Complete association between CHCF1 genotype and enterotoxigenic Escherichia coli F4ab-associated post-weaning diarrhea in a pig challenge trial

The early-life fecal microbiota is associated with litter of origin but not with susceptibility to ETEC F4ab-mediated post-weaning diarrhea in CHCF1 genotyped pigs

INTRODUCTION

Universal biomarkers in the fecal microbiota that predict susceptibility to post-weaning diarrhea (PWD) would be valuable for future intervention strategies. Genetic susceptibility to enterotoxigenic E. coli (ETEC) infection in pigs is a major determinant of PWD and may unfavourably alter early-life gut microbiota composition. We investigated whether pigs genetically susceptible to ETEC F4ab/ac had different fecal microbiota composition and diversity pre- and post-weaning compared to genetically resistant pigs.

METHOD

Fecal microbiotas were characterized using long-read sequencing of the 16S rRNA gene in 24 CHCF1 heterozygous susceptible (RS) and 24 CHCF1 homozygous resistant (RR) pigs. These pigs were tested at early lactation (post-natal day (PND) 8) and late lactation (PND 22), which are critical periods for microbiota development and immune maturation. Twelve pigs from each group were weaned and transported to an experimental facility at PND 23, and were tested again at PND 24, prior to an ETEC F4ab challenge. This enabled studying immediate fecal microbiota changes after weaning and investigating whether CHCF1 RS pigs had compromised microbiotas compared to CHCF1 RR pigs preceding infection.

RESULTS

Across time, CHCF1 RS pigs had a higher number of observed OTUs (coef: 103, 95% CI [18.90; 192.76], p = 0.01) compared to CHCF1 RR pigs. There were no significant differences in the overall bacterial communities or differentially abundant taxa between genotypes. Littermates had bacterial communities more similar to each other compared to non-littermates during lactation (PND 8: R2 = 0.2, p = 0.001 and PND 22: R2 = 0.23, p = 0.001) and the litter effect persisted after weaning (PND 24: R2 = 0.4, p = 0.001).

CONCLUSION

We did not find major differences in the fecal microbiota between CHCF1 genotypes, pre- or post-weaning, that could help explain subsequent susceptibility to ETEC F4ab-mediated PWD. Litter explained a major part of the variation in the overall fecal bacterial community between pigs in the study.

Selection for Resilience in Livestock Production Systems

Selective breeding for improved animal resilience is becoming critical to increase the sustainability of production systems. Despite the existence of a genetic component for resilience, breeding for improved resilience has been limited by the absence of a consensus on its definition and quantifying method. In this work, we provide a review of (i) the definition of resilience and related concepts such as robustness, resistance, and tolerance; (ii) possible quantifying methods for resilience; (iii) its genetic background; and (iv) insights about its improvement through selective breeding. We suggest that a resilient animal may be defined as an individual that is able to cope with a perturbation(s) and rapidly bounce back to normal functioning if altered. Furthermore, since challenging conditions lead to trade-offs and, consequently, deviations between basic physiological functions, we suggest using these deviations as indicators for resilience. These resilience indicators may also be used as proxies to study the genetic determinism and background of resilience in livestock species. Finally, we discuss possible strategies to improve resilience and review the implementation of associated genetic markers for resilience indicators in selection schemes.

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.

Effect of dietary tall oil fatty acids and hydrolysed yeast in SNP2-positive and SNP2-negative piglets challenged with F4 enterotoxigenic Escherichia coli

