Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana

Abstract

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.

Genomic Analysis Reveals the Genetic Determinants Associated With Antibiotic Resistance in the Zoonotic Pathogen Campylobacter spp. Distributed Globally

“…Notably, 3 of the AR genes had not been previously reported in Campylobacter: lnu(AN2), putatively associated with lincosamides resistance, and 2 putative β-lactams resistance genes, bla OXA−493 and bla OXA−576 . Two β-lactamases coding genes, bla OXA−61 and bla OXA−184 , were the most abundant AR genes in the analyzed genomes from C. coli and C. jejuni, which is consistent with the results from previous studies (Griggs et al, 2009;Weis et al, 2016;Zhao et al, 2016;de Vries et al, 2018;Fabre et al, 2018;Whitehouse et al, 2018). In contrast, in the analyzed genomes from species other than C. coli and C. jejuni, the bla OXA−493 β-lactamase coding gene was the predominant (Supplementary File S1).…”

“…By its importance for public health and food safety, it is necessary to know the resistome of the genus Campylobacter; the resistome is defined as the collection of AR determinants in a specific bacteria or ecological niche (D'Costa et al, 2006;Wright, 2007;Hu et al, 2017). A very high correlation between the genotype and phenotype for AR has been observed in Campylobacter (Zhao et al, 2016;de Vries et al, 2018;Whitehouse et al, 2018). Therefore, the identification of the Campylobacter genotypes associated with AR could help to choose the best antibiotic treatment against infections by Campylobacter species.…”

Anthropogenic landscapes increase Campylobacter jejuni infections in urbanizing banded mongoose (Mungos mungo): A one health approach

“…epidemiology, surveillance and risk assessment, complicating public health prevention and control strategies [48]. The majority of Campylobacter-positive human samples (82.1%) were C. jejuni, which is similar to previous reports for southern Botswana (94.7%, 95% CI 75.4-99.1%) [26]. The nature of environmental reservoirs may influence exposure and transmission of Campylobacter species with C. jejuni appearing to have a greater survival in the environment than other species (reviewed in [9]).…”

Genomic epidemiology ofCampylobacter jejuniassociated with asymptomatic pediatric infection in the Peruvian Amazon

“…In contrast to the profusion of poultry-associated lineages, there was a striking paucity of host generalist ST-21 and ST-45 clonal complexes [40] that are among the most common diseasecausing lineages in Europe and North America. This has previously been observed in another LMICs, with very few ST-21 complex isolates cultured in surveys from Africa, SE Asia and South America [84][85][86][87][88]. Ruminant specialist lineages were also rare among the Peruvian pediatric samples (6.1 %) and the most common cattle associated lineage (ST-61 complex [25]) was completely absent.…”