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Antimicrobial resistance (AMR) is a global emerging problem for food safety and public health. Retail meat is one of the vehicles that may transmit antimicrobial resistant bacteria to humans. Here we assessed the phenotypic and genotypic resistance of non-typhoidal Salmonella from retail meat collected in California in 2019 by the National Antimicrobial Resistance Monitoring System (NARMS) Retail Food Surveillance program. A total of 849 fresh meat samples were collected from randomly selected grocery stores in Northern and Southern California from January to December 2019. The overall prevalence of Salmonella was 15.31 %, with a significantly higher occurrence in Southern (28.38%) than in Northern (5.22 %) California. The prevalence of Salmonella in chicken (24.01 %) was higher (p < 0.001) compared to ground turkey (5.42 %) and pork (3.08 %) samples. No Salmonella were recovered from ground beef samples. The prevalence of Salmonella in meat with reduced antibiotic claim (20.35 %) was higher (p < 0.001) than that with conventional production (11.96 %). Salmonella isolates were classified into 25 serotypes with S. Kentucky (47.73 %), S. typhimurium (11.36 %), and S. Alachua (7.58 %) as predominant serotypes. Thirty-two out of 132 (24.24 %) Salmonella isolates were susceptible to all tested antimicrobial drugs, while 75.76 % were resistant to one or more drugs, 62.88 % to two or more drugs, and 9.85 % to three or more drugs. Antimicrobials that Salmonella exhibited high resistance to were tetracycline (82/132, 62.12 %) and streptomycin (79/132, 59.85 %). No significant difference was observed between reduced antibiotic claim and conventional production in the occurrence of single and multidrug resistance. A total of 23 resistant genes, a D87Y mutation of gyrA, and 23 plasmid replicons were identified from resistant Salmonella isolates. Genotypic and phenotypic results were well correlated with an overall sensitivity of 96.85 %. S. infantis was the most resistant serotype which also harbored the IncFIB (pN55391) plasmid replicon and gyrA (87) mutation. Data from Northern and Southern California in this study helps us to understand the AMR trends in Salmonella from retail meat sold in the highly populous and demographically diverse state of California., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

This article follows-up on our recently published work, which evaluated the impact of the addition of an alfalfa leaf-derived adsorbent in the aflatoxin B 1 (AFB 1 )-contaminated diet in regard to the production parameters, blood cell count, serum biochemistry, liver enzymes, and liver histology of turkey poults. This paper presents complementary results on microbial community, ileal morphology, barrier function, and immunity. For this purpose, 350 1-day-old female turkey poults were randomly distributed into five groups: (1) Control, AFB 1 -free diet; (2) AF, AFB 1 -contaminated diet at 250 ng/g; (3) alfalfa, AFB 1 -free diet + 0.5% ( w / w ) adsorbent; (4) alfalfa + AF, AFB 1 -contaminated diet at 250 ng/g + 0.5% ( w / w ) adsorbent; and (5) YCW + AF, AFB 1 -contaminated diet at 250 ng/g + 0.5% ( w / w ) commercial yeast cell wall-based adsorbent (reference group). In general, in the AF group, the growth of opportunistic pathogens was promoted, which lead to gut dysbacteriosis, mainly influenced by Streptococcus lutetiensis . Conversely, a significant increase in beneficial bacteria ( Faecalibacterium and Coprococcus catus ) was promoted by the addition of the plant-based adsorbent. Moreover, the AF group had the lowest villus height and a compromised barrier function, as evidenced by a significant ( p < 0.05) increase in fluorescein isothiocyanate dextran (FITC-d), but these negative effects were almost reversed by the addition of the alfalfa adsorbent. Furthermore, the AF + YCW and alfalfa + AF groups exhibited a significant increase in the cutaneous basophil hypersensitivity response compared to the rest of the experimental groups. Taken together, these results pointed out that the alfalfa counteracts the adverse effects of AFB 1 in poults, facilitating the colonization of beneficial bacteria and improving the barrier function of the turkey poults.

Turkey litter waste is lignocellulosic and keratinous, requiring prior enzymatic treatment to facilitate fiber hydrolysis and utilization by microorganisms in anaerobic digestion (AD) process. The understanding of the performance of microorganisms in AD can be facilitated through molecular biology and bioinformatics tools. This study aimed to determine the taxonomic profile and functional prediction of microbial communities in the AD of turkey litter waste subjected to enzymatic pretreatment and correlate it with operational parameters. The tests involved the use of turkey litter (T) at 25 g L -1 of volatile solids, a granular inoculum (S) (10% m/v), and the addition of cellulase (C), and pectinase (P) enzymes at four concentrations. The use of enzymes increased methane production by 19% (turkey litter, inoculum, and cellulase-TSC4) and 15% (turkey litter, inoculum, and enzymatic pectinase-TSP4) compared to the control (turkey litter and inoculum-TS), being more effective in TSC4 (667.52 mLCH 4 ), where there was consumption of acetic, butyric, and propionic acids. The pectinase assay (TSP4) showed a methane production of 648 mLCH 4 and there was the accumulation of metabolites. Cellulolytic microorganisms Bacteroides, Ruminofilibacter, Lachnospiraceae, Ruminococcaceae, and Methanosaeta were favored in TSC4. In TSP4, the predominant genus was Macellibacteroides and Methanosarcina, and genes involved in methylotrophic methanogenesis were also found (mtaB, mtmB, and mtbB). Enzymes involved in hydrogenotrophic methanogenesis were identified in both assays (TSC4 and TSP4). Molecular tools helped to understand the metabolic routes involved in AD with enzymatic treatment, allowing the elaboration of strategies to improve the sustainable degradation of turkey litter waste., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The spread of antimicrobial-resistant bacteria is a significant concern, as it can lead to increased morbidity and mortality in both humans and animals. Whole-genome sequencing (WGS) is a powerful tool that can be used to conduct a comprehensive analysis of the genetic basis of antimicrobial resistance (AMR). We compared the phenotypic and genotypic AMR profiles of 97 Salmonella isolates derived from chicken and turkey diagnostic samples. We focused AMR analysis on 5 antimicrobial classes: aminoglycoside, beta-lactam, phenicol, tetracycline, and trimethoprim. The overall sensitivity and specificity of WGS in predicting phenotypic antimicrobial resistance in the Salmonella isolates were 93.4% and 99.8%, respectively. There were 16 disagreement instances, including 15 that were phenotypically resistant but genotypically susceptible; the other instance involved phenotypic susceptibility but genotypic resistance. Of the isolates examined, 67 of 97 (69%) carried at least 1 resistance gene, with 1 isolate carrying as many as 12 resistance genes. Of the 31 AMR genes analyzed, 16 were identified as aminoglycoside-resistance genes, followed by 4 beta-lactam-resistance, 3 tetracycline-resistance, 2 sulfonamide-resistance, and 1 each of fosfomycin-, quinolone-, phenicol-, trimethoprim-, bleomycin-, and colistin-resistance genes. Most of the resistance genes found were located on plasmids., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Background: Ornithobacterium rhinotracheal (ORT) infects numerous birds, particularly chickens and turkeys. ORT is an emerging bacterial pathogen of global concern in the poultry industry. As ORT is rapidly spreading throughout commercial poultry, it requires intensive studies of its epidemiology, diagnostic procedures, molecular typing, virulence genes and antimicrobial resistance., Objectives: The present study was conducted in isolation and identification of ORT from slaughtered turkeys., Methods: Cleft palate swabs of 200 were collected from slaughtered turkeys and cultured on blood agar. ORT was characterized using biochemical tests and PCR targeting the ORT 16S rRNA gene. Virulence genes of isolates were determined targeting adenylate kinase (adk), copA and virulence-associated protein D (vapD) genes. Additionally, diversity of ORT isolates was performed by enterobacterial repetitive intergenic consensus (ERIC) and RAPD PCR. Disk diffusion was used to determine the antibiotic sensitivity of the isolates., Results: ORT was identified in 23 (11.5%) samples using both the biochemical tests and PCR. The result of detecting virulence genes showed that all the isolates (23: 100%) had the adk gene, whereas two (8.7%) isolates had the copA gene, and seven (30.43%) isolates had the vapD gene. Molecular typing of isolates revealed 21 different patterns by RAPD PCR assay using M13 primer and 20 distinct patterns by ERIC PCR test. Both ERIC and RAPD PCR were distinctive methods for investigating the genetic diversity of ORT isolates. The antibiotic resistance test showed that 18 (78.26%) isolates were resistant to gentamicin, amikacin, cefazolin, streptomycin and penicillin. All isolates (100%) were resistant to cloxacillin and fosfomycin., Conclusions: This study showed the prevalence of ORT in turkey and high resistance of this bacterium to many common veterinary antibiotics. Moreover, both ERIC and RAPD PCR are distinctive methods for investigating the genetic diversity of ORT isolates. These data may help monitor antibiotic resistance and typing of ORT in epidemiological studies and serve as the foundation for designing region-specific vaccines for future use., (© 2024 The Author(s). Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

