4.6 Article

Genomic Analysis of Ciprofloxacin-Resistant Salmonella enterica Serovar Kentucky ST198 From Spanish Hospitals

Journal

FRONTIERS IN MICROBIOLOGY
Volume 12, Issue -, Pages -

Publisher

FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2021.720449

Keywords

Salmonella enterica serovar Kentucky; ST198; SGI1-K; IS26; fluoroquinolone resistance; multidrug resistance; whole genome sequencing; phylogenetic analysis

Categories

Funding

  1. Fondo de Investigacion Sanitaria, Instituto de Salud Carlos III, Ministerio de Economia y Competitividad [FIS PI17/00474]
  2. Spain, co-funded by European Regional Development Fund of the European Union: a way to making Europe [BP17-018]
  3. Severo Ochoa for support of Research and Teaching in the Principality of Asturias

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This study characterized all ciprofloxacin-resistant Salmonella enterica serovar Kentucky (S. Kentucky) isolates detected in five Spanish hospitals from 2009 to 2018 through whole genome sequencing. The isolates all belonged to sequence type 198 and exhibited resistances to multiple antibiotics mediated by various resistance genes, with a close genetic relationship observed between isolates from different hospitals.
Salmonella enterica serovar Kentucky (S. Kentucky) with sequence type (ST) 198 and highly resistant to ciprofloxacin (ST198-Cip(R)) has emerged as a global MDR clone, posing a threat to public health. In the present study, whole genome sequencing (WGS) was applied to characterize all Cip(R) S. Kentucky detected in five Spanish hospitals during 2009-2018. All Cip(R) isolates (n = 13) were ST198 and carried point mutations in the quinolone resistance-determining regions (QRDRs) of both gyrA (resulting in Ser83Phe and Asp87Gly, Asp87Asn, or Asp87Tyr substitutions in GyrA) and parC (with Thr57Ser and Ser80Ile substitutions in ParC). Resistances to other antibiotics (ampicillin, chloramphenicol, gentamicin, streptomycin, sulfonamides, and tetracycline), mediated by the bla(TEM-1B), catA1, aacA5, aadA7, strA, strB, sul1, and tet(A) genes, and arranged in different combinations, were also observed. Analysis of the genetic environment of the latter resistance genes revealed the presence of multiple variants of SGI1 (Salmonella genomic island 1)-K and SGI1-P, where all these resistance genes except catA1 were placed. IS26 elements, found at multiple locations within the SGI1 variants, have probably played a crucial role in their generation. Despite the wide diversity of SGI1-K- and SGI1-P-like structures, phylogenetic analysis revealed a close relationship between isolates from different hospitals, which were separated by a minimum of two and a maximum of 160 single nucleotide polymorphisms. Considering that S. enterica isolates resistant to fluoroquinolones belong to the high priority list of antibiotic-resistant bacteria compiled by the World Health Organization, continuous surveillance of the S. Kentucky ST198-CIP(R) clone is required.

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