Genotypic diversity among multidrug resistant Pseudomonas aeruginosa and Acinetobacter species at Mulago Hospital in Kampala, Uganda

Abstract

Background: Multidrug resistant Pseudomonas aeruginosa and Acinetobacter species are common causes of nosocomial infections worldwide. Recently we reported the occurrence of carbapenem resistant Enterobacteriaceae, P. aeruginosa and Acinetobacter species at Mulago National Referral Hospital in Kampala, Uganda, but the isolates were not analyzed for genetic relatedness. Herein we report the intra-species genotypic diversity among P. aeruginosa and Acinetobacter baumannii isolated from hospitalized patients and the environment at Mulago Hospital, using repetitive elements-based PCR (Rep-PCR) genotyping.

Results: A total of 736 specimens from hospitalized patients were processed for culture and sensitivity testing yielding 9 (1.2%) P. aeruginosa and 7 (0.95%) A. baumannii. Similarly, 100 samples from the hospital environment were processed yielding 33 (33%) P. aeruginosa and 13 (13%) A. baumannii. Altogether, 62 non-repetitive isolates were studied (42 P. aeruginosa and 20 A. baumannii), of which 38% (16/42) P. aeruginosa and 40% (8/20) A. baumannii were multidrug resistant (isolates resistant to three or more classes of antimicrobials). Carbapenem resistance prevalence was 33 and 21% for P. aeruginosa from patients and the environment, respectively, while it was 14 and 86% for A. baumannii from patients and environment, respectively. Cluster analysis of the Rep-PCR fingerprints revealed a high level of genetic diversity among the isolates within each species as few isolates were clustered (at 100% level of similarity). More to this, the clustered isolates revealed a complex nature of multidrug resistant P. aeruginosa and A. baumannii clones circulating at Mulago Hospital. Importantly, certain isolates from the environment and patients were clustered, implying that hospitalized patients at Mulago were probably infected with strains from the environment.

Conclusions: The prevalence of multidrug resistant P. aeruginosa and A. baumannii is high at Mulago Hospital but carbapenem resistance prevalence remains relatively low in isolates from hospitalized patients. Importantly, the prevalence of carbapenem resistance in isolates from the environment is high implying the infection control practices at the hospital might be inadequate.

Keywords: Antimicrobial resistance AMR; Carbapenems; Genotyping; Gram negative bacteria; Hospital environment; Hospitalized patients; Rep-PCR; Sub-Saharan Africa.

Fig. 1

Dendrogram based on Dice’s coefficient of similarity using UPGMA method implemented by the Bionumerix program showing relationships between A. baumannii isolates according to BOXAIR-PCR genotyping. E isolate from hospital environment; H isolate from hospitalized patient. The susceptibility profiles (extreme right panel) for carbapenem-resistant isolates are indicated in brown font. AK amikacin, CN gentamicin, IMP imipenem, MEM meropenem, CAZ ceftazidime, FEP cefepime, ATM aztreonam, TZP piperacillin/tazobactam, CIP ciprofloxacin, SXT trimethoprim/sulfamethoxazole. ^bMultidrug-resistance pattern; ^cSXT-susceptible carbapenem-resistant A. baumannii

Fig. 2

Dendrogram based on Dice’s coefficient of similarity using UPGMA method implemented by the Bionumerix program showing relationships between A. baumannii isolates according to REP-PCR genotyping. E isolate from hospital environment; H isolate from hospitalized patient. The susceptibility profiles (extreme right panel) for carbapenem-resistant isolates are indicated in brown font. AK amikacin, CN gentamicin, IMP imipenem, MEM meropenem, CAZ ceftazidime, FEP cefepime, ATM aztreonam, TZP piperacillin/tazobactam, CIP ciprofloxacin, SXT trimethoprim/sulfamethoxazole. ^bMultidrug-resistance pattern; ^cSXT-susceptible carbapenem-resistant A. baumannii

Fig. 3

Dendrogram based on Dice’s coefficient of similarity using the UPGMA method implemented by the Bionumerix program showing relationships between P. aeruginosa isolates according to BOXAIR-PCR genotyping. E isolate from hospital environment; H isolate from hospitalized patient. The susceptibility profiles (extreme right panel) for carbapenem-resistant isolates are indicated in brown font. AK Amikacin, CN gentamicin, IMP imipenem, MEM meropenem, CAZ ceftazidime, FEP cefepime, ATM aztreonam, TZP piperacillin/tazobactam, CIP ciprofloxacin. ^bMultidrug-resistance pattern