Development of the Tonsil Microbiome in Pigs and Effects of Stress on the Microbiome.

Tonsils, lympho-epithelial tissues located at the junction of the oropharynx and nasopharynx, play a key role in surveillance, colonization, and persistence of inhaled and ingested pathogens. In pigs, the tonsils are a reservoir for numerous bacteria and viruses, including host-specific pathogens and potential zoonotic pathogens as well as commensal organisms. However, there are no in depth studies of the development of the tonsillar microbiome in pigs, or any mammal, over time. The goal of this study was to follow the development of the tonsil microbiome in healthy pigs from birth to market weight. Samples were collected using tonsil brushes from 16 piglets (4 each from 4 sows) at newborn, 1, 2, 3, and 4 weeks of age, and from 8 of those piglets at 6, 8, 10, 12, 16, and 19 weeks of age. Bacterial DNA was isolated from each sample and 16S rDNA genes were amplified and sequenced. Sequence analysis showed that members of the Streptococcaceae, Pasteurellaceae, and Moraxellaceae were present at all time points and represent the three most abundant families identified. Other community members appeared transiently or increased or decreased significantly with disruption events or stress. We observed four significant shifts in the tonsil community that coincided with well-defined disruption events: weaning plus addition of Carbadox plus movement to the nursery at week 3, removal of Carbadox and addition of Tylan at week 5, removal of Tylan and habitat change at week 9, and habitat change at week 16. Weaning triggered a bloom of Streptococcaeae and decrease of Moraxellaceae. The shift from Carbadox to Tylan led to reduction in Proteobacteria and Streptococcaceae but an increase in other Firmicutes, accompanied by a dramatic increase in community richness. Cessation of Tylan coincided with a return to a less rich community, and a bloom in Clostridiales. The final shift in habitat was accompanied by a decrease in Clostridiales and increase in Proteobacteria. The tonsillar microbiome of older pigs resembled the previously described mature core tonsillar microbiome. This study demonstrates a temporal succession in the development of the pig tonsillar microbiome, and significant community shifts that correlate with disruption events.

Prevalence and characteristics of Shiga toxin-producing Escherichia coli in finishing pigs: Implications on public health.

Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens, which can cause serious illnesses, including hemorrhagic colitis and hemolytic uremic syndrome. To study the epidemiology of STEC in finishing pigs and examine the potential risks they pose for human STEC infections, we conducted a longitudinal cohort study in three finishing sites. Six cohorts of pigs (2 cohorts/site, 20 pigs/cohort) were randomly selected, and fecal samples (n=898) were collected every two weeks through their finishing period. Eighty-two pigs (68.3%) shed STEC at least once, and the proportion of STEC-positive pigs varied across sites (50-97.5%) and cohorts (15-100%). Clinically important serotypes, O157:H7 (stx2c, eae) and O26:H11 (stx1a, eae), were recovered from two pigs at sites C and A, respectively. The most common serotype isolated was O59:H21 (stx2e), which was particularly prevalent in site B as it was recovered from all STEC positive pigs (n=39). Each cohort showed different patterns of STEC shedding, which were associated with the prevalent serotype. The median shedding duration of STEC in pigs was 28days, consistent with our prior study. However, among pigs shedding O59:H21 at least once, pigs in cohort B2 had a significantly longer shedding duration of 42days (P<0.05) compared to other cohorts. Stx2e was the most commonly observed stx variant in finishing pigs (93.9%), in accordance with the previous studies. Stx2e has been reported to be significantly associated with edema disease in pigs, however, the pathogenicity in humans warrants further investigations. Nonetheless, our findings affirm that pigs are an important reservoir for human STEC infections, and that the circulating serotypes in a cohort and site management factors may significantly affect the prevalence of STEC. Molecular characterization of STEC isolates and epidemiological studies to identify risk factors for shedding in pigs are strongly warranted to further address the significance to public health and to develop mitigation strategies.

Genome Sequences of 34 Shiga Toxin-Producing Escherichia coli Isolates from Swine and Other Sources.

Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne pathogens that can be carried by various animals. The swine STEC population is partially composed of host-specific strains that are often not well characterized. In this work, the genome sequences of a number of swine STEC strains are presented.

Intestinal Microbial Community Dynamics of White-Tailed Deer (Odocoileus virginianus) in an Agroecosystem.