Cellulitis is an important disease in commercial turkey farms associated with significant economic loss. Although the etiology of cellulitis is not fully elucidated, Clostridium septicum (C. septicum) is one of the main causes of this infectious disease. In this study, we report the development of a quantitative real-time PCR (qRT PCR) assay targeting the alpha-toxin gene (csa), which involves a prior 15-cyle PCR using a nested pair of primers to increase the detection sensitivity. Additionally, the TaqMan probe was employed to increase the target-specificity of the assay. The performance of our nested qRT-PCR assay was evaluated using Clostridium isolates from turkey farms, representing both septicum and non-septicum species, as well as sponge swab samples from turkey farms. Our step-by-step development of the assay showed that the csa gene is a suitable target for specific detection of C. septicum strains and that the inclusion of nested PCR step significantly increased the detection sensitivity of the final qRT PCR assay. The performance of the assay was also validated by a high correlation of the threshold cycle numbers of the qRT PCR assay with the relative abundance of C. septicum read counts in 16S rRNA gene microbiota profiles of the C. septicum-containing samples from turkey farms., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

Foodborne infections with antimicrobial-resistant Campylobacter spp. remain an important public health concern. Publicly available data collected by the National Antimicrobial Resistance Monitoring System for Enteric Bacteria related to antimicrobial resistance (AMR) in Campylobacter spp. isolated from broiler chickens and turkeys at the slaughterhouse level across the United States between 2013 and 2021 were analysed. A total of 1,899 chicken-origin (1,031 Campylobacter coli (C. coli) and 868 Campylobacter jejuni (C. jejuni) ) and 798 turkey-origin (673 C. coli and 123 C. jejuni ) isolates were assessed. Chicken isolates exhibited high resistance to tetracycline (43.65%), moderate resistance to ciprofloxacin (19.5%), and low resistance to clindamycin (4.32%) and azithromycin (3.84%). Turkey isolates exhibited very high resistance to tetracycline (69%) and high resistance to ciprofloxacin (39%). The probability of resistance to all tested antimicrobials, except for tetracycline, significantly decreased during the latter part of the study period. Turkey-origin Campylobacter isolates had higher odds of resistance to all antimicrobials than isolates from chickens. Compared to C. jejuni isolates, C. coli isolates had higher odds of resistance to all antimicrobials, except for ciprofloxacin. The study findings emphasize the need for poultry-type-specific strategies to address differences in AMR among Campylobacter isolates.

Salmonella enterica Agona (S. Agona) and Salmonella enterica Saintpaul (S. Saintpaul) are among the emerging drug-resistant Salmonella in turkey production and processing. Rapid solutions to control emerging and uncommon serotypes such as S. Agona and S. Saintpaul are needed. This study tested pimenta essential oil (PEO) as a processing antibacterial against S. Agona and S. Saintpaul in experiments representative of different stages of turkey processing. The compound effectively reduced S. Agona and S. Saintpaul in nutrient broth studies and with mature biofilm assays. PEO was tested against a combination of S. Agona and S. Saintpaul in ground turkey meat and nonprocessed breast meat. In the first experiment with ground turkey, samples were inoculated with a mixture of S. Agona and S. Saintpaul (∼3 log 10 CFU/g) and treated with PEO at different concentrations (0% PEO, 0.25% PEO, 0.5% PEO, 1% PEO, 2% PEO, and 2.5% PEO). In the second experiment with turkey breast, samples inoculated with ∼3 log 10 CFU/g (SA+SP) were dipped in different concentrations of PEO with chitosan (CN) for 2 min. In both these experiments, samples were stored at 4°C, and Salmonella recovery was carried out at 0, 1, 3, 5, and 7 d. All experiments followed a completely randomized design and were repeated 6 times (n = 6). Statistical analysis was done using the PROC-ANOVA procedure of SAS. In the ground turkey meat, PEO at or above 2% reduced 2 log 10 CFU/g of Salmonella by day 1. PEO at 2.5% in ground turkey meat resulted in enrichment-negative samples by 1 min, indicative of the rapid killing effect of the compound at a high concentration of PEO (P ≤ 0.05). A maximum reduction of 1.7 log 10 CFU Salmonella/g of turkey breast meat was obtained after 2 min of dip treatment containing CN and 2.5% PEO. Results indicate that PEO could be used as a plant-based processing antibacterial against S. Agona and S. Saintpaul in turkey processing. Upscaling to plant-level studies is necessary before recommending its usage., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Antimicrobial-resistant bacteria are a growing public health threat. In 2017 the U.S. Food and Drug Administration implemented Veterinary Feed Directive (VFD) rules changes to limit medically important antimicrobial use in food-producing animals, combating antimicrobial-resistant bacteria. The effect of the VFD rule changes on the occurrence of bacteria resistant to medically-important antimicrobials in retail meats is yet to be investigated in the U.S. This study investigates whether the VFD rule changes affected the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the U.S., Methods: Multivariable mixed effect logistic regression models were used to analyze 2002-2019 retail meats surveillance data from the National Antimicrobial Resistance Monitoring System (NARMS) in the U.S. Variables included VFD rule changes, meat type, quarter of year, and raising claims. A potential association between these variables and the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats was estimated., Results: Analysis included data regarding tetracycline-resistant Salmonella (n = 8,501), Escherichia (n = 20, 283), Campylobacter (n = 9,682), and erythromycin-resistant Campylobacter (n = 10,446) in retail meats. The odds of detecting tetracycline-resistant Escherichia (OR = 0.60), Campylobacter (OR = 0.89), and erythromycin-resistant Campylobacter (OR = 0.43) in chicken breast significantly decreased after the VFD rule changes, compared to the pre-VFD rule change period. The odds of detecting tetracycline-resistant Salmonella (0.66), Escherichia (OR = 0.56), and Campylobacter (OR = 0.33) in ground turkey also significantly decreased. However, the odds of detecting tetracycline-resistant Salmonella (OR = 1.49) in chicken breast and erythromycin-resistant Campylobacter (OR = 4.63) in ground turkey significantly increased. There was no significant change in the odds of detecting tetracycline-resistant Salmonella and Escherichia in ground beef or pork chops., Conclusions: The implementation of VFD rule changes had a beneficial effect by reducing the occurrence of tetracycline-resistant and erythromycin-resistant bacteria in chicken and ground turkey. Ongoing surveillance of antimicrobial resistance and antimicrobial use could complement the implementation of stewardship such as VFD rule in food-producing animals in the U.S., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Sarkar, Okafor. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Infections with Ornithobacterium rhinotracheale are causing respiratory diseases that require antibiotic treatment in poultry worldwide. In the field, this agent is known to often be resistant to many antimicrobials, complicating therapeutic interventions. Therefore, there is a clear need to monitor trends in resistance development. In the present study, antibiotic resistance profiles of 64 O. rhinotracheale strains isolated from diseased turkeys from 2002 to 2021 were investigated against 19 antimicrobial substances by the microdilution method. Susceptibility toward chloramphenicol, carbapenem, and sulfamethozaxole combination was found for all strains. Most isolates were also susceptible to penicillins (98%-100%), with the exception of oxacillin, cephalosporins (84%-100%), tetracycline (89%), and tylosin (88%). In the case of quinolones, 89% of isolates showed intermediate resistance to enrofloxacin, whereas 90% showed full resistance to nalidixic acid. Full resistance to the tested aminoglycosides and colistin was revealed for all strains. Eighteen different AMR profiles were elucidated; more than half of the isolates (53%) shared the same AMR profile. Similar susceptibility profiles of O. rhinotracheale isolates were found on the different farms, proving some stability over the years. All isolates were classified as multidrug resistant. Multiple outbreaks within a flock or in successive flocks within a farm comprised 46 O. rhinotracheale isolates. Here, occasional changes in susceptibility for some antimicrobial substances were observed. In general, most of the changes occurred in quinolones, followed by tetracycline switching mainly from intermediate resistance to full resistance and vice versa. The present surveillance provides actual data on effective antibiotic treatments in case of disease outbreaks and contributes to the One Health concept acknowledging the important link between animal and human health.

Bacterial communities in the reproductive tract of avian species play an important role in keeping birds healthy and encouraging growth. Infection can occur during egg formation with pathogens that can be transmitted to the embryo. In this study, we investigated the bacterial composition in the turkey reproductive tract using a taxa identification based on the amplicon sequence of the V3-V4 region of the 16S rRNA gene. The microbial composition and relative abundance of bacteria differed between individual birds. Among the 19 phyla detected in turkey oviduct were unique taxa like Planctomycetes or Petescibacteria. Differences in composition of bacterial diversity were found at the family and genus level. Oviducts contained also several genus with well-recognized avian pathogens like Escherichia-Shigella, Enterococcus, Staphylococcus, and Ornithobacterium. Some of the bacteria described in this study have not been so far identified in turkeys. The objective of this study was to identify bacterial communities in the turkey oviduct and compared the composition of the oviduct with that in chickens broadening the knowledge of the microbial composition in the reproductive tract of poultry., (© 2022. The Author(s).)