Reduction of post-weaning diarrhoea caused by ETEC is a principal objective in pig farming in terms of welfare benefits. This study determined the effects of genetic susceptibility and dietary strategies targeting inflammation and fimbriae adherence on F4-ETEC shedding and diarrhoea in weaned piglets in an experimental challenge model. A DNA marker test targeting single nucleotide polymorphism 2 (SNP2) identified piglets as heterozygous (SNP2+, susceptible) or homozygous (SNP2-, resistant) to developing F4ac-ETEC diarrhoea. A total of 50 piglets, 25 SNP2+ and 25 SNP2-, were weaned at 30 days of age and equally distributed to different treatments (n = 10): Positive control (PC): piglets fed with a negative control diet and provided with colistin via drinking water; Negative control (NC): piglets fed with a negative control diet; Tall oil fatty acids (TOFA): piglets fed with a negative control diet + 1.0 g TOFA/kg feed; Yeast hydrolysate (YH): piglets fed with a negative control diet + 1.5 g YH/kg feed derived from Saccharomyces cerevisiae; and Combination (COM): piglets fed with a negative control diet + 1.0 g TOFA and 1.5 g YH/kg feed. On day 10 post-weaning, all piglets were infected with F4-ETEC by oral administration. Piglets fed with PC, TOFA, YH or COM had a lower faecal shedding of F4-ETEC than NC piglets (P < 0.001), which was also shorter in duration for PC and TOFA piglets than for NC piglets (P < 0.001). Piglets in PC, TOFA, YH and COM had a shorter diarrhoea duration versus NC when classified as SNP2+ (P = 0.02). Furthermore, PC, TOFA and YH piglets grew more than NC and COM piglets in the initial post-inoculation period (P < 0.001). In addition, the level of faecal F4-ETEC shedding and the percentage of pigs that developed F4-ETEC diarrhoea (72 vs. 32%, P < 0.01) following infection were higher, and the duration of F4-ETEC diarrhoea longer (2.6 vs. 0.6 days, P < 0.001), in SNP2+ piglets than in SNP2- piglets, and led to reduced growth performance (P = 0.03). In conclusion, piglets fed with TOFA, YH or their combination, irrespective of their SNP2 status, are more resilient to F4-ETEC infection. Moreover, SNP2+ piglets show a higher level of F4-ETEC shedding and diarrhoea prevalence than SNP2- piglets, confirming an association between SNP2 and F4ac-ETEC susceptibility.

Effects of early postnatal gastric and colonic microbiota transplantation on piglet gut health

BACKGROUND

Diarrhea is a major cause of reduced growth and mortality in piglets during the suckling and weaning periods and poses a major threat to the global pig industry. Diarrhea and gut dysbiosis may in part be prevented via improved early postnatal microbial colonization of the gut. To secure better postnatal gut colonization, we hypothesized that transplantation of colonic or gastric content from healthy donors to newborn recipients would prevent diarrhea in the recipients in the post-weaning period. Our objective was to examine the impact of transplanting colonic or gastric content on health and growth parameters and paraclinical parameters in recipient single-housed piglets exposed to a weaning transition and challenged with enterotoxigenic Escherichia coli (ETEC).

METHODS

Seventy-two 1-day-old piglets were randomized to four groups: colonic microbiota transplantation (CMT, n = 18), colonic content filtrate transplantation (CcFT, n = 18), gastric microbiota transplantation (GMT, n = 18), or saline (CON, n = 18). Inoculations were given on d 2 and 3 of life, and all piglets were milk-fed until weaning (d 20) and shortly after challenged with ETEC (d 24). We assessed growth, diarrhea prevalence, ETEC concentration, organ weight, blood parameters, small intestinal morphology and histology, gut mucosal function, and microbiota composition and diversity.

RESULTS

Episodes of diarrhea were seen in all groups during both the milk- and the solid-feeding phase, possibly due to stress associated with single housing. However, CcFT showed lower diarrhea prevalence on d 27, 28, and 29 compared to CON (all P < 0.05). CcFT also showed a lower ETEC prevalence on d 27 (P < 0.05). CMT showed a higher alpha diversity and a difference in beta diversity compared to CON (P < 0.05). Growth and other paraclinical endpoints were similar across groups.

CONCLUSION

In conclusion, only CcFT reduced ETEC-related post-weaning diarrhea. However, the protective effect was marginal, suggesting that higher doses, more effective modalities of administration, longer treatment periods, and better donor quality should be explored by future research to optimize the protective effects of transplantation.