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

Introduction: Pseudomonas aeruginosa () and () can cause difficult-to-treat infections. We characterized molecular epidemiology of ceftazidime-resistant and carbapenem-resistant at a tertiary hospital in Ethiopia.

Materials And Methods: Non-fermenting gram-negative bacilli ( = 80) isolated from admitted patients were subjected for species identification by MALDI-TOF. species resistant to ceftazidime or meropenem, and species 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 species isolated, 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 species. Moreover, 92% (12/13) of species non-susceptible to ceftazidime and/or meropenem, and 89.4% (17/19) of species encoded multiple resistance genes for at least three classes of antimicrobials. The prevalent β - lactamase genes were (53.8%, 7/13), (23.0%, 3/13) among , and (57.8%, 11/19) among . The -like β - lactamase, (63.1%, 12/19) was the most prevalent carbapenemase gene among isolates. Single isolates from both , and were detected with the . Sequence type (ST)1 and ST274 were the prevalent sequence types. A cgMLST analysis of the ST1 isolates showed that they were closely related and belonged to the international clonal complex one (ICC1). Similarly, ST274 isolates were clonally related.

Conclusion: The prevalence of MDR isolates of and spp. was high. isolates were clonally spreading in the admission wards at the hospital. Emergence of in the intensive care, and surgical wards of the hospital is a severe threat that requires urgent intervention.