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter , Enterococcus , Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported ( n = 15 factors; 42%), followed by biosecurity ( n = 11; 31%) and management practices ( n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production, causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminate antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study, we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analyses of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella, and Escherichia coli compared to domestic turkeys. E. coli strains isolated from wild and domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule ( kpsII and kpsIII ) or siderophore ( iroN and fyuA ) synthesis than were those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. IMPORTANCE Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study, we compare the microbiota of wild and domestic turkeys. The results suggest that free-ranging wild turkeys carry a distinct microbiome compared to farm-raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to that of farm-raised birds. The microbiomes of wild turkeys may be used to guide the development of new ways to control disease in large-scale poultry production.

Salmonella Heidelberg (SH) is a highly invasive human pathogen for which turkeys can serve as reservoir hosts. Colonization of turkeys with SH may result in potential contamination and is a greater challenge to prevent in comminuted products. Antimicrobial efficacy of 3 GRAS-status plant-derived antimicrobials (PDAs), lemongrass essential oil (LG), citral (CIT), and trans-cinnamaldehyde (TC), against SH in ground turkey, a comminuted product implicated in several outbreaks, was evaluated in this study. Ground turkey samples inoculated with ∼3.50 log 10 CFU/g of a three-strain SH cocktail were treated with either LG, CIT, or TC at either 0.5, 1, or 2% (vol/wt). Samples were stored at 4°C, and bacterial enumeration was performed on d 0, 1, 3, and 5. Appropriate controls were included alongside all treatments. Fluorescence microscopy was performed to evaluate the direct impact of the PDAs against SH in vitro. Appearance and aroma difference testing of raw patties was also performed for select treatments with trained sensory panelists. Treatment with 2% TC yielded a 2.5 log 10 CFU/g reduction by d 1 and complete reduction by d 5 (P < 0.05). By d 3, 2% CIT and 2% LG resulted in SH reduction of at least 1.7 log 10 CFU/g (P < 0.05). Addition of 1% TC resulted in reduction of at least 1.8 log 10 CFU/g by d 3 (P < 0.05). Participants could distinguish PDA-treated raw patties by aroma. Most participants (7/11) could not distinguish patties treated with 0.5% TC based on appearance. Microscopic images indicate that all PDAs resulted in disruption of the SH membrane. Results of the present study indicate that the three tested PDAs, LG, CIT, and TC are effective against SH in ground turkey, indicating their potential use as interventions to mitigate Salmonella contamination in comminuted turkey products., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Avian mycoplasmosis, mainly caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS), is an economically important disease of poultry industry. The present study was aimed to develop duplex PCR as a rapid, specific and economical method for accurate detection of MG and MS in poultry and its comparison with single (monoplex) MG/MS PCR. During present investigation, a total of 146 poultry flocks having clinical history of respiratory disease were screened. Pooled tissue samples (trachea, lungs and air sacs) from 4-5 birds of each flock were collected during necropsy at disease investigation laboratories, Hisar, Haryana, India. The single and duplex PCR assays were standardized using primers of intergenic spacer region (IGSR; 16S-23S rRNA) for MG and hemagglutinin vlhA gene for MS, with expected amplicon size of 812 bp and 1200 bp products, respectively. In single PCR, 6.85%, 2.74% and 2.74% tissue samples were found positive for MG, MS and both MG and MS, respectively. However, duplex PCR showed, 7.53%, 2.74% and 1.37% positivity for MG, MS and both MG and MS, respectively. Taking the results of monoplex PCR as a gold standard, sensitivity and specificity of the developed duplex PCR was found to be 94.44% and 100%, respectively. Moreover, Cohen's kappa statistic (k = 0.97) measured a 'perfect' agreement between monoplex and duplex PCR assays. The positive and negative predictive values of duplex PCR was found to be 1.0 and 0.9922, respectively at 95% confidence interval (CI), as compared to monoplex PCR. The simultaneous use of two genes in a duplex PCR was more rapid and economical than two separate single PCR reactions., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Colibacillosis is a common bacterial disease in broiler production worldwide. It is emerging as a serious health concern in turkey production. Until recently, the disease was managed through antimicrobial therapy. However, such preventive strategies are no longer considered sustainable, and the advent of a live commercial vaccine registered for turkeys has modified health management plans in turkey production systems. In a French farming cooperative representing 10% of the country's turkey production, the vaccine was prescribed in two categories of farms: those with recurrent colibacillosis where an O78 Escherichia coli strain had been isolated, and those with sporadic outbreaks, where other serotypes had been documented. The commercial vaccine was administered in the first and third week of age. Performance data were collected retrospectively for all flocks produced over a 4-yr period from 37 turkey farm members of the cooperative. Segregated flocks from recurrent or sporadic farms, and whether or not vaccination had been performed, were analyzed and recorded. In farms with sporadic colibacillosis, vaccination significantly improved mortality rate and all performance parameters (average condemnation rate at the slaughterhouse, average feed conversion ratio, average weight per slaughtered turkey in each flock, average economic margin per flock, and performance index). Farms with recurrent outbreaks had comparable results, except for average flock mortality and condemnation rates, which were numerically reduced in vaccinated flocks compared to flocks that had not been vaccinated. This retrospective study contributes to the weight of evidence in favor of colibacillosis control through vaccination in turkey production.

Colibacillosis is a common bacterial disease in broiler production worldwide. It is emerging as a serious health concern in turkey production. Until recently, the disease was managed through antimicrobial therapy. However, such preventive strategies are no longer considered sustainable, and the advent of a live commercial vaccine registered for turkeys has modified health management plans in turkey production systems. In a French farming cooperative representing 10% of the country's turkey production, the vaccine was prescribed in two categories of farms: those with recurrent colibacillosis where an O78 Escherichia coli strain had been isolated, and those with sporadic outbreaks, where other serotypes had been documented. The commercial vaccine was administered in the first and third week of age. Performance data were collected retrospectively for all flocks produced over a 4-yr period from 37 turkey farm members of the cooperative. Segregated flocks from recurrent or sporadic farms, and whether or not vaccination had been performed, were analyzed and recorded. In farms with sporadic colibacillosis, vaccination significantly improved mortality rate and all performance parameters (average condemnation rate at the slaughterhouse, average feed conversion ratio, average weight per slaughtered turkey in each flock, average economic margin per flock, and performance index). Farms with recurrent outbreaks had comparable results, except for average flock mortality and condemnation rates, which were numerically reduced in vaccinated flocks compared to flocks that had not been vaccinated. This retrospective study contributes to the weight of evidence in favor of colibacillosis control through vaccination in turkey production.

Background: Escherichia coli is a bacterial species widely distributed among mammals and avian species, and also a member of the normal intestinal microbiota. However, some E. coli strains of different pathotypes can cause disease in both humans and animals. Atypical enteropathogenic E. coli (aEPEC) can infect both animals and humans or influence the severity of other ongoing infections., Results: In the present study, a total of 332 samples were collected from ducks, geese, turkeys, chickens, and pigeons from the Hungarian Veterinary Diagnostic Directorate, two slaughterhouses, two pigeon keepers and one backyard chicken farm. E. coli was isolated and verified from 319 samples. The isolates were screened by PCR for diarrheagenic E. coli pathotypes. Altogether seven atypical enteropathogenic E. coli (aEPEC) strains were identified: two from four-week-old dead turkeys, two from force-fed geese, and three from pigeons. No further pathotypes were identified in the collection. The atypical EPEC strains were classified phylogenetically to B1, B2, and F, and four out of the seven aEPEC isolates proved to be multidrug resistant. Serotypes of aEPEC strains were uniform collected from same farms and showed diversity between their origins with O76, O145, O109 serogroups., Conclusions: This is the first report in the literature about aEPEC in goose (Anser anser domestica). Furthermore, this is the first isolation of aEPEC from turkeys and pigeons in Hungary. The uneven distribution of aEPEC in different age groups of poultry suggests that aEPEC disappears with growing up, but stress (e.g.: force-feeding) and concurrent diseases might promote its reappearance in the intestine., (© 2021. The Author(s).)

