.pdf |archive-date=2022-10-09 |url-status=live | year=1995 | title=Table 5 }}</ref>
! Rank|| Cause of death || Deaths 2002<br /> (in millions) || Percentage of<br /> all deaths || Deaths 1993<br /> (in millions)|| 1993 Rank
|- style="background:#ffdead;"
||N/A|| style="background:#ffdead;"| All infectious diseases || style="background:#ffdead;"|14.7 || style="background:#ffdead; text-align:center;"|25.9% || style="background:#ffdead;"| 16.4 || style="background:#ffdead; text-align:center;"|32.2%
|-
| 1 ||[[Lower respiratory tract infection|Lower respiratory infections]]<ref>Lower respiratory infections include various [[pneumonia]]s, [[influenza]]s and [[acute bronchitis]].</ref>
||3.9 || style="text-align:center;"|6.9%||4.1||1
|-
| 2 |||[[HIV]]/[[AIDS]] ||2.8 || style="text-align:center;"|4.9% || 0.7||7
|-
| 3 ||[[Gastroenteritis|Diarrheal diseases]]<ref>Diarrheal diseases are caused by many different organisms, including [[cholera]], [[botulism]], and ''[[Escherichia coli|E. coli]]'' <!-- THIS APPEARS TO BE A LIST OF TWO DISEASES and ONE ORGANISM -->to name a few. See also: [[Intestinal infectious diseases]]</ref>||1.8 || style="text-align:center;"|3.2% ||3.0||2
|-
| 4 ||[[Tuberculosis]] (TB)|| 1.6 || style="text-align:center;"|2.7% ||2.7 ||3
|-
| 5 ||[[Malaria]] ||1.3 || style="text-align:center;"|2.2% ||2.0 ||4
|-
| 6 || [[Measles]] ||0.6 || style="text-align:center;"|1.1% ||1.1 ||5
|-
| 7 ||[[Pertussis]] ||0.29|| style="text-align:center;"|0.5% ||0.36 ||7
|-
| 8 ||[[Tetanus]] ||0.21 || style="text-align:center;"|0.4% ||0.15 ||12
|-
| 9 ||[[Meningitis]]||0.17 || style="text-align:center;"|0.3% ||0.25 ||8
|-
| 10 ||[[Syphilis]]||0.16 || style="text-align:center;"|0.3% ||0.19 || 11
|-
| 11 ||[[Hepatitis B]] ||0.10 || style="text-align:center;"|0.2% ||0.93 || 6
|-
| 12–17 ||[[Tropical disease]]s (6)<ref>Tropical diseases include [[Chagas disease]], [[dengue fever]], [[filariasis|lymphatic filariasis]], [[leishmaniasis]], [[onchocerciasis]], [[schistosomiasis]] and [[trypanosomiasis]].</ref> ||0.13 || style="text-align:center;"|0.2% ||0.53 ||9, 10, 16–18
|-
| style="text-align:left;" colspan=6| {{small|''Note: Other causes of death include maternal and perinatal conditions (5.2%), nutritional deficiencies (0.9%),<br /> noncommunicable conditions (58.8%), and injuries (9.1%).''}}
|}

The top three single agent/disease killers are [[HIV]]/[[AIDS]], [[tuberculosis|TB]] and [[malaria]]. While the number of deaths due to nearly every disease have decreased, deaths due to HIV/AIDS have increased fourfold. Childhood diseases include [[pertussis]], [[poliomyelitis]], [[diphtheria]], [[measles]] and [[tetanus]]. Children also make up a large percentage of lower respiratory and diarrheal deaths. In 2012, approximately 3.1 million people have died due to lower respiratory infections, making it the number 4 leading cause of death in the world.<ref>{{Cite web|title = WHO {{!}} The top 10 causes of death|url = https://www.who.int/mediacentre/factsheets/fs310/en/|publisher = WHO|access-date = 2015-09-24|archive-date = 2017-05-30|archive-url = https://web.archive.org/web/20170530121727/http://www.who.int/mediacentre/factsheets/fs310/en/|url-status = live}}</ref>

