Rectal Carriage of Sequence Type 307 Klebsiella pneumoniae High‐Risk Clone Harboring Multiple Carbapenemase Genes in Community Hospitals Gauteng, South Africa

TL;DR

This study found that a high-risk strain of Klebsiella pneumoniae, ST307, is common in community hospitals in South Africa and carries multiple drug resistance genes.

Contribution

The study identifies ST307 as a significant reservoir of carbapenemase genes in community hospitals and highlights the role of IncX3 plasmids in spreading resistance.

Findings

24% of rectal screening samples were carbapenemase positive, with 25% being ST307 isolates.

45% of ST307 isolates carried the bla_OXA-181 gene on IncX3 plasmids.

ST307 isolates showed significantly higher levels of antimicrobial resistance compared to non-ST307 isolates.

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 bla
OXA‐181 on IncX3 plasmids. Occurrence of bla
OXA‐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 bla
NDM
+bla
OXA‐48‐like, four bla
NDM
+bla
OXA‐181, three bla
KPC
+bla
OXA‐181, and one bla
OXA‐181+bla
VIM. One ST307 isolate harbored three carbapenemase genes (bla
NDM
+bla
OXA‐48
+bla
OXA‐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.

Graphical presentation of rectal carriage of carbapenem‐resistant Klebsiella pneumoniae, highlighting ST307 high‐risk clone and IncX3 plasmid‐associated bla
OXA‐181. This study highlights the threat linked to horizontal gene transfer of AMR genes by epidemic plasmids from Klebsiella pneumoniae high‐risk clones to other bacterial species.

Figures