Genomic analysis of a multidrug-resistant Klebsiella pneumoniae ST11 strain recovered from Barbary deer (Cervus elaphus barbarus) in Akfadou Forest, Algeria

Abstract

Objectives: The emergence and worldwide spread of carbapenemase-producing Enterobacterales (CPE) is a great public-health concern. This study aimed to screen for the presence of CPE isolates from Barbary deer in Akfadou Forest, Béjaïa (Algeria). Methods: Faecal samples (n = 39) were obtained from Barbary deer in Akfadou Forest between March–June 2018. Whole-genome sequencing (WGS) was performed to characterise one representative strain of Klebsiella pneumoniae. Data analysis was performed using online tools. Results: A total of 13 carbapenem-resistantK. pneumoniae isolates were obtained. The isolates showed an identical antimicrobial resistance pattern and were susceptible to colistin and fosfomycin. WGS analysis revealed the complete resistome of K. pneumoniae strain CF21, including blaNDM-1, blaCTX-M-15, blaSHV-182, blaDHA-1, blaOXA-1, aac(3)-IIa, aac(3)-IId, aac(6ʹ)-Ib-cr, rmtC, sul1, qnrB9, fosA, tetA, dfrA14, catA2, catB3 and mphA. Multilocus sequence typing (MLST) analysis assigned this strain to the international clone ST11. Plasmid analysis showed that this K. pneumoniae strain possesses five different plasmids including IncA/C2, IncFIA(HI1), IncFIB(K), IncFII(K) and ColRNAI. Conclusion: This study reports a multidrug-resistantK. pneumoniae strain recovered from Barbary deer in Algeria and confirms that wild animals could serve as a reservoir of antimicrobial resistance genes.

Keywords

• Klebsiella pneumonia
• Antimicrobial resistance genes
• Wild animal
• WGS
• Algeria