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10. Evidence for the efficacy of pre-harvest agricultural practices in mitigating food-safety risks to fresh produce in North America

Author

Devarajan, Naresh, primary, Weller, Daniel L., additional, Jones, Matthew, additional, Adell, Aiko D., additional, Adhikari, Achyut, additional, Allende, Ana, additional, Arnold, Nicole L., additional, Baur, Patrick, additional, Beno, Sarah M., additional, Clements, Donna, additional, Olimpi, Elissa M., additional, Critzer, Faith, additional, Green, Hyatt, additional, Gorski, Lisa, additional, Ferelli Gruber, Angela, additional, Kovac, Jasna, additional, McGarvey, Jeffery, additional, Murphy, Claire M., additional, Murphy, Sarah I., additional, Navarro-Gonzalez, Nora, additional, Owen, Jeb P., additional, Pires, Alda F. A., additional, Richard, Nicole, additional, Samaddar, Sandipan, additional, Schmidt, Radomir, additional, Scow, Kate, additional, Shariat, Nikki W., additional, Smith, Olivia M., additional, Spence, Austin R., additional, Stoeckel, Don, additional, Tran, Thao D. H., additional, Wall, Gretchen, additional, and Karp, Daniel S., additional

Published
2023
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14. Evidence for the efficacy of pre-harvest agricultural practices in mitigating food-safety risks to fresh produce in North America

Author

Center for Produce Safety (US), Department of Agriculture (US), Agricultural Research Service (US), Allende, Ana [0000-0002-5622-4332], Devarajan, Naresh, Weller, Daniel L., Jones, Matthew, Adell, Aiko D., Adhikari, Achyut, Allende, Ana, Baur, Arnold Patrick, Beno, Sarah M., Clements, Donna, Critzer, Faith, Green, Hyatt, Gorski, Lisa, Ferelli Gruber, Angela, Kovac, Jasna, McGarvey, Jeffery, M. Murphy, Claire, Murphy, Sarah I., Navarro-Gonzalez, Nora, Owen, Jeb P., Pires, Alda F. A., Richard, Nicole, Samaddar, Sandipan, Schmidt, Radomir, Scow, Kate, Shariat, Nikki W., Smith, Olivia M., Spence, Austin R., Stoeckel, Don, Tran, Thao D. H., Wall, Gretchen, Daniel S. Karp, Center for Produce Safety (US), Department of Agriculture (US), Agricultural Research Service (US), Allende, Ana [0000-0002-5622-4332], Devarajan, Naresh, Weller, Daniel L., Jones, Matthew, Adell, Aiko D., Adhikari, Achyut, Allende, Ana, Baur, Arnold Patrick, Beno, Sarah M., Clements, Donna, Critzer, Faith, Green, Hyatt, Gorski, Lisa, Ferelli Gruber, Angela, Kovac, Jasna, McGarvey, Jeffery, M. Murphy, Claire, Murphy, Sarah I., Navarro-Gonzalez, Nora, Owen, Jeb P., Pires, Alda F. A., Richard, Nicole, Samaddar, Sandipan, Schmidt, Radomir, Scow, Kate, Shariat, Nikki W., Smith, Olivia M., Spence, Austin R., Stoeckel, Don, Tran, Thao D. H., Wall, Gretchen, and Daniel S. Karp

Abstract

Consumption of contaminated produce remains a leading cause of foodborne illness. Increasingly, growers are altering agricultural practices and farm environments to manage food-safety hazards, but these changes often result in substantial economic, social, and environmental costs. Here, we present a comprehensive evidence synthesis evaluating the efficacy of soil, non-crop vegetation, animal, landscape, and irrigation water management strategies aimed at reducing produce-safety risk in North America. We systematically summarized findings from 78 peer-reviewed papers on the effect of 21 management practices on the prevalence, abundance, or survival of four foodborne pathogens (i.e., E. coli, Salmonella spp., Listeria spp., and Campylobacter spp.), resulting in 113 summaries. We then organized a 30-member expert panel, who used these summaries to evaluate the impact of each practice on food-safety outcomes. While more than half of the practices were too understudied to confidently evaluate their impact on food safety, the panel did identify several practices that were associated with reduced preharvest food-safety risks, including not using raw manure, separating crop and livestock production, and choosing low-risk irrigation sources. The panel also identified practices that appear ineffective at reducing food-safety risks, such as the removal of non-crop vegetation. Overall, these findings provide insights into the food-safety impacts of agricultural and land management practices that growers, auditors, and extension personnel can use to co-manage produce preharvest environments for food safety and other aims

Published
2023

15. The New Microbiology: From Microbiomes to CRISPR

Author

Obe, Tomi and Shariat, Nikki W.

Subjects
The New Microbiology: From Microbiomes to CRISPR (Nonfiction work) -- Cossart, Pascale, Books -- Book reviews, Health
Abstract

Pascale Cossart; ASM Press, Washington DC, USA, 2018; ISBN: 978-1-683-67010-0; Pages: 200; Price: US $30.00 Infections, diseases, epidemics, and pandemics are some of the words that come to mind when [...]