===Historic pandemics===
{{See also|List of epidemics}}
[[File:Marseille-peste-Serre.jpg|thumb|The [[Great Plague of Marseille]] in 1720 killed 100,000 people in the city and the surrounding provinces.]]
With their potential for unpredictable and explosive impacts, infectious diseases have been major actors in human [[history]].<ref name=Fauci2012>{{cite journal |vauthors=Fauci AS, Morens DM |title=The perpetual challenge of infectious diseases |journal=New England Journal of Medicine |volume=366 |issue=5 |pages=454–61 |date=2012 |pmid=22296079 |doi=10.1056/NEJMra1108296 |doi-access=free }}</ref> A [[pandemic]] (or global [[epidemic]]) is a disease that affects people over an extensive geographical area. For example:
* [[Plague of Justinian]], from 541 to 542, killed between 50% and 60% of Europe's population.<ref>[http://eee.uci.edu/clients/bjbecker/PlaguesandPeople/lecture3.html "Infectious and Epidemic Disease in History"] {{webarchive |url=https://archive.today/20120712145547/http://eee.uci.edu/clients/bjbecker/PlaguesandPeople/lecture3.html |date=July 12, 2012 }}</ref>
* The [[Black Death]] of 1347 to 1352 killed 25 million in Europe over five years. The plague reduced the old world population from an estimated 450 million to between 350 and 375 million in the 14th century.
* The introduction of [[smallpox]], measles, and [[typhus]] to the areas of Central and South America by European explorers during the 15th and 16th centuries caused pandemics among the native inhabitants. Between 1518 and 1568 disease pandemics are said to have caused the population of [[Mexico]] to fall from 20 million to 3 million.<ref name= Dobson>{{cite journal| vauthors = Dobson AP, Carter ER| year = 1996| url = http://www.erin.utoronto.ca/~w3gwynne/BIO418/Dobson1996.pdf| title = Infectious Diseases and Human Population History| journal = BioScience| volume = 46| issue = 2| doi = 10.2307/1312814| pages = 115–26| jstor = 1312814| s2cid = 89361444 | doi-access = free| access-date = 2013-11-27| archive-date = 2016-03-03| archive-url = https://web.archive.org/web/20160303231520/http://www.erin.utoronto.ca/~w3gwynne/BIO418/Dobson1996.pdf| url-status = live}}</ref>
* The first European [[influenza]] epidemic occurred between 1556 and 1560, with an estimated mortality rate of 20%.<ref name= Dobson/>
* [[Smallpox]] killed an estimated 60 million Europeans during the 18th century<ref>{{Cite web |title=NCpedia {{!}} NCpedia |url=https://www.ncpedia.org/anchor/smallpox |access-date=2023-11-17 |website=www.ncpedia.org |archive-date=2023-03-28 |archive-url=https://web.archive.org/web/20230328055149/https://www.ncpedia.org/anchor/smallpox |url-status=live }}</ref> (approximately 400,000 per year).<ref>[https://archive.today/20090601172056/http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=vacc.chapter.3 Smallpox and Vaccinia]. ''National Center for Biotechnology Information.''</ref> Up to 30% of those infected, including 80% of the children under 5 years of age, died from the disease, and one-third of the survivors went blind.<ref>{{cite journal |title=Smallpox: The Triumph over the Most Terrible of the Ministers of Death|first=Nicolau|last=Barquet|date=15 October 1997 |journal=Annals of Internal Medicine|volume=127|issue=8_Part_1|pages=635–42|doi=10.7326/0003-4819-127-8_Part_1-199710150-00010|pmid=9341063|s2cid=20357515}}</ref>
* In the 19th century, [[tuberculosis]] killed an estimated one-quarter of the adult population of Europe;<ref>[https://www.cdc.gov/TB/pubs/mdrtb/default.htm Multidrug-Resistant "Tuberculosis"]. ''Centers for Disease Control and Prevention.'' {{webarchive |url=https://web.archive.org/web/20100309043219/http://www.cdc.gov/TB/pubs/mdrtb/default.htm |date=March 9, 2010 }}</ref> by 1918 one in six deaths in France were still caused by TB.
* The Influenza Pandemic of 1918 (or the [[Spanish flu]]) killed 25–50 million people (about 2% of world population of 1.7 billion).<ref>{{cite web|url=http://www.history.navy.mil/library/online/influenza_main.htm|archive-url=https://web.archive.org/web/20060220113240/http://www.history.navy.mil/library/online/influenza_main.htm|archive-date=20 February 2006|title=Influenza of 1918 (Spanish Flu) and the US Navy|date=20 February 2006}}</ref> Today [[Influenza]] kills about 250,000 to 500,000 worldwide each year.
* In 2021, COVID-19 emerged as a major global health crisis, directly causing 8.7 million deaths, making it one of the leading causes of mortality worldwide.<ref>{{Cite web |title=Leading causes of death |url=https://www.who.int/data/gho/data/themes/mortality-and-global-health-estimates/ghe-leading-causes-of-death |website=World Health Organization |access-date=2024-12-30}}</ref>

