Antimicrobial susceptibility of intestinal bacteria from Swiss poultry flocks before the ban of antimicrobial growth promoters

Antimicrobial Resistance, Biofilm Formation, and Virulence Genes in Enterococcus Species from Small Backyard Chicken Flocks

Backyard birds are small flocks that are more common in developing countries. They are used for poultry meat and egg production. However, they are also implicated in the maintenance and transmission of several zoonotic diseases, including multidrug-resistant bacteria. Enterococci are one of the most common zoonotic bacteria. They colonize numerous body sites and cause a wide range of serious nosocomial infections in humans. Therefore, the objective of the present study was to investigate the diversity in Enterococcus spp. in healthy birds and to determine the occurrence of multidrug resistance (MDR), multi-locus sequence types, and virulence genes and biofilm formation. From March 2019 to December 2020, cloacal swabs were collected from 15 healthy backyard broiler flocks. A total of 90 enterococci strains were recovered and classified according to the 16S rRNA sequence into Enterococcus faecalis (50%); Enterococcus faecium (33.33%), Enterococcus hirae (13.33%), and Enterococcus avium (3.33%). The isolates exhibited high resistance to tetracycline (55.6%), erythromycin (31.1%), and ampicillin (30%). However, all of the isolates were susceptible to linezolid. Multidrug resistance (MDR) was identified in 30 (33.3%) isolates. The enterococci AMR-associated genes ermB, ermA, tetM, tetL, vanA, cat, and pbp5 were identified in 24 (26.6%), 11 (12.2%), 39 (43.3%), 34 (37.7%), 1 (1.1%), 4 (4.4%), and 23 (25.5%) isolates, respectively. Of the 90 enterococci, 21 (23.3%), 27 (30%), and 36 (40%) isolates showed the presence of cylA, gelE, and agg virulence-associated genes, respectively. Seventy-three (81.1%) isolates exhibited biofilm formation. A statistically significant correlation was obtained for biofilm formation versus the MAR index and MDR. Multi-locus sequence typing (MLST) identified eleven and eight different STs for E. faecalis and E. faecium, respectively. Seven different rep-family plasmid genes (rep1–2, rep3, rep5–6, rep9, and rep11) were detected in the MDR enterococci. Two-thirds (20/30; 66.6%) of the enterococci were positive for one or two rep-families. In conclusion, the results show that healthy backyard chickens could act as a reservoir for MDR and virulent Enterococcus spp. Thus, an effective antimicrobial stewardship program and further studies using a One Health approach are required to investigate the role of backyard chickens as vectors for AMR transmission to humans.

Staphylococci in poultry intestines: a comparison between farmed and household chickens

Both pathogenic as well as nonpathogenic species of staphylococci have been reported in poultry, but these studies have not compared staphylococcal flora of both farmed and household broiler chickens. Staphylococci from farmed (n = 51) and household chicken intestines (n = 43) were isolated and tested for resistance to antimicrobials, presence of resistance genes, and inhibitory activity against other bacteria; correlation of resistance phenotype and genotype was also evaluated. At least 12 staphylococcal species were identified; Staphylococcus carnosus subspecies carnosus was the predominant species from both sources. Most farmed chicken staphylococci were resistant to tigecycline (38/51; 74.8%) while the highest level of resistance among the household chicken staphylococci was to clindamycin (31/43; 72.1%). The mecA gene was only detected in staphylococci from household chickens, whereas ermC and tetK or tetM were found in staphylococci from both groups of birds. Multidrug resistance (resistance ≥ 2 antimicrobial classes) was observed in 88% of resistant staphylococci ranging from 2 to 8 classes and up to 10 antimicrobials. Isolates produced inhibitory activity against 7 clinical bacterial strains primarily Enterococcus faecalis (25/88; 28.4%) and Escherichia coli (22/88; 25%). This study demonstrated that the staphylococcal population among farmed and household chickens varies by species and resistance to antimicrobials. These results may reflect the influence of the environment or habitat of each bird type on the intestinal microflora. As resistance in the staphylococci to antimicrobials used to treat human infections was detected, further study is warranted to determine strategies to prevent transfer of these resistant populations to humans via contamination of the poultry meat.

