Controlling Salmonella: strategies for feed, the farm, and the processing plant

Controlling Salmonella in poultry is an ongoing food safety measure and while significant progress has been made, there is a need to continue to evaluate different strategies that include understanding Salmonella-poultry interaction, Salmonella-microbiota interactions, Salmonella genetics and response to adverse conditions, and preharvest and postharvest parameters that enable persistence. The purpose of this symposium is to discuss different strategies to consider from feed milling to the farm to the processing environment. This Poultry Science Association symposium paper is divided into 5 different sections that covers 1) immunological aspects of Salmonella control, 2) application of Salmonella genetics for targeted control strategies in poultry production, 3) improving poultry feed hygienics: utilizing feed manufacture techniques and equipment to improve feed hygienics, 4) practical on farm interventions for controlling Salmonella-what works and what may not work, and 5) monitoring and mitigating Salmonella in poultry. These topics elucidate the critical need to establish control strategies that will improve poultry gut health and limit conditions that exposes Salmonella to stress causing alterations to virulence and pathogenicity both at preharvest and postharvest poultry production. This information is relevant to the poultry industry's continued efforts to ensure food safety poultry production.

Scientometric Evaluation of 100-year history of Poultry Science (1921-2020)

To have a better contribution to the poultry production community, the Poultry Science Association founded journals including Poultry Science (PS) at 1921. Now, after 100 yr of publishing, PS ranks between the top 10 journals in the category of “agriculture, dairy, and animal science”. One hundred years after publishing the first paper in PS, the poultry industry has been completely revolutionized. Hence, it will be interesting to establish scientometrics study of the PS development during the last century. Therefore, based on findings of the current study, among countries/authors’ collaborations, future research fronts, and possibility of hot topics in the coming years may be predictable. Accordingly, a total of 22,451 articles were retrieved. For content analyses, according to the PS categorization for subject areas, 14 different subject areas were developed, including “behavior, breeding and quantitative genetics, education and extension, health and welfare, immunology, management and environment, metabolism and nutrition, microbiology and virology, modeling, molecular biology, physiology and anatomy, production, products, processing and marketing, and reproduction”. Considering the 100-yr of PS, the most frequent subject area was “nutrition and metabolism” (14,109 articles), and “modeling” (1,114 articles) attracted less scholarly attention. However, considering the last decade (2011–2020), the most important subject area was “molecular biology” (1,420 of 2,466 articles; 57.58%), followed by “modeling” (544 of 1,144 articles; 48.88%). Moreover, the most frequent poultry species/strains were broilers (retrieved in 6,156 articles), followed by laying hens, turkeys, and quail. Considering collaboration of countries and researchers, it can be said that a total number of 108 countries contributed to PS, with the most prolific country being United States (with 9,421 articles; 43.16%), followed by China, Canada, the Netherlands, and Japan. Among the authors, Harms RH (287 articles), and Siegel PB (208) were the most prolific authors, and Siegel PB and Dunnington EA (71 articles) had more collaborations. To study keyword trends, including 3 time periods broilers was the central co-occurrent keyword, while the importance of chickens and turkeys declined during the time. Salmonella spp. was a constant representative of poultry microbiology during 100 yr. While “nutrition and metabolism” was the most important subject area, nutrition-related keywords (major items) were not concentrated and co-occurred with a variety of keywords from different subject areas. While “molecular biology” ranked first over the past decade, the importance of “nutrition and metabolism” should not be ignored. In fact, in recent years, molecular basis of the nutrition has been studied. In big-data era and due to developing the molecular biology technologies, it seems that using mathematical modeling and computational methodologies will increase and probably remains as one of the most attractive research areas for scientists at least in the upcoming future decades.

Salmonella in Chicken Meat: Consumption, Outbreaks, Characteristics, Current Control Methods and the Potential of Bacteriophage Use

The control of Salmonella in chicken processing plants is an ongoing challenge for many factories around the globe, especially with the increasing demand for poultry escalating processing throughputs. Foodborne outbreaks due to Salmonella still pose a prominent risk to public health. As chicken meat is a good reservoir for Salmonella, it is important for chicken processing plants to continuously optimize methods to reduce the incidence of Salmonella on their products. Current methods include the use of chemical antimicrobials such as chlorine-containing compounds and organic acids. However, these current methods are decreasing in popularity due to the rising rate of Salmonella resistance, coupled with the challenge of preserving the sensory properties of the meat, along with the increasing stringency of antimicrobial use. Bacteriophages are becoming more appealing to integrate into the large-scale hurdle concept. A few factors need to be considered for successful implementation, such as legislation, and application volumes and concentrations. Overall, bacteriophages show great potential because of their host specificity, guaranteeing an alternative outcome to the selective pressure for resistant traits placed by chemicals on whole microbial communities.

