Antibiotic-induced gut dysbiosis elicits gut-brain axis relevant multi-omic signatures and behavioral and neuroendocrine changes in a nonhuman primate model.

Emerging evidence indicates that antibiotic-induced dysbiosis can play an etiological role in the pathogenesis of neuropsychiatric disorders. However, most of this evidence comes from rodent models. The objective of this study was to evaluate if antibiotic-induced gut dysbiosis can elicit changes in gut metabolites and behavior indicative of gut-brain axis disruption in common marmosets (Callithrix jacchus) - a nonhuman primate model often used to study sociability and stress. We were able to successfully induce dysbiosis in marmosets using a custom antibiotic cocktail (vancomycin, enrofloxacin and neomycin) administered orally for 28 days. This gut dysbiosis altered gut metabolite profiles, behavior, and stress reactivity. Increase in gut Fusobacterium spp. post-antibiotic administration was a novel dysbiotic response and has not been observed in any rodent or human studies to date. There were significant changes in concentrations of several gut metabolites which are either neurotransmitters (e.g., GABA and serotonin) or have been found to be moderators of gut-brain axis communication in rodent models (e.g., short-chain fatty acids and bile acids). There was an increase in affiliative behavior and sociability in antibiotic-administered marmosets, which might be a coping mechanism in response to gut dysbiosis-induced stress. Increase in urinary cortisol levels after multiple stressors provides more definitive proof that this model of dysbiosis may cause disrupted communication between gut and brain in common marmosets. This study is a first attempt to establish common marmosets as a novel model to study the impact of severe gut dysbiosis on gut-brain axis cross-talk and behavior.

Antibiotic-induced gut dysbiosis and cognitive, emotional, and behavioral changes in rodents: a systematic review and meta-analysis.

There are previous epidemiological studies reporting associations between antibiotic use and psychiatric symptoms. Antibiotic-induced gut dysbiosis and alteration of microbiota-gut-brain axis communication has been proposed to play a role in this association. In this systematic review and meta-analysis, we reviewed published articles that have presented results on changes in cognition, emotion, and behavior in rodents (rats and mice) after antibiotic-induced gut dysbiosis. We searched three databases-PubMed, Web of Science, and SCOPUS to identify such articles using dedicated search strings and extracted data from 48 articles. Increase in anxiety and depression-like behavior was reported in 32.7 and 40.7 percent of the study-populations, respectively. Decrease in sociability, social novelty preference, recognition memory and spatial cognition was found in 18.1, 35.3, 26.1, and 62.5 percent of the study-populations, respectively. Only one bacterial taxon (increase in gut Proteobacteria) showed statistically significant association with behavioral changes (increase in anxiety). There were no consistent findings with statistical significance for the potential biomarkers [Brain-derived neurotrophic factor (BDNF) expression in the hippocampus, serum corticosterone and circulating IL-6 and IL-1ß levels]. Results of the meta-analysis revealed a significant association between symptoms of negative valence system (including anxiety and depression) and cognitive system (decreased spatial cognition) with antibiotic intake (p < 0.05). However, between-study heterogeneity and publication bias were statistically significant (p < 0.05). Risk of bias was evaluated to be high in the majority of the studies. We identified and discussed several reasons that could contribute to the heterogeneity between the results of the studies examined. The results of the meta-analysis provide promising evidence that there is indeed an association between antibiotic-induced gut dysbiosis and psychopathologies. However, inconsistencies in the implemented methodologies make generalizing these results difficult. Gut microbiota depletion using antibiotics may be a useful strategy to evaluate if and how gut microbes influence cognition, emotion, and behavior, but the heterogeneity in methodologies used precludes any definitive interpretations for a translational impact on clinical practice.

Maternal-Child Microbiome and Impact on Growth and Neurodevelopment in Infants and Children: A Scoping Review.

