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Jaradat ZW, Al-Mousa WA, Elbetieha AM, Ababneh QO, Al-Nabulsi AA, Jang H, Gangiredla J, Patel IR, Gopinath GR, Tall BD. Virulence, antimicrobial susceptibility, and phylogenetic analysis of Cronobacter sakazakii isolates of food origins from Jordan. J Appl Microbiol 2022; 133:2528-2546. [PMID: 35858752 DOI: 10.1111/jam.15723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022]
Abstract
AIMS to characterize a collection of Cronobacter sakazakii isolates collected from various origins in Jordan. METHODS AND RESULTS the isolates were characterized using 16S rRNA sequencing, DNA microarray, multi-locus sequence typing (MLST), O-serotyping, virulence gene identification, and antibiotic susceptibility testing. The identities and phylogenetic relatedness revealed that C. sakazakii sequence type 4 (ST4) and Csak O:1 serotype was the most prevalent STs and serovars among these C. sakazakii strains. PCR screening of putative virulence genes showed that the siderophore-interacting protein gene (sip) and iron acquisition gene clusters (eitCBAD and iucABCD/iutA) were the most detected genes with noticeable variability in the type 6 secretion system (T6SS) and filamentous hemagglutinin/adhesion (FHA) gene loci. The antibiotic resistance profiles revealed that the majority of the isolates were susceptible to all antibiotics used despite harboring a class C β-lactamase resistance gene. CONCLUSIONS the results described in this report provide additional insights about the considerable genotypic and phenotypic heterogeneity within C. sakazakii. SIGNIFICANCE AND IMPACT OF THE STUDY the information reported in this study might be of great value in understanding the origins of C. sakazakii isolates, in addition to their diversity and variability, which might be helpful in preventing future outbreaks of this pathogen.
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Affiliation(s)
- Ziad W Jaradat
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, P. O Box 3030, 22110, Jordan
| | - Waseem A Al-Mousa
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, P. O Box 3030, 22110, Jordan
| | - Ahmed M Elbetieha
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, P. O Box 3030, 22110, Jordan
| | - Qutaiba O Ababneh
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid, P. O Box 3030, 22110, Jordan
| | - Anas A Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, P. O Box 3030, 22110, Irbid, Jordan
| | - Hyein Jang
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 20708, Laurel, MD
| | - Jayanthi Gangiredla
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 20708, Laurel, MD
| | - Isha R Patel
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 20708, Laurel, MD
| | - Gopal R Gopinath
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 20708, Laurel, MD
| | - Ben D Tall
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, 20708, Laurel, MD
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Jang H, Eshwar A, Lehner A, Gangiredla J, Patel IR, Beaubrun JJG, Chase HR, Negrete F, Finkelstein S, Weinstein LM, Ko K, Addy N, Ewing L, Woo J, Lee Y, Seo K, Jaradat Z, Srikumar S, Fanning S, Stephan R, Tall BD, Gopinath GR. Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. Microorganisms 2022; 10:microorganisms10071396. [PMID: 35889115 PMCID: PMC9319161 DOI: 10.3390/microorganisms10071396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.
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Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Junia Jean-Gilles Beaubrun
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Hannah R. Chase
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Leah M. Weinstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Katie Ko
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Nicole Addy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Laura Ewing
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Jungha Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Youyoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Ziad Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
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Gopinath GR, Jang H, Beaubrun JJG, Gangiredla J, Mammel MK, Müller A, Tamber S, Patel IR, Ewing L, Weinstein LM, Wang CZ, Finkelstein S, Negrete F, Muruvanda T, Allard M, Sockett DC, Pagotto F, Tall BD, Stephan R. Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes. Microorganisms 2022; 10:microorganisms10061199. [PMID: 35744717 PMCID: PMC9228720 DOI: 10.3390/microorganisms10061199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/04/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.
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Affiliation(s)
- Gopal R. Gopinath
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Correspondence: ; Tel.: +1-240-402-3612
| | - Hyein Jang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Junia Jean-Gilles Beaubrun
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
- Biological Analysis Division, Public Health Command Europe Laboratory Sciences, Room 102, Bldg 3810, Kirchberg Kaserne, RP 66849 Landstuhl, Germany
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Mark K. Mammel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Andrea Müller
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
| | - Sandeep Tamber
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Isha R. Patel
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Laura Ewing
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Leah M. Weinstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Caroline Z. Wang
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Samantha Finkelstein
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Flavia Negrete
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Tim Muruvanda
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Marc Allard
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD 20740, USA; (T.M.); (M.A.)
| | - Donald C. Sockett
- Wisconsin Veterinary Diagnostic Laboratory, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards/Health Canada, Ottawa, ON K1A 0K9, Canada; (S.T.); (F.P.)
| | - Ben D. Tall
- Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.J.-G.B.); (J.G.); (M.K.M.); (I.R.P.); (L.E.); (L.M.W.); (C.Z.W.); (S.F.); (F.N.); (B.D.T.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.M.); (R.S.)
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Negrete FJ, Ko K, Jang H, Hoffmann M, Lehner A, Stephan R, Fanning S, Tall BD, Gopinath GR. Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities. Gut Pathog 2022; 14:23. [PMID: 35668537 PMCID: PMC9169379 DOI: 10.1186/s13099-022-00500-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cronobacter sakazakii is a foodborne pathogen that causes septicemia, meningitis, and necrotizing enterocolitis in neonates and infants. The current research details the full genome sequences of two extremely persistent C. sakazakii strains (H322 and GK1025B) isolated from powdered infant formula (PIF) manufacturing settings. In addition, the genetic attributes associated with five plasmids, pH322_1, pH322_2, pGK1025B_1, pGK1025B_2, and pGK1025B_3 are described. Materials and Methods Using PacBio single-molecule real-time (SMRT®) sequencing technology, whole genome sequence (WGS) assemblies of C. sakazakii H322 [Sequence type (ST)83, clonal complex [CC] 83) and GK1025B (ST64, CC64) were generated. Plasmids, also sequenced, were aligned with phylogenetically related episomes to determine, and identify conserved and missing genomic regions. Results A truncated ~ 13 Kbp type 6 secretion system (T6SS) gene cluster harbored on virulence plasmids pH322_2 and pGK1025B_2, and a second large deletion (~ 6 Kbp) on pH322_2, which included genes for a tyrosine-type recombinase/integrase, a hypothetical protein, and a phospholipase D was identified. Within the T6SS of pH322_2 and pGK1025B_2, an arsenic resistance operon was identified which is in common with that of plasmids pSP291_1 and pESA3. In addition, PHASTER analysis identified an intact 96.9 Kbp Salmonella SSU5 prophage gene cluster in pH322_1 and pGK1025B_1 and showed that these two plasmids were phylogenetically related to C. sakazakii plasmids: pCS1, pCsa767a, pCsaC757b, pCsaC105731a. Plasmid pGK1025B_3 was identified as a novel conjugative Cronobacter plasmid. Furthermore, WGS analysis identified a ~ 16.4 Kbp type 4 secretion system gene cluster harbored on pGK1025B_3, which contained a phospholipase D gene, a key virulence factor in several host–pathogen diseases. Conclusion These data provide high resolution information on C. sakazakii genomes and emphasizes the need for furthering surveillance studies to link genotype to phenotype of strains from previous investigations. These results provide baseline data necessary for future in-depth investigations of C. sakazakii that colonize PIF manufacturing facility settings and genomic analyses of these two C. sakazakii strains and five associated plasmids will contribute to a better understanding of this pathogen's survival and persistence within various “built environments” like PIF manufacturing facilities. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-022-00500-5.
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Jang H, Chase HR, Gangiredla J, Grim CJ, Patel IR, Kothary MH, Jackson SA, Mammel MK, Carter L, Negrete F, Finkelstein S, Weinstein L, Yan Q, Iversen C, Pagotto F, Stephan R, Lehner A, Eshwar AK, Fanning S, Farber J, Gopinath GR, Tall BD, Pava-Ripoll M. Analysis of the Molecular Diversity Among Cronobacter Species Isolated From Filth Flies Using Targeted PCR, Pan Genomic DNA Microarray, and Whole Genome Sequencing Analyses. Front Microbiol 2020; 11:561204. [PMID: 33101235 PMCID: PMC7545074 DOI: 10.3389/fmicb.2020.561204] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/03/2020] [Indexed: 11/17/2022] Open
Abstract
Cronobacter species are opportunistic pathogens capable of causing life-threatening infections in humans, with serious complications arising in neonates, infants, immuno-compromised individuals, and elderly adults. The genus is comprised of seven species: Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite a multiplicity of genomic data for the genus, little is known about likely transmission vectors. Using DNA microarray analysis, in parallel with whole genome sequencing, and targeted PCR analyses, the total gene content of two C. malonaticus, three C. turicensis, and 14 C. sakazaki isolated from various filth flies was assessed. Phylogenetic relatedness among these and other strains obtained during surveillance and outbreak investigations were comparatively assessed. Specifically, microarray analysis (MA) demonstrated its utility to cluster strains according to species-specific and sequence type (ST) phylogenetic relatedness, and that the fly strains clustered among strains obtained from clinical, food and environmental sources from United States, Europe, and Southeast Asia. This combinatorial approach was useful in data mining for virulence factor genes, and phage genes and gene clusters. In addition, results of plasmidotyping were in agreement with the species identity for each strain as determined by species-specific PCR assays, MA, and whole genome sequencing. Microarray and BLAST analyses of Cronobacter fly sequence datasets were corroborative and showed that the presence and absence of virulence factors followed species and ST evolutionary lines even though such genes were orthologous. Additionally, zebrafish infectivity studies showed that these pathotypes were as virulent to zebrafish embryos as other clinical strains. In summary, these findings support a striking phylogeny amongst fly, clinical, and surveillance strains isolated during 2010–2015, suggesting that flies are capable vectors for transmission of virulent Cronobacter spp.; they continue to circulate among United States and European populations, environments, and that this “pattern of circulation” has continued over decades.
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Affiliation(s)
- Hyein Jang
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Hannah R Chase
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Christopher J Grim
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Isha R Patel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Mahendra H Kothary
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Scott A Jackson
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Mark K Mammel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Laurenda Carter
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Flavia Negrete
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Samantha Finkelstein
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Leah Weinstein
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - QiongQiong Yan
- WHO Collaborating Centre for Cronobacter, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Carol Iversen
- WHO Collaborating Centre for Cronobacter, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zürich, Zurich, Switzerland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zürich, Zurich, Switzerland
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, University of Zürich, Zurich, Switzerland
| | - Seamus Fanning
- WHO Collaborating Centre for Cronobacter, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Jeffery Farber
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Gopal R Gopinath
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Ben D Tall
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD, United States
| | - Monica Pava-Ripoll
- Center of Food Safety and Applied Nutrition, U. S. Food & Drug Administration, College Park, MD, United States
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6
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Jang H, Gopinath GR, Eshwar A, Srikumar S, Nguyen S, Gangiredla J, Patel IR, Finkelstein SB, Negrete F, Woo J, Lee Y, Fanning S, Stephan R, Tall BD, Lehner A. The Secretion of Toxins and Other Exoproteins of Cronobacter: Role in Virulence, Adaption, and Persistence. Microorganisms 2020; 8:E229. [PMID: 32046365 PMCID: PMC7074816 DOI: 10.3390/microorganisms8020229] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 12/29/2022] Open
Abstract
: Cronobacter species are considered an opportunistic group of foodborne pathogenic bacteria capable of causing both intestinal and systemic human disease. This review describes common virulence themes shared among the seven Cronobacter species and describes multiple exoproteins secreted by Cronobacter, many of which are bacterial toxins that may play a role in human disease. The review will particularly concentrate on the virulence factors secreted by C. sakazakii, C. malonaticus, and C. turicensis, which are the primary human pathogens of interest. It has been discovered that various species-specific virulence factors adversely affect a wide range of eukaryotic cell processes including protein synthesis, cell division, and ion secretion. Many of these factors are toxins which have been shown to also modulate the host immune response. These factors are encoded on a variety of mobile genetic elements such as plasmids and transposons; this genomic plasticity implies ongoing re-assortment of virulence factor genes which has complicated our efforts to categorize Cronobacter into sharply defined genomic pathotypes.
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Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich CH-8006 Zürich, Switzerland; (A.E.); (R.S.); (A.L.)
| | - Shabarinath Srikumar
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin Belfield, Dublin 4, D04 V1W8, Ireland; (S.S.); (S.N.); (S.F.)
| | - Scott Nguyen
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin Belfield, Dublin 4, D04 V1W8, Ireland; (S.S.); (S.N.); (S.F.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Samantha B. Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - JungHa Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - YouYoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin Belfield, Dublin 4, D04 V1W8, Ireland; (S.S.); (S.N.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich CH-8006 Zürich, Switzerland; (A.E.); (R.S.); (A.L.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (F.N.); (J.W.); (Y.L.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich CH-8006 Zürich, Switzerland; (A.E.); (R.S.); (A.L.)
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7
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Negrete F, Jang H, Gangiredla J, Woo J, Lee Y, Patel IR, Chase HR, Finkelstein S, Wang CZ, Srikumar S, Nguyen S, Eshwar A, Stephan R, Lehner A, Fanning S, Tall BD, Gopinath GR. Genome-wide survey of efflux pump-coding genes associated with Cronobacter survival, osmotic adaptation, and persistence. Curr Opin Food Sci 2019. [DOI: 10.1016/j.cofs.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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8
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Finkelstein S, Negrete F, Jang H, Gangiredla J, Mammel M, Patel IR, Chase HR, Woo J, Lee Y, Wang CZ, Weinstein L, Tall BD, Gopinath GR. Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages. Microorganisms 2019; 7:E554. [PMID: 31726673 PMCID: PMC6920972 DOI: 10.3390/microorganisms7110554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 12/28/2022] Open
Abstract
Cronobacter species are a group of foodborne pathogenic bacteria that cause both intestinal and systemic human disease in individuals of all age groups. Little is known about the mechanisms that Cronobacter employ to survive and persist in foods and other environments. Toxin-antitoxin (TA) genes are thought to play a role in bacterial stress physiology, as well as in the stabilization of horizontally-acquired re-combinatorial elements such as plasmids, phage, and transposons. TA systems have been implicated in the formation of a persistence phenotype in some bacterial species including Escherichia coli and Salmonella. This project's goal was to understand the phylogenetic relatedness among TA genes present in Cronobacter. Preliminary studies showed that two typical toxin genes, fic and hipA followed species evolutionary lines. A local database of 22 TA homologs was created for Cronobacter sakazakii and a Python version 3 shell script was generated to extract TA FASTA sequences present in 234 C. sakazakii genomes previously sequenced as part of Center for Food Safety and Applied Nutrition's (CFSAN) GenomeTrakr project. BLAST analysis showed that not every C. sakazakii strain possessed all twenty-two TA loci. Interestingly, some strains contained either a toxin or an antitoxin component, but not both. Five common toxin genes: ESA_00258 (parDE toxin-antitoxin family), ESA_00804 (relBE family), ESA_01887 (relBE family), ESA_03838 (relBE family), and ESA_04273 (YhfG-Fic family) were selected for PCR analysis and the primers were designed to detect these genes. PCR analysis showed that 55 of 63 strains possessed three of these genes Sequence analysis identified homologs of the target genes and some of the strains were PCR-negative for one or more of the genes, pointing to potential nucleotide polymorphisms in those loci or that these toxin genes were absent. Phylogenetic studies using a Cronobacter pan genomic microarray showed that for the most part TAs follow species evolutionary lines except for a few toxin genes possessed by some C. malonaticus and C. universalis strains; this demonstrates that some TA orthologues share a common phylogeny. Within the C. sakazakii strains, the prevalence and distribution of these TA homologs by C. sakazakii strain BAA-894 (a powdered infant formula isolate) followed sequence-type evolutionary lineages. Understanding the phylogeny of TAs among the Cronobacter species is essential to design future studies to realize the physiological mechanisms and roles for TAs in stress adaptation and persistence of Cronobacter within food matrices and food processing environments.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Ben D. Tall
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 MuirKirk Rd, Laurel, MD 20708, USA; (S.F.); (F.N.); (H.J.); (J.G.); (M.M.); (I.R.P.); (H.R.C.); (J.W.); (Y.L.); (C.Z.W.); (L.W.); (G.R.G.)
