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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] [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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2
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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] [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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3
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Yi M, He P, Li J, Zhang J, Lin L, Wang L, Zhao L. A portable toolbox based on time-resolved fluoroimmunoassay and immunomagnetic separation for Cronobacter sakazakii on-site detection in dairy. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Gao Y, Ye Y, Xu J, Wu Q, Yao B, Chen W. Rapid and easy quantitative identification of Cronobacter spp. in infant formula milk powder by isothermal strand-exchange-amplification based molecular capturing lateral flow strip. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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The protealysin operon encodes emfourin, a prototype of a novel family of protein metalloprotease inhibitors. Int J Biol Macromol 2020; 169:583-596. [PMID: 33385454 DOI: 10.1016/j.ijbiomac.2020.12.170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023]
Abstract
Protealysin is a Serratia proteamaculans metalloproteinase of the M4 peptidase family and the prototype of a large group of protealysin-like proteases (PLPs). PLPs are likely involved in bacterial interaction with plants and animals as well as in bacterial pathogenesis. We demonstrated that the PLP genes in bacteria colocalize with the genes of putative conserved proteins. In S. proteamaculans, these two genes form a bicistronic operon. The putative S. proteamaculans protein that we called emfourin (M4in) was expressed in Escherichia coli and characterized. M4in forms a complex with protealysin with a 1:1 stoichiometry and is a potent slow-binding competitive inhibitor of protealysin (Ki = 52 ± 14 pM); besides, M4in is not secreted from S. proteamaculans constitutively. A comparison of amino acid sequences of M4in and its homologs with those of known inhibitors suggests that M4in is the prototype of a new family of protein inhibitors of proteases.
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Molecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk. Foods 2020; 10:foods10010020. [PMID: 33374633 PMCID: PMC7822459 DOI: 10.3390/foods10010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 12/21/2022] Open
Abstract
Cronobacter spp. are opportunistic pathogens of the Enterobacteriaceae family. The organism causes infections in all age groups, but the most serious cases occur in outbreaks related to neonates with meningitis and necrotizing enterocolitis. The objective was to determine the in silico and in vitro putative virulence factors of six Cronobacter sakazakii strains isolated from powdered milk (PM) in the Czech Republic. Strains were identified by MALDI-TOF MS and whole-genome sequencing (WGS). Virulence and resistance genes were detected with the Ridom SeqSphere+ software task template and the Comprehensive Antibiotic Resistance Database (CARD) platform. Adherence and invasion ability were performed using the mouse neuroblastoma (N1E-115 ATCCCRL-2263) cell line. The CRISPR-Cas system was searched with CRISPRCasFinder. Core genome MLST identified four different sequence types (ST1, ST145, ST245, and ST297) in six isolates. Strains 13755-1B and 1847 were able to adhere in 2.2 and 3.2 × 106 CFU/mL, while 0.00073% invasion frequency was detected only in strain 1847. Both strains 13755-1B and 1847 were positive for three (50.0%) and four virulence genes, respectively. The cpa gene was not detected. Twenty-eight genes were detected by WGS and grouped as flagellar or outer membrane proteins, chemotaxis, hemolysins, and invasion, plasminogen activator, colonization, transcriptional regulator, and survival in macrophages. The colistin-resistance-encoding mcr-9.1 and cephalothin-resis-encoding blaCSA genes and IncFII(pECLA) and IncFIB(pCTU3) plasmids were detected. All strains exhibited CRISPR matrices and four of them two type I-E and I-F matrices. Combined molecular methodologies improve Cronobacter spp. decision-making for health authorities to protect the population.
