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Volume 4, Issue 7

Genetic characterization of Infantis from South Africa, 2004–2016 Open Access

Abstract

Infantis is presenting an increasing risk to public health. Of particular concern are the reports of pESI, a multidrug resistance (MDR) encoding megaplasmid, in isolates from multiple countries, but little is known about its presence or diversity in South Africa. Whole genome sequences of 387 . Infantis isolates from South Africa (2004–2020) were analysed for genetic phylogeny, recombination frequency, antimicrobial resistance (AMR) determinants, plasmid presence and overall gene content. The population structure of South African . Infantis was substantially different to . Infantis reported elsewhere; only two thirds of isolates belonged to eBG31, while the remainder were identified as eBG297, a much rarer group globally. Significantly higher levels of recombination were observed in the eBG297 isolates, which was associated with the presence of prophages. The majority of isolates were putatively susceptible to antimicrobials (335/387) and lacked any plasmids (311/387); the megaplasmid pESI was present in just one isolate. A larger proportion of eBG31 isolates, 19% (49/263), contained at least one AMR determinant, compared to eBG297 at 2% (3/124). Comparison of the pan-genomes of isolates from either eBG identified 943 genes significantly associated with eBG, with 43 found exclusively in eBG31 isolates and 34 in eBG297 isolates. This, along with the single nucleotide polymorphism distance and difference in resistance profiles, suggests that eBG31 and eBG297 isolates occupy different niches within South Africa. If antibiotic-resistant . Infantis emerges in South Africa, probably through the spread of the pESI plasmid, treatment of this infection would be compromised.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): AMR , eBG297 , eBG31 and Salmonella Infantis
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award BB/R012504/1)
    • Principle Award Recipient: JohnWain
  • National Institute for Health Research Health Protection Research Unit (Award NIHR200892)
    • Principle Award Recipient: MarieAnne Chattaway
  • National Institute for Health Research Health Protection Research Unit
    • Principle Award Recipient: ApplicableNot
  • UKMRC Strategic Innovation Health Partnerships
    • Principle Award Recipient: KarenH. Keddy
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Genetic characterization of Salmonella Infantis from South Africa, 2004–2016
Access Microbiology 4, 000371 (2022); https://doi.org/10.1099/acmi.0.000371
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