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9
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Jang H, Woo J, Lee Y, Negrete F, Finkelstein S, Chase HR, Addy N, Ewing L, Beaubrun JJG, Patel I, Gangiredla J, Eshwar A, Jaradat ZW, Seo K, Shabarinath S, Fanning S, Stephan R, Lehner A, Tall BD, Gopinath GR. Draft genomes of Cronobacter sakazakii strains isolated from dried spices bring unique insights into the diversity of plant-associated strains. Stand Genomic Sci 2018; 13:35. [PMID: 30519380 PMCID: PMC6267090 DOI: 10.1186/s40793-018-0339-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/10/2018] [Indexed: 01/16/2023] Open
Abstract
Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazakii, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the C. sakazakii genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated C. sakazakii genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for Cronobacter species. The presence of the genes identified in this study can support the remarkable phenotypic traits of C. sakazakii such as the organism's capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.
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Affiliation(s)
- Hyein Jang
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Jungha Woo
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Youyoung Lee
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Flavia Negrete
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Samantha Finkelstein
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Hannah R. Chase
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Nicole Addy
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Laura Ewing
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Junia Jean Gilles Beaubrun
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Isha Patel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Ziad W. Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, 22110 Jordan
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, 05029 South Korea
| | - Srikumar Shabarinath
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Ireland
- WHO Collaborating Centre for Cronobacter, Belfield, Dublin 4, Ireland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Ireland
- WHO Collaborating Centre for Cronobacter, Belfield, Dublin 4, Ireland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Ben D. Tall
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
| | - Gopal R. Gopinath
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708 USA
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10
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Carter L, Chase HR, Gieseker CM, Hasbrouck NR, Stine CB, Khan A, Ewing-Peeples LJ, Tall BD, Gopinath GR. Analysis of enterotoxigenic Bacillus cereus strains from dried foods using whole genome sequencing, multi-locus sequence analysis and toxin gene prevalence and distribution using endpoint PCR analysis. Int J Food Microbiol 2018; 284:31-39. [PMID: 29990637 DOI: 10.1016/j.ijfoodmicro.2018.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 06/08/2018] [Accepted: 06/21/2018] [Indexed: 10/28/2022]
Abstract
Bacillus cereus strains were isolated from dried foods, which included international brands of spices from South East Asia, Mexico and India purchased from several retail stores, samples of powdered infant formula (PIF), medicated fish feed and dietary supplements. The genetic diversity of 64 strains from spices and PIF was determined using a multiplex endpoint PCR assay designed to identify hemolysin BL, nonhemolytic enterotoxin, cytotoxin K, and enterotoxin FM toxin genes. Thirteen different B. cereus toxigenic gene patterns or profiles were identified among the strains. Randomly selected B. cereus strains were sequenced and compared with reference Genomic Groups from National Center Biotechnology Information using bioinformatics tools. A comprehensive multi-loci sequence analysis (MLSA) was designed using alleles from 25 known MLST genes specifically tailored for use with whole genome assemblies. A cohort of representative genomes of strains from a few FDA regulated commodities like dry foods and medicated fish feed was used to demonstrate the utility of the 25-MLSA approach for rapid clustering and identification of Genome Groups. The analysis clustered the strains from medicated fish feed, dry foods, and dietary supplements into phylogenetically-related groups. 25-MLSA also pointed to a greater diversity of B. cereus strains from foods and feed than previously recognized. Our integrated approach of toxin gene PCR, and to our knowledge, whole genome sequencing (WGS) based sequence analysis, may be the first of its kind that demonstrates enterotoxigenic potential and genomic diversity in parallel.
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Affiliation(s)
- Laurenda Carter
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA.
| | - Hannah R Chase
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Charles M Gieseker
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Nicholas R Hasbrouck
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Cynthia B Stine
- U. S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Ashraf Khan
- Division of Microbiology, National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Laura J Ewing-Peeples
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Ben D Tall
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
| | - Gopal R Gopinath
- U. S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment, Laurel, MD 20708 USA
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11
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Gopinath GR, Cinar HN, Murphy HR, Durigan M, Almeria M, Tall BD, DaSilva AJ. A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes. Gut Pathog 2018; 10:15. [PMID: 29643938 PMCID: PMC5891936 DOI: 10.1186/s13099-018-0242-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 04/01/2018] [Indexed: 11/10/2022] Open
Abstract
Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations.
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Affiliation(s)
- G R Gopinath
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - H N Cinar
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - H R Murphy
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - M Durigan
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - M Almeria
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - B D Tall
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
| | - A J DaSilva
- Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA
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12
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Gopinath GR, Chase HR, Gangiredla J, Eshwar A, Jang H, Patel I, Negrete F, Finkelstein S, Park E, Chung T, Yoo Y, Woo J, Lee Y, Park J, Choi H, Jeong S, Jun S, Kim M, Lee C, Jeong H, Fanning S, Stephan R, Iversen C, Reich F, Klein G, Lehner A, Tall BD. Genomic characterization of malonate positive Cronobacter sakazakii serotype O:2, sequence type 64 strains, isolated from clinical, food, and environment samples. Gut Pathog 2018; 10:11. [PMID: 29556252 PMCID: PMC5845375 DOI: 10.1186/s13099-018-0238-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 03/02/2018] [Indexed: 02/06/2023] Open
Abstract
Background Malonate utilization, an important differential trait, well recognized as being possessed by six of the seven Cronobacter species is thought to be largely absent in Cronobacter sakazakii (Csak). The current study provides experimental evidence that confirms the presence of a malonate utilization operon in 24 strains of sequence type (ST) 64, obtained from Europe, Middle East, China, and USA; it offers explanations regarding the genomic diversity and phylogenetic relatedness among these strains, and that of other C. sakazakii strains. Results In this study, the presence of a malonate utilization operon in these strains was initially identified by DNA microarray analysis (MA) out of a pool of 347 strains obtained from various surveillance studies involving clinical, spices, milk powder sources and powdered infant formula production facilities in Ireland and Germany, and dried dairy powder manufacturing facilities in the USA. All ST64 C. sakazakii strains tested could utilize malonate. Zebrafish embryo infection studies showed that C. sakazakii ST64 strains are as virulent as other Cronobacter species. Parallel whole genome sequencing (WGS) and MA showed that the strains phylogenetically grouped as a separate clade among the Csak species cluster. Additionally, these strains possessed the Csak O:2 serotype. The nine-gene, ~ 7.7 kbp malonate utilization operon was located in these strains between two conserved flanking genes, gyrB and katG. Plasmidotyping results showed that these strains possessed the virulence plasmid pESA3, but in contrast to the USA ST64 Csak strains, ST64 Csak strains isolated from sources in Europe and the Middle East, did not possess the type six secretion system effector vgrG gene. Conclusions Until this investigation, the presence of malonate-positive Csak strains, which are associated with foods and clinical cases, was under appreciated. If this trait was used solely to identify Cronobacter strains, many strains would likely be misidentified. Parallel WGS and MA were useful in characterizing the total genome content of these Csak O:2, ST64, malonate-positive strains and further provides an understanding of their phylogenetic relatedness among other virulent C. sakazakii strains. Electronic supplementary material The online version of this article (10.1186/s13099-018-0238-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gopal R Gopinath
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Hannah R Chase
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Jayanthi Gangiredla
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Athmanya Eshwar
- 2Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Hyein Jang
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Isha Patel
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Flavia Negrete
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Samantha Finkelstein
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Eunbi Park
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - TaeJung Chung
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - YeonJoo Yoo
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - JungHa Woo
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - YouYoung Lee
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Jihyeon Park
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Hyerim Choi
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Seungeun Jeong
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Soyoung Jun
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Mijeong Kim
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Chaeyoon Lee
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - HyeJin Jeong
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
| | - Séamus Fanning
- 3UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin & WHO Collaborating Centre for Cronobacter, Belfield, Dublin 4, Ireland
| | - Roger Stephan
- 2Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Carol Iversen
- 2Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland.,3UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin & WHO Collaborating Centre for Cronobacter, Belfield, Dublin 4, Ireland
| | - Felix Reich
- 4Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Günter Klein
- 4Institute for Food Quality and Safety, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Angelika Lehner
- 2Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Ben D Tall
- 1Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708 USA
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13
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Benahmed F, Wang H, Beaubrun JJG, Gopinath GR, Cheng CM, Hanes DE, Hammack TS, Rasmussen M, Davidson MK. Detection of Salmonella enterica subsp. enterica Serovar Cubana from Naturally Contaminated Chick Feed. J Food Prot 2017; 80:1815-1820. [PMID: 28981377 DOI: 10.4315/0362-028x.jfp-16-344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Because some significant outbreaks of human salmonellosis have been traced to contaminated animal feed, the rapid and efficient detection of Salmonella in feed is essential. However, the current U.S. Food and Drug Administration Bacteriological Analytical Manual (BAM) culture method that uses lactose broth as a preenrichment medium has not reliably supported the results of real-time PCR assays for certain foods. We evaluated the BAM culture method and a quantitative real-time PCR (qPCR) assay using two preenrichment media, modified buffered peptone water and lactose broth, to detect Salmonella enterica subsp. enterica serovar Cubana in naturally contaminated chick feed. After 24 h of incubation, the qPCR method was as sensitive as the culture method when modified buffered peptone water was used as the preenrichment medium but less sensitive than culture when lactose broth was used. After 48 h of incubation, detection of Salmonella Cubana by qPCR and by culture in either preenrichment medium was equivalent. We also compared the performance of the traditional serotyping method, which uses pure cultures of Salmonella grown on blood agar, to two molecular serotyping methods. The serotyping method based on whole genome sequencing also requires pure cultures, but the PCR-based molecular serotyping method can be done directly with the enriched culture medium. The PCR-based molecular serotyping method provided simple and rapid detection and identification of Salmonella Cubana. However, whole genome sequencing allows accurate identification of many Salmonella serotypes and highlights variations in the genomes, even in tight genomic clusters. We also compared the genome of the chick feed isolate with 58 Salmonella Cubana strains in GenBank and found that the chick feed isolate was very closely related to an isolate from a foodborne outbreak involving alfalfa sprouts.
