Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species

Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublin...

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Published inPloS one Vol. 7; no. 11; p. e49455
Main Authors Joseph, Susan, Desai, Prerak, Ji, Yongmei, Cummings, Craig A., Shih, Rita, Degoricija, Lovorka, Rico, Alain, Brzoska, Pius, Hamby, Stephen E., Masood, Naqash, Hariri, Sumyya, Sonbol, Hana, Chuzhanova, Nadia, McClelland, Michael, Furtado, Manohar R., Forsythe, Stephen J.
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 16.11.2012
Public Library of Science (PLoS)
Subjects
Adhesins
Baby foods
Bacteremia
Bacteria
Bacterial infections
Bacterial Secretion Systems - genetics
Base Sequence
Bioinformatics
Biology
Brain research
Comparative analysis
Copper
Cronobacter
Cronobacter - genetics
Cronobacter - pathogenicity
Deoxyribonucleic acid
Divergence
DNA
DNA sequencing
E coli
Enterobacter
Enterocolitis
Escherichia coli
Evolution, Molecular
Factories
Fimbriae, Bacterial - genetics
Food contamination
Gene sequencing
Genes
Genetic research
Genome, Bacterial - genetics
Genomes
Genomics
Infections
Likelihood Functions
Medicine
Meningitis
Metals
Models, Genetic
Molecular Sequence Data
Multigene Family - genetics
Neonates
Nucleotide sequence
Phylogeny
Prophages
Science
Secretion
Sequence Analysis, DNA
Silver
Species
Species Specificity
Tellurite
Vaccines
Veterinary Science
Virulence
Virulence Factors - genetics
United States > US
California
Online AccessGet full text

