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Giraud-Gatineau A, Texier G, Fournier PE, Raoult D, Chaudet H. Using MALDI-TOF spectra in epidemiological surveillance for the detection of bacterial subgroups with a possible epidemic potential. BMC Infect Dis 2021; 21:1109. [PMID: 34711189 PMCID: PMC8554970 DOI: 10.1186/s12879-021-06803-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Background For the purpose of epidemiological surveillance, the Hospital University Institute Méditerranée infection has implemented since 2013 a system named MIDaS, based on the systematic collection of routine activity materials, including MALDI-TOF spectra, and results. The objective of this paper is to present the pipeline we use for processing MALDI-TOF spectra during epidemiological surveillance in order to disclose proteinic cues that may suggest the existence of epidemic processes in complement of incidence surveillance. It is illustrated by the analysis of an alarm observed for Streptococcus pneumoniae. Methods The MALDI-TOF spectra analysis process looks for the existence of clusters of spectra characterized by a double time and proteinic close proximity. This process relies on several specific methods aiming at contrasting and clustering the spectra, presenting graphically the results for an easy epidemiological interpretation, and for determining the discriminating spectra peaks with their possible identification using reference databases. Results The use of this pipeline in the case of an alarm issued for Streptococcus pneumoniae has made it possible to reveal a cluster of spectra with close proteinic and temporal distances, characterized by the presence of three discriminant peaks (5228.8, 5917.8, and 8974.3 m/z) and the absence of peak 4996.9 m/z. A further investigation on UniProt KB showed that peak 5228.8 is possibly an OxaA protein and that the absent peak may be a transposase. Conclusion This example shows this pipeline may support a quasi-real time identification and characterization of clusters that provide essential information on a potentially epidemic situation. It brings valuable information for epidemiological sensemaking and for deciding on the continuation of the epidemiological investigation, in particular the involving of additional costly resources to confirm or invalidate the alarm. Clinical trials registration NCT03626987. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06803-3.
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Affiliation(s)
- Audrey Giraud-Gatineau
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Gaetan Texier
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
| | - Pierre-Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Hervé Chaudet
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France. .,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France.
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Giraud-Gatineau A, Texier G, Garnotel E, Raoult D, Chaudet H. Insights Into Subspecies Discrimination Potentiality From Bacteria MALDI-TOF Mass Spectra by Using Data Mining and Diversity Studies. Front Microbiol 2020; 11:1931. [PMID: 32903575 PMCID: PMC7438549 DOI: 10.3389/fmicb.2020.01931] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/22/2020] [Indexed: 12/25/2022] Open
Abstract
Bacterial identification at subspecies level is critical in clinical care and epidemiological investigations due to the different epidemic potentialities of a species. For this purpose, matrix-assisted laser desorption ionization – time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed in place of molecular genotyping, but with some result discrepancies. The aim of this work is to methodically mine the expression diversities of MALDI-TOF bacterial species spectra and their possible latent organization in order to evaluate their subspecies specific expression. Peak expression diversities of MALDI-TOF spectra coming from routine identifications have been analyzed using Hill numbers, rarefaction curves, and peak clustering. Some size effect critical thresholds were estimated using change point analyses. We included 167,528 spectra corresponding to 405 species. Species spectra diversities have a broad size-dependent variability, which may be influenced by the kind of sampling. Peak organization is characterized by the presence of a main cluster made of the most frequently co-occurring peaks and around 20 secondary clusters grouping less frequently co-occurring peaks. The 35 most represented species in our sample are distributed in two groups depending on the focusing of their protein synthesis activity on the main cluster or not. Our results may advocate some analogy with genomics studies of bacteria, with a main species-related cluster of co-occurring peaks and several secondary clusters, which may host peaks able to discriminate bacterial subgroups. This systematic study of the expression diversities of MALDI-TOF spectra shows that latent organization of co-occurring peaks supports subspecies discrimination and may explain why studies on MALDI-TOF-based typing exhibit some result divergences.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
| | - Gaetan Texier
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
| | - Eric Garnotel
- Hôpital d'Instruction des Armées Laveran, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
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3
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Garner D, Kathariou S. Fresh Produce-Associated Listeriosis Outbreaks, Sources of Concern, Teachable Moments, and Insights. J Food Prot 2016; 79:337-44. [PMID: 26818997 DOI: 10.4315/0362-028x.jfp-15-387] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Foodborne transmission of Listeria monocytogenes was first demonstrated through the investigation of the 1981 Maritime Provinces outbreak involving coleslaw. In the following two decades, most listeriosis outbreaks involved foods of animal origin, e.g., deli meats, hot dogs, and soft cheeses. L. monocytogenes serotype 4b, especially epidemic clones I, II, and Ia, were frequently implicated in these outbreaks. However, since 2008 several outbreaks have been linked to diverse types of fresh produce: sprouts, celery, cantaloupe, stone fruit, and apples. The 2011 cantaloupe-associated outbreak was one of the deadliest foodborne outbreaks in recent U.S. history. This review discusses produce-related outbreaks of listeriosis with a focus on special trends, unusual findings, and potential paradigm shifts. With the exception of sprouts, implicated produce types were novel, and outbreaks were one-time events. Several involved serotype 1/2a, and in the 2011 cantaloupe-associated outbreak, serotype 1/2b was for the first time conclusively linked to a common-source outbreak of invasive listeriosis. Also in this outbreak, for the first time multiple strains were implicated in a common-source outbreak. In 2014, deployment of whole genome sequencing as part of outbreak investigation validated this technique as a pivotal tool for outbreak detection and speedy resolution. In spite of the unusual attributes of produce-related outbreaks, in all but one of the investigated cases (the possible exception being the coleslaw outbreak) contamination was traced to the same sources as those for outbreaks associated with other vehicles (e.g., deli meats), i.e., the processing environment and equipment. The public health impact of farm-level contamination remains uncharacterized. This review highlights knowledge gaps regarding virulence and other potentially unique attributes of produce outbreak strains, the potential for novel fresh produce items to become unexpectedly implicated in outbreaks, and the key role of good control strategies in the processing environment.
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Affiliation(s)
- Danisha Garner
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695-7624, USA
| | - Sophia Kathariou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695-7624, USA.
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4
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Doijad S, Lomonaco S, Poharkar K, Garg S, Knabel S, Barbuddhe S, Jayarao B. Multi-Virulence-Locus Sequence Typing of 4bListeria monocytogenesIsolates Obtained from Different Sources in India over a 10-Year Period. Foodborne Pathog Dis 2014; 11:511-6. [DOI: 10.1089/fpd.2013.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Swapnil Doijad
- ICAR Research Complex for Goa, Old Goa, Goa, India
- Penn State Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania
| | - Sara Lomonaco
- Penn State Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Sandeep Garg
- Department of Microbiology, Goa University, Goa, India
| | - Stephen Knabel
- Penn State Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Bhushan Jayarao
- Penn State Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania
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5
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Ochiai Y, Mochizuki M, Yamada F, Takano T, Hondo R, Ueda F. Genetic Classification of Listeria monocytogenes Serotype 4b Strains, Including Epidemic Clones, Isolated from Retail Meat in the Tokyo Metropolitan Area. Jpn J Infect Dis 2014; 67:258-63. [DOI: 10.7883/yoken.67.258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Conservation of genomic localization and sequence content of Sau3AI-like restriction-modification gene cassettes among Listeria monocytogenes epidemic clone I and selected strains of serotype 1/2a. Appl Environ Microbiol 2010; 76:5577-84. [PMID: 20581194 DOI: 10.1128/aem.00648-10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a food-borne pathogen with a clonal population structure and apparently limited gene flow between strains of different lineages. Strains of epidemic clone I (ECI) have been responsible for numerous outbreaks and invariably have DNA that is resistant to digestion by Sau3AI, suggesting methylation of cytosine at GATC sites. A putative restriction-modification (RM) gene cassette has been identified in the genome of the ECI strain F2365 and all other tested ECI strains but is absent from other strains of the same serotype (4b). Homologous RM cassettes have not been reported among L. monocytogenes isolates of other serotypes. Furthermore, conclusive evidence for the involvement of this RM cassette in the Sau3AI resistance phenotype of ECI strains has been lacking. In this study, we describe a highly conserved RM cassette in certain strains of serotypes 1/2a and 4a that have Sau3AI-resistant DNA. In these strains the RM cassette was in the same genomic location as in the ECI reference strain F2365. The cassette included a gene encoding a putative recombinase, suggesting insertion via site-specific recombination. Deletion of the RM cassette in the ECI strain F2365 and the serotype 1/2a strain A7 rendered the DNA of both strains susceptible to Sau3AI digestion, providing conclusive evidence that the cassette includes a gene required for methylation of cytosine at GATC sites in both strains. The findings suggest that, in addition to its presence in ECI strains, this RM cassette and the accompanying genomic DNA methylation is also encountered among selected strains of other lineages.
