Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Carroll, Laura M.; Bakker, Henk D.; Siler, Julie D.; Warchocki, Steven; Kent, David J.; Lyalina, Svetlana; Davis, Margaret A.; Sischo, William M.; Besser, Thomas E.; Warnick, Lorin D.; Pereira, Richard Van Vleck

doi:10.1128/aem.00140-17

Cited by 92 publications

(124 citation statements)

References 66 publications

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“…Previously, WGS has been used to differentiate drug-resistant S. enterica isolates from different locations, which can exhibit notable differences in resistant-relevant genotypic and phenotypic characteristics (34). Other research has shown WGS can be valuable in predicting phenotypic resistance among both S. enterica (34, 35) and E. coli (36). In the current study, WGS analyses revealed that all our Subgroup B2 isolates carried bla TEM - 1 and tetA.…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s

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Cao

Luo

et al. 2018

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20advances understanding of SE and the role mice may play in SE contamination and 44 spread among poultry population. Our data was able to identify SE isolates from 45 different farms or years of collection. Moreover, the annotations of clade-defining SNPs 46 provided information about possible protein functions among these SE isolates from 47 each subgroup. Clade-defining or farm-unique biomarkers were useful for rapid 48 detection and outbreak investigations. 49 homogeneous isolates (1, 7, 15). Application of WGS have also been useful in other 74 microorganisms, including E. coli (16), Vibrio cholera (17), and Staphylococcus aureus 75 (18). 76 Importantly, WGS can be also applied to historic isolates, some of which have been 77 stored for decades. Data from those historic isolates should allow us to understand the 78 origin and persistence of important traits. In this current project, we sequenced 91 SE 79 isolated from 82 mice at poultry farms during the 1990s, which lets us to compare both 80 site and host-adaptions with those of isolates from more recent sampling. Documenting 81 these genomes and fitting them into large-scale phylogeny projects such as 82 GenomeTrakr 83 (https://www.fda.gov/Food/FoodScienceResearch/WholeGenomeSequencingProgram 84 WGS/ucm363134.htm) and NCBI Pathogen Detection Isolates Browser 85 (https://www.ncbi.nlm.nih.gov/pathogens/) will refine our understanding of SE 86 contamination and spread in poultry facilities (19). Further, identifying and 87 characterizing biomarkers can facilitate the development of rapid and reliable tests that 88 could guide appropriate interventions during future outbreaks. 89 6 Materials and Methods 90 Bacterial isolates 91 Ninety-one SE isolates from mouse spleens (n=62) and intestines (n=29), collected 92 from 15 poultry farms in Pennsylvania during 1995-1998, are listed in Table 1. Among 93 these isolates, eight pairs were isolated from the spleen and intestine of the same 94 mouse; these were designated as m1 through m8. These isolates are archived under 95 Bioproject Number PRJNA186035 (https://www.ncbi.nlm.nih.gov/bioproject/186035). 96 Whole genome sequencing and assembly 97Genomic DNA was extracted after incubation of culture for 16 hours at 37 ºC in 98Trypticase Soy Broth (TSB) using the DNeasy Blood and Tissue Kit (Qiagen Inc, 99

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Section: Discussionmentioning

confidence: 99%

Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s

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Cao

Luo

et al. 2018

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“…Partial genes only accounted for 6.4% of streptomycin discrepancies, suggesting this observation is not due to potential non-functional genes. While the mechanism of discordance between streptomycin resistance genes and susceptibility is unclear, this relationship has been observed in multiple surveys of Enterobacteriaceae (14, 16, 51, 54, 55). [also see S. 8]…”

Section: Resultsmentioning

confidence: 97%

Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates

Feldgarden¹,

Brover²,

Dh³

et al. 2019

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“…Similar phylogeographical separation has also been observed in S. Dublin as well. Strains isolated from New York and Washington states cluster into distinct clades (9). We did not consider within country clustering due to the paucity of certain samples metadata (lack of specific region details).…”

Section: Discussionmentioning

confidence: 99%

“…Current genomics of S. Dublin has primarily focused upon the identification of antimicrobial resistance (AMR) homologues and mobile genetic elements such as prophages and plasmids (9–11). S. Dublin genome diversification appears to be driven by horizontal gene transfer and genome degradation resulting in pseudogenes (11).…”

Section: Introductionmentioning

confidence: 99%

Geography Shapes the Population Genomics ofSalmonella entericaDublin

Fenske

Thachil

McDonough

et al. 2019

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Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that 27 can cause serious systemic infections in humans. Despite the increasing prevalence of human 28 infections and the negative impact on agricultural processes, little is known about the population 29 structure of the serotype. To this end, we compiled a manually curated dataset comprising of 880 30 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that 31 region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin 32 in the UK are genomically distinct from US, Brazilian and African strains. The geographical 33 partitioning impacts the composition of the core genome as well as the ancillary genome. 34Antibiotic resistance genes are almost exclusively found in US genomes and is mediated by an 35IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in 36 the serotype. Comparison of S. Dublin to a closely related serotype, Salmonella enterica 37 serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not 38 found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and 39 catabolism of carbohydrates and virulence genes associated with type VI secretion systems and 40 fimbria assembly respectively. 41 IMPORTANCE S. Dublin is a bovine-adapted strain that can also cause human infections. 42Typical S. Dublin human infections are characterized by invasion of tissue that ultimately 43 traverses to the bloodstream causing life-threatening systemic cases. The preferred course of 44 treatment for such infection is the administration of antibiotics. Thus, it is important to study the 45 population structure of the serotype to monitor and identify which strains present the greatest 46 threats to public health. Consequently, in this work, it was found that S. Dublin genomic features 47 are greatly influenced by the region in which they populate. Our analysis found that most S. 48Dublin isolates from the US are distinct and have gained multidrug resistance through a new 49 hybrid plasmid. Thus, it would be expected that infections in the US would respond less 50 favorably to the first line of therapy and the region acts as the major source of a multidrug-51 resistant S. Dublin.

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Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

Cited by 92 publications

References 66 publications

Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s

Whole genome sequence analysis of 91SalmonellaEnteritidis isolates from mice caught on poultry farms in the mid 1990s

Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates

Geography Shapes the Population Genomics ofSalmonella entericaDublin

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