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International audience; Enterotoxigenic Escherichia coli (ETEC) is the aetiological agent of postweaning diarrhoea (PWD) in piglets. The SNPs located on the Mucine 4 (MUC4) and Fucosyltransferase 1 (FUT1) genes have been associated with the susceptibility to ETEC F4 and ETEC F18, respectively. The interplay between the MUC4 and FUT1 genotypes to ETEC infection and the use of amoxicillin in modifying the intestinal microbiota during a natural infection by multiresistant ETEC strains have never been investigated. The aim of this study was to evaluate the effects of the MUC4 and FUT1 genotypes and the administration of amoxicillin through different routes on the presence of diarrhoea and the faecal microbiota composition in piglets naturally infected with ETEC. Seventy-one piglets were divided into three groups: two groups differing by amoxicillin administration routes-parenteral (P) or oral (O) and a control group without antibiotics (C). Faecal scores, body weight, presence of ETEC F4 and F18 were investigated 4 days after the arrival in the facility (T0), at the end of the amoxicillin administration (T1) and after the withdrawal period (T2). The faecal bacteria composition was assessed by sequencing the 16S rRNA gene. We described that MUC4 and FUT1 genotypes were associated with the presence of ETEC F4 and ETEC F18. The faecal microbiota was influenced by the MUC4 genotypes at T0. We found the oral administration to be associated with the presence of diarrhoea at T1 and T2. Furthermore, the exposure to amoxicillin resulted in significant alterations of the faecal microbiota. Overall, MUC4 and FUT1 were confirmed as genetic markers for the susceptibility to ETEC infections in pigs. Moreover, our data highlight that group amoxicillin treatment may produce adverse outcomes on pig health in course of multiresistant ETEC infection. Therefore, alternative control measures able to maintain a healthy faecal microbiota in weaners are recommended.

The transmission of antimicrobial resistance bacteria from animals to humans has become an important concern. The extended-spectrum beta-lactamase (ESBL) -AmpC- producing Escherichia coli (ESBL-AmpC EC) and quinolones resistant E. coli are of particular interest. The present study aimed to evaluate the load and prevalence of antibiotic-resistant commensal E. coli along the goose production cycle on 2 free-range farms in central Italy. On A farm, oxytetracycline was administered, while the B farm did not use antibiotics during the geese productive cycle. One hundred geese of 1-day-old from the same batch were divided into the two farms. At hatching, the animals showed an average of E. coli loads was 6.83 ± 0.48 log CFU/g, and 0.28 ± 0.28, 0, 5.12 ± 0.54 log CFU/g for E. coli resistant to nalidixic acid (E. colinal), to cefotaxime (E. colicef) and to tetracyclines (E. colitet), respectively. The loads of E. coli, E. colinal, E. colicef and E. colitet on 224 environmental faecal pools were determined at 8 time points. Antimicrobial susceptibility and molecular characterization of E. colicef isolates were performed. The ANOVA was used to assess the difference in bacterial loads between the two farms. We described more than 50% of resistances for tetracyclines in both farms, and sulphonamides and cephazolin in the A farm. The loads of E. coli and E. colinal in faeces were estimated at approximately 6–7 log (CFU/g) and 5–6 log (CFU/g) in the two farms, respectively. The average load of extended-spectrum beta-lactamase Escherichia coli (ESBL EC) in goose faeces varied broadly along the production cycle: in the first weeks, a sharp increase was observed in both farms, while later on A farm, the burden of ESBL EC remained steady until the end of the production cycle and on B farm the load dramatically decreased from 6 wk of age onward. An increase in the proportion of E. colinal was observed on A farm shortly after the antibiotic administration. Our study shows that the dynamics of antibiotic-resistant E. coli in farmed geese are similar to the ones observed in broilers. However, the risk of the emergence of antibiotic-resistant commensal E. coli, might be mitigated by the adoption of good management practices, including prudent use of antibiotics.

Ancienne clé UT "early access" : 000486708300001; International audience; Understanding gut microbiota similarities and differences across breeds in horses has the potential to advance approaches aimed at personalized microbial modifications, particularly those involved in improving sport athletic performance. Here, we explore whether faecal microbiota composition based on faecal 16S ribosomal RNA gene sequencing varies across six different sport breeds at two time points 8 months apart within a cohort of 189 healthy horses cared for under similar conditions. Lusitano horses presented the smallest and Hanoverians the greatest bacterial diversity. We found subtle but significant differences in beta-diversity between Lusitano, Anglo Arabian and the central European breeds, and we reproduced these results across the two time points. Repeat sampling of subjects showed community to be temporally more stable in Lusitano and Anglo Arabian breeds. Additionally, we found that 27 genera significantly varied in abundance across breeds. Overall, 33% of these taxa overlapped with previously identified taxa that were associated with genetic variation in humans or other species. However, a non-significant correlation was observed between microbial composition and the host pedigree-based kinship. Despite a notable variation in the diversity and composition of the faecal microbiota, breed exerted limited effects on the equine faecal microbiota.

