Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel blaADC-257
Mai M. Zafer, Amira F. A. Hussein, Mohamed H. Al‐Agamy, Hesham H. Radwan, Samira M. Hamed
Abstract
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 IS Aba14 in ST85 Pas isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel bla ADC allele ( bla ADC-257 ) with an upstream IS Aba1 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. Tn 2006 -associated bla OXA-23 was carried by M20. bla OXA-94 genes were preceded by IS Aba1 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.