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. 2022 Jan 24;29(1):7.
doi: 10.1186/s12929-022-00786-2.

Genomic diversity and antimicrobial resistance of Campylobacter spp. from humans and livestock in Nigeria

Benshak J Audu  1 , Strachan Norval  2 , Lopes Bruno  3 , Ramjee Meenakshi  3 , Macrae Marion  3 , Ken J Forbes  3
Affiliations

Genomic diversity and antimicrobial resistance of Campylobacter spp. from humans and livestock in Nigeria

Benshak J Audu et al. J Biomed Sci. .

Abstract

Background: Campylobacter spp. are zoonotic pathogens, ubiquitous and are found naturally as commensals in livestock from where they can be transmitted to humans directly or through animal products. The genomic diversity and antimicrobial resistance profile of Campylobacter was investigated with a focus on C. jejuni and C. coli in humans and livestock (poultry and cattle) from Nigeria.

Methods: 586 human stool samples and 472 faecal samples from livestock were cultured for thermophilic Campylobacter species on modified charcoal cefoperazone deoxycholate agar (mCCDA). Culture in combination with whole genome sequencing identified and confirmed the presence of Campylobacter in humans and animals from the study area. Further analysis of the sequences was performed to determine multilocus sequence types and genetic determinants of antimicrobial resistance to fluoroquinolone, betalactam, tetracycline and macrolide classes of antimicrobials.

Results: From the human stool samples tested, 50 (9%) were positive of which 33 (66%) were C. jejuni, 14 (28%) were C. coli while 3 (6%) were C. hyointestinalis. In livestock, 132 (28%) were positive. Thirty one (7%) were C. jejuni while 101 (21%) were C. coli. Whole genome sequencing and MLST of the isolates revealed a total of 32 sequence types (STs) identified from 47 human isolates while 48 STs were identified in 124 isolates from livestock indicating a population which was overall, genetically diverse with a few more dominant strains. The antimicrobial resistance profiles of the isolates indicated a higher prevalence of resistance in Campylobacter isolated from livestock than in humans. Generally, resistance was greatest for betalactams (42%) closely followed by fluoroquinolones (41%), tetracyclines (15%) and lastly macrolides (2%). Multidrug resistance to three or more antimicrobials was observed in 24 (13%) isolates from humans (n = 1, 4%) and chicken (n = 23, 96%).

Conclusions: This study has further contributed information about the epidemiology, genetic diversity and antimicrobial resistance profile of thermophilic Campylobacter in Nigeria.

Keywords: Antimicrobial resistance; Campylobacter; Clonal complex; Multilocus sequence typing; Sequence type.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Sequence Type diversity of isolates in samples from animals and humans
Fig. 2
Fig. 2
A population snapshot of human, chicken and cattle strains using eBURST. ** STs are indicated by dots which are linked by a line if they are SLVs while the primary founder by a blue dot. Relative abundance of the STs is reflected by the area of the dot
Fig. 3
Fig. 3
Simpson’s Diversity Index of Campylobacter STs in human and chicken
Fig. 4
Fig. 4
Pairwise Nei’s genetic distance between human and chicken isolates calculated at the 7-locus MLST level
Fig. 5
Fig. 5
Rarefaction analysis of human and chicken strains. *Dashed lines indicate 95% bootstrapped CI
See this image and copyright information in PMC

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