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The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water–plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing  Escherichia coli  ( n =3),  Klebsiella pneumoniae  ( n =5),  Serratia fonticola  ( n =10), and  Salmonella enterica  ( n =1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with  bla  CTX-M-15  being the dominant ESBL encoding gene and  bla  ACT -types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the  K. pneumoniae  strains, compared to the other genera tested. From one farm,  bla  CTX-M-15 -positive  K. pneumoniae  strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing  K. pneumoniae  ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However,  bla  CTX-M-15  was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in  K. pneumoniae  ( n =4) strains. In one  E. coli  and five  K. pneumoniae  strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635–0.721 in  S. fonticola , 0.852–0.931 in  E. coli , 0.796–0.899 in  K. pneumoniae , and 0.939 in the  S. enterica  strain. The presence of MDR ESBL/AmpC-producing  E. coli ,  K. pneumoniae ,  S. fonticola , and  S. enterica  with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.

frontiers in microbiology

Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa