Identification and Virulence of Enterobacter Sakazakii
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CHAPTER 1: General Introduction and Aims 1.1 the Genus Cronobacter: an Introduction
Diversity and virulence of the genus Cronobacter revealed by multilocus sequence typing (MLST) and comparative genomic analysis Susan Manju Joseph A thesis submitted in partial fulfilment of the requirements of Nottingham Trent University for the degree of Doctor of Philosophy July 2013 Experimental work contained in this thesis is original research carried out by the author, unless otherwise stated, in the School of Science and Technology at the Nottingham Trent University. No material contained herein has been submitted for any other degree, or at any other institution. This work is the intellectual property of the author. You may copy up to 5% of this work for private study, or personal, non-commercial research. Any re-use of the information contained within this document should be fully referenced, quoting the author, title, university, degree level and pagination. Queries or requests for any other use, or if a more substantial copy is required, should be directed in the owner(s) of the Intellectual Property Rights. Susan Manju Joseph ACKNOWLEDGEMENTS I would like to express my immense gratitude to my supervisor Prof. Stephen Forsythe for having offered me the opportunity to work on this very exciting project and for having been a motivating and inspiring mentor as well as friend through every stage of this PhD. His constant encouragement and availability for frequent meetings have played a very key role in the progress of this research project. I would also like to thank my co-supervisors, Dr. Alan McNally and Prof. Graham Ball for all the useful advice, guidance and participation they provided during the course of this PhD study. -
Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species Where C. Sakazakii Homologs Follow Sequence Type Lineages
microorganisms Article Prevalence, Distribution, and Phylogeny of Type Two Toxin-Antitoxin Genes Possessed by Cronobacter Species where C. sakazakii Homologs Follow Sequence Type Lineages Samantha Finkelstein, Flavia Negrete, Hyein Jang, Jayanthi Gangiredla, Mark Mammel, Isha R. Patel, Hannah R. Chase, JungHa Woo, YouYoung Lee, Caroline Z. Wang, Leah Weinstein, Ben D. Tall * and Gopal R. Gopinath Center of Food Safety and Applied Nutrition, U. S. Food and Drug Administration, 8301 MuirKirk Rd, Laurel, MD 20708, USA; sfi[email protected] (S.F.); [email protected] (F.N.); [email protected] (H.J.); [email protected] (J.G.); [email protected] (M.M.); [email protected] (I.R.P.); [email protected] (H.R.C.); [email protected] (J.W.); [email protected] (Y.L.); [email protected] (C.Z.W.); [email protected] (L.W.); [email protected] (G.R.G.) * Correspondence: [email protected] Received: 4 October 2019; Accepted: 9 November 2019; Published: 12 November 2019 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. -
Biocontrol of Cronobacter Spp. Using Bacteriophage in Infant Formula
i Biocontrol of Cronobacter spp. using Bacteriophage in Infant Formula by Reza Abbasifar A Thesis presented to The University of Guelph In partial fulfillment of requirements for the degree of Doctor of Philosophy in Food Science Guelph, Ontario, Canada © Reza Abbasifar, May, 2013 ii ABSTRACT Biocontrol of Cronobacter spp. using Bacteriophage in Infant Formula Reza Abbasifar Advisor: Dr. Mansel W. Griffiths University of Guelph, 2013 Co-Advisor: Dr. Parviz M. Sabour The purpose of this research was to explore the potential application of lytic phages to control Cronobacter spp. in infant formula. More than two hundred and fifty phages were isolated from various environmental samples against different strains of Cronobacter spp. Selected phages were characterized by morphology, host range, and cross infectivity. The genomes of five novel Cronobacter phages [vB_CsaM_GAP31 (GAP31), vB_CsaM_GAP32 (GAP32), vB_CsaP_GAP52 (GAP52), vB_CsaM_GAP161 (GAP161), vB_CsaP_GAP227 (GAP227)] were sequenced. Phage GAP32 possess the second largest phage genome sequenced to date, and it is proposed that GAP32 belongs to a new genus of “Gap32likeviruses”. Phages GAP52 and GAP227 are the first C. sakazakii podoviruses whose genomes have been sequenced. None of the sequenced genomes showed homology to virulent or lysogenic genes. In addition, in vivo administration of phage GAP161 in the hemolymph of Galleria mellonella larvae showed no negative effects on the wellbeing of the larvae and could effectively prevent Cronobacter infection in the larvae. A cocktail of five phages was highly effective for biocontrol of three Cronobacter sakazakii strains present as a mixed culture in both broth media and contaminated reconstituted infant formula. This phage cocktail could be iii potentially used to control C. -
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/Ijsem.0.001485