BACKGROUND: Pathologic changes in the microbiome (dysbiosis) have been implicated in affecting the growth and neurodevelopment of infants and children. There is evidence to suggest that prenatal and postnatal stressors may be a factor in dysbiosis and there is also a growing body of evidence to suggest that interventions may reduce this negative impact. A scoping review was undertaken to identify association between maternal and/or child microbiome with child growth and neurodevelopment. Additionally, intervention studies such as use of nutritional supplementation and its impact on the microbiome, growth and neurodevelopment were reviewed. METHODS: An exhaustive literature search identified 654 relevant citations. After review of abstracts, 557 were eliminated, and 97 remained for full text review. We identified and reported on 42 articles which met inclusion criteria. RESULTS: Seven studies examined associations between microbiome and neurodevelopment and 36 studies evaluated anthropometric measurements, most commonly weight, and microbiota relationships. One study evaluated both growth and neurodevelopment and microbiota. Fourteen studies evaluated supplemental nutrients. Preterm, low birth weight (LBW), and very low birth weight (VLBW) infants were most studied. Findings were inconclusive for consistent associations between microbiota and growth and neurodevelopment. Further, there were no consistent conclusive changes with prescribed treatment interventions. DISCUSSION: There is a need for high-quality longitudinal studies evaluating repeated developmental assessment measures using consistent microbial analysis techniques to inform conclusions regarding the association between microbiome and infant and child growth and neurodevelopment. Additional intervention studies that may mitigate dysbiosis are warranted.

Design, Biological Evaluation, and Computer-Aided Analysis of Dihydrothiazepines as Selective Antichlamydial Agents.

Chlamydia trachomatis (CT) causes the most prevalent sexually transmitted bacterial disease in the United States. The lack of drug selectivity is one of the main challenges of the current antichlamydial pharmacotherapy. The metabolic needs of CT are controlled, among others, by cylindrical proteases and their chaperones (e.g., ClpX). It has been shown that dihydrothiazepines can disrupt CT-ClpXP. Based on this precedent, we synthesized a dihydrothiazepine library and characterized its antichlamydial activity using a modified semi-high-throughput screening assay. Then, we demonstrated their ability to inhibit ClpX ATPase activity in vitro, supporting ClpX as a target. Further, our lead compound displayed a promising selectivity profile against CT, acceptable cytotoxicity, no mutagenic potential, and good in vitro stability. A two-dimensional quantitative structure-activity relationship (2D QSAR) model was generated as a support tool in the identification of more potent antichlamydial molecules. This study suggests dihydrothiazepines are a promising starting point for the development of new and selective antichlamydial drugs.

Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.

Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.

Global Distribution of Extended Spectrum Cephalosporin and Carbapenem Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis.

Third generation cephalosporins and carbapenems are considered critically important antimicrobials in human medicine. Food animals such as swine can act as reservoirs of antimicrobial resistance (AMR) genes/bacteria resistant to these antimicrobial classes, and potential dissemination of AMR genes or resistant bacteria from pigs to humans is an ongoing public health threat. The objectives of this systematic review and meta-analysis were to: (1) estimate global proportion and animal-level prevalence of swine E. coli phenotypically resistant to third generation cephalosporins (3GCs) and carbapenems at a country level; and (2) measure abundances and global distribution of the genetic mechanisms that confer resistance to these antimicrobial classes in these E. coli isolates. Articles from four databases (CAB Abstracts, PubMed/MEDLINE, PubAg, and Web of Science) were screened to extract relevant data. Overall, proportion of E. coli resistant to 3GCs was lower in Australia, Europe, and North America compared to Asian countries. Globally, <5% of all E. coli were carbapenem-resistant. Fecal carriage rates (animal-level prevalence) were consistently manifold higher as compared to pooled proportion of resistance in E. coli isolates. bla CTX-M were the most common 3GC resistance genes globally, with the exception of North America where bla CMY were the predominant 3GC resistance genes. There was not a single dominant bla CTX-M gene subtype globally and several bla CTX-M subtypes were dominant depending on the continent. A wide variety of carbapenem-resistance genes (bla NDM-, VIM-, IMP-, OXA-48, and KPC-) were identified to be circulating in pig populations globally, albeit at very-low frequencies. However, great statistical heterogeneity and a critical lack of metadata hinders the true estimation of prevalence of phenotypic and genotypic resistance to these antimicrobials. Comparatively frequent occurrence of 3GC resistance and emergence of carbapenem resistance in certain countries underline the urgent need for improved AMR surveillance in swine production systems in these countries.