Despite initiatives to improve the safety of poultry products in the United States, progress has stalled, and salmonellosis incidence is still above Healthy People 2020's goal. One strategy to manage Salmonella and verify process control in poultry establishments is to implement microbiological criteria (MC) linked to public health outcomes. Concentration-based MC have been used by the food industry; however, the public health impact of such approaches is only starting to be assessed. This study evaluated the public health impact of a concentration-based MC for Salmonella in raw ground turkey consumed in the United States using a quantitative risk assessment modeling approach. The distribution of Salmonella concentration in ground turkey was derived from USDA-FSIS monitoring surveys. Other variables and parameters were derived from public databases, literature, and expert opinion. Based on considered concentrations, implementing a MC of 1 cell/g led to an estimated 46.1% reduction (preventable fraction, PF) in the mean probability of illness when consumer cooking and cross-contamination were included. The PF was consistent across scenarios including or excluding cross-contamination and cooking, with slightly lower mean PF when cross-contamination was included. The proportion of lots not compliant with the 1 cell/g MC was 1.05% in the main scenarios and increased nonlinearly when higher Salmonella concentrations were assumed. Assumptions on concentration variability across lots and within lots had a large impact, highlighting the benefit of reducing this uncertainty. These approach and results can help inform the development of MC to monitor and control Salmonella in ground turkey products., (© 2020 The Authors. Risk Analysis published by Wiley Periodicals LLC on behalf of Society for Risk Analysis.)

Microbiological spoilage of meat is considered as a process which involves mainly bacterial metabolism leading to degradation of meat sensory qualities. Studying spoilage requires the collection of different types of experimental data encompassing microbiological, physicochemical and sensorial measurements. Within this framework, the objective herein was to carry out a multiblock path modelling workflow to decipher causality relationships between different types of spoilage-related responses: composition of microbiota, volatilome and off-odour profiles. Analyses were performed with the Path-ComDim approach on a large-scale dataset collected on fresh turkey sausages. This approach enabled to quantify the importance of causality relationships determined a priori between each type of responses as well as to identify important responses involved in spoilage, then to validate causality assumptions. Results were very promising: the data integration confirmed and quantified the causality between data blocks, exhibiting the dynamical nature of spoilage, mainly characterized by the evolution of off-odour profiles caused by the production of volatile organic compounds such as ethanol or ethyl acetate. This production was possibly associated with several bacterial species like Lactococcus piscium, Leuconostoc gelidum, Psychrobacter sp. or Latilactobacillus fuchuensis. Likewise, the production of acetoin and diacetyl in meat spoilage was highlighted. The Path-ComDim approach illustrated here with meat spoilage can be applied to other large-scale and heterogeneous datasets associated with pathway scenarios and represents a promising key tool for deciphering causality in complex biological phenomena., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Due to the increasing spread of multidrug-resistant (MDR) bacteria, phage therapy is considered one of the most promising methods for addressing MDR bacteria. Escherichia coli lives symbiotically in the intestines of humans and some animals, and most strains are beneficial in terms of maintaining a healthy digestive tract. However, some E. coli strains can cause serious zoonotic diseases, including diarrhea, pneumonia, urinary tract infections, and hemolytic uremic syndrome. In this study, we characterized a newly isolated Myoviridae phage, vB&#95;EcoM&#95;APEC. The phage vB&#95;EcoM&#95;APEC was able to infect E. coli APEC O78, which is the most common MDR E. coli serotype in turkeys. Additionally, the phage's host range included Klebsiella pneumoniae and other E. coli strains. The genome of phage vB&#95;EcoM&#95;APEC (GenBank accession number MT664721) was 35,832 bp in length, with 52 putative open reading frames (ORFs) and a GC content of 41.3%. The genome of vB&#95;EcoM&#95;APEC exhibited low similarity (79.1% identity and 4.0% coverage) to the genome of Acinetobacter phage vB&#95;AbaM&#95;IME284 (GenBank no. MH853787.1) according to the nucleotide Basic Local Alignment Search Tool (BLASTn). Phylogenetic analysis revealed that vB&#95;EcoM&#95;APEC was a novel phage, and its genome sequence showed low similarity to other available phage genomes. Gene annotation indicated that the protein encoded by orf11 was an endolysin designated as LysO78, which exhibited 64.7% identity (91.0% coverage) with the putative endolysin of Acinetobacter baumannii phage vB&#95;AbaM&#95;B9. The LysO78 protein belongs to glycoside hydrolase family 19, and was described as being a chitinase class I protein. LysO78 is a helical protein with 12 α-helices containing a large domain and a small domain in terms of the predicted three-dimensional structure. The results of site-directed mutagenesis indicated that LysO78 contained the catalytic residues E54 and E64. The purified endolysin exhibited broad-spectrum bacteriolytic activity against Gram-negative strains, including the genera Klebsiella , Salmonella , Shigella , Burkholderia , Yersinia , and Pseudomonas , as well as the species Chitinimonas arctica , E. coli , Ralstonia solanacearum , and A. baumannii . An enzymatic assay showed that LysO78 had highly lytic peptidoglycan hydrolases activity (64,620,000 units/mg) against E. coli APEC O78, and that LysO78 had lytic activity in the temperature range of 4-85 °C, with an optimal temperature of 28 °C and optimal pH of 8.0, and was active at pH 3.0-12.0. Overall, the results suggested that LysO78 might be a promising therapeutic agent for controlling MDR E. coli APEC O78 and nosocomial infections caused by multidrug-resistant bacteria.

Across the world, many commercial poultry flocks and captive birds are threatened by infection with Aspergillus fumigatus. Susceptibility to aspergillosis varies among birds; among galliform birds specifically, morbidity and mortality rates seem to be greater in turkeys than in chickens. Little is known regarding the features of avian immune responses after inhalation of Aspergillus conidia, and to date, scarce information on inflammatory responses during aspergillosis exists. Thus, in the present study, we aimed to improve our understanding of the interactions between A. fumigatus and economically relevant galliform birds in terms of local innate immune responses. Intra-tracheal aerosolization of A. fumigatus conidia in turkey and chicken poults led to more severe clinical signs and lung lesions in turkeys, but leukocyte recovery from lung lavages was higher in chickens at 1dpi only. Interestingly, only chicken CD8+ T lymphocyte proportions increased after infection. Furthermore, the lungs of infected chickens showed an early upregulation of pro-inflammatory cytokines, including IL-1β, IFN-γ and IL-6, whereas in turkeys, most of these cytokines showed a downregulation or a delayed upregulation. These results confirmed the importance of an early pro-inflammatory response to ensure the development of an appropriate anti-fungal immunity to avoid Aspergillus dissemination in the respiratory tract. In conclusion, we show for the first time that differences in local innate immune responses between chickens and turkeys during aspergillosis may determine the outcome of the disease., (© The Author(s) 2020. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.)

The objective of this study was to determine the chemical composition and antibacterial activity of Trachyspermum ammi essential oil (TAEO). Moreover, the present study comparatively investigated TAEO in the forms of emulsion and Nano-emulsion in alginate-based edible coatings against inoculated Listeria monocytogenes in turkey fillets during 12 days in cold storage (at a temperature of 4 ± 1 °C). Alginate solutions with two levels of TAEO (in emulsion and Nano-emulsion forms) were prepared in this study. The bacterial count was performed on days 0, 1, 2, 4, 8, and 12. Based on the obtained results of the current study, a comparison of different treatments with the blank samples (without any coating) showed that the highest considerable result was observed in the samples with Nano-emulsion coating (P < 0.05). Nano-emulsion loaded alginate coating prevented the growth of listeria in turkey fillets even after 12 days of cold storage. According to the findings of this study, the application of alginate edible coatings containing TAEO, especially in Nano-form, can be very effective in controlling the growth of L. monocytogenes, as a foodborne pathogen, during storage; therefore, it is a good choice to be applied in the meat industry., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Pasteurella multocida is a bacterial pathogen with the ability to infect a multitude of hosts including humans, companion animals, livestock, and wildlife. This study used bioinformatic approaches to explore the genomic diversity of 656 P. multocida isolates and epidemiological associations between host factors and specific genotypes. Isolates included in this study originated from a variety of hosts, including poultry, cattle, swine, rabbits, rodents, and humans, from five different continents. Multi-locus sequence typing identified 69 different sequence types. In-silico methodology for determining capsular serogroup was developed, validated, and applied to all genome sequences, whereby capsular serogroups A, B, D, and F were found. Whole genome phylogeny was constructed from 237,670 core single nucleotide variants (SNVs) and demonstrated an overall lack of host or capsular serogroup specificity, with the exception of isolates from bovine sources. Specific SNVs within the srlB gene were identified in P. multocida subsp. septica genomes, representing specific mutations that may be useful for differentiating one of the three known subspecies. Significant associations were identified between capsular serogroup and virulence factors, including capsular serogroup A and OmpH1, OmpH3, PlpE, and PfhB1; capsular serogroup B and HgbA and PtfA; and capsular serogroup F and PtfA and PlpP. Various mobile genetic elements were identified including those similar to ICEPmu1, ICEhin1056, and IncQ1 plasmids, all of which harbored multiple antimicrobial resistance-encoding genes. Additional analyses were performed on a subset of 99 isolates obtained from turkeys during fowl cholera outbreaks from a single company which revealed that multiple strains of P. multocida were circulating during the outbreak, instead of a single, highly virulent clone. This study further demonstrates the extensive genomic diversity of P. multocida, provides epidemiological context to the various genotyping schemes that have traditionally been used for differentiating isolates, and introduces additional tools for P. multocida molecular typing., Competing Interests: JN is employed by Blue House Veterinary LLC. MS and BW are employed by Select Genetics. There are no patents, products in development or marketed products to declare. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Campylobacter cause gastroenteritis in humans and may be shed in the feces of livestock and poultry species, including cattle, chicken, turkey, and swine. However, a synthesis of the prevalence on farms in the United States and Canada is currently lacking. Thus, our objective was to conduct a systematic review and meta-analysis to estimate the prevalence of Campylobacter coli , Campylobacter jejuni , and Campylobacter spp. on livestock and poultry farms operated under commercial conditions in the United States and Canada. The relevant literature was identified and examined for eligibility based on a priori inclusion and exclusion criteria. Relevant data were extracted, and a meta-analysis was performed. The data were transformed using the Freeman-Tukey arcsine transformation to stabilize the variance. A separate meta-analysis was performed for each animal species, level of sampling (individual versus pooled), and species of Campylobacter , for a total of 29 meta-analyses. C. jejuni and Campylobacter spp. were present in all livestock and poultry species of interest, whereas C. coli was found in all species of interest with the exception of chickens. Furthermore, substantial heterogeneity was observed in most meta-analyses. In an attempt to account for this, subgroup analyses were performed on potential moderators. However, with the exception of beef cattle, where studies in feedlot cattle reported a consistently higher prevalence compared with adult cattle on pasture, significant heterogeneity remained in the majority of meta-analyses after accounting for potential moderators. The results of this review can be used to inform future risk assessment, consumer and producer awareness, and resource allocation, and identify gaps for future research.