===Emerging diseases===
In most cases, microorganisms live in harmony with their hosts via [[mutualism (biology)|mutual]] or [[commensalism|commensal]] interactions. Diseases can emerge when existing parasites become pathogenic or when new pathogenic parasites enter a new host.

# [[Coevolution]] between [[parasite]] and [[host (biology)|host]] can lead to hosts becoming [[Immune tolerance|resistant]] to the parasites or the parasites may evolve greater [[virulence]], leading to [[immunopathology|immunopathological disease]].
# Human activity is involved with many [[emerging infectious disease]]s, such as [[environment (ecology)|environmental change]] enabling a parasite to occupy new [[ecological niche|niches]]. When that happens, a [[pathogen]] that had been confined to a remote habitat has a wider distribution and possibly a new [[host (biology)|host organism]]. Parasites jumping from nonhuman to human hosts are known as [[zoonosis|zoonoses]]. Under disease invasion, when a parasite invades a new host species, it may become pathogenic in the new host.<ref name= Krauss>{{cite book |author=Krauss H |title=Zoonoses: Infectious Diseases Transmissible from Animals to Humans |publisher=ASM Press |location=Washington, D.C. |year=2003 |edition=3rd |isbn=978-1-55581-236-2 |author2=Weber A |author3=Appel M }}</ref>

Several human activities have led to the emergence of [[zoonotic]] human pathogens, including viruses, bacteria, protozoa, and rickettsia,<ref>{{cite journal | title=Summer buzz | author=Potter P | journal=Emerg Infect Dis |date=July 2013 | volume=19 | issue=3 | doi=10.3201/eid1907.AC1907 | page=1184| pmc=3903457 }}</ref> and spread of [[Vector (epidemiology)|vector-borne]] diseases,<ref name= Krauss /> see also [[globalization and disease]] and [[wildlife disease]]:
* Encroachment on wildlife [[habitat]]s. The construction of new villages and housing developments in rural areas force animals to live in dense populations, creating opportunities for microbes to mutate and emerge.<ref>{{cite journal |author=Peter Daszak |author2=Andrew A. Cunningham |author3=Alex D. Hyatt |title=Emerging Infectious Diseases of Wildlife – Threats to Biodiversity and Human Health |journal=Science |volume=287 |issue=5452 |date=27 January 2000 |pages=443–49 |pmid= 10642539 |doi=10.1126/science.287.5452.443 |bibcode=2000Sci...287..443D }}</ref>
* Changes in [[agriculture]]. The introduction of new crops attracts new crop pests and the microbes they carry to farming communities, exposing people to unfamiliar diseases.
* The destruction of [[rain forests]]. As countries make use of their rain forests, by building roads through forests and clearing areas for settlement or commercial ventures, people encounter insects and other animals harboring previously unknown microorganisms.
* Uncontrolled [[urbanization]]. The rapid growth of cities in many developing countries tends to concentrate large numbers of people into crowded areas with poor sanitation. These conditions foster transmission of contagious diseases.
* Modern [[transport]]. Ships and other cargo carriers often harbor unintended "passengers", that can spread diseases to faraway destinations. While with international jet-airplane travel, people infected with a disease can carry it to distant lands, or home to their families, before their first symptoms appear.

