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Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts
Escherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of...
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| Published in: | The Journal of infection 2018-12, Vol.77 (6), p.534-543 |
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| container_issue | 6 |
| container_start_page | 534 |
| container_title | The Journal of infection |
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| creator | Dale, Adam P. Pandey, Anish K. Hesp, Richard J. Belogiannis, Konstantinos Laver, Jay R. Shone, Clifford C. Read, Robert C. |
| description | Escherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of virulence factor (VF) genes amongst bacteraemia isolates from neutropaenic patients would be lower than isolates from immunocompetent patients.
Immunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing.
Isolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p |
| doi_str_mv | 10.1016/j.jinf.2018.10.011 |
| format | article |
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Immunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing.
Isolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p < 0.0001). Number of VF genes (OR 1.21, 95% CIs 1.01–1.46, p = 0.039) and urinary catheter/recurrent urinary tract infection (OR 12.82, 95% CIs 1.24–132.65, p = 0.032) were independent predictors of bacteraemia secondary to UTIF vs. non-UTIF in immunocompetent patients. papA, papC, papE/F, papG, agn43, tia, iut, fyuA, kpsM and sat were significantly more prevalent amongst UTIF- vs non-UTIF-originating isolates amongst immunocompetent patients, while papC, papE/F, papG, agn43, tia, fyuA, hlyA, usp and clb were significantly more prevalent amongst UTIF- vs NPUFI-associated isolates.
Bacteraemia-associated E. coli strains originating from UTIF have distinct VF gene profiles from strains associated with non-UTIF- and NPUFI. This diversity must be addressed in the design of future vaccines to ensure adequate coverage of strains responsible for site-specific disease.</description><identifier>ISSN: 0163-4453</identifier><identifier>EISSN: 1532-2742</identifier><identifier>DOI: 10.1016/j.jinf.2018.10.011</identifier><identifier>PMID: 30391630</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Adult ; Aged ; Aged, 80 and over ; Antimicrobial resistance ; Bacteraemia ; Bacteremia - microbiology ; Escherichia coli ; Escherichia coli - genetics ; Escherichia coli - isolation & purification ; Escherichia coli - pathogenicity ; Escherichia coli Infections - blood ; Escherichia coli Infections - urine ; ExPEC ; Female ; Genome, Bacterial ; Humans ; Immunocompetence ; Male ; Middle Aged ; Neutropaenia ; Neutropenia - microbiology ; Phylogeny ; Prospective Studies ; Sequence Analysis, DNA ; United Kingdom ; Urinary Tract Infections - microbiology ; Virulence ; Virulence factor ; Virulence Factors - genetics ; Whole Genome Sequencing ; Young Adult</subject><ispartof>The Journal of infection, 2018-12, Vol.77 (6), p.534-543</ispartof><rights>2018 The Authors</rights><rights>Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.</rights><rights>2018 The Authors 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c521t-ec2729fc39ca5d67bd595d486c5d7dc2c601cfb45ece05a32ca2c74e423f1c913</citedby><cites>FETCH-LOGICAL-c521t-ec2729fc39ca5d67bd595d486c5d7dc2c601cfb45ece05a32ca2c74e423f1c913</cites><orcidid>0000-0003-3314-5989 ; 0000-0001-8163-7481 ; 0000-0002-4297-6728</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30391630$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dale, Adam P.</creatorcontrib><creatorcontrib>Pandey, Anish K.</creatorcontrib><creatorcontrib>Hesp, Richard J.</creatorcontrib><creatorcontrib>Belogiannis, Konstantinos</creatorcontrib><creatorcontrib>Laver, Jay R.</creatorcontrib><creatorcontrib>Shone, Clifford C.</creatorcontrib><creatorcontrib>Read, Robert C.</creatorcontrib><title>Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts</title><title>The Journal of infection</title><addtitle>J Infect</addtitle><description>Escherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of virulence factor (VF) genes amongst bacteraemia isolates from neutropaenic patients would be lower than isolates from immunocompetent patients.
Immunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing.
Isolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p < 0.0001). Number of VF genes (OR 1.21, 95% CIs 1.01–1.46, p = 0.039) and urinary catheter/recurrent urinary tract infection (OR 12.82, 95% CIs 1.24–132.65, p = 0.032) were independent predictors of bacteraemia secondary to UTIF vs. non-UTIF in immunocompetent patients. papA, papC, papE/F, papG, agn43, tia, iut, fyuA, kpsM and sat were significantly more prevalent amongst UTIF- vs non-UTIF-originating isolates amongst immunocompetent patients, while papC, papE/F, papG, agn43, tia, fyuA, hlyA, usp and clb were significantly more prevalent amongst UTIF- vs NPUFI-associated isolates.
