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Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam

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ABSTRACT

We investigated the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans. Detection of mcr-1–carrying bacteria in chicken samples was associated with colistin use and detection in human samples with exposure to mcr-1–positive chickens.

No MeSH data available.


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Phylogenetic analyses of mcr-1–positive Escherichia coli isolated from chickens and chicken farmers, Vietnam, 2012–2013. Maximum-likelihood tree of 22 mcr-1–carrying E. coli isolated from 15 chicken fecal samples and 3 human fecal swab samples (underlined), constructed by using CSI Phylogeny 1.4 (https://cge.cbs.dtu.dk//services/CSIPhylogeny/), shows a genome-wide single-nucleotide polymorphism (SNP) comparison. A total of 74,585 SNPs were concatenated for pairwise comparison (difference between pairs 0–32,267 SNPs). The multilocus sequence types (ST) are indicated next to the isolate names. The ST155 isolates CG05C.C1 and CG05C.C2 differ by 1 SNP; the ST10 isolates CG48C.A2 and CG48C.G2 differ by 1 SNP and 1 antimicrobial resistance gene; the ST156 isolates CT48C.C1 and CT48C.C2 differ by 4 SNPs and 3 antimicrobial resistance genes; and the ST50 isolates CT67C.C1 and CT67C.C2 are phenotypically different but have 0 SNP differences and originate from the same sample and are therefore likely to be highly related or identical. Scale bar indicates number of nucleotide substitutions per site.
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Figure 1: Phylogenetic analyses of mcr-1–positive Escherichia coli isolated from chickens and chicken farmers, Vietnam, 2012–2013. Maximum-likelihood tree of 22 mcr-1–carrying E. coli isolated from 15 chicken fecal samples and 3 human fecal swab samples (underlined), constructed by using CSI Phylogeny 1.4 (https://cge.cbs.dtu.dk//services/CSIPhylogeny/), shows a genome-wide single-nucleotide polymorphism (SNP) comparison. A total of 74,585 SNPs were concatenated for pairwise comparison (difference between pairs 0–32,267 SNPs). The multilocus sequence types (ST) are indicated next to the isolate names. The ST155 isolates CG05C.C1 and CG05C.C2 differ by 1 SNP; the ST10 isolates CG48C.A2 and CG48C.G2 differ by 1 SNP and 1 antimicrobial resistance gene; the ST156 isolates CT48C.C1 and CT48C.C2 differ by 4 SNPs and 3 antimicrobial resistance genes; and the ST50 isolates CT67C.C1 and CT67C.C2 are phenotypically different but have 0 SNP differences and originate from the same sample and are therefore likely to be highly related or identical. Scale bar indicates number of nucleotide substitutions per site.

Mentions: The MIC of colistin for the 22 mcr-1–carrying E. coli isolates ranged 3–4 mg/L. Because the Etest might underestimate the true MIC (10), these results indicate reduced susceptibility. Single-nucleotide polymorphism (SNP)–based phylogenetic analyses of the core genomes showed little genomic similarity between isolates, but the analyses did show many isolates belonged to the same multilocus sequence types (n = 14) (Figure). Analysis of the acquired resistance genes, reflecting the presence of an accessory genome, showed a large variation in resistance gene content, with only the tet(A) gene, encoding for tetracycline resistance, present in all genomes (Technical Appendix 2 Table). De novo bacterial genome assembly was performed, and the contigs carrying mcr-1 were analyzed. A replication origin could be located in 5 isolates, leading to the identification of plasmid incompatibility groups IncHI2 (1 isolate), IncI2 (2 isolates), and combined IncHI2 and IncHI2A (2 isolates). Transposon ISAplI, initially described as carrying the mcr-1 gene (2), was identified in 18 of 22 contigs.