==Germ theory of disease==
{{Main|Germ theory of disease}}
In [[Classical antiquity|Antiquity]], the [[Ancient Greece|Greek]] historian [[Thucydides]] ({{circa|460}} – {{circa|400 BCE}}) was the first person to write, in his account of the [[plague of Athens]], that diseases could spread from an infected person to others.<ref>{{Cite web |title=Annals of medical history. v.1 1917. |url=https://hdl.handle.net/2027/mdp.39015016778261?urlappend=%3Bseq=28 |access-date=2023-11-17 |website=HathiTrust |page=14 | hdl=2027/mdp.39015016778261?urlappend=%3Bseq=28 |language=en |archive-date=2023-11-17 |archive-url=https://web.archive.org/web/20231117122937/https://babel.hathitrust.org/cgi/imgsrv/html?id=mdp.39015016778261&seq=31 |url-status=live }}</ref><ref>{{Cite book |last1=Thucydides |url=http://archive.org/details/pelocrawleyr00thucuoft |title=History of the Peloponnesian War, done into English by Richard Crawley |last2=Crawley |first2=Richard |date=1914 |publisher=London Dent |others=Robarts - University of Toronto |pages=131–132}}</ref> In his ''On the Different Types of Fever'' ({{circa|175 AD}}), the Greco-Roman physician [[Galen]] speculated that plagues were spread by "certain seeds of plague", which were present in the air.<ref>{{Cite journal |last=Nutton |first=V |date=January 1983 |title=The seeds of disease: an explanation of contagion and infection from the Greeks to the Renaissance. |journal=Medical History |volume=27 |issue=1 |pages=1–34 |doi=10.1017/s0025727300042241 |issn=0025-7273 |pmc=1139262 |pmid=6339840 }}</ref> In the [[Sushruta Samhita]], the ancient Indian physician [[Sushruta]] theorized: "Leprosy, fever, consumption, diseases of the eye, and other infectious diseases spread from one person to another by sexual union, physical contact, eating together, sleeping together, sitting together, and the use of same clothes, garlands and pastes."<ref>{{Cite journal|last1=Rastogi|first1=Nalin|last2=Rastogi|first2=R|date=1985-01-01|title=Leprosy in ancient India|url=https://www.researchgate.net/publication/16797371|journal=International Journal of Leprosy and Other Mycobacterial Diseases|volume=52|issue=4|pages=541–43|pmid=6399073}}</ref><ref>{{Cite book|last1=Susruta|url=http://archive.org/details/englishtranslati00susruoft|title=An English translation of the Sushruta samhita, based on original Sanskrit text. Edited and published by Kaviraj Kunja Lal Bhishagratna. With a full and comprehensive introd., translation of different readings, notes, comparative views, index, glossary and plates|last2=Bhishagratna|first2=Kunja Lal|date=1907–1916|publisher=Calcutta|others=Gerstein – University of Toronto}}</ref> This book has been dated to about the sixth century BC.<ref>{{Cite book|last=Hoernle|first=A. F. Rudolf (August Friedrich Rudolf)|url=http://archive.org/details/studiesinmedicin01hoeruoft|title=Studies in the medicine of ancient India|date=1907|publisher=Oxford : At the Clarendon Press|others=Gerstein – University of Toronto}}</ref>

