Pathogenomics

During the earlier times when genomics was being studied, scientists found it challenging to sequence genetic information.{{cite journal | vauthors = Pallen MJ, Wren BW | title = Bacterial pathogenomics | journal = Nature | volume = 449 | issue = 7164 | pages = 835–42 | date = October 2007 | pmid = 17943120 | doi = 10.1038/nature06248 | bibcode = 2007Natur.449..835P | s2cid = 4313623 }} The field began to explode in 1977 when Fred Sanger, PhD, along with his colleagues, sequenced the DNA-based genome of a bacteriophage, using a method now known as the Sanger Method.{{cite journal | vauthors = Brownlee GG |date=2015-08-19 |title=Frederick Sanger CBE CH OM. 13 August 1918 — 19 November 2013 |journal=Biographical Memoirs of Fellows of the Royal Society |volume=61 |pages=437–466 |doi=10.1098/rsbm.2015.0013 |doi-access=free }}{{Cite book|title=Prescott's microbiology|last=Willey | first = Joanne M | name-list-style = vanc | publisher=McGraw-Hill Education |year=2020 |isbn=9781260211887 |location=New York, New York |pages=431–432 |oclc=1039422993 }}{{cite web |url=https://www.yourgenome.org/facts/ |title=Timeline: Organisms that have had their genomes sequenced |date=19 January 2015|website=Your Genome |access-date=9 November 2019}} The Sanger Method for sequencing DNA exponentially advanced molecular biology and directly led to the ability to sequence genomes of other organisms, including the complete human genome.

The Haemophilus influenza genome was one of the first organism genomes sequenced in 1995 by J. Craig Venter and Hamilton Smith using whole genome shotgun sequencing.{{cite journal | vauthors = Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM | display-authors = 6 | title = Whole-genome random sequencing and assembly of Haemophilus influenzae Rd | journal = Science | volume = 269 | issue = 5223 | pages = 496–512 | date = July 1995 | pmid = 7542800 | doi = 10.1126/science.7542800 | bibcode = 1995Sci...269..496F }} Since then, newer and more efficient high-throughput sequencing, such as Next Generation Genomic Sequencing (NGS) and Single-Cell Genomic Sequencing, have been developed. While the Sanger method is able to sequence one DNA fragment at a time, NGS technology can sequence thousands of sequences at a time.{{cite web | url= https://www.illumina.com/science/technology/next-generation-sequencing/ngs-vs-sanger-sequencing.html |title=Key Differences between next-generation sequencing and Sanger sequencing }} With the ability to rapidly sequence DNA, new insights developed, such as the discovery that since prokaryotic genomes are more diverse than originally thought, it is necessary to sequence multiple strains in a species rather than only a few.{{cite journal | vauthors = Fraser-Liggett CM | title = Insights on biology and evolution from microbial genome sequencing | journal = Genome Research | volume = 15 | issue = 12 | pages = 1603–10 | date = December 2005 | pmid = 16339357 | doi = 10.1101/gr.3724205 | doi-access = free }} E.coli was an example of why this is important, with genes encoding virulence factors in two strains of the species differing by at least thirty percent. Such knowledge, along with more thorough study of genome gain, loss, and change, is giving researchers valuable insight into how pathogens interact in host environments and how they are able to infect hosts and cause disease.