The intestinal microbiota has important functions that contribute to host health. The compositional dynamics of microbial communities are affected by many factors, including diet and presence of pathogens. In contrast to humans and domestic mammals, the composition and seasonal dynamics of intestinal microbiota of wildlife species remain comparatively understudied. White-tailed deer (Odocoileus virginianus) is an ecologically and economically important wildlife species that inhabits agricultural ecosystems and is known to be a reservoir of enteric pathogens. Nevertheless, there is a lack of knowledge of white-tailed deer intestinal microbiota diversity and taxonomic composition. This study's first objective was to characterize and compare the intestinal microbiota of 66 fecal samples from white-tailed deer collected during two sampling periods (March and June) using 16S rDNA pyrosequencing. Associations between community diversity and composition and factors including season, sex, host genetic relatedness, and spatial location were quantified. Results revealed that white-tailed deer intestinal microbiota was predominantly comprised of phyla Firmicutes and Proteobacteria, whose relative frequencies varied significantly between sampling periods. The second objective was to examine the associations between the presence of Escherichia coli and Salmonella, and microbiota composition and diversity. Results indicated that relative abundance of some microbial taxa varied when a pathogen was present. This study provides insights into microbial compositional dynamics of a wildlife species inhabiting coupled natural and agricultural landscapes. Data focus attention on the high prevalence of Proteobacteria particularly during the summer and highlight the need for future research regarding the role of white-tailed deer as a natural pathogen reservoir in agroecosystems.

Association between thermal environment and Salmonella in fecal samples from dairy cattle in midwestern United States.

The objective of this study was to describe the association between thermal measures in the barn environment (pen temperature and humidity) and fecal shedding of Salmonella in dairy cattle. A repeated cross-sectional study was conducted within a commercial dairy herd located in the midwestern United States. Five pooled fecal samples were collected monthly from each pen for 9 mo and submitted for microbiological culture. Negative binomial regression methods were used to test the association [incidence rate ratio (IRR)] between Salmonella pen status (the count of Salmonella-positive pools) and thermal environmental parameters [average temperature and temperature humidity index (THI)] for 3 time periods (48 h, 72 h, and 1 wk) before fecal sampling. Salmonella was cultured from 10.8% [39/360; 95% confidence interval (CI): 7.8% to 14.5%] of pooled samples. The highest proportion of positive pools occurred in August. The IRR ranged from 1.26 (95% CI: 1.15 to 1.39, THI 1 wk) to 4.5 (95% CI: 2.13 to 9.51, heat exposure 1 wk) across all thermal parameters and lag time periods measured. For example, the incidence rate of Salmonella-positive pools increased by 54% for every 5°C increment in average temperature (IRR = 1.54; 95% CI: 1.29 to 1.85) and 29% for every 5-unit increase in THI (IRR = 1.29; 95% CI: 1.16 to 1.42) during the 72 h before sampling. The incidence rate ratio for pens exposed to higher temperatures (> 25°C) was 4.5 times (95% CI: 2.13 to 9.51) the incidence rate ratio for pens exposed to temperatures < 25°C in the 72 h before sampling. Likewise, the incidence rate ratio for pens exposed to THI > 70 was 4.23 times greater (95% CI: 2.1 to 8.28) than when the THI was < 70 in the 72 h before sampling. An association was found between the thermal environment and Salmonella shedding in dairy cattle. Further research is warranted in order to fully understand the component risks associated with the summer season and increased Salmonella shedding.

