Antibiotic resistance and novel Sequence Types of Klebsiella spp. in human, animal, and food sources: a One Health perspective from Northern Nigeria

This study aimed to evaluate the genomic characteristics of Klebsiella spp. from human, animal, and food sources, and to establish their clonal relationships with globally circulating sequence types (STs). Using both phenotypic and next-generation sequencing approaches, a total of 300 samples comprising food samples (n = 180) and human clinical samples (n = 120) were collected and analyzed. Of these, 45 Klebsiella spp. were isolated from human (n = 16), animal (n = 15), and food (n = 14) sources. K. pneumoniae was the predominant species (34/45; 75.5%), followed by K. variicola subsp. variicola (4/45; 8.8%), K. quasipneumoniae (3/45; 6.6%), K. pneumoniae subsp. similipneumoniae (2/45; 4.4%), K. aerogenes (1/45; 2.2%), and K. michiganensis (1/45; 2.2%). Considering all the sources, 57.8 % of the isolates resulted in resistant to trimethoprim-sulfamethoxazole, while a lower percentage of strains showed resistance to aztreonam (17.8%), cefpodoxime (17.8%), cefotaxime (22.2%), ceftazidime (22.2%), ciprofloxacin (24.4%), colistin (15.6%), gentamicin (8.9%), levofloxacin (2.2%) and tobramycin (11.1%). In general, resistant strains were detected more frequently in samples of human and animal origin than in those of food origin. A total of 17 distinct STs were identified, including 9 novel STs. The fluoroquinolones resistance was mainly attributed to the presence of gene qnrS1 (33%), while strB (22%), strA (17.7%), and aac (6′)-Ibr-cr (11.1%) for aminoglycoside. β-lactam resistance genes bla_CTX−M, bla_SHV, bla_TEM, bla_OXA, and bla_OKP-_B were considerably present in human (15/16; 93.7%) and animal (17/19; 89.5%) isolates. Among ESBL-encoding genes, bla_OXY-1 (1/10; 10%) was exclusively found in food samples. The emergence of antibiotic-resistant and novel lineages of Klebsiella spp., with identical STs across human, animal, and food niches, indicates clonal expansion of high-risk strains. Surveillance and control of ESBL-producing Enterobacteriaceae using the One Health approach are urgently needed in Northern Nigeria.

Importance

. This study contributes to the understanding of the epidemiology of Klebsiella spp. in Nigeria. The study highlights that even in regions with relatively limited use of last resort antibiotics, high-risk global clones are circulating. These findings, aligned with the One Health approach, and emphasize the close interconnection between human, animal, and food sources, which facilitates the spread of common clones. Given the continuous emergence of new resistance mechanisms in Klebsiella spp., ongoing surveillance across Africa is warranted, employing both classical and molecular methods. In this study, next-generation sequencing enabled a comprehensive assessment of the circulating bacterial species, resistome, plasmidome, and virulome.