Molecular characterisation of carbapenem resistant acinetobacter baumannii clinical isolates from Mulago Hospital Orthopaedic Ward

Abstract

Acinetobacter baumannii is an opportunistic nosocomial pathogen that causes various infections in patients. Due to the rapid development of antibiotic resistance, Acinetobacter baumannii has emerged as carbapenem-resistant causing a threat to its treatment. This study was conducted to determine the molecular characteristics of carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates obtained from Mulago Hospital Orthopedic Ward. A total of 13 archived glycerol stock cells were cultured and DNA was extracted. Whole-genome sequencing was done using the Illumina platform to produce sequences for bioinformatics analysis. Following analyses using Rapid Microbial Analysis Pipeline (rMAP), five samples (two from environment and three from index patients) passed the quality controls and were subjected to further analyses. Several antibiotic resistance mechanisms were identified with multi-drug efflux pumps being most prevalent followed by enzymatic degradation of drugs (Betalactamases). Five superfamilies of efflux pumps were identified where adeABC and adeIJK efflux were associated with multidrug resistance including carbapenems. In enzymatic degradation, Classes A, B, C and D beta-lactamases were identified with Class D (Oxacillinases) being the most prevalent (44%). These oxacillinases included OXA-69 as the most encountered (3 isolates), blaOXA-230, blaOXA-58, blaOXA-60, blaOXA-98, blaADC-2, blaADC-30, blaADC-73, blaNDM-1. Other genes identified in CRAB multidrug resistant isolates included mphA, sul2, tet(39), dfrA20, AAC(3)- IId, APH(3)-Ib, APH(3)-Ia and APH(6)-Id. The entA, entB, and papX were the identified virulence factors. From multi-locus sequence typing, A. baumannii study isolates belonged to two sequence types (ST) with ST1 having 3 isolates and ST52 which had only one isolate. One of the study isolate (ID089) could not be assigned a sequence type for the Pasteur scheme and this isolate presented many genes common to only itself compared to others. Based on a phylogenetic analysis of the samples, along with other A. baumannii strains deposited in NCBI, it appears that there may be a transmission of this pathogen between patients and the environment. Specifically, samples ORTHO037E and ID186 shared a common ancestor. The study revealed the presence of multiple oxacillinases, with at least one found in each sample. These findings suggest a potential threat in the treatment of CRAB infections and call for close monitoring where a study to compare presence of gene and its expression in the bacteria is key