L'objectif de cette étude est de décrire l'association entre les mesures thermiques de l'étable (température et humidité des enclos) et l'excrétion fécale de Salmonella chez les bovins laitiers. Une étude transversale répétée a été réalisée dans un troupeau laitier commercial situé dans la région du Midwest des États-Unis. 5 échantillons composites de fèces ont été récoltés de chaque stalle d'une manière mensuelle pendant neuf mois puis soumis pour culture microbiologique. Des méthodes de régression binomiale négative ont été utilisées pour tester l'association (ratio de taux d'incidence, IRR) entre la présence de Salmonella dans les enclos (nombre d'échantillons positifs à Salmonella) et les paramètres environnementaux [température moyenne, index humidité température (THI) pour 3 périodes (48 h, 72 h, 1 semaine)]. Salmonella a été cultivée de 10,8 % (39/360; I.C. 95 % 7,8 %­14,5 %) des échantillons composites. La plus grande proportion d'échantillons positifs ont été collectés durant le mois d'août. Le rapport des taux d'incidence (IRR) a varié de 1,26 (IIR = 1,26; I.C. à 95 % 1,15 à 1,39) à 4,5 (IRR = 4,5; I.C. à 95 % 2,13 à 9,51) pour tous les paramètres thermiques et les des périodes étudiés. Par exemple, l'augmentation d'échantillons Salmonella positifs est de 54 % par incrément de cinq °C de température moyenne (IRR = 1,54; I.C. à 95 % 1,29 à 1,85) et de 29 % pour chaque augmentation de cinq unités de THI (IRR = 1,29; IC à 95 % 1,16 à 1,42) dans les 72 heures avant l'échantillonnage. Le ratio de taux d'incidence pour les enclos exposés à de hautes temperatures (> 25 °C) était 4,5 fois (I.C. à 95 % 2,13 à 9,51) supérieur au ratio de taux d'incidence des enclos exposés à des temperatures < 25 °C. De même, Le ratio de taux d'incidence des enclos exposés à des THI > 70 est de 4,23 (I.C. à 95 % 2,16­8,28) superieur a ceux dont le THI est < 70 dans les 72 heures précédant l'échantionnage. Une association a été trouvée entre les mesures thermiques et l'excrétion de Salmonella chez les bovins laitiers. Plus de recherches sont requises pour comprendre entièrement les risques associés à la saison estivale et à l'excrétion de Salmonella.(Traduit par les autuers).

Factors Associated with Shiga Toxin-Producing Escherichia coli Shedding by Dairy and Beef Cattle.

UNLABELLED: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome. Cattle are the primary reservoir for STEC, and food or water contaminated with cattle feces is the most common source of infections in humans. Consequently, we conducted a cross-sectional study of 1,096 cattle in six dairy herds (n = 718 animals) and five beef herds (n = 378 animals) in the summers of 2011 and 2012 to identify epidemiological factors associated with shedding. Fecal samples were obtained from each animal and cultured for STEC. Multivariate analyses were performed to identify risk factors associated with STEC positivity. The prevalence of STEC was higher in beef cattle (21%) than dairy cattle (13%) (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.25, 2.47), with considerable variation occurring across herds (range, 6% to 54%). Dairy cattle were significantly more likely to shed STEC when the average temperature was >28.9°C 1 to 5 days prior to sampling (OR, 2.5; 95% CI, 1.25, 4.91), during their first lactation (OR, 1.8; 95% CI, 1.1, 2.8), and when they were <30 days in milk (OR, 3.9; 95% CI, 2.1, 7.2). These data suggest that the stress or the negative energy balance associated with lactation may result in increased STEC shedding frequencies in Michigan during the warm summer months. Future prevention strategies aimed at reducing stress during lactation or isolating high-risk animals could be implemented to reduce herd-level shedding levels and avoid transmission of STEC to susceptible animals and people. IMPORTANCE: STEC shedding frequencies vary considerably across cattle herds in Michigan, and the shedding frequency of strains belonging to non-O157 serotypes far exceeds the shedding frequency of O157 strains, which is congruent with human infections in the state. Dairy cattle sampled at higher temperatures, in their first lactation, and early in the milk production stage were significantly more likely to shed STEC, which could be due to stress or a negative energy balance. Future studies should focus on the isolation of high-risk animals to decrease herd shedding levels and the potential for contamination of the food supply.

Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine.

Salmonella enterica (nontyphoidal) is one of the major causes of foodborne diseases in the United States and worldwide. Molecular typing methods are significant tools used to better understand the transmission and ecology of Salmonella in order to implement pre-harvest control measures. The objectives of this study were to describe the Salmonella genotypes, the distribution of isolate subtypes from different ecological niches (i.e., barn environment, nursery, and individual pigs) and their evolution over time in a longitudinal study conducted in three finishing sites (housing pigs from 10 weeks of age until slaughter at 24-26 weeks of age). Among the 107 Salmonella isolates submitted for pulsed-field gel electrophoresis (PFGE) analysis, there were 25 distinct subtypes. PFGE genotyping results were consistent with the serotype findings. A large number of distinguishable PFGE patterns (i.e., within the same serovar) were observed and different combinations of subtypes were identified within and across sites and cohorts. New subtypes may result of the introduction of new strains, genetic changes, or ongoing transmission of evolved strains within the production system. The same subtypes were detected intermittently during the study period, which suggests the persistence of indistinguishable subtypes in this production system. In addition, this study suggests persistence of the same subtype over several cohorts of pigs and potential residual contamination from the barn. Factors affecting adaptation and transmission of Salmonella within and among ecological systems (e.g., finishing pigs, nursery, and environment) should be further investigated. Understanding genotypic diversity of Salmonella in different ecological niches during pre-harvest may contribute to the development of more targeted and cost effective control programs during nursery and finishing phases.