Poultry production is the fastest growing meat sector worldwide. In the last five years, growing concerns have been expressed by international health agencies and consumers about the transmission of antibiotic-resistant bacteria from poultry meat to human. Consequently, poultry producers have adopted alternative production systems based on reduced antibiotic usage, including organic and antibiotic-free (AF) production. However, the effect of these production systems on the antibiotic resistance of the gut flora in slaughtered poultry has been poorly investigated. We hypothesized that organic and AF production systems reduce the risk of antibiotic resistance in the commensal Escherichia coli of broilers at slaughter compared with conventional production. Cecal content from broilers raised in conventional (292), AF (291), or organic (272) flocks (855 broilers in total) belonging to the same company was sampled. E. coli loads [colony-forming units (CFU/g)] and numbers of E. coli resistant to nalidixic acid (E. colinal) were determined for each sample. Antibiotic susceptibility of one isolate per sample was evaluated using the disc diffusion method; colistin resistance was determined by using the broth microdilution method. The differences in bacterial loads from the three production types were evaluated using one-way ANOVA. Differences in the proportion of resistant isolates in the three production lines were evaluated using Pearson's χ2 or Fisher's test. The strength of the association was evaluated by using odds ratio (OR), with the conventional production type as a reference (OR = 1). Overall, the analysis revealed a high level of resistance (50% or higher) to ampicillin, cefazolin, sulfonamides, nalidixic acid, and tetracycline, independently of the production type. High proportion of ciprofloxacin resistance (52%) was observed, with 4.5% isolates resistant to cefotaxime and 1.8% resistant to colistin. The average loads (log CFU/g cecal content) of E. colinal were determined as 6.84 for AF, 6.38 for organic type, and 7.27 for conventional type. The difference was significant (p AF > organic) was confirmed by qualitative data. However, the magnitude of the effect, measured as a reduced risk of resistance, varied broadly for the antibiotics tested. These findings suggest that poultry production systems alternative to the conventional broiler production are associated with reduced frequency of antibiotic-resistant E. coli among the commensal gut flora, posing a lower risk to the environment and the consumer.

Pasteurella multocida is a widespread pathogen associated with major animal diseases of economic significance. Despite this, little is known about the capsular types, virulence gene pattern, and antimicrobial susceptibility of isolates from hosts affected by different diseases, and no data are available in Italy. One hundred eighty six isolates of P. multocida, were taken from different species in different states of health in several Italian regions, and were tested for genes encoding for capsular types (cap) and major virulence factors (tbpA, toxA, hgbB and pfhA). Antimicrobial susceptibility was investigated with the agar diffusion test. The majority of isolates was capA+. However, the distribution differed according to species and disease of origin, with a greater heterogeneity in isolates from rabbits; capE was never found, while capB was detected once. Only capA+ and capF+ strains tested positive for pfhA. Conversely, almost all capD+ isolates were hgbB+. In bovine respiratory disease, pfhA+/tbpA+/capA+ isolates predominated, while tbpA+/toxA+/capD+ isolates predominated in sheep. Overall, low levels of resistance were found, with full susceptibility to ceftiofur and florfenicol. Lower susceptibility to older antimicrobials was recorded, since only approximately 1/3 of the isolates showed susceptibility to tylosin and erythromycin, and resistance to tetracycline (7.5%), and trimethoprim - sulphametoxazole (4.8%) was also observed.

In rabbit, P. multocida is considered a predominant pathogenic agent; despite this, few data on the molecular epidemiology are available so far. The aim of this work was to characterize P. multocida isolates from rabbit affected by various diseases in Italy. Comparison was made to reference strains from other countries. Thirty-nine isolates were tested using PCRs to detect the genes coding capsular antigens, virulence factors and lipopolysaccharide structures (LPS). Multilocus sequence typing (MLST) was performed and 19 STs registered that belonged to 9 clonal complexes. Italian isolates were all related to P. multocida subsp. P. multocida. Three sequence types dominated (ST9, ST50 and ST74). The isolates were assigned to capsular types A (20/39), D (9/39) and F (10/39), to virulence genes pfhA (13/39), hgbB (21/39) and pfhA+hgbB (4/39) (one without virulence factors) and the isolates either belonged to the LPS genotypes 3 (22/39) or 6 (17/39). The clonal relationships of the Italian strains from rabbit had similarity to previously reported rabbit isolates that belonged to ST9, ST74, ST204 and ST206, however, they differed from other rabbit references strains that belonged to six other STs. In particular, ST9 with capsular type F has been previously reported from diseased rabbit in Czech Republic and ST74 has been observed for older rabbit isolates. ST50 has probably been reported from Spain. ST9 and ST50 have previously also been reported from birds and pig, respectively, whereas ST74 has exclusively been reported from pig. It remains to be investigated if the isolates obtained from diseased rabbit in Italy represent introductions from other host or they are primarily of rabbit origin.

Contaminated pork is a significant source of foodborne Salmonella infections. Pork is contaminated at the slaughterhouse; however, the mechanisms driving Salmonella contamination of carcasses are still poorly understood. The aim of this study was to investigate whether the amount of Salmonella carried by slaughtered pigs in their guts has an influence on carcass contamination. On that account, we tested whether the number of carcasses contaminated during a slaughter day was associated with the prevalence of highly contaminated pigs (HCP: Salmonella caecal loads ≥ 3log/g), or with the prevalence of pigs that simply carry Salmonella spp. in their guts. Three hundred and six pigs were sampled in a slaughterhouse from Central Italy. Salmonella loads in the caecum and on the carcass of each pig were estimated by the most probable number (MPN) technique. The overall prevalence of Salmonella was 34.64% and 7.19% for the caeca and carcasses, respectively. S . Derby and Salmonella enterica 4,[5],12:i:– were the most frequently isolated serovars. The prevalence of HCP was 11.44%. We found a higher number of contaminated carcasses on days of high prevalence of HCP than on days of low prevalence of HCP ( p = 0.0011). Conversely, carcass contamination did not vary with the prevalence of pigs that simply carried Salmonella spp. in their guts ( p = 0.7970). Therefore, the prevalence of HCP, but not the prevalence of pigs carrying Salmonella spp., was related to carcass contamination. Taken together, these findings suggest that reduction of Salmonella loads in the guts of slaughtered pigs would result in fewer contaminated carcasses, and consequently, help to minimise the risk of human infection due to the consumption of contaminated pork.