Sef fimbria operon construction, expression, and function for direct rapid detection of Salmonella Enteritidis

Salmonella Enteritidis (SE) causes both horizontal and vertical transmission of diseases in poultry industry and is also one of the main causes of human food poisoning. Sequence analysis of the sef operon of poultry-derived Salmonella serotypes showed the presence of an entire sef operon in SE, whereas only sef pseudogenes were found in Salmonella Gallinarum and Salmonella Pullorum. Subsequently, the sef operon of SE was cloned into the pBR322 plasmid and expressed in a modified Escherichia coli strain SE5000. sef operon expression was demonstrated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, western blot, agglutination assay, and transmission electron microscopy. The results showed that SE5000+Sef, but not SE5000+pBR322, could specifically react with SE-positive chicken serum in an agglutination assay, which could be clearly visualized by the naked eye within less than 2 min. In contrast, SE5000+Sef could not be recognized in Salmonella Gallinarum- and Salmonella Pullorum-positive chicken sera. Next, taking advantage of the exclusive presence of an entire sef operon in SE, we set up an agglutination-based detection system to monitor the dynamics of Sef-targeted antibody from SE-infected chicks for 47 days. Using the proposed detection method, SE was readily detectable starting from 2 weeks post-infection. Finally, we compared the proposed SE5000+Sef-based detection system with commercially available agglutination antigen using the classical bacterial isolation and identification procedure as reference. The results showed that the SE5000+Sef system was more consistent with the results of bacterial isolation and identification with almost 100% accuracy. We established a simple, sensitive, and cheap agglutination method for rapid and specific detection of SE-infected chickens, which can facilitate epidemiological investigation and eradication of SE infections. KEY POINTS: • Only the Salmonella Enteritidis serotype expressed Sef fimbriae in chicken infected with SE. • A rapid, large-scale method of detection by the naked eye of detection of SE-infected chicken is presented.

Molecular-based identification and detection of Salmonella in food production systems: current perspectives

Salmonella remains a prominent cause of foodborne illnesses and can originate from a wide range of food products. Given the continued presence of pathogenic Salmonella in food production systems, there is a consistent need to improve identification and detection methods that can identify this pathogen at all stages in food systems. Methods for subtyping have evolved over the years, and the introduction of whole genome sequencing and advancements in PCR technologies have greatly improved the resolution for differentiating strains within a particular serovar. This, in turn, has led to the continued improvement in Salmonella detection technologies for utilization in food production systems. In this review, the focus will be on recent advancements in these technologies, as well as potential issues associated with the application of these tools in food production. In addition, the recent and emerging research developments on Salmonella detection and identification methodologies and their potential application in food production systems will be discussed.

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.

An Efficient Multiplex PCR-Based Assay as a Novel Tool for Accurate Inter-Serovar Discrimination of Salmonella Enteritidis, S. Pullorum/Gallinarum and S. Dublin

Salmonella enterica serovars Enteritidis, Pullorum/Gallinarum, and Dublin are infectious pathogens causing serious problems for pig, chicken, and cattle production, respectively. Traditional serotyping for Salmonella is costly and labor-intensive. Here, we established a rapid multiplex PCR method to simultaneously identify three prevalent Salmonella serovars Enteritidis, Pullorum/Gallinarum, and Dublin individually for the first time. The multiplex PCR-based assay focuses on three genes tcpS, lygD, and flhB. Gene tcpS exists only in the three Salmonella serovars, and lygD exists only in S. Enteritidis, while a truncated region of flhB gene is only found in S. Pullorum/Gallinarum. The sensitivity and specificity of the multiplex PCR assay using three pairs of specific primers for these genes were evaluated. The results showed that this multiplex PCR method could accurately identify Salmonella Enteritidis, Pullorum/Gallinarum, and Dublin from eight non-Salmonella species and 27 Salmonella serovars. The least concentration of genomic DNA that could be detected was 58.5 pg/μL and the least number of cells was 100 CFU. Subsequently, this developed method was used to analyze clinical Salmonella isolates from one pig farm, one chicken farm, and one cattle farm. The results showed that blinded PCR testing of Salmonella isolates from the three farms were in concordance with the traditional serotyping tests, indicating the newly developed multiplex PCR system could be used as a novel tool to accurately distinguish the three specific Salmonella serovars individually, which is useful, especially in high-throughput screening.