Recommendations for the role of social science research in One Health.

The social environment has changed rapidly as technology has facilitated communication among individuals and groups in ways not imagined 20 years ago. Communication technology increasingly plays a role in decision-making about health and environmental behaviors and is being leveraged to influence that process. But at its root is the fundamental need to understand human cognition, communication, and behavior. The concept of 'One Health' has emerged as a framework for interdisciplinary work that cuts across human, animal, and ecosystem health in recognition of their interdependence and the value of an integrated perspective. Yet, the science of communication, information studies, social psychology, and other social sciences have remained marginalized in this emergence. Based on an interdisciplinary collaboration, this paper reports on a nascent conceptual framework for the role of social science in 'One Health' issues and identifies a series of recommendations for research directions that bear additional scrutiny and development.

Organic or antibiotic-free labeling does not impact the recovery of enteric pathogens and antimicrobial-resistant Escherichia coli from fresh retail chicken.

We investigated the implied health benefits of retail chicken breast labeled as "organic" or "antibiotic-free" when compared to conventional products based on frequency of contamination by Salmonella spp., Campylobacter spp., and coliform bacteria resistant to fluoroquinolones, extended-spectrum cephalosporins, or carbapenems. We purchased 231 prepackaged chicken breasts from 99 grocery stores representing 17 retail chains in Ohio, Michigan, and Pennsylvania from June to September 2012. Ninety-six (41.5%) packages were labeled "antibiotic free" and 40 (17.3%) were labeled "organic," with the remaining 95 (41.1%) making neither label claim. Salmonella were recovered from 56 (24.2%) packages, and the recovery rate was not different between product types. Five percent of packages contained Salmonella carrying the extended-spectrum cephalosporin resistance gene bla(CMY-2), representing 21.4% of Salmonella isolates. Campylobacter spp. were recovered from 10.8% of packages, with observed recovery rates similar for the three product types. Using selective media, we recovered Escherichia coli harboring bla(CMY-2) from over half (53.7%) of packages, with similar recovery rates for all product types. In addition, we recovered E. coli carrying bla(CTX-M) from 6.9% of packages, and E. coli with QRDR mutations from 8.2% of packages. Fluoroquinolone-resistant E. coli recovered using selective media were more common (p<0.05) in conventional (18.9%) compared to organic (0) and antibiotic-free (2.1%) packages. Our results indicate that, regardless of product type, fresh retail chicken breast is commonly contaminated with enteric pathogens associated with foodborne illness and commensal bacteria harboring genes conferring resistance to critically important antimicrobial drugs.

Diverse virulence gene content of Shiga toxin-producing Escherichia coli from finishing swine.

Shiga toxin-producing Escherichia coli (STEC) infections are a critical public health concern because they can cause severe clinical outcomes, such as hemolytic uremic syndrome, in humans. Determining the presence or absence of virulence genes is essential in assessing the potential pathogenicity of STEC strains. Currently, there is limited information about the virulence genes carried by swine STEC strains; therefore, this study was conducted to examine the presence and absence of 69 virulence genes in STEC strains recovered previously from finishing swine in a longitudinal study. A subset of STEC strains was analyzed by pulsed-field gel electrophoresis (PFGE) to examine their genetic relatedness. Swine STEC strains (n = 150) were analyzed by the use of a high-throughput real-time PCR array system, which included 69 virulence gene targets. Three major pathotypes consisted of 16 different combinations of virulence gene profiles, and serotypes were determined in the swine STEC strains. The majority of the swine STEC strains (n = 120) belonged to serotype O59:H21 and carried the same virulence gene profile, which consisted of 9 virulence genes: stx2e, iha, ecs1763, lpfAO113, estIa (STa), ehaA, paa, terE, and ureD. The eae, nleF, and nleH1-2 genes were detected in one swine STEC strain (O49:H21). Other genes encoding adhesins, including iha, were identified (n = 149). The PFGE results demonstrated that swine STEC strains from pigs raised in the same finishing barn were closely related. Our results revealed diverse virulence gene contents among the members of the swine STEC population and enhance understanding of the dynamics of transmission of STEC strains among pigs housed in the same barn.

