Risk factors associated with Salmonella prevalence, its antibiotic resistance, and egg antibiotic residues in the layer farming environment

Background and Aim:

Human salmonellosis with non-typhoidal Salmonella remains a global public health concern related to the consumption of contaminated eggs and egg-based products. This study aimed to examine the prevalence of Salmonella, antimicrobial-resistant Salmonella, and egg antibiotic residues concerning risk factors associated with Salmonella contamination in eggs, the layer farming environment, and laying hens kept in battery-cage closed-housing systems.

Materials and Methods:

This study used a repeated cross-sectional design to collect 488 samples from eggs, laying hens, and the farm environment on one laying farm for Salmonella detection according to ISO 6579:2002/AMD 1:2007. Salmonella-positive samples were further tested for serotype and antimicrobial susceptibility using the disk diffusion test. The layer farm contact person was interviewed at the sampling time to evaluate the risk factors associated with Salmonella contamination using logistic regression analysis. For each month, 24 eggs (144 eggs in total) were also randomly sampled from the collection egg area at the farm for antibiotic residue detection using the European Four Plate Test.

Results:

The highest Salmonella prevalence rates were in the samples from the layer pen floors, followed by the egg sizing machine (ESM) and eggshells at 65.5%, 52.5%, and 15%, respectively. Salmonellaenterica serovar Corvallis was the dominant serovar (48.38%), followed by Mbandaka (37.76%), Braenderup (14.29%), and Typhimurium (4.08%). Rodent presence at the farm and the frequency of changing the disinfectant foot dip were significant factors related to Salmonella contamination on the pen floors (odds ratio [OR]=22.5, 95% confidence interval [CI]=2.11-240.48, p=0.01; OR=24, 95% CI=2.78-206.96, p=0.004, respectively). Hand-washing before sorting and cleaning the ESM were the significant factors (OR=13, 95% CI=1.2-140.73, p=0.04). The most resistant Salmonella isolates were resistant to oxytetracycline. One isolate of S. enterica Typhimurium was resistant to cefotaxime, enrofloxacin, and oxytetracycline. The antibiotic residues in the egg yolks were streptomycin, enrofloxacin, and tetracycline at prevalence rates of 36.11%, 11.81%, and 7.64%, respectively. Streptomycin was the most abundant residue in the albumen and yolk, followed by tetracycline.

Conclusion:

Salmonella prevalence in layer farming with a closed-housing system is related to effective biosecurity and hygiene issues, such as rodent control, clean farm equipment, and good worker hygiene. In addition, eggs’ antibiotic residues may be related to treating antimicrobial-resistant Salmonella isolates and medicated feed with inappropriate antibiotic withdrawal time.

Salmonella and Escherichia coli Prevalence in Meat and Produce Sold at Farmers' Markets in Northern California

ABSTRACT

As the number of farmers' markets and other direct-to-consumer marketing channels increases, it is crucial to understand the potential risks associated with consuming directly marketed animal products and fresh produce. The overall aim of this project was to assess the prevalence of Salmonella and Escherichia coli in animal products and produce sold at farmers' markets in Northern California and to evaluate the food safety risks associated with consuming meat (e.g., beef, pork, and poultry) and fresh produce purchased from farmers' markets. Animal products and produce were purchased from a total of 44 certified farmers' markets in Northern California. Salmonella was found in 6 (1.8%) of 338 animal products and in 0 (0%) of 128 produce samples; E. coli was found in 40 (31.3%) of 128 fresh produce samples. E. coli concentration in produce ranged from 0 to 2.96, with an overall average of 0.13 log (most probable number + 1)/100 mL. Salmonella isolates were resistant to nalidixic acid and tetracycline. The results from this study highlight the need for further training on mitigation strategies to reduce contamination of animal products and fresh produce by foodborne pathogens.

HIGHLIGHTS

Self-made Salmonella Pullorum agglutination antigen development and its potential practical application

Pullorum disease caused by Salmonella Pullorum is one of the most important infectious diseases in the poultry industry worldwide, which leads to serious economic losses in many developing countries because of its high mortality rate in young chicks. The traditional slide agglutination test with low cost, fast reaction, and on-site detection has been widely used in the diagnosis of Pullorum disease. However, in practice, the test performance is with the disadvantages of false positive results and unstable detection results. In this paper, we developed self-made agglutination antigens prepared by local isolates in the poultry farm and compare the detection performance with commercial agglutination antigens (China Institute of Veterinary Drug Control) and Group D Salmonella ELISA kit (BioChek UK Ltd). The results of detecting 200 serum samples indicated that the consistency of commercial agglutination antigen detecting in 2 times was only 79.5%. Using the ELISA kit as the reference method, the commercial agglutination antigen detecting results of the Kappa test were only moderately consistent (0.58 ∼ 0.59). Meanwhile, positive and total coincidence rates of the self-made agglutination antigen test with more reliable repeat could reach 97.4 and 88%, respectively, and the result of Kappa test was highly consistent (0.75). The Receiver Operating Characteristic curve analysis clarified that the area under the receiver-operating-characteristic curve values of self-made and commercial agglutination antigen tests could reach 0.861 and 0.804, respectively. These results were coincident when detecting known positive serum from the infected chickens. It's worth mentioning that the visible positive reaction of self-made agglutination antigen test appeared faster and stronger than commercial antigen test. In conclusion, self-made Salmonella Pullorum agglutination antigen developed in this study was much better than commercial agglutination antigen and is expected to be a valuable tool in the diagnosis of the epidemiology of Salmonella Pullorum.

