Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon
A multidrug-resistant (MDR) Campylobacter coli ( C. coli ) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the C. coli is...
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| Veröffentlicht in: | Folia microbiologica 2022-04, Vol.67 (2), p.319-328 |
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| creator | Halimeh, Fatima Bachir Rafei, Rayane Diene, Seydina M. Osman, Marwan Kassem, Issmat I. Jamal Akoum, Randa Moudani, Walid Hamze, Monzer Rolain, Jean-Marc |
| description | A multidrug-resistant (MDR)
Campylobacter coli
(
C. coli
) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the
C. coli
isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The
bla
OXA-61
, which is associated with beta-lactam resistance, was also detected in the
C. coli
genome. A set of 30 genes associated with the virulence in
C. coli
was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of
Campylobacter
isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of
Campylobacter
in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant. |
| doi_str_mv | 10.1007/s12223-021-00921-w |
| format | Article |
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Campylobacter coli
(
C. coli
) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the
C. coli
isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The
bla
OXA-61
, which is associated with beta-lactam resistance, was also detected in the
C. coli
genome. A set of 30 genes associated with the virulence in
C. coli
was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of
Campylobacter
isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of
Campylobacter
in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant.</description><identifier>ISSN: 0015-5632</identifier><identifier>EISSN: 1874-9356</identifier><identifier>DOI: 10.1007/s12223-021-00921-w</identifier><identifier>PMID: 34997523</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Amides ; Aminoglycoside antibiotics ; Aminoglycosides ; Antibiotics ; Antimicrobial agents ; Antimicrobial resistance ; Applied Microbiology ; Bacteriology ; Biomedical and Life Sciences ; Campylobacter ; Campylobacter coli ; Campylobacteriosis ; Cardiology and cardiovascular system ; Diarrhea ; Drug resistance ; Emerging diseases ; Environmental Engineering/Biotechnology ; Epidemiology ; Gene sequencing ; Genes ; Genomes ; Human health and pathology ; Immunology ; Infectious diseases ; Life Sciences ; Microbiology ; Microbiology and Parasitology ; Multidrug resistance ; Multidrug resistant organisms ; Mutation ; Nucleotide sequence ; Original Article ; Parasitology ; Phenotypes ; rRNA 16S ; Virology ; Virulence ; Whole genome sequencing ; β-Lactam antibiotics</subject><ispartof>Folia microbiologica, 2022-04, Vol.67 (2), p.319-328</ispartof><rights>Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2021</rights><rights>2021. Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i.</rights><rights>Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2021.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c409t-f05a33c89743b8d3e641e069617ed5b85f89820e9667cf02cf13f3483f3a9da33</citedby><cites>FETCH-LOGICAL-c409t-f05a33c89743b8d3e641e069617ed5b85f89820e9667cf02cf13f3483f3a9da33</cites><orcidid>0000-0001-7466-5118 ; 0000-0002-2978-9573 ; 0000-0002-2402-4467 ; 0000-0002-6466-2324 ; 0000-0002-6235-2760</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s12223-021-00921-w$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s12223-021-00921-w$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,777,781,882,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34997523$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://amu.hal.science/hal-03663664$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Halimeh, Fatima Bachir</creatorcontrib><creatorcontrib>Rafei, Rayane</creatorcontrib><creatorcontrib>Diene, Seydina M.</creatorcontrib><creatorcontrib>Osman, Marwan</creatorcontrib><creatorcontrib>Kassem, Issmat I.</creatorcontrib><creatorcontrib>Jamal Akoum, Randa</creatorcontrib><creatorcontrib>Moudani, Walid</creatorcontrib><creatorcontrib>Hamze, Monzer</creatorcontrib><creatorcontrib>Rolain, Jean-Marc</creatorcontrib><title>Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon</title><title>Folia microbiologica</title><addtitle>Folia Microbiol</addtitle><addtitle>Folia Microbiol (Praha)</addtitle><description>A multidrug-resistant (MDR)
Campylobacter coli
(
C. coli
) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the
C. coli
isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The
bla
OXA-61
, which is associated with beta-lactam resistance, was also detected in the
C. coli
genome. A set of 30 genes associated with the virulence in
C. coli
was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of
Campylobacter
isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of
Campylobacter
in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant.</description><subject>Amides</subject><subject>Aminoglycoside antibiotics</subject><subject>Aminoglycosides</subject><subject>Antibiotics</subject><subject>Antimicrobial agents</subject><subject>Antimicrobial resistance</subject><subject>Applied Microbiology</subject><subject>Bacteriology</subject><subject>Biomedical and Life Sciences</subject><subject>Campylobacter</subject><subject>Campylobacter coli</subject><subject>Campylobacteriosis</subject><subject>Cardiology and cardiovascular system</subject><subject>Diarrhea</subject><subject>Drug resistance</subject><subject>Emerging diseases</subject><subject>Environmental Engineering/Biotechnology</subject><subject>Epidemiology</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genomes</subject><subject>Human health and pathology</subject><subject>Immunology</subject><subject>Infectious diseases</subject><subject>Life Sciences</subject><subject>Microbiology</subject><subject>Microbiology and Parasitology</subject><subject>Multidrug resistance</subject><subject>Multidrug resistant