Prevalence of class A ESBL, class B and D carbapenemase encoding genes (CTX-M, TEM, SHV, NDM, IMP, OXA-48) in gram-negative bacterial pathogens isolated from various clinical samples collected from northern region of United Arab Emirates

Abstract

Objective The aim of this study was to assess the prevalence of class A ESBL, class B and D carbapenemase encoding genes (blaCTX-M, blaTEM, blaSHV, blaNDM, blaIMP and blaOXA-48) in gram-negative bacterial pathogens isolated from various clinical samples collected from northern region of UAE. Methods A laboratory based experimental study was conducted from October 14, 2021, to June 30, 2022. A total of 3670 various clinical samples (urine, blood, pus, and sputum) were obtained from patients attending the in and out-patient departments of Thumbay University Hospital and various other hospitals of Northern Emirates of UAE, processed for routine bacterial culture examination and determined their antibiotic sensitivity pattern especially ESBL and carbapenem resistance using MicroScan Neg Breakpoint Combo 50 panel. Molecular detection of class A ESBL, class B and D carbapenemase encoding genes (blacTX-M, blaTEM, blaSHV blaNDM, blaIMP & blaOXA-48) were performed on the ESBL and carbapenemase producing gram negative bacteria. Partial genomic sequencing and phylogenetic tree analysis was performed on the most predominant ESBL gene blaCTX-M. Results In total, 1098 bacterial cultures were obtained, of which 833 were gram negative bacteria and among them, 209 (25.1%) were ESBL producers and 40 (4.8%) were both ESBL and carbapenemase producers. In all the 249 bacterial isolates, the ESBL and carbapenemase encoding genes (blaCTX-M, blaTEM, blaSHV, blaNDM & blaIMP) were detected except blaOXA-48. The blaCTX-M (n=72) was the predominantly harbored gene followed by blaTEM (n=56) and blaSHV (n=29), mostly detected in E. coli (n=157), then K. pneumoniae (n=41), P. aeruginosa (n=18) & A. baumannii (n=7). The blaNDM & blaIMP were detected in K. pneumoniae (n=4), A. baumannii (n=3) and P. aeruginosa (n=2) for blaIMP. The gene combinations such as blaCTX-M+TEM (n=15), blaCTX-M+SHV (n=15), blaCTX-M+TEM+SHV (n=6) were co-harbored in 36 E. coli and in the K. pneumoniae, the blaCTX-M+TEM (n=15), blaCTX-M+SHV (n=15), blaTEM+SHV (n=3), blaTEM+NDM (n=1) were detected. The blaCTX-M+TEM, blaCTX-M+SHV & blaCTX-M+TEM+SHV+IMP were detected in one P. aeruginosa and in one A. baumannii, the blaTEM+NDM, blaTEM+IMP & blaCTX-M+TEM+SHV+IMP were detected. Conclusion The highest bacterial culture positivity was detected in the urine samples. 25.1% of the Gram-ve bacteria were only ESBL producers and 4.8% were both the ESBL & carbapenemase producers. 44.5% of ESBL & carbapenemase producing bacteria harbored the blaCTX-M and mostly detected in the E. coli, then K. pneumoniae and P. mirabilis. Multiple gene combinations were detected in 5% P. aeruginosa, 10% A. baumannii and 3.82% E. coli. This finding highlights the importance of molecular detection of ESBL & carbapenemase producing genes to emphasize the monitor and control the development of multi drug resistant Gram-ve bacterial pathogens.