Caribbean multi-centre study of Klebsiella pneumoniae: whole genome sequencing, antimicrobial resistance and virulence factors.
The surveillance of antimicrobial resistant isolates has proven to be one of the most valuable tools to understand the global rise of multidrug-resistant bacterial pathogens. We report the first insights into the current situation in the Caribbean, where a pilot project to monitor antimicrobial resistance through phenotypic resistance measurements combined with whole-genome sequencing was set up in collaboration with the Caribbean Public Health Agency (CARPHA). Our first study focused on Klebsiella pneumoniae, a highly relevant organism amongst the Gram-negative opportunistic pathogens world-wide today causing hospital, as well as community-acquired, infections. Our results show that not only carbapenem resistance, but also hypervirulent strains, are circulating in patients in the Caribbean. Our current data does not allow us to infer their prevalence in the population. We argue for the urgent need to further support antimicrobial resistance surveillance and stewardship in this almost uncharted territory, which can make a significant impact on the reduction of antimicrobial usage. DATA SUMMARY-Raw sequencing data is deposited at the sequence read archive (SRA), and assemblies are deposited at GenBank, accession numbers for all are given in Dataset S1. -The data of measured resistance phenotypes (Vitek) is also provided in Dataset S1. -The tree file and associated metadata can be investigated and downloaded through the free online platform microreact (https://microreact.org/project/S1-a7KAkV).{checkmark} I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. {boxtimes} Significance as a BioResource to the communityThis BioResource contains whole-genome sequence data of 270 Klebsiella pneumoniae isolates, information about encoded resistance genes and the phylogeny of the isolates, their distribution in the global K. pneumoniae population, and their resistance phenotype data as determined by the VITEK 2 compact system. The isolates are recent (2017 through 2018) and represent clinically relevant patient isolates from 15 different sites in 12 Caribbean states. These data will be of interest for researchers working on K. pneumoniae and other opportunistic pathogens as well as those interested in mobile genetic elements carrying antimicrobial resistance cassettes. Our data is the only recent survey of antimicrobial resistant opportunistic pathogens from multiple sites within the Caribbean, and is of high significance for the global surveillance of K. pneumoniae and antimicrobial resistance elements. This BioResource is made available through data tables provided with this article, as well deposition of the raw data in the relevant archives, and an interactive platform (microreact) to enquire and download analyses (phylogenetic tree, metadata).