{"entity": "researcher", "timestamp": "2026-06-17T07:28:45.912Z", "family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "affiliations": ["Department of Food Science, Cornell University, Ithaca, New York, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf"}}, "publications": [{"entity": "publication", "iuid": "1ea481b2eda848ba8b5b32273d7f0922", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ea481b2eda848ba8b5b32273d7f0922.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ea481b2eda848ba8b5b32273d7f0922"}}, "title": "Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.", "authors": [{"family": "Cohn", "given": "Alexa R", "initials": "AR"}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM", "orcid": "0000-0002-3677-0192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/02112eccb0664819af916a3c3dc79daa.json"}}, {"family": "Liao", "given": "Jingqiu", "initials": "J", "orcid": "0000-0002-2579-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac812840b9814e919ed1dca12a484c87.json"}}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Cheng", "given": "Rachel A", "initials": "RA", "orcid": "0000-0002-5932-7011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b1b7638c9c4ec7bad01d1ad6497b6a.json"}}], "type": "journal article", "published": "2022-11-30", "journal": {"title": "Front Microbiol", "issn": "1664-302X", "volume": "13", "pages": "1005215", "issn-l": "1664-302X"}, "abstract": "Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome. Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.", "doi": "10.3389/fmicb.2022.1005215", "pmid": "36532462", "labels": {"DDLS Fellow": null, "Laura Carroll": null}, "xrefs": [{"db": "pmc", "key": "PMC9748477"}], "notes": [], "created": "2023-05-13T11:52:27.912Z", "modified": "2025-04-29T07:05:49.849Z"}, {"entity": "publication", "iuid": "204a710ec66d401d8f64c2559f2bbffd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/204a710ec66d401d8f64c2559f2bbffd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/204a710ec66d401d8f64c2559f2bbffd"}}, "title": "Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil.", "authors": [{"family": "Kipper", "given": "Di\u00e9ssy", "initials": "D"}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Mascitti", "given": "Andrea K", "initials": "AK"}, {"family": "Streck", "given": "Andr\u00e9 F", "initials": "AF", "orcid": "0000-0002-4798-0777", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7e3f45fa7b4a4937bdd166ef667549e0.json"}}, {"family": "Fonseca", "given": "Andr\u00e9 S K", "initials": "ASK"}, {"family": "Ikuta", "given": "Nilo", "initials": "N"}, {"family": "Tondo", "given": "Eduardo C", "initials": "EC"}, {"family": "Wiedmann", "given": "Martin", "initials": "M", "orcid": "0000-0002-4168-5662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ff5ceeea60684abeb83951c53f7b6e31.json"}}, {"family": "Lunge", "given": "Vagner R", "initials": "VR", "orcid": "0000-0003-4012-8650", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33c4324875e6436d9cb3433bf215a1bb.json"}}], "type": "journal article", "published": "2021-10-14", "journal": {"title": "Applied and environmental microbiology", "issn": "1098-5336", "volume": "87", "issue": "21", "pages": "e0103621", "issn-l": "0099-2240"}, "abstract": "Salmonella enterica serovar Heidelberg is isolated from poultry-producing regions around the world. In Brazil, S. Heidelberg has been frequently detected in poultry flocks, slaughterhouses, and chicken meat. The goal of the present study was to assess the population structure, recent temporal evolution, and some important genetic characteristics of S. Heidelberg isolated from Brazilian poultry farms. Phylogenetic analysis of 68 S. Heidelberg genomes sequenced here and additional whole-genome data from NCBI demonstrated that all isolates from the Brazilian poultry production chain clustered into a monophyletic group, here called S. Heidelberg Brazilian poultry lineage (SH-BPL). Bayesian analysis defined the time of the most recent common ancestor (tMRCA) as 2004, and the overall population size (N) was constant until 2008, when an \u223c10-fold eN increase was observed until circa 2013. SH-BPL presented at least two plasmids with replicons ColpVC (en = 68; 100%), IncX1 (n = 66; 97%), IncA/C2 (n = 65; 95.5%), ColRNAI (n = 43; 63.2%), IncI1 (n = 32; 47%), ColMG828, Col156, IncHI2A, IncHI2, IncQ1, IncX4, IncY, and TrfA (each with n < 4; <4% each). Antibiotic resistance genes were found, with high frequencies of fosA7 (n = 68; 100%), mdf(A) (n = 68; 100%), tet(34) (n = 68; 100%), sul2 (n = 64; 94.1%), and blaCMY-2 (n = 56; 82.3%), along with an overall multidrug resistance (MDR) profile. Ten Salmonella pathogenicity islands (SPI1 to SPI5, SPI9, and SPI11 to SPI14) and 139 virulence genes were also detected. The SH-BPL profile was like those of other previous S. Heidelberg isolates from poultry around the world in the 1990s. In conclusion, the present study demonstrates the recent introduction (2004) and high level of dissemination of an MDR S. Heidelberg lineage in Brazilian poultry operations. IMPORTANCES. Heidelberg is the most frequent serovar in several broiler farms from the main Brazilian poultry-producing regions. Therefore, avian-source foods (mainly chicken carcasses) commercialized in the country and exported to other continents are contaminated with this foodborne pathogen, generating several national and international economic losses. In addition, isolates of this serovar are usually resistant to antibiotics and can cause human invasive and septicemic infection, representing a public health concern. This study demonstrates the use of whole-genome sequencing (WGS) to obtain epidemiological information for one S. Heidelberg lineage highly spread among Brazilian poultry farms. This information will help to define biosecurity measures to control this important Salmonella serovar in