Molecular characterization of multidrug resistant acinetobacter baumanii from patients at selected tertiary health care institutions in Uganda

Abstract

Acinetobacter baumannii is a gram-negative non-motile bacterium known to be an opportunistic pathogen. It is responsible for health care and community- acquired infections causing a range of infections including skin and soft tissue, urinary tract infections, bacteremia, ventilator associated pneumonia, etc. Mortality rates for A. baumannii infections have been reported at over 60% and the pathogenesis of the bacterium is attributed to its various virulent factors like the outer membrane protein, capsule formation and biofilm formation etc. There is a major rise in the number of multidrug resistant strains of A. baumannii with many being extended drug resistant and pan-drug resistant. A total of 13 A. baumannii isolates were retrieved for this study from three tertiary healthcare facilities in Uganda; Kiruddu National Referral Hospital, Bwera general hospital and Bombo General Military Hospital. Kirby-Bauer disc diffusion test was performed to confirm the MDR status of the isolates following CLSI guidelines and was followed with whole genome sequencing (WGS) for genotypic characterization of the resistant determinants and virulent genes. All the isolates were 100% resistant to ceftazidime, ceftriaxone, piperacillin/tazobactam, cotrimoxazole, cefotaxime, cefepime and ciprofloxacin while 92% of the isolates were resistant to meropenem and 84.6% resistant to amikacin and gentamicin. WGS revealed various AMR determinants and virulent genes among the isolates. Fifteen virulent genes i.e. OmpA, AdeFGH efflux pump, bap, Csupili, PNAG, phospholipase C and D, LPS, acinetobactin, heme utilization gene, abal/abaR, bfmR/bfms, PbpG which were present in all isolates and katA gene which was only present in ST2 isolates and PilE only present in isolate MUWRP11105 of ST52 were revealed. Multiple AMR determinants including blaOXA -23 like genes, blaOXA- 51 genes, gyrA, parC, blaNDM-1 etc. Pasteur multi-locus sequence typing (MLST) reveled 4 sequence types; ST1, ST2, ST52 and ST2589 with 46.1%, 38.4%, 7.6% and 7.6% isolates belonging respectively. Two international high-risk clone IC 1 and IC 2 were revealed to be circulating among the three healthcare facilities.