Shiga toxin-producing Escherichia coli in swine: the public health perspective.

Shiga toxin-producing Escherichia coli (STEC) strains are food-borne pathogens that are an important public health concern. STEC infection is associated with severe clinical diseases in human beings, including hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS), which can lead to kidney failure and death. Cattle are the most important STEC reservoir. However, a number of STEC outbreaks and HUS cases have been attributed to pork products. In swine, STEC strains are known to be associated with edema disease. Nevertheless, the relationship between STEC of swine origin and human illness has yet to be determined. This review critically summarizes epidemiologic and biological studies of swine STEC. Several epidemiologic studies conducted in multiple regions of the world have demonstrated that domestic swine can carry and shed STEC. Moreover, animal studies have demonstrated that swine are susceptible to STEC O157:H7 infection and can shed the bacterium for 2 months. A limited number of molecular epidemiologic studies, however, have provided conflicting evidence regarding the relationship between swine STEC and human illness. The role that swine play in STEC transmission to people and the contribution to human disease frequency requires further evaluation.

Enumeration of salmonella in feces of naturally infected pigs.

Quantification of Salmonella in asymptomatic pigs can be used to institute control measures and to assess risk of carcass contamination during slaughter. The objective of this study was to quantify the fecal concentration of Salmonella in naturally infected pigs. Individual fecal samples (positive [n=443], negative [n=1225] determined by microbiological culture) were submitted for direct quantitative real-time polymerase chain reaction (q-PCR). Direct q-PCR categorized 99.6% (1220/1225) of culture negative samples as negative. For culture positive samples, 15.4% (68/443) were detected by q-PCR, but only 3.4% (15/443) were within the direct q-PCR quantifiable range (≥ 10(3) colony-forming units [CFU]/g of feces). Of these latter samples, the concentration range was 1.06 × 10(3) to 1.73 × 10(6) CFU/g feces. Of the 15 samples with high Salmonella concentrations, seven were collected from one pig and three samples were collected from its penmates. Direct q-PCR may be an alternative to traditional culture-dependent methods for detection of pigs with high fecal concentrations of Salmonella, but not for detection of pigs shedding low concentrations of Salmonella, which represented the majority of pigs in this study. When high shedding was detected it was clustered within a single pig and its penmates. These data contribute to quantitative risk assessments of the association between concentrations of Salmonella shed by pigs during the finishing phase and risk of carcass contamination at slaughter.

Scoping review on search queries and social media for disease surveillance: a chronology of innovation.

BACKGROUND: The threat of a global pandemic posed by outbreaks of influenza H5N1 (1997) and Severe Acute Respiratory Syndrome (SARS, 2002), both diseases of zoonotic origin, provoked interest in improving early warning systems and reinforced the need for combining data from different sources. It led to the use of search query data from search engines such as Google and Yahoo! as an indicator of when and where influenza was occurring. This methodology has subsequently been extended to other diseases and has led to experimentation with new types of social media for disease surveillance. OBJECTIVE: The objective of this scoping review was to formally assess the current state of knowledge regarding the use of search queries and social media for disease surveillance in order to inform future work on early detection and more effective mitigation of the effects of foodborne illness. METHODS: Structured scoping review methods were used to identify, characterize, and evaluate all published primary research, expert review, and commentary articles regarding the use of social media in surveillance of infectious diseases from 2002-2011. RESULTS: Thirty-two primary research articles and 19 reviews and case studies were identified as relevant. Most relevant citations were peer-reviewed journal articles (29/32, 91%) published in 2010-11 (28/32, 88%) and reported use of a Google program for surveillance of influenza. Only four primary research articles investigated social media in the context of foodborne disease or gastroenteritis. Most authors (21/32 articles, 66%) reported that social media-based surveillance had comparable performance when compared to an existing surveillance program. The most commonly reported strengths of social media surveillance programs included their effectiveness (21/32, 66%) and rapid detection of disease (21/32, 66%). The most commonly reported weaknesses were the potential for false positive (16/32, 50%) and false negative (11/32, 34%) results. Most authors (24/32, 75%) recommended that social media programs should primarily be used to support existing surveillance programs. CONCLUSIONS: The use of search queries and social media for disease surveillance are relatively recent phenomena (first reported in 2006). Both the tools themselves and the methodologies for exploiting them are evolving over time. While their accuracy, speed, and cost compare favorably with existing surveillance systems, the primary challenge is to refine the data signal by reducing surrounding noise. Further developments in digital disease surveillance have the potential to improve sensitivity and specificity, passively through advances in machine learning and actively through engagement of users. Adoption, even as supporting systems for existing surveillance, will entail a high level of familiarity with the tools and collaboration across jurisdictions.