Predicting Salmonella prevalence associated with meteorological factors in pastured poultry farms in southeastern United States

Consumer demand has increased for pastured poultry products as the drive for sustainable farming practices and ethical treatments of livestock have become popular in the press. It is necessary to identify the important meteorological factors associated with the prevalence of Salmonella in the pastured poultry settings since the presence of Salmonella in the environment could lead to contamination of the final product. The objective of this study was to develop a model to describe the relationship between meteorological factors and the presence of Salmonella on the pastured poultry farms. The random forest method was used to develop a model where 83 meteorological factors were included as the predicting variables. The soil model identified humidity as the most important variable associated with Salmonella prevalence, while high wind gust speed and average temperature were identified as important meteorological variables in the feces model. The developed models were robust in predicting the prevalence of Salmonella in pastured poultry farms with the area under receiver operating characteristic (ROC) curve values of 0.884 and 0.872 for the soil model and feces model, respectively. The predictive models developed in this study can provide users with practical and effective tools to make informed decisions with scientific evidence regarding the meteorological parameters that are important to monitor for increased on-farm Salmonella prevalence.

Gastrointestinal microbiomes of broilers and layer hens in alternative production systems

Alternative poultry production systems consisting of free-range or pasture flock raised poultry continues to increase in popularity. Based on the perceived benefits of poultry products generated from these alternative poultry production systems, they have commercial appeal to consumers. Several factors impact the health and well being of birds raised and maintained in these types of production systems. Exposure to foodborne pathogens and potential for colonization in the gastrointestinal tract has to be considered with these types of production systems. The gastrointestinal tract microbial composition and function of birds grown and maintained in alternative poultry operations may differ depending on diets, breed, and age of bird. Dietary variety and foraging behavior are potential influential factors on bird nutrition. The gastrointestinal tract microbiomes of birds raised under alternative poultry production systems are now being characterized with next-generation sequencing to identify individual microbial members and assess the impact of different factors on the diversity of microbial populations. In this review, the gastrointestinal tract microbiota contributions to free-range or pasture-raised broiler and egg layer production systems, subsequent applications, and potential future directions will be discussed.

Protective Effect of Vitamin E on laying performance, antioxidant capacity, and immunity in laying hens challenged with Salmonella Enteritidis

Vitamin E (VE) has proven to function as potent lipid-soluble antioxidant, a signaling molecule, and a regulator of the immune system. The objective of the study was to assess the protective effect of VE on laying performance, antioxidant capacity, and immunity in laying hens exposed to Salmonella Enteritidis (SE). A total of 80 32-week-old salmonella-free double negative Hy-Line brown laying hens were randomly assigned to 4 treatments with 20 replicates each (1 bird per replicate) according to a 2 × 2 factorial design with 2 VE supplementation levels [0 IU/kg (VE0) vs. 30 IU/kg (VE30)], and 2 challenge treatments [SE vs. physiological saline solution (PS)]. During the last 3 D of week 43 of age, birds were orally challenged with 1.0 mL suspension of 109 cfu/mL S. Enteritidis daily, whereas the birds of negative treatments (VE0) received the same volume of PS. The egg mass of VE0 treatment decreased (P < 0.05) in contrast to VE treatment after challenge. The serum concentrations of interleukins (IL-1β and IL-6) and malondialdehyde (MDA) levels of SE treatments increased (P < 0.05) at week 44 and week 46, respectively. In both VE30 treatments, the decrease (P < 0.05) in birds' mortality was associated with higher IgA, IgG, IgM concentrations at week 44, and higher IgA, IgM concentrations at week 46. There is an interaction (P < 0.05) between SE challenge and VE levels with regard to feed conversion, daily egg mass, and serum MDA, IgA, and IgM levels. It can be concluded that supplemental VE (30 IU/kg) in diets for laying hens may alleviate oxidative and immune stress due to SE challenge.

