Characterization of Genomic Diversity among Carbapenem-Resistant Escherichia coli Clinical Isolates and Antibacterial Efficacy of Silver Nanoparticles from Pakistan

The emergence of carbapenem-resistant Escherichia coli (E. coli) is considered an important threat to public health resulting in resistance accumulation due to antibiotics misuse and selection pressure. This warrants periodic efforts to investigate and develop strategies for infection control. A total of 184 carbapenem-resistant clinical strains of E. coli were characterized for resistance pattern, resistance genes, plasmids, sequence types and in vitro efficacy of silver nanoparticles (AgNPs). Carbapenem resistance was prevalent in E. coli isolated from female patients (64.7%), urine samples (40.8%) and surgical wards (32.1%). Polymyxin-B showed higher susceptibility. ESBLs and carbapenemases were produced in 179 and 119 isolates, respectively. Carbapenemase-encoding genes were observed among 104 strains with bla(NDM-1) (45.1%), bla(OXA-48) (27%), bla(NDM-7) (3.8%), bla(NDM-1)/bla(OXA-48) (15.4%), bla(NDM-7)/bla(OXA-48) (2.9%), bla(OXA-48)/bla(VIM) (3.8%) and bla(NDM-1)/bla(VIM) (2%). ESBL resistance genes were detected in 147 isolates, namely bla(SHV) (24.9%), bla(CTX-M) (17.7%), bla(TEM) (4.8%), bla(SHV)/bla(CTX-M) (29.2%), bla(SHV)/bla(TEM) (15%) and bla(CTX-M)/bla(TEM) (8.8%). ST405 (44.4%) and ST131 (29.2%) were more frequent sequence types with ST101 (9.7%), ST10 (9.7%) and ST648 (7%). The replicon types IncFII, IncFIIK, IncA/C, IncN and IncL/M were detected. The combination of MEM/AgNPs remained effective against carbapenemase-positive E. coli. We reported genetically diverse E. coli strains coharboring carbapenemases/ESBLs from Pakistan. Moreover, this study highlights the enhanced antibacterial activity of MEM/AgNPs and may be used to manage bacterial infections.