Mycoplasma gallisepticum and Mycoplasma synoviae are bacterial pathogens that cause disease in poultry, adversely affecting their health and welfare, and are a financial burden on producers. This manuscript describes the results of the MycoPath project that is the first international antimicrobial susceptibility programme for mycoplasma pathogens isolated from poultry. Improved comparative analysis of minimal inhibitory concentration (MIC) results from participating countries was facilitated by using one laboratory determining all MICs. Chicken and turkey isolates were obtained from France, Germany, Great Britain, Hungary, Italy and Spain during 2014-2016. One isolate per farm was retained. The MIC of seven antimicrobial agents was determined using a broth microdilution method, with Friis Medium ( M. gallisepticum ) or Modified Chanock's Medium ( M. synoviae ). Of the 222 isolates recovered, 82 were M. gallisepticum and 130 were M. synoviae. M. gallisepticum MIC 50/90 values were 0.12/0.5, 2/8, 0.5/4, 0.12/>64, 0.008/0.062, 0.008/32, 0.062/4 mg/l for doxycycline, enrofloxacin, oxytetracycline, spiramycin, tiamulin, tilmicosin and tylosin, respectively. For M. synoviae , the values were 0.5/1, 8/16, 0.5/1, 0.5/8, 0.25/0.5, 0.062/2 and 0.062/16 mg/l respectively . A bimodal MIC distribution for the fluoroquinolone (enrofloxacin) and the macrolides (spiramycin, tilmicosin and tylosin) indicate that both species have sub-populations that are less susceptible in vitro to those antimicrobials. Some differences in susceptibilities were observed according to host species, Mycoplasma species, and country of origin. This study provides a baseline of novel data for future monitoring of antimicrobial resistance in poultry Mycoplasma species. Additionally, this information will facilitate the selection of the antimicrobial agents most likely to be effective, thus ensuring their minimal use with targeted and correct therapeutic treatments. Highlights First large-scale pan-European collection of representative Mg and Ms isolates.MIC values assessed in central laboratory for Mg and Ms from chickens and turkeys.Range of MIC values for 82 Mg and 130 Ms isolates to seven licenced antibiotics shown.Data can be used to help determine Mg and Ms veterinary-specific breakpoints.

Almost two decades ago, in addition to a compulsory M. gallisepticum (Mg) monitoring programme of breeding stock based on European Union regulations, the Dutch poultry industry added national regulations to further reduce the Mg prevalence in Dutch commercial poultry. Currently, all commercial chicken and turkey flocks except broilers are monitored for Mg. All breeding flocks on a farm where one or more flocks tested Mg positive are culled. Mg positive layer pullets are channelled and layer pullets placed on Mg positive multi-age farms are vaccinated. The monitoring data obtained were analysed covering a period of 17 years. Moreover, 31 Dutch Mg isolates from the same period were analysed by multilocus sequence typing (MLST) and compared to available PubMLST data. The results show that in breeding stock the seroprevalence decreased from 1.6% to 0.0%, in commercial layers from 6.3% to 1.9%, and in meat turkeys from 17.6% to 2.4%. The MLST results showed the presence of closely related and identical sequence types (STs) within the different Dutch poultry types. Similar STs were found in Northern and Southern Europe only. The results show a fast decline in the Mg prevalence since 2001, although in layers the Mg prevalence has stabilized and suggests backyard poultry might pose a risk for commercial poultry. The need for Mg control across poultry sectors and in trade was confirmed by the similarity in STs found in different types of poultry and regions. These results from the Dutch poultry industry can be extrapolated to Mg control in general.

The respiratory tracts of turkeys play important roles in the overall health and performance of the birds. Understanding the bacterial communities present in the respiratory tracts of turkeys can be helpful to better understand the interactions between commensal or symbiotic microorganisms and other pathogenic bacteria or viral infections. The aim of this study was the characterization of the bacterial communities of upper respiratory tracks in commercial turkeys using NGS sequencing by the amplification of 16S rRNA gene with primers designed for hypervariable regions V3 and V4 (MiSeq, Illumina). From 10 phyla identified in upper respiratory tract in turkeys, the most dominated phyla were Firmicutes and Proteobacteria. Differences in composition of bacterial diversity were found at the family and genus level. At the genus level, the turkey sequences present in respiratory tract represent 144 established bacteria. Several respiratory pathogens that contribute to the development of infections in the respiratory system of birds were identified, including the presence of Ornithobacterium and Mycoplasma OTUs. These results obtained in this study supply information about bacterial composition and diversity of the turkey upper respiratory tract. Knowledge about bacteria present in the respiratory tract and the roles they can play in infections can be useful in controlling, diagnosing and treating commercial turkey flocks.

Salmonella spp. remains the most significant foodborne pathogen in south Brazil, but its epidemiology tends to change over time. Using official and surrogate data, a microbial subtyping model attributed different Salmonella serovars to laying hens, pigs, broilers, and turkeys from 2005 to 2015 in Rio Grande do Sul (RS). Additional to the subtyping model, three sub-analyses of outbreak data attributed Salmonella spp. in humans to animal and non-animal food. Laying hens/eggs was the most important source of human salmonellosis in RS, with almost 40% (159 cases; 95% credibility interval, 43-247) attribution proportion, followed by pigs reared in Santa Catarina, a neighbor state (34.5%). The Salmonella serovars Enteritidis and Typhimurium were the most common serovars involved. Source-related parameters had wide credibility intervals but showed a higher risk of illness from contaminated eggs than from the other three animal-food sources. Analysis of the outbreak data corroborated the findings and indicated signs of decreasing importance for eggs and increasing importance for pork consumption., (Copyright © 2020 Elsevier B.V. All rights reserved.)

A dairy-originated probiotic bacterium, Propionibacterium freudenreichii subsp. freudenreichii B3523 (PF) was found to be effective in reducing multidrug-resistant Salmonella Heidelberg (MDR SH) colonization in turkey poults (2-week-old) and growing (7-week-old) and finishing (12-week-old) turkeys. In this study, we explored the potential for microbiome modulation in the cecum of turkeys of different age groups due to PF supplementation in conjunction with MDR SH challenge. One-day-old commercial turkey poults were allocated to 3 treatment groups: negative control (N; turkeys without PF supplementation or SH challenge), SH control (S; turkeys challenged with SH without PF supplementation), and test group (P; turkeys supplemented with PF and challenged with SH). Turkeys were supplemented with 10 10  CFU PF in 5-gallon (18.9 L) water until 7 or 12 week of age. At the 6th or 11 th wk, turkeys were challenged with SH at 10 6 and 10 8  CFU/bird by crop gavage, respectively. After 2 and 7 d of challenge (2-d postinoculation [PI] and 7-d PI, respectively), cecal samples were collected and microbiome analysis was conducted using Illumina MiSeq. The experiments were repeated twice with 8 and 10 turkeys/group for 7- and 12-wk studies, respectively. Results indicated that the species richness and abundance (Shannon diversity index) was similar among the treatment groups. However, treatments caused apparent clustering of the samples among each other (P < 0.05). Firmicutes was the predominant phylum in the growing and finishing turkey cecum which was evenly distributed among the treatments except on wk 12 where the relative abundance of Firmicutes was significantly higher in P than in N (P = 0.02). The MDR SH challenge resulted in modulation of microflora such as Streptococcus, Gordonibacter, and Turicibacter (P < 0.05) in the S groups compared with the P and N groups, known to be associated with inflammatory responses in birds and mammals. The supplementation of PF increased the relative abundance of carbohydrate-fermenting and short-chain fatty acid-producing genera in the P group compared with the S group (P < 0.05). Moreover, the results revealed that PF supplementation potentially modulated the beneficial microbiota in the P group, which could mitigate SH carriage in turkeys., (Copyright © 2020. Published by Elsevier Inc.)

