High prevalence and co-existence of SHV and CTX-M genes in extensively drug-resistant (XDR) Gram-negative bacteria isolated from hospital settings in Faisalabad District, Pakistan.

BACKGROUND: Hospital-acquired infections (HAIs) associated with increasing antimicrobial resistance (AMR) are becoming a global health challenge, causing AMR spread and a serious health threat. This study was designed to evaluate the phenotypic and genotypic status of AMR in Gram-negative HAI-associated bacteria, to gain a current insight into the local settings. METHODS AND RESULTS: Kirby-Bauer method and Double Disc Synergy Test were used for phenotypic assessment of AMR and extended-spectrum β-lactamase (ESBL) producers, respectively. Genes encoding antimicrobial resistance, ESBLs, and carbapenemases were identified by PCR followed by Sanger sequencing. Among 102 HAI samples, 62 were Gram-negative, identified as Escherichia coli (E. coli) (42.2%), Klebsiella pneumoniae (K. pneumoniae) (21.1%), and Pseudomonas aeruginosa (P. aeruginosa) (6.6%) by PCR. All K. pneumoniae and (95%) E. coli isolates exhibited multidrug resistance. K. pneumoniae isolates (95%) showed resistance against ceftazidime, cefotaxime, ceftriaxone, and aztreonam, and (89%) isolates were resistant to amoxicillin-clavulanic acid, ofloxacin, and cefepime (E. coli isolates (84%), (84%), (78%), (76%), (76%), and (73%) were resistant against cefotaxime, ceftriaxone, aztreonam, ceftazidime, doripenem, and colistin, respectively. Genotypically, the mcr-2 gene was detected in 5% K. pneumoniae isolates. Phenotypically, 63% isolates were identified as ESBL producers with high genetic prevalence of SHV-12 (78.9%) and SHV-1 (57.8%) in K. pneumoniae and CTX-M1 (60.5%) in E. coli. Notably, one K. pneumoniae isolate harbored all class-A ESBL genes, which is a novel finding. Co-existence of CTX-M1 + SHV-1 + TEM-1, SHV-1 + SHV-12 + TEM-1, and CTX-M1 + CTX-M15 + TEM-1 genes was dominant. CONCLUSION: The HAIs caused by extensively drug-resistant and ESBL-producing K. pneumoniae and E. coli were dominant, with less prevalence of moderately drug-resistant Pseudomonas isolates.