Global Distribution of Fluoroquinolone and Colistin Resistance and Associated Resistance Markers in Escherichia coli of Swine Origin - A Systematic Review and Meta-Analysis.

Background: Fluoroquinolones and polymyxins (colistin) are considered as critical drugs for human medicine. Antimicrobials of these classes are also used in swine production worldwide and this usage can contribute to selection of antimicrobial resistance (AMR), which is a threat to both human and animal health. Given the dynamic epidemiology of AMR, updating our knowledge regarding distribution and trends in the proportion of resistant bacteria is of critical importance. Objectives: The aim of this systematic review and meta-analysis was to describe the global prevalence of phenotypic and genotypic resistance to fluoroquinolones and colistin in Escherichia coli collected from swine. Results: Four databases (PubMed, PubAg, Web of Science, and CAB abstracts) and reports of national surveillance programs were scanned and 360 articles were included in the analysis. We identified higher prevalence levels of fluoroquinolone and colistin resistance in isolates from pig populations in Asia compared to Europe. The heterogeneity of pooled estimates was also higher in Asian countries suggesting that prevalence of AMR is still not fully characterized. There was a major knowledge gap about the situation of AMR in South American and African countries. We also identified key deficiencies in how AMR data was reported in the studies. A meta-analysis using 6,167 publicly available genomes of swine E. coli established the prevalence and global distribution of genetic determinants that can lead to fluoroquinolone and colistin resistance. Conclusion: This study provides the most comprehensive information on prevalence of phenotypic and genotypic resistance to key antimicrobials in pig populations globally. There is a need to establish national surveillance programs and effective policies, particularly in certain world regions, to curtail the threat of evolution of resistant isolates in swine production that can potentially contribute to public health detrimentally.

Host Identity and Geographic Location Significantly Affect Gastrointestinal Microbial Richness and Diversity in Western Lowland Gorillas (Gorilla gorilla gorilla) under Human Care.

The last few decades have seen an outpouring of gastrointestinal (GI) microbiome studies across diverse host species. Studies have ranged from assessments of GI microbial richness and diversity to classification of novel microbial lineages. Assessments of the "normal" state of the GI microbiome composition across multiple host species has gained increasing importance for distinguishing healthy versus diseased states. This study aimed to determine baselines and trends over time to establish "typical" patterns of GI microbial richness and diversity, as well as inter-individual variation, in three populations of western lowland gorillas (Gorilla gorilla gorilla) under human care at three zoological institutions in North America. Fecal samples were collected from 19 western lowland gorillas every two weeks for seven months (n = 248). Host identity and host institution significantly affected GI microbiome community composition (p < 0.05), although host identity had the most consistent and significant effect on richness (p = 0.03) and Shannon diversity (p = 0.004) across institutions. Significant changes in microbial abundance over time were observed only at Denver Zoo (p < 0.05). Our results suggest that individuality contributes to most of the observed GI microbiome variation in the study populations. Our results also showed no significant changes in any individual's microbial richness or Shannon diversity during the 7-month study period. While some microbial taxa (Prevotella, Prevotellaceae and Ruminococcaceae) were detected in all gorillas at varying levels, determining individual baselines for microbial composition comparisons may be the most useful diagnostic tool for optimizing non-human primate health under human care.

Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States.

Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). blaCMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), blaCTX-M (carried by IncF, IncHI2, and IncN plasmids), and blaSHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb'-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health.IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.

Prevalence and trend analysis of antimicrobial resistance in clinical Escherichia coli isolates collected from diseased pigs in the USA between 2006 and 2016.

