Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel blaADC-257

Acinetobacter baumannii has become a major challenge to clinicians worldwide due to its high epidemic potential and acquisition of antimicrobial resistance. This work aimed at investigating antimicrobial resistance determinants and their context in four extensively drug-resistant (XDR) NDM-producing A. baumannii clinical isolates collected between July and October 2020 from Kasr Al-Ainy Hospital, Cairo, Egypt. A total of 20 A. baumannii were collected and screened for acquired carbapenemases (bla(NDM), bla(VIM) and bla(IMP)) using PCR. Four NDM producer A. baumannii isolates were identified and selected for whole-genome sequencing, in silico multilocus sequence typing, and resistome analysis. Antimicrobial susceptibility profiles were determined using disk diffusion and broth microdilution tests. All bla(NDM)-positive A. baumannii isolates were XDR. Three isolates belonged to high-risk international clones (IC), namely, IC2 corresponding to ST570(Pas)/1701(Oxf) (M20) and IC9 corresponding to ST85(Pas)/ST1089(Oxf) (M02 and M11). For the first time, we report bla(NDM-1) gene on the chromosome of an A. baumannii strain that belongs to sequence type ST164(Pas)/ST1418(Oxf). Together with AphA6, bla(NDM-1) was bracketed by two copies of ISAba14 in ST85(Pas) isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel bla(ADC) allele (bla(ADC-257)) with an upstream ISAba1 element was identified in M19 (ST/CC164(Pas) and ST1418(Oxf)/CC234(Oxf)). bla(ADC) genes harbored by M02 and M11 were uniquely interrupted by IS1008. Tn2006-associated bla(OXA-23) was carried by M20. bla(OXA-94) genes were preceded by ISAba1 element in M02 and M11. AbGRI3 was carried by M20 hosting the resistance genes aph(3`)-Ia, aac(6`)-Ib`, catB8, ant(3``)-Ia, sul1, armA, msr(E), and mph(E). Nonsynonymous mutations were identified in the quinolone resistance determining regions (gyrA and parC) of all isolates. Resistance to colistin in M19 was accompanied by missense mutations in lpxACD and pmrABC genes. The current study provided an insight into the genomic background of XDR phenotype in A. baumannii recovered from patients in Egypt. WGS revealed strong association between resistance genes and diverse mobile genetic elements with novel insertion sites and genetic organizations.

Automated summary

Acinetobacter baumannii has become a major challenge for clinicians worldwide due to its high epidemic potential and antimicrobial resistance. This study investigated antimicrobial resistance determinants in XDR NDM-producing A. baumannii isolates from Egypt. Genomic analysis revealed a strong association between resistance genes, diverse mobile genetic elements, and unique genetic arrangements.