Clinical and molecular analysis of ESBL, carbapenemase, and colistin-resistant bacteria in UTI patients

Molecular analysis of antibiotic-resistant gene in urobacteria

Abstract

Uropathogens, particularly bacteria, can infect any part of the urinary tract and cause bacteriuria. Our study aimed to examine the antibiotic-resistant profile, associated risk factors, and phenotypic and genotypic features of ESBL, carbapenemase, and mcr resistance genes in multidrug-resistant bacteria. Samples were inoculated on culture media, identified using standard biochemical tests, and species confirmation was performed via 16S rRNA gene amplification. Furthermore, antibiotic susceptibilities were evaluated using the Kirby-Bauer disc diffusion method. The phenotypically confirmed resistant strains were further inspected for ESBL, carbapenemases, and mcr variants using PCR. Merely 57.24% (83/145) of the samples exhibited growth. Of these, 39.70% (33/83) were identified as Klebsiella pneumoniae, 27.70% (23/83) as Escherichia coli, 10.80% (9/83) as Pseudomonas aeruginosa, 9.60% (8/83) as Staphylococcus aureus, 7.20% (6/83) as Proteus mirabilis, and 4.80% (4/83) as Staphylococcus saprophyticus. Overall, 22.54% (16/71) of the gram-negative strains were confirmed molecularly to have resistant genes. The ESBL – producers accounted for 21.74% (5/23) of E. coli, 21.21% (7/33) of K. pneumoniae, and 22.22% (2/9) of P. aeruginosa. Likewise, carbapenemase-harboring strains included 6.06% (2/33) of K. pneumoniae, 4.35% (1/23) of E. coli, and 11.11% (1/9) of P. aeruginosa. Notably, 3.03% (1/33) of K. pneumoniae, 8.70% (2/23) of E. coli, and 11.11% (1/9) of P. aeruginosa strains tested positive for the mcr-1 gene. None of the Proteus strains showed any resistant genes. The most common variants were bla_SHV-11 (non-ESBL) and bla_CTX-M-15 (ESBL) accounted for 28.57% (4/14) each, bla_TEM-116 accounted for 14.29% (2/14), bla_SHV-1, bla_SHV-75, bla_TEM-1 and bla_OXA-1 accounted for 7.14% (1/14) each of the ESBL. Similarly, the carbapenemase variants included bla_OXA-48, bla_NDM-1, bla_VIM-1, and bla_KPC-2, each accounting for 25.0% (1/4), while 37.50% (6/16) of the strains exhibited co-existence of different gene variants. Based on our findings, it can be concluded that females, especially those in middle age, were more infected. These pathogens exhibited a wide range of ESBL, carbapenemase, and mcr-1 variants. Imipenem was suggested as the preferred medication.