Abstract
To understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.
Highlights
The emergence and spread of carbapenem-resistant Enterobacterales (CRE) is considered to be one of the most serious antibiotic resistance threats [1]
To understand the reasons of its successful emergence and spread, we used whole genome sequencing (WGS) to assess the resistome, the capsular locus, the carbapenemase carrying plasmid types, as well as the level of core genome similarity of selected K. pneumoniae ST14 isolated in countries of the Arabian Peninsula, which were compared to whole genomes of K. pneumoniae ST14 isolated at other geographical locations
761 independent CRKP strains isolated between June 2011 and June 2016 in 33 hospitals of five countries of the Arabian Peninsula from a collection described earlier [11] were screened by PFGE [12], to select isolates exhibiting ≥ 80% similar patterns to 23 known CRKP-ST14 identified earlier in the UAE [7,8,9]
Summary
The emergence and spread of carbapenem-resistant Enterobacterales (CRE) is considered to be one of the most serious antibiotic resistance threats [1]. The majority of CRE is Klebsiella pneumoniae, which are carbapenem resistant due to the production of carbapenemases (CRKP) [2] This worldwide trend is observed in countries of the Arabian Peninsula [3,4,5]. K. pneumoniae ST14 is one of such clones producing various carbapenemases that have been reported from four continents [2, 5, 6] including the Arabian Peninsula [3, 7,8,9] Earlier, this clone was shown to have high prevalence among CRE isolated in the United Arab Emirates [8, 10]. To understand the reasons of its successful emergence and spread, we used whole genome sequencing (WGS) to assess the resistome, the capsular locus, the carbapenemase carrying plasmid types, as well as the level of core genome similarity of selected K. pneumoniae ST14 isolated in countries of the Arabian Peninsula, which were compared to whole genomes of K. pneumoniae ST14 isolated at other geographical locations
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