AUTHOR=Sewunet Tsegaye , Asrat Daniel , Woldeamanuel Yimtubezinash , Aseffa Abraham , Giske Christian G. 

TITLE=Molecular epidemiology and antimicrobial susceptibility of Pseudomonas spp. and Acinetobacter spp. from clinical samples at Jimma medical center, Ethiopia

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.951857

DOI=10.3389/fmicb.2022.951857

ISSN=1664-302X

ABSTRACT=Introduction: Pseudomonas aeruginosa (P. aeruginosa) and Acinetobacter baumannii (A. baumannii) can cause difficult-to-treat infections. We characterized molecular epidemiology of ceftazidime-resistant P. aeruginosa and carbapenem-resistant A. baumannii at a tertiary hospital in Ethiopia.
Materials and Methods: Non-fermenting gram-negative bacilli (n=80) isolated from admitted patients were subjected for species identification by MALDI-TOF. P. aeruginosa isolates resistant to ceftazidime or meropenem, and A. baumannii isolates resistant to meropenem, or imipenem were selected for whole genome sequencing. DNA extracted with EZ1 Advanced XL instrument (Qiagen, Hilden, Germany) was sequenced on Illumina (HiSeq2500) using libraries prepared by NEXTRA-kits (Illumina). Raw reads were assembled using SPAdes 3.13.0, and assembled genomes were used to query databases for resistome profile and sequence types.
 Result: Among Pseudomonas isolates 31.7% (13/41), and 7.3% (3/41) were non-susceptible to ceftazidime, and meropenem respectively. Carbapenem-resistance was 56.4% (22/39) among Acinetobacter isolates. Moreover, 92% (12/13) of Pseudomonas species, and 89.4% (17/19) of Acinetobacter species encoded multiple resistance genes for at least three classes of antimicrobials. The prevalent lactamase genes were blaOXA-486 (53.8%, 7/13), blaCTX-M-15 (23.0%, 3/13) among Pseudomonas, and blaGES-11 (57.8%, 11/19) among Acinetobacter. The blaOXA-51-like lactamase, blaOXA-69 (63:1% (12/19) was the most prevalent carbapenemase gene among Acinetobacter isolates. Single isolates from both P. aeruginosa, and A. baumannii were detected with the blaNDM-1. Sequence type (ST)1 A. baumannii and ST274 P. aeruginosa were the prevalent sequence types. A cgMLST analysis of the ST1 A. baumannii isolates showed that they were closely related and belonged to the international clonal complex one (ICC1). Similarly, ST274 P. aeruginosa isolates were clonally related. 
Conclusion: The prevalence of MDR isolates of Pseudomonas and Acinetobacter isolates was high. Emergence of blaNDM-1 in the intensive care, and surgical wards of the hospital is a severe threat that requires urgent intervention.