Molecular Characterization and Detection of Plasmid-Mediated Quinolone Resistance (qnrA, qnrB, qnrD) Genes among Multidrug-Resistant Salmonella enterica Serovar Typhi Isolates from Clinical Specimens in Bauchi, Northeastern Nigeria
H. I. Liyo *
Department of Epidemiology and Biostatistics, Federal University of Health Sciences, Azare, Bauchi, Nigeria.
M. I. Liyo
Department of Microbiology, Federal, University, Gashua, Yobe, Nigeria.
A. Shehu
Department of Microbiology, Federal, University, Gashua, Yobe, Nigeria.
A. Magaji
Department of Microbiology, Abubakar Tafawa Balewa University, Bauchi, Nigeria.
A. Salisu
Department of Microbiology, Abubakar Tafawa Balewa University, Bauchi, Nigeria.
S. Z. M. Kabeer
Department of Microbiology, Federal University of Health Sciences, Azare (FUHSA), Bauchi state, Nigeria.
S. Ismai’l
Department of Microbiology, Federal, University, Gashua, Yobe, Nigeria.
Y. Saheed
Department of Microbiology, Yobe State University, Damaturu, Nigeria.
P. Moses
Department of Microbiology, Federal, University, Gashua, Yobe, Nigeria.
F. M. Ado
Department of Microbiology, University of Abuja, Abuja, Nigeria.
A. Usman
College of Nursing Science, Maiduguri, Borno State, Nigeria.
A. B. Zamo
Department of Medical Microbiology/Immunology, Federal University of Health Sciences Teaching Hospital, Azare (FUHSTHA), Bauchi State, Nigeria.
I. Mustapha
Department of Medical Laboratory Technicians, Galtima Mai Kyari College of Health Technology, Nguru, Yobe State, Nigeria.
H. S. Musa
National Health Insurance Authority, Bauchi State Office, Bauchi, Nigeria.
M. Y. Iliyasu
Department of Microbiology, Federal, University, Gashua, Yobe, Nigeria.
A. U. Kura
Department of Pharmacology, Sa’adu Zungur University, Bauchi, Nigeria.
*Author to whom correspondence should be addressed.
Abstract
Background: Salmonella enterica serovar Typhi remains a leading cause of enteric fever with 9 million cases and 110,000 deaths annually, disproportionately affecting low- and middle-income countries (Lamichhane et al., 2024). Multidrug-resistant (MDR) S. typhi and plasmid-mediated quinolone resistance (PMQR) determinants, particularly qnr genes, pose a major public health threat within the One Health framework because of their potential for rapid horizontal dissemination via mobile genetic elements (Djordjevic et al., 2024; Argimón et al., 2021).
Aim: This study aimed to molecularly identify MDR S. typhi isolates and detect qnrA, qnrB and qnrD genes among clinical isolates in Bauchi, Northeastern Nigeria.
Place and Duration of Study: Department of Microbiology, Abubakar Tafawa Balewa University, Bauchi, and Abubakar Tafawa Balewa University Teaching Hospital (ATBUTH), Bauchi, Nigeria, between January 2024 and December 2024.
Methodology: This was a cross-sectional laboratory-based study. Ethical approval: ATBUTH/HREC/2024/012. A total of 138 clinical samples (blood, n = 66; stool, n = 72) were collected with informed consent. Samples were cultured on Salmonella-Shigella Agar and Xylose Lysine Deoxycholate Agar. Presumptive Salmonella isolates were confirmed biochemically (Triple Sugar Iron, citrate, urease, H2S, motility) and serologically using polyvalent O and H antisera. Antimicrobial susceptibility testing (AST) was performed using the Kirby–Bauer disc diffusion in accordance with CLSI M100, 33rd edition (Clinical and Laboratory Standards Institute, 2023) using 12 antibiotics: ampicillin (10µg), chloramphenicol (30µg), trimethoprim-sulfamethoxazole (25µg), ciprofloxacin (5µg), nalidixic acid (30µg), ceftriaxone (30µg), cefotaxime (30µg), azithromycin (15µg), gentamicin (10µg), tetracycline (30µg), amoxicillin-clavulanate (30µg) and ofloxacin (5µg). MDR was defined as resistance to ≥1 agent in ≥3 antimicrobial categories (Magiorakos et al., 2012). MDR isolates were confirmed by PCR targeting the 16S rRNA gene (RIBOSE-1/RIBOSE-2, 789bp), followed by Sanger sequencing and BLAST analysis (≥98.7% identity threshold) (Stackebrandt and Ebers, 2006; Altschul et al., 1990). PMQR genes (qnrA, 516 bp; qnrB, 469 bp; qnrD, 691 bp) were screened by gene-specific PCR (Robicsek et al., 2006; Cavaco et al., 2009) and phylogenetic analysis was performed in MEGA 11 using the Neighbour-Joining method, 1,000 bootstrap replicates and the Kimura two-parameter model (Kimura, 1980; Tamura et al., 2021).
Results: Five (3.62%) Salmonella isolates were recovered (blood: 2/66, 3.03%; stool: 3/72, 4.16%). Two isolates (40%) were multidrug-resistant (MDR) (resistant to ampicillin, chloramphenicol, SXT, nalidixic acid, tetracycline). Sequencing of the 16S rRNA gene showed 99.10% and 98.77% identity with S. typhi reference strains CP156169.1 and CP029896.1. Phylogenetic analysis clustered the isolates with global S. typhi strains. Among MDR isolates, qnrA was detected in 2/2 (100%), qnrB in 1/2 (50%), qnrD 0%. Overall occurrence in the study population: qnrA 2/138 (1.45%), qnrB 1/138 (0.72%).
Conclusion: This study confirms the circulation of PMQR determinants (qnrA, qnrB) among MDR S. typhi in Bauchi. Although the prevalence was low (1.45%), their presence in clinical isolates indicates a potential risk of reduced fluoroquinolone effectiveness. Continued molecular surveillance within a One Health framework, antimicrobial stewardship, and WASH interventions are recommended. Future studies should use whole-genome sequencing for plasmid characterization.
Keywords: Salmonella enterica serovar Typhi, multidrug-resistance, plasmid-mediated quinolone resistance, qnrA, qnrB, qnrD, 16S rRNA, antimicrobial susceptibility, polymerase chain reaction