Role of enterotoxigenic Escherichia coli prophage in spreading antibiotic resistance in a porcine‐derived environment

Abstract

Enterotoxigenic Escherichia coli (ETEC) cause acute secretory diarrhoea in pigs, posing a great economic loss to the swine industry. This study analysed the prevalence and genetic characteristics of prophages from 132 ETEC isolates from symptomatic pigs to determine their potential for spreading antibiotic resistance. A total of 1105 potential prophages were identified, and the distribution of the genome size showed three 'overlapping' trends. Similarity matrix comparison showed that prophages correlated with the ETEC lineage distribution, and further identification of these prophages corroborated the lineage specificity. In total, 1206 antibiotic resistance genes (ARGs) of 52 different categories were identified in 132 ETEC strains; among these, 2.65% (32/1206) of ARGs were found to be carried by prophages. Analysis of flanking sequences showed that almost all the ARGs could be grouped into two types: 'bla TEM-1B ' and 'classic class 1 integron (IntI1)'. They co-occurred with a strictly conserved recombinase and transposon Tn3 family but with a difference: the 'bla TEM-1B type' prophages exhibited a classic Tn2 transposon structure with 100% sequence identity, whereas the 'IntI1 type' co-occurred with the TnAs2 transposon with only 84% sequence identity. These results imply that ARGs might be pervasive in natural bacterial populations through transmission by transposable bacteriophages.

Distribution of Antimicrobial Resistance and Virulence Genes within the Prophage-Associated Regions in Nosocomial Pathogens

“…Phage or prophage-carrying AMR genes are reported to be minor HGT agents ( 37 , 38 ). In recent years, however, several studies have reported that AMR genes are present in the phage or prophage region ( 39 – 42 ), implying that they are associated with the prophage region more than expected. Nevertheless, there have been few reports comprehensively identifying and analyzing AMR/VF genes located in the prophage region of nosocomial AMR pathogens.…”

Comprehensive Scanning of Prophages in Lactobacillus : Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems

“…The prevalence of ARGs in Lactobacillus is well known, and many strains show phenotypic multidrug resistance ( 48 ). Foodborne drug-resistant bacteria may promote the transfer of ARGs to other commensal microorganisms in the human gastrointestinal tract ( 49 ), thus posing a threat to public health and food safety ( 50 ), while a complete prophage is a crucial carrier and reservoir of ARGs ( 51 ), leading to the widespread dissemination of antibiotic resistance ( 52 ). Therefore, ubiquitous prophages should arouse our attention to assess the risk of antibiotic resistance transfer in Lactobacillus .…”

Prophage elements function as reservoir for antibiotic resistance and virulence genes in nosocomial pathogens

“…Phage or prophage-carrying AMR genes are reported to be minor HGT agents (34, 35). In recent years, however, several studies have reported that AMR genes are present in the phage or prophage region (36–39), implying that they are associated with the prophage region more than expected. Nevertheless, there have been few reports comprehensively identifying and analyzing AMR/VF genes encoded in the prophage region of nosocomial AMR pathogens.…”