With this high influx of new information, there has arisen a higher demand for bioinformatics so scientists can properly analyze the new data. In response, software and other tools have been developed for this purpose.{{cite journal | vauthors = Oakeson KF, Wagner JM, Mendenhall M, Rohrwasser A, Atkinson-Dunn R | title = Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory | language = en-us | journal = Emerging Infectious Diseases | volume = 23 | issue = 9 | pages = 1441–1445 | date = September 2017 | pmid = 28820135 | pmc = 5572866 | doi = 10.3201/eid2309.170416 }} Also, as of 2008, the amount of stored sequences was doubling every 18 months, making urgent the need for better ways to organize data and aid research.{{cite web | vauthors = Lathe W, Williams J, Mangan M, Karolchik D | title = Genomic data resources: challenges and promises. | work = Nature Education | date = 2008 | volume = 1 | issue = 3 | pages = 2 | url = https://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721/ }} In response, many publicly accessible databases and other resources have been created, including the NCBI pathogen detection program, the Pathosystems Resource Integration Centre (PATRIC),{{Cite journal |last1=Davis |first1=James J. |last2=Wattam |first2=Alice R. |last3=Aziz |first3=Ramy K. |last4=Brettin |first4=Thomas |last5=Butler |first5=Ralph |last6=Butler |first6=Rory M. |last7=Chlenski |first7=Philippe |last8=Conrad |first8=Neal |last9=Dickerman |first9=Allan |last10=Dietrich |first10=Emily M. |last11=Gabbard |first11=Joseph L. |date=2020-01-08 |title=The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities |journal=Nucleic Acids Research |volume=48 |issue=D1 |pages=D606–D612 |doi=10.1093/nar/gkz943 |issn=1362-4962 |pmc=7145515 |pmid=31667520}} Pathogenwatch,{{Cite journal |last1=Argimón |first1=Silvia |last2=Yeats |first2=Corin A. |last3=Goater |first3=Richard J. |last4=Abudahab |first4=Khalil |last5=Taylor |first5=Benjamin |last6=Underwood |first6=Anthony |last7=Sánchez-Busó |first7=Leonor |last8=Wong |first8=Vanessa K. |last9=Dyson |first9=Zoe A. |last10=Nair |first10=Satheesh |last11=Park |first11=Se Eun |date=2021-05-17 |title=A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch |journal=Nature Communications |volume=12 |issue=1 |pages=2879 |doi=10.1038/s41467-021-23091-2 |issn=2041-1723 |pmc=8128892 |pmid=34001879|bibcode=2021NatCo..12.2879A }} the Virulence Factor Database (VFDB) of pathogenic bacteria,{{Cite web|url=http://www.mgc.ac.cn/cgi-bin/VFs/v5/main.cgi|title=VFDB: Virulence Factors of Bacterial Pathogens|website=www.mgc.ac.cn|access-date=2019-11-08}} the Victors database of virulence factors in human and animal pathogens.{{Cite journal |last1=Sayers |first1=Samantha |last2=Li |first2=Li |last3=Ong |first3=Edison |last4=Deng |first4=Shunzhou |last5=Fu |first5=Guanghua |last6=Lin |first6=Yu |last7=Yang |first7=Brian |last8=Zhang |first8=Shelley |last9=Fa |first9=Zhenzong |last10=Zhao |first10=Bin |last11=Xiang |first11=Zuoshuang |date=2019-01-08 |title=Victors: a web-based knowledge base of virulence factors in human and animal pathogens |journal=Nucleic Acids Research |volume=47 |issue=D1 |pages=D693–D700 |doi=10.1093/nar/gky999 |issn=1362-4962 |pmc=6324020 |pmid=30365026}} Until 2022, the most sequenced pathogens are Salmonella enterica and E. coli - Shigella. The sequencing technologies, the bioinformatics tools, the databases, statistics related to pathogen genomes and the applications in forensics, epidemiology, clinical practice and food safety have been extensively reviewed.

Pathogens may be prokaryotic (archaea or bacteria), single-celled eukarya or viruses. Prokaryotic genomes have typically been easier to sequence due to smaller genome size compared to Eukarya. Due to this, there is a bias in reporting pathogenic bacterial behavior. Regardless of this bias in reporting, many of the dynamic genomic events are similar across all the types of pathogen organisms. Genomic evolution occurs via gene gain, gene loss, and genome rearrangement, and these "events" are observed in multiple pathogen genomes, with some bacterial pathogens experiencing all three. Pathogenomics does not focus exclusively on understanding pathogen-host interactions, however. Insight of individual or cooperative pathogen behavior provides knowledge into the development or inheritance of pathogen virulence factors. Through a deeper understanding of the small sub-units that cause infection, it may be possible to develop novel therapeutics that are efficient and cost-effective.{{cite journal | vauthors = Rappuoli R | title = Reverse vaccinology, a genome-based approach to vaccine development | journal = Vaccine | volume = 19 | issue = 17–19 | pages = 2688–91 | date = March 2001 | pmid = 11257410 | doi = 10.1016/S0264-410X(00)00554-5 }}