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Affiliation(s)
- Faiza Benahmed
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
| | - Hua Wang
- 2 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, Maryland 20740
| | - Junia Jean-Gilles Beaubrun
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Gopal R Gopinath
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Chorng-Ming Cheng
- 4 U.S. Food and Drug Administration, Pacific Regional Laboratory Southwest, Irvine, California 92612, USA (retired)
| | - Darcy E Hanes
- 3 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Virulence Assessment, Laurel, Maryland 20708; and
| | - Thomas S Hammack
- 2 U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, Division of Microbiology, College Park, Maryland 20740
| | - Mark Rasmussen
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
| | - Maureen K Davidson
- 1 U.S. Food and Drug Administration, Center for Veterinary Medicine, Division of Animal and Food Microbiology, Laurel, Maryland 20708
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14
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Chase HR, Gopinath GR, Eshwar AK, Stoller A, Fricker-Feer C, Gangiredla J, Patel IR, Cinar HN, Jeong H, Lee C, Negrete F, Finkelstein S, Stephan R, Tall BD, Lehner A. Comparative Genomic Characterization of the Highly Persistent and Potentially Virulent Cronobacter sakazakii ST83, CC65 Strain H322 and Other ST83 Strains. Front Microbiol 2017; 8:1136. [PMID: 28694793 PMCID: PMC5483470 DOI: 10.3389/fmicb.2017.01136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Cronobacter (C.) sakazakii is an opportunistic pathogen and has been associated with serious infections with high mortality rates predominantly in pre-term, low-birth weight and/or immune compromised neonates and infants. Infections have been epidemiologically linked to consumption of intrinsically and extrinsically contaminated lots of reconstituted powdered infant formula (PIF), thus contamination of such products is a challenging task for the PIF producing industry. We present the draft genome of C. sakazakii H322, a highly persistent sequence type (ST) 83, clonal complex (CC) 65, serotype O:7 strain obtained from a batch of non-released contaminated PIF product. The presence of this strain in the production environment was traced back more than 4 years. Whole genome sequencing (WGS) of this strain together with four more ST83 strains (PIF production environment-associated) confirmed a high degree of sequence homology among four of the five strains. Phylogenetic analysis using microarray (MA) and WGS data showed that the ST83 strains were highly phylogenetically related and MA showed that between 5 and 38 genes differed from one another in these strains. All strains possessed the pESA3-like virulence plasmid and one strain possessed a pESA2-like plasmid. In addition, a pCS1-like plasmid was also found. In order to assess the potential in vivo pathogenicity of the ST83 strains, each strain was subjected to infection studies using the recently developed zebrafish embryo model. Our results showed a high (90-100%) zebrafish mortality rate for all of these strains, suggesting a high risk for infections and illness in neonates potentially exposed to PIF contaminated with ST83 C. sakazakii strains. In summary, virulent ST83, CC65, serotype CsakO:7 strains, though rarely found intrinsically in PIF, can persist within a PIF manufacturing facility for years and potentially pose significant quality assurance challenges to the PIF manufacturing industry.
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Affiliation(s)
- Hannah R Chase
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Gopal R Gopinath
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Andrea Stoller
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Claudia Fricker-Feer
- Quality Assurance and Food Safety Department, Hochdorf Swiss Nutrition LtdHochdorf, Switzerland
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Isha R Patel
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Hediye N Cinar
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - HyeJin Jeong
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - ChaeYoon Lee
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
| | - Ben D Tall
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, LaurelMD, United States
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of ZurichZurich, Switzerland
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15
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Tall BD, Gangiredla J, Grim CJ, Patel IR, Jackson SA, Mammel MK, Kothary MH, Sathyamoorthy V, Carter L, Fanning S, Iversen C, Pagotto F, Stephan R, Lehner A, Farber J, Yan QQ, Gopinath GR. Use of a Pan-Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology. Microarrays (Basel) 2017; 6:microarrays6010006. [PMID: 28273858 PMCID: PMC5374366 DOI: 10.3390/microarrays6010006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/08/2017] [Accepted: 02/21/2017] [Indexed: 11/24/2022]
Abstract
Cronobacter (previously known as Enterobacter sakazakii) is a genus of Gram-negative, facultatively anaerobic, oxidase-negative, catalase-positive, rod-shaped bacteria of the family Enterobacteriaceae. These organisms cause a variety of illnesses such as meningitis, necrotizing enterocolitis, and septicemia in neonates and infants, and urinary tract, wound, abscesses or surgical site infections, septicemia, and pneumonia in adults. The total gene content of 379 strains of Cronobacter spp. and taxonomically-related isolates was determined using a recently reported DNA microarray. The Cronobacter microarray as a genotyping tool gives the global food safety community a rapid method to identify and capture the total genomic content of outbreak isolates for food safety, environmental, and clinical surveillance purposes. It was able to differentiate the seven Cronobacter species from one another and from non-Cronobacter species. The microarray was also able to cluster strains within each species into well-defined subgroups. These results also support previous studies on the phylogenic separation of species members of the genus and clearly highlight the evolutionary sequence divergence among each species of the genus compared to phylogenetically-related species. This review extends these studies and illustrates how the microarray can also be used as an investigational tool to mine genomic data sets from strains. Three case studies describing the use of the microarray are shown and include: (1) the determination of allelic differences among Cronobacter sakazakii strains possessing the virulence plasmid pESA3; (2) mining of malonate and myo-inositol alleles among subspecies of Cronobacter dublinensis strains to determine subspecies identity; and (3) lastly using the microarray to demonstrate sequence divergence and phylogenetic relatedness trends for 13 outer-membrane protein alleles among 240 Cronobacter and phylogenetically-related strains. The goal of this review is to describe microarrays as a robust tool for genomics research of this assorted and important genus, a criterion toward the development of future preventative measures to eliminate this foodborne pathogen from the global food supply.
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Affiliation(s)
- Ben D Tall
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Christopher J Grim
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Isha R Patel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Scott A Jackson
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
- Complex Microbial Systems Group Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Mark K Mammel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Mahendra H Kothary
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Venugopal Sathyamoorthy
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Laurenda Carter
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Belfield, Dublin D04 N2E5, Ireland.
| | - Carol Iversen
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH Scotland, UK.
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards, Health Canada, Ottawa, ON K1A 0K9, Canada.
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstr. 272, CH-8057 Zurich, Switzerland.