Bacteraemia-associated E. coli strains originating from UTIF have distinct VF gene profiles from strains associated with non-UTIF- and NPUFI. This diversity must be addressed in the design of future vaccines to ensure adequate coverage of strains responsible for site-specific disease.</description><subject>Adult</subject><subject>Aged</subject><subject>Aged, 80 and over</subject><subject>Antimicrobial resistance</subject><subject>Bacteraemia</subject><subject>Bacteremia - microbiology</subject><subject>Escherichia coli</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - isolation & purification</subject><subject>Escherichia coli - pathogenicity</subject><subject>Escherichia coli Infections - blood</subject><subject>Escherichia coli Infections - urine</subject><subject>ExPEC</subject><subject>Female</subject><subject>Genome, Bacterial</subject><subject>Humans</subject><subject>Immunocompetence</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Neutropaenia</subject><subject>Neutropenia - microbiology</subject><subject>Phylogeny</subject><subject>Prospective Studies</subject><subject>Sequence Analysis, DNA</subject><subject>United Kingdom</subject><subject>Urinary Tract Infections - microbiology</subject><subject>Virulence</subject><subject>Virulence factor</subject><subject>Virulence Factors - genetics</subject><subject>Whole Genome Sequencing</subject><subject>Young Adult</subject><issn>0163-4453</issn><issn>1532-2742</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNp9kc-KFDEQxoMo7rj6Ah4kRy895k-nZwMiyLKuwoIXPYdMdfVMDd3JmKQHfC8f0LSzu-jFS0KqvvpVVT7GXkuxlkJ27w7rA4VhrYS8qoG1kPIJW0mjVaM2rXrKVlWkm7Y1-oK9yPkghLDads_ZhRba1pxYsV-3GOKEmceB32TYYyLYk-cQR-JbDwWTx6kGKMfRl0WYaEfBFwo7PqQ48TnVZ_rJS6pyPkSgWh2Kp8CnmJCfKM0jBsDG51yzldLzHYbKKnsf6hEznlEhhuYB9wfkQ88DziXFo8dAwKu25Jfs2eDHjK_u70v2_dPNt-vPzd3X2y_XH-8aMEqWBkFtlB1AW_Cm7zbb3ljTt1cdmH7Tg4JOSBi2rUFAYbxW4BVsWmyVHiRYqS_ZhzP3OG8n7AFD3XF0x0RTndBFT-7fTKC928WT65TVWrYV8PYekOKPGXNxE2XAcfQB45ydkloIY61YeqmzFFLMOeHw2EYKt9jtDm6x2y12L7Fqdy168_eAjyUP_lbB-7MA6zedCJPLQIsXPSWE4vpI_-P_BrN9wxA</recordid><startdate>201812</startdate><enddate>201812</enddate><creator>Dale, Adam P.</creator><creator>Pandey, Anish K.</creator><creator>Hesp, Richard J.</creator><creator>Belogiannis, Konstantinos</creator><creator>Laver, Jay R.</creator><creator>Shone, Clifford C.</creator><creator>Read, Robert C.</creator><general>Elsevier Ltd</general><general>W.B. Saunders</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-3314-5989</orcidid><orcidid>https://orcid.org/0000-0001-8163-7481</orcidid><orcidid>https://orcid.org/0000-0002-4297-6728</orcidid></search><sort><creationdate>201812</creationdate><title>Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts</title><author>Dale, Adam P. ; Pandey, Anish K. ; Hesp, Richard J. ; Belogiannis, Konstantinos ; Laver, Jay R. ; Shone, Clifford C. ; Read, Robert C.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c521t-ec2729fc39ca5d67bd595d486c5d7dc2c601cfb45ece05a32ca2c74e423f1c913</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Adult</topic><topic>Aged</topic><topic>Aged, 80 and over</topic><topic>Antimicrobial resistance</topic><topic>Bacteraemia</topic><topic>Bacteremia - microbiology</topic><topic>Escherichia coli</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - isolation & purification</topic><topic>Escherichia coli - pathogenicity</topic><topic>Escherichia coli Infections - blood</topic><topic>Escherichia coli Infections - urine</topic><topic>ExPEC</topic><topic>Female</topic><topic>Genome, Bacterial</topic><topic>Humans</topic><topic>Immunocompetence</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Neutropaenia</topic><topic>Neutropenia - microbiology</topic><topic>Phylogeny</topic><topic>Prospective Studies</topic><topic>Sequence Analysis, DNA</topic><topic>United Kingdom</topic><topic>Urinary Tract Infections - microbiology</topic><topic>Virulence</topic><topic>Virulence factor</topic><topic>Virulence Factors - genetics</topic><topic>Whole Genome Sequencing</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Dale, Adam P.