Progress 12/18/14 to 09/30/17
Outputs
Target Audience:Key beneficiaries will be dairy and produce farmers in NY as well as small scale and artisan food processors that may be at a higher risk of Salmonella Cerro introduction from environmental sources. This project will specifically provide data that may help dairy and produce farmers reduce introduction of Salmonella thus reducing animal disease issues and produce contamination (and associated recalls), respectively. Farm workers and their families are also beneficiaries as this project will ultimately reduce the risk of zoonotic animal - farm worker transmission. Finally, NYS Dept. of Health and NYS Ag & Mkts will be beneficiaries as the data collected will allow both agencies to rapidly develop and implement improved subtyping methods and surveillance strategies for Salmonella Cerro as well as other Salmonella serotypes. Ultimately, all NYS and US citizens will benefit as this project has the potential to reduce foodborne illness transmission. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided training opportunities in Salmonella research and genomics for (i) one post-doctoral fellows, who was partially supported by this grant, and (ii) a PhD student that contributed to this project, but was supported by an NSF graduate fellowship. The post-doctoral fellow supported by this project has since taken a food microbiology faculty position at Penn State; supporting the success of this project in training food safety scientists. How have the results been disseminated to communities of interest?All genome sequences have been made available through SRA under the BioProject ID PRJNA308933. In addition findings have bene communicated formally through peer-reviewed publications as well as informally to veterinarians and public health staff (e.g., at the New York State Department of Health). What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
To better understand the transmission patterns and drivers of geographic spread of the recently emerged Salmonella serotype Cerro, we studied the genomic similarity and microevolution of Salmonella Cerro isolates from the northeast U.S. and Texas. Eighty-three out of 86 isolates were confirmed as multilocus sequence type 367. We identified core genome SNPs in 57 upstate New York (NY), 2 Pennsylvania (PA), and 27 Texas S. Cerro isolates from dairy cattle, farm environments, raw milk, and one human clinical case and used them to construct a tip-dated phylogeny. S. Cerro isolates clustered in three distinct clades, including (i) clade I (n = 3; 2013) comprising isolates from northwest Texas (NTX), (ii) clade II (n = 14; 2009-2011, 2014) comprising isolates from NY, and (iii) clade III comprising isolates from NY, PA, and central Texas (CTX) in subclade IIIa (n = 45; 2008-2014), and only CTX isolates in subclade IIIb (n D 24; 2013). Temporal phylogenetic analysis estimated the divergence of these three clades from the most recent common ancestor in approximately 1980. The CTX clade IIIb was estimated to have evolved and diverged from the NY ancestor around 2004. Furthermore, gradual temporal loss of genes encoding a D-alanine transporter, involved in virulence, was observed. These genes were present in the isolates endemic to NTX clade I and were gradually lost in clades II and III. The virulence gene orgA, which is part of the Salmonella Pathogenicity Island 1, was lost in a subgroup of Texas isolates in clades I and IIIb. All S. Cerro isolates had an additional cytosine inserted in a cytosine-rich region of the virulence gene sopA, resulting in premature termination of translation likely responsible for loss of pathogenic capacity in humans. A group of closely related NY isolates was characterized by the loss of hydrogen sulfide production due to the truncation or complete loss of phsA. Our data suggest the ability of Salmonella to rapidly diverge and adapt to specific niches (e.g., bovine niche), and to modify virulence-related characteristics such as the ability to utilize tetrathionate as an alternative electron acceptor, which is commonly used to detect Salmonella. Overall, our results illustrate the opportunity to correlate clinical outcome data and genetic data for S. Cerro isolates, such as truncations in virulence genes. Our results not only provide new insights into the emergence and spread of novel Salmonella pheno- and pathotypes, but also illustrate how genomics data can be used to allow for improved, serotype and subtype specific risk assessments that take into account differences in virulence phenotypes among different Salmonella
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Kovac, J., K. J. Cummings, L. D. Rodriguez-Rivera, L. M. Carroll, A. Thachil, and M. Wiedmann. 2017. Temporal genomic phylogeny reconstruction indicates a geospatial transmission path of Salmonella Cerro in the United States and a clade-specific loss of hydrogen sulfide production. Front. Microbiol. 8:737. doi: 10.3389/fmicb.2017.00737
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Miller, R., and M. Wiedmann. 2016. The cytolethal distending toxin produced by nontyphoidal Salmonella serotypes Javiana, Montevideo, Oranienburg, and Mississippi, induces DNA damage in a manner similar to serotype Typhi. mBio Dec 20;7(6). pii: e02109-16. doi: 10.1128/mBio.02109-16
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Miller, R., and M Wiedmann. 2016. Dynamic Duo- The Salmonella Cytolethal Distending Toxin Combines ADP-Ribosyltransferase and Nuclease Activities in a Novel Form of the Cytolethal Distending Toxin. Toxins (Basel). 2016 Apr 25;8(5). pii: E121. doi: 10.3390/toxins8050121