Cover

Abstract Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
AbstractList Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. Methodology/Principal Findings We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Conclusions/Significance Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages. Methodology/Principal Findings We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes. Conclusions/Significance Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages.BACKGROUNDSpecies of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including bacteraemia, meningitis, and necrotising enterocolitis. The genus is composed of seven species: C. sakazakii, C. malonaticus, C. turicensis, C. dublinensis, C. muytjensii, C. universalis, and C. condimenti. Clinical cases are associated with three species, C. malonaticus, C. turicensis and, in particular, with C. sakazakii multilocus sequence type 4. Thus, it is plausible that virulence determinants have evolved in certain lineages.We generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes.METHODOLOGY/PRINCIPAL FINDINGSWe generated high quality sequence drafts for eleven Cronobacter genomes representing the seven Cronobacter species, including an ST4 strain of C. sakazakii. Comparative analysis of these genomes together with the two publicly available genomes revealed Cronobacter has over 6,000 genes in one or more strains and over 2,000 genes shared by all Cronobacter. Considerable variation in the presence of traits such as type six secretion systems, metal resistance (tellurite, copper and silver), and adhesins were found. C. sakazakii is unique in the Cronobacter genus in encoding genes enabling the utilization of exogenous sialic acid which may have clinical significance. The C. sakazakii ST4 strain 701 contained additional genes as compared to other C. sakazakii but none of them were known specific virulence-related genes.Genome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.CONCLUSIONS/SIGNIFICANCEGenome comparison revealed that pair-wise DNA sequence identity varies between 89 and 97% in the seven Cronobacter species, and also suggested various degrees of divergence. Sets of universal core genes and accessory genes unique to each strain were identified. These gene sequences can be used for designing genus/species specific detection assays. Genes encoding adhesins, T6SS, and metal resistance genes as well as prophages are found in only subsets of genomes and have contributed considerably to the variation of genomic content. Differences in gene content likely contribute to differences in the clinical and environmental distribution of species and sequence types.
Audience Academic
Author Brzoska, Pius
Joseph, Susan
Cummings, Craig A.
Hariri, Sumyya
Rico, Alain
Hamby, Stephen E.
Sonbol, Hana
McClelland, Michael
Shih, Rita
Furtado, Manohar R.
Masood, Naqash
Ji, Yongmei
Degoricija, Lovorka
Desai, Prerak
Chuzhanova, Nadia
Forsythe, Stephen J.
AuthorAffiliation 3 Life Technologies Corporation, Foster City, California, United States of America
6 Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
5 Bioinformatics and Biomathematics Group, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
1 Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
Emory University, United States of America
4 Life Technologies Corporation, Darmstadt, Germany
2 Vaccine Research Institute San Diego, San Diego, California, United States of America
AuthorAffiliation_xml – name: 3 Life Technologies Corporation, Foster City, California, United States of America
– name: 5 Bioinformatics and Biomathematics Group, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
– name: 2 Vaccine Research Institute San Diego, San Diego, California, United States of America
– name: Emory University, United States of America
– name: 1 Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
– name: 4 Life Technologies Corporation, Darmstadt, Germany
– name: 6 Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
Author_xml – sequence: 1
  givenname: Susan
  surname: Joseph
  fullname: Joseph, Susan
– sequence: 2
  givenname: Prerak
  surname: Desai
  fullname: Desai, Prerak
– sequence: 3
  givenname: Yongmei
  surname: Ji
  fullname: Ji, Yongmei
– sequence: 4
  givenname: Craig A.
  surname: Cummings
  fullname: Cummings, Craig A.
– sequence: 5
  givenname: Rita
  surname: Shih
  fullname: Shih, Rita
– sequence: 6
  givenname: Lovorka
  surname: Degoricija
  fullname: Degoricija, Lovorka
– sequence: 7
  givenname: Alain
  surname: Rico
  fullname: Rico, Alain
– sequence: 8
  givenname: Pius
  surname: Brzoska
  fullname: Brzoska, Pius
– sequence: 9
  givenname: Stephen E.
  surname: Hamby
  fullname: Hamby, Stephen E.
– sequence: 10
  givenname: Naqash
  surname: Masood
  fullname: Masood, Naqash
– sequence: 11
  givenname: Sumyya
  surname: Hariri
  fullname: Hariri, Sumyya
– sequence: 12
  givenname: Hana
  surname: Sonbol
  fullname: Sonbol, Hana
– sequence: 13
  givenname: Nadia
  surname: Chuzhanova
  fullname: Chuzhanova, Nadia
– sequence: 14
  givenname: Michael
  surname: McClelland
  fullname: McClelland, Michael
– sequence: 15
  givenname: Manohar R.
  surname: Furtado
  fullname: Furtado, Manohar R.
– sequence: 16
  givenname: Stephen J.
  surname: Forsythe
  fullname: Forsythe, Stephen J.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23166675$$D View this record in MEDLINE/PubMed
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Current address: The University of Chicago Booth School of Business, Chicago, Illinois, United States of America
Current address: Sequenta, Inc., South San Francisco, California, United States of America
Competing Interests: The authors have the following interests. YJ was employed by Life Technologies, RS is an employee of Life Technologies, LD is an employee of Life Technologies, PB is an employee of Life Technologies, AR was employed by Life Technologies, CAC was employed by Life Technologies and owns stock in the company, MF is an employee of Life Technologies and owns stock in LIFE. This work was funded by Life Technologies who also performed the genome sequencing. In addition, one of the co-authors, Craig Cummings is now an employee of Sequenta, Inc. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.
Conceived and designed the experiments: YJ CC SJ SJF. Performed the experiments: SJ SH HS YJ AR. Analyzed the data: YJ PD LD PB RS CC SEH NM SJ SH HS AR NC MM SJF. Contributed reagents/materials/analysis tools: MM MF. Wrote the paper: YJ CC MM SEH NC SJ SJF.
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Snippet Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases, including...
Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases,...
Background Species of Cronobacter are widespread in the environment and are occasional food-borne pathogens associated with serious neonatal diseases,...
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SubjectTerms Adhesins
Baby foods
Bacteremia
Bacteria
Bacterial infections
Bacterial Secretion Systems - genetics
Base Sequence
Bioinformatics
Biology
Brain research
Comparative analysis
Copper
Cronobacter
Cronobacter - genetics
Cronobacter - pathogenicity
Deoxyribonucleic acid
Divergence
DNA
DNA sequencing
E coli
Enterobacter
Enterocolitis
Escherichia coli
Evolution, Molecular
Factories
Fimbriae, Bacterial - genetics
Food contamination
Gene sequencing
Genes
Genetic research
Genome, Bacterial - genetics
Genomes
Genomics
Infections
Likelihood Functions
Medicine
Meningitis
Metals
Models, Genetic
Molecular Sequence Data
Multigene Family - genetics
Neonates
Nucleotide sequence
Phylogeny
Prophages
Science
Secretion
Sequence Analysis, DNA
Silver
Species
Species Specificity
Tellurite
Vaccines
Veterinary Science
Virulence
Virulence Factors - genetics
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Title Comparative Analysis of Genome Sequences Covering the Seven Cronobacter Species
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https://pubmed.ncbi.nlm.nih.gov/PMC3500316
https://doaj.org/article/cf6e6020440d4df782de12a51f936d4d
http://dx.doi.org/10.1371/journal.pone.0049455
Volume 7
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