1
|
Gmeiner A, Njage PMK, Hansen LT, Aarestrup FM, Leekitcharoenphon P. Predicting Listeria monocytogenes virulence potential using whole genome sequencing and machine learning. Int J Food Microbiol 2024; 410:110491. [PMID: 38000216 DOI: 10.1016/j.ijfoodmicro.2023.110491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Contamination with food-borne pathogens, such as Listeria monocytogenes, remains a big concern for food safety. Hence, rigorous and continuous microbial surveillance is a standard procedure. At this point, however, the food industry and authorities only focus on detection of Listeria monocytogenes without characterization of individual strains into groups of more or less concern. As whole genome sequencing (WGS) gains increasing interest in the industry, this methodology presents an opportunity to obtain finer resolution of microbial traits such as virulence. Within this study, we therefore aimed to explore the use of WGS in combination with Machine Learning (ML) to predict L. monocytogenes virulence potential on a sub-species level. The WGS datasets used in this study for ML model training consisted of i) national surveillance isolates (n = 169, covering 38 MLST types) and ii) publicly available isolates acquired through the GenomeTrakr network (n = 2880, spanning 80 MLST types). We used the clinical frequency, i.e., ratio of the number of clinical isolates to total amount of isolates, as estimate for virulence potential. The predictive performance of input features from three different genomic levels (i.e., virulence genes, pan-genome genes, and single nucleotide polymorphisms (SNPs)) and six machine learning algorithms (i.e., Support Vector Machine with a linear kernel, Support Vector Machine with a radial kernel, Random Forrest, Neural Networks, LogitBoost, and Majority Voting) were compared. Our machine learning models predicted sub-species virulence potential with nested cross-validation F1-scores up to 0.88 for the majority voting classifier trained on national surveillance data and using pan-genome genes as input features. The validation of the pre-trained ML models based on 101 previously in vivo studied isolates resulted in F1-scores up to 0.76. Furthermore, we found that the more rapid and less computationally intensive raw read alignment yields comparably accurate models as de novo assembly. The results of our study suggest that a majority voting classifier trained on pan-genome genes is the best and most robust choice for the prediction of clinical frequency. Our study contributes to more rapid and precise characterization of L. monocytogenes virulence and its variation on a sub-species level. We further demonstrated a possible application of WGS data in the context of microbial hazard characterization for food safety. In the future, predictive models may assist case-specific microbial risk management in the food industry. The python code, pre-trained models, and prediction pipeline are deposited at (https://github.com/agmei/LmonoVirulenceML).
Collapse
Affiliation(s)
- Alexander Gmeiner
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark.
| | - Patrick Murigu Kamau Njage
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Lisbeth Truelstrup Hansen
- National Food Institute, Technical University of Denmark, Research Group for Food Microbiology and Hygiene, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| |
Collapse
|
2
|
Genomic Analysis of Prophages Recovered from Listeria monocytogenes Lysogens Found in Seafood and Seafood-Related Environment. Microorganisms 2021; 9:microorganisms9071354. [PMID: 34206706 PMCID: PMC8303350 DOI: 10.3390/microorganisms9071354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 11/23/2022] Open
Abstract
A prophage is a phage-related sequence that is integrated into a bacterial chromosome. Prophages play an important role in bacterial evolution, survival, and persistence. To understand the impact of Listeria prophages on their host genome organizations, this work sequenced two L. monocytogenes strains (134LM and 036LM), previously identified as lysogens by mitomycin C induction. Draft genomes were generated with assembly sizes of 2,953,877 bp and 3,000,399 bp. One intact prophage (39,532 bp) was inserted into the comK gene of the 134LM genome. Two intact prophages (48,684 bp and 39,488 bp) were inserted in tRNA-Lys and elongation-factor genes of the 036LM genome. The findings confirmed the presence of three corresponding induced phages previously obtained by mitomycin C induction. Comparative genomic analysis of three prophages obtained in the newly sequenced lysogens with 61 prophages found in L. monocytogenes genomes, available in public databases, identified six major clusters using whole genome-based phylogenetic analysis. The results of the comparative genomic analysis of the prophage sequences provides knowledge about the diversity of Listeria prophages and their distribution among Listeria genomes in diverse environments, including different sources or geographical regions. In addition, the prophage sequences and their insertion sites contribute to the genomic diversity of L. monocytogenes genomes. These data of prophage sequences, prophage insertion sites, and prophage sequence comparisons, together with ANIb confirmation, could be useful for L. monocytogenes classification by prophages. One potential development could be refinement of prophage typing tools for monitoring or surveillance of L. monocytogenes contamination and transmission.
Collapse
|
3
|
Sebastián M, Arilla-Luna S, Bellalou J, Yruela I, Medina M. The Biosynthesis of Flavin Cofactors in Listeria monocytogenes. J Mol Biol 2019; 431:2762-2776. [PMID: 31132361 DOI: 10.1016/j.jmb.2019.05.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/26/2022]
Abstract
Listeria monocytogenes is riboflavin auxotrophic, but it has two genes envisaged to transform riboflavin into FMN and FAD after its uptaked by specialized transporters. One encodes a bifunctional type I FAD synthase (FADS, herein LmFADS-1), while the other produces a protein similar to type I at the FMN:ATP adenylyltransferase (FMNAT) site but with a shorter C-