Dynamic genomes with high plasticity are necessary to allow pathogens, especially bacteria, to survive in changing environments. With the assistance of high throughput sequencing methods and in silico technologies, it is possible to detect, compare and catalogue many of these dynamic genomic events. Genomic diversity is important when detecting and treating a pathogen since these events can change the function and structure of the pathogen.{{cite encyclopedia |url= https://www.britannica.com/science/gene-flow |title=Gene flow {{!}} genetics | encyclopedia =Encyclopedia Britannica |access-date=2019-11-04 }}{{cite book |last1=Griffiths |first1=Anthony JF |last2=Miller |first2=Jeffrey H. |last3=Suzuki |first3=David T. |last4=Lewontin |first4=Richard C. |last5=Gelbart |first5=William M. | name-list-style = vanc |date=2000 | chapter = Sources of variation |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK22012/ |title = An Introduction to Genetic Analysis |publisher=W.H. Freeman | edition = 7th | isbn = 978-0-7167-3771-1 }} There is a need to analyze more than a single genome sequence of a pathogen species to understand pathogen mechanisms. Comparative genomics is a methodology which allows scientists to compare the genomes of different species and strains.{{Cite web|url=https://www.genome.gov/about-genomics/fact-sheets/Comparative-Genomics-Fact-Sheet|title=Comparative Genomics Fact Sheet|website=Genome.gov|language=en|access-date=2019-11-13}} There are several examples of successful comparative genomics studies, among them the analysis of Listeria{{cite journal | vauthors = Hain T, Chatterjee SS, Ghai R, Kuenne CT, Billion A, Steinweg C, Domann E, Kärst U, Jänsch L, Wehland J, Eisenreich W, Bacher A, Joseph B, Schär J, Kreft J, Klumpp J, Loessner MJ, Dorscht J, Neuhaus K, Fuchs TM, Scherer S, Doumith M, Jacquet C, Martin P, Cossart P, Rusniock C, Glaser P, Buchrieser C, Goebel W, Chakraborty T | display-authors = 6 | title = Pathogenomics of Listeria spp | journal = International Journal of Medical Microbiology | volume = 297 | issue = 7–8 | pages = 541–57 | date = November 2007 | pmid = 17482873 | doi = 10.1016/j.ijmm.2007.03.016 }} and Escherichia coli.{{cite journal | vauthors = Perna NT, Plunkett G, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Pósfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalanta ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR | display-authors = 6 | title = Genome sequence of enterohaemorrhagic Escherichia coli O157:H7 | journal = Nature | volume = 409 | issue = 6819 | pages = 529–33 | date = January 2001 | pmid = 11206551 | doi = 10.1038/35054089 | bibcode = 2001Natur.409..529P | doi-access = free }} Some studies have attempted to address the difference between pathogenic and non-pathogenic microbes. This inquiry proves to be difficult, however, since a single bacterial species can have many strains, and the genomic content of each of these strains varies.

Varying microbe strains and genomic content are caused by different forces, including three specific evolutionary events which have an impact on pathogen resistance and ability to cause disease, a: gene gain, gene loss, and genome rearrangement.

Gene loss occurs when genes are deleted. The reason why this occurs is still not fully understood,{{cite journal | vauthors = Koskiniemi S, Sun S, Berg OG, Andersson DI | title = Selection-driven gene loss in bacteria | journal = PLOS Genetics | volume = 8 | issue = 6 | pages = e1002787 | date = June 2012 | pmid = 22761588 | pmc = 3386194 | doi = 10.1371/journal.pgen.1002787 | doi-access = free }} though it most likely involves adaptation to a new environment or ecological niche.{{cite journal | vauthors = Bliven KA, Maurelli AT | title = Antivirulence genes: insights into pathogen evolution through gene loss | journal = Infection and Immunity | volume = 80 | issue = 12 | pages = 4061–70 | date = December 2012 | pmid = 23045475 | pmc = 3497401 | doi = 10.1128/iai.00740-12 }}{{cite journal | vauthors = Ward PN, Holden MT, Leigh JA, Lennard N, Bignell A, Barron A, Clark L, Quail MA, Woodward J, Barrell BG, Egan SA, Field TR, Maskell D, Kehoe M, Dowson CG, Chanter N, Whatmore AM, Bentley SD, Parkhill J | display-authors = 6 | title = Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis | journal = BMC Genomics | volume = 10 | pages = 54 | date = January 2009 | pmid = 19175920 | pmc = 2657157 | doi = 10.1186/1471-2164-10-54 | doi-access = free }} Some researchers believe gene loss may actually increase fitness and survival among pathogens. In a new environment, some genes may become unnecessary for survival, and so mutations are eventually "allowed" on those genes until they become inactive "pseudogenes." These pseudogenes are observed in organisms such as Shigella flexneri, Salmonella enterica,{{cite journal | vauthors = Parkhill J, Dougan G, James KD, Thomson NR, Pickard D, Wain J, Churcher C, Mungall KL, Bentley SD, Holden MT, Sebaihia M, Baker S, Basham D, Brooks K, Chillingworth T, Connerton P, Cronin A, Davis P, Davies RM, Dowd L, White N, Farrar J, Feltwell T, Hamlin N, Haque A, Hien TT, Holroyd S, Jagels K, Krogh A, Larsen TS, Leather S, Moule S, O'Gaora P, Parry C, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG | display-authors = 6 | title = Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18 | journal = Nature | volume = 413 | issue = 6858 | pages = 848–52 | date = October 2001 | pmid = 11677608 | doi = 10.1038/35101607 | bibcode = 2001Natur.413..848P | doi-access = free }} and Yersinia pestis. Over time, the pseudogenes are deleted, and the organisms become fully dependent on their host as either endosymbionts or obligate intracellular pathogens, as is seen in Buchnera, Myobacterium leprae, and Chlamydia trachomatis. These deleted genes are also called Anti-virulence genes (AVG) since it is thought they may have prevented the organism from becoming pathogenic. In order to be more virulent, infect a host and remain alive, the pathogen had to get rid of those AVGs. The reverse process can happen as well, as was seen during analysis of Listeria strains, which showed that a reduced genome size led to a non-pathogenic Listeria strain from a pathogenic strain. Systems have been developed to detect these pseudogenes/AVGs in a genome sequence.