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7
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DNA probes for unambiguous identification of Listeria monocytogenes epidemic clone II strains. Appl Environ Microbiol 2010; 76:3061-8. [PMID: 20305032 DOI: 10.1128/aem.03064-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes epidemic clone II (ECII) strains have been responsible for two major multistate outbreaks of food-borne listeriosis in the United States, but their prevalence and ecology remain poorly understood. In this study, we describe DNA probes that unambiguously identify this clonal group. These probes were able to differentiate ECII strains of outbreak, sporadic, or environmental origin from other L. monocytogenes strains of the same serotype (4b).
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8
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Chen J, Chen Q, Jiang J, Hu H, Ye J, Fang W. Serovar 4b complex predominates among Listeria monocytogenes isolates from imported aquatic products in China. Foodborne Pathog Dis 2010; 7:31-41. [PMID: 19735205 DOI: 10.1089/fpd.2009.0353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Listeria monocytogenes, the causative organism of listeriosis, is primarily transmitted to humans through contaminated food. In this study, we examined 1275 batches of aquatic products imported from 29 countries and found that 36 batches from 8 countries were contaminated by Listeria (2.8%), with L. monocytogenes accounting for 2.6% (33/1275) and L. innocua for 0.2% (3/1275). Of the 23 selected L. monocytogenes isolates (from the 33 identified), 15 (65.2%) were of serovar 4b complex (4b, 4d, or 4e), three (13.0%) of 1/2a or 3a, four (17.4%) of 1/2b or 3b, and one (4.4%) of 1/2c or 3c. Notably, four of the 23 isolates belonged to epidemic clone I (ECI) and another four were associated with epidemic clone II (ECII), two highly clonal 4b clusters responsible for most of the documented listeriosis outbreaks. In the multilocus sequence typing scheme based on the concatenated genes gyrB-dapE-hisJ-sigB-ribC-purM-betL-gap-tuf, serovar 4b complex isolates from imported aquatic products exhibited significant genetic diversity. While the four ECI isolates were genetically related to those from Chinese diseased animals, both lacking one proline-rich repeat of ActA, the four ECII isolates were located between 1/2b or 3b strains. As the L. monocytogenes isolates from imported aquatic products possessed a nearly complete set of major infection-related genes, they demonstrated virulence potential in mouse model.
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Affiliation(s)
- Jianshun Chen
- Zhejiang University Institute of Preventive Veterinary Medicine, and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, Zhejiang, China
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9
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Akya A, Pointon A, Thomas C. Listeria monocytogenes does not survive ingestion by Acanthamoeba polyphaga. MICROBIOLOGY-SGM 2009; 156:809-818. [PMID: 19892759 DOI: 10.1099/mic.0.031146-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Listeria monocytogenes is a ubiquitous bacterium capable of infecting humans, particularly pregnant women and immunocompromised individuals. Although the intracellular invasion and pathogenesis of listeriosis in mammalian tissues has been well studied, little is known about the ecology of L. monocytogenes , and in particular the environmental reservoir for this bacterium has not been identified. This study used short-term co-culture at 15, 22 and 37 degrees C to examine the interaction of L. monocytogenes strains with Acanthamoeba polyphaga ACO12. Survival of L. monocytogenes cells phagocytosed by monolayers of trophozoites was assessed by culture techniques and microscopy. A. polyphaga trophozoites eliminated bacterial cells within a few hours post-phagocytosis, irrespective of the incubation temperature used. Wild-type L. monocytogenes and a phenotypic listeriolysin O mutant were unable to either multiply or survive within trophozoites. By contrast, Salmonella enterica serovar Typhimurium C5 cells used as controls were able to survive and multiply within A. polyphaga trophozoites. The data presented indicate that A. polyphaga ACO12 is unlikely to harbour L. monocytogenes, or act as an environmental reservoir for this bacterium.
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Affiliation(s)
- Alisha Akya
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide 5005, Australia
| | - Andrew Pointon
- South Australian Research and Development Institute, Glenside, South Australia
| | - Connor Thomas
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide 5005, Australia
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10
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Cotter PD, Draper LA, Lawton EM, Daly KM, Groeger DS, Casey PG, Ross RP, Hill C. Listeriolysin S, a novel peptide haemolysin associated with a subset of lineage I Listeria monocytogenes. PLoS Pathog 2008; 4:e1000144. [PMID: 18787690 PMCID: PMC2522273 DOI: 10.1371/journal.ppat.1000144] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Accepted: 08/07/2008] [Indexed: 11/18/2022] Open
Abstract
Streptolysin S (SLS) is a bacteriocin-like haemolytic and cytotoxic virulence factor that plays a key role in the virulence of Group A Streptococcus (GAS), the causative agent of pharyngitis, impetigo, necrotizing fasciitis and streptococcal toxic shock syndrome. Although it has long been thought that SLS and related peptides are produced by GAS and related streptococci only, there is evidence to suggest that a number of the most notorious Gram-positive pathogenic bacteria, including Listeria monocytogenes, Clostridium botulinum and Staphylococcus aureus, produce related peptides. The distribution of the L. monocytogenes cluster is particularly noteworthy in that it is found exclusively among a subset of lineage I strains; i.e., those responsible for the majority of outbreaks of listeriosis. Expression of these genes results in the production of a haemolytic and cytotoxic factor, designated Listeriolysin S, which contributes to virulence of the pathogen as assessed by murine- and human polymorphonuclear neutrophil-based studies. Thus, in the process of establishing the existence of an extended family of SLS-like modified virulence peptides (MVPs), the genetic basis for the enhanced virulence of a proportion of lineage I L. monocytogenes may have been revealed.
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Affiliation(s)
- Paul D. Cotter
- Department of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (PDC); (CH)
| | | | - Elaine M. Lawton
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Karen M. Daly
- Department of Microbiology, University College Cork, Cork, Ireland
| | | | - Pat G. Casey
- Department of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - R. Paul Ross
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Moorepark Food Research Centre, Teagasc, Moorepark, Fermoy, Cork, Ireland
| | - Colin Hill
- Department of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- * E-mail: (PDC); (CH)
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11
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Sperry KEV, Kathariou S, Edwards JS, Wolf LA. Multiple-locus variable-number tandem-repeat analysis as a tool for subtyping Listeria monocytogenes strains. J Clin Microbiol 2008; 46:1435-50. [PMID: 18256218 PMCID: PMC2292909 DOI: 10.1128/jcm.02207-07] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Revised: 01/18/2008] [Accepted: 01/28/2008] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes, like many other food-borne bacteria, has certain strains that are commonly linked to outbreaks. Due to the relatively low numbers of affected individuals, outbreaks of L. monocytogenes can be difficult to detect. The current technique of molecular subtyping in PulseNet laboratories to identify genetically similar strains is pulsed-field gel electrophoresis (PFGE). While PFGE is state-of-the-art, interlaboratory comparisons are difficult because the results are highly susceptible to discrepancies due to even minor variations in experimental conditions and the subjectivity of band marking. This research was aimed at the development of a multiple-locus variable-number tandem-repeat analysis (MLVA) that can be implemented in PulseNet laboratories to replace or complement existing protocols. MLVA has proven to be a rapid and highly discriminatory tool for subtyping many bacteria. In this study, a novel MLVA method for L. monocytogenes strains was developed utilizing eight loci multiplexed into two PCRs. The PCR products were separated by capillary gel electrophoresis for high throughput and accurate sizing, and the fragment sizes were analyzed and clustered based on the number of repeats. When tested against a panel of 193 epidemiologically linked and nonlinked isolates, this MLVA for L. monocytogenes strains demonstrates strong epidemiological concordance. Since MLVA is a high-throughput screening method that is fairly inexpensive, easy to perform, rapid, and reliable, it is well suited to interlaboratory comparisons during epidemiological investigations of food-borne illness.
