Phenotypic And Genotypic Characterization of Extended Spectrum Beta- Lactamase-Producing Clinical Isolates of Escherichia coli and Klebsiella pneumoniae in Two Kenyan Facilities: A National Referral and a Level Five Hospital

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Abstract Background The emergence of antimicrobial resistance (AMR) and multidrug resistance (MDR) among Escherichia coli and Klebsiella pneumoniae, especially through the production of extended spectrum β-lactamases (ESBLs), limits therapeutic options and poses a significant public health threat. Objective The aim of this study was to phenotypically and genotypically characterise the ESBL-associated AMR and MDR of Escherichia coli and Klebsiella pneumoniae isolates from patient samples in two Kenyan Hospitals. Methods We collected 138 E. coli and 127 K. pneumoniae isolates from various clinical specimens at the two health facilities from January 2020 to Feb 2021. ESBL production and antibiotic susceptibility of the isolates were phenotypically confirmed using a standard procedure. Molecular analysis was done through conventional Polymerase Chain Reaction (PCR) with appropriate primers for gadA, rpoB, blaTEM, blaSHV, blaOXA, blaCTX-M-group-1, blaCTX-M-group-2, blaCTX-M-group-9, and blaCTX-M-group-8/25 genes, sequencing and BLASTn analysis. Results Most E. coli (82.6%) and K. pneumoniae (92.9%) isolates were ESBL producers, with the highest resistance was against Ceftriaxone (69.6% among E. coli and 91.3% among K. pneumoniae) and Amoxicillin/clavulanic acid (70.9% among K. pneumoniae). The frequency of MDR was 39.9% among E. coli and 13.4% among K. pneumoniae isolates. The commonest MDR phenotypes among the E. coli isolates were CRO-FEB-AZM-LVX and CRO-AZM-LVX, while the FOX-CRO-AMC-MI-TGC-FM, FOX-CRO-FEP-AMC-TZP-AZM-LVX-MI, and CRO-AMC-TZP-AZM-MI were the most frequent among K. pneumoniae isolates. Notably, the FOX-CRO-FEP-AMC-TZP-AZM-LVX-MI phenotype was observed in both ESBL-positive and ESBL-negative K. pneumoniae isolates. The most frequent ESBL genes were blaTEM (42%), blaSHV (40.6%), and blaOXA (34.1%) among E. coli, and blaTEM (89%), blaSHV (82.7%), blaOXA (76.4%), and blaCTX−M−group−1 (72.5%) among K. pneumoniae isolates. The blaSHV and blaOXA, and blaTEM genotypes were predominantly associated with FOX-CRO-FEP-MEM and CRO-FEP MDR, and CRO AMR phenotypes, among E. coli isolates from Embu Level V (16.7%) and Kenyatta National Hospital (7.0%) respectively. Conclusions The high proportion of ESBL-producing E. coli and K. pneumoniae isolates increases the utilization of last-resort antibiotics, jeopardizing antimicrobial chemotherapy. Furthermore, the antimicrobial resistance patterns exhibited towards extended-spectrum cephalosporins, beta-lactam/beta-lactamase inhibitor combinations, fluoroquinolones, and macrolides show the risk of co-resistance associated with ESBL-producing isolates responsible for MDR.

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