Evaluation of occurrence, antimicrobial resistance rates, and antibiotic resistance determinants in Klebsiella pneumoniae from hospitalised patients in Lagos, Nigeria

The study investigated the prevalence, antimicrobial resistance patterns, and resistance determinants of multidrug-resistant (MDR) Klebsiella pneumoniae isolated from hospitalized patients in Lagos, Nigeria. One thousand four hundred and forty clinical samples (400 urine, 700 blood, and 340 stool) were collected from inpatients admitted to four public hospitals in Lagos between May 2021 and July 2023. The samples were analysed microbiologically. The isolates were identified using API 20E. and were subjected to in vitro antibiotic susceptibility testing, extended-spectrum beta-lactamases (ESβLs), β-lactamase AmpC, and carbapenemases. The real-time polymerase chain reaction (real-time PCR) was used to determine antibiotic resistance genes, including ESBLs and carbapenemases, using specific primers. Three Klebsiella species were reported in this study, with an overall prevalence of 5.97% (86/1440). Of this, 4.5% (65/1440) K. pneumoniae, 1.04% (15/1440) K. oxytoca, and the least prevalent 0.42% (6/1440) K. aerogenes were documented. K. pneumoniae was isolated in all the age groups, but was highest in groups 1–10 years. There was no statistically significant association (P-value > 0.05) between the occurrence of K. pneumoniae and age groups or sex. Over 80% of K. pneumoniae isolates were MDR and were 100% resistant to cephalosporins, carbapenems, and polymyxin antibiotics. Six resistant patterns were recorded, with CAZ-CTX-CPM-CIP-CRO-AUG-GM-CO-IMP-MEM-ETP-DOR being the most frequently encountered pattern, at 46.2%. Specifically, 16 of the 20 isolates (80.0%) harboured one or two ESBL genes such as blaSHV, blaTEM and blaCTX−M, and carbapenemase genes including blaIMP, blaVIM, blaNDM, blaKPC, and blaOXA−48. This study revealed the presence of MDR K.pneumoniae and the emerging isolates with the co-existence of ESBL, AmpC, and carbapenemase genes. Surveillance, early detection, and adherence to antibiotic policies are essential to mitigate the spread.