File:Improved Figure1. copy.png

One of the key forces driving gene gain is thought to be horizontal (lateral) gene transfer (LGT).{{cite journal | vauthors = Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbø CL, Case RJ, Doolittle WF | display-authors = 6 | title = Lateral gene transfer and the origins of prokaryotic groups | journal = Annual Review of Genetics | volume = 37 | pages = 283–328 | year = 2003 | pmid = 14616063 | doi = 10.1146/annurev.genet.37.050503.084247 }} It is of particular interest in microbial studies because these mobile genetic elements may introduce virulence factors into a new genome.{{cite journal | vauthors = Lima WC, Paquola AC, Varani AM, Van Sluys MA, Menck CF | title = Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism | journal = FEMS Microbiology Letters | volume = 281 | issue = 1 | pages = 87–97 | date = April 2008 | pmid = 18318843 | doi = 10.1111/j.1574-6968.2008.01083.x | doi-access = free }} A comparative study conducted by Gill et al. in 2005 postulated that LGT may have been the cause for pathogen variations between Staphylococcus epidermidis and Staphylococcus aureus.{{cite journal | vauthors = Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM | display-authors = 6 | title = Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain | journal = Journal of Bacteriology | volume = 187 | issue = 7 | pages = 2426–38 | date = April 2005 | pmid = 15774886 | pmc = 1065214 | doi = 10.1128/JB.187.7.2426-2438.2005 }} There still, however, remains skepticism about the frequency of LGT, its identification, and its impact.{{cite journal | vauthors = Bapteste E, Boucher Y | title = Lateral gene transfer challenges principles of microbial systematics | journal = Trends in Microbiology | volume = 16 | issue = 5 | pages = 200–7 | date = May 2008 | pmid = 18420414 | doi = 10.1016/j.tim.2008.02.005 }} New and improved methodologies have been engaged, especially in the study of phylogenetics, to validate the presence and effect of LGT.{{cite journal | vauthors = Huang J, Gogarten JP | title = Ancient horizontal gene transfer can benefit phylogenetic reconstruction | journal = Trends in Genetics | volume = 22 | issue = 7 | pages = 361–6 | date = July 2006 | pmid = 16730850 | doi = 10.1016/j.tig.2006.05.004 }} Gene gain and gene duplication events are balanced by gene loss, such that despite their dynamic nature, the genome of a bacterial species remains approximately the same size.{{cite journal | vauthors = Mira A, Ochman H, Moran NA | title = Deletional bias and the evolution of bacterial genomes | journal = Trends in Genetics | volume = 17 | issue = 10 | pages = 589–96 | date = October 2001 | pmid = 11585665 | doi = 10.1016/S0168-9525(01)02447-7 }}

Mobile genetic insertion sequences can play a role in genome rearrangement activities.{{cite journal | vauthors = Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeño-Tárraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PC, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG | display-authors = 6 | title = Genome sequence of Yersinia pestis, the causative agent of plague | journal = Nature | volume = 413 | issue = 6855 | pages = 523–7 | date = October 2001 | pmid = 11586360 | doi = 10.1038/35097083 | bibcode = 2001Natur.413..523P | author-link1 = Julian Parkhill | doi-access = free }} Pathogens that do not live in an isolated environment have been found to contain a large number of insertion sequence elements and various repetitive segments of DNA. The combination of these two genetic elements is thought help mediate homologous recombination. There are pathogens, such as Burkholderia mallei,{{cite journal | vauthors = Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM | display-authors = 6 | title = Structural flexibility in the Burkholderia mallei genome | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 39 | pages = 14246–51 | date = September 2004 | pmid = 15377793 | pmc = 521142 | doi = 10.1073/pnas.0403306101 | bibcode = 2004PNAS..10114246N | doi-access = free }} and Burkholderia pseudomallei{{cite journal | vauthors = Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J | display-authors = 6 | title = Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 39 | pages = 14240–5 | date = September 2004 | pmid = 15377794 | pmc = 521101 | doi = 10.1073/pnas.0403302101 | doi-access = free }} which have been shown to exhibit genome-wide rearrangements due to insertion sequences and repetitive DNA segments. At this time, no studies demonstrate genome-wide rearrangement events directly giving rise to pathogenic behavior in a microbe. This does not mean it is not possible. Genome-wide rearrangements do, however, contribute to the plasticity of bacterial genome, which may prime the conditions for other factors to introduce, or lose, virulence factors.