Zoonotic Transmission of mcr-1 Colistin Resistance Gene from Small-Scale Poultry Farms, Vietnam
Phylogenetic analyses of mcr-1–positive Escherichia coli isolated from chickens and chicken farmers, Vietnam, 2012–2013. Maximum-likelihood tree of 22 mcr-1–carrying E. coli isolated from 15 chicken fecal samples and 3 human fecal swab samples (underlined), constructed by using CSI Phylogeny 1.4 (https://cge.cbs.dtu.dk//services/CSIPhylogeny/), shows a genome-wide single-nucleotide polymorphism (SNP) comparison. A total of 74,585 SNPs were concatenated for pairwise comparison (difference between pairs 0–32,267 SNPs). The multilocus sequence types (ST) are indicated next to the isolate names. The ST155 isolates CG05C.C1 and CG05C.C2 differ by 1 SNP; the ST10 isolates CG48C.A2 and CG48C.G2 differ by 1 SNP and 1 antimicrobial resistance gene; the ST156 isolates CT48C.C1 and CT48C.C2 differ by 4 SNPs and 3 antimicrobial resistance genes; and the ST50 isolates CT67C.C1 and CT67C.C2 are phenotypically different but have 0 SNP differences and originate from the same sample and are therefore likely to be highly related or identical. Scale bar indicates number of nucleotide substitutions per site.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5382726&req=5

Figure 1: Phylogenetic analyses of mcr-1–positive Escherichia coli isolated from chickens and chicken farmers, Vietnam, 2012–2013. Maximum-likelihood tree of 22 mcr-1–carrying E. coli isolated from 15 chicken fecal samples and 3 human fecal swab samples (underlined), constructed by using CSI Phylogeny 1.4 (https://cge.cbs.dtu.dk//services/CSIPhylogeny/), shows a genome-wide single-nucleotide polymorphism (SNP) comparison. A total of 74,585 SNPs were concatenated for pairwise comparison (difference between pairs 0–32,267 SNPs). The multilocus sequence types (ST) are indicated next to the isolate names. The ST155 isolates CG05C.C1 and CG05C.C2 differ by 1 SNP; the ST10 isolates CG48C.A2 and CG48C.G2 differ by 1 SNP and 1 antimicrobial resistance gene; the ST156 isolates CT48C.C1 and CT48C.C2 differ by 4 SNPs and 3 antimicrobial resistance genes; and the ST50 isolates CT67C.C1 and CT67C.C2 are phenotypically different but have 0 SNP differences and originate from the same sample and are therefore likely to be highly related or identical. Scale bar indicates number of nucleotide substitutions per site.
Mentions: The MIC of colistin for the 22 mcr-1–carrying E. coli isolates ranged 3–4 mg/L. Because the Etest might underestimate the true MIC (10), these results indicate reduced susceptibility. Single-nucleotide polymorphism (SNP)–based phylogenetic analyses of the core genomes showed little genomic similarity between isolates, but the analyses did show many isolates belonged to the same multilocus sequence types (n = 14) (Figure). Analysis of the acquired resistance genes, reflecting the presence of an accessory genome, showed a large variation in resistance gene content, with only the tet(A) gene, encoding for tetracycline resistance, present in all genomes (Technical Appendix 2 Table). De novo bacterial genome assembly was performed, and the contigs carrying mcr-1 were analyzed. A replication origin could be located in 5 isolates, leading to the identification of plasmid incompatibility groups IncHI2 (1 isolate), IncI2 (2 isolates), and combined IncHI2 and IncHI2A (2 isolates). Transposon ISAplI, initially described as carrying the mcr-1 gene (2), was identified in 18 of 22 contigs.

View Article: PubMed Central - PubMed

ABSTRACT

We investigated the consequences of colistin use in backyard chicken farms in Vietnam by examining the prevalence of mcr-1 in fecal samples from chickens and humans. Detection of mcr-1–carrying bacteria in chicken samples was associated with colistin use and detection in human samples with exposure to mcr-1–positive chickens.

No MeSH data available.


Related in: MedlinePlus