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstr. 272, CH-8057 Zurich, Switzerland.
| | - Jeffery Farber
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Qiong Q Yan
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Belfield, Dublin D04 N2E5, Ireland.
| | - Gopal R Gopinath
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, Laurel, MD 20708, USA.
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16
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Kothary MH, Gopinath GR, Gangiredla J, Rallabhandi PV, Harrison LM, Yan QQ, Chase HR, Lee B, Park E, Yoo Y, Chung T, Finkelstein SB, Negrete FJ, Patel IR, Carter L, Sathyamoorthy V, Fanning S, Tall BD. Analysis and Characterization of Proteins Associated with Outer Membrane Vesicles Secreted by Cronobacter spp. Front Microbiol 2017; 8:134. [PMID: 28232819 PMCID: PMC5299011 DOI: 10.3389/fmicb.2017.00134] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/19/2017] [Indexed: 02/02/2023] Open
Abstract
Little is known about secretion of outer membrane vesicles (OMVs) by Cronobacter. In this study, OMVs isolated from Cronobacter sakazakii, Cronobacter turicensis, and Cronobacter malonaticus were examined by electron microscopy (EM) and their associated outer membrane proteins (OMP) and genes were analyzed by SDS-PAGE, protein sequencing, BLAST, PCR, and DNA microarray. EM of stained cells revealed that the OMVs are secreted as pleomorphic micro-vesicles which cascade from the cell's surface. SDS-PAGE analysis identified protein bands with molecular weights of 18 kDa to >100 kDa which had homologies to OMPs such as GroEL; OmpA, C, E, F, and X; MipA proteins; conjugative plasmid transfer protein; and an outer membrane auto-transporter protein (OMATP). PCR analyses showed that most of the OMP genes were present in all seven Cronobacter species while a few genes (OMATP gene, groEL, ompC, mipA, ctp, and ompX) were absent in some phylogenetically-related species. Microarray analysis demonstrated sequence divergence among the OMP genes that was not captured by PCR. These results support previous findings that OmpA and OmpX may be involved in virulence of Cronobacter, and are packaged within secreted OMVs. These results also suggest that other OMV-packaged OMPs may be involved in roles such as stress response, cell wall and plasmid maintenance, and extracellular transport.
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Affiliation(s)
| | | | | | | | | | - Qiong Q Yan
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, WHO Collaborating Centre for Cronobacter, University College, Dublin Dublin, Ireland
| | | | - Boram Lee
- U. S. Food and Drug Administration Laurel, MD, USA
| | - Eunbi Park
- U. S. Food and Drug Administration Laurel, MD, USA
| | - YeonJoo Yoo
- U. S. Food and Drug Administration Laurel, MD, USA
| | | | | | | | - Isha R Patel
- U. S. Food and Drug Administration Laurel, MD, USA
| | | | | | - Séamus Fanning
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, WHO Collaborating Centre for Cronobacter, University College, Dublin Dublin, Ireland
| | - Ben D Tall
- U. S. Food and Drug Administration Laurel, MD, USA
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17
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Cinar HN, Qvarnstrom Y, Wei-Pridgeon Y, Li W, Nascimento FS, Arrowood MJ, Murphy HR, Jang A, Kim E, Kim R, da Silva A, Gopinath GR. Comparative sequence analysis of Cyclospora cayetanensis apicoplast genomes originating from diverse geographical regions. Parasit Vectors 2016; 9:611. [PMID: 27899155 PMCID: PMC5129617 DOI: 10.1186/s13071-016-1896-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 11/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyclospora cayetanensis is an emerging coccidian parasite that causes endemic and epidemic diarrheal disease called cyclosporiasis, and this infection is associated with consumption of contaminated produce or water in developed and developing regions. Food-borne outbreaks of cyclosporiasis have occurred almost every year in the USA since the 1990s. Investigations of these outbreaks are currently hampered due to lack of molecular epidemiological tools for trace back analysis. The apicoplast of C. cayetanensis, a relict non-photosynthetic plastid with an independent genome, provides an attractive target to discover sequence polymorphisms useful as genetic markers for detection and trace back analysis of the parasite. Distinct differences in the apicoplast genomes of C. cayetanensis could be useful in designing advanced molecular methods for rapid detection and, subtyping and geographical source attribution, which would aid outbreak investigations and surveillance studies. METHODS To obtain the genome sequence of the C. cayetanensis apicoplast, we sequenced the C. cayetanensis genomic DNA extracted from clinical stool samples, assembled and annotated a 34,146 bp-long circular sequence, and used this sequence as a reference genome in this study. We compared the genome and the predicted proteome to the data available from other apicomplexan parasites. To initialize the search for genetic markers, we mapped the raw sequence reads from an additional 11 distinct clinical stool samples originating from Nepal, New York, Texas, and Indonesia to the apicoplast reference genome. RESULTS We identified several high quality single nucleotide polymorphisms (SNPs) and small insertion/deletions spanning the apicoplast genome supported by extensive sequencing reads data, and a 30 bp sequence repeat at the terminal spacer region in a Nepalese sample. The predicted proteome consists of 29 core apicomplexan peptides found in most of the apicomplexans. Cluster analysis of these C. cayetanensis apicoplast genomes revealed a familiar pattern of tight grouping with Eimeria and Toxoplasma, separated from distant species such as Plasmodium and Babesia. CONCLUSIONS SNPs and sequence repeats identified in this study may be useful as genetic markers for identification and differentiation of C. cayetanensis isolates found and could facilitate outbreak investigations.
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Affiliation(s)
- Hediye Nese Cinar
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA.
| | - Yvonne Qvarnstrom
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yuping Wei-Pridgeon
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wen Li
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Fernanda S Nascimento
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael J Arrowood
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Helen R Murphy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - AhYoung Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Eunje Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - RaeYoung Kim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Alexandre da Silva
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Gopal R Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
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18
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Affiliation(s)
- Ben D Tall
- a Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration , Laurel , MD , USA
| | - Hannah R Chase
- a Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration , Laurel , MD , USA
| | - Gopal R Gopinath
- a Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration , Laurel , MD , USA
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19
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Kothary MH, Franco AA, Tall BD, Gopinath GR, Datta AR. Purification and Characterization of a Rabbit Serum Factor That Kills Listeria Species and Other Foodborne Bacterial Pathogens. Foodborne Pathog Dis 2016; 13:441-7. [PMID: 27455064 DOI: 10.1089/fpd.2015.2109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In an in-vitro assay, rabbit serum, but not human serum, killed Listeria monocytogenes, a foodborne pathogen. The aim of our study was to purify and partially characterize this killing factor. Listericidin was purified from rabbit serum by a single-step ion-exchange chromatography with DEAE-Sephadex A-50 and its antimicrobial activity was assessed by a microdilution method. Listericidin is a protein with a molecular weight of 9 kDa and an isoelectric point of 8.1. It kills L. monocytogenes at 4°C, 25°C, and 37°C, and its activity is resistant to heat (boiling) and acidic conditions (pH <2). Listericidin's activity is inhibited by sodium chloride and various growth media, is sensitive to proteolytic enzymes and is enhanced by calcium chloride, and is neutralized by monoclonal antibodies to human complement C3a. However, the listericidin reacts weakly with these antibodies in an ELISA. The first 33 N-terminal residues of listericidin (SVQLTEKRMDKVGQYTNKELRKXXEDGMRDNPM) have homology to various complement C3a components. Listericidin also kills other Listeria spp., Vibrio spp., Salmonella spp., Escherichia spp., Cronobacter spp., and Bacillus spp. The listericidin peptide purified in a single-step chromatography is pH and heat stable, and has a broad antimicrobial spectrum against major foodborne pathogens in addition to L. monocytogenes.