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Key beneficiaries will be dairy and produce farmers in NY as well as small scale and artisan food processors that may be at a higher risk of Salmonella Cerro introduction from environmental sources. This project will specifically provide data that may help dairy and produce farmers reduce introduction of Salmonella thus reducing animal disease issues and produce contamination (and associated recalls), respectively. Farm workers and their families are also beneficiaries as this project will ultimately reduce the risk of zoonotic animal - farm worker transmission. Finally, NYS Dept. of Health and NYS Ag & Mkts will be beneficiaries as the data collected will allow both agencies to rapidly develop and implement improved subtyping methods and surveillance strategies for Salmonella Cerro as well as other Salmonella serotypes. Ultimately, all NYS and US citizens will benefit as this project has the potential to reduce foodborne illness transmission. Key beneficiaries will be dairy and produce farmers in NY as well as small scale and artisan food processors that may be at a higher risk of Salmonella Cerro introduction from environmental sources. This project will specifically provide data that may help dairy and produce farmers reduce introduction of Salmonella thus reducing animal disease issues and produce contamination (and associated recalls), respectively. Farm workers and their families are also beneficiaries as this project will ultimately reduce the risk of zoonotic animal - farm worker transmission. Finally, NYS Dept. of Health and NYS Ag & Mkts will be beneficiaries as the data collected will allow both agencies to rapidly develop and implement improved subtyping methods and surveillance strategies for Salmonella Cerro as well as other Salmonella serotypes. Ultimately, all NYS and US citizens will benefit as this project has the potential to reduce foodborne illness transmission. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided training opportunities in Salmonella research and genomics for (i) a post-doctoral fellow, who was partially supported by this grants as well as a PhD student that contributed to this project, but was supported by an NSF graduate fellowship. The post-doctoral fellow supported by this project has been offered a food microbiology faculty position at Penn State; this further supports the success of this project in training food safety scientists. How have the results been disseminated to communities of interest?Thus far, preliminary results have predominately been communicated informally to veterinarians and public health staff (e.g., at the New York State Department of Health). More formal communications and presentations are planned for project year 3 and a manuscript for publication is currently in progress. In addition, all genome sequences have been made available through SRA under the BioProject ID PRJNA308933. What do you plan to do during the next reporting period to accomplish the goals?Over the next reporting period, we will finish our data analyses and prepare a manuscript for publication. We also plan to identify relevant and promising candidate genes that may be important for the emergence and spread of Salmonella Cerro; these genes could also be used to pursue follow-up experiments that may involve generation and characterization of appropriate null mutants.
Impacts
What was accomplished under these goals?
We identified core genome SNPs for 57 upstate New York (NY), 2 Pennsylvania (PA) and 27 Texas Salmonella Cerro isolated from dairy cattle, farm environment and one human clinical case. Subsequently, we carried out detection of regions of recombination with Gubbins. Final simple SNPs were used to construct tip-dated phylogeny in BEAST using general time-reversible substitution model, lognormal relaxed molecular clock and constant population model. BLAST was used to identify genomic traits that have been associated with impaired virulence of S. Cerro in humans. Isolates clustered in three distinct clades, including (i) on clade comprising isolates from Northwest Texas (NTX), (ii) one clad comprising isolates from NY and PA, and (iii) a third clade comprising isolates from NY and central Texas (CTX), this clade was separated in two robust subclades. Temporal phylogenetic analysis estimated the divergence of these three clades from the most recent common ancestor in early 1990s. The central Texas clade was estimated to evolved and diverge from the NY ancestor in mid-2000s. A group of closely related NY isolates was characterized by the loss of hydrogen sulfide production. Furthermore, gradual temporal loss of genes encoding D-alanine transporter, involved in virulence, was observed. These genes were present in the isolates endemic in NTX and were completely lost in CTX clade that has evolved from Northeastern ancestor. All Salmonella Cerro isolates had an additional cytosine inserted in cytosine rich region of sopA virulence factor, resulting in premature termination of translation likely responsible for loss of pathogenic capacity in humans. Our data show the ability of emerging Salmonella to rapidly evolve and expand in animal populations, which is of concern to the US dairy farmers and industry
Publications
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Progress 12/18/14 to 09/30/15
Outputs
