Diversity and phage sensitivity to phages of porcine enterotoxigenic Escherichia coli.

Enterotoxigenic Escherichia coli (ETEC) is a diverse and poorly characterized E. coli pathotype that causes diarrhea in humans and animals. Phages have been proposed for the veterinary biocontrol of ETEC, but effective solutions require understanding of porcine ETEC diversity that affects phage infection. Here, we sequenced and analyzed the genomes of the PHAGEBio ETEC collection, gathering 79 diverse ETEC strains isolated from European pigs with post-weaning diarrhea (PWD). We identified the virulence factors characterizing the pathotype and several antibiotic resistance genes on plasmids, while phage resistance genes and other virulence factors were mostly chromosome encoded. We experienced that ETEC strains were highly resistant to Enterobacteriaceae phage infection. It was only by enrichment of numerous diverse samples with different media and conditions, using the 41 ETEC strains of our collection as hosts, that we could isolate two lytic phages that could infect a large part of our diverse ETEC collection: vB_EcoP_ETEP21B and vB_EcoS_ETEP102. Based on genome and host range analyses, we discussed the infection strategies of the two phages and identified components of lipopolysaccharides ( LPS) as receptors for the two phages. Our detailed computational structural analysis highlights several loops and pockets in the tail fibers that may allow recognition and binding of ETEC strains, also in the presence of O-antigens. Despite the importance of receptor recognition, the diversity of the ETEC strains remains a significant challenge for isolating ETEC phages and developing sustainable phage-based products to address ETEC-induced PWD.IMPORTANCEEnterotoxigenic Escherichia coli (ETEC)-induced post-weaning diarrhea is a severe disease in piglets that leads to weight loss and potentially death, with high economic and animal welfare costs worldwide. Phage-based approaches have been proposed, but available data are insufficient to ensure efficacy. Genome analysis of an extensive collection of ETEC strains revealed that phage defense mechanisms were mostly chromosome encoded, suggesting a lower chance of spread and selection by phage exposure. The difficulty in isolating lytic phages and the molecular and structural analyses of two ETEC phages point toward a multifactorial resistance of ETEC to phage infection and the importance of extensive phage screenings specifically against clinically relevant strains. The PHAGEBio ETEC collection and these two phages are valuable tools for the scientific community to expand our knowledge on the most studied, but still enigmatic, bacterial species-E. coli.

Phylogenetic and pathotype analysis of Escherichia coli swine isolates from Southern Brazil / Análise filogenética e de patotipos de Escherichia coli isoladas de suínos no Sul do Brazil

The current study evaluated the presence of virulence factors by a multiplex PCR technique and then phylogenetically classified the studied strains into groups A, B1, B2 and D, according to Clermont et al. (2000), in 152 intestinal and extraintestinal swine isolates of Escherichia coli. Seventy seven isolates tested were positive for virulence factors. Phylogenetic characterization placed 21 samples into group A, 65 into B1, 19 into B2 and 47 into D. Fourteen urine samples were classified as uropathogenic E. coli (UPEC), nine were both UPEC and enterotoxigenic E. coli (ETEC) and four were ETEC only. The most common phylogenetic classifications were B1 and D groups. Of the analyzed fecal samples, 25 were classified as ETEC. Phylogenetically, the group of higher occurrence was B1, followed by B2, A and D. For the small intestine samples, 20 were classified as ETEC. Phylogenetic analysis found groups B1 and A to be the most commons in these samples. Six isolated tissue samples were classified as ETEC and most of them were designated as group D by phylogenetic classification. The phylogenetic analysis could be employed in veterinary laboratories in the E. coli isolates screening, including the possibility of vaccine strain selection and epidemiological searches.

O presente estudo teve por objetivo avaliar a presença de diferentes fatores de virulência em 152 isolados de Escherichia coli intestinais e extra-intestinais provenientes de suínos pela técnica de PCR multiplex e classificá-los nos grupos filogenéticos A, B1, B2 e D, de acordo com Clermont et al. (2000). Setenta e sete isolados foram positivos para pelo menos um fator de virulência. Através da caracterização filogenética, 21 isolados foram caracterizados como pertencentes ao grupo A, 65 ao grupo B1, 19 ao grupo B2 e 47 isolados ao grupo D. Quatorze isolados de urina foram caracterizados como E. coli uropatogênica (UPEC); nove apresentaram fatores de UPEC e E. coli enterotoxigênica (ETEC) simultaneamente e quatro foram classificados como ETEC. Na classificação filogenética, os isolados provenientes de amostras de urina classificaram-se principalmente nos grupos D e B1. Das amostras de fezes analisadas, 25 demonstraram fatores de virulência característicos do patotipo ETEC. Filogeneticamente, o grupo de maior ocorrência foi o B1 seguido de B2, A e D. Em relação às cepas isoladas de intestino delgado, 20 foram caracterizadas como ETEC. Pela filogenia, 23 isolados classificaram-se nos grupos A ou B1. Seis isolados de tecidos foram qualificados como ETEC e a maioria deles foram designados como pertencentes ao grupo D, pela classificação filogenética. A análise filogenética pode ser empregada em laboratórios de diagnóstico veterinário como um screening para isolados de E. coli, incluindo a possibilidade de seleção de cepas vacinais e levantamentos epidemiológicos.