One Health approach to investigate antimicrobial resistance and public health risk of foodborne pathogens in Gauteng and Limpopo provinces, South Africa

Abstract

Globally, antimicrobial resistance (AMR) in foodborne pathogenic bacteria of the family Enterobacteriaceae has continued to rise. There is an increase in public health concerns about the spread of multi-drug resistant (MDR) foodborne pathogenic E. coli (PEC) and Salmonella enterica of zoonotic importance. This study aimed to characterise and investigate the profiles and resistome of zoonotic foodborne PEC and S. enterica using a One Health approach.

Between May 2019 and August 2020, faecal samples from swine and poultry, hand swabs from workers and environmental run-off water samples were collected from commercial abattoirs and farms in Gauteng and Limpopo provinces of South Africa. Similarly, effluents from wastewater treatment plants (WWTPs) and a tertiary hospital setting were collected. The PEC and S. enterica isolates detected were screened for phenotypic antimicrobial susceptibility testing (AST) for extended-spectrum beta-lactamases (ESBL), carbapenem and colistin resistance. Additionally, all PEC and S. enterica isolates were characterised using M-PCR assays to detect AMR genes for ESBL, carbapenems and colistin genes. Genetic relatedness of isolates was determined using pulsed-field gel electrophoresis (PFGE) and representative isolates were sequenced using whole genome sequencing (WGS). A pilot study compared resistomes from run-off water effluent samples from swine and poultry abattoirs and a WWTP using culture-dependent method and shotgun metagenomics.

A total of 542 samples were collected from swine (n = 198), poultry (n = 220), human hand swabs (n = 108), abattoir/farm run-off water (n = 11) and effluents samples (n = 5) from WWTPs and a hospital setting. The M-PCR assays detected a prevalence of 26.2% (142/542) and 2.2% (12/542) of PEC and S. enterica, respectively. The AST results detected resistance to ESBLs and colistin in PEC and S. enterica, respectively. No Carbapenem or colistin resistance was observed among PEC and S. enterica isolates. Dendrogram showed both PEC and S. enterica isolates clustered together according to the sampling site indicating genetic relatedness among isolates from the same site. Whole genome sequencing detected an array of virulence genes including: eae, stx1 and stx2 and AMR genes such as blaCTX-M-14 and blaTEM-1B. Mobile genetic elements associated with virulence and AMR were also reported such as the IncF variants and IncQ1 replicon types in PEC and S. enterica respectively. This study reported for the first time in Africa, the stx2k subtype in a PEC strain and the S. Typhimurium monophasic variant I 4,[5],12:i:- clonal group ST34 strain from animal and food sources. The culture-dependent method identified PEC in only the poultry wastewater effluent. Shotgun metagenomics did not detect the presence of PEC and S. enterica at genus and species levels in all three wastewater effluents which may indicate a low abundance of these bacterial pathogens in samples collected. The sul1 AMR gene was detected simultaneously with the culture-dependent method and shotgun metagenomics. Shotgun metagenomics identified Aliarcobacter cryaerophilus, an emerging foodborne pathogen, from the WWTP sample.

The detection of diverse PEC and S. enterica strains in swine, poultry, human hands and environmental run-off water in this study emphasises the need for continuous monitoring of foodborne pathogenic bacteria in abattoirs and farms across South Africa using a One Health Approach.