A basic form of contagion theory was proposed by [[Ancient Iranian medicine|Persian]] physician [[Ibn Sina]] (known as Avicenna in Europe) in ''[[The Canon of Medicine]]'' (1025), which later became the most authoritative medical textbook in Europe up until the 16th century. In Book IV of the ''Canon'', Ibn Sina discussed [[epidemics]], outlining the classical [[miasma theory]] and attempting to blend it with his own early contagion theory. He mentioned that people can transmit disease to others by breath, noted contagion with [[tuberculosis]], and discussed the transmission of disease through water and dirt.<ref>{{cite book |last1=Byrne |first1=Joseph Patrick |title=Encyclopedia of the Black Death |date=2012 |publisher=[[ABC-CLIO]] |isbn=978-1-59884-253-1 |page=29 |url=https://books.google.com/books?id=5KtDfvlSrDAC&pg=PA29}}</ref> The concept of invisible contagion was later discussed by several [[medicine in the medieval Islamic world|Islamic scholars]] in the [[Ayyubid Sultanate]] who referred to them as ''[[najasat]]'' ("impure substances"). The [[fiqh]] scholar [[Ibn al-Haj al-Abdari]] ({{circa|1250}}–1336), while discussing [[Islamic dietary laws|Islamic diet]] and [[Islamic hygienical jurisprudence|hygiene]], gave warnings about how contagion can contaminate water, food, and garments, and could spread through the water supply, and may have implied contagion to be unseen particles.<ref>{{cite book |last1=Reid |first1=Megan H. |title=Law and Piety in Medieval Islam |date=2013 |publisher=[[Cambridge University Press]] |isbn=978-1-107-06711-0 |pages=106, 114, 189–90 |url=https://books.google.com/books?id=5fJ4AAAAQBAJ}}</ref>

When the [[Black Death]] [[bubonic plague]] reached [[Al-Andalus]] in the 14th century, the Arab physicians Ibn Khatima ({{circa|1369}}) and [[Ibn al-Khatib]] (1313–1374) hypothesised that infectious diseases were caused by "minute bodies" and described how they can be transmitted through garments, vessels and earrings.<ref>{{cite journal |last1=Majeed |first1=Azeem |title=How Islam changed medicine |journal=[[BMJ]] |date=22 December 2005 |volume=331 |issue=7531 |pages=1486–87 |doi=10.1136/bmj.331.7531.1486 |pmid=16373721 |pmc=1322233 |issn=0959-8138}}</ref> Ideas of contagion became more popular in Europe during the [[Renaissance]], particularly through the writing of the Italian physician [[Girolamo Fracastoro]].<ref>{{cite journal | author = Beretta M | title = The revival of Lucretian atomism and contagious diseases during the renaissance | journal = Medicina Nei Secoli | volume = 15 | issue = 2 | pages = 129–54 | year = 2003 | pmid = 15309812 }}</ref> [[Anton van Leeuwenhoek]] (1632–1723) advanced the science of [[microscopy]] by being the first to observe microorganisms, allowing for easy visualization of bacteria.

In the mid-19th century [[John Snow (physician)|John Snow]] and [[William Budd]] did important work demonstrating the contagiousness of typhoid and cholera through contaminated water. Both are credited with decreasing epidemics of cholera in their towns by implementing measures to prevent contamination of water.<ref>{{cite journal | author = Moorhead Robert | date = November 2002 | title = William Budd and typhoid fever | journal = J R Soc Med | volume = 95 | issue = 11| pages = 561–64 | pmc=1279260 | pmid=12411628 | doi=10.1177/014107680209501115}}</ref> [[Louis Pasteur]] proved beyond doubt that certain diseases are caused by infectious agents, and developed a vaccine for [[rabies]]. [[Robert Koch]] provided the study of infectious diseases with a scientific basis known as [[Koch's postulates]]. [[Edward Jenner]], [[Jonas Salk]] and [[Albert Sabin]] developed effective vaccines for [[smallpox]] and [[polio]], which would later result in the [[eradication of infectious diseases|eradication]] and near-eradication of these diseases, respectively. [[Alexander Fleming]] discovered the world's first [[antibiotic]], [[penicillin]], which Florey and Chain then developed. [[Gerhard Domagk]] developed [[sulfonamide (medicine)|sulphonamides]], the first broad spectrum [[Chemical synthesis|synthetic]] antibacterial drugs.{{citation needed|date=April 2023}}