Differential Effects of Bacitracin Methylene Disalicylate (BMD) on the Distal Colon and Cecal Microbiota of Young Broiler Chickens

Antibiotics have been used extensively for growth promotion in poultry, along with other food production animals, as well as therapeutically to treat infectious diseases. However, with concerns over selection for drug antibiotic resistant bacteria the practice of using subtherapeutic doses of antibiotics is under increased scrutiny. Consequently, we assessed the impact of the commonly used antibiotic bacitracin methylene disalicylate (BMD) on the gastrointestinal microbiota of chickens. For this we administered therapeutic doses of BMD as a feed additive and 16s rRNA gene amplicon sequencing to measure changes in taxonomic abundance on the distal colon and cecal microbiota of young broiler chickens. While BMD treatment was found to impact the abundance of selected taxa and overall beta diversity, significant changes were, in general, limited to the colon of the treated birds. Selected taxa at the phylum, class, and genus levels that were most impacted were identified. The composition of the cecum remained relatively stable in BMD-treated animals. As poultry production practices seek alternatives to growth promoting antibiotic feed additives, manipulation of the gastrointestinal microbiota holds promise. These results suggest that targeting the cecum may offer a means to promote changes to the microbiota that maximize the benefits for the hosts.

An Investigation of Enterococcus Species Isolated from the African Buffalo (Syncerus caffer) in Serengeti National Park, Tanzania

We isolated Enterococcus species that colonized in the African buffalo (Syncerus caffer) in order to investigate their genetic relatedness and antimicrobial susceptibility. A total of 219 isolates were obtained and a 16S rRNA gene sequence analysis showed they were classified into Enterococcus avium, E. casseliflavus, E. faecalis, E. faecium, E. hirae, or E. mundtii. Multilocus sequence typing of E. faecalis and E. faecium isolates indicated that some of the isolates showed an evolutionary distance that was far from the primary founders. The antimicrobial susceptibility of the enterococcal isolates suggested that the significant transmission of antimicrobial resistance via human intervention had not yet occurred.

Influence of antimicrobial feed additives on broiler commensal posthatch gut microbiota development and performance

The effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 (Lachnospiraceae), OTU 186/188 (Lactobacillus johnsonii), OTU 220 (Lachnospiraceae), OTUs 284 to 288 (unclassified bacterial spp. or Ruminococcaceae), OTU 296/298 (unclassified bacterium or Clostridiales), and OTU 480/482 (Oxalobacteraceae) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 (Lactobacillus crispatus), OTU 152 (Lactobacillus reuteri or unclassified Clostridiales), OTU 198/200 (Subdoligranulum spp.), and OTU 490/492 (unclassified bacterium or Enterobacteriaceae) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.

Probiotics: from research to consumer

Intestinal microflora has metabolic, trophic and protective functions, and can be modified in pathological conditions and by the exogenous administration of probiotics. Probiotics are defined as living microorganisms which resist gastric, bile, and pancreatic secretions, attach to epithelial cells and colonize the human intestine. In the last twenty years research has been focused on the identification of the role of planktonic flora and adhesive bacteria in health and disease, and on the requisite of bacterial strains to become probiotic product which can be marketed. Probiotics can be commercialized either as nutritional supplements, pharmaceuticals or foods, but the marketing as a pharmaceutical product requires significant time, complex and costly research, and the demonstration of a well-defined therapeutic target. This review examines the sequential steps of research which, from the identification of a possible probiotic strain, lead to its production and marketing, summarizing the whole process existing behind its development, through its growth in laboratory, the studies performed to test its resistance to human secretions and stability, microencapsulation technologies, and safety tests.

Effect of porcine-derived mucosal competitive exclusion culture on antimicrobial resistance in Escherichia coli from growing piglets

While use of antimicrobial drugs in livestock production has made a significant impact on animal health, welfare, and productivity, interest in suitable alternatives such as pre/probiotics, organic acids, and cultures of normal flora or "competitive exclusion" cultures from young animals has increased significantly in the wake of the antimicrobial resistance issue. The present study was undertaken to determine the effect of porcine-derived mucosal competitive exclusion (PCE) culture on both the antimicrobial susceptibility of commensal E. coli and on growth performance in piglets. Two replicate trials were conducted using growing piglets fed standard antimicrobial-free production diets. Piglets in the treatment group were orally dosed with PCE (10(10) cfu/mL) twice within 24 h of birth, at weaning, and 18-24 h post-weaning; control group piglets were dosed with sterile broth as a placebo. Fecal samples from all piglets were cultured for commensal E. coli at dosing times and when feed type was changed. A significantly higher proportion of E. coli from PCE-treated piglets demonstrated resistance to tetracycline (p < 0.0001), and streptomycin (p < 0.0001) when compared to controls. Resistance to streptomycin resistance in E. coli from piglets treated with PCE culture was variable, returning to baseline levels by day 21 (weaning). Piglets treated with the PCE culture demonstrated improved feed efficiencies when compared to control piglets (p < 0.005) during feeding of the starter and first growth diets. The PCE culture used in the present study had previously been shown to effectively exclude Salmonella in pigs. To the best of the authors' knowledge, this is the first report characterizing the effect of a competitive exclusion culture on antimicrobial resistance of commensal E. coli.