International Journal of Systematic and Evolutionary Microbiology (2016), 66, 5575–5599 DOI 10.1099/ijsem.0.001485 Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov. Mobolaji Adeolu,† Seema Alnajar,† Sohail Naushad and Radhey S. Gupta Correspondence Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Radhey S. Gupta L8N 3Z5, Canada [email protected] Understanding of the phylogeny and interrelationships of the genera within the order ‘Enterobacteriales’ has proven difficult using the 16S rRNA gene and other single-gene or limited multi-gene approaches. In this work, we have completed comprehensive comparative genomic analyses of the members of the order ‘Enterobacteriales’ which includes phylogenetic reconstructions based on 1548 core proteins, 53 ribosomal proteins and four multilocus sequence analysis proteins, as well as examining the overall genome similarity amongst the members of this order. The results of these analyses all support the existence of seven distinct monophyletic groups of genera within the order ‘Enterobacteriales’. In parallel, our analyses of protein sequences from the ‘Enterobacteriales’ genomes have identified numerous molecular characteristics in the forms of conserved signature insertions/deletions, which are specifically shared by the members of the identified clades and independently support their monophyly and distinctness. Many of these groupings, either in part or in whole, have been recognized in previous evolutionary studies, but have not been consistently resolved as monophyletic entities in 16S rRNA gene trees. The work presented here represents the first comprehensive, genome- scale taxonomic analysis of the entirety of the order ‘Enterobacteriales’. -
Phage S144, a New Polyvalent Phage Infecting Salmonella Spp. and Cronobacter Sakazakii
International Journal of Molecular Sciences Article Phage S144, a New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii Michela Gambino 1 , Anders Nørgaard Sørensen 1 , Stephen Ahern 1 , Georgios Smyrlis 1, Yilmaz Emre Gencay 1 , Hanne Hendrix 2, Horst Neve 3 , Jean-Paul Noben 4 , Rob Lavigne 2 and Lone Brøndsted 1,* 1 Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark; [email protected] (M.G.); [email protected] (A.N.S.); [email protected] (S.A.); [email protected] (G.S.); [email protected] (Y.E.G.) 2 Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; [email protected] (H.H.); [email protected] (R.L.) 3 Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 24103 Kiel, Germany; [email protected] 4 Biomedical Research Institute and Transnational University Limburg, Hasselt University, BE3590 Diepenbeek, Belgium; [email protected] * Correspondence: [email protected] Received: 25 June 2020; Accepted: 21 July 2020; Published: 22 July 2020 Abstract: Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. -
Cronobacter: an Emerging Opportunistic Pathogen Associated with Neonatal Meningitis, Sepsis and Necrotizing Enterocolitis
Journal of Perinatology (2013) 33, 581–585 & 2013 Nature America, Inc. All rights reserved 0743-8346/13 www.nature.com/jp STATE-OF-THE-ART Cronobacter: an emerging opportunistic pathogen associated with neonatal meningitis, sepsis and necrotizing enterocolitis CJ Hunter1,2 and JF Bean1 Members of the genus Cronobacter are an emerging group of opportunist Gram-negative pathogens. This genus was previously thought to be a single species, called Enterobacter sakazakii. Cronobacter spp. typically affect low-birth-weight neonates, causing life-threatening meningitis, sepsis and necrotizing enterocolitis. Outbreaks of disease have been associated with contaminated infant formula, although the primary environmental source remains elusive. Advanced understanding of these bacteria and better classification has been obtained by improved detection techniques and genomic analysis. Research has begun to characterize the virulence factors and pathogenic potential of Cronobacter. Investigations into sterilization techniques and protocols for minimizing the risk of contamination have been reviewed at national and international forums. In this review, we explore the clinical impact of Cronobacter neonatal and pediatric infections, discuss virulence and pathogenesis, and review prevention and treatment strategies. Journal of Perinatology (2013) 33, 581–585; doi:10.1038/jp.2013.26; published online 28 March 2013 Keywords: Cronobacter sakazakii; meningitis; necrotizing enterocolitis; neonatal infections; infant formula INTRODUCTION single clinical setting.10 Cronobacter neonatal infection rates Cronobacter is an emerging genus of opportunistic Gram-negative remain low and are reported in the USA as one Cronobacter pathogens associated with potentially fatal neonatal infections, infection per 100 000 infants, 8.7 per 100 000 low-birth-weight including meningitis, sepsis and necrotizing enterocolitis (NEC).1 neonates, and one Cronobacter infection per 10 660 very low- 13 These infections typically affect our smallest and most vulnerable birth-weight neonates. -
