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Volume 8, Issue 12

An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream isolates from South-West Nigeria hospitals Open Access

Abstract

bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016–2018 bloodstream isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10–ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely origin, identical to those of avian pathogenic Sanji, and serotyped as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , cpsACP , Escherichia coli , genomic surveillance , Nigeria and ST131
Funding
This study was supported by the:
  • Bill and Melinda Gates Foundation (Award INV-036234)
    • Principle Award Recipient: IrukaN Okeke
  • Medical Research Council (Award MR/L00464X/1)
    • Principle Award Recipient: IrukaN Okeke
  • National Institute for Health Research (Award 16_136_111)
    • Principle Award Recipient: DavidM Aanensen
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-12-16
2024-05-01
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An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals
M Gen 8, 000863 (2022); https://doi.org/10.1099/mgen.0.000863
/content/journal/mgen/10.1099/mgen.0.000863
/content/journal/mgen/10.1099/mgen.0.000863
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