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12
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Galbraith EA, Antonopoulos DA, White BA. Application of suppressive subtractive hybridization to uncover the metagenomic diversity of environmental samples. Methods Mol Biol 2008; 410:295-333. [PMID: 18642606 DOI: 10.1007/978-1-59745-548-0_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Metagenomics addresses the collective genetic structure and functional composition of a microbial environmental sample without the bias or necessity for culturing the microorganisms from the community in question. Metagenomic studies are now beginning to take advantage of the plethora of complete genome sequences and the associated tools, such as bacterial artificial chromosome (BAC) and fosmid vectors, to discover novel genes and survey the structure and function of microbial communities. Complementary and less expensive methods to compare genomes from individual microbes have been utilized in comparative genomic studies. Suppressive subtractive hybridization (SSH) is one such approach, which has been utilized to compare the genomic content of closely related species of bacteria. Recently, SSH has also been used as a comparative method to examine the microbial diversity (i.e., species composition) and functional differences (i.e., gene composition) in the genomic content of two different rumen environmental communities. Through a series of hybridizations and pblymerase chain reaction (PCR) amplifications, metagenomic differences between two environmental samples can be isolated by SSH. Subsequent DNA sequencing and bioinformatic analyses allow the putative identification of these differences.
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13
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Chen Y, Knabel SJ. Multiplex PCR for simultaneous detection of bacteria of the genus Listeria, Listeria monocytogenes, and major serotypes and epidemic clones of L. monocytogenes. Appl Environ Microbiol 2007; 73:6299-304. [PMID: 17693562 PMCID: PMC2075000 DOI: 10.1128/aem.00961-07] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex PCR assay which combines detection of bacteria of the genus Listeria, Listeria monocytogenes serotypes 1/2a and 4b, and epidemic clones I, II, and III of L. monocytogenes was developed. The assay provides a rapid, reliable, and inexpensive method for screening and subgrouping this important food-borne pathogen.
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Affiliation(s)
- Yi Chen
- The Pennsylvania State University, Food Science Department, 436 Food Science Building, University Park, PA 16802, USA.
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14
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Franciosa G, Scalfaro C, Maugliani A, Floridi F, Gattuso A, Hodzic S, Aureli P. Distribution of epidemic clonal genetic markers among Listeria monocytogenes 4b isolates. J Food Prot 2007; 70:574-81. [PMID: 17388044 DOI: 10.4315/0362-028x-70.3.574] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent genome sequencing of isolates of Listeria monocytogenes serotype 4b implicated in some major outbreaks of foodborne listeriosis has revealed unique genetic markers in these isolates. The isolates were grouped into two distinct epidemic clones, ECI and ECII. In the present study, selected ECI- and ECII-specific genetic markers were detected in 16 and 15 of 89 L. monocytogenes 4b isolates, respectively. The ECI markers were found in 6 of 34 clinical isolates, 9 of 50 food isolates, and 1 of 5 environmental isolates, and the ECII markers were detected in 7 of 34 clinical isolates, 7 of 50 food isolates, and 1 of 5 environmental isolates. Hence, of the isolates with the epidemic clonal genetic markers, 38% (13 of 34) were of clinical origin, 32% (16 of 50) were of food origin, and 40% (2 of 5) were of environmental origin. The predominance of the epidemic clonal markers among the clinical and environmental isolates supports the hypothesis that these markers are correlated with the pathogenic potential of strains and with their environmental persistence. Several isolates had only one epidemic clonal marker, either the ECI-specific marker 133 or the ECII-specific marker 4bSF18. Pulsed-field gel electrophoresis analysis revealed higher genomic diversity among the strains with ECII-like characteristics than among those strains carrying the ECI-specific genetic markers.
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Affiliation(s)
- Giovanna Franciosa
- Laboratory of Food Microbial Hazards, National Center for Food Quality and Risk Assessment, Istituto Superiore di Sanità, Rome, Italy
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Ducey TF, Page B, Usgaard T, Borucki MK, Pupedis K, Ward TJ. A single-nucleotide-polymorphism-based multilocus genotyping assay for subtyping lineage I isolates of Listeria monocytogenes. Appl Environ Microbiol 2006; 73:133-47. [PMID: 17085705 PMCID: PMC1797101 DOI: 10.1128/aem.01453-06] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a facultative intracellular pathogen responsible for food-borne disease with high mortality rates in humans and is the leading microbiological cause of food recalls. Lineage I isolates of L. monocytogenes are a particular public health concern because they are responsible for most sporadic cases of listeriosis and the vast majority of epidemic outbreaks. Rapid, reproducible, and sensitive methods for differentiating pathogens below the species level are required for effective pathogen control programs, and the CDC PulseNet Task Force has called for the development and validation of DNA sequence-based methods for subtyping food-borne pathogens. Therefore, we developed a multilocus genotyping (MLGT) assay for L. monocytogenes lineage I isolates based on nucleotide variation identified by sequencing 23,251 bp of DNA from 22 genes distributed across seven genomic regions in 65 L. monocytogenes isolates. This single-well assay of 60 allele-specific probes captured 100% of the haplotype information contained in approximately 1.5 Mb of comparative DNA sequence and was used to reproducibly type a total of 241 lineage I isolates. The MLGT assay provided high discriminatory power (Simpson's index value, 0.91), uniquely identified isolates from the eight listeriosis outbreaks examined, and differentiated serotypes 1/2b and 4b as well as epidemic clone I (ECI), ECIa, and ECII. In addition, the assay included probes for a previously characterized truncation mutation in inlA, providing for the identification of a specific virulence-attenuated subtype. These results demonstrate that MLGT represents a significant new tool for use in pathogen surveillance, outbreak detection, risk assessment, population analyses, and epidemiological investigations. DNA sequences were deposited in the GenBank database under accession numbers DQ 812146 to DQ 812517, DQ 843664 to DQ 844598, and AY 512391 to AY 512502.
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Affiliation(s)
- Thomas F Ducey
- Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL 61604, USA
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Kathariou S, Graves L, Buchrieser C, Glaser P, Siletzky RM, Swaminathan B. Involvement of closely related strains of a new clonal group of Listeria monocytogenes in the 1998-99 and 2002 multistate outbreaks of foodborne listeriosis in the United States. Foodborne Pathog Dis 2006; 3:292-302. [PMID: 16972778 DOI: 10.1089/fpd.2006.3.292] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In 1998-99, a multistate outbreak of listeriosis in the United States was associated with contaminated hot dogs and was caused by a strain of Listeria monocytogenes serotype 4b that had been only rarely encountered before in the national PulseNet database. Upon further characterization, the strains from this outbreak were designated as Epidemic Clone II (ECII). ECII isolates exhibited diversification in a genomic region ("region 18") that was otherwise conserved among L. monocytogenes of serotype 4b. Additional unique genetic markers were identified through genome sequencing of one of the isolates from the 1998-99 outbreak. In 2002, another multistate outbreak of listeriosis also involved bacteria of serotype 4b and was attributed to contaminated turkey deli meats. Molecular subtyping data revealed that the macrorestriction patterns of the isolates from the 1998-99 and 2002 outbreaks were closely related. In addition, the 2002 outbreak isolates harbored chromosomal genetic markers found to be unique to, and typical of, the 1998-99 outbreak isolates, including diversification in genomic region 18. Macroarray- based subtyping using chromosomal sequences confirmed the close genetic relatedness between the isolates from the two outbreaks. Genomic content was highly conserved among isolates from each outbreak, with differences detected only in prophage and internalin-like gene sequences. However, since these differences were observed among isolates from each of the outbreaks, they did not differentiate the 1998-99 isolates as a group from those of the 2002 outbreak. Two of 15 randomly chosen serotype 4b clinical isolates from a non-outbreak period (calendar year 2003) appeared to be closely related to the 1998-99 and 2002 outbreak isolates. These findings suggest that both multistate outbreaks of listeriosis in the United States involved closely related members of a single clonal group (ECII) that had not been identified in outbreaks prior to 1998. Since the outbreaks involved different food vehicles and processing plants, the findings suggest establishment of ECII in a still unidentified reservoir in the United States, from which the organisms were introduced to different processing plants.