===Medical specialists===
The [[medicine|medical treatment]] of infectious diseases falls into the [[specialty (medicine)|medical field]] of [[infectious disease (medical specialty)|Infectious Disease]] and in some cases the study of propagation pertains to the field of [[Epidemiology]]. Generally, infections are initially diagnosed by [[primary care]] physicians or [[internal medicine]] specialists. For example, an "uncomplicated" [[pneumonia]] will generally be treated by the [[internist]] or the [[pulmology|pulmonologist]] (lung physician). The work of the infectious diseases specialist therefore entails working with both patients and general practitioners, as well as [[Research|laboratory scientists]], [[immunology|immunologists]], [[bacteriologist]]s and other specialists.<ref>{{Cite book |last=Evans |first=Alfred S. |chapter=Epidemiological Concepts |date=2009-05-29 |title=Bacterial Infections of Humans |pages=1–50 |doi=10.1007/978-0-387-09843-2_1 |pmc=7176254|isbn=978-0-387-09842-5 }}</ref>

An infectious disease team may be alerted when:{{citation needed|date=April 2023}}
* The disease has not been definitively diagnosed after an initial workup
* The patient is [[immunocompromised]] (for example, in [[AIDS]] or after [[chemotherapy]]);
* The [[infectious agent]] is of an uncommon nature (e.g. [[tropical disease]]s);
* The disease has not responded to first line [[antibiotic]]s;
* The disease might be dangerous to other patients, and the patient might have to be isolated

==Society and culture==
Several studies have reported associations between pathogen load in an area and human behavior. Higher pathogen load is associated with decreased size of ethnic and religious groups in an area. This may be due high pathogen load favoring avoidance of other groups, which may reduce pathogen transmission, or a high pathogen load preventing the creation of large settlements and armies that enforce a common culture. Higher pathogen load is also associated with more restricted sexual behavior, which may reduce pathogen transmission. It also associated with higher preferences for health and attractiveness in mates. Higher [[fertility rate]]s and shorter or less parental care per child is another association that may be a compensation for the higher mortality rate. There is also an association with [[polygyny]] which may be due to higher pathogen load, making selecting males with a high genetic resistance increasingly important. Higher pathogen load is also associated with more collectivism and less individualism, which may limit contacts with outside groups and infections. There are alternative explanations for at least some of the associations although some of these explanations may in turn ultimately be due to pathogen load. Thus, polygyny may also be due to a lower male: female ratio in these areas but this may ultimately be due to male infants having increased mortality from infectious diseases. Another example is that poor socioeconomic factors may ultimately in part be due to high pathogen load preventing economic development.<ref name="pmid19683831">{{cite journal | author = Nettle D | title = Ecological influences on human behavioural diversity: a review of recent findings | journal = Trends Ecol. Evol. | volume = 24 | issue = 11 | pages = 618–24 | year = 2009 | pmid = 19683831 | doi = 10.1016/j.tree.2009.05.013 | bibcode = 2009TEcoE..24..618N }}</ref>