Isolation of Cronobacter Spp.(Formerly Enterobacter Sakazakii) from Infant
BMC Microbiology BioMed Central Research article Open Access Isolation of Cronobacter spp. (formerly Enterobacter sakazakii) from infant food, herbs and environmental samples and the subsequent identification and confirmation of the isolates using biochemical, chromogenic assays, PCR and 16S rRNA sequencing Ziad W Jaradat*†, Qotaiba O Ababneh†, Ismail M Saadoun, Nawal A Samara and Abrar M Rashdan Address: Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, P. O. Box 3030, Irbid-22110, Jordan Email: Ziad W Jaradat* - [email protected]; Qotaiba O Ababneh - [email protected]; Ismail M Saadoun - [email protected]; Nawal A Samara - [email protected]; Abrar M Rashdan - [email protected] * Corresponding author †Equal contributors Published: 27 October 2009 Received: 10 March 2009 Accepted: 27 October 2009 BMC Microbiology 2009, 9:225 doi:10.1186/1471-2180-9-225 This article is available from: http://www.biomedcentral.com/1471-2180/9/225 © 2009 Jaradat et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Cronobacter spp. (formerly Enterobacter sakazakii), are a group of Gram-negative pathogens that have been implicated as causative agents of meningitis and necrotizing enterocolitis in infants. The pathogens are linked to infant formula; however, they have also been isolated from a wide range of foods and environmental samples. Results: In this study, 233 samples of food, infant formula and environment were screened for the presence of Cronobacter spp. -
Pan-Genome Analysis of the Emerging Foodborne Pathogen Cronobacter Spp
Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation Grim, C. J., Kotewicz, M. L., Power, K. A., Gopinath, G., Franco, A. A., Jarvis, K. G., Yan, Q. Q., Jackson, S. A., Sathyamoorthy, V., Hu, L., Pagotto, F., Iversen, C., Lehner, A., Stephan, R., Fanning, S., & Tall, B. D. (2013). Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation. BMC Genomics, 14, [366]. https://doi.org/10.1186/1471- 2164-14-366 Published in: BMC Genomics Document Version: Publisher's PDF, also known as Version of record Queen's University Belfast - Research Portal: Link to publication record in Queen's University Belfast Research Portal Publisher rights © 2013 Grim et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. General rights Copyright for the publications made accessible via the Queen's University Belfast Research Portal is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The Research Portal is Queen's institutional repository that provides access to Queen's research output. Every effort has been made to ensure that content in the Research Portal does not infringe any person's rights, or applicable UK laws. -
Cronobocter Condimenti Sp. Novv Isolated from Spiced Meat And
1 i Cronobocter condimenti sp. novv isolated from spiced meat and 2 Cronobocter universalis sp. novv a novel species designation for 3 Cronobocter sp. genomospecies 1, recovered from a leg infection, 4 water, and food ingredients 5 6 Susan Joseph1, Esin Cetinkaya2, Hana Drahovska3, Arturo Levican4, Maria J. Figueras4 and 7 Stephen J. Forsythe1 8 1School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, 9 UK, NG118NS. 10 2 Food Engineering Department, Engineering Faculty, Ankara University, Turkey 11 3 Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 12 Bratislava, Slovakia 13 4 Unit of Microbiology, Rovira i Virgili University, IISPV, Sant Llorenc, 21, 43201 Reus, Spain 14 15 Running title: Two new Cronobacter species. 16 Subject category: New taxa 17 18 Author for correspondence: Stephen J Forsythe. School of Science and Technology, 19 Nottingham Trent University, Clifton Lane, Nottingham, UK, NG11 8NS. Tel: +115 8483529, 20 Fax: +115 8486636. Email: [email protected]. 21 22 The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene (1361 bp) of strains 23 1330T, NCTC 9529T, 1435, 731 and 96 are FN539031, EF059877, JN205049, JN205050 and 24 JN205051 respectively; the accession numbers for the genes atpD, fusA, glnS, gltB, gyrB, 25 infB, ppsA of strains 1330T, NCTC 9529T, C. sakazakii ATCC 29544T, C. malonaticus LMG 26 23826T, C. turicensis LMG 23827T, C. muytjensii ATCC 51329T, C. dublinensis LMG 23823Tand 27 Citrobacter koseri CDC 3613-631 used in MLSA are from JF268258 to JF268314; they can also 28 be directly accessed from the Cronobacter MLST database website 29 (http://www.pubMLST.org/cronobacter) developed by Keith Jolley and sited at the 30 University of Oxford (Jolley et al. -
Precise Species Identification by Whole-Genome Sequencing of Enterobacter Bloodstream Infection, China Wenjing Wu,1 Li Wei,1 Yu Feng, Yi Xie, Zhiyong Zong
