Application of a CRISPR Sequence-Based Method for a Large-Scale Assessment of Salmonella Serovars in Ontario Poultry Production Environments

Accurate detection of all Salmonella serovars present in a sample is important in surveillance programs. Current detection protocols are limited to detection of a predominant serovar, missing identification of less abundant serovars in a sample. An alternative method, called CRISPR-SeroSeq, serotyping by sequencing of amplified CRISPR spacers, was employed to detect multiple serovars in a sample without the need of culture isolation. The CRISPR-SeroSeq method successfully detected 34 most frequently reported Salmonella serovars in pure cultures and target serovars at 104 CFU/mL in 27 Salmonella-negative environmental enrichment samples post-spiked with one of 15 different serovars, plus 2 additional serovars at 1 log CFU/mL higher abundance. When the method was applied to 442 naturally contaminated environmental samples collected from 192 poultry farms, 25 different serovars were detected from 430 of the samples. In 73.1% of the samples, 2 to 7 serovars were detected, with Salmonella Kiambu (55.7%), Salmonella Infantis (48.4%), Salmonella Kentucky (27.1%), Salmonella Livingstone (26.6%), and Salmonella Mbandaka/Montevideo (23.4%) being the most prevalent on the farms. Single isolates from 384 samples were also analyzed using a traditional serotyping method, and the same serovar identified by culture was detected by CRISPR-SeroSeq in 96.1% (369/384) of samples, with the former missing detection of additional and sometimes critical serovars. The surveillance data obtained via CRISPR-SeroSeq revealed a significant emergence of Salmonella Kiambu and Salmonella Rissen on poultry farms in Ontario. The results highlight the effectiveness of the CRISPR-SeroSeq approach in detecting multiple Salmonella serovars in poultry environmental samples under applied conditions, providing updated surveillance information on Salmonella serovars on poultry farms in Ontario. IMPORTANCE The CRISPR-SeroSeq method represents an alternative molecular tool to the traditional culture-based serotyping method that can detect multiple Salmonella serovars in a sample and provide rapid serovar results without the need of selective enrichment and culture isolation. The evaluation results can facilitate implementation of the method in routine Salmonella surveillance on poultry farms and in outbreak investigations. The application of the method can increase the accuracy of current serovar prevalence information. The results highlight the effectiveness of the validated method and the need for monitoring Salmonella serovars in poultry environments to improve current surveillance programs. The updated surveillance data provide timely information on emergence of different Salmonella serovars on poultry farms in Ontario and support on-farm risk assessment and risk management of Salmonella.

Cellular and molecular events in early and mid gestation porcine implantation sites: a review

Commercial, North American pork breeds (Sus scrofa) experience significant loss of genetically-normal conceptuses during the peri-implantation (attachment) period and at mid-gestation (day 50 to 90 of the 114 day porcine gestation interval). Although exact causes for these losses are not defined, asynchronous in-utero development and deficits in vascularization of the endometrium and placenta appear to be involved. Understanding of normal maternal-fetal dialogue is critical to develop breeding or therapeutic strategies that improve fetal health and overall litter size in commercial pigs. The non-invasive, epitheliochorial porcine placenta permits investigation of maternal or fetal compartments without cross contaminating cells. We developed and use protocols to capture single, homogenous populations of porcine cells (endometrial lymphocytes, dendritic or endothelial cells) from histological sections using laser capture microdissection (LCM), a powerful tool for study of gene expression that reflects the in vivo environment. These data are compared with gene expression in biopsies of endometrium and of trophoblast from the same, attachment sites. Here we review justifications for selection of the genes we have studied and our published and in progress work. These data provide new insights into the roles of the endometrial immune environment in the regulation of the success and failure of porcine conceptuses.

A review of molecular contrasts between arresting and viable porcine attachment sites

Significant spontaneous fetal loss of unknown cause occurs in North American commercial swine. About 30% of conceptuses, thought to be genetically normal, are lost during the peri-attachment period. An additional 20% are lost at mid-pregnancy. Littermate endometrial and trophoblast biopsies were studied by quantitative real-time PCR for gene expression, and immunohistochemistry for protein expression at gestation day (gd)15-23 and 50. RNA analyses were also conducted on endometrial lymphocytes and arterial endothelial cells removed from biopsies by laser capture microdissection. Genes were selected for study from human literature and cloned as required. As in humans, angiogenic, cytokine, chemokine and chemokine decoy receptor gene expression occurs at the porcine maternal-fetal interface. In each tissue studied, distinct patterns of expression are found between early and mid-pregnancy, as well as between viable and arresting conceptus attachment sites. These changes involve both endometrial lymphocytes and dendritic cells. Restriction in endometrial angiogenesis, reduction in expression of the chemokine decoy receptor D6, and reduction in dendritic cell numbers contribute to fetal arrest. In peri-attachment loss, interferon-gamma is more abundantly transcribed than tumor necrosis factor-alpha, but this ratio is reversed during midgestation failure. Further characterization of spontaneous fetal loss in pigs will identify targets for modification by hog producers and may provide a model for identification of antecedents to fetal loss in humans.

Immunological mechanisms affecting angiogenesis and their relation to porcine pregnancy success

Prenatal mortality due to loss of lymphocyte-promoted endometrial angiogenesis is being investigated as a major cause of litter reductions during pregnancy in pigs. This review discusses immune mechanisms influencing porcine endometrial angiogenesis as well as additional signalling molecules that may play important roles in the compromise of peri-implantation and mid-gestation fetal pig survival. These include dendritic cells, signalling molecules such as toll-like receptors, chemokines and ficolins. Together these cells and molecules regulate immune responses and, ideally, protect the mother and prevent immune-based conceptus losses. Dendritic cells were recently shown to be angiogenic. Their tolerogenic role at the maternal-fetal interface coupled with the ability to secrete and respond to angiogenic factors suggests that dendritic cells are the key coordinators of angiogenesis at the porcine maternal-fetal interface. Chemokines coordinate the localization of immune effector and endothelial cells. The balance between pro-angiogenic and anti-angiogenic chemokines is addressed in relation to conceptus viability. Ficolins, components of the lectin-mediated complement activation pathway, are used for self/non-self recognition. Together, these components of the immune system could regulate lymphocyte- and non-lymphocyte-promoted endometrial angiogenesis to determine conceptus survival.