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Affiliation(s)
- S Kathariou
- Department of Food Science, North Carolina State University, Raleigh, North Carolina 27695-7624, USA.
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17
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Wei W, Cao Z, Zhu YL, Wang X, Ding G, Xu H, Jia P, Qu D, Danchin A, Li Y. Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228. BMC Genomics 2006; 7:112. [PMID: 16684363 PMCID: PMC1482698 DOI: 10.1186/1471-2164-7-112] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Accepted: 05/10/2006] [Indexed: 11/16/2022] Open
Abstract
Background Staphylococcus epidermidis, long regarded as an innocuous commensal bacterium of the human skin, is the most frequent cause of nosocomial infections associated with implanted medical devices. This conditional pathogen provides a model of choice to study genome landmarks correlated with the transition between commensalism and pathogenicity. Traditional investigations stress differences in gene content. We focused on conserved genes that have accumulated small mutation differences during the transition. Results A comparison of strain ATCC12228, a non-biofilm forming, non-infection associated strain and strain RP62A, a methicillin-resistant biofilm clinical isolate, revealed consistent variation, mostly single-nucleotide polymorphisms (SNPs), in orthologous genes in addition to the previously investigated global changes in gene clusters. This polymorphism, scattered throughout the genome, may reveal genes that contribute to adaptation of the bacteria to different environmental stimuli, allowing them to shift from commensalism to pathogenicity. SNPs were detected in 931 pairs of orthologs with identical gene length, accounting for approximately 45% of the total pairs of orthologs. Assuming that non-synonymous mutations would mark recent evolution, and hence be associated to the onset of the pathogenic process, analysis of ratios of non-synonymous SNPs vs synonymous SNPs suggested hypotheses about possible pathogenicity determinants. The N/S ratios for virulence factors and surface proteins differed significantly from that of average SNPs. Of those gene pairs, 40 showed a disproportionate distribution of dN vs dS. Among those, the presence of the gene encoding methionine sulfoxide reductase suggested a possible involvement of reactive oxygen species. This led us to uncover that the infection associated strain was significantly more resistant to hydrogen peroxide and paraquat than the environmental strain. Some 16 genes of the list were of unknown function. We could suggest however that they were likely to belong to surface proteins or considered in priority as important for pathogenicity. Conclusion Our study proposed a novel approach to identify genes involved in pathogenic processes and provided some insight about the molecular mechanisms leading a commensal inhabitant to become an invasive pathogen.
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Affiliation(s)
- Wu Wei
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai, China
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
| | - ZhiWei Cao
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
| | - Yu-Li Zhu
- Department of Medical Molecular Virology, Institute of Medical microbiology, Shanghai Medical School of Fudan University, 138 YiXue Yuan Road, Shanghai, China
| | - XiaoJing Wang
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai, China
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
| | - GuoHui Ding
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai, China
| | - Hao Xu
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
| | - PeiLin Jia
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai, China
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
| | - Di Qu
- Department of Medical Molecular Virology, Institute of Medical microbiology, Shanghai Medical School of Fudan University, 138 YiXue Yuan Road, Shanghai, China
| | - Antoine Danchin
- Genetics of Bacterial Genomes/URA 2171 CNRS, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - YiXue Li
- Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Graduate School of the Chinese Academy of Sciences, 320 YueYang Road, Shanghai, China
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai, China
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18
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Folsom JP, Siragusa GR, Frank JF. Formation of biofilm at different nutrient levels by various genotypes of Listeria monocytogenes. J Food Prot 2006; 69:826-34. [PMID: 16629025 DOI: 10.4315/0362-028x-69.4.826] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Strains of Listeria monocytogenes differ in their ability to form biofilms. The objectives of this study were to determine whether genetically related strains have similar biofilm-forming capacities and what effect nutrient concentration has on the ability of different strains to produce biofilms. Biofilms of 30 strains of L. monocytogenes, obtained from a variety of sources were grown on stainless steel in tryptic soy broth (TSB) or in a 1:10 dilution of TSB (DTSB) for 24 h at 32 degrees C. The amount of biofilm formed was determined with image analysis after cells were stained with bisBenzimide H 33258 (Hoechst 33258). The strains were genetically subtyped by repetitive element sequence-based PCR (rep-PCR) with the primer set rep-PRODt and rep-PROG5. Data were analyzed with an analysis of variance and Duncan's multiple range test. Eleven strains produced the same amount of biofilm in both media. Fourteen strains produced more biofilm in TSB than in DTSB. Five strains produced more biofilm in DTSB than in TSB. Serotype 4b strains produced more biofilm in TSB than did serotype 1/2a strains, whereas serotype 1/2a strains produced more biofilm in DTSB than did serotype 4b strains. Growth in DTSB resulted in decreased biofilm accumulation for serotype 4b strains. There was no correlation between genetic subtype and the amount of biofilm accumulation. These results indicate that strains of serotype 1/2a and serotype 4b differ in the regulation of their biofilm phenotype. The poor biofilm accumulation of serotype 4b isolates when grown in DTSB could be a factor in the predominance of serogroup 1/2 strains in food processing plants, where nutrients may be limited.
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Affiliation(s)
- James P Folsom
- Department of Food Science and Technology, University of Georgia, Athens 30602-7610, USA
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19
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Kimura B. Recent Advances in the Study of the Genotypic Diversity and Ecology of Listeria monocytogenes. Microbes Environ 2006. [DOI: 10.1264/jsme2.21.69] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Bon Kimura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology
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20
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Zhang C, Nietfeldt J, Zhang M, Benson AK. Functional consequences of genome evolution in Listeria monocytogenes: the lmo0423 and lmo0422 genes encode sigmaC and LstR, a lineage II-specific heat shock system. J Bacteriol 2005; 187:7243-53. [PMID: 16237008 PMCID: PMC1272999 DOI: 10.1128/jb.187.21.7243-7253.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes strains belonging to phylogenetic lineage II (serotypes 1/2a, 1/2c, and 3a) carry a lineage-specific genome segment encoding a putative sigma subunit of RNA polymerase (lmo0423, herein referred to as sigC), a gene of unknown function (lmo0422) similar to the padR family of regulators, and a gene that is similar to the rodA-ftsW family of cell wall morphology genes (lmo0421). To understand the function of this set of genes, their expression patterns and the effects of null mutations in the lineage II L. monocytogenes strain 10403S were examined. The data are consistent with the three genes comprising an operon (the sigC operon) that is highly induced by temperature upshift. The operon is transcribed from three different promoters, the proximal of which (P1) depends upon sigC itself. Null mutations in sigC or lmo0422 increase the death rate at lethal temperatures and cause loss of thermal adaptive response, whereas the lmo0421 mutation causes only a loss of the adaptive response component. Only the sigC mutation affects transcription from the P1 promoter, whereas ectopic expression of lmo0422 from the P(SPAC) promoter complements the individual lmo0422 and sigC null mutations, showing that lmo0422 is the actual thermal resistance regulator or effector while sigC provides a mechanism for temperature-dependent transcription of lmo0422 from P1. Our genetic and phylogenetic analyses are consistent with lmo0422-renamed lstR (for lineage-specific thermal regulator)-and sigC comprising a system of thermal resistance that was ancestral to the genus Listeria and was subsequently lost during divergence of the lineage I L. monocytogenes population.