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7
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Hayman MM, Edelson-Mammel SG, Carter PJ, Chen YI, Metz M, Sheehan JF, Tall BD, Thompson CJ, Smoot LA. Prevalence of Cronobacter spp. and Salmonella in Milk Powder Manufacturing Facilities in the United States. J Food Prot 2020; 83:1685-1692. [PMID: 32421786 DOI: 10.4315/jfp-20-047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/13/2020] [Indexed: 12/29/2022]
Abstract
ABSTRACT The U.S. Food and Drug Administration (FDA) conducted a sampling assignment in 2014 to ascertain the prevalence of Cronobacter spp. and Salmonella in the processing environment of facilities manufacturing milk powder. Cronobacter was detected in the environment of 38 (69%) of 55 facilities. The average prevalence of Cronobacter in 5,671 subsamples (i.e., swabs and sponges from different facility locations) was 4.4%. In the 38 facilities where Cronobacter was detected, the average prevalence of positive environmental subsamples was 6.25%. In 20 facilities where zone information of the sampling location was complete, Cronobacter was most frequently detected in zone 4, followed by zone 3, then zone 2, with zone 1 yielding the lowest percentage of positive samples. The prevalence of Cronobacter across the zones was statistically different (P < 0.05). There was no significant association between product type (i.e., lactose, whey products, buttermilk powder, and nonfat dried milk) and prevalence of Cronobacter in the facility. Salmonella was detected in the environment of three (5.5%) of the 55 facilities; all three facilities produced dried whey product. The overall prevalence of Salmonella in 5,714 subsamples was 0.16%. In facilities in which Salmonella was detected, the average prevalence was 2.5%. Salmonella was most frequently detected in zone 4, followed by zone 3. Salmonella was not detected in zone 1 or zone 2. The disparity between Salmonella and Cronobacter prevalence indicates that additional measures may be required to reduce or eliminate Cronobacter from the processing environment. HIGHLIGHTS
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Affiliation(s)
- Melinda M Hayman
- Office of Food Safety (ORCID: https://orcid.org/0000-0002-8918-3290 [M.M.H.]), U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Sharon G Edelson-Mammel
- Office of Food Safety (ORCID: https://orcid.org/0000-0002-8918-3290 [M.M.H.]), U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Peggy J Carter
- Office of Regulatory Affairs, Office of Regulatory Science, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Y I Chen
- Office of Regulatory Science, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Monica Metz
- Office of Food Safety (ORCID: https://orcid.org/0000-0002-8918-3290 [M.M.H.]), U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - John F Sheehan
- Office of Food Safety (ORCID: https://orcid.org/0000-0002-8918-3290 [M.M.H.]), U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Ben D Tall
- Office of Applied Research and Safety Assessment, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Clinton J Thompson
- Office of Analytics and Outreach, U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
| | - Leslie A Smoot
- Office of Food Safety (ORCID: https://orcid.org/0000-0002-8918-3290 [M.M.H.]), U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive HFS-316, College Park, Maryland 20740, USA
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8
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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] [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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9
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Nguyen SV, Muthappa DM, Eshwar AK, Buckley JF, Murphy BP, Stephan R, Lehner A, Fanning S. Comparative genomic insights into Yersinia hibernica - a commonly misidentified Yersinia enterocolitica-like organism. Microb Genom 2020; 6:mgen000411. [PMID: 32701425 PMCID: PMC7643974 DOI: 10.1099/mgen.0.000411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/07/2020] [Indexed: 11/18/2022] Open
Abstract
Food-associated outbreaks linked to enteropathogenic Yersinia enterocolitica are of concern to public health. Pigs and their meat are recognized risk factors for transmission of Y. enterocolitica. This study aimed to describe the comparative genomics of Y. enterocolitica along with a number of misclassified Yersinia isolates, now constituting the recently described Yersinia hibernica. The latter was originally cultured from an environmental sample taken at a pig slaughterhouse. Unique features were identified in the genome of Y. hibernica, including a novel integrative conjugative element (ICE), denoted as ICEYh-1 contained within a 255 kbp region of plasticity. In addition, a zebrafish embryo infection model was adapted and applied to assess the virulence potential among Yersinia isolates including Y. hibernica.
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Affiliation(s)
- Scott Van Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Dechamma Mundanda Muthappa
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Athmanya K. Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
| | - James F. Buckley
- Veterinary Food Safety Laboratory, Cork County Council, Inniscarra, Co. Cork and Department of Microbiology, National University of Ireland, Cork, College Road, Cork, Ireland
| | - Brenda P. Murphy
- Veterinary Food Safety Laboratory, Cork County Council, Inniscarra, Co. Cork and Department of Microbiology, National University of Ireland, Cork, College Road, Cork, 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
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
- Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast BT9 5AG, UK
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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] [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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11
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12
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Eshwar AK, Wolfrum N, Stephan R, Fanning S, Lehner A. Interaction of matrix metalloproteinase-9 and Zpx inCronobacter turicensisLMG 23827Tmediated infections in the zebrafish model. Cell Microbiol 2018; 20:e12888. [DOI: 10.1111/cmi.12888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 12/18/2022]
Affiliation(s)
| | - Nina Wolfrum
- Institute for Veterinary Bacteriology; University of Zurich; Zurich Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene; University of Zurich; Zurich Switzerland
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South; University College Dublin; Dublin Ireland
| | - Angelika Lehner
- Institute for Food Safety and Hygiene; University of Zurich; Zurich Switzerland
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13
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Lehner A, Tall BD, Fanning S, Srikumar S. Cronobacter spp.—Opportunistic Foodborne Pathogens: an Update on Evolution, Osmotic Adaptation and Pathogenesis. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0089-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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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] [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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15
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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] [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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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 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] [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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