Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States

Lorraine D. Rodriguez-Rivera, Andrea I. Moreno Switt, Lovorka Degoricija, Rixun Fang, Craig A. Cummings, Manohar R. Furtado, Martin Wiedmann, Henk C. Den Bakker

Resultado de la investigación: Article

11 Citas (Scopus)

Resumen

Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here " NY bovine clade" ), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.

Idioma originalEnglish
Número de artículo427
PublicaciónBMC Genomics
Volumen15
N.º1
DOI
EstadoPublished - 4 jun 2014

Huella dactilar

Salmonella
Virulence
Metagenomics
Serogroup
Clone Cells
Genome
Salmonella enterica
Nonsense Codon
Gene Deletion

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Medicine(all)

Citar esto

Rodriguez-Rivera, L. D., Moreno Switt, A. I., Degoricija, L., Fang, R., Cummings, C. A., Furtado, M. R., ... Den Bakker, H. C. (2014). Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States. BMC Genomics, 15(1), [427]. https://doi.org/10.1186/1471-2164-15-427
Rodriguez-Rivera, Lorraine D. ; Moreno Switt, Andrea I. ; Degoricija, Lovorka ; Fang, Rixun ; Cummings, Craig A. ; Furtado, Manohar R. ; Wiedmann, Martin ; Den Bakker, Henk C. / Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States. En: BMC Genomics. 2014 ; Vol. 15, N.º 1.
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title = "Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States",
abstract = "Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here {"} NY bovine clade{"} ), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.",
author = "Rodriguez-Rivera, {Lorraine D.} and {Moreno Switt}, {Andrea I.} and Lovorka Degoricija and Rixun Fang and Cummings, {Craig A.} and Furtado, {Manohar R.} and Martin Wiedmann and {Den Bakker}, {Henk C.}",
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Rodriguez-Rivera, LD, Moreno Switt, AI, Degoricija, L, Fang, R, Cummings, CA, Furtado, MR, Wiedmann, M & Den Bakker, HC 2014, 'Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States', BMC Genomics, vol. 15, n.º 1, 427. https://doi.org/10.1186/1471-2164-15-427

Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States. / Rodriguez-Rivera, Lorraine D.; Moreno Switt, Andrea I.; Degoricija, Lovorka; Fang, Rixun; Cummings, Craig A.; Furtado, Manohar R.; Wiedmann, Martin; Den Bakker, Henk C.

En: BMC Genomics, Vol. 15, N.º 1, 427, 04.06.2014.

Resultado de la investigación: Article

TY - JOUR

T1 - Genomic characterization of Salmonella Cerro ST367, an emerging Salmonella subtype in cattle in the United States

AU - Rodriguez-Rivera, Lorraine D.

AU - Moreno Switt, Andrea I.

AU - Degoricija, Lovorka

AU - Fang, Rixun

AU - Cummings, Craig A.

AU - Furtado, Manohar R.

AU - Wiedmann, Martin

AU - Den Bakker, Henk C.

PY - 2014/6/4

Y1 - 2014/6/4

N2 - Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here " NY bovine clade" ), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.

AB - Background: Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar.Results: In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here " NY bovine clade" ), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone.Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche.Conclusions: Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts.

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U2 - 10.1186/1471-2164-15-427

DO - 10.1186/1471-2164-15-427

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