Molecular epidemiology of carbapenem-resistant Enterobacterales colonization in an intensive care unit.

Abstract

Background: Due to the high association with mortality and morbidity, carbapenem-resistant Enterobacterales (CRE) in general, and carbapenem-resistant Klebsiella pneumoniae, in particular, have been listed as high-priority pathogens by the World Health Organization (WHO) for the research and development of new antibiotics. Concomitant resistance to multiple antibiotics of different classes, impedes efficient clinical management of CRE infections. We characterized carbapenemase-producing K. pneumoniae (CPKP) isolates from sequential rectal screening of patients in a single intensive care unit (ICU) in a public hospital in the uMgungundlovu District of Kwazulu-Natal, South Africa, collected over one month. Method: Ninety-seven rectal swabs collected from consenting adult patients (n=31) on day 1, 3, 7 and weekly thereafter were screened for carbapenemase-production using Chrome-ID selective media. Fourteen CPKP were subjected to speciation and antibiotic susceptibility testing using the VITEK 2® automated system and their clonality was ascertained by ERIC/PCR. A sub-sample of eight isolates from five patients underwent whole genome sequencing (WGS) on the Illumina MiSeq platform followed by bioinformatics analysis to delineate the resistome, virulome, mobilome, clonality and phylogeography. Results: All isolates (100%) were resistant to ertapenem and meropenem and 71.4% (n=10) were resistant to imipenem. All isolates harbored the blaOXA-181 carbapenemase (100%, n=8) and also carried other β-lactamase genes such as OXA-1, CTX-M-15, TEM-1B and SHV-1. IncF, IncX3, and Col plasmid replicons groups and class I integrons (ln191 and ln27) were detected. All isolates belonged to the same sequence type ST307 and capsular serotypes (K102, O2v2) and several were associated with a single bed located in the ICU. All but one isolate carried the same plasmid multilocus sequence type [K7:A-:B-] and the same virulence repertoire was identified reflecting the epidemiological relationships between isolates. BlaOXA-181 were presumably located on a multi-replicon plasmid similar to that of E. coli p010_B-OXA181, and isolates were aligned with several South African and international clades, demonstrating horizontal and vertical transboundary distribution. Conclusion: OXA-181-producing K. pneumoniae belonging to ST307 was found to be potentially endemic in the hospital ICU environment of a public hospital in KwaZulu-Natal South Africa. The presence of a myriad of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in different permutations and combinations presents challenges to clinical management and infection prevention and control measures. This necessitates a CRE screening programme and strict infection prevention and control measures to detect and eliminate this endemic clone.