Single Nucleotide Polymorphisms, or SNPs, allow for a wide array of genetic variation among humans as well as pathogens. They allow researchers to estimate a variety of factors: the effects of environmental toxins, how different treatment methods affect the body, and what causes someone's predisposition to illnesses.{{Cite web |url= https://ghr.nlm.nih.gov/primer/genomicresearch/snp |title=What are single nucleotide polymorphisms (SNPs)? |website=Genetics Home Reference|language=en|access-date=2019-11-08}} SNPs play a key role in understanding how and why mutations occur. SNPs also allows for scientists to map genomes and analyze genetic information.

File:Pan-genome-graphics.png

Pan-genome overview The most recent definition of a bacterial species comes from the pre-genomic era. In 1987, it was proposed that bacterial strains showing >70% DNA·DNA re-association and sharing characteristic phenotypic traits should be considered to be strains of the same species.{{cite journal | vauthors = Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, Khouri H, Radune D, Dimitrov G, Watkins K, O'Connor KJ, Smith S, Utterback TR, White O, Rubens CE, Grandi G, Madoff LC, Kasper DL, Telford JL, Wessels MR, Rappuoli R, Fraser CM | display-authors = 6 | title = Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome" | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 39 | pages = 13950–5 | date = September 2005 | pmid = 16172379 | pmc = 1216834 | doi = 10.1073/pnas.0506758102 | bibcode = 2005PNAS..10213950T | doi-access = free }} The diversity within pathogen genomes makes it difficult to identify the total number of genes that are associated within all strains of a pathogen species. It has been thought that the total number of genes associated with a single pathogen species may be unlimited, although some groups are attempting to derive a more empirical value.{{cite journal | vauthors = Lapierre P, Gogarten JP | title = Estimating the size of the bacterial pan-genome | journal = Trends in Genetics | volume = 25 | issue = 3 | pages = 107–10 | date = March 2009 | pmid = 19168257 | doi = 10.1016/j.tig.2008.12.004 }} For this reason, it was necessary to introduce the concept of pan-genomes and core genomes.{{cite journal | vauthors = Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R | title = The microbial pan-genome | journal = Current Opinion in Genetics & Development | volume = 15 | issue = 6 | pages = 589–94 | date = December 2005 | pmid = 16185861 | doi = 10.1016/j.gde.2005.09.006 }} Pan-genome and core genome literature also tends to have a bias towards reporting on prokaryotic pathogenic organisms. Caution may need to be exercised when extending the definition of a pan-genome or a core-genome to the other pathogenic organisms because there is no formal evidence of the properties of these pan-genomes.{{cn|date=June 2022}}

A core genome is the set of genes found across all strains of a pathogen species. A pan-genome is the entire gene pool for that pathogen species, and includes genes that are not shared by all strains. Pan-genomes may be open or closed depending on whether comparative analysis of multiple strains reveals no new genes (closed) or many new genes (open) compared to the core genome for that pathogen species. In the open pan-genome, genes may be further characterized as dispensable or strain specific. Dispensable genes are those found in more than one strain, but not in all strains, of a pathogen species. Strain specific genes are those found only in one strain of a pathogen species. The differences in pan-genomes are reflections of the life style of the organism. For example, Streptococcus agalactiae, which exists in diverse biological niches, has a broader pan-genome when compared with the more environmentally isolated Bacillus anthracis. Comparative genomics approaches are also being used to understand more about the pan-genome.{{cite journal | vauthors = Tettelin H, Riley D, Cattuto C, Medini D | title = Comparative genomics: the bacterial pan-genome | journal = Current Opinion in Microbiology | volume = 11 | issue = 5 | pages = 472–7 | date = October 2008 | pmid = 19086349 | doi = 10.1016/j.mib.2008.09.006 }} Recent discoveries show that the number of new species continue to grow with an estimated 10³¹ bacteriophages on the planet with those bacteriophages infecting 10²⁴ others per second, the continuous flow of genetic material being exchanged is difficult to imagine.