Published
2022
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19. Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

Author

Fu, Yezhi, primary, M’ikanatha, Nkuchia M., additional, Lorch, Jeffrey M., additional, Blehert, David S., additional, Berlowski-Zier, Brenda, additional, Whitehouse, Chris A., additional, Li, Shaoting, additional, Deng, Xiangyu, additional, Smith, Jared C., additional, Shariat, Nikki W., additional, Nawrocki, Erin M., additional, and Dudley, Edward G., additional

Published
2022
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27. Salmonella Genomics and Population Analyses Reveal High Inter- and Intraserovar Diversity in Freshwater

Author

Deaven, Abigail M., primary, Ferreira, Christina M., additional, Reed, Elizabeth A., additional, Chen See, Jeremy R., additional, Lee, Nora A., additional, Almaraz, Eduardo, additional, Rios, Paula C., additional, Marogi, Jacob G., additional, Lamendella, Regina, additional, Zheng, Jie, additional, Bell, Rebecca L., additional, and Shariat, Nikki W., additional

Published
2021
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29. High-resolution Serotyping Reveals SalmonellaSurveillance Challenges in the Turkey Industry

Author

Cason, Emily E., Carlson, Anna V., Siemens, Angela L., and Shariat, Nikki W.

Abstract

•Turkey final products include Salmonellaserovars not found upstream.•Salmonellacontamination in turkeys is complex, and serovars differ among product types.•Farm sampling at load-out poorly reflects Salmonelladetected at processing.•A live attenuated SalmonellaTyphimurium vaccine strain was found in final products.•Discrepancies exist between molecular and conventional Salmonellaprevalence.

Published
2024
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32. Poultry Processing Interventions Reduce SalmonellaSerovar Complexity on Postchill Young Chicken Carcasses as Determined by Deep Serotyping

Author

Richards, Amber K., Siceloff, Amy T., Simmons, Mustafa, Tillman, Glenn E., and Shariat, Nikki W.

Abstract

•At hot rehang, 48.4% (74/153) of carcasses contained two or more serovars.•At postchill, 7.9% (3/38) of carcasses contained two or more serovars.•Serovar Kentucky was most frequent at hot rehang (72.5%) and postchill (73.7%).•There was high serovar concordance between paired sample types (87.1%; 27/31).

Published
2024
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35. Prevalence of Group I Salmonella Kentucky in domestic food animals from Pennsylvania and overlap with human clinical CRISPR sequence types.

Author

Rauch, Hallie E., Vosik, Dorothy, Kariyawasam, Subhashinie, M’ikanatha, Nkuchia, and Shariat, Nikki W.

Subjects
SALMONELLA, HEALTH of food animals, CRISPRS, PUBLIC health, POULTRY products
Abstract

Abstract: Although infrequently associated with illness in humans, Salmonella enterica, subsp. enterica serovar Kentucky is the most common non‐clinical, non‐human serovar reported in the United States, being largely found in poultry and poultry products, as well as being associated with cattle. This serovar is polyphyletic and can be separated into two groups, Group I and II, based on CRISPR‐typing analysis. In Salmonella Kentucky isolates from human clinical samples in Pennsylvania, both lineages are equally represented. The goal of this study was to determine whether both groups were also represented in domestic food animals in Pennsylvania. We analysed the CRISPR arrays from 67 Salmonella Kentucky isolates used PCR and sequencing of CRISPR arrays or analysis of whole genome sequences to analyse the CRISPR arrays and Across a collection of 67 Salmonella Kentucky isolates that includes those collected from farms, veterinary clinical samples as well as isolates from retail meats, we show that Group I Salmonella Kentucky are the exclusive lineage present. We reveal that the specific subtype of over a quarter of these animal isolates are also found to be responsible for causing human salmonellosis in the same region over the same time period. [ABSTRACT FROM AUTHOR]

Published
2018
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36. Population Analyses Reveal Preenrichment Method and Selective Enrichment Media Affect SalmonellaSerovars Detected on Broiler Carcasses

Author

Cox, Nelson A., Berrang, Mark E., House, Sandra L., Medina, David, Cook, Kimberly L., and Shariat, Nikki W.

Abstract

Poultry is a major Salmonellareservoir, but conventional culture-based methods typically identify the most abundant serovars while those less abundant remain undetected. Choice of enrichment procedure also introduces bias, and for broiler carcasses, a 1-min rinse before preenrichment is insufficient to release all Salmonellapresent. The inability to assess serovar diversity means that serovars more often associated with human illness may be masked by more abundant Salmonella. CRISPR-SeroSeq (serotyping by sequencing clustered regularly interspaced short palindromic repeats), an amplicon-based, next-generation sequencing tool, allows detection of multiple serovars and maps the relative serovar frequencies in a sample. To address the preceding limitations, CRISPR-SeroSeq was used on broiler carcasses collected prechilled at a commercial plant. Standard carcass rinse aliquot preenrichments and whole carcass preenrichments that were enriched in Rappaport-Vassiliadis (RV) and tetrathionate (TT) broths were compared. On average, five serovars were observed per carcass, including nine on one carcass. CRISPR-SeroSeq detected serovars comprising as little as 0.005% of the population. CRISPR-SeroSeq data matched (28 of 32) standard culture analysis for abundant serovars. Salmonellaserovars Kentucky, Typhimurium, and Schwarzengrund were found on each carcass. Overall, serovar diversity was higher in whole carcass preenrichments that were enriched in RV (P< 0.05). Serovar Schwarzengrund was present at higher frequencies in whole carcass preenrichments compared with rinse aliquot preenrichments (ttest, P< 0.05), suggesting it adheres more strongly to the carcass. Salmonellaserovar Enteritidis was enriched eightfold more in TT than in RV, and serovars Schwarzengrund and Reading were preferentially enriched in RV. Comparison of preenriched and enriched samples suggests that selective enrichment in RV or TT was inhibitory to some serovars. This article addresses limitations of Salmonellasurveillance protocols and provides information related to Salmonellapopulation dynamics.