</creatorcontrib><creatorcontrib>Pandey, Anish K.</creatorcontrib><creatorcontrib>Hesp, Richard J.</creatorcontrib><creatorcontrib>Belogiannis, Konstantinos</creatorcontrib><creatorcontrib>Laver, Jay R.</creatorcontrib><creatorcontrib>Shone, Clifford C.</creatorcontrib><creatorcontrib>Read, Robert C.</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The Journal of infection</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dale, Adam P.</au><au>Pandey, Anish K.</au><au>Hesp, Richard J.</au><au>Belogiannis, Konstantinos</au><au>Laver, Jay R.</au><au>Shone, Clifford C.</au><au>Read, Robert C.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts</atitle><jtitle>The Journal of infection</jtitle><addtitle>J Infect</addtitle><date>2018-12</date><risdate>2018</risdate><volume>77</volume><issue>6</issue><spage>534</spage><epage>543</epage><pages>534-543</pages><issn>0163-4453</issn><eissn>1532-2742</eissn><abstract>Escherichia coli is the leading cause of bacteraemia. In an era of emerging multi-drug-resistant strains, development of effective preventative strategies will be informed by knowledge of strain diversity associated with specific infective syndromes/patient groups. We hypothesised that the number of virulence factor (VF) genes amongst bacteraemia isolates from neutropaenic patients would be lower than isolates from immunocompetent patients.
Immunocompetent and neutropaenic adults with E. coli bacteraemia were recruited prospectively and the source of bacteraemia determined. VF gene profiles were established in silico following whole genome sequencing.
Isolates from individual patients were monoclonal. Strains from immunocompetent patients with urinary tract infective foci (UTIF) harboured more VF genes (median number of VF genes 16, range 8–24) than isolates from both immunocompetent patients with non-UTIF (10, 2–22, p = 0.0058) and neutropaenic patients with unknown focus of infection (NPUFI) (8, 3–13, p < 0.0001). Number of VF genes (OR 1.21, 95% CIs 1.01–1.46, p = 0.039) and urinary catheter/recurrent urinary tract infection (OR 12.82, 95% CIs 1.24–132.65, p = 0.032) were independent predictors of bacteraemia secondary to UTIF vs. non-UTIF in immunocompetent patients. papA, papC, papE/F, papG, agn43, tia, iut, fyuA, kpsM and sat were significantly more prevalent amongst UTIF- vs non-UTIF-originating isolates amongst immunocompetent patients, while papC, papE/F, papG, agn43, tia, fyuA, hlyA, usp and clb were significantly more prevalent amongst UTIF- vs NPUFI-associated isolates.
Bacteraemia-associated E. coli strains originating from UTIF have distinct VF gene profiles from strains associated with non-UTIF- and NPUFI. This diversity must be addressed in the design of future vaccines to ensure adequate coverage of strains responsible for site-specific disease.</abstract><cop>England</cop><pub>Elsevier Ltd</pub><pmid>30391630</pmid><doi>10.1016/j.jinf.2018.10.011</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0003-3314-5989</orcidid><orcidid>https://orcid.org/0000-0001-8163-7481</orcidid><orcidid>https://orcid.org/0000-0002-4297-6728</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Adult Aged Aged, 80 and over Antimicrobial resistance Bacteraemia Bacteremia - microbiology Escherichia coli Escherichia coli - genetics Escherichia coli - isolation & purification Escherichia coli - pathogenicity Escherichia coli Infections - blood Escherichia coli Infections - urine ExPEC Female Genome, Bacterial Humans Immunocompetence Male Middle Aged Neutropaenia Neutropenia - microbiology Phylogeny Prospective Studies Sequence Analysis, DNA United Kingdom Urinary Tract Infections - microbiology Virulence Virulence factor Virulence Factors - genetics Whole Genome Sequencing Young Adult |
| title | Genomes of Escherichia coli bacteraemia isolates originating from urinary tract foci contain more virulence-associated genes than those from non-urinary foci and neutropaenic hosts |
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