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MESH Headings
- Adaptation, Physiological
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Biological Evolution
- Colony Count, Microbial
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/physiology
- Evolution, Molecular
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genome, Bacterial
- Hot Temperature
- Listeria monocytogenes/genetics
- Listeria monocytogenes/physiology
- Membrane Proteins/genetics
- Membrane Proteins/physiology
- Multigene Family
- Operon
- Phylogeny
- Promoter Regions, Genetic
- RNA, Bacterial/analysis
- RNA, Messenger/analysis
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Sequence Homology
- Sigma Factor/genetics
- Sigma Factor/physiology
- Synteny
- Transcription, Genetic
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Affiliation(s)
- Chaomei Zhang
- Department of Food Science and Technology, University of Nebraska, 330 Food Industry Complex, Lincoln, NE 68583-0919, USA
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21
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Eifert JD, Curtis PA, Bazaco MC, Meinersmann RJ, Berrang ME, Kernodle S, Stam C, Jaykus LA, Kathariou S. Molecular Characterization ofListeria monocytogenesof the Serotype 4b Complex (4b, 4d, 4e) from Two Turkey Processing Plants. Foodborne Pathog Dis 2005; 2:192-200. [PMID: 16156700 DOI: 10.1089/fpd.2005.2.192] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most foodborne outbreaks of listeriosis have been found to involve a small number of closely related strains of Listeria monocytogenes serotype 4b. The ecology of these organisms and their reservoirs in nature or in the processing plant environment, however, remain poorly understood. Surveys of environmental samples from two turkey processing plants in the United States indicated presence of L. monocytogenes of the serotype 4b complex (serotype 4b and the closely related serotypes 4d and 4e). In addition, environmental and raw product samples from one plant repeatedly yielded isolates with genetic markers typical of two major serotype 4b epidemic clonal groups, ECI and ECII. The pulsed field gel electrophoresis (PFGE) profiles of these isolates, however, were clearly distinct from those of confirmed epidemic-associated strains. Furthermore, we observed minor but consistent differences in PFGE profiles of isolates that harbored ECI- or ECII-specific genetic markers, and that were obtained at different sampling times from the same plant. The findings suggest processing plant persistence (or repeated introductions) and genomic diversification of L. monocytogenes serotype 4b isolates that harbor ECI- or ECII-specific genetic markers. Such diversification would need to be taken into consideration in further efforts to elucidate the evolution and epidemiology of these organisms.
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Affiliation(s)
- J D Eifert
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, USA
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22
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Olier M, Garmyn D, Rousseaux S, Lemaître JP, Piveteau P, Guzzo J. Truncated internalin A and asymptomatic Listeria monocytogenes carriage: in vivo investigation by allelic exchange. Infect Immun 2005; 73:644-8. [PMID: 15618209 PMCID: PMC538994 DOI: 10.1128/iai.73.1.644-648.2005] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Allelic exchange of the region coding for the C terminus of InlA between one epidemic (with an 80-kDa InlA) and one asymptomatic (with a 47-kDa InlA) carriage Listeria monocytogenes strain confirmed the need for this region for internalin entry in vitro. Interestingly, restoration of internalin A functionality did not result in full virulence in chicken embryo assays.
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Affiliation(s)
- Maïwenn Olier
- Laboratoire de Microbiologie, UMR INRA 1232, Université de Bourgogne, 1 Esplanade Erasme, 21000 Dijon, France
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23
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Evans MR, Swaminathan B, Graves LM, Altermann E, Klaenhammer TR, Fink RC, Kernodle S, Kathariou S. Genetic markers unique to Listeria monocytogenes serotype 4b differentiate epidemic clone II (hot dog outbreak strains) from other lineages. Appl Environ Microbiol 2004; 70:2383-90. [PMID: 15066835 PMCID: PMC383029 DOI: 10.1128/aem.70.4.2383-2390.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A small number of closely related strains of Listeria monocytogenes serotype 4b, designated epidemic clone I (ECI), have been implicated in numerous outbreaks of food-borne listeriosis described during the past two decades in Europe and North America. In 1998 to 1999, a multistate outbreak traced to contaminated hot dogs involved a different strain type of serotype 4b, with genetic fingerprints rarely encountered before. In spite of the profound economic and public health impact of this outbreak, the implicated bacteria (designated epidemic clone II [ECII]) have remained poorly characterized genetically, and nucleotide sequences specific for these strains have not been reported. Using genome sequence information, PCR, and Southern blots, we identified DNA fragments which appeared to be either absent or markedly divergent in the hot dog outbreak strains but conserved among other serotype 4b strains. PCR with primers derived from these fragments as well as Southern blots with the amplicons as probes readily differentiated ECII from other serotype 4b strains. The serotype 4b-specific region harboring these fragments was adjacent to inlA, which encodes a well-characterized virulence determinant. The findings suggest that ECII strains have undergone divergence in portions of a serotype-specific region that is conserved in other serotype 4b strains. Although the mechanisms that drive this divergence remain to be identified, DNA-based tools from this region can facilitate the detection and further characterization of strains belonging to this lineage.
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Affiliation(s)
- Matthew R Evans
- Department of Food Science, North Carolina State University, Raleigh, North Carolina 27695, USA
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24
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Ward TJ, Gorski L, Borucki MK, Mandrell RE, Hutchins J, Pupedis K. Intraspecific phylogeny and lineage group identification based on the prfA virulence gene cluster of Listeria monocytogenes. J Bacteriol 2004; 186:4994-5002. [PMID: 15262937 PMCID: PMC451661 DOI: 10.1128/jb.186.15.4994-5002.2004] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Accepted: 04/23/2004] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a serious food-borne pathogen that can cause invasive disease in humans and other animals and has been the leading cause of food recalls due to microbiological concerns in recent years. In order to test hypotheses regarding L. monocytogenes lineage composition, evolution, ecology, and taxonomy, a robust intraspecific phylogeny was developed based on prfA virulence gene cluster sequences from 113 L. monocytogenes isolates. The results of the multigene phylogenetic analyses confirm that L. monocytogenes comprises at least three evolutionary lineages, demonstrate that lineages most frequently (lineage 1) and least frequently (lineage 3) associated with human listeriosis are sister-groups, and reveal for the first time that the human epidemic associated serotype 4b is prevalent among strains from lineage 1 and lineage 3. In addition, a PCR-based test for lineage identification was developed and used in a survey of food products demonstrating that the low frequency of association between lineage 3 isolates and human listeriosis cases likely reflects rarity of exposure and not reduced virulence for humans as has been previously suggested. However, prevalence data do suggest lineage 3 isolates may be better adapted to the animal production environment than the food-processing environment. Finally, analyses of haplotype diversity indicate that lineage 1 has experienced a purge of genetic variation that was not observed in the other lineages, suggesting that the three L. monocytogenes lineages may represent distinct species within the framework of the cohesion species concept.
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Affiliation(s)
- Todd J Ward
- Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University St., Peoria, IL 61604, USA.
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25
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Johnson J, Jinneman K, Stelma G, Smith BG, Lye D, Messer J, Ulaszek J, Evsen L, Gendel S, Bennett RW, Swaminathan B, Pruckler J, Steigerwalt A, Kathariou S, Yildirim S, Volokhov D, Rasooly A, Chizhikov V, Wiedmann M, Fortes E, Duvall RE, Hitchins AD. Natural atypical Listeria innocua strains with Listeria monocytogenes pathogenicity island 1 genes. Appl Environ Microbiol 2004; 70:4256-66. [PMID: 15240309 PMCID: PMC444784 DOI: 10.1128/aem.70.7.4256-4266.2004] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Accepted: 04/05/2004] [Indexed: 11/20/2022] Open
Abstract
Identification of bona fide Listeria isolates into the six species of the genus normally requires only a few tests. Aberrant isolates do occur, but even then only one or two extra confirmatory tests are generally needed for identification to species level. We have discovered a hemolytic-positive, rhamnose and xylose fermentation-negative Listeria strain with surprising recalcitrance to identification to the species level due to contradictory results in standard confirmatory tests. The issue had to be resolved by using total DNA-DNA hybridization testing and then confirmed by further specific PCR-based tests including a Listeria microarray assay. The results show that this isolate is indeed a novel one. Its discovery provides the first fully documented instance of a hemolytic Listeria innocua strain. This species, by definition, is typically nonhemolytic. The L. innocua isolate contains all the members of the PrfA-regulated virulence gene cluster (Listeria pathogenicity island 1) of L. monocytogenes. It is avirulent in the mouse pathogenicity test. Avirulence is likely at least partly due to the absence of the L. monocytogenes-specific allele of iap, as well as the absence of inlA, inlB, inlC, and daaA. At least two of the virulence cluster genes, hly and plcA, which encode the L. monocytogenes hemolysin (listeriolysin O) and inositol-specific phospholipase C, respectively, are phenotypically expressed in this L. innocua strain. The detection by PCR assays of specific L. innocua genes (lin0198, lin0372, lin0419, lin0558, lin1068, lin1073, lin1074, lin2454, and lin2693) and noncoding intergenic regions (lin0454-lin0455 and nadA-lin2134) in the strain is consistent with its L. innocua DNA-DNA hybridization identity. Additional distinctly different hemolytic L. innocua strains were also studied.