==Fossil record==
{{Main|Paleopathology}}
[[File:Herrerasaurus1.JPG|thumb|150px|right|alt=Skull of dinosaur with long jaws and teeth.|''[[Herrerasaurus]]'' skull]]
Evidence of infection in [[Fossil|fossil remains]] is a subject of interest for [[paleopathologists]], scientists who study occurrences of injuries and illness in extinct life forms. Signs of infection have been discovered in the bones of carnivorous dinosaurs. When present, however, these infections seem to tend to be confined to only small regions of the body. A skull attributed to the early carnivorous dinosaur ''[[Herrerasaurus ischigualastensis]]'' exhibits pit-like wounds surrounded by swollen and porous bone. The unusual texture of the bone around the wounds suggests they were affected by a short-lived, non-lethal infection. Scientists who studied the skull speculated that the bite marks were received in a fight with another ''Herrerasaurus''. Other carnivorous dinosaurs with documented evidence of infection include ''[[Acrocanthosaurus]]'', ''[[Allosaurus]]'', ''[[Tyrannosaurus]]'' and a tyrannosaur from the [[Kirtland Formation]]. The infections from both tyrannosaurs were received by being bitten during a fight, like the ''Herrerasaurus'' specimen.<ref name="molnar-pathology">Molnar, R. E., 2001, "Theropod paleopathology: a literature survey": In: ''Mesozoic Vertebrate Life'', edited by Tanke, D. H., and Carpenter, K., Indiana University Press, pp. 337–63.</ref>

==Outer space==
{{main|Effect of spaceflight on the human body|Medical treatment during spaceflight|Space medicine}}
A 2006 [[Space Shuttle]] experiment found that ''[[Salmonella typhimurium]]'', a bacterium that can cause [[food poisoning]], became more [[virulent]] when cultivated in [[Outer space|space]].<ref name="ASU-20070923">{{cite web |last=Caspermeyer |first=Joe |title=Space flight shown to alter ability of bacteria to cause disease |url=https://biodesign.asu.edu/news/space-flight-shown-alter-ability-bacteria-cause-disease |date=23 September 2007 |website=[[Arizona State University]] |access-date=14 September 2017 |archive-date=14 September 2017 |archive-url=https://web.archive.org/web/20170914172718/https://biodesign.asu.edu/news/space-flight-shown-alter-ability-bacteria-cause-disease }}</ref> On April 29, 2013, scientists in [[Rensselaer Polytechnic Institute]], funded by [[NASA]], reported that, during [[spaceflight]] on the [[International Space Station]], [[microbes]] seem to adapt to the [[space environment]] in ways "not observed on Earth" and in ways that "can lead to increases in growth and virulence".<ref name="PLos-20130429">{{cite journal  |vauthors=Kim W, etal |title=Spaceflight Promotes Biofilm Formation by Pseudomonas aeruginosa |date=April 29, 2013 |journal=[[PLOS ONE]] |volume=8 |issue=4 |page=e6237 |doi=10.1371/journal.pone.0062437 |pmid=23658630 |pmc=3639165 |bibcode=2013PLoSO...862437K |doi-access=free }}</ref> More recently, in 2017, [[bacteria]] were found to be more resistant to [[antibiotic]]s and to thrive in the near-weightlessness of space.<ref name="GZM-20170913">{{cite web |last=Dvorsky |first=George |title=Alarming Study Indicates Why Certain Bacteria Are More Resistant to Drugs in Space |url=https://gizmodo.com/alarming-study-indicates-why-certain-bacteria-are-more-1805666249 |date=13 September 2017 |website=[[Gizmodo]] |access-date=14 September 2017 |archive-date=14 September 2017 |archive-url=https://web.archive.org/web/20170914011750/http://gizmodo.com/alarming-study-indicates-why-certain-bacteria-are-more-1805666249 |url-status=live }}</ref> [[Microorganism]]s have been observed to survive the [[vacuum]] of outer space.<ref name=Dose>{{cite journal | title=ERA-experiment "space biochemistry" | journal=Advances in Space Research | volume=16 | issue=8 | year=1995 | pages=119–29 | doi=10.1016/0273-1177(95)00280-R | pmid=11542696 | last1=Dose | first1=K. | last2=Bieger-Dose | first2=A. | last3=Dillmann | first3=R. | last4=Gill | first4=M. | last5=Kerz | first5=O. | last6=Klein | first6=A. | last7=Meinert | first7=H. | last8=Nawroth | first8=T. | last9=Risi | first9=S. | last10=Stridde | first10=C. | bibcode=1995AdSpR..16h.119D | url=http://publications.ub.uni-mainz.de/opus/volltexte/2008/11364/pdf/11364.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://publications.ub.uni-mainz.de/opus/volltexte/2008/11364/pdf/11364.pdf |archive-date=2022-10-09 |url-status=live }}{{Dead link|date=August 2018 |bot=InternetArchiveBot |fix-attempted=yes }}</ref><ref name='Horneck'>{{cite journal | title=Biological responses to space: results of the experiment "Exobiological Unit" of ERA on EURECA I | journal=Adv. Space Res. | year=1995 | author1=Horneck G. |author2=Eschweiler, U. |author3=Reitz, G. |author4=Wehner, J. |author5=Willimek, R. |author6=Strauch, K. | volume=16 | issue=8 | pages=105–18| pmid=11542695 | bibcode=1995AdSpR..16h.105H |doi=10.1016/0273-1177(95)00279-N}}</ref>