Published
2019
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37. Buffered Peptone Water Formulation Does Not Influence Growth of pESI-positive Salmonella entericaSerovar Infantis

Author

McMillan, Elizabeth A., Berrang, Mark E., Read, Quentin D., Rasamsetti, Surendra, Richards, Amber K., Shariat, Nikki W., and Frye, Jonathan G.

Abstract

•Ser. Infantis does not grow faster or to a higher final concentration in nBPW than in BPW.•When used to simulate poultry carcass sampling, nBPW does not perform differently than BPW.•It is unlikely that the use of nBPW is related to the increased detection of ser. Infantis on poultry samples.

Published
2023
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38. Assessing Salmonellaprevalence and complexity through processing using different culture methods

Author

Rasamsetti, Surendra, Berrang, Mark E., Cox, Nelson A., and Shariat, Nikki W.

Abstract

Conventional Salmonellasurveillance requires a week for isolation, confirmation, and subsequent serotyping. We previously showed that this could be reduced by 24 h by combining the pre-enrichment and enrichment steps into a single selective pre-enrichment step and was tested on directly after picking. The goal of this study was 2-fold: 1) to evaluate the use of selective pre-enrichment through each step of processing, including postintervention when the Salmonellaload is reduced, and 2) to assess any changes in serovar populations in Salmonellapositive samples. Duplicate carcass drip samples, each representative of 500 broiler carcasses, were collected by catching processing water drip under moving carcass shackle lines in each of three commercial broiler slaughter plants. Samples were collected post-pick, post-inside-outside bird wash (IOBW), and post-chill; duplicate wing rinses were performed pre- and post-antimicrobial parts dip. Each processing plant was sampled 6 times for a total of 180 samples collected. The number of Salmonellapositives identified with selective pre-enrichment conditions (48/180) was similar to traditional selective enrichment culture conditions (52/180), showed good concordance in recovery rate between the 2 culture methods (Fisher's exact test, P = 0.72). We also found that the incidence of Salmonellareduced dramatically after antimicrobial intervention (post-pick 66.7% vs. post chill 8.3%). When serovar populations were evaluated in Salmonellapositive samples using CRISPR-SeroSeq, we detected four different Salmonellaserovars, Kentucky, Infantis, Schwarzengrund, and Typhimurium, and their incidence rose between post-pick and post-IOBW. The relative abundance of Infantis within individual samples increased between post-pick and post-IOBW while the relative abundance of the other 3 serovars decreased. These results suggest that a selective pre-enrichment step reduces the time required for Salmonellaisolation without negatively affecting detection and serovar profiles in culture positive samples were not altered between culture conditions used.

Published
2022
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39. Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.

Author

Yezhi Fu, M'ikanatha, Nkuchia M., Lorch, Jeffrey M., Blehert, David S., Berlowski-Zier, Brenda, Whitehouse, Chris A., Shaoting Li, Xiangyu Deng, Smith, Jared C., Shariat, Nikki W., Nawrocki, Erin M., and Dudleya, Edward G.

Subjects
*SALMONELLA enterica serovar typhimurium, *SALMONELLA enterica, *WATER birds, *PASSERIFORMES, *DOMESTIC animals, *GULLS
Abstract

Salmonella enterica serovar Typhimurium is typically considered a host generalist; however, certain isolates are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium isolates from wild birds collected in 30 U.S. states during 1978-2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (Aequornithes), and larids (gulls and terns) represented three distinct lineages and certain S. Typhimurium CRISPR types presented in individual lineages. We also showed that lineages formed by wild bird isolates differed from most isolates originating from domestic animal sources, and that genomes from these lineages substantially improved source attribution of Typhimurium genomes to wild birds by a machine learning classifier. Furthermore, virulence gene signatures that differentiated S. Typhimurium from passerines, water birds, and larids were detected. Passerine isolates tended to lack S. Typhimurium-specific virulence plasmids. Isolates from the passerine, water bird, and larid lineages had close genetic relatedness with human clinical isolates, including those from a 2021 U.S. outbreak linked to passerine birds. These observations indicate that S. Typhimurium from wild birds in the United States are likely host-adapted, and the representative genomic data set examined in this study can improve source prediction and facilitate outbreak investigation. [ABSTRACT FROM AUTHOR]

Published
2022
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