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Affiliation(s)
- Mahendra H Kothary
- Division of Virulence Assessment, Food and Drug Administration , Laurel, Maryland
| | - Augusto A Franco
- Division of Virulence Assessment, Food and Drug Administration , Laurel, Maryland
| | - Ben D Tall
- Division of Virulence Assessment, Food and Drug Administration , Laurel, Maryland
| | - Gopal R Gopinath
- Division of Virulence Assessment, Food and Drug Administration , Laurel, Maryland
| | - Atin R Datta
- Division of Virulence Assessment, Food and Drug Administration , Laurel, Maryland
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20
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Eshwar AK, Tall BD, Gangiredla J, Gopinath GR, Patel IR, Neuhauss SCF, Stephan R, Lehner A. Linking Genomo- and Pathotype: Exploiting the Zebrafish Embryo Model to Investigate the Divergent Virulence Potential among Cronobacter spp. PLoS One 2016; 11:e0158428. [PMID: 27355472 PMCID: PMC4927158 DOI: 10.1371/journal.pone.0158428] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/15/2016] [Indexed: 12/04/2022] Open
Abstract
Bacteria belonging to the genus Cronobacter have been recognized as causative agents of life-threatening systemic infections primarily in premature, low-birth weight and immune-compromised neonates. Apparently not all Cronobacter species are linked to infantile infections and it has been proposed that virulence varies among strains. Whole genome comparisons and in silico analysis have proven to be powerful tools in elucidating potential virulence determinants, the presence/absence of which may explain the differential virulence behaviour of strains. However, validation of these factors has in the past been hampered by the availability of a suitable neonatal animal model. In the present study we have used zebrafish embryos to model Cronobacter infections in vivo using wild type and genetically engineered strains. Our experiments confirmed the role of the RepF1B-like plasmids as “virulence plasmids” in Cronobacter and underpinned the importantce of two putative virulence factors—cpa and zpx—in in vivo pathogenesis. We propose that by using this model in vivo infection studies are now possible on a large scale level which will boost the understanding on the virulence strategies employed by these pathogens.
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Affiliation(s)
- Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, Maryland, United States of America
| | | | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
- * E-mail:
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21
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Yan Q, Wang J, Gangiredla J, Cao Y, Martins M, Gopinath GR, Stephan R, Lampel K, Tall BD, Fanning S. Comparative Genotypic and Phenotypic Analysis of Cronobacter Species Cultured from Four Powdered Infant Formula Production Facilities: Indication of Pathoadaptation along the Food Chain. Appl Environ Microbiol 2015; 81:4388-402. [PMID: 25911470 PMCID: PMC4475896 DOI: 10.1128/aem.00359-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Cronobacter species are opportunistic pathogens commonly found in the environment. Among the seven Cronobacter species, Cronobacter sakazakii sequence type 4 (ST-4) is predominantly associated with recorded cases of infantile meningitis. This study reports on a 26-month powdered infant formula (PIF) surveillance program in four production facilities located in distinct geographic regions. The objective was to identify the ST(s) in PIF production environments and to investigate the phenotypic features that support their survival. Of all 168 Cronobacter isolates, 133 were recovered from a PIF production environment, 31 were of clinical origin, and 4 were laboratory type strains. Sequence type 1 (n = 84 isolates; 63.9%) was the dominant type in PIF production environments. The majority of these isolates clustered with an indistinguishable pulsotype and persisted for at least an 18-month period. Moreover, DNA microarray results identified two phylogenetic lineages among ST-4 strains tested. Thereafter, the ST-1 and -4 isolates were phenotypically compared. Differences were noted based on the phenotypes expressed by these isolates. The ST-1 PIF isolates produced stronger biofilms at both 28°C and 37°C, while the ST-4 clinical isolates exhibited greater swimming activity and increased binding to Congo red dye. Given the fact that PIF is a low-moisture environment and that the clinical environment provides for an interaction between the pathogen and its host, these differences may be consistent with a form of pathoadaptation. These findings help to extend our current understanding of the epidemiology and ecology of Cronobacter species in PIF production environments.
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Affiliation(s)
- Qiongqiong Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Juan Wang
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Jayanthi Gangiredla
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, OARSA, Silver Spring, Maryland, USA
| | - Yu Cao
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Marta Martins
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Gopal R Gopinath
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, OARSA, Silver Spring, Maryland, USA
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Keith Lampel
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, OARSA, Silver Spring, Maryland, USA
| | - Ben D Tall
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, OARSA, Silver Spring, Maryland, USA
| | - Séamus Fanning
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
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22
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Tall BD, Gangiredla J, Gopinath GR, Yan Q, Chase HR, Lee B, Hwang S, Trach L, Park E, Yoo Y, Chung T, Jackson SA, Patel IR, Sathyamoorthy V, Pava-Ripoll M, Kotewicz ML, Carter L, Iversen C, Pagotto F, Stephan R, Lehner A, Fanning S, Grim CJ. Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp. Front Pediatr 2015; 3:36. [PMID: 25984509 PMCID: PMC4415424 DOI: 10.3389/fped.2015.00036] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/08/2015] [Indexed: 11/13/2022] Open
Abstract
Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas.
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Affiliation(s)
- Ben Davies Tall
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Jayanthi Gangiredla
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Gopal R Gopinath
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Qiongqiong Yan
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin , Dublin , Ireland ; WHO Collaborating Centre for Cronobacter , Dublin , Ireland
| | - Hannah R Chase
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Boram Lee
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Seongeun Hwang
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Larisa Trach
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Eunbi Park
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - YeonJoo Yoo
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - TaeJung Chung
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Scott A Jackson
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Isha R Patel
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Venugopal Sathyamoorthy
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Monica Pava-Ripoll
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , College Park, MD , USA
| | - Michael L Kotewicz
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Laurenda Carter
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
| | - Carol Iversen
- College of Life Sciences, University of Dundee , Dundee , UK
| | - Franco Pagotto
- Food Directorate, Bureau of Microbial Hazards/Health Canada , Ottawa, ON , Canada
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich , Zurich , Switzerland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich , Zurich , Switzerland
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin , Dublin , Ireland ; WHO Collaborating Centre for Cronobacter , Dublin , Ireland
| | - Christopher J Grim
- Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration , Laurel, MD , USA
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23
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Stephan R, Grim CJ, Gopinath GR, Mammel MK, Sathyamoorthy V, Trach LH, Chase HR, Fanning S, Tall BD. Re-examination of the taxonomic status of Enterobacter helveticus, Enterobacter pulveris and Enterobacter turicensis as members of the genus Cronobacter and their reclassification in the genera Franconibacter gen. nov. and Siccibacter gen. nov. as Franconibacter helveticus comb. nov., Franconibacter pulveris comb. nov. and Siccibacter turicensis comb. nov., respectively. Int J Syst Evol Microbiol 2014; 64:3402-3410. [PMID: 25028159 PMCID: PMC4179279 DOI: 10.1099/ijs.0.059832-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Recently, a taxonomical re-evaluation of the genus Enterobacter, based on multi-locus sequence typing (MLST) analysis, has led to the proposal that the species Enterobacter pulveris, Enterobacter helveticus and Enterobacter turicensis should be reclassified as novel species of the genus Cronobacter. In the present work, new genome-scale analyses, including average nucleotide identity, genome-scale phylogeny and k-mer analysis, coupled with previously reported DNA–DNA hybridization values and biochemical characterization strongly indicate that these three species of the genus Enterobacter are not members of the genus Cronobacter, nor do they belong to the re-evaluated genus Enterobacter. Furthermore, data from this polyphasic study indicated that all three species constitute two new genera. We propose reclassifying Enterobacter pulveris and Enterobacter helveticus in the genus Franconibacter gen. nov. as Franconibacter pulveris comb. nov. (type strain 601/05T = LMG 24057T = DSM 19144T) and Franconibacter helveticus comb. nov. (type strain 513/05T = LMG 23732T = DSM 18396T), respectively, and Enterobacter turicensis in the genus Siccibacter gen. nov. as Siccibacter turicensis comb. nov. (type strain 508/05T = LMG 23730T = DSM 18397T).
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Affiliation(s)
- Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | | | | | | | | | | | | | - Séamus Fanning
- WHO Collaborating Centre for Cronobacter, Belfield, Dublin, Ireland.,UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College, Dublin, Ireland
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24
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Tall BD, Chen Y, Yan Q, Gopinath GR, Grim CJ, Jarvis KG, Fanning S, Lampel KA. Cronobacter: an emergent pathogen causing meningitis to neonates through their feeds. Sci Prog 2014; 97:154-72. [PMID: 25108996 PMCID: PMC10365370 DOI: 10.3184/003685014x13994743930498] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The recognition of Cronobacter as a public health concern was raised when powdered infant formula (PIF) was linked to several neonatal meningitis outbreaks. It is an opportunistic pathogen that causes necrotising enterocolitis, infantile septicaemia, and meningitis which carries a high mortality rate among neonates. It has been also linked with cases of infection in adults and elderly. Over the past decade, much focus has been made on developing sensitive and specific characterisation, detection, and isolation methods to ascertain the quality of foods, notably contamination of PIF with Cronobacter and to understand its ability to cause disease. Whole genome sequencing has unveiled several putative virulence factors, yet the full capacity of the pathogenesis of Cronobacter has not yet been elucidated.
