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

Abstract

Salmonella enterica serovar Kentucky (S. Kentucky) with sequence type (ST) 198 and highly resistant to ciprofloxacin (ST198-CipR) 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 CipRS. Kentucky detected in five Spanish hospitals during 2009–2018. All CipR 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 blaTEM–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-CIPR clone is required.

Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland

“…5 ). An additional Spanish isolate (LSP_314_17) reportedly associated with travel to Bali, Indonesia [ 23 ] also fell into this cluster (1–10 pairwise cgSNPs) ( Fig. 5 ).…”

“…Of the 43 cases in the UK, 14 cases were linked with travel to Indonesia, five cases with travel to other Asian countries, and four cases with travel in Europe or Africa; one case was not associated with travel within 28 days, and for 19 patients the travel history was not documented (). An additional Spanish isolate (LSP_314_17) reportedly associated with travel to Bali, Indonesia [23] also fell into this cluster (1–10 pairwise cgSNPs) (). Genomic data of this isolate was not available via EnteroBase.…”

“…Long-read sequencing of five selected isolates identified resistance gene clusters integrated at various chromosomal positions or on plasmids. Only one of those carried a resistance gene cluster in SGI-1, which was identified as a dominant integration site in earlier studies [13, 17, 23].…”

“…Human S . Kentucky infections in Europe and North America are often associated with travel to Asia or Africa [20–25]. In the EU, approximately half of all human S .…”

“…Poultry are assumed to be a major reservoir of ST198 and recent surveillance studies indicate the circulation of ST198-CIP R clones in poultry farms in Europe and Asia [17][18][19][20]. Human S. Kentucky infections in Europe and North America are often associated with travel to Asia or Africa [20][21][22][23][24][25]. In the EU, approximately half of all human S. Kentucky cases are acquired outside of the EU [26].…”