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

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 (blaNDM, blaVIM and blaIMP) 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 blaNDM-positive A. baumannii isolates were XDR. Three isolates belonged to high-risk international clones (IC), namely, IC2 corresponding to ST570Pas/1701Oxf (M20) and IC9 corresponding to ST85Pas/ST1089Oxf (M02 and M11). For the first time, we report blaNDM-1 gene on the chromosome of an A. baumannii strain that belongs to sequence type ST164Pas/ST1418Oxf. Together with AphA6, blaNDM-1 was bracketed by two copies of ISAba14 in ST85Pas isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel blaADC allele (blaADC-257) with an upstream ISAba1 element was identified in M19 (ST/CC164Pas and ST1418Oxf/CC234Oxf). blaADC genes harbored by M02 and M11 were uniquely interrupted by IS1008. Tn2006-associated blaOXA-23 was carried by M20. blaOXA-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.

Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

“…Within RI-PER-7, the rifampin resistance gene arr-2 was only carried by M03. Colistin resistance in M19 was found to be associated with mutations in pmrB (H89L), pmrC (I42V, I212V, R323K, A354S, and V470I), IpxA (Y131H and Y231H), IpxC (C120R, N287D, and K130T), and lpxD (V631 and E117K), as described before (Zafer et al, 2021).…”

“…Genes coding the chloramphenicol efflux pumps FloR and CmlA5 were also identified. FloR efflux pump-coding gene was carried by M02 and M11 (2/18, 11.1%) in association with sul2 gene and ISs, as described before (Zafer et al, 2021). A novel cmlA/floR-like gene variant was identified in five isolates (27.7%).…”

“…These included all GC9 isolates, one GC2 isolate (M20), as well as M19 (ST164 Pas /1418 Oxf ) and its phylogenetically related isolate M10. The genetic environment of bla NDM−1 was described in our previous study (Zafer et al, 2021). We reported, for the first time, a novel transposon in which both bla NDM−1 and aphA6 were enclosed by two direct copies of ISAba14.…”

Rectal Colonization and Nosocomial Transmission of Carbapenem-Resistant Acinetobacter baumannii in an Intensive Care Unit, Southwest Nigeria

“…The ST1089 (IC9) strains were the second most common lineage in this study. These strains have been isolated from clinical samples and hospital environments, particularly from studies in Northern Africa and in the Middle East, and are frequently reported to carry blaNDM-1 and blaOXA-94 carbapenem resistance genes (32,(33)(34)(35)(36)(37)(38)(39). An ST1089 strain carrying blaNDM-1 was also isolated from raw milk in a dairy farm in Algeria (40).…”

Emergence of a Carbapenem-Resistant Klebsiella pneumoniae Isolate Co-harbouring Dual blaNDM– 6-Carrying Plasmids in China

“…Tn 125 , which is formed by IS Aba125 , is the most common transposable element involved in the interspecies transmission of bla NDM among Acinetobacter spp. and Enterobacteriaceae ( Bontron et al, 2016 ; Zafer et al, 2021 ). IS Aba125 in the upstream (intact or interrupt) provides a strong promoter for driving the expression of bla NDM ( Poirel et al, 2011 ; Toleman et al, 2012 ).…”