Target Audience:Key beneficiaries will be dairy and produce farmers in NY as well as small scale and artisan food processors that may be at a higher risk of Salmonella Cerro introduction from environmental sources. This project will specifically provide data that may help dairy and produce farmers reduce introduction of Salmonella thus reducing animal disease issues and produce contamination (and associated recalls), respectively. Farm workers and their families are also beneficiaries as this project will ultimately reduce the risk of zoonotic animal - farm worker transmission. Finally, NYS Dept. of Health and NYS Ag & Mkts will be beneficiaries as the data collected will allow both agencies to rapidly develop and implement improved subtyping methods and surveillance strategies for Salmonella Cerro. Ultimately, all NYS and US citizens will benefit as this project has the potential to reduce foodborne illness transmission. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project provided training opportunities in Salmonella research and genomics for (i) a post-doctoral fellow, who was partially supported by this grants as well as a PhD student that contributed to this project, but was supported by an NSF graduate fellowship. How have the results been disseminated to communities of interest?Thus far, preliminary results have predominately been communicated informally to veterinarians and public health staff (e.g., at the New York State Department of Health). More formal communications and presentations are planned for project year 2. What do you plan to do during the next reporting period to accomplish the goals?Over the next reporting period we will focus on phenotypic characterization experiments to identify potential competitive advantages of different Cerro strains in different environments and hosts (AIM 2). Genome sequence data will also be used to characterize Cerro isolates to identify subtypes within the serotype. These data will then be analyzed along with Geographical Information System (GIS) coordinates for isolation location to identify specific risk factors for presence or dispersal of Salmonella Cerro (along bird flyways, major waterways etc.). This will help us to provide specific recommendations for farmers how to reduce the risk of Cerro introduction into dairy farms or onto produce fields.
Impacts
What was accomplished under these goals?
A total of 86 Salmonella enterica Cerro isolated from animal (n = 43), environmental (n = 41), food (n = 1) and human (n = 1) from New York state (as well as comparison isolates form Texas) were selected for the comparative genomic analysis. All animal isolates were of bovine origin and were selected to represent clinical and sub-clinical cases. The environmental isolates were obtained from farm environment, water or soil. A single food isolate was isolated from raw milk, and a single human isolate was a sporadic case of infection that occurred in New York State. Bacterial strains selected for the analyses were isolated within 2009 to 2014. Among the 86 isolates, 13 were sequenced at Cornell University Core facility on an Illumina MiSeq platform using Illumina Nextera XT library kit. The rest of the isolates were sequenced at Texas A&M University sequencing facility on an Illumina HiSeq platform using Bioo Scientific NextFlex library kit. The whole genome sequence (WGS) reads were used to confirm serotype in silico using SeqSero program. The WGS were assembled de novo using SPAdes 3.6.0. The core genome single nucleotide polymorphisms (SNPs) were identified using kSNP v2 and used to build a Maximum likelihood phylogeny in the same program. The 86 isolates clustered in 12 distinct clades. Majority of identified clades included isolates from a single state. Geospatial and temporal clustering will be further investigated. Further analysis will be carried out also to identify clade-specific genetic features and their association with virulence in animals. Furthermore, WGS data was used to confirm presence of key genes involved in hydrogen sulfide production pathway. Hydrogen sulfide is one of the key identification features exploited in classical microbiological isolation procedures for Salmonella. High prevalence of non-hydrogen producing Salmonella isolates can therefore complicate isolation and identification procedures for Salmonella. We have searched for presence of eleven genes that were involved in a functional association network of thiosulfate reductase (encoded by phsA), as determined by STRING database of known and predicted protein interactions. The genes identified by STRING were STY2774 asrA, asrC, cysJ, cyst, phsB, phsC, ttrA, ttrB and ttr, encoding anaerobic reductase protein, anaerobic sulfite reductase subunits A and C, sulfite reductase flavoprotein sububit alpha, SMT1943 tRNA gene, thiosulfate reductase electron transport protein, thiosulfate reductase cytochrome B subunit and tetrathionate reductase subunits A, B and C, respectively. The representative sequences for these eleven genes (called reference sequences) were extracted from NCBI Gene. Nucleotide reference sequences were used for BLAST searches against the local WGS database that contained the Salmonella Cerro genomes. All eleven reference sequences were identified in all except three isolates (FSL R9-1904, FSL R9-1131, FSL R9-1902). Isolate FSL R9-1904 was isolated in 2012 and FSL R9-1131 and FSL R9-1902 were isolated in 2013. The shorter variant of the gene encoding a thiosulfate reductase (phsA; Sakano et al., 2013) was identified also in isolates FSL R9-1904 and FSL R9-1902 (75% of the full length), as well as FSL R9-1131 (52% of the full length). The rest of the eleven genes were not detected in these isolates. The non-production of hydrogen sulfide will be confirmed in phenotypic experiments to confirm the congruence with in results of in silico analysis.
Publications
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