Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria

Diane E Kawa; Isabella A Tickler; Fred C Tenover; Shuwaram A Shettima

doi:10.3390/tropicalmed8110500

Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria

Trop Med Infect Dis. 2023 Nov 16;8(11):500. doi: 10.3390/tropicalmed8110500.

Authors

Diane E Kawa¹, Isabella A Tickler², Fred C Tenover³, Shuwaram A Shettima⁴

Affiliations

¹ Department of Medical and Scientific Affairs, Cepheid, Sunnyvale, CA 94089, USA.
² Department of Medical and Scientific Affairs, Cepheid, 20090 Milan, Italy.
³ College of Arts and Sciences, University of Dayton, Dayton, OH 45469, USA.
⁴ Department of Medical Microbiology, Parasitology and Immunology, Modibbo Adama University Teaching Hospital, Yola 640001, Adamawa State, Nigeria.

Abstract

Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby-Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included bla_CTX-M, bla_SHV, and bla_TEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either bla_CTX-M-15 or bla_{CTX-M-1 4} and phenotypically produced ESBLs. The bla_NDM-7 and bla_VIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained bla_NDM-7, while bla_NDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6')-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL bla_CTX-M-15, the serine carbapenemase, bla_OXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance.

Keywords: Nigeria; Yola; beta-lactamase; carbapenem resistance; carbapenemase; fluoroquinolone resistance.

Grants and funding

N/A/Cepheid