Prevalence and risk factors associated with Campylobacter spp. and Salmonella enterica in livestock raised on diversified small-scale farms in California

Diversified farms are operations that raise a variety of crops and/or multiple species of livestock, with the goal of utilising the products of one for the growth of the other, thus fostering a sustainable cycle. This type of farming reflects consumers' increasing demand for sustainably produced, naturally raised or pasture-raised animal products that are commonly produced on diversified farms. The specific objectives of this study were to characterise diversified small-scale farms (DSSF) in California, estimate the prevalence of Salmonella enterica and Campylobacter spp. in livestock and poultry, and evaluate the association between farm- and sample-level risk factors and the prevalence of Campylobacter spp. on DSSF in California using a multilevel logistic model. Most participating farms were organic and raised more than one animal species. Overall Salmonella prevalence was 1.19% (95% confidence interval (CI95) 0.6-2), and overall Campylobacter spp. prevalence was 10.8% (CI95 = 9-12.9). Significant risk factors associated with Campylobacter spp. were farm size (odds ratio (OR)10-50 acres: less than 10 acres = 6, CI95 = 2.11-29.8), ownership of swine (OR = 9.3, CI95 = 3.4-38.8) and season (ORSpring: Coastal summer = 3.5, CI95 = 1.1-10.9; ORWinter: Coastal summer = 3.23, CI95 = 1.4-7.4). As the number of DSSF continues to grow, evaluating risk factors and management practices that are unique to these operations will help identify risk mitigation strategies and develop outreach materials to improve the food safety of animal and vegetable products produced on DSSF.

Increasing Frequencies of Antibiotic Resistant Non-typhoidal Salmonella Infections in Michigan and Risk Factors for Disease

Non-typhoidal Salmonella (NTS) are important enteric pathogens causing over 1 million foodborne illnesses in the U.S. annually. The widespread emergence of antibiotic resistance in NTS isolates has limited the availability of antibiotics that can be used for therapy. Since Michigan is not part of the FoodNet surveillance system, few studies have quantified antibiotic resistance frequencies and identified risk factors for NTS infections in the state. We obtained 198 clinical NTS isolates via active surveillance at four Michigan hospitals from 2011 to 2014 for classification of serovars and susceptibility to 24 antibiotics using broth microdilution. The 198 isolates belonged to 35 different serovars with Enteritidis (36.9%) predominating followed by Typhimurium (19.5%) and Newport (9.7%), though the proportion of each varied by year, residence, and season. The number of Enteritidis and Typhimurium cases was higher in the summer, while Enteritidis cases were significantly more common among urban vs. rural residents. A total of 30 (15.2%) NTS isolates were resistant to ≥1 antibiotic and 15 (7.5%) were resistant to ≥3 antimicrobial classes; a significantly greater proportion of Typhimurium isolates were resistant compared to Enteritidis isolates and an increasing trend in the frequency of tetracycline resistance and multidrug resistance was observed over the 4-year period. Resistant infections were associated with longer hospital stays as the mean stay was 5.9 days for patients with resistant isolates relative to 4.0 days for patients infected with susceptible isolates. Multinomial logistic regression indicated that infection with serovars other than Enteritidis [Odds ratio (OR): 3.8, 95% confidence interval (CI): 1.23-11.82] as well as infection during the fall (OR: 3.0; 95% CI: 1.22-7.60) were independently associated with resistance. Together, these findings demonstrate the importance of surveillance, monitoring resistance frequencies, and identifying risk factors that can aid in the development of new prevention strategies.

A Microbiomic Analysis of a Pasture-Raised Broiler Flock Elucidates Foodborne Pathogen Ecology Along the Farm-To-Fork Continuum

While conventionally grown poultry continues to dominate the U. S. poultry industry, there is an increasing demand for locally-grown, "all natural" alternatives. The use of next generation sequencing allows for not only the gross (e.g., community structure) but also fine-scale (e.g., taxa abundances) examination of these complex microbial communities. This data provides a better understanding of how a pasture flock's microbiome changes throughout the production life cycle and how that change in microbial ecology changes foodborne pathogens in alternative poultry production systems. In order to understand this ecology better, pooled broiler samples were taken during the entire flock life cycle, from pre-hatch gastrointestinal samples (N = 12) to fecal samples from the brood (N = 5), and pasture (N = 10) periods. Additional samples were taken during processing, including skin and feather rinsates (N = 12), ceca (N = 12), and whole carcass rinses (N = 12), and finally whole carcasss rinsates of final products (N = 3). Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum, as well as what environmental factors may be influencing these shifts. Significant microbiome shifts occurred during the life cycle of the pasture broiler flock, with the brood and pasture fecal samples and cecal samples being very distinct from the other pre-hatch, processing, and final product samples. Throughout these varied microbiomes, there was a stable core microbiome containing 13 taxa. Within this core microbiome, five taxa represented known foodborne pathogens (Salmonella, Campylobacter) or potential/emerging pathogens (Pseudomonas, Enterococcus, Acinetobacter) whose relative abundances varied throughout the farm-to-fork continuum, although all were more prevalent in the fecal samples. Additionally, of the 25 physiochemical and nutrient variables measured from the fecal samples, the carbon to nitrogen ratio was one of the most significant variables to warrant further investigations because it impacted both general fecal microbial ecology and Campylobacter and Enterococcus taxa within the core fecal microbiomes. These findings demonstrate the need for further longitudinal, farm-to-fork studies to understand the ecology of the microbial ecology of pasture production flocks to improve animal, environmental, and public health.