Evaluation of new broth media for microdilution antibiotic susceptibility testing of Lactobacilli, Pediococci, Lactococci, and Bifidobacteria

Nine pure or mixed broth media were evaluated for their suitabilities to determine MICs in a microdilution test of 19 antibacterial agents for lactic acid bacteria (LAB) of the genera Lactobacillus, Pediococcus, Lactococcus, and Bifidobacterium. A mixed formulation of Iso-Sensitest broth (90%) and deMan-Rogosa-Sharpe broth (10%) with or without supplementation with L-cysteine, referred to as the LAB susceptibility test medium, provided the most optimal medium basis in terms of growth support of nonenterococcal LAB and correct indication of MICs of international control strains.

Use of folic acid casei medium reveals trimethoprim susceptibility of Lactobacillus species

AIM

Lactobacilli have been reported to have intrinsic resistance to trimethoprim. The susceptibility of lactobacilli to trimethoprim on different media was investigated in order to search for a phenotypic test method that could indicate the presence of acquired resistance genes.

METHODS AND RESULTS

Strains of Lactobacillus acidophilus, Lact. paracasei, Lact. rhamnosus and Lact. plantarum were susceptibility tested with E-tests on folic acid casei medium (FACM), MRS and defined medium 1. The effects of addition or removal of nucleosides and thymidine phosphorylase were investigated. E-tests on FACM yielded reproducible minimal inhibitory concentrations (MICs) for trimethoprim but addition of nucleosides was necessary for growth of Lact. acidophilus. MICs for the tested strains were 0.125-0.19, 0.25-3 and 0.064-0.19 microg ml(-1) for Lact. paracasei, Lact. rhamnosus and Lact. plantarum, respectively. With the addition of deoxyuridine and deoxyadenosine to FACM the MICs of Lact. acidophilus were 0.064-1 microg ml(-1).

CONCLUSIONS, SIGNIFICANCE AND IMPACT OF THE STUDY

Lactobacilli do not have intrinsic resistance to trimethoprim. The results show that trimethoprim susceptibility testing of the tested Lactobacillus species is possible and indicate that transferable resistance genes are absent in all the tested strains.

Broad-spectrum protein biosensors for class-specific detection of antibiotics

The dramatically increasing prevalence of multi-drug-resistant human pathogenic bacteria and related mortality requires two key actions: (i) decisive initiatives for the detection of novel antibiotics and (ii) a global ban for use of antibiotics as growth promotants in stock farming. Both key actions entail technology for precise, high-sensitive detection of antibiotic substances either to detect and validate novel anti-infective structures or to enforce the non-use of clinically relevant antibiotics. We have engineered prokaryotic antibiotic response regulators into a molecular biosensor configuration able to detect tetracycline, streptogramin, and macrolide antibiotics in spiked liquids including milk and serum at ng/mL concentrations and up to 2 orders of magnitude below current Swiss and EC threshold values. This broad-spectrum, class-specific, biosensor-based assay has been optimized for use in a storable ready-to-use and high-throughput-compatible ELISA-type format. At the center of the assay is an antibiotic sensor protein whose interaction with specific DNA fragments is responsive to a particular class of antibiotics. Binding of biosensor protein to the cognate DNA chemically linked to a solid surface is converted into an immuno-based colorimetric readout correlating with specific antibiotics concentrations.

Prevalence and antimicrobial resistance of enterococcus species isolated from retail meats

From March 2001 to June 2002, a total of 981 samples of retail raw meats (chicken, turkey, pork, and beef) were randomly obtained from 263 grocery stores in Iowa and cultured for the presence of Enterococcus spp. A total of 1,357 enterococcal isolates were recovered from the samples, with contamination rates ranging from 97% of pork samples to 100% of ground beef samples. Enterococcus faecium was the predominant species recovered (61%), followed by E. faecalis (29%), and E. hirae (5.7%). E. faecium was the predominant species recovered from ground turkey (60%), ground beef (65%), and chicken breast (79%), while E. faecalis was the predominant species recovered from pork chops (54%). The incidence of resistance to many production and therapeutic antimicrobials differed among enterococci recovered from retail meat samples. Resistance to quinupristin-dalfopristin, a human analogue of the production drug virginiamycin, was observed in 54, 27, 9, and 18% of E. faecium isolates from turkey, chicken, pork, and beef samples, respectively. No resistance to linezolid or vancomycin was observed, but high-level gentamicin resistance was observed in 4% of enterococci, the majority of which were recovered from poultry retail meats. Results indicate that Enterococcus spp. commonly contaminate retail meats and that dissimilarities in antimicrobial resistance patterns among enterococci recovered from different meat types may reflect the use of approved antimicrobial agents in each food animal production class.