Precise Species Identification by Whole-Genome Sequencing of Enterobacter Bloodstream Infection, China Wenjing Wu,1 Li Wei,1 Yu Feng, Yi Xie, Zhiyong Zong (2), E. agglomerans to genus Pantoea (3), and E. sakazakii The clinical importance of Enterobacter spp. remains unclear because phenotype-based Enterobacter spe- to genus Cronobacter (4). Currently, 14 Enterobacter spp. cies identification is unreliable. We performed a genomic with validly published names exist, and 3 additional En- study on 48 cases of Enterobacter-caused bloodstream terobacter spp. have tentative species designations await- infection by using in silico DNA–DNA hybridization to ing validation under the rules of the International Code identify precise species. Strains belonged to 12 species; of Nomenclature of Bacteria (Bacteriological Code) Enterobacter xiangfangensis (n = 21) and an unnamed (Appendix 1 Table 1, https://wwwnc.cdc.gov/EID/ species (taxon 1, n = 8) were dominant. Most (63.5%) article/27/1/19-0154-App1.pdf). Enterobacter strains (n = 349) with genomes in Gen- Several Enterobacter spp., such as E. asburiae, Bank from human blood are E. xiangfangensis; taxon 1 E. cloacae, and E. hormaechei, cause infections in hu- (19.8%) was next most common. E. xiangfangensis and mans (1). Enterobacter strains extracted from clinical taxon 1 were associated with increased deaths (20.7% samples are usually reported as E. cloacae, and some- vs. 15.8%), lengthier hospitalizations (median 31 d vs. 19.5 d), and higher resistance to aztreonam, cefepime, times E. asburiae, E. hormaechei, or E. kobei, by auto- ceftriaxone, piperacillin-tazobactam, and tobramycin. mated microbial identification systems such as Vi- Strains belonged to 37 sequence types (STs); ST171 (E. -
Insights Into the Emergent Bacterial Pathogen Cronobacter Spp., Generated by Multilocus Sequence Typing and Analysis
REVIEW ARTICLE published: 22 November 2012 doi: 10.3389/fmicb.2012.00397 Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis Susan Joseph and Stephen J. Forsythe* Pathogen Research Group, School of Science and Technology, Nottingham Trent University, Nottingham, UK Edited by: Cronobacter spp. (previously known as Enterobacter sakazakii) is a bacterial pathogen Danilo Ercolini, Università degli Studi affecting all age groups, with particularly severe clinical complications in neonates and di Napoli Federico II, Italy infants. One recognized route of infection being the consumption of contaminated infant Reviewed by: formula. As a recently recognized bacterial pathogen of considerable importance and Anderson D. Sant’Ana, University of São Paulo, Brazil regulatory control, appropriate detection, and identification schemes are required. The Giorgio Giraffa, Agriculture Research application of multilocus sequence typing (MLST) and analysis (MLSA) of the seven alle- Council, Fodder and Dairy les atpD, fusA, glnS, gltB, gyrB, infB, and ppsA (concatenated length 3036 base pairs) Productions Research Centre, Italy has led to considerable advances in our understanding of the genus. This approach is *Correspondence: Stephen J. Forsythe, Pathogen supported by both the reliability of DNA sequencing over subjective phenotyping and Research Group, School of Science the establishment of a MLST database which has open access and is also curated; and Technology, Nottingham Trent http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of University, Clifton Lane, Nottingham the newly recognized genus, instrumental in the formal recognition of new Cronobacter NG11 8NS, UK. e-mail: [email protected] species (C. -
Cronobacter, the Emergent Bacterial Pathogen Enterobacter Sakazakii
Forsythe et al. BMC Genomics 2014, 15:1121 http://www.biomedcentral.com/1471-2164/15/1121 RESEARCH ARTICLE Open Access Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis Stephen J Forsythe1*, Benjamin Dickins1 and Keith A Jolley2 Abstract Background: Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. This paper presents the application of Next Generation Sequencing (NGS) to Cronobacter which has led to the establishment of the Cronobacter PubMLST genome and sequence definition database (http://pubmlst.org/ cronobacter/) containing over 1000 isolates with metadata along with the recognition of specific clonal lineages linked to neonatal meningitis and adult infections Results: Whole genome sequencing and multilocus sequence typing (MLST) has supports the formal recognition of the genus Cronobacter composed of seven species to replace the former single species Enterobacter sakazakii.Applyingthe 7-loci MLST scheme to 1007 strains revealed 298 definable sequence types, yet only C. sakazakii clonal complex 4 (CC4) was principally associated with neonatal meningitis. This clonal lineage has been confirmed using ribosomal-MLST (51-loci) and whole genome-MLST (1865 loci) to analyse 107 whole genomes via the Cronobacter PubMLST database. This database has enabled the retrospective analysis of historic cases and outbreaks following re-identification of those strains. Conclusions: The Cronobacter PubMLST database offers a central, open access, reliable sequence-based repository for researchers.