Salmonella is a leading cause of foodborne illness (i.e., salmonellosis) outbreaks, which on occasion are attributed to ground turkey. The poultry industry uses Salmonella prevalence as an indicator of food safety. However, Salmonella prevalence is only one of several factors that determine risk of salmonellosis. Consequently, a model for predicting risk of salmonellosis from individual lots of ground turkey as a function of Salmonella prevalence and other risk factors was developed. Data for Salmonella contamination (prevalence, number, and serotype) of ground turkey were collected at meal preparation. Scenario analysis was used to evaluate effects of model variables on risk of salmonellosis. Epidemiological data were used to simulate Salmonella serotype virulence in a dose-response model that was based on human outbreak and feeding trial data. Salmonella prevalence was 26% (n = 100) per 25 g of ground turkey, whereas Salmonella number ranged from 0 to 1.603 with a median of 0.185 log per 25 g. Risk of salmonellosis (total arbitrary units (AU) per lot) was affected (p ≤ 0.05) by Salmonella prevalence, number, and virulence, by incidence and extent of undercooking, and by food consumption behavior and host resistance but was not (p > 0.05) affected by serving size, serving size distribution, or total bacterial load of ground turkey when all other risk factors were held constant. When other risk factors were not held constant, Salmonella prevalence was not correlated (r = -0.39; p = 0.21) with risk of salmonellosis. Thus, Salmonella prevalence alone was not a good indicator of poultry food safety because other factors were found to alter risk of salmonellosis. In conclusion, a more holistic approach to poultry food safety, such as the process risk model developed in the present study, is needed to better protect public health from foodborne pathogens like Salmonella., (Published 2020. This article is a U.S. Government work and is in the public domain in the USA.)

Salmonella Infantis carrying extended spectrum β-lactamase bla CTX-M-65 on a pESI-like megaplasmid has recently emerged in United States poultry. In order to determine the carriage rate and gene content variability of this plasmid in U.S. Salmonella Infantis, whole genome sequences of Salmonella isolates from humans and animals in the U.S. and internationally containing the pESI-like plasmid were analyzed. The U.S. Department of Agriculture Food Safety and Inspection Service (FSIS) identified 654 product sampling isolates containing pESI-like plasmids through hazard analysis and critical control point (HACCP) verification testing in 2017 and 2018. The Centers for Disease Control and Prevention identified 55 isolates with pESI-like plasmids in 2016-2018 through the National Antimicrobial Resistance Monitoring System. Approximately 49% of pESI-like plasmids from FSIS verification isolates and 71% from CDC NARMS contained bla CTX-M-65 . Pan-plasmid genome analysis was also performed. All plasmids contained traN and more than 95% contained 172 other conserved genes; 61% contained bla CTX-M-65 . In a hierarchical clustering analysis, some plasmids from U.S. animal sources clustered together and some plasmids from South America clustered together, possibly indicating multiple plasmid lineages. However, most plasmids contained similar genes regardless of origin. Carriage of the pESI-like plasmid in U.S. appears to be limited to Salmonella Infantis and carriage rates increased from 2017 to 2018.

Antimicrobial resistance (AMR) is a global threat in humans and animals, and antimicrobial usage (AMU) has been identified as a main trigger of AMR. The purpose of this work was to compare data on AMR in clinical and non-clinical isolates of Escherichia coli in German broilers and turkeys between 2014 and 2017. Furthermore, we investigated AMR changes over time and the association of changes in AMU with changes in AMR. Data on clinical and non-clinical isolates together with data on therapy frequency of broilers and turkeys were collected from German monitoring systems. Logistic regression analyses were performed to assess the association between the explanatory factors (AMU, year and isolate type) and the dependent variable (AMR). In broilers, the analysis showed lower resistance proportions of clinical isolates of E. coli to ampicillin and colistin (ampicillin: Odds ratio (OR) and 95% confidence interval (CI) = 0.44 (0.3-0.64), p<0.001; colistin: OR and 95% CI = 0.75 (0.73-0.76), p<0.001) but higher proportions for cefotaxime (OR and 95% CI = 4.58 (1.56-15.1), p = 0.007). Resistance to ampicillin, gentamicin and tetracycline was less frequent in clinical isolates in turkeys (ampicillin: OR and 95% CI = 0.4 (0.29-0.53), p<0.001; gentamicin: OR and 95% CI = 0.5 (0.26-0.94), p = 0.035; tetracycline: OR and 95% CI = 0.4 (0.29-0.55), p<0.001). The analysis found decreasing associations of AMU with resistance to tetracycline in turkeys and to colistin in broilers. Year was associated with a decrease in resistance to colistin in broilers and to tetracycline in turkeys. Differences in resistance found in this study between clinical and non-clinical isolates might play an important role in resistance prevalence. This study indicated that further data analyses over longer time intervals are required to clarify the differences found between clinical and non-clinical isolates and to assess the long-term effects of changes in AMU on the prevalence of AMR., Competing Interests: The authors have declared that no competing interests exist.

The objective of this study was to compare the prevalence and antimicrobial resistance (AMR) rates of Campylobacter spp. isolated from conventional and organic turkey meat sold at retail in Germany. Samples of conventional ( N  = 527) and organic ( N  = 245) fresh turkey meat without skin were collected at retail markets throughout Germany and tested for Campylobacter spp.. Campylobacter isolates were tested for resistance to six antimicrobials (gentamicin, streptomycin, ciprofloxacin, nalidixic acid, erythromycin, and tetracycline) using broth microdilution. Prevalence of Campylobacter spp. was higher in organic (32.7%) than in conventional (19.4%) turkey meat. The proportion of fully susceptible isolates was lower in Campylobacter coli (6.8%) than in Campylobacter jejuni (33.9%) and higher in isolates from organic (38.4%) than from conventional production (17.4%). Overall, resistance rates were the highest to ciprofloxacin, nalidixic acid, and tetracycline. Resistance to erythromycin was only observed in C. coli and resistance to gentamicin was absent. Overall, resistance rates to tetracycline and fluoroquinolones were higher in isolates from conventional (60.9% and 78.9%) than from organic meat (32.9% and 58.9%, respectively). However, this significant difference was only observed for C. jejuni , but not for C. coli . Further studies are needed to identify the reasons for the differences in the association of production type of turkeys with AMR in the different Campylobacter spp. and the critical parameters for the reduction of AMR in Campylobacter from turkey meat.

Meat products contain valuable nutrients that are important for human health and development but are also highly susceptible to colonization by microorganisms. This can lead to spoilage and serious foodborne illnesses. Natural antimicrobial peptides, produced by many organisms as part of their innate immune system to fight microbial infections, have great potential as food preservatives. In this study, we explored the effect of ternary antimicrobial random peptide mixtures (RPMs) on food spoilage bacteria in minced turkey meat. Amendment of RPMs to meat led to significant reductions in bacterial abundance in experimental tests, and RPMs worked synergistically with nitrite to reduce bacterial loads. Using high-throughput 16S ribosomal RNA gene amplicon sequencing, we characterized the effect of RPMs and nitrite on meat microbial community structure before and during incubation under refrigerated conditions. Our findings reveal strong antimicrobial activity for RPMs against spoilage bacteria in meat, including Listeria monocytogenes and Pseudomonas putida. These results demonstrate the potential of RPMs as a safer preservative for reducing spoilage in meat and other food products., (Copyright © 2020. Published by Elsevier Ltd.)

The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA , is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli , confers gentamicin resistance to E. coli , and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification., (Copyright © 2020 American Society for Microbiology.)

Salmonella is a major causative agent of foodborne illness and rapid identification of this pathogen is essential to prevent disease. Currently most assays require high bacterial burdens or prolonged enrichment to achieve acceptable performance. A reduction in testing time without loss of sensitivity is critical to allow food processors to safely decrease product holding time. To meet this need, a method was developed to detect Salmonella using luciferase reporter bacteriophages. Bacteriophages were engineered to express NanoLuc, a novel optimized luciferase originating from the deep-sea shrimp Oplophorus gracilirostris. NanoLuc-expressing bacteriophages had a limit of detection of 10-100 CFU per mL in culture without enrichment. Luciferase reporters demonstrated a broad host range covering all Salmonella species with one reporter detecting 99.3% of 269 inclusivity strains. Cross-reactivity was limited and only observed with other members of the Enterobacteriaceae family. In food matrix studies, a cocktail of engineered bacteriophages accurately detected 1 CFU in either 25 g of ground turkey with a 7 h enrichment or 100 g of powdered infant formula with a 16 h enrichment. Use of the NanoLuc reporter assay described herein resulted in a considerable reduction in enrichment time without a loss of sensitivity.