Multiple genetic elements of human-affecting pathogens contribute to the transfer of virulence factors: plasmids, pathogenicity island, prophages, bacteriophages, transposons, and integrative and conjugative elements.{{cite journal | vauthors = Gennari M, Ghidini V, Caburlotto G, Lleo MM | title = Virulence genes and pathogenicity islands in environmental Vibrio strains nonpathogenic to humans | journal = FEMS Microbiology Ecology | volume = 82 | issue = 3 | pages = 563–73 | date = December 2012 | pmid = 22676367 | doi = 10.1111/j.1574-6941.2012.01427.x | doi-access = free | bibcode = 2012FEMME..82..563G }} Pathogenicity islands and their detection are the focus of several bioinformatics efforts involved in pathogenomics.{{cite journal | vauthors = Langille MG, Brinkman FS | title = IslandViewer: an integrated interface for computational identification and visualization of genomic islands | journal = Bioinformatics | volume = 25 | issue = 5 | pages = 664–5 | date = March 2009 | pmid = 19151094 | pmc = 2647836 | doi = 10.1093/bioinformatics/btp030 }}{{cite journal | vauthors = Guy L | title = Identification and characterization of pathogenicity and other genomic islands using base composition analyses | journal = Future Microbiology | volume = 1 | issue = 3 | pages = 309–16 | date = October 2006 | pmid = 17661643 | doi = 10.2217/17460913.1.3.309 }} It is a common belief that "environmental bacterial strains" lack the capacity to harm or do damage to humans. However, recent studies show that bacteria from aquatic environments have acquired pathogenic strains through evolution. This allows for the bacteria to have a wider range in genetic traits and can cause a potential threat to humans from which there is more resistance towards antibiotics.

File:Staphylococcus aureus biofilm 01.jpg

Microbe-host interactions tend to overshadow the consideration of microbe-microbe interactions. Microbe-microbe interactions though can lead to chronic states of infirmity that are difficult to understand and treat.

Biofilms are an example of microbe-microbe interactions and are thought to be associated with up to 80% of human infections.{{Cite web| title=Research on microbial biofilms (PA-03-047) | url=http://grants.nih.gov/grants/guide/pa-files/PA-03-047.html | date=2002-12-20 | publisher=NIH, National Heart, Lung, and Blood Institute}} Recently it has been shown that there are specific genes and cell surface proteins involved in the formation of biofilm.{{cite journal | vauthors = Valle J, Vergara-Irigaray M, Merino N, Penadés JR, Lasa I | title = sigmaB regulates IS256-mediated Staphylococcus aureus biofilm phenotypic variation | journal = Journal of Bacteriology | volume = 189 | issue = 7 | pages = 2886–96 | date = April 2007 | pmid = 17277051 | pmc = 1855799 | doi = 10.1128/JB.01767-06 }} These genes and also surface proteins may be characterized through in silico methods to form an expression profile of biofilm-interacting bacteria. This expression profile may be used in subsequent analysis of other microbes to predict biofilm microbe behaviour, or to understand how to dismantle biofilm formation.

Pathogens have the ability to adapt and manipulate host cells, taking full advantage of a host cell's cellular processes and mechanisms.

A microbe may be influenced by hosts to either adapt to its new environment or learn to evade it. An insight into these behaviours will provide beneficial insight for potential therapeutics. The most detailed outline of host-microbe interaction initiatives is outlined by the Pathogenomics European Research Agenda. Its report emphasizes the following features:

File:Host-pathogen analysis.png

• Microarray analysis of host and microbe gene expression during infection. This is important for identifying the expression of virulence factors that allow a pathogen to survive a host's defense mechanism. Pathogens tend to undergo an assortment of changed in order to subvert and hosts immune system, in some case favoring a hyper variable genome state.{{cite journal | vauthors = Hogardt M, Hoboth C, Schmoldt S, Henke C, Bader L, Heesemann J | title = Stage-specific adaptation of hypermutable Pseudomonas aeruginosa isolates during chronic pulmonary infection in patients with cystic fibrosis | journal = The Journal of Infectious Diseases | volume = 195 | issue = 1 | pages = 70–80 | date = January 2007 | pmid = 17152010 | doi = 10.1086/509821 | doi-access = free }} The genomic expression studies will be complemented with protein-protein interaction networks studies.
• Using RNA interference (RNAi) to identify host cell functions in response to infections. Infection depends on the balance between the characteristics of the host cell and the pathogen cell. In some cases, there can be an overactive host response to infection, such as in meningitis, which can overwhelm the host's body. Using RNA, it will be possible to more clearly identify how a host cell defends itself during times of acute or chronic infection.{{cite journal | vauthors = Cheng LW, Viala JP, Stuurman N, Wiedemann U, Vale RD, Portnoy DA | title = Use of RNA interference in Drosophila S2 cells to identify host pathways controlling compartmentalization of an intracellular pathogen | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 102 | issue = 38 | pages = 13646–51 | date = September 2005 | pmid = 16157870 | pmc = 1224656 | doi = 10.1073/pnas.0506461102 | bibcode = 2005PNAS..10213646C | doi-access = free }} This has also been applied successfully is Drosophila.
• Not all microbe interactions in host environment are malicious. Commensal flora, which exists in various environments in animals and humans may actually help combating microbial infections. The human flora, such as the gut for example, is home to a myriad of microbes.{{cite journal | vauthors = Hattori M, Taylor TD | title = The human intestinal microbiome: a new frontier of human biology | journal = DNA Research | volume = 16 | issue = 1 | pages = 1–12 | date = February 2009 | pmid = 19147530 | pmc = 2646358 | doi = 10.1093/dnares/dsn033 }}

The diverse community within the gut has been heralded to be vital for human health. There are a number of projects under way to better understand the ecosystems of the gut.{{cite journal | vauthors = Hooper LV, Gordon JI | title = Commensal host-bacterial relationships in the gut | journal = Science | volume = 292 | issue = 5519 | pages = 1115–8 | date = May 2001 | pmid = 11352068 | doi = 10.1126/science.1058709 | bibcode = 2001Sci...292.1115H | s2cid = 44645045 }} The sequence of commensal Escherichia coli strain SE11, for example, has already been determined from the faecal matter of a healthy human and promises to be the first of many studies.{{cite journal | vauthors = Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T, Itoh K, Hattori M | display-authors = 6 | title = Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult | journal = DNA Research | volume = 15 | issue = 6 | pages = 375–86 | date = December 2008 | pmid = 18931093 | pmc = 2608844 | doi = 10.1093/dnares/dsn026 }} Through genomic analysis and also subsequent protein analysis, a better understanding of the beneficial properties of commensal flora will be investigated in hopes of understanding how to build a better therapeutic.{{cite journal | vauthors = Zoetendal EG, Rajilic-Stojanovic M, de Vos WM | title = High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota | journal = Gut | volume = 57 | issue = 11 | pages = 1605–15 | date = November 2008 | pmid = 18941009 | doi = 10.1136/gut.2007.133603 | s2cid = 34347318 }}

The "eco-evo" perspective on pathogen-host interactions emphasizes the influences ecology and the environment on pathogen evolution. The dynamic genomic factors such as gene loss, gene gain and genome rearrangement, are all strongly influenced by changes in the ecological niche where a particular microbial strain resides. Microbes may switch from being pathogenic and non-pathogenic due to changing environments. This was demonstrated during studies of the plague, Yersinia pestis, which apparently evolved from a mild gastrointestinal pathogen to a very highly pathogenic microbe through dynamic genomic events.{{cite journal | vauthors = Achtman M, Morelli G, Zhu P, Wirth T, Diehl I, Kusecek B, Vogler AJ, Wagner DM, Allender CJ, Easterday WR, Chenal-Francisque V, Worsham P, Thomson NR, Parkhill J, Lindler LE, Carniel E, Keim P | display-authors = 6 | title = Microevolution and history of the plague bacillus, Yersinia pestis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 51 | pages = 17837–42 | date = December 2004 | pmid = 15598742 | pmc = 535704 | doi = 10.1073/pnas.0408026101 | bibcode = 2004PNAS..10117837A | doi-access = free }} In order for colonization to occur, there must be changes in biochemical makeup to aid survival in a variety of environments. This is most likely due to a mechanism allowing the cell to sense changes within the environment, thus influencing change in gene expression.{{cite journal | vauthors = Oyston PC, Dorrell N, Williams K, Li SR, Green M, Titball RW, Wren BW | title = The response regulator PhoP is important for survival under conditions of macrophage-induced stress and virulence in Yersinia pestis | journal = Infection and Immunity | volume = 68 | issue = 6 | pages = 3419–25 | date = June 2000 | pmid = 10816493 | pmc = 97616 | doi = 10.1128/IAI.68.6.3419-3425.2000 }} Understanding how these strain changes occur from being low or non-pathogenic to being highly pathogenic and vice versa may aid in developing novel therapeutics for microbial infections.

