Limited Genetic Diversity of blaCMY-2-Containing IncI1-pST12 Plasmids from Enterobacteriaceae of Human and Broiler Chicken Origin in The Netherlands
Drijver, Evert P M den; Stohr, Joep J J M; Verweij, Jaco J; Verhulst, Carlo; Velkers, Francisca C; Stegeman, Arjan; Bergh, Marjolein F Q Kluytmans-van den; Kluytmans, Jan A J W; Group, I-Health Study
(2020) Microorganisms, volume 8, issue 11, pp. 1 - 13
(Article)
Abstract
Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission. We compared IncI1-pST12 plasmids from both human and livestock origin and explored the degree of sequence similarity between plasmids from Enterobacteriaceae with different epidemiological links. Short-read sequence data of Enterobacteriaceae cultured from humans and broilers were screened for
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the presence of both a blaCMY-2 gene and an IncI1-pST12 replicon. Isolates were long-read sequenced on a MinION sequencer (OxfordNanopore Technologies). After plasmid reconstruction using hybrid assembly, pairwise single nucleotide polymorphisms (SNPs) were determined. The plasmids were annotated, and a pan-genome was constructed to compare genes variably present between the different plasmids. Nine Escherichia coli sequences of broiler origin, four Escherichia coli sequences, and one Salmonella enterica sequence of human origin were selected for the current analysis. A circular contig with the IncI1-pST12 replicon and blaCMY-2 gene was extracted from the assembly graph of all fourteen isolates. Analysis of the IncI1-pST12 plasmids revealed a low number of SNP differences (range of 0-9 SNPs). The range of SNP differences overlapped in isolates with different epidemiological links. One-hundred and twelve from a total of 113 genes of the pan-genome were present in all plasmid constructs. Next generation sequencing analysis of blaCMY-2-containing IncI1-pST12 plasmids isolated from Enterobacteriaceae with different epidemiological links show a high degree of sequence similarity in terms of SNP differences and the number of shared genes. Therefore, statements on the horizontal transfer of these plasmids based on genetic identity should be made with caution.
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Keywords: AmpC β-lactamase, BlaCMY-2, IncI1, Plasmid, Microbiology (medical), Virology, Microbiology, Journal Article
ISSN: 2076-2607
Publisher: MDPI AG
Note: Funding Information: Funding: The i-4-1-Health project was financed by the Interreg V Flanders-The Netherlands program, the cross-border cooperation program with financial support from the European Regional Development Fund (ERDF). Additional financial support was received from the Dutch Ministry of Health, Welfare and Sport, the Dutch Ministry of Economic Affairs, the Province of Noord-Brabant, the Belgian Department of Agriculture and Fisheries, the Province of Antwerp and the Province of East-Flanders. Selective and non-selective agar plates, ETEST® strips and VITEK® 2 AST cards were provided by bioMérieux (Marcy l’Etoile, France); FecalSwabs® and tryptic soy broths are provided by Copan Italy (Brescia, Italy). The authors were free to publish the results from the project without interference from the funding bodies, bioMérieux or Copan Italy. Funding Information: The i-4-1-Health project was financed by the Interreg V Flanders-The Netherlands program, the cross-border cooperation program with financial support from the European Regional Development Fund (ERDF). Additional financial support was received from the Dutch Ministry of Health, Welfare and Sport, the Dutch Ministry of Economic Affairs, the Province of Noord-Brabant, the Belgian Department of Agriculture and Fisheries, the Province of Antwerp and the Province of East-Flanders. Selective and non-selective agar plates, ETEST? strips and VITEK? 2 AST cards were provided by bioM?rieux (Marcy l?Etoile, France); FecalSwabs? and tryptic soy broths are provided by Copan Italy (Brescia, Italy). The authors were free to publish the results from the project without interference from the funding bodies, bioM?rieux or Copan Italy. Publisher Copyright: © 2020 by the authors. Licensee MDPI, Basel, Switzerland.
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