organisms</subject><subject>Mutation</subject><subject>Nucleotide sequence</subject><subject>Original Article</subject><subject>Parasitology</subject><subject>Phenotypes</subject><subject>rRNA 16S</subject><subject>Virology</subject><subject>Virulence</subject><subject>Whole genome sequencing</subject><subject>β-Lactam 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sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon</title><author>Halimeh, Fatima Bachir ; Rafei, Rayane ; Diene, Seydina M. ; Osman, Marwan ; Kassem, Issmat I. ; Jamal Akoum, Randa ; Moudani, Walid ; Hamze, Monzer ; Rolain, Jean-Marc</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c409t-f05a33c89743b8d3e641e069617ed5b85f89820e9667cf02cf13f3483f3a9da33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amides</topic><topic>Aminoglycoside antibiotics</topic><topic>Aminoglycosides</topic><topic>Antibiotics</topic><topic>Antimicrobial agents</topic><topic>Antimicrobial resistance</topic><topic>Applied Microbiology</topic><topic>Bacteriology</topic><topic>Biomedical and Life Sciences</topic><topic>Campylobacter</topic><topic>Campylobacter coli</topic><topic>Campylobacteriosis</topic><topic>Cardiology and cardiovascular system</topic><topic>Diarrhea</topic><topic>Drug resistance</topic><topic>Emerging diseases</topic><topic>Environmental Engineering/Biotechnology</topic><topic>Epidemiology</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genomes</topic><topic>Human health and pathology</topic><topic>Immunology</topic><topic>Infectious diseases</topic><topic>Life Sciences</topic><topic>Microbiology</topic><topic>Microbiology and Parasitology</topic><topic>Multidrug resistance</topic><topic>Multidrug resistant organisms</topic><topic>Mutation</topic><topic>Nucleotide sequence</topic><topic>Original Article</topic><topic>Parasitology</topic><topic>Phenotypes</topic><topic>rRNA 16S</topic><topic>Virology</topic><topic>Virulence</topic><topic>Whole genome sequencing</topic><topic>β-Lactam antibiotics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Halimeh, Fatima Bachir</creatorcontrib><creatorcontrib>Rafei, 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Central Basic</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Folia microbiologica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Halimeh, Fatima Bachir</au><au>Rafei, Rayane</au><au>Diene, Seydina M.</au><au>Osman, Marwan</au><au>Kassem, Issmat I.</au><au>Jamal Akoum, Randa</au><au>Moudani, Walid</au><au>Hamze, Monzer</au><au>Rolain, Jean-Marc</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon</atitle><jtitle>Folia microbiologica</jtitle><stitle>Folia Microbiol</stitle><addtitle>Folia Microbiol (Praha)</addtitle><date>2022-04-01</date><risdate>2022</risdate><volume>67</volume><issue>2</issue><spage>319</spage><epage>328</epage><pages>319-328</pages><issn>0015-5632</issn><eissn>1874-9356</eissn><abstract>A multidrug-resistant (MDR)
Campylobacter coli
(
C. coli
) strain was isolated from a 2-month-old newborn who suffered from severe diarrhea in Lebanon. Here, whole-genome sequencing (WGS) analysis was deployed to determine the genetic basis of antimicrobial resistance and virulence in the
C. coli
isolate and to identify its epidemiological background (sequence type). The identity of the isolate was confirmed using API® Campy, MALDI-TOF, and 16S rRNA gene sequencing analysis. The antimicrobial susceptibility phenotype was determined using the disk diffusion assay. Our analysis showed that resistance to macrolide and quinolone was potentially associated with the presence of multiple point mutations in antibiotic targets on the chromosomal DNA. Furthermore, tetracycline and aminoglycoside resistance were encoded by genes on a pTet plasmid. The
bla
OXA-61
, which is associated with beta-lactam resistance, was also detected in the
C. coli
genome. A set of 30 genes associated with the virulence in
C. coli
was detected using WGS analysis. MLST analysis classified the isolate as belonging to a new sequence type (ST-9588), a member of ST-828 complex which is mainly associated with humans and chickens. Taking together, this study provides the first WGS analysis of
Campylobacter
isolated from Lebanon. The detection of a variety of AMR and virulence determinants strongly emphasizes the need for studying the burden of
Campylobacter
in Lebanon and the Middle East and North Africa (MENA) region, where information on campylobacteriosis is scant.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>34997523</pmid><doi>10.1007/s12223-021-00921-w</doi><tpages>10</tpages><orcidid>https://orcid.org/0000-0001-7466-5118</orcidid><orcidid>https://orcid.org/0000-0002-2978-9573</orcidid><orcidid>https://orcid.org/0000-0002-2402-4467</orcidid><orcidid>https://orcid.org/0000-0002-6466-2324</orcidid><orcidid>https://orcid.org/0000-0002-6235-2760</orcidid></addata></record> |
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| ispartof | Folia microbiologica, 2022-04, Vol.67 (2), p.319-328 |
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| language | eng |
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| source | SpringerLink Journals - AutoHoldings |
| subjects | Amides Aminoglycoside antibiotics Aminoglycosides Antibiotics Antimicrobial agents Antimicrobial resistance Applied Microbiology Bacteriology Biomedical and Life Sciences Campylobacter Campylobacter coli Campylobacteriosis Cardiology and cardiovascular system Diarrhea Drug resistance Emerging diseases Environmental Engineering/Biotechnology Epidemiology Gene sequencing Genes Genomes Human health and pathology Immunology Infectious diseases Life Sciences Microbiology Microbiology and Parasitology Multidrug resistance Multidrug resistant organisms Mutation Nucleotide sequence Original Article Parasitology Phenotypes rRNA 16S Virology Virulence Whole genome sequencing β-Lactam antibiotics |
| title | Genome sequence of a multidrug-resistant Campylobacter coli strain isolated from a newborn with severe diarrhea in Lebanon |
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