Feeding and lighting practices on small-scale extensive pastured poultry commercial farms in the United States

As commercial free-range and pastured poultry production has gained increased popularity in the United States in recent years, there is a greater need to understand basic husbandry practices including feeding and lighting practices. Because husbandry practices vary greatly between individual commercial pastured poultry and free-range operations, gaining knowledge across a wide cross-section of producers is necessary to better understand current practices. Specifically, because feed is considered the most expensive part of poultry production with respect to operating cost, in collaboration with the American Pastured Poultry Producers Association, an on-line survey of commercial free-range and pastured poultry producers was conducted aimed primarily at evaluating feeding and lighting practices. Data were collected from 14 commercial pastured (n = 13) and free-range (n = 1) producers (6 broiler, 1 layer, and 7 broiler/layer facilities) across 9 U.S. states. Results showed that these operations most commonly use Cornish Cross for broiler production and ISA Brown and Australorp for egg production. Only 1 of the 14 farms calculates feed conversion ratio on a monthly basis. Estimates of Hen Month Egg Production (HMEP) resulted in HMEP percentages that were over 100% in 6 of the 7 farms that provided data. 5 of the 7 farms that have layers used supplemental lighting but do not use a lux meter. These lack of data reflect an important challenge with this segment of the poultry industry. Extension based outreach focused on enabling data collection and record-keeping and analysis are necessary. Despite its small sample size, this study's results provide some valuable insights with respect to feeding equipment and the current state of data collection for this segment of the poultry industry.

Frequent human-poultry interactions and low prevalence of Salmonella in backyard chicken flocks in Massachusetts

The backyard chicken (BYC) movement in the USA has increased human contact with poultry and subsequently, human contact with the pathogen Salmonella. However, to date, there have been few studies assessing prevalence of Salmonella in backyard flocks, despite the known public health risk this zoonotic bacterium poses. The objective of this study was to characterize human-BYC interactions and assess the prevalence of Salmonella among BYC flocks. We interviewed 50 BYC owners using a structured questionnaire to determine flock and household characteristics that facilitate contact with BYC and that may be associated with Salmonella in the BYC environment. Composite faecal material, cloacal swabs and dust samples from 53 flocks housed on 50 residential properties in the Greater Boston, Massachusetts area were tested for Salmonella using standard culture techniques and confirmed using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometer. Microbroth dilution and whole genome sequencing were used to determine phenotypic and genotypic resistance profiles, respectively, and sequence results were used to determine multilocus sequencing type. No owners self-reported a diagnosis of salmonellosis in the household. Over 75% of a subset of owners reported that they and their children consider BYC pets. This perception is evident in how owners reported interacting with their birds. Salmonella enterica subspecies enterica serotype Kentucky ST152 (serogroup C)-a strain not commonly associated with human infection-was confirmed in one flock, or 2% of tested flocks, and demonstrated resistance to tetracycline and streptomycin. We detected Salmonella at low prevalence in BYC. Further study of the health effects of exposure to zoonotic gastrointestinal pathogens such as Salmonella among families with BYC is warranted.

Operational challenges and opportunities in pastured poultry operations in the United States

As pastured poultry production has gained increased popularity in the United States in recent years, there is a growing need for research and outreach efforts aimed at this sector of poultry production. In order to get familiarized with American pastured poultry producers, we conducted an online questionnaire aimed primarily at evaluating what operational challenges are faced by producers and what educational opportunities should be initiated by researchers. Results showed that pastured poultry farms largely vary in total number of acres farmed and total number of birds kept. The vast majority of farms (96%) rotate their flocks on pasture and include livestock species (78%) in their rotation systems. Mobile coops are the preferred housing option provided by producers (88%). The most common source of mortality listed by respondents was predation (52%), followed by "other" (32%). However, predation was not selected as the most important challenge by the majority of respondents. Sixty-four percent of participants instead mentioned providing adequate feed at reasonable cost as the major challenge in raising poultry on pasture, followed again by "other" (52%) and lack of processing facilities for small numbers of birds (40%). Finally, the topics considered by respondents as the most helpful to learn more about were how to improve egg production rate and/or feed conversion ratio (67%), followed by how to improve pasture condition and optimum vegetative cover all year round (62%). Despite its small sample size, this study's results provide some valuable insights of challenges encountered and information needed on pastured poultry farms.