Abstract
Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.
Highlights
Escherichia coli is the most frequently isolated Gram-negative pathogen affecting human health [1]
Our study collection consisted of 103/335 (31 %) strains of E. coli isolated from rectal swabs of pigs from two farms in New South Wales, Australia, that were PCR-positive for the class 1 integron integrase gene, intI1
We identified 37 distinct sequence types, 21 of which were previously isolated from swine, as reported by the E. coli multilocus sequence typing (MLST) database
Summary
Escherichia coli is the most frequently isolated Gram-negative pathogen affecting human health [1]. Isolates are frequently resistant to multiple antibiotics and modelling studies forecast that multidrug resistant (MDR; resistant to three or more classes of antimicrobials) E. coli infections will account for 30 % of 10 million fatal MDR infections annually by 2050 [2]. In addition to the pathogenic variants, commensal E. coli comprise an important component of the gut microbiota. E. coli are shed into the environment in high numbers. Each gram of faeces from commercially reared pigs contains between 104 and 108 E. coli [3]. It is important to understand the characteristics of these E. coli given the huge quantities of faeces generated and disseminated by intensive pig production. The world’s largest producer of swine, produces an estimated 0.618 billion to 1.29 billion metric tonnes of swine faeces each year [4, 5]
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