Prevalence of Yersinia enterocolitica in antimicrobial-free and conventional antimicrobial use swine production.

Swine are the primary reservoir for foodborne illness associated with Yersinia enterocolitica. The use of antimicrobials in animal agriculture has been hypothesized as having a potential role in the increase in prevalence of zoonotic pathogens. The objective of this study was to compare the frequency of Y. enterocolitica fecal shedding in swine reared on farms with conventional antimicrobial use policies to farms that were antimicrobial free (ABF). Swine farms were selected from three regions in the United States. In each region, farms were categorized based on antimicrobial use policy. Fecal samples were collected from pigs on-farm within 48 h of harvest. The overall proportion of Y. enterocolitica and ail-harboring Y. enterocolitica-positive pigs was 10.9% and 4.0%, respectively. There were increased odds (odds ratio [OR] 6.8, 95% confidence interval [CI] 3.46-13.28) for a pig to be Y. enterocolitica positive if it was reared on an ABF farm as compared to a conventional farm. There was no significant association between farm antimicrobial use policy and isolation of an ail-harboring Y. enterocolitica from an individual pig (OR 1.8, 95% CI 0.90-3.61). The association of antimicrobial use policy with Y. enterocolitica shedding in feces should be interpreted cautiously, as antimicrobial use cannot be separated from other management factors (e.g., confinement or outdoor housing), which may be associated with risk of Y. enterocolitica in swine.

Yersinia enterocolitica of porcine origin: carriage of virulence genes and genotypic diversity.

Yersinia enterocolitica is an important foodborne pathogen, and pigs are recognized as a major reservoir and potential source of pathogenic strains to humans. A total of 172 Y. enterocolitica recovered from conventional and antimicrobial-free pig production systems from different geographic regions (North Carolina, Ohio, Michigan, Wisconsin, and Iowa) were investigated to determine their pathogenic significance to humans. Phenotypic and genotypic diversity of the isolates was assessed using antibiogram, serogrouping, and amplified fragment length polymorphism (AFLP). Carriage of chromosomal and plasmid-borne virulence genes were investigated using polymerase chain reaction. A total of 12 antimicrobial resistance patterns were identified. More than two-thirds (67.4%) of Y. enterocolitica were pan-susceptible, and 27.9% were resistant against ß-lactams. The most predominant serogroup was O:3 (43%), followed by O:5 (25.6%) and O:9 (4.1%). Twenty-two of 172 (12.8%) isolates were found to carry Yersinia adhesion A (yadA), a virulence gene encoded on the Yersinia virulence plasmid. Sixty-nine (40.1%) isolates were found to carry ail gene. The ystA and ystB genes were detected in 77% and 26.2% of the strains, respectively. AFLP genotyping of isolates showed wide genotypic diversity and were grouped into nine clades with an overall genotypic similarity of 66.8-99.3%. AFLP analysis revealed that isolates from the same production system showed clonal relatedness, while more than one genotype of Y. enterocolitica circulates within a farm.

Escherichia coli and Klebsiella pneumoniae producing CTX-M cephalosporinase from swine finishing barns and their association with antimicrobial use.

We report the recovery of Escherichia coli or Klebsiella pneumoniae containing the extended-spectrum ß-lactamase gene bla(CTX-M) from 24 of 1,495 (1.6%) swine fecal samples in 8 of 50 (16%) finishing barns located in 5 U.S. states. We did not detect an association between antimicrobial use and recovery of bla(CTX-M).

Antimicrobial susceptibility, pulsed-field gel electrophoresis, and multi-locus sequence typing of Campylobacter coli in swine before, during, and after the slaughter process.