Differential ex vivo responses of primary leukocytes from turkey pedigree lines to Salmonella Heidelberg

Escalating product recalls as a consequence of Salmonella-contaminated poultry products have resulted in detrimental economic impacts in the poultry industry. One potential long-term alternative method to Salmonella prevention is genetic selection to improve innate resistance. This study evaluated the ex vivo effects of Salmonella Heidelberg (SH) on phagocytic and bactericidal leukocyte function in turkeys from six pedigree lines (A-F). Day-of-hatch poults (n = 48) were placed and raised in cages (2 birds/gender/genetic line/cage) to 35 d when heterophils and peripheral blood mononuclear cells (PBMCs) were extracted from males and females of each line. Cells were used in phagocytic and bactericidal assays to determine the ex vivo effects of SH on turkey leukocyte activity. Data were analyzed using the Fit Model platform in JMP Pro 10.0 (SAS Institute Inc.) with differences considered significant at P ≤ 0.05 and data reported as LS Means with SEM. Although genetic line had no significant effect on phagocytosis of SH by heterophils and PBMCs, cumulatively, female cells exhibited higher phagocytosis potential than those from males. The main effect of gender was significant on bactericidal activity of PBMCs when incubated at a 1:10 and 1:100 PBMC to SH ratio. Genetic line also had a significant effect on bactericidal activity of PBMCs with cells from line F exhibiting the best activity. These results suggest that gender had a marked cumulative effect on phagocytosis of SH by heterophils and PBMCs while both genetic line and gender had a prominent effect on bacterial killing of SH by turkey PBMCs. Once able to determine genetic markers associated with these immune responses to Salmonella, genetic selection for increased resistance may become feasible in turkeys.

Development of multiplex PCR assay for simultaneous detection of Salmonella genus, Salmonella subspecies I, Salm. Enteritidis, Salm. Heidelberg and Salm. Typhimurium

AIMS

The aim of this research was to develop multiplex PCR assay that could simultaneously detect Salmonella genus, Salmonella subsp. I, Salm. Enteritidis, Heidelberg and Typhimurium because these Salmonella serovars are the most common isolates associated with poultry products.

METHODS AND RESULTS

Five primers were utilized to establish multiplex PCR and applied to Salmonella isolates from chickens and farm environments. These isolates were identified as Salmonella subsp. I and 16 of 66 isolates were classified as Salm. Enteritidis, while Heidelberg or Typhimurium was not detected. We also spiked three Salmonella strains on chicken breast meat to evaluate the specificity and sensitivity of multiplex PCR as well as qPCR to optimize quantification of Salmonella in these samples. The optimized multiplex PCR and qPCR could detect approx. 2·2 CFU of Salmonella per gram after 18 h enrichment.

CONCLUSIONS

The multiplex PCR and qPCR would provide rapid and consistent results. Also, these techniques would be useful for the detection and quantification of Salmonella in contaminated poultry, foods and environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

The strategy for the rapid detection of Salmonella serovars in poultry is needed to further reduce the incidence of salmonellosis in humans. The optimized multiplex PCR will be useful to detect prevalent Salmonella serovars in poultry products.

Application of Molecular Approaches for Understanding Foodborne Salmonella Establishment in Poultry Production

Salmonellosis in the United States is one of the most costly foodborne diseases. Given that Salmonella can originate from a wide variety of environments, reduction of this organism at all stages of poultry production is critical. Salmonella species can encounter various environmental stress conditions which can dramatically influence their survival and colonization. Current knowledge of Salmonella species metabolism and physiology in relation to colonization is traditionally based on studies conducted primarily with tissue culture and animal infection models. Consequently, while there is some information about environmental signals that control Salmonella growth and colonization, much still remains unknown. Genetic tools for comprehensive functional genomic analysis of Salmonella offer new opportunities for not only achieving a better understanding of Salmonella pathogens but also designing more effective intervention strategies. Now the function(s) of each single gene in the Salmonella genome can be directly assessed and previously unknown genetic factors that are required for Salmonella growth and survival in the poultry production cycle can be elucidated. In particular, delineating the host-pathogen relationships involving Salmonella is becoming very helpful for identifying optimal targeted gene mutagenesis strategies to generate improved vaccine strains. This represents an opportunity for development of novel vaccine approaches for limiting Salmonella establishment in early phases of poultry production. In this review, an overview of Salmonella issues in poultry, a general description of functional genomic technologies, and their specific application to poultry vaccine developments are discussed.