The goal of this study was to determine the frequency of resistance to extended-spectrum cephalosporins (ESCs) in Escherichia coli and other Enterobacterales from turkeys in Canada and characterize the associated resistance determinants. Pooled fecal samples were collected in 77 turkey farms across British Columbia, Québec, and Ontario. Isolates were obtained with and without selective enrichment cultures and compared to isolates from diagnostic submissions of suspected colibacillosis cases in Ontario. Isolates were identified using MALDI-TOF and susceptibility to ESCs was assessed by disk diffusion. The presence of blaCMY, blaCTX-M, blaTEM, and blaSHV was tested by PCR. Transformation experiments were used to characterize blaCMY plasmids. Genome sequencing with short and long reads was performed on a representative sample of blaCTX-M-positive isolates to assess isolates relatedness and characterize blaCTX-M plasmids. For the positive enrichment cultures (67% of total samples), 93% (587/610) were identified as E. coli, with only a few other Enterobacterales species identified. The frequency of ESC resistance was low in E. coli isolates from diagnostic submission (4%) and fecal samples without selective enrichment (5%). Of the ESC-resistant Enterobacterales isolates from selective enrichments, 71%, 18%, 14%, and 8% were positive for blaCMY, blaTEM, blaCTX-M, and blaSHV, respectively. IncI1 followed by IncK were the main incompatibility groups identified for blaCMY plasmids. The blaCTX-M-1 gene was found repeatedly on IncI1 plasmids of the pMLST type 3, while blaCTX-M-15, blaCTX-M-55, and blaCTX-M-65 were associated with a variety of IncF plasmids. Clonal spread of strains carrying blaCTX-M genes between turkey farms was observed, as well as the presence of an epidemic blaCTX-M-1 plasmid in unrelated E. coli strains. In conclusion, Enterobacterales resistant to ESCs were still widespread at low concentration in turkey feces two years after the cessation of ceftiofur use. Although blaCMY-2 is the main ESC resistance determinant in E. coli from Canadian turkeys, blaCTX-M genes also occur which are often carried by multidrug resistance plasmids. Both clonal spread and horizontal gene transfer are involved in parallel in the spread of blaCTX-M genes in Enterobacterales from Canadian turkeys., Competing Interests: The authors have declared that no competing interests exist.

The feed supplementation of probiotic microorganisms is a promising method for detoxification of ochratoxin A (OTA) in poultry. The aim of the study was to investigate the effect of newly elaborated synbiotics on the turkey performance, the intestinal microbiota and its enzymatic activity in turkeys (0-15 weeks) fed OTA contaminated feed (198.6-462.0 µg/kg) compared to control group (OTA-free feed). The studies determined the composition of intestinal microorganisms by the culture method and the activity of fecal enzymes by spectrophotometry. It was found that OTA had an adverse effect on the body weight, the intestinal microbiota and the fecal enzymes activity in turkeys. On the other hand, synbiotics resulted in an increase in the count of beneficial bacteria while reducing the number of potential pathogens in the digestive tract. Moreover, synbiotics caused an increase in the activity of α-glucosidase and α-galactosidase, while decreasing the activity of potentially harmful fecal enzymes (β-glucosidase, β-galactosidase, β-glucuronidase) in the turkey's excreta. Results indicate a beneficial effect of elaborated synbiotics on the health of turkeys and a reduction of the negative impact of OTA contaminated feed. These synbiotics can be successfully used as feed additives for turkeys.

Mycoplasma gallisepticum causes respiratory diseases and reproduction disorders in turkeys and chickens. The infection has considerable economic impact due to reduced meat and egg production. Because elimination programmes are not feasible in a large number of poultry farms, vaccination remains the only effective measure of disease control. Differentiating vaccine strains from field isolates is necessary in the control of vaccination programmes and diagnostics. The aim of this study was to develop a polymerase chain reaction based mismatch amplification mutation assay (MAMA) for the discrimination of K vaccine strain (K 5831, Vaxxinova Japan K.K.). After determining the whole genome sequence of the K strain, primers were designed to detect seven different vaccine-specific single nucleotide polymorphisms. After evaluating preliminary results, the MAMA-K-fruA test detecting a single guanine-adenine substitution within the fruA gene (G88A) was found to be the most applicable assay to distinguish the K vaccine strain from field isolates. The detected K strain-specific single nucleotide polymorphism showed genetic stability after serial passage in vitro, but this stability test should still be evaluated in vivo as well, investigating a large number of K strain re-isolates. The MAMA-K-fruA assay was tested on a total of 280 culture and field samples. The designed assay had 10 2 and 10 3 template copy number/µl sensitivity in melt-curve analysis based and agarose-gel based assays, respectively, and showed no cross reaction with other avian Mycoplasma species. The new MAMA provides a time- and cost-effective molecular tool for the control of vaccination programmes and for diagnostics.

Communities of gut bacteria (microbiota) are known to play roles in resistance to pathogen infection and optimal weight gain in turkey flocks. However, knowledge of turkey respiratory microbiota and its link to gut microbiota is lacking. This study presents a 16S rRNA gene-based census of the turkey respiratory microbiota (nasal cavity and trachea) alongside gut microbiota (cecum and ileum) in two identical commercial Hybrid Converter turkey flocks raised in parallel under typical field commercial conditions. The flocks were housed in adjacent barns during the brood stage and in geographically separated farms during the grow-out stage. Several bacterial taxa, primarily Staphylococcus , that were acquired in the respiratory tract at the beginning of the brood stage persisted throughout the flock cycle. Late-emerging predominant taxa in the respiratory tract included Deinococcus and Corynebacterium Tracheal and nasal microbiota of turkeys were identifiably distinct from one another and from gut microbiota. Nevertheless, gut and respiratory microbiota changed in parallel over time and appeared to share many taxa. During the brood stage, the two flocks generally acquired similar gut and respiratory microbiota, and their average body weights were comparable. However, there were qualitative and quantitative differences in microbial profiles and body weight gain trajectories after the flocks were transferred to geographically separated grow-out farms. Lower weight gain corresponded to the emergence of Deinococcus and Ornithobacterium in the respiratory tract and Fusobacterium and Parasutterella in gut. This study provides an overview of turkey microbiota under field conditions and suggests several hypotheses concerning the respiratory microbiome. IMPORTANCE Turkey meat is an important source of animal protein, and the industry around its production contributes significantly to the agricultural economy. The microorganisms present in the gut of turkeys are known to impact bird health and flock performance. However, the respiratory microbiota in turkeys is entirely unexplored. This study has elucidated the microbiota of respiratory tracts of turkeys from two commercial flocks raised in parallel throughout a normal flock cycle. Further, the study suggests that bacteria originating in the gut or in poultry house environments influence respiratory communities; consequently, they induce poor performance, either directly or indirectly. Future attempts to develop microbiome-based interventions for turkey health should delimit the contributions of respiratory microbiota and aim to limit disturbances to those communities., (Copyright © 2020 American Society for Microbiology.)

Acinetobacter baumannii (A. baumannii) is a miscellaneous bacterium with ability of extensive antibiotic resistance. A. baumannii strains have also been isolated from animal origins. The objective of our atudy was characterization of A. baumannii antibiotic resistance and virulence traits from turkey and chicken raw meat. Of 576 turkey and 424 chicken specimens during 2017-2019, 200 (120 from turkey and 80 from chicken) isolates were identified as A. baumannii. Virulence factors and antibiotic resistance patterns of A. baumannii were determined using polymerase chain reaction (PCR) technique and Kirby-Bauer test. All the isolates were resistant to tetracycline and cefoxitin and 81 % and 56 % of them produced ESBLs and carbapenemases. Also 74 % of them (34 % from chicken and 40 % from turkey) were multidrug-resistant (MDR) A. baumannii. Colistin and fosfomycin non-susceptibility was detected among 12 % and 10 % of them, respectively. The existence of tetA, dfrA, tetB, bla oxa-51-like , bla oxa-23-like , sul1, bla oxa-24-like , bla oxa-58-like , fosA3 and mcr-1 genes accounted for 80 %, 71 %, 70.5 %, 66 %, 62 %, 43 %, 34 %, 22 %, 11 % and 13 % of them, repectively. Additionally, predominant virulence factors included the fimH, afa/draBC, sfa/foc DE, cnfI and cnf2 genes. The rate of antibiotic resistance genes and virulence factors was not significantly different between turkey and chicken (p > 0.05). High rate of antibiotic non-susceptibility even against last-line resorts in poultry products is a concern and suggest that animals play a potential role as reservoirs of transmission of MDR A. baumannii., Competing Interests: Declaration of Competing Interest The authors certify that they have NO affiliations with or involvement in any organization or entity with any financial interest or nonfinancial in the subject matter or materials discussed in this manuscript., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale , which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined. Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades. IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates., (Copyright © 2020 American Society for Microbiology.)

Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source. IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans., (Copyright © 2020 Miller et al.)

This paper presents the impact on antimicrobial resistance (AMR) in poultry and pig bacteria of the French EcoAntibio plan, a public policy to reduce antimicrobial use in animals. The analysis was performed using sales data of veterinary antimicrobials and AMR data from bacteria obtained at slaughterhouse and from diseased animals. From 2011-2018, fluoroquinolones exposure decreased by 71.5 % for poultry and 89.7 % for pigs. For Campylobacter jejuni isolated from broilers at slaughterhouses, ciprofloxacin resistance increased from 51 % in 2010 to 63 % in 2018, whereas for turkeys the percentages varied from 56 % in 2014 to 63 % in 2018. For commensal E. coli isolated from the caecal content of broilers at slaughterhouses, the resistance to ciprofloxacin - assessed using an epidemiological cut-off value - increased in broiler isolates from 30.7 % in 2010 to 38.1 % in 2018. In turkeys, the percentage of resistant E. coli isolates decreased from 21.3 % in 2014 to 15.2 % in 2018, whereas in pigs, it increased from 1.9 % in 2009 to 5.5 % in 2017. However, for E. coli isolated from diseased animals, when the breakpoints of 2018 were applied, resistance to fluoroquinolones significantly decreased between 2010 and 2018 from 9.0%-5.4% for broilers/hens, from 7.4 % to 3.4 % for turkeys and from 9.4 % to 3.6 % for pigs. These data show that the major, rapid decrease in the exposition to fluoroquinolones had contrasting effects on resistance in the diverse bacterial collections. Co-selection or fitness of resistant strains may explain why changes in AMR do not always closely mirror changes in use., Competing Interests: Declaration of Competing Interest None., (Copyright © 2020 Elsevier B.V. All rights reserved.)

The aim of this article is to report on antimicrobial resistance (AMR) in commensal Escherichia coli from livestock from several European countries. The relationships with antimicrobial usage (AMU) at country level and harmonized indicators to cover the most relevant AMR aspects for human health in animal production were also investigated. E. coli were isolated in faeces from broilers and fattening pigs (from nine countries), and fattening turkeys and veal calves (from three countries) and screened against a fixed antimicrobial panel. AMU data were collected at farm and average treatment incidences stratified by antimicrobial class, country and livestock species were calculated. Associations between AMR and AMU at country level were analysed. Independent of animal species, the highest resistance was observed for ampicillin, sulphamethoxazole, tetracycline and trimethoprim. E. coli from broilers showed the highest resistance level for (fluoro)quinolones, and multidrug resistance peaked in broilers and fattening turkeys. Colistin resistance was observed at very low levels with the exception of fattening turkeys. High resistance to third- and fourth-generation cephalosporins was detected in broilers and fattening turkeys. The lowest levels of resistance were for meropenem, azithromycin and tigecycline (<1 %). Significant correlations between resistance and usage at country level were detected in broilers for polymyxins and aminoglycosides, and in fattening pigs for cephalosporins, amphenicols, fluoroquinolones and polymyxins. None of the correlations observed between AMR and AMU were statistically significant for fattening turkey and veal calves. The strength of the analysis performed here is the correlation of aggregated data from the same farms at country level for both AMU and AMR within antimicrobial classes.

Two independent studies were performed, each with a 3 × 2 factorial arrangement to compare the response in broilers and turkeys to phytase and xylanase supplementation on cecal fermentation and microbial populations. For both studies, 960 Ross 308 and 960 BUT 10 (1-day-old) were allocated to 1 of 6 experimental treatments: (1) control diet, containing the standard dose (100 g/ton) of phytase (STD-Xyl); (2) the control diet with 100 g/ton of xylanase (STD + Xyl); (3) the control diet supplemented on top with 2 fold the standard dose of phytase (200 g/ton), also referred as superdosing (SD-Xyl); (4) the superdosed diet with 100 g/ton of xylanase (SD + Xyl); (5) the control diet supplemented with 5-fold the standard dose of phytase (500 g/ton), also referred as megadosing (MD-Xyl); and (6) the megadosed diet with 100 g/ton of xylanase (MD + Xyl). Each treatment had 8 replicates of 20 animals. Broiler and turkey diets, based on wheat, soybean meal, rapeseed, and barley, and water were available ad libitum. On day 28, the cecal contents from 5 birds per pen were collected. The profile of short-chain fatty acids (SCFA) and microbiome structure (by % guanidine and cytosine [G + C] method) were analyzed. Selected % G + C fractions were used for 16S rDNA sequencing for the identification of bacteria. No treatment effects were noted on SCFA concentrations in either broilers or turkeys. Broilers fed MD diets had greater proportions of unclassified Clostridiales, Mollicutes (RF9) and Faecalibacterium. Xylanase supplementation in broilers resulted in lower proportions of Lactobacillus but increased Mollicutes (RF9), unclassified Ruminococcus, unclassified Clostridiales, and Bifidobacterium. The microbiome in turkeys was unaffected by phytase supplementation, but xylanase supplementation increased the proportions of Lachnospiraceae (Incertae sedis), Lactobacillus, and Bifidobacterium. Supplementation of turkey diets with increasing doses of phytase did not affect the cecal microbiota in contrast to what was observed in broilers. In contrast, xylanase supplementation in both species led to significant changes in the microbial populations, suggesting a positive influence through the provision of oligosaccharides., (Copyright © 2019. Published by Elsevier Inc.)

The mcr-1 gene has been identified in bacterial isolates obtained from humans, animals, environment, and food, including Salmonella spp., which is one of the major foodborne pathogens worldwide. The aim of this study was to evaluate the presence of mcr-1 gene in Salmonella spp. from food produced in Brazil and to characterize the isolates harboring this gene. A total of 490 Salmonella spp. isolates from the Brazilian National Program for the Control of Foodborne Pathogens were screened for the presence of mcr-1 gene by polymerase chain reaction (PCR). Whole genome sequencing (WGS) was performed in positive isolates to characterize the sequence type (ST), plasmid families and resistance genes. Antimicrobial susceptibility tests were performed by broth microdilution. Selected isolates were submitted to conjugation experiments using the Escherichia coli J53 as a receptor. We detected eight isolates harboring the mcr-1 gene; seven belonged to Salmonella enterica serovar Typhimurium and its monophasic variant 4,[5],12:i:-, and one belonged to serovar Saintpaul. Seven of the mcr-1 positive isolates displayed a high rate of resistance to other antibiotics in addition to colistin. Analysis of the WGS indicated that the ST 19 was the most common ST among the mcr-1 positive isolates. The mcr-1 gene was located in an IncX4 plasmid of ∼33 kb, with no additional resistance genes and with high identity with a plasmid obtained from a clinical isolate of E. coli mcr-1 positive in Brazil. All plasmids harboring the mcr-1 gene were able to conjugate. Our results suggest the spread of a single plasmid type in Brazil harboring the mcr-1 among Salmonella spp. The horizontal transfer of this mobile element has been contributing to the spread of the colistin resistance in the country.

We investigated the occurrence of plasmid-mediated colistin resistance in Enterobacteriaceae in turkey meat produced in the Czech Republic as well as in turkey meat imported into the Czech Republic from other European Union countries. Seventeen samples of raw turkey meat from the Czech Republic (n = 4), Hungary (n = 2), Poland (n = 6) and Germany (n = 5) were cultured in peptone water at 37 °C overnight and the enriched cultures were tested for the presence of mcr-1-5 genes. PCR-positive enriched cultures were inoculated onto selective agar with colistin (3.5 mg/L). A minimal inhibitory concentration (MIC) of colistin was determined by using the broth microdilution method in PCR-positive isolates. In addition, a macrorestriction analysis was performed using XbaI endonuclease. Of 17 meat samples, 12 samples from Poland (6/6), Germany (3/5) and the Czech Republic (3/4) proved positive for the presence of the mcr-1 gene. Forty-two isolates carrying the mcr-1 gene were obtained: Escherichia coli (n = 39) revealing 32 distinct XbaI profiles and Klebsiella pneumoniae (n = 3) with 2 distinct XbaI profiles. The minimal inhibitory concentration (MIC) of the mcr-1 positive isolates was as follows: 4 mg/L (n = 28), 8 mg/L (n = 12), 32 mg/L (n = 1) and 64 mg/L (n = 1). The high prevalence (70.6%; 12/17 samples) of mcr-1-mediated colistin-resistant Enterobacteriaceae found in the turkey meat samples analysed in this study, builds on previously published evidence that poultry, and their products, represent a substantial risk for the dissemination of plasmid-mediated colistin resistance in Europe.