Antimicrobial resistance (AMR) is an emerging threat to both human and animal health. Antimicrobial use and resistance in food animal production, including swine, has received increased scrutiny as a source of resistant foodborne pathogens. Continuous surveillance of AMR in bacterial isolates of swine origin can guide in conservation of antimicrobials used in both human and swine medicine. The objective of this study was to evaluate the prevalence and trends of the phenotypic AMR in Escherichia coli of swine origin isolated from clinical samples at the Minnesota Veterinary Diagnostic laboratory between 2006 and 2016. The prevalence of resistance to ampicillin, tetracyclines and sulphadimethoxine remained greater than 50% throughout the period. There was a drastic change in enrofloxacin resistance, increasing from less than 1% to more than 20% between 2006 and 2016 (annual relative increase of 57% between 2006 and 2013 and 16% between 2013 and 2016). The prevalence of resistance to other antimicrobials remained constant (ceftiofur, oxytetracycline and chlortetracycline) or changed significantly (annual relative changes of less than 10%) for at least some time-period between 2006 and 2016 (ampicillin, florfenicol, gentamicin, neomycin, sulphadimethoxine, trimethoprim-sulphamethoxazole and spectinomycin). Rarefaction analysis revealed an increase in the number of unique combinations of AMRs per year. Network analysis was performed by estimating and plotting partial correlations between minimum inhibitory concentrations (MICs) of various antimicrobials. An increase in strength of these networks was observed, particularly in networks created after 2010, which can be indicative of increased multiple AMR in these isolates. These results provide valuable insight into the trends in AMR in E. coli of swine origin in the USA and act as supplementary information to the existing active AMR surveillance systems.

Prevalence and time trend analysis of antimicrobial resistance in respiratory bacterial pathogens collected from diseased pigs in USA between 2006-2016.

Swine respiratory disease complex (SRDC) causes massive economic losses to the swine industry and is a major animal welfare concern. Antimicrobials are mainstay in treatment and control of SRDC. However, there is a lack of data on the prevalence and trends in resistance to antimicrobials in bacterial pathogens associated with SRDC. The objective of this study was to estimate the prevalence and changes in resistance to 13 antimicrobials in swine bacterial pathogens (Streptococcus suis, Pasteurella multocida, Actinobacillus suis and Haemophilus parasuis) in the U.S.A using data collected at University of Minnesota Veterinary Diagnostic Laboratory between 2006 and 2016. For antimicrobials for which breakpoints were available, prevalence of resistance remained below 10% except for tetracycline in S. suis and P. multocida isolates, and these prevalence estimates remained consistently low over the years despite statistical significance (p < .05) in trend analysis. For antimicrobial-bacterial combinations without available breakpoints, the odds of isolates being resistant increased by >10% annually for 7 and 1 antimicrobials in H. parasuis and S. suis isolates respectively, and decreased >10% annually for 4 and 1 antimicrobials in A. suis and H. parasuis isolates, respectively, according to the ordinal regression models. Clinical implications of changes in AMR for A. suis and H. parasuis should be interpreted cautiously due to the lack of interpretive criteria and challenges in antimicrobial susceptibility tests in the case of H. parasuis. Future studies should focus on surveillance of antimicrobial resistance and establishment of standardized susceptibility testing methodologies and interpretive criteria for these animal pathogens of critical importance.

Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States.