Campylobacter spp in human, chickens, pigs and their antimicrobial resistance

Campylobacter spp. have been identified as etiologic agents in outbreaks and sporadic cases of gastroenteritis in developed countries. In developing countries, most reported Campylobacter infections are in children. Previously reported prevalences of Campylobacter spp. in children in Southeast Asia range from 2.9% to 15%. The frequency and pattern of occurrence of Campylobacter spp. differ between developed and developing countries, especially in the number of cases reported in adults and the presence of any seasonal patterns in occurrence. Although the severity of Campylobacter infection in adults was different between developed and developing countries, the clinical symptoms of infection in adults resulting from infection in developing countries was similar to those in developed countries. Many different animal species maintain Campylobacter spp. with no clinical signs. There do not appear to be significantly different colonization rates of Campylobacter in food animals between developed and developing countries. The role of C. jejuni as a primary pathogen in farm animals is uncertain. C. jejuni can be found in feces of diarrheic and healthy calves and piglets. Campylobacter with resistance to antimicrobial agents have been reported in both developed and developing countries, and the situation seems to deteriorate more rapidly in developing countries, where there is widespread and uncontrolled use of antibiotics resistance was observed at high levels in food animals in both developed and developing countries. Studies suggested an association between antimicrobial use in food animals and the development of resistance in human isolates in developed countries.

Molecular characterization of tet(M) genes in Lactobacillus isolates from different types of fermented dry sausage

The likelihood that products prepared from raw meat and milk may act as vehicles for antibiotic-resistant bacteria is currently of great concern in food safety issues. In this study, a collection of 94 tetracycline-resistant (Tc(r)) lactic acid bacteria recovered from nine different fermented dry sausage types were subjected to a polyphasic molecular study with the aim of characterizing the host organisms and the tet genes, conferring tetracycline resistance, that they carry. With the (GTG)(5)-PCR DNA fingerprinting technique, the Tc(r) lactic acid bacterial isolates were identified as Lactobacillus plantarum, L. sakei subsp. carnosus, L. sakei subsp. sakei, L. curvatus, and L. alimentarius and typed to the intraspecies level. For a selection of 24 Tc(r) lactic acid bacterial isolates displaying unique (GTG)(5)-PCR fingerprints, tet genes were determined by means of PCR, and only tet(M) was detected. Restriction enzyme analysis with AccI and ScaI revealed two different tet(M) allele types. This grouping was confirmed by partial sequencing of the tet(M) open reading frame, which indicated that the two allele types displayed high sequence similarities (>99.6%) with tet(M) genes previously reported in Staphylococcus aureus MRSA 101 and in Neisseria meningitidis, respectively. Southern hybridization with plasmid profiles revealed that the isolates contained tet(M)-carrying plasmids. In addition to the tet(M) gene, one isolate also contained an erm(B) gene on a different plasmid from the one encoding the tetracycline resistance. Furthermore, it was also shown by PCR that the tet(M) genes were not located on transposons of the Tn916/Tn1545 family. To our knowledge, this is the first detailed molecular study demonstrating that taxonomically and genotypically diverse Lactobacillus strains from different types of fermented meat products can be a host for plasmid-borne tet genes.

Vancomycin-resistant enterococci in shellfish, unchlorinated waters, and chicken

Vancomycin-resistant enterococci (VRE) have been a cause of increasing concern chiefly regarding the infection of hospital patients. There is suspicion, but limited evidence, that food and environmental spread may be important. Biomonitoring by examination of bivalve shellfish was used to assess the occurrence of VRE entering the environment. Using pre-enrichment and Lewisham and Slanetz and Bartley agars, 2/125 (1.6%) of shellfish were found to contain enterococci resistant to high levels of vancomycin. Lewisham agar allows relatively rapid identification of VRE. In a second phase of the work using pre-enrichment and Slanetz and Bartley agar, 4/151 (2.7%) shellfish and 5/27 (18.5%) raw chickens contained VRE. Using filtration and pre-enrichment, no VRE were found in 54 unchlorinated water samples. The study shows that environmental prevalence of VRE is low, and that raw chickens are frequently contaminated.