Editorial: Mechanisms of Persistence, Survival, and Transmission of Bacterial Foodborne Pathogens in Production Animals

Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting

Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.

To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

BACKGROUND

Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile.

RESULTS

Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131.

CONCLUSIONS

This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Effect of Antibiotic, Phytobiotic and Probiotic Supplementation on Growth, Blood Indices and Intestine Health in Broiler Chicks Challenged with Clostridium perfringens

Simple Summary

Necrotic enteritis is one of the most important economic issues in the poultry industry, associated with sudden death rates of up to 50%. However, there is limited information on the role of probiotics and/or phytobiotic compounds on the treatment and prevention of Clostridium perfringens infections in broiler chicks. This study aimed to assess the effects of probiotic compounds (Maxus, CloStat, Sangrovit Extra, CloStat + Sangrovit Extra and Gallipro Tech) on the growth performance, blood biochemistry and intestinal health of broiler chicks in vivo. The results demonstrated that the inclusion of probiotic and/or phytobiotic compounds has a positive effect on performance, blood constituents, liver histopathology, intestinal morphology and histopathology. Furthermore, a notable reduction in both lesion scores was observed when probiotics and phytobiotics alone or in combination were included in the diets.

Abstract

This study evaluated the effects of feed additives on the growth, blood biochemistry and intestinal health of broiler chicks. A total of 378 of broiler chicks (Ross 308) were randomly allotted to seven groups. Chicks were fed a basal diet with 0.0 (control negative), 0.0 (control positive), 0.1, 0.5, 0.12, 0.5 + 0.12 and 0.2 g Kg⁻¹ of Maxus, CloStat, Sangrovit Extra, CloStat + Sangrovit Extra and Gallipro Tech, respectively for 35 days. After 15 days, the chicks were inoculated with Clostridium perfringens. All feed additives were found to enhance growth performance and feed efficiency. The best feed conversion ratio was found in the Negative Control, CloStat + Sangrovit Extra and Gallipro Tect groups, respectively. A notable increase in villus length, total villus area, small intestine weight, ilium weight and total lesion score was found in chicks supplemented with Bacillus subtilis. Besides, the dietary inclusion of phytobiotic compounds showed potential in reducing the serum Alanine aminotransferase (ALT) concentration and increasing the glucose levels. All intestine and liver histopathological signs were reduced in chicks fed a probiotic-supplemented diet. Our findings indicate that supplementation with probiotics and phytobiotics alone or in combined form can be used to enhance performance, intestine health and blood constituents against C. perfringens infection in broiler chicks.