Nontyphoidal Salmonella enterica (NTS) poses a major public health risk worldwide that is amplified by the existence of antimicrobial-resistant strains, especially those resistant to quinolones and extended-spectrum cephalosporins (ESC). Little is known on the dissemination of plasmids harboring the acquired genetic determinants that confer resistance to these antimicrobials across NTS serotypes from livestock in the United States. NTS isolates (n = 183) from U.S. swine clinical cases retrieved during 2014 to 2016 were selected for sequencing based on their phenotypic resistance to enrofloxacin (quinolone) or ceftiofur (3rd-generation cephalosporin). De novo assemblies were used to identify chromosomal mutations and acquired antimicrobial resistance genes (AARGs). In addition, plasmids harboring AARGs were identified using short-read assemblies and characterized using a multistep approach that was validated by long-read sequencing. AARGs to quinolones [qnrB15, qnrB19, qnrB2, qnrD, qnrS1, qnrS2, and aac(6')Ib-cr] and ESC (blaCMY-2, blaCTX-M-1, blaCTX-M-27, and blaSHV-12) were distributed across serotypes and were harbored by several plasmids. In addition, chromosomal mutations associated with resistance to quinolones were identified in the target enzyme and efflux pump regulation genes. The predominant plasmid harboring the prevalent qnrB19 gene was distributed across serotypes. It was identical to a plasmid previously reported in S. enterica serovar Anatum from swine in the United States (GenBank accession number KY991369.1) and similar to Escherichia coli plasmids from humans in South America (GenBank accession numbers GQ374157.1 and JN979787.1). Our findings suggest that plasmids harboring AARGs encoding mechanisms of resistance to critically important antimicrobials are present in multiple NTS serotypes circulating in swine in the United States and can contribute to resistance expansion through horizontal transmission.

Characterization of Campylobacter jejuni, Campylobacter upsaliensis, and a novel Campylobacter sp. in a captive non-human primate zoological collection.

BACKGROUND: The aim of this study was to longitudinally investigate the prevalence and characterization of Campylobacter spp. from non-human primates primate (NHP) with a history of endemic diarrhea housed at Como Park Zoo. METHODS: Fecal samples from 33 symptom-free NHP belonging to eight different species were collected weekly for 9 weeks. Species-level characterization and phylogenetic analysis of isolates included biochemical testing and 16S rRNA sequencing. RESULTS: Campylobacter spp. were isolated from the feces of 42% (14/33) of the primates. Three Campylobacter spp. (C upsaliensis, C jejuni, and novel Campylobacter sp.) were identified from three NHP species. A possible positive host Campylobacter species-specificity was observed. However, no statistical association was observed between the isolation of Campylobacter spp. and age and sex of the animal. CONCLUSIONS: The study revealed the value of conducting repeated fecal sampling to establish the overall prevalence of Campylobacter in zoo-maintained NHP; it also importantly identifies a novel Campylobacter sp. isolated from white-faced saki monkeys.

The Possible Influence of Non-synonymous Point Mutations within the FimA Adhesin of Non-typhoidal Salmonella (NTS) Isolates in the Process of Host Adaptation.

Non-typhoidal Salmonella (NTS) remains a global pathogen that affects a wide range of animal species. We analyzed a large number of NTS isolates of different host origins, including Salmonella Heidelberg (n = 80, avian), S. Dublin (50, bovine), S. Typhimurium var 5- (n = 40, porcine), S. 4,5,12,:i:- (n = 40, porcine), S. Cerro (n = 16, bovine), and S. Montevideo (n = 14, bovine), using virulence profiling of the bcfC, mgtC, ssaC, invE, pefA, stn, sopB, and siiE virulence-associated genes, a biofilm production assay, pulsed field gel electrophoresis, and the full-length sequencing of the fimA (adhesin) and iroN (receptor) genes. We determined a key amino acid substitution, A169 (i.e., threonine changed to alanine at position 169), in the FimA protein that changed ligand affinity of FimA toward N-acetyl-D-glucosamine. This finding clearly indicates the important role of non-synonymous single nucleotide polymorphism (nsSNPs) in adhesin functionality that may impact the host tropism of NTS. This nsSNP was found in S. Heidelberg and S. Cerro isolates. Although this was not the case for the IroN receptor, the phylogeny of this receptor and different host origins of NTS isolates were positively correlated, suggesting existence of specific host immune selective pressures on this unique receptor in S. enterica. We found that pefA, a gene encoding major fimbrial subunit, was the most-segregative virulence factor. It was associated with S. Heidelberg, S. Typhimurium var 5- and S. 4,5,12,:i:- but not with the rest of NTS strains. Further, we observed a significantly higher frequency of non-biofilm producers among NTS strains that do not carry pefA (42.5%) compared to S. Heidelberg (2.5%) and S. Typhimurium var 5- (7.5%) and S. 4,5,12,:i:- (0%). This study provides new insights into the host adaptation of avian and mammalian NTS isolates that are based on the bacterial antigens FimA and IroN as well as the interrelationships between host adaptation, overall genetic relatedness, and virulence potential in these NTS isolates.