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Affiliation(s)
- J Johnson
- Food and Drug Administration, Bothell, Washington 98021, USA
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26
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Yildirim S, Lin W, Hitchins AD, Jaykus LA, Altermann E, Klaenhammer TR, Kathariou S. Epidemic clone I-specific genetic markers in strains of Listeria monocytogenes serotype 4b from foods. Appl Environ Microbiol 2004; 70:4158-64. [PMID: 15240296 PMCID: PMC444779 DOI: 10.1128/aem.70.7.4158-4164.2004] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Accepted: 03/08/2004] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes contamination of ready-to-eat foods has been implicated in numerous outbreaks of food-borne listeriosis. However, the health hazards posed by L. monocytogenes detected in foods may vary, and speculations exist that strains actually implicated in illness may constitute only a fraction of those that contaminate foods. In this study, examination of 34 serogroup 4 (putative or confirmed serotype 4b) isolates of L. monocytogenes obtained from various foods and food-processing environments, without known implication in illness, revealed that many of these strains had methylation of cytosines at GATC sites in the genome, rendering their DNA resistant to digestion by the restriction endonuclease Sau3AI. These strains also harbored a gene cassette with putative restriction-modification system genes as well as other, genomically unlinked genetic markers characteristic of the major epidemic-associated lineage of L. monocytogenes (epidemic clone I), implicated in numerous outbreaks in Europe and North America. This may reflect a relatively high fitness of strains with these genetic markers in foods and food-related environments relative to other serotype 4b strains and may partially account for the repeated involvement of such strains in human food-borne listeriosis.
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Affiliation(s)
- Suleyman Yildirim
- North Carolina State University, Department of Food Science, Campus Box 7624, Raleigh, NC 27695-7624, USA
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27
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Doumith M, Cazalet C, Simoes N, Frangeul L, Jacquet C, Kunst F, Martin P, Cossart P, Glaser P, Buchrieser C. New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect Immun 2004; 72:1072-83. [PMID: 14742555 PMCID: PMC321639 DOI: 10.1128/iai.72.2.1072-1083.2004] [Citation(s) in RCA: 204] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a food-borne bacterial pathogen that causes a wide spectrum of diseases, such as meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13 L. monocytogenes serovars described, invasive disease is mostly associated with serovar 4b strains. To investigate the genetic diversity of L. monocytogenes strains with different virulence potentials, we partially sequenced an epidemic serovar 4b strain and compared it with the complete sequence of the nonepidemic L. monocytogenes EGDe serovar 1/2a strain. We identified an unexpected genetic divergence between the two strains, as about 8% of the sequences were serovar 4b specific. These sequences included seven genes coding for surface proteins, two of which belong to the internalin family, and three genes coding for transcriptional regulators, all of which might be important in different steps of the infectious process. Based on the sequence information, we then characterized the gene content of 113 Listeria strains by using a newly designed Listeria array containing the "flexible" part of the sequenced Listeria genomes. Hybridization results showed that all of the previously identified virulence factors of L. monocytogenes were present in the 93 L. monocytogenes strains tested. However, distinct patterns of the presence or absence of other genes were identified among the different L. monocytogenes serovars and Listeria species. These results allow new insights into the evolution of L. monocytogenes, suggesting that early divergence of the ancestral L. monocytogenes serovar 1/2c strains from the serovar 1/2b strains led to two major phylogenetic lineages, one of them including the serogroup 4 strains, which branched off the serovar 1/2b ancestral lineage, leading (mostly by gene loss) to the species Listeria innocua. The identification of 30 L. monocytogenes-specific and several serovar-specific marker genes, such as three L. monocytogenes serovar 4b-specific surface protein-coding genes, should prove powerful for the rapid tracing of listeriosis outbreaks, but it also represents a fundamental basis for the functional study of virulence differences between L. monocytogenes strains.
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Affiliation(s)
- Michel Doumith
- Laboratoire des Listeria, Centre National de Référence des Listeria, World Health Organization Collaborating Center for Foodborne Listeriosis, Institut Pasteur, 75724 Paris 15, France
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28
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Zhang C, Zhang M, Ju J, Nietfeldt J, Wise J, Terry PM, Olson M, Kachman SD, Wiedmann M, Samadpour M, Benson AK. Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations. J Bacteriol 2003; 185:5573-84. [PMID: 12949110 PMCID: PMC193770 DOI: 10.1128/jb.185.18.5573-5584.2003] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.
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Affiliation(s)
- Chaomei Zhang
- Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska 68583, USA
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Porto ACS, Wonderling L, Call JE, Luchansky JB. Use of pulsed-field gel electrophoresis to monitor a five-strain mixture of Listeria monocytogenes in frankfurter packages. J Food Prot 2003; 66:1465-8. [PMID: 12929838 DOI: 10.4315/0362-028x-66.8.1465] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In a previous study, the viability of a five-strain mixture of Listeria monocytogenes (including Scott A [serotype 4b, clinical isolate], 101M [serotype 4b, beef-pork sausage isolate], F6854 [serotype 1/2a, turkey frankfurter isolate], H7776 [serotype 4b, frankfurter isolate], and MFS-2 [serotype 1/2a, pork plant isolate]) was monitored during refrigerated storage of frankfurters prepared with and without 3.0% added potassium lactate. Throughout a 90-day period of storage at 4 degrees C, the initial inoculum level of 20 CFU per package remained relatively constant in packages containing frankfurters prepared with potassium lactate, but pathogen counts increased to 4.6 log10 CFU in packages containing frankfurters prepared without added potassium lactate. To determine which of the five strains persisted under these conditions, randomly selected colonies obtained after 28 and 90 days of refrigerated storage of frankfurters were analyzed by pulsed-field gel electrophoresis (PFGE) with the restriction enzyme SmaI to generate distinct banding patterns for each of the five strains. Then, with the use of PFGE as a tool for identification, the percentages of the strains on days 28 and 90 of the growth study were compared. In the absence of any added potassium lactate in the product, 43% of the 58 isolates recovered on day 28 were identified as strain Scott A, 12% were identified as strain 101M, 22% were identified as strain F6854, 10% were identified as strain H7776, and 12% were identified as strain MFS-2. However, by day 90, an appreciable number (83%) of the 60 isolates analyzed were identified as strain MFS-2. In packages containing frankfurters formulated with 3.0% potassium lactate, all five strains were present at frequencies of 5 to 36% among the 19 isolates tested on day 28; however, by day 90, strain MFS-2 made up the statistical majority (63%) of the 27 isolates tested. The results of this study indicate that strain MFS-2, a serotype 1/2a isolate recovered from a pork processing plant, was more persistent than strains Scott A, 101M, F6854, or H7776 during the extended refrigerated storage of frankfurters.
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Affiliation(s)
- Anna C S Porto
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Microbial Food Safety Research Unit, 600 East Mermaid Lane, Wyndmoor, Pennsylvania 19038, USA
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Ramnath M, Rechinger KB, Jänsch L, Hastings JW, Knøchel S, Gravesen A. Development of a Listeria monocytogenes EGDe partial proteome reference map and comparison with the protein profiles of food isolates. Appl Environ Microbiol 2003; 69:3368-76. [PMID: 12788738 PMCID: PMC161492 DOI: 10.1128/aem.69.6.3368-3376.2003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A partially annotated proteome reference map of the food pathogen Listeria monocytogenes was developed for exponentially growing cells under standardized, optimal conditions by using the sequenced strain EGDe (serotype 1/2a) as a model organism. The map was developed by using a reproducible total protein extraction and two-dimensional (2-D) polyacrylamide gel electrophoresis analysis procedure, and it contained 33 identified proteins representing the four main protein functional classes. In order to facilitate analysis of membrane proteins, a protein compartmentalization procedure was assessed. The method used provided partial fractionation of membrane and cytosolic proteins. The total protein 2-D profiles of three serotype 1/2a strains and one serotype 1/2b strain isolated from food were compared to the L. monocytogenes EGDe proteome. An average of 13% of the major protein spots in the food strain proteomes were not matched in the strain EGDe proteome. The variation was greater for the less intense spots, and on average 28% of these spots were not matched. Two of the proteins identified in L. monocytogenes EGDe were missing in one or more of the food isolates. These two proteins were proteins involved in the main glycolytic pathway and in metabolism of coenzymes and prosthetic groups. The two corresponding genes were found by PCR amplification to be present in the four food isolates. Our results show that the L. monocytogenes EGDe reference map is a valuable starting point for analyses of strains having various origins and could be useful for analyzing the proteomes of different isolates of this pathogen.
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Affiliation(s)
- Manilduth Ramnath
- Department of Biochemistry, University of Stellenbosch, 7602 Matieland, South Africa
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Wagner M, Allerberger F. Characterization of Listeria monocytogenes recovered from 41 cases of sporadic listeriosis in Austria by serotyping and pulsed-field gel electrophoresis. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2003; 35:227-34. [PMID: 12648841 DOI: 10.1016/s0928-8244(02)00445-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
41 clinical Listeria monocytogenes strains recovered from seven feto-maternal and 34 non-pregnancy associated cases of human listeriosis documented between 1997 and 2000 underwent serotyping and typing by pulsed-field gel electrophoresis (PFGE) applying the enzymes AscI, ApaI and SmaI. The pulsotypes of the clinical strains were compared to the pulsotypes of three L. monocytogenes strains isolated from healthy fecal carriers and nine reference strains isolated from seven outbreaks in Europe and the USA. The 41 clinical strains of Austrian provenance showed 37 pulsotypes. Five sets of two Austrian strains each were indistinguishable by PFGE typing. Epidemiological links were absent between these indistinguishable isolates. One unique pulsotype (AB) was found in three fecal isolates. Five pulsotypes (A, Q, R, AC and AD) were distinguished among the strains associated with outbreaks. Clusters consisting of two, five and six Austrian strains each were indistinguishable from the outbreak-associated pulsotypes A, Q and R, respectively, after PFGE analysis with AscI. Three strains of AscI pulsotype Q and five strains of AscI pulsotype R could be further differentiated by restriction with ApaI and SmaI. One strain each from sporadic cases shared a combined pulsotype with the outbreak strains of pulsotypes A and R, respectively. These PFGE data suggest that a similar genetic background can be found in strains which have been contributing to outbreaks world-wide and in isolates associated with sporadic listeriosis in Austria.
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Affiliation(s)
- Martin Wagner
- Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria.
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Olier M, Pierre F, Rousseaux S, Lemaître JP, Rousset A, Piveteau P, Guzzo J. Expression of truncated Internalin A is involved in impaired internalization of some Listeria monocytogenes isolates carried asymptomatically by humans. Infect Immun 2003; 71:1217-24. [PMID: 12595435 PMCID: PMC148840 DOI: 10.1128/iai.71.3.1217-1224.2003] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2002] [Revised: 09/24/2002] [Accepted: 11/08/2002] [Indexed: 11/20/2022] Open
Abstract
Fourteen human carriage Listeria monocytogenes isolates were compared to sporadic and epidemic-associated human strains in order to ascertain the pathogenic behavior of these unrecognized asymptomatic strains. Experimental infection of 14-day-old chick embryos revealed that the majority of the carriage strains were attenuated for virulence. Of the 10 attenuated carriage strains, 5 were affected in their invasion capacities in vitro. Western blot analysis with antibody directed against InlA, the surface protein implicated in the internalization in host cells, allowed correlation between the ability of the carriage strains to enter Caco-2 cells and InlA expression. Indeed, these five carriage strains produced truncated forms of InlA. Four of the five truncated forms of InlA had an apparent molecular mass of 47 kDa. In order to assess the existence of a genetic lineage, partial sequences of inlA gene of these four strains were compared and revealed that they had a high degree of sequence conservation at the gene (99.86%) and amino acid (100%) levels. Comparison of their nucleotide sequences with that of the corresponding segment of inlA from EGD-e and Scott A strains, taken as epidemic references, showed more divergence. Taken together, these observations suggest the presence of specific traits that characterize L. monocytogenes strains isolated during asymptomatic carriage. Some of these traits could provide some explanations about the determinants that make them unable to cause systemic human infection.
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Affiliation(s)
- Maïwenn Olier
- Laboratoire de Microbiologie Equipe PG2MA, UMR INRA 1082, ENSBANA, 21000 Dijon, France
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Call DR, Borucki MK, Besser TE. Mixed-genome microarrays reveal multiple serotype and lineage-specific differences among strains of Listeria monocytogenes. J Clin Microbiol 2003; 41:632-9. [PMID: 12574259 PMCID: PMC149708 DOI: 10.1128/jcm.41.2.632-639.2003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epidemiological studies and analysis of putative virulence genes have shown that Listeria monocytogenes has diverged into several phylogenetic divisions. We hypothesize that similar divergence has occurred for many genes that influence niche-specific fitness and virulence and that identifying these differences may offer new opportunities for the detection, treatment, and control of this important pathogen. To explore this issue further, we developed a microarray composed of fragmented DNA taken from 10 strains of L. monocytogenes. We then hybridized genomic DNA from 50 different strains to replicate arrays and analyzed the resulting hybridization patterns. A simple Euclidean distance metric permitted the reconstruction of previously described genetic relationships between serotypes, and only four microarray probes were needed to discriminate between the most important serotypes (1/2a, 1/2b, 1/2c, and 4). We calculated an index of linkage equilibrium from the microarray data and confirmed that L. monocytogenes has a strongly clonal population structure (I(A) = 3.85). Twenty-nine informative probes were retrieved from the library and sequenced. These included genes associated with repairing UV-damaged DNA, salt tolerance, biofilm formation, heavy metal transport, ferrous iron transport, and teichoic acid synthesis. Several membrane-bound lipoproteins and one internalin were identified, plus three phage sequences and six sequences with unknown function. Collectively, these data confirm that many genes have diverged between lineages of L. monocytogenes. Furthermore, these results demonstrate the value of mixed-genome microarrays as a tool for deriving biologically useful information and for identifying and screening genetic markers for clinically important microbes.
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Affiliation(s)
- Douglas R Call
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, Washington 99164-7040, USA.
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Doolittle WF, Boucher Y, Nesbø CL, Douady CJ, Andersson JO, Roger AJ. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Philos Trans R Soc Lond B Biol Sci 2003; 358:39-57; discussion 57-8. [PMID: 12594917 PMCID: PMC1693099 DOI: 10.1098/rstb.2002.1185] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.
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Affiliation(s)
- W F Doolittle
- Genome Atlantic, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada.
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Abstract
Several virulence factors of Listeria monocytogenes have been identified and extensively characterized at the molecular and cell biologic levels, including the hemolysin (listeriolysin O), two distinct phospholipases, a protein (ActA), several internalins, and others. Their study has yielded an impressive amount of information on the mechanisms employed by this facultative intracellular pathogen to interact with mammalian host cells, escape the host cell's killing mechanisms, and spread from one infected cell to others. In addition, several molecular subtyping tools have been developed to facilitate the detection of different strain types and lineages of the pathogen, including those implicated in common-source outbreaks of the disease. Despite these spectacular gains in knowledge, the virulence of L. monocytogenes as a foodborne pathogen remains poorly understood. The available pathogenesis and subtyping data generally fail to provide adequate insight about the virulence of field isolates and the likelihood that a given strain will cause illness. Possible mechanisms for the apparent prevalence of three serotypes (1/2a, 1/2b, and 4b) in human foodborne illness remain unidentified. The propensity of certain strain lineages (epidemic clones) to be implicated in common-source outbreaks and the prevalence of serotype 4b among epidemic-associated stains also remain poorly understood. This review first discusses current progress in understanding the general features of virulence and pathogenesis of L. monocytogenes. Emphasis is then placed on areas of special relevance to the organism's involvement in human foodborne illness, including (i) the relative prevalence of different serotypes and serotype-specific features and genetic markers; (ii) the ability of the organism to respond to environmental stresses of relevance to the food industry (cold, salt, iron depletion, and acid); (iii) the specific features of the major known epidemic-associated lineages; and (iv) the possible reservoirs of the organism in animals and the environment and the pronounced impact of environmental contamination in the food processing facilities. Finally, a discussion is provided on the perceived areas of special need for future research of relevance to food safety, including (i) theoretical modeling studies of niche complexity and contamination in the food processing facilities; (ii) strain databases for comprehensive molecular typing; and (iii) contributions from genomic and proteomic tools, including DNA microarrays for genotyping and expression signatures. Virulence-related genomic and proteomic signatures are expected to emerge from analysis of the genomes at the global level, with the support of adequate epidemiologic data and access to relevant strains.
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Affiliation(s)
- Sophia Kathariou
- Food Science Department, North Carolina State University, Raleigh 27695, USA.
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Nesbø CL, Nelson KE, Doolittle WF. Suppressive subtractive hybridization detects extensive genomic diversity in Thermotoga maritima. J Bacteriol 2002; 184:4475-88. [PMID: 12142418 PMCID: PMC135253 DOI: 10.1128/jb.184.16.4475-4488.2002] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparisons between genomes of closely related bacteria often show large variations in gene content, even between strains of the same species. Such studies have focused mainly on pathogens; here, we examined Thermotoga maritima, a free-living hyperthermophilic bacterium, by using suppressive subtractive hybridization. The genome sequence of T. maritima MSB8 is available, and DNA from this strain served as a reference to obtain strain-specific sequences from Thermotoga sp. strain RQ2, a very close relative (approximately 96% identity for orthologous protein-coding genes, 99.7% identity in the small-subunit rRNA sequence). Four hundred twenty-six RQ2 subtractive clones were sequenced. One hundred sixty-six had no DNA match in the MSB8 genome. These differential clones comprise, in sum, 48 kb of RQ2-specific DNA and match 72 genes in the GenBank database. From the number of identical clones, we estimated that RQ2 contains 350 to 400 genes not found in MSB8. Assuming a similar genome size, this corresponds to 20% of the RQ2 genome. A large proportion of the RQ2-specific genes were predicted to be involved in sugar transport and polysaccharide degradation, suggesting that polysaccharides are more important as nutrients for this strain than for MSB8. Several clones encode proteins involved in the production of surface polysaccharides. RQ2 encodes multiple subunits of a V-type ATPase, while MSB8 possesses only an F-type ATPase. Moreover, an RQ2-specific MutS homolog was found among the subtractive clones and appears to belong to a third novel archaeal type MutS lineage. Southern blot analyses showed that some of the RQ2 differential sequences are found in some other members of the order Thermotogales, but the distribution of these variable genes is patchy, suggesting frequent lateral gene transfer within the group.
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Affiliation(s)
- Camilla L Nesbø
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Czuprynski CJ, Faith NG, Steinberg H. Ability of the Listeria monocytogenes strain Scott A to cause systemic infection in mice infected by the intragastric route. Appl Environ Microbiol 2002; 68:2893-900. [PMID: 12039747 PMCID: PMC123921 DOI: 10.1128/aem.68.6.2893-2900.2002] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2001] [Accepted: 03/21/2002] [Indexed: 11/20/2022] Open
Abstract
Listeriosis is an important food-borne disease that causes high rates of morbidity and mortality. For reasons that are not clear, most large outbreaks of human listeriosis involve Listeria monocytogenes serotype 4b. Relatively little is known about the pathogenesis of listeriosis following gastrointestinal exposure to food-borne disease isolates of L. monocytogenes. In the present study, we investigated the pathogenesis of systemic infection by the food-borne isolate Scott A in an intragastric (i.g.) mouse challenge model. We found that the severity of infection with L. monocytogenes Scott A was increased in mice made neutropenic by administration of monoclonal antibody RB6-8C5. This observation was similar to a previous report on a study with the laboratory strain L. monocytogenes EGD. Prior administration of sodium bicarbonate did not enhance the virulence of L. monocytogenes strain Scott A for i.g. inoculated mice. Following i.g. inoculation of mice, two serotype 4b strains of L. monocytogenes (Scott A and 101M) achieved a greater bacterial burden in the spleen and liver and elicited more severe histopathological damage to those organs than did a serotype 1/2a strain (EGD) and a serotype 1/2b stain (CM). Of the four strains tested, only strain CM exhibited poor survival in synthetic gastric fluid in vitro. The other three strains exhibited similar patterns of survival at pHs of greater than 5 and relatively rapid (<30 min) loss of viability at pHs of less than 5.0. Growth of L. monocytogenes Scott A at temperatures of 12.5 to 37 degrees C did not affect its ability to cause systemic infection in i.g. inoculated mice. These observations suggest that the serotype 4b L. monocytogenes strains Scott A and 101M possess one or more virulence determinants that make them better able to cause systemic infection following inoculation via the g.i. tract than do the serotype 1/2 strains EGD and CM.
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Affiliation(s)
- Charles J Czuprynski
- Department of Pathobiological Sciences School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin 53706, USA.
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Abstract
The purpose of this paper is to provide guidance to food processors in controlling Listeria monocytogenes in food-processing environments. Of particular concern are outbreaks of a few to several hundred scattered cases involving an unusually virulent strain that has become established in the food-processing environment and contaminates multiple lots of food over days or months of production. The risk is highest when growth occurs in a food before it is eaten by a susceptible population. The information presented in this paper provides the basis for the establishment of an environmental sampling program, the organization and interpretation of the data generated by this program, and the response to Listeria-positive results. Results from such a program, including examples of niches, are provided. Technologies and regulatory policies that can further enhance the safety of ready-to-eat foods are discussed.
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Affiliation(s)
- R B Tompkin
- ConAgra Refrigerated Prepared Foods, Downers Grove, Illinois 60515, USA.
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Tran HL, Kathariou S. Restriction fragment length polymorphisms detected with novel DNA probes differentiate among diverse lineages of serogroup 4 Listeria monocytogenes and identify four distinct lineages in serotype 4b. Appl Environ Microbiol 2002; 68:59-64. [PMID: 11772609 PMCID: PMC126560 DOI: 10.1128/aem.68.1.59-64.2002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes of serotype 4b has been implicated in numerous outbreaks of food-borne listeriosis and in ca. 40% of sporadic cases. Strains of this serotype appear to be relatively homogeneous genetically, and molecular markers specific for distinct serotype 4b lineages have not been frequently identified. Here we show that DNA fragments derived from the putative mannitol permease locus of Listeria monocytogenes had an unexpectedly high potential to differentiate among different strains of serotype 4b when used as probes in Southern blotting of EcoRI-digested genomic DNA, yielding four distinct restriction fragment length polymorphism (RFLP) patterns. Strains of two epidemic-associated lineages, including the major epidemic clone implicated in several outbreaks in Europe and North America, had distinct RFLPs which differed from those of all other serotype 4b strains that we screened but which were encountered among strains of serotypes 1/2b and 3b. In addition, three serogroup 4 lineages were found to have unique RFLPs that were not encountered among any other L. monocytogenes strains. One was an unusual lineage of serotype 4b, and the other two were members of the serotype 4a and 4c group. The observed polymorphisms may reflect evolutionary relationships among lineages of L. monocytogenes and may facilitate detection and population genetic analysis of specific lineages.
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Affiliation(s)
- Huyen L Tran
- Department of Microbiology, University of Hawaii, Honolulu, Hawaii, USA
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