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Affiliation(s)
- Ben D. Tall
- Center for Food Safety and Applied Nutrition, Food and Drug Administration in Laurel, Maryland
| | - Yi Chen
- FDA in College Park, Maryland
| | | | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, FDA, in Laurel, Maryland
| | | | - Karen G. Jarvis
- Center for Food Safety and Applied Nutrition, FDA, in Laurel, Maryland
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25
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Yan Q, Power KA, Cooney S, Fox E, Gopinath GR, Grim CJ, Tall BD, McCusker MP, Fanning S. Complete genome sequence and phenotype microarray analysis of Cronobacter sakazakii SP291: a persistent isolate cultured from a powdered infant formula production facility. Front Microbiol 2013; 4:256. [PMID: 24032028 PMCID: PMC3759002 DOI: 10.3389/fmicb.2013.00256] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 08/13/2013] [Indexed: 11/13/2022] Open
Abstract
Outbreaks of human infection linked to the powdered infant formula (PIF) food chain and associated with the bacterium Cronobacter, are of concern to public health. These bacteria are regarded as opportunistic pathogens linked to life-threatening infections predominantly in neonates, with an under developed immune system. Monitoring the microbiological ecology of PIF production sites is an important step in attempting to limit the risk of contamination in the finished food product. Cronobacter species, like other microorganisms can adapt to the production environment. These organisms are known for their desiccation tolerance, a phenotype that can aid their survival in the production site and PIF itself. In evaluating the genome data currently available for Cronobacter species, no sequence information has been published describing a Cronobacter sakazakii isolate found to persist in a PIF production facility. Here we report on the complete genome sequence of one such isolate, Cronobacter sakazakii SP291 along with its phenotypic characteristics. The genome of C. sakazakii SP291 consists of a 4.3-Mb chromosome (56.9% GC) and three plasmids, denoted as pSP291-1, [118.1-kb (57.2% GC)], pSP291-2, [52.1-kb (49.2% GC)], and pSP291-3, [4.4-kb (54.0% GC)]. When C. sakazakii SP291 was compared to the reference C. sakazakii ATCC BAA-894, which is also of PIF origin, the annotated genome data identified two interesting functional categories, comprising of genes related to the bacterial stress response and resistance to antimicrobial and toxic compounds. Using a phenotypic microarray (PM), we provided a full metabolic profile comparing C. sakazakii SP291 and the previously sequenced C. sakazakii ATCC BAA-894. These data extend our understanding of the genome of this important neonatal pathogen and provides further insights into the genotypes associated with features that can contribute to its persistence in the PIF environment.
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Affiliation(s)
- Qiongqiong Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference and Training on Cronobacter, School of Public Health, Physiotherapy and Population Science, University College Dublin Dublin, Ireland
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26
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de la Cruz N, Bromberg S, Pasko D, Shimoyama M, Twigger S, Chen J, Chen CF, Fan C, Foote C, Gopinath GR, Harris G, Hughes A, Ji Y, Jin W, Li D, Mathis J, Nenasheva N, Nie J, Nigam R, Petri V, Reilly D, Wang W, Wu W, Zuniga-Meyer A, Zhao L, Kwitek A, Tonellato P, Jacob H. The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res 2005; 33:D485-91. [PMID: 15608243 PMCID: PMC540004 DOI: 10.1093/nar/gki050] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Rat Genome Database (RGD) (http://rgd.mcw.edu) aims to meet the needs of its community by providing genetic and genomic infrastructure while also annotating the strengths of rat research: biochemistry, nutrition, pharmacology and physiology. Here, we report on RGD's development towards creating a phenome database. Recent developments can be categorized into three groups. (i) Improved data collection and integration to match increased volume and biological scope of research. (ii) Knowledge representation augmented by the implementation of a new ontology and annotation system. (iii) The addition of quantitative trait loci data, from rat, mouse and human to our advanced comparative genomics tools, as well as the creation of new, and enhancement of existing, tools to enable users to efficiently browse and survey research data. The emphasis is on helping researchers find genes responsible for disease through the use of rat models. These improvements, combined with the genomic sequence of the rat, have led to a successful year at RGD with over two million page accesses that represent an over 4-fold increase in a year. Future plans call for increased annotation of biological information on the rat elucidated through its use as a model for human pathobiology. The continued development of toolsets will facilitate integration of these data into the context of rat genomic sequence, as well as allow comparisons of biological and genomic data with the human genomic sequence and of an increasing number of organisms.
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Affiliation(s)
- Norberto de la Cruz
- Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53213, USA
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27
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Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath GR, Wu GR, Matthews L, Lewis S, Birney E, Stein L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005; 33:D428-32. [PMID: 15608231 PMCID: PMC540026 DOI: 10.1093/nar/gki072] [Citation(s) in RCA: 810] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes. Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathways. The Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although our primary curational domain is pathways from Homo sapiens, we regularly create electronic projections of human pathways onto other organisms via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed.
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Affiliation(s)
- G Joshi-Tope
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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28
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Joshi-Tope G, Vastrik I, Gopinath GR, Matthews L, Schmidt E, Gillespie M, D'Eustachio P, Jassal B, Lewis S, Wu G, Birney E, Stein L. The Genome Knowledgebase: a resource for biologists and bioinformaticists. Cold Spring Harb Symp Quant Biol 2004; 68:237-43. [PMID: 15338623 DOI: 10.1101/sqb.2003.68.237] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- G Joshi-Tope
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11790, USA
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29
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Twigger SN, Nie J, Ruotti V, Yu J, Chen D, Li D, Mathis J, Narayanasamy V, Gopinath GR, Pasko D, Shimoyama M, De La Cruz N, Bromberg S, Kwitek AE, Jacob HJ, Tonellato PJ. Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human data. Genome Res 2004; 14:651-60. [PMID: 15060006 PMCID: PMC383309 DOI: 10.1101/gr.1974504] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Integration of the large variety of genome maps from several organisms provides the mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease. The release of the rat genome sequence provides new information for studies using the rat model and is a key reference against which existing and new rat physiological results can be aligned. Previously, we described comparative maps of the rat, mouse, and human based on EST sequence comparisons combined with radiation hybrid maps. Here, we use new data and introduce the Integrated Genomics Environment, an extensive database of curated and integrated maps, markers, and physiological results. These results are integrated by using VCMapview, a java-based map integration and visualization tool. This unique environment allows researchers to relate results from cytogenetic, genetic, and radiation hybrid studies to the genome sequence and compare regions of interest between human, mouse, and rat. Integrating rat physiology with mouse genetics and clinical results from human by using the respective genomes provides a novel route to capitalize on comparative genomics and the strengths of model organism biology.
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Affiliation(s)
- Simon N Twigger
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.