The Prevalence of Extended-Spectrum Beta-Lactamase-Producing Multidrug-Resistant Escherichia Coli in Poultry Chickens and Variation According to Farming Practices in Punjab, India.

BACKGROUND: Agricultural use of antimicrobials in subtherapeutic concentrations is increasing in response to the rising demand for food animal products worldwide. In India, the use of antimicrobials in food animal production is unregulated. Research suggests that many clinically important antimicrobials are used indiscriminately. This is the largest study to date in India that surveys poultry production to test for antimicrobial resistance and the occurrence of extended-spectrum ß-lactamases (ESBLs) modulated by farming and managerial practices. OBJECTIVES: Our goal was to survey poultry production for resistance to eleven clinically relevant antimicrobials and phenotypic occurrence of ESBLs as modulated by farming and managerial practices. METHODS: Eighteen poultry farms from Punjab were surveyed, and 1,556 Escherichia coli isolates from 530 birds were tested for susceptibility to 11 antimicrobials using the disk diffusion method and validated using VITEK 2 (bioMérieux, Marcy-L'Étoile, France). Samples from 510 of these birds were phenotypically tested for ESBL production using the combination disk method and confirmed using VITEK 2. Generalized linear mixed models were used to infer differences in resistance profiles associated with different farming practices and facility types. RESULTS: Resistance profiles were significantly different between broiler and layer farms. Broiler farms were 2.2 [ampicillin (AMP), p=0.017] to 23 [nalidixic acid (NX), p<0.001] times more likely to harbor resistant E. coli strains than layer farms. Adjusting for farm type (broiler vs. layer), the odds of resistance (although not statistically significant) to all antimicrobials except nitrofurantoin (NIT) were higher in independent facilities (IUs) as compared to contracted facilities (CFs). Increased prevalence of multidrug resistance (MDR; 94% compared to 60% in layers), including prevalence of ESBL-producing strains (87% compared to 42% in layers), was observed in broiler farms. CONCLUSIONS: Our findings suggest that unregulated use of clinically relevant antimicrobials in Indian broiler and layer farms may contribute to the emergence of resistance and support the need to curb the nontherapeutic use of medically important antimicrobials in food animal production. https://doi.org/10.1289/EHP292.

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment.

Gut health is paramount for commercial poultry production, and improved methods to assess gut health are critically needed to better understand how the avian gastrointestinal tract matures over time. One important aspect of gut health is the totality of bacterial populations inhabiting different sites of the avian gastrointestinal tract, and associations of these populations with the poultry farm environment, since these bacteria are thought to drive metabolism and prime the developing host immune system. In this study, a single flock of commercial turkeys was followed over the course of 12 weeks to examine bacterial microbiome inhabiting the ceca, ileum, and corresponding poultry litter. Furthermore, the effects of low-dose, growth-promoting penicillin treatment (50 g/ton) in feed on the ileum bacterial microbiome were also examined during the early brood period. The cecum and ileum bacterial communities of turkeys were distinct, yet shifted in parallel to one another over time during bird maturation. Corresponding poultry litter was also distinct yet more closely represented the ileal bacterial populations than cecal bacterial populations, and also changed parallel to ileum bacterial populations over time. Penicillin applied at low dose in feed significantly enhanced early weight gain in commercial poults, and this correlated with predictable shifts in the ileum bacterial populations in control versus treatment groups. Overall, this study identified the dynamics of the turkey gastrointestinal microbiome during development, correlations between bacterial populations in the gastrointestinal tract and the litter environment, and the impact of low-dose penicillin on modulation of bacterial communities in the ileum. Such modulations provide a target for alternatives to low-dose antibiotics.