Genotypic Characterization of Hypervirulent Enterobacterales Isolates From Intensive Care Unit Patients at the Kenyatta National Hospital

Abstract

Introduction: Intensive care units (ICUs) are hotspots for antibiotic resistance emergence, propagated by misuse and overuse of broad-spectrum antibiotics. The emergence of multidrug-resistant bacteria, including potentially dangerous hypervirulent strains result in severe and hard-to-treat infections, posing significant public health threats. The aim of this study was to establish the presence of hypervirulent Enterobacterales bacteria among isolates obtained from ICU patients at Kenya's Kenyatta National Hospital. Methods: The study was a retrospective laboratory study that involved the analysis of 40 Extended Spectrum Beta-Lactamase (ESBL) and carbapenemase-producing Enterobacterales isolates from diverse clinical samples including tracheal aspirates, urine, blood and pus swabs. These isolates were subjected to culture, identification, and antibiotic susceptibility testing using VITEK®2. DNA was extracted and whole-genome sequencing was performed using the Oxford Nanopore MinION protocol. Bioinformatic tools ResFinder 2.1, Virulence Finder 2.0, Plasmid Finder databases 2.1, and the virulence factor database were used to analyze the bacterial genomes for AMR genes, virulence genes, and plasmids. Results: Out of 33 viable isolates, 22 were successfully identified and sequenced, consisting of 15 Escherichia coli and 7 Klebsiella pneumoniae isolates. These isolates exhibited multidrug-resistant traits, with nearly complete resistance to beta-lactam antibiotics. Carbapenem resistance was rare, except in one E. coli isolate. No carbapenemase genes were found, however ESBL production was evident across the Enterobacterales isolates, with presence of genes encoding β-lactamases such as blaOXA-1 (13/22, 59%), blaOXA-534 (3/22, 13%), blaCTX-M-15 (18/22, 82%), blaEC (13/22, 59%), blaTEM (7/22, 32%), blaCMY (1/22, 5%), blaSHV (8/22, 36%), and ompK (6/22, 27%) encode ESBL production and consequently resistance to cephalosporins. Notably, key hypervirulent genes were identified among E. coli isolates, including attachment-fimH- (15/15, 100%), toxin production sat- (5/15, 33%), biofilm formation csgA- (14/15, 93%), and capsule formation kspE- (10/15, 67%). For K. pneumoniae isolates, notable efflux pump transporters were acrAB- (4/7, 57%), and mtrD- (1/7, 14%). Conclusion: The existence of ESBL-producing Enterobacterales, associated with resistance to multiple classes of antibiotics and heightened virulence, presents a substantial healthcare risk for ICU patients. Therefore, health care workers should strictly observe infection prevention protocols and exercise judicious antibiotic usage to reduce the dissemination of AMR.