Brazilian and worldwide poultry operations.", "doi": "10.1128/AEM.01036-21", "pmid": "34406824", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC8516049"}], "notes": [], "created": "2025-03-18T17:27:36.310Z", "modified": "2025-03-18T17:27:36.482Z"}, {"entity": "publication", "iuid": "0975152f3c0e48d89ba780a04681382b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0975152f3c0e48d89ba780a04681382b"}}, "title": "Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica.", "authors": [{"family": "Liao", "given": "Jingqiu", "initials": "J", "orcid": "0000-0002-2579-8157", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac812840b9814e919ed1dca12a484c87.json"}}, {"family": "Orsi", "given": "Renato Hohl", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-07-00", "journal": {"title": "Environ. Microbiol.", "issn": "1462-2920", "volume": "22", "issue": "7", "pages": "2811-2828", "issn-l": "1462-2912"}, "abstract": "Genetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York and Washington states to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.", "doi": "10.1111/1462-2920.15014", "pmid": "32337816", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T17:25:39.817Z", "modified": "2025-03-18T17:25:39.889Z"}, {"entity": "publication", "iuid": "5afc72774c7c476086ecf048588acc1d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5afc72774c7c476086ecf048588acc1d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5afc72774c7c476086ecf048588acc1d"}}, "title": "Paenibacillus odorifer, the Predominant Paenibacillus Species Isolated from Milk in the United States, Demonstrates Genetic and Phenotypic Conservation of Psychrotolerance but Clade-Associated Differences in Nitrogen Metabolic Pathways.", "authors": [{"family": "Beno", "given": "Sarah M", "initials": "SM"}, {"family": "Cheng", "given": "Rachel A", "initials": "RA", "orcid": "0000-0002-5932-7011", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4b1b7638c9c4ec7bad01d1ad6497b6a.json"}}, {"family": "Orsi", "given": "Renato H", "initials": "RH", "orcid": "0000-0003-4933-9817", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/faa4bd30679547898c7bd57690ba18bf.json"}}, {"family": "Duncan", "given": "Diana R", "initials": "DR"}, {"family": "Guo", "given": "Xiaodong", "initials": "X"}, {"family": "Kovac", "given": "Jasna", "initials": "J", "orcid": "0000-0002-9465-4552", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d18e6f5bd24644e18030b59391d1a755.json"}}, {"family": "Carroll", "given": "Laura M", "initials": "LM"}, {"family": "Martin", "given": "Nicole H", "initials": "NH"}, {"family": "Wiedmann", "given": "Martin", "initials": "M"}], "type": "journal article", "published": "2020-01-22", "journal": {"title": "mSphere", "issn": "2379-5042", "volume": "5", "issue": "1", "issn-l": "2379-5042"}, "abstract": "Paenibacillus is a spore-forming bacterial genus that is frequently isolated from fluid milk and is proposed to play a role in spoilage. To characterize the genetic and phenotypic diversity of Paenibacillus spp., we first used rpoB allelic typing data for a preexisting collection of 1,228 Paenibacillus species isolates collected from raw and processed milk, milk products, and dairy environmental sources. Whole-genome sequencing (WGS) and average nucleotide identity by BLAST (ANIb) analyses performed for a subset of 58 isolates representing unique and overrepresented rpoB allelic types in the collection revealed that these isolates represent 21 different Paenibacillus spp., with P. odorifer being the predominant species. Further genomic characterization of P. odorifer isolates identified two distinct phylogenetic clades, clades A and B, which showed significant overrepresentation of 172 and 164 ortholog clusters and 94 and 52 gene ontology (GO) terms, respectively. While nitrogen fixation genes were found in both clades, multiple genes associated with nitrate and nitrite reduction were overrepresented in clade A isolates; additional phenotypic testing demonstrated that nitrate reduction is specific to isolates in clade A. Hidden Markov models detected 9 to 10 different classes of cold shock-associated genetic elements in all P. odorifer isolates. Phenotypic testing revealed that all isolates tested here can grow in skim milk broth at 6\u00b0C, suggesting that psychrotolerance is conserved in P. odorifer Overall, our data suggest that Paenibacillus spp. isolated from milk in the United States represent broad genetic diversity, which may provide challenges for targeted-control strategies aimed at reducing fluid milk spoilage.IMPORTANCE Although Paenibacillus species isolates are frequently isolated from pasteurized fluid milk, the link between the genetic diversity and phenotypic characteristics of these isolates was not well understood, especially as some Bacillales isolated from milk are unable to grow at refrigeration temperatures. Our data demonstrate that Paenibacillus spp. isolated from fluid milk represent tremendous interspecies diversity, with P. odorifer being the predominant Paenibacillus sp. isolated. Furthermore, genetic and phenotypic data support that P. odorifer is well suited to transition from a soil-dwelling environment, where nitrogen fixation (and other nitrate/nitrite reduction pathways present only in clade A) may facilitate growth, to fluid milk, where its multiple cold shock-associated adaptations enable it to grow at refrigeration temperatures throughout the storage of milk. Therefore, efforts to reduce bacterial contamination of milk will require a systematic approach to reduce P. odorifer contamination of raw milk.", "doi": "10.1128/mSphere.00739-19", "pmid": "31969477", "labels": {"Laura Carroll": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7407005"}, {"db": "pii", "key": "5/1/e00739-19"}], "notes": [], "created": "2025-03-18T17:25:13.299Z", "modified": "2025-03-18T17:25:13.415Z"}]}