Shared Extended-Spectrum β-Lactamase-Producing Salmonella Serovars between Agricultural and Aquatic Environments Revealed through invA Amplicon Sequencing

The presence of antibiotic-resistant Salmonella spp. in the environment is of great public health interest, worldwide. Furthermore, its extended-spectrum β-lactamase (ESBL)-producing strains constitute an emerging global health concern due to their limited treatment options in hospital. Therefore, this study aimed at characterising and tracking nonresistant and ESBL-producing Salmonella spp. from agricultural settings to nearby water sources highlighting their antibiotic resistance genes (ARG) and virulence factor (VF) distribution using a combination of both culture-dependent and independent methods. Furthermore, this study investigated the diversity and shared serovars among sampled matrices using amplicon sequencing of the invasion gene A (invA) of Salmonella spp. The results showed that soil had the highest prevalence of Salmonella spp. (62.5%, 65/104) and ESBL-producing Salmonella (34.6%, 36/104). For typed ARG, the most commonly detected gene was blaOXA with 75% (30/40), followed by blaCTX-M 67.5% (27/40),blaTEM 40% (16/40) and sul1 30% (12/40) gene; blaSHV gene was not detected in isolated ESBL-producing Salmonella spp. For VF, the most detected gene was invA (96.9%, 38/40), followed by spaM (17.5%, 7/40), spiC (40%, 16/40), orfL (32.5%, 13/40), misL 32.5% (13/40) and pipD 32.5 (13/40). For diversity analysis, soil, manure, irrigation water and nearby freshwater revealed 81, 68, 12 and 9 serovars, respectively. Soil, manure, irrigation water and freshwater stream samples shared five serovars, which indicated circulation of ESBL-producing Salmonella spp. within the agricultural environment and nearby water sources. Soil is therefore identified as one of the major reservoirs of ESBL-producing Salmonella spp. It is concluded that agricultural environment contamination may have a direct relationship with the presence of antibiotic-producing Salmonella in freshwater streams.

Multilocus-based phylogenetic analysis of extended-spectrum beta-lactamase Escherichia coli O157:H7 uncovers related strains between agriculture and nearby water sources

This study aimed to uncover related strains of extended-spectrum beta-lactamase Escherichia coli O157:H7 between agricultural matrices (soil, manure and irrigation water) and nearby water sources using multilocus-based phylogenetic analysis. Resistant and nonresistant E. coli O157:H7 were isolated, identified and characterised using standard microbiological methods. The results showed that soil samples had a high prevalence of E. coli O157:H7 (31.73%) and ESBL-producing E. coli O157:H7 (22.11%). Multilocus sequencing typing (MLST) analysis revealed that all ESBL-producing E. coli O157:H7 were identified as ST11. Phylogenetic analysis of E. coli O157:H7 indicated that irrigation water might be a reservoir for E. coli O157:H7. For antibiotic-resistant genes (ARG), the most common was bla_TEM in 85% (n = 34), followed by bla_OXA in 70% (n = 28), bla_NDM and sul1 30% (n = 12) and lastly mcr-1, which was only found in one soil isolate. The results showed that ESBL-producing E. coli O157:H7 isolates were intermixed in three clades, indicating close relatedness between isolated strains from different matrices.