Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France
ABSTRACT: Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypica...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-03-01
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| Series: | Journal of Global Antimicrobial Resistance |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213716522000194 |
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| author | Afaf Hamame Bernard Davoust Jean-Marc Rolain Seydina M. Diene |
| author_facet | Afaf Hamame Bernard Davoust Jean-Marc Rolain Seydina M. Diene |
| author_sort | Afaf Hamame |
| collection | DOAJ |
| description | ABSTRACT: Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mcr genes in France. Samples collected from a pig farm in Avignon (Vaucluse department) were subjected to molecular screening targeting mcr variants. Methods: Samples were cultured on selective Lucie-Bardet-Jean-Marc-Rolain medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing. Whole-genome sequencing and bioinformatic genome analysis were performed. Results: Selective culture of stools revealed the presence of an E. coli strain named Q4552 harbouring mcr-1.1 and mcr-3.5 genes, which is also resistant to 14 antibiotics. Genome sequencing and assembly yielded a complete and circular chromosome and eight different plasmids. Sequence analysis demonstrated an integration of a mobile genetic element carrying mcr-1.1 in the chromosome, whereas mcr-3.5 was in the plasmid and its resistome was composed of 22 resistance genes. The Q4552 strain was identified as an ST-843 clone that belonged to the clonal complex Cplx-568 and is the only ST type of this cplx-568 that has been isolated from animals, humans, and the environment. Conclusion: We report the first co-occurrence of mcr-1 and mcr-3 genes in France from a pathogenic E. coli isolated from a pig. Because this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor the bacterium are urgently required to avoid its spread and zoonotic transmission to humans. |
| first_indexed | 2024-12-18T10:37:54Z |
| format | Article |
| id | doaj.art-89fac6bf696d4e9895b2006fdde126ed |
| institution | Directory Open Access Journal |
| issn | 2213-7165 |
| language | English |
| last_indexed | 2024-12-18T10:37:54Z |
| publishDate | 2022-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Global Antimicrobial Resistance |
| spelling | doaj.art-89fac6bf696d4e9895b2006fdde126ed2022-12-21T21:10:42ZengElsevierJournal of Global Antimicrobial Resistance2213-71652022-03-0128174179Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in FranceAfaf Hamame0Bernard Davoust1Jean-Marc Rolain2Seydina M. Diene3Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix Marseille Univ, IRD, APHM, MEPHI, Faculté de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, FranceAix Marseille Univ, IRD, APHM, MEPHI, Faculté de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; Corresponding author. MEPHI, IHU-Méditerranée Infection, Faculté Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France.ABSTRACT: Objectives: Colistin is considered a last-resort antibiotic against carbapenem-resistant isolates. Currently, this antibiotic is facing the emergence of mobilised colistin resistance (mcr) genes, which confer colistin resistance. This study conducted genomic characterisation of an atypical multidrug-resistant Escherichia coli harbouring two mcr genes in France. Samples collected from a pig farm in Avignon (Vaucluse department) were subjected to molecular screening targeting mcr variants. Methods: Samples were cultured on selective Lucie-Bardet-Jean-Marc-Rolain medium. Growing bacteria were identified using MALDI-TOF, followed by antibiotic susceptibility testing. Whole-genome sequencing and bioinformatic genome analysis were performed. Results: Selective culture of stools revealed the presence of an E. coli strain named Q4552 harbouring mcr-1.1 and mcr-3.5 genes, which is also resistant to 14 antibiotics. Genome sequencing and assembly yielded a complete and circular chromosome and eight different plasmids. Sequence analysis demonstrated an integration of a mobile genetic element carrying mcr-1.1 in the chromosome, whereas mcr-3.5 was in the plasmid and its resistome was composed of 22 resistance genes. The Q4552 strain was identified as an ST-843 clone that belonged to the clonal complex Cplx-568 and is the only ST type of this cplx-568 that has been isolated from animals, humans, and the environment. Conclusion: We report the first co-occurrence of mcr-1 and mcr-3 genes in France from a pathogenic E. coli isolated from a pig. Because this clone (ST-843) has been reported in zoonotic transmissions, programs to monitor the bacterium are urgently required to avoid its spread and zoonotic transmission to humans.http://www.sciencedirect.com/science/article/pii/S2213716522000194mcr genesmcr-1mcr-3Colistin resistanceWhole-genome sequencing |
| spellingShingle | Afaf Hamame Bernard Davoust Jean-Marc Rolain Seydina M. Diene Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France Journal of Global Antimicrobial Resistance mcr genes mcr-1 mcr-3 Colistin resistance Whole-genome sequencing |
| title | Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France |
| title_full | Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France |
| title_fullStr | Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France |
| title_full_unstemmed | Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France |
| title_short | Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France |
| title_sort | genomic characterisation of an mcr 1 and mcr 3 producing escherichia coli strain isolated from pigs in france |
| topic | mcr genes mcr-1 mcr-3 Colistin resistance Whole-genome sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2213716522000194 |
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