Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae isolates obtained from community-acquired urinary tract infections and rectal carriage isolates

Abstract

Antimicrobial resistance (AMR) due to Enterobacterales is a worldwide public health threat. The continuous emergence of multidrug resistant (MDR) bacteria in developing countries with poor sanitation programmes, inactive antimicrobial policies and inadequate infection control infrastructures can affect the health of community members with significant financial burden. South Africa has a high burden of infectious diseases and AMR. Contributing factors to these problems include the use of antimicrobials as growth promoters in food-producing animals and the overuse and misuse of antimicrobials. Among Enterobacterales, Klebsiella pneumoniae (K. pneumoniae) has emerged as the major driver of AMR globally. Klebsiella pneumoniae strains expressing carbapenem-hydrolysing enzymes have been associated with several hospital outbreaks in South Africa. These enzymes are disseminated by K. pneumoniae high-risk clones [sequence type (ST)-307 and non-ST307] and epidemic plasmid [incompatibility group (Inc)-X3]. There is paucity of information on the circulating K. pneumoniae high-risk clones isolated from urine and rectal carriage of patients in South Africa. Active surveillance of K. pneumoniae clones isolated from urine of patients is necessary to implement treatment strategies to manage urinary colonisation or infection. Early screening of at-risk-patients for carbapenem-resistant K. pneumoniae (CRKp) colonisation in hospitals will aid epidemiological monitoring to combat the spread of K. pneumoniae high-risk clones globally. Aim of this study was to investigate the molecular epidemiology of K. pneumoniae obtained from urine and rectal carriage isolates. A total of 446 carbapenemase-producing K. pneumoniae isolates were recovered from urine (n=194; 43%) and rectal carriage (n=252; 57%). Isolates were collected from the Ampath National Reference Laboratory (Ampath-MDRC), Pretoria, between February 2021 and May 2022. Patients’ demographic data were collected. This study employed phenotypic and molecular methods. The molecular methods included polymerase chain reaction (PCR) to detect ST307, IncX3 plasmid and carbapenemase genes [beta-(β)-lactamase genes encoding oxacillinase (blaOXA)-181, New Delhi metallo-β-lactamase (blaNDM), K. pneumoniae carbapenemase (blaKPC), Verona integron-encoded metallo-β-lactamase (blaVIM)]. Repetitive extragenic palindromic (REP)-PCR was used to determine the genetic relatedness among ST307 and non-ST307 isolates. Twenty-three carbapenemase-producing K. pneumoniae isolated from urine (n=10) and rectal carriage (n=13), selected based on the presence of carbapenemase genes were subjected to whole genome sequencing (WGS). The sequenced isolates exhibited MDR, extensively drug resistant and pandrug resistant phenotypes. Ten STs were detected. Among the 23 isolates, three were ST307. The non-ST307 clones include ST2497 (n=5) and ST17 (n=4). The ST17 strains were exclusively isolated from rectal carriage. Co-existence of carbapenemase genes were observed in 10 isolates. The predominant carbapenemase genes among the sequenced isolates were blaOXA-181 (n=11) and blaNDM (n=11). Most isolates were associated with plasmids, bacteriophages and acquired virulence determinants. In this study, K. pneumoniae high-risk clones acquired additional AMR and virulence traits. The high-risk clones were associated with several mobile genetic elements, including the IncX3 plasmid. This study provides insights into the epidemiology of CRKp in South Africa, highlighting the importance of infection prevention and control and antimicrobial therapeutic strategies based on the prevailing high-risk clones in different patient populations. This is essential for successful treatment and prevention of infectious diseases associated with AMR in South Africa.