The objective of this study was to determine persistence of clonal strains from farm to retail by assessing the clonal relatedness of Campylobacter coli isolated on farm, peri-harvest, and at processing from 11 individually identified pigs. Phenotypic (antimicrobial susceptibility) and genotypic (pulsed field gel electrophoresis [PFGE] and multi-locus sequence typing [MLST]) characterization of isolates was conducted. There was high genetic diversity of Campylobacter isolates from on-farm fecal samples. Campylobacter isolates from farm, post-evisceration, hide, and carcass samples showed similar phenotypes and belonged to the same genotypic clusters based on PFGE and sequence types (STs) based on MLST. Five STs that have not been previously reported were identified (ST-4083, ST-4084, ST-4085, ST-4086, ST-4087). Despite high genotypic diversity of C. coli on farm, retail meat products were consistently contaminated with isolates of the same STs, particularly ST854 and ST1056, as isolates collected from previous stages confirming persistence of strains from pre- to post-harvest.

Quantification of Campylobacter and Salmonella in cattle before, during, and after the slaughter process.

Salmonella and Campylobacter cause a significant number of human illnesses globally, most of which are food related. Cattle can be asymptomatic carriers of both of these pathogens. The objective of this study was to determine the association between the concentration of Salmonella and Campylobacter pre- and postharvest in cattle. Samples were collected from each of 98 individually identified cattle during the periharvest and postharvest period. For each animal, four different phases were sampled: on farm (fecal sample), poststunning and exsanguination (hide sponge and rectal content sample [lairage]), prechilling (carcass sponge), and final product (ground meat). Salmonella and Campylobacter were cultured and quantified at each stage by using the direct dilution and most probable number (MPN) method. Salmonella was not isolated from any sample. The proportion (%) of samples that were Campylobacter positive was 77, 82, 97, 55, and 12 for farm, rectal content, hide, carcass, and meat samples respectively. The mean Campylobacter concentration for each sample was as follows: fecal sample from farm, 3.7×10(4) cfu/g; rectal content sample from lairage, 1.6×10(5) cfu/g; hide sponge, 0.9 cfu/cm(2); carcass sponge, 8.7 cfu/half carcass; and meat, 1.1 cfu/g. There were no associations between Campylobacter concentrations for any two sample types. This lack of association could indicate that there is an environmental reservoir that can contaminate the final meat product, or since the majority of animals were positive entering the slaughter process, that the process itself reduces the load of Campylobacter regardless of the initial concentration. In addition, contamination of beef may be more strongly associated with periharvest practices than animal carriage rates.

Ceftiofur use in finishing swine barns and the recovery of fecal Escherichia coli or Salmonella spp. resistant to ceftriaxone.

The objective of this study was to investigate the association between ceftiofur use policy in finishing swine barns and recovery of fecal Escherichia coli or Salmonella spp. resistant to ceftriaxone. The study population included 54 finishing swine barns from three companies located in North Carolina. The barns were each classified according to their reported therapeutic ceftiofur use rates of "Rare," "Moderate," and "Common." Fecal samples from the barns were cultured for the presence of E. coli and Salmonella spp. resistant to ceftriaxone using selective media designed to recover rare organisms expressing the AmpC ß-lactamase phenotype. A total of 1899 swine fecal samples yielded 1193 E. coli (63%) resistant to ceftriaxone. Recovery rates by ceftiofur use classification were 45% for Rare, 73% for Moderate, and 68% Common ceftiofur use groups. Barns reporting Rare ceftiofur use had a lower odds of recovery of E. coli (OR=0.32; p<0.001) resistant to ceftriaxone compared to Common use barns. The overall Salmonella spp. prevalence was 63.8% (n=714). Of these, 65 Salmonella were resistant to ceftriaxone with the highest rate (6%) found in the Common ceftiofur use group, followed by Rare (4.1%) and Moderate (0.15%). The odds of recovery of Salmonella resistant to ceftriaxone were similar for barns with ceftiofur use classified as Rare and Common. Samples from barns with ceftiofur use classified as Moderate had a lower odds (OR=0.02; p<0.01) of recovery of Salmonella resistant to ceftriaxone than barns classified as Common. Our result is consistent with the hypothesis that the use of ceftiofur in finishing swine barns, beyond its rare application, may influence the recovery of enteric E. coli with resistance to cephalosporin drugs, although other unmeasured factors appear to be important in the recovery of cephalosporin-resistant Salmonella. The dissemination of enteric bacteria with resistance to cephalosporins has the potential to impact both veterinary and human therapeutic treatment options.