Detection, Occurrence, Grow Th and Inactivation of Cronobacter Spp

Total Page:16

File Type:pdf, Size:1020Kb

Detection, Occurrence, Grow Th and Inactivation of Cronobacter Spp kaft_def.qxd 20/03/2010 11:36 Page 1 Detection, occurrence, growth of andinactivation Detection, occurrence, growth and inactivation of Cronobacter spp. (Enterobacter sakazakii) Cronobacter spp. M.C. Kandhai 2010 Kandhai M.C. spp. Chantal Kandhai Propositions 1. In the last decennium, detection methods for Cronobacter spp. have been improved, which has led to an increase in the isolation of Cronobacter spp. from a wide variety of food products and environments. This fact in itself is not a reason to consider Cronobacter spp. as an emerging pathogen. 2. The use of sterile liquid formulae is an effective control measure to reduce the probability of infections in low and very low birth weight infants due to Cronobacter spp.. 3. As, generally, pathogens are relevant in foods only at such low numbers that multiplication is required to allow their detection, the enrichment step must be regarded as the most important step in the entire detection procedure. Yet, relatively little research effort is dedicated to optimizing this procedure. 4. Improvements in food safety management can only successfully be achieved in a food enterprise when there is a true food safety culture in the food enterprise. 5. Children are an extraordinary gift and enhance their mother's career by improving her multitasking skills. 6. Patience is the most important virtue in joint scientific writing. Propositions belonging to the thesis, entitled: “Detection, occurrence, growth, and inactivation of Cronobacter spp. (Enterobacter sakazakii)” M.C. Kandhai Wageningen, 23 April 2010. Detection, occurrence, growth and inactivation of Cronobacter spp. (Enterobacter sakazakii) M.C. Kandhai Thesis committee Thesis supervisors Prof. dr. L.G.M. Gorris Chairholder of the European Chair in Food Safety Microbiology Wageningen University Prof. dr. ir. M.H. Zwietering Professor of Food Microbiology Wageningen University Thesis co-supervisor Dr. ir. M.W. Reij Researcher and Lecturer at Laboratory of Food Microbiology Wageningen University Other members Prof.dr.ir. M.A.J.S. van Boekel, Wageningen University Prof. S. Fanning, UCD Center for Food Safety, Ireland Prof. dr. ir. A.H. Havelaar, University of Utrecht Dr. ir. A.E. Heuvelink, Food and Consumer Product Safety Authority, Zutphen This research was conducted under the auspices of the Graduate School of Voeding, Levensmiddelentechnologie, Agrobiotechnologie en Gezondheid (VLAG). Detection, occurrence, growth and inactivation of Cronobacter spp. (Enterobacter sakazakii) M.C. Kandhai Thesis Submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Doctorate Board to be defended in public on Friday 23 April 2010 at 4 PM in the Aula. M.C. Kandhai Detection, occurrence, growth and inactivation of Cronobacter spp. (Enterobacter sakazakii), 240 pages. Thesis, Wageningen University, Wageningen, NL (2010) With references, with summaries in Dutch and English ISBN 978-90-8585-556-9 To Fons, Aditya, Sarada & Ishaan “Life is constantly changing. Whatever time you have is yours, for tomorrow might never come” Abstract The genus Cronobacter consists of Gram-negative, motile, non-spore forming, facultative anaerobic bacteria, and was originally defined as one species “Enterobacter sakazakii” within the genus Enterobacter in 1980. Cronobacter spp. have been documented as a rare cause of outbreaks and sporadic cases of neonatal meningitis, necrotizing enterocolitis, and sepsis in infants with a high mortality. Among these infants, those at greatest risk are infants less than 2 months of age, particularly pre-term infants, low birth weight (LBW) infants (< 2500 g), and immuno-compromised infants. At the onset of the work for this thesis, Cronobacter spp. had been isolated from milk- based powdered formulae which have a direct link to the sub-population at greatest risk. However, there was a need to more closely investigate whether and where Cronobacter spp. occurs in environments in which these powdered are manufactured and packed but also to investigate other sources which could lead to exposure of vulnerable sub-populations. The main objective of this study was to develop isolation and detection methods that would allow quick and reliable investigation into the occurrence of the micro-organism in potential sources. Furthermore, more insight into the growth behavior of Cronobacter spp. in reconstituted infant formula was necessary in order to provide data to be used in Microbiological Risk Assessment (MRA) dedicated to this particular food product. A selective enrichment method was developed for the rapid and reliable enrichment and detection of Cronobacter spp. in environmental samples. The detection method which was developed is based on two features of Cronobacter spp. combined: their yellow pigmented colonies when grown on tryptone soy agar and their constitutive -glucosidase, which can be detected in a 4-h colorimetric assay. The initially developed method and refinements thereof were applied for routine screening for the presence of Cronobacter spp. in environmental samples and a variety of food products manufactured or marketed in The Netherlands. The detection method described in this thesis has been the basis for a series of media for Cronobacter spp. that have recently been commercialized. Quantitative data on product contamination at manufacture, during preparation, and also growth after reconstitution are required in order to assess the risk associated with Cronobacter spp. exposure. Next to that, tools are needed to asses the micro-organisms growth potential as well as its inactivation (thus, its survival) due to specific control measures applied. In this thesis, predictive growth models were developed that capture key growth parameters. Minimum– and maximum temperatures estimated with the Secondary Rosso equation were 3.6 ºC and 47.6 ºC, respectively. The estimated lag time of the micro- organisms was found to vary from 83.3 ± 18.7 h at 10 ºC to 1.73 ± 0.43 h at 37 ºC and could be described with the hyperbolic model and reciprocal square root relation. The models for growth rates and lag times as a function of temperatures obtained during this study allow estimating the potential growth of Cronobacter spp. in reconstituted infant formula stored at any temperature below 47 C. As growth rates of Cronobacter at refrigeration temperatures are relatively small, caregivers are advised to store reconstituted infant at low temperature as a control measure to prevent microbial growth. It is evident that storage of reconstituted formula in a refrigerator may require a significant amount of the time before the formula reach the targeted refrigeration temperature. Therefore, a mathematical model was built to predict the temperature profile and the resulting growth of Cronobacter spp. during cooling, i.e. under dynamic temperature conditions. Predictions showed that proliferation of Cronobacter spp. during cooling strongly depends on the size of the container used for storage and that it may be prevented by limiting the volume to be cooled to portion-size only or by reconstituting at temperatures of 25 °C or lower. The survival of two Cronobacter strains in dry powdered infant formula (PIF) was tested and compared to the survival of six other bacterial strains after inoculation and storage at several temperatures between 7 and 42 ºC. The effect of temperature on survival in PIF, was described using both the Weibull distribution model and the log-linear model. Differences were found in the rate of survival that can be due to difference in the resistance to inactivation in dry environments between Cronobacter species, which could be relevant to consider when establishing quantitative risk assessments on consumer risks related to PIF. The research described in this thesis contributes to the existing knowledge on the natural habitat of Cronobacter spp. and its occurrence and behavior in PIF. The models developed for quantifying the growth of Cronobacter spp. in reconstituted formulae under various conditions can be applied in risk assessments set-up to estimate the probability of vulnerable sub-populations becoming ill after consuming infant formulae. International and national governmental bodies may use these predictive models in risk assessments and to establish guidelines for health care professionals to provide effective hygiene training to parents and professional caregivers to ensure that PIF is prepared handled and stored appropriately. Contents Abstract 6 Chapter 1 Introduction 11 Chapter 2 A new protocol for the detection of Cronobacter spp. applied to environmental samples 43 Chapter 3 A simple and rapid cultural method for enrichment of Cronobacter spp. in environmental samples 55 Chapter 4 Occurrence of Cronobacter spp. in food production environments and households 69 Chapter 5 A study into the prevalence of Cronobacter spp. in The Netherlands 77 Chapter 6 The effect of pre-culturing conditions on the lag time and specific growth rate of Cronobacter spp. in reconstituted infant formula 109 Chapter 7 Growth of Cronobacter spp. under dynamic temperature conditions occurring during cooling of reconstituted powdered infant formula 133 Chapter 8 Survival of Cronobacter spp. in comparison to other bacteria in dry infant formulae 165 Chapter 9 Discussion, and concluding remarks 193 Samenvatting 227 Acknowledgement 231 List of publications 233 Curriculum vitae 237 Overview of
Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • View Preprint
    A peer-reviewed version of this preprint was published in PeerJ on 16 June 2020. View the peer-reviewed version (peerj.com/articles/9376), which is the preferred citable publication unless you specifically need to cite this preprint. Gao H, Yin X, Jiang X, Shi H, Yang Y, Wang C, Dai X, Chen Y, Wu X. 2020. Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China. PeerJ 8:e9376 https://doi.org/10.7717/peerj.9376 Diversity and pathogenicity of microbial communities causing grape sour rot in eastern coastal areas of China Huanhuan Gao Corresp., Equal first author, 1, 2 , Xiangtian Yin Equal first author, 1 , Xilong Jiang 1 , Hongmei Shi 1 , Yang Yang 1 , Xiaoyan Dai 1, 2 , Yingchun Chen 1 , Xinying Wu Corresp. 1 1 Shandong Academy of Grape, Jinan, China 2 Shandong Academy of Agricultural Sciences, Institute of Plant Protection, Jinan, China Corresponding Authors: Huanhuan Gao, Xinying Wu Email address: [email protected], [email protected] Background As a polymicrobial disease, grape sour rot can lead to the decrease in the yield of grape berries and wine quality. The diversity of microbial communities in sour rot-infected grapes depends on the planting location of grapes and the identified methods. The east coast of China is one of the most important grape and wine regions in China and even in the world. Methods To identify the pathogenic microorganism s causing sour rot in table grapes of eastern coastal areas of China, the diversity and abundance of the bacteria and fungi were assessed based on two methods, including traditional culture-methods, and 16S rRNA and ITS gene high-throughput sequencing .
    [Show full text]
  • The Microbiological Safety of Low Water Activity Foods and Spices Food Microbiology and Food Safety
    Food Microbiology and Food Safety Practical Approaches Joshua B. Gurtler Michael P. Doyle Je rey L. Kornacki Editors The Microbiological Safety of Low Water Activity Foods and Spices Food Microbiology and Food Safety Series Editor: Michael P. Doyle Food Microbiology and Food Safety Series The Food Microbiology and Food Safety series is published in conjunction with the International Association for Food Protection, a non-profi t association for food safety professionals. Dedicated to the life-long educational needs of its Members, IAFP provides an information network through its two scientifi c journals (Food Protection Trends and Journal of Food Protection), its educational Annual Meeting, international meetings and symposia, and interaction between food safety professionals. Series Editor Michael P. Doyle, Regents Professor and Director of the Center for Food Safety, University of Georgia, Griffi th, GA, USA Editorial Board Francis F. Busta, Director, National Center for Food Protection and Defense, University of Minnesota, Minneapolis, MN, USA Patricia Desmarchelier, Food Safety Consultant, Brisbane, Australia Jeffrey Farber, Bureau of Microbial Hazards, Ottawa, ON, Canada David Golden, Professor of Microbiology, Department of Food Science and Technology, University of Tennessee, Knoxville, TN, USA Vijay Juneja, Supervisory Lead Scientist, USDA-ARS, Philadelphia, PA, USA More information about this series at http://www.springer.com/series/7131 Joshua B. Gurtler • Michael P. Doyle Jeffrey L. Kornacki Editors The Microbiological Safety of Low Water Activity Foods and Spices Editors Joshua B. Gurtler Michael P. Doyle U.S. Department of Agriculture ARS, University of Georgia Center of Food Safety Eastern Regional Research Center Griffi n , GA , USA Food Safety Intervention Technologies Wyndmoor , PA , USA Jeffrey L.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Comparative Analysis of Cronobacter Sp. with Respect to Genomic Diversity and Physiology
    COMPARATIVE ANALYSIS OF CRONOBACTER SP. WITH RESPECT TO GENOMIC DIVERSITY AND PHYSIOLOGY EVA KUCEROVA A thesis submitted in partial fulfilment of the requirements Nottingham Trent University for the degree of Doctor of Philosophy. This research programme was carried out in collaboration with Nottingham University, UK and Vaccine Research Institute of San Diego, California, US November 2010 i 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. ii i ABSTRACT In recent years, some outbreaks of bacterial infection in neonatal intensive care units have been traced to powdered infant formula contaminated with Cronobacter species, causing life-threatening diseases such as necrotizing enterocolitis and meningitis. This study for the first time presents growth data and whole genome comparisons for five different species of Cronobacter after the taxonomic revision by Iversen et al. (2008). Growth data for 28 bacterial strains across 21 bacterial species in casein- and whey-dominant infant formula at temperatures 21, 27, 37, 41 and 44oC were determined, covering category A and B organisms as defined by WHO 2006. The data revealed potential of some Cronobacter species to grow at 44oC, posing a significant risk of infection by the bacterium when following the current formula preparation guidelines.
    [Show full text]
  • Comparison of Incl/M Plasmids Using the Neighbor-Joining Method on Basis Repa and Exca Genes
    Current Research in Bioinformatics Original Research Paper Comparison of IncL/M Plasmids Using the Neighbor-Joining Method on Basis repA and excA Genes Touati Abdelaziz and Mairi Assia Laboratoire d’Ecologie Microbienne, FSNV, Université de Bejaia, 06000 Bejaia, Algérie Article history Abstract: The aim of this study is to make comparison of IncL/M groups Received: 25-12-2019 on basis of two genes candidates’ repA and excA genes. The sequences of Revised: 11-02-2020 27 plasmids were compared using the neighbor-joining method. This Accepted: 12-02-2020 method was used to construct a phylogenetic tree for the nucleotide sequences of two genes (repA and excA), using the program MEGA X Corresponding Author: Touati Abdelaziz software. The evolutionary distances were computed using the maximum Laboratoire d’Ecologie composite likelihood method. The neighbor-joining method analysis Microbienne, FSNV, Université showed different results based on the gene used for comparison. The repA de Bejaia, 06000 Bejaia, gene was more accurate than excA gene to distinguish between different Algérie incL/M plasmids. This study suggested that IncL/M plasmids harboring Email: [email protected] different antibiotic resistance genes have evolved differently. Keywords: Plasmids, IncL/M Type, Phylogenetic Analysis, repA Gene, excA Gene Introduction the prevalence of particular plasmids may vary depending on the source and geographical site, they have been The dissemination of antimicrobial resistance in increasingly isolated from bacteria of human, animal and Gram-negative bacteria has been largely attributed to the environmental origin (Rozwandowicz et al., 2018; horizontal transfer of plasmid-located resistance genes Touati and Mairi, 2019). In a recent review, Touati and (Carattoli, 2013).
    [Show full text]
  • X2018;Nissabacter Archeti’
    AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE-LA TIMONE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE Présentée et soutenue le 24 Novembre 2017 Par En vue de l’obtention du grade de Docteur de l’Université Aix-Marseille Spécialité : Génomique et Bio-informatique REAL-TIME GENOMICS TO DECIPHER ATYPICAL BACTERIA IN CLINICAL MICROBIOLOGY COMPOSITION DU JURY Président du Jury Professeur Anthony Levasseur Examinateur Professeur Ruimy Raymond Rapporteur1 Professeur Marie Kempf Rapporteur2 Professeur Estelle Jumas-Bilak Directeur de Thèse Professeur Jean-Marc Rolain Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE CNSR-IRD UMR7278, IHU MEDITERRANEE INFECTION AIX-MARSEILLE UNIVERSITE FACULTE DE MEDECINE-LA TIMONE ECOLE DOCTORALE DES SCIENCES DE LA VIE ET DE LA SANTE Présentée et soutenue le 24 Novembre 2017 Par En vue de l’obtention du grade de Docteur de l’Université Aix-Marseille Spécialité : Génomique et Bio-informatique REAL-TIME GENOMICS TO DECIPHER ATYPICAL BACTERIA IN CLINICAL MICROBIOLOGY COMPOSITION DU JURY Président du Jury Professeur Anthony Levasseur Examinateur Professeur Ruimy Raymond Rapporteur1 Professeur Marie Kempf Rapporteur2 Professeur Estelle Jumas-Bilak Directeur de Thèse Professeur Jean-Marc Rolain Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE CNSR-IRD UMR7278, IHU MEDITERRANEE INFECTION 1 CONTENT Avant-propos Résumé /Abstract Introduction Chapter I: Review Articles I: Real-time genomics and the impact of bacterial genome recombination in clinical microbiology Kodjovi D. Mlaga, Seydina M. Diene, R. Ruimy, J-M Rolain. (Submitted in Genome Biology and Evolution) Chapter II: Comparative genomic applied in clinical microbiology Articles II: Using MALDI-TOF MS typing method to decipher outbreak: the case of Staphylococcus saprophyticus causing urinary tract infections (UTIs) in Marseille, France.
    [Show full text]