File:Babyimmunization.jpg

Human health has greatly improved and the mortality rate has declined substantially since the second world war because of improved hygiene due to changing public health regulations, as well as more readily available vaccines and antibiotics.{{cite journal | vauthors = Pompe S, Simon J, Wiedemann PM, Tannert C | title = Future trends and challenges in pathogenomics. A Foresight study | journal = EMBO Reports | volume = 6 | issue = 7 | pages = 600–5 | date = July 2005 | pmid = 15995675 | pmc = 1369123 | doi = 10.1038/sj.embor.7400472 }} Pathogenomics will allow scientists to expand what they know about pathogenic and non-pathogenic microbes, thus allowing for new and improved vaccines. Pathogenomics also has wider implication, including preventing bioterrorism.

Reverse vaccinology is relatively new. While research is still being conducted, there have been breakthroughs with pathogens such as Streptococcus and Meningitis.{{cite journal | vauthors = Sette A, Rappuoli R | title = Reverse vaccinology: developing vaccines in the era of genomics | journal = Immunity | volume = 33 | issue = 4 | pages = 530–41 | date = October 2010 | pmid = 21029963 | pmc = 3320742 | doi = 10.1016/j.immuni.2010.09.017 }} Methods of vaccine production, such as biochemical and serological, are laborious and unreliable. They require the pathogens to be in vitro to be effective.{{cite journal | vauthors = Rappuoli R | title = Reverse vaccinology | journal = Current Opinion in Microbiology | volume = 3 | issue = 5 | pages = 445–50 | date = October 2000 | pmid = 11050440 | doi = 10.1016/S1369-5274(00)00119-3 }} New advances in genomic development help predict nearly all variations of pathogens, thus making advances for vaccines. Protein-based vaccines are being developed to combat resistant pathogens such as Staphylococcus and Chlamydia.

In 2005, the sequence of the 1918 Spanish influenza was completed. Accompanied with phylogenetic analysis, it was possible to supply a detailed account of the virus' evolution and behavior, in particular its adaptation to humans.{{cite journal | vauthors = Taubenberger JK, Reid AH, Lourens RM, Wang R, Jin G, Fanning TG | title = Characterization of the 1918 influenza virus polymerase genes | journal = Nature | volume = 437 | issue = 7060 | pages = 889–93 | date = October 2005 | pmid = 16208372 | doi = 10.1038/nature04230 | bibcode = 2005Natur.437..889T | s2cid = 4405787 | doi-access = free }} Following the sequencing of the Spanish influenza, the pathogen was also reconstructed. When inserted into mice, the pathogen proved to be incredibly deadly.{{cite journal | vauthors = Tumpey TM, Basler CF, Aguilar PV, Zeng H, Solórzano A, Swayne DE, Cox NJ, Katz JM, Taubenberger JK, Palese P, García-Sastre A | display-authors = 6 | title = Characterization of the reconstructed 1918 Spanish influenza pandemic virus | journal = Science | volume = 310 | issue = 5745 | pages = 77–80 | date = October 2005 | pmid = 16210530 | doi = 10.1126/science.1119392 | bibcode = 2005Sci...310...77T | citeseerx = 10.1.1.418.9059 | s2cid = 14773861 }} The 2001 anthrax attacks shed light on the possibility of bioterrorism as being more of a real than imagined threat. Bioterrorism was anticipated in the Iraq war, with soldiers being inoculated for a smallpox attack.{{Cite web|url=http://www.cdi.org/terrorism/smallpox.cfm|title=Terrorism Project)|date=2002-12-20|publisher=Center for Defense Information}} Using technologies and insight gained from reconstruction of the Spanish influenza, it may be possible to prevent future deadly planted outbreaks of disease. There is a strong ethical concern however, as to whether the resurrection of old viruses is necessary and whether it does more harm than good.{{cite journal | vauthors = van Aken J | title = Ethics of reconstructing Spanish flu: is it wise to resurrect a deadly virus? | journal = Heredity | volume = 98 | issue = 1 | pages = 1–2 | date = January 2007 | pmid = 17035950 | doi = 10.1038/sj.hdy.6800911 | s2cid = 32686445 }} The best avenue for countering such threats is coordinating with organizations which provide immunizations. The increased awareness and participation would greatly decrease the effectiveness of a potential epidemic. An addition to this measure would be to monitor natural water reservoirs as a basis to prevent an attack or outbreak. Overall, communication between labs and large organizations, such as Global Outbreak Alert and Response Network (GOARN), can lead to early detection and prevent outbreaks.

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Category:Microbiology

Category:Pathogen genomics