==See also==
{{div col|colwidth=30em}}
* [[Biological hazard]]
* [[Blood-borne disease]]
* [[Coinfection]]
* [[Copenhagen Consensus]]
* [[Cordon sanitaire (medicine)|Cordon sanitaire]]
* [[Epidemiological transition]]
* [[Foodborne illness]]
* [[Hospital-acquired infection]]
* [[Eradication of infectious diseases]]
* [[Infection control]]
* [[Isolation (health care)]]
* [[List of causes of death by rate]]
* [[List of diseases caused by insects]]
* [[List of infectious diseases]]
* [[Mathematical modelling of infectious disease]]
* [[Multiplicity of infection]]
* [[Neglected tropical diseases]]
* [[Outline of infectious disease concepts]]
* [[Sentinel surveillance]]
* [[Spillover infection]]
* [[Threshold host density]]
* [[Transmission (medicine)]]
* [[Vaccine-preventable diseases]]
* [[Waterborne diseases]]
{{div col end}}

== References ==
{{Reflist}}

==External links==
{{Medical resources
 | DiseasesDB =28832
 | ICD10 = {{ICD10|A|00||a|00}}-{{ICD10|B|99||b|99}}
 | ICD9 = {{ICD9|001-139}}
 | ICDO =
 | OMIM =
 | OMIM_mult =
 | MedlinePlus =
 | eMedicineSubj =
 | eMedicineTopic =
 | eMedicine_mult =
 | MeshID = D003141
}}
{{Commons category|Infectious diseases and disorders}}
* [https://www.ecdc.europa.eu/en European Center for Disease Prevention and Control]
* [https://www.cdc.gov/ U.S. Centers for Disease Control and Prevention],
* [https://www.idsociety.org/ Infectious Disease Society of America] (IDSA)
* [https://web.archive.org/web/20070817112159/http://www.vrc.nih.gov/ Vaccine Research Center] Information concerning vaccine research clinical trials for Emerging and re-Emerging Infectious Diseases.
* ''[https://www.sciencedirect.com/journal/microbes-and-infection Microbes & Infection]'' (journal)

{{Infectious disease}}
{{Concepts in infectious disease}}
{{History of infectious disease}}
{{Medicine}}
{{Pathology}}
{{Vaccines}}
{{Disease groups}}
{{Portal bar|Medicine|Viruses}}
{{Authority control}}

{{DEFAULTSORT:Infection}}
[[Category:Infectious diseases| ]]
[[Category:Epidemiology]]