Rectal carriage of sequence type 307 Klebsiella pneumoniae high-risk clone harboring multiple carbapenemase genes in community hospitals Gauteng, South Africa

Abstract

Asymptomatic rectal carriers are recognized as reservoirs of carbapenem-resistant Klebsiella pneumoniae (CRKp), which can spread epidemic high-risk clones [e.g., sequence types (ST)-307] and plasmids [incompatibility group (Inc)-X3] in hospitals, with possible transmission into the community. This study investigated the epidemiology and characteristics of CRKp high-risk clones ST307 among rectal carriage isolates from community hospitals. A carbapenemase positivity rate of 24% was observed for all rectal screening performed during hospital admission (February to August 2021) in Gauteng, South Africa; 252 CRKp isolates were characterized. Antimicrobial susceptibility was performed using the VITEK 2 automated system, and polymerase chain reaction assays were used to detect K. pneumoniae ST307, carbapenemase genes, and associated mobile genetic elements (MGEs e.g., IncX3, IS3000). Of the 252 isolates, 25% (64/252) were ST307 positive and 75% (188/252) were non-ST307. Among the 64 ST307, 45% (29/64) harbored blaOXA-181 on IncX3 plasmids. Occurrence of blaOXA-181 among ST307 (69%; 44/64) when compared to non-ST307 (48%; 91/188) was statistically significant (p-value = 0.002). Fourteen isolates, including two ST307, harbored double carbapenemase genes. Carbapenemase gene combinations include six blaNDM+blaOXA-48-like, four blaNDM +blaOXA-181, three blaKPC+blaOXA-181, and one blaOXA-181+blaVIM. One ST307 isolate harbored three carbapenemase genes (blaNDM+blaOXA-48+blaOXA-181). Level of antimicrobial resistance was significantly (p-value < 0.001) associated with the occurrence of ST307, comprising 73% (47/64) extensively drug resistant. This study highlights the need for rectal screening of XDR clones and plasmids using simple and cost-effective genomic methodologies suitable for low- and middle-income countries for local risk management and control of infectious diseases in hospitals.