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30
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Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MDF, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R. Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004; 2:e162. [PMID: 15103394 PMCID: PMC393292 DOI: 10.1371/journal.pbio.0020162] [Citation(s) in RCA: 267] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 04/01/2004] [Indexed: 01/08/2023] Open
Abstract
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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Affiliation(s)
- Tadashi Imanishi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takeshi Itoh
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 2Bioinformatics Laboratory, Genome Research Department, National Institute of Agrobiological SciencesIbarakiJapan
| | - Yutaka Suzuki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
| | - Claire O'Donovan
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Satoshi Fukuchi
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | | | - Roberto A Barrero
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Takuro Tamura
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 8BITS CompanyShizuokaJapan
| | - Yumi Yamaguchi-Kabata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Motohiko Tanino
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Kei Yura
- 9Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research InstituteKyotoJapan
| | - Satoru Miyazaki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Kazuho Ikeo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Keiichi Homma
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Arek Kasprzyk
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Tetsuo Nishikawa
- 10Reverse Proteomics Research InstituteChibaJapan
- 11Central Research Laboratory, HitachiTokyoJapan
| | - Mika Hirakawa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Jean Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Danielle Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Jennifer Ashurst
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Libin Jia
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Mitsuteru Nakao
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Michael A Thomas
- 17Department of Biological Sciences, Idaho State UniversityPocatello, IdahoUnited States of America
| | - Nicola Mulder
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Youla Karavidopoulou
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Lihua Jin
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Sangsoo Kim
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | | | - Boris Lenhard
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Eric Eveno
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoshiyuki Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Chisato Yamasaki
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Jun-ichi Takeda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Craig Gough
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Phillip Hilton
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Yasuyuki Fujii
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hiroaki Sakai
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Susumu Tanaka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Clara Amid
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Matthew Bellgard
- 24Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch UniversityMurdoch, Western AustraliaAustralia
| | - Maria de Fatima Bonaldo
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Hidemasa Bono
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Susan K Bromberg
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Anthony J Brookes
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Elspeth Bruford
- 28HUGO Gene Nomenclature Committee, University College LondonLondonUnited Kingdom
| | | | - Claude Chelala
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Christine Couillault
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | | | - Marie-Anne Debily
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | | | - Inna Dubchak
- 32Lawrence Berkeley National Laboratory, BerkeleyCaliforniaUnited States of America
| | - Toshinori Endo
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | | | - Eduardo Eyras
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kaoru Fukami-Kobayashi
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Gopal R. Gopinath
- 36Genome Knowledgebase, Cold Spring Harbor LaboratoryCold Spring Harbor, New YorkUnited States of America
| | - Esther Graudens
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoonsoo Hahn
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Michael Han
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Ze-Guang Han
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Kousuke Hanada
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideki Hanaoka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Erimi Harada
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Katsuyuki Hashimoto
- 38Division of Genetic Resources, National Institute of Infectious DiseasesTokyoJapan
| | - Ursula Hinz
- 34Swiss Institute of BioinformaticsGenevaSwitzerland
| | - Momoki Hirai
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Teruyoshi Hishiki
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Ian Hopkinson
- 41Department of Primary Care and Population Sciences, Royal Free University College Medical School, University College LondonLondonUnited Kingdom
- 42Clinical and Molecular Genetics Unit, The Institute of Child HealthLondonUnited Kingdom
| | - Sandrine Imbeaud
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Hidetoshi Inoko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Alexander Kanapin
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Yayoi Kaneko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Takeya Kasukawa
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Janet Kelso
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Paul Kersey
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | | | | | - Bernhard Korn
- 46RZPD Resource Center for Genome ResearchHeidelbergGermany
| | - Vladimir Kuryshev
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Izabela Makalowska
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Takashi Makino
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shuhei Mano
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Regine Mariage-Samson
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Jun Mashima
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideo Matsuda
- 49Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka UniversityOsakaJapan
| | - Hans-Werner Mewes
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Shinsei Minoshima
- 50Medical Photobiology Department, Photon Medical Research Center, Hamamatsu University School of MedicineShizuokaJapan
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | | | - Hideki Nagasaki
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Naoki Nagata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Rajni Nigam
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Osamu Ogasawara
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | | | - Masafumi Ohtsubo
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Norihiro Okada
- 53Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of TechnologyKanagawaJapan
| | - Toshihisa Okido
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Satoshi Oota
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Motonori Ota
- 54Global Scientific Information and Computing Center, Tokyo Institute of TechnologyTokyoJapan
| | - Toshio Ota
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Tetsuji Otsuki
- 55Molecular Biology Laboratory, Medicinal Research Laboratories, Taisho Pharmaceutical CompanySaitamaJapan
| | | | - Annemarie Poustka
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Shuang-Xi Ren
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Naruya Saitou
- 56Department of Population Genetics, National Institute of GeneticsShizuokaJapan
| | - Katsunaga Sakai
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shigetaka Sakamoto
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Ryuichi Sakate
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Ingo Schupp
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Florence Servant
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Stephen Sherry
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Rie Shiba
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Nobuyoshi Shimizu
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Mary Shimoyama
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | | | - Bento Soares
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Charles Steward
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Makiko Suwa
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Mami Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Aiko Takahashi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Gen Tamiya
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Hiroshi Tanaka
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | - Todd Taylor
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Joseph D Terwilliger
- 58Columbia University and Columbia Genome CenterNew York, New YorkUnited States of America
| | - Per Unneberg
- 59Department of Biotechnology, Royal Institute of TechnologyStockholmSweden
| | - Vamsi Veeramachaneni
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Shinya Watanabe
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Laurens Wilming
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Norikazu Yasuda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hyang-Sook Yoo
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Marvin Stodolsky
- 60Biology Division and Genome Task Group, Office of Biological and Environmental Research, United States Department of EnergyWashington, D.CUnited States of America
| | - Wojciech Makalowski
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Mitiko Go
- 61Faculty of Bio-Science, Nagahama Institute of Bio-Science and TechnologyShigaJapan
| | - Kenta Nakai
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Toshihisa Takagi
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Minoru Kanehisa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Yoshiyuki Sakaki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - John Quackenbush
- 62Institute for Genomic ResearchRockville, MarylandUnited States of America
| | - Yasushi Okazaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Yoshihide Hayashizaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Winston Hide
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Ranajit Chakraborty
- 63Center for Genome Information, Department of Environmental Health, University of CincinnatiCincinnati, OhioUnited States of America
| | - Ken Nishikawa
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideaki Sugawara
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Yoshio Tateno
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Zhu Chen
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
- 64State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Second Medical UniversityShanghaiChina
| | | | - Peter Tonellato
- 65PointOne SystemsWauwatosa, WisconsinUnited States of America
| | - Rolf Apweiler
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kousaku Okubo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Lukas Wagner
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Stefan Wiemann
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Robert L Strausberg
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Takao Isogai
- 10Reverse Proteomics Research InstituteChibaJapan
- 66Graduate School of Life and Environmental Sciences, University of TsukubaIbarakiJapan
| | - Charles Auffray
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Nobuo Nomura
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takashi Gojobori
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 67Department of Genetics, Graduate University for Advanced StudiesShizuokaJapan
| | - Sumio Sugano
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
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Chiou S, Yoo J, Loh KC, Guzman RC, Gopinath GR, Rajkumar L, Chou YC, Yang J, Popescu NC, Nandi S. Identification of rat mammary tumor-1 gene (RMT-1), which is highly expressed in rat mammary tumors. Cancer Lett 2001; 174:45-55. [PMID: 11675151 DOI: 10.1016/s0304-3835(01)00668-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Full-term pregnancy early in life results in a permanent reduction in lifetime breast cancer risk in women. Parous rats and mice are also refractory to chemical carcinogenesis. Therefore, investigation of the differences between mammary glands from virgin and parous rats would provide valuable information regarding the protective effects of early full-term pregnancy. In this report, we examined the gene expression patterns in mammary glands from virgin and parous Lewis rats. Using differential display technology, a novel 4.2 kb cDNA, designated rat mammary tumor-1 (RMT-1) was isolated. Northern blot analysis of RMT-1 showed that RMT-1 expression was higher in the pre-pubertal and pubertal stages during rat mammary gland development while it was down-regulated in mammary glands from mature virgin and parous rats. RMT-1 expression was highest in rat mammary cancers compared with either the mammary glands of virgin or parous rats. At the Northern blot sensitivity level, RMT-1 expression was found only in the mammary gland. Northern blot analysis also showed that the expression of this gene was found in 74% of N-methyl-nitrosourea (MNU)-induced mammary cancers while it was not found in MNU-induced cancers from other organs. The examination of the RMT-1 gene structure revealed that it consists of five exons spanning 5.9 kb. Using fluorescence in situ hybridization, the gene was localized on rat chromosome 1 band q 43-51. The present data show that there is a correlation between high RMT-1 expression and rat mammary carcinogenesis or decreased RMT-1 expression and parity associated refractoriness to chemically induced mammary carcinogenesis. However, whether or not RMT-1 gene has a functional role in these processes remains to be investigated.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- Disease Models, Animal
- Exons/genetics
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- In Situ Hybridization, Fluorescence
- Mammary Neoplasms, Experimental/chemically induced
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/prevention & control
- Molecular Sequence Data
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Parity/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
- Rats, Inbred Lew
- Restriction Mapping
- Sexual Abstinence
- Sexual Maturation/genetics
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Affiliation(s)
- S Chiou
- Cancer Research Laboratory and the Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA.
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