Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads
Many virulence factors have been described for opportunistic pathogens within the genus Aeromonas. Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas fr...
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| creator | Talagrand-Reboul, Emilie Latif-Eugenín, Fadua Beaz-Hidalgo, Roxana Colston, Sophie Figueras, Maria-Jose Graf, Joerg Jumas-Bilak, Estelle Lamy, Brigitte |
| description | Many virulence factors have been described for opportunistic pathogens within the genus Aeromonas. Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains. |
| doi_str_mv | 10.1371/journal.pone.0201428 |
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Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0201428</identifier><identifier>PMID: 30110345</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aeromonads ; Aeromonas ; Analysis ; Assaying ; Bacteriology ; Biodiversity ; Biology and Life Sciences ; Cloning ; Cytotoxicity ; Deoxyribonucleic acid ; Diagnostic systems ; DNA ; E coli ; Epidemiology ; Fish ; Food contamination & poisoning ; Genes ; Genetic aspects ; Genetic diversity ; Genetics ; Genomes ; Homology ; Life Sciences ; Medicine and Health Sciences ; Microbiology and Parasitology ; Opportunist infection ; Polymerase chain reaction ; Population studies ; Populations and Evolution ; Proteins ; Redesign ; Research and Analysis Methods ; Sensitivity ; Sensitivity analysis ; Species diversity ; Strains (organisms) ; Virulence ; Virulence (Microbiology) ; Virulence factors</subject><ispartof>PloS one, 2018-08, Vol.13 (8), p.e0201428-e0201428</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Talagrand-Reboul et al. 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Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. 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Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.</description><subject>Aeromonads</subject><subject>Aeromonas</subject><subject>Analysis</subject><subject>Assaying</subject><subject>Bacteriology</subject><subject>Biodiversity</subject><subject>Biology and Life Sciences</subject><subject>Cloning</subject><subject>Cytotoxicity</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnostic systems</subject><subject>DNA</subject><subject>E coli</subject><subject>Epidemiology</subject><subject>Fish</subject><subject>Food contamination & poisoning</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Homology</subject><subject>Life Sciences</subject><subject>Medicine and Health Sciences</subject><subject>Microbiology and 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Polymerase Chain Reactions (PCRs) are commonly used in population studies of aeromonads to detect virulence-associated genes in order to better understand the epidemiology and emergence of Aeromonas from the environment to host, but their performances have never been thoroughly evaluated. We aimed to determine diagnostic sensitivity and specificity of PCR assays for the detection of virulence-associated genes in a collection of Aeromonas isolates representative for the genetic diversity in the genus. Thirty-nine Aeromonas strains belonging to 27 recognized species were screened by published PCR assays for virulence-associated genes (act, aerA, aexT, alt, ascFG, ascV, ast, lafA, lip, ser, stx1, stx2A). In parallel, homologues of the 12 putative virulence genes were searched from the genomes of the 39 strains. Of the 12 published PCR assays for virulence factors, the comparison of PCR results and genome analysis estimated diagnostic sensitivities ranging from 34% to 100% and diagnostic specificities ranged from 71% to 100% depending upon the gene. To improve the detection of virulence-associated genes in aeromonads, we have designed new primer pairs for aerA/act, ser, lafA, ascFG and ascV, which showed excellent diagnostic sensitivity and specificity. Altogether, the analysis of high quality genomic data, which are more and more easy to obtain, provides significant improvements in the genetic detection of virulence factors in bacterial strains.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30110345</pmid><doi>10.1371/journal.pone.0201428</doi><tpages>e0201428</tpages><orcidid>https://orcid.org/0000-0001-9767-0753</orcidid><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
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| subjects | Aeromonads Aeromonas Analysis Assaying Bacteriology Biodiversity Biology and Life Sciences Cloning Cytotoxicity Deoxyribonucleic acid Diagnostic systems DNA E coli Epidemiology Fish Food contamination & poisoning Genes Genetic aspects Genetic diversity Genetics Genomes Homology Life Sciences Medicine and Health Sciences Microbiology and Parasitology Opportunist infection Polymerase chain reaction Population studies Populations and Evolution Proteins Redesign Research and Analysis Methods Sensitivity Sensitivity analysis Species diversity Strains (organisms) Virulence Virulence (Microbiology) Virulence factors |
| title | Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-21T19%3A32%3A16IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-driven%20evaluation%20and%20redesign%20of%20PCR%20tools%20for%20improving%20the%20detection%20of%20virulence-associated%20genes%20in%20aeromonads&rft.jtitle=PloS%20one&rft.au=Talagrand-Reboul,%20Emilie&rft.date=2018-08-15&rft.volume=13&rft.issue=8&rft.spage=e0201428&rft.epage=e0201428&rft.pages=e0201428-e0201428&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0201428&rft_dat=%3Cgale_plos_%3EA550356585%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2088776050&rft_id=info:pmid/30110345&rft_galeid=A550356585&rft_doaj_id=oai_doaj_org_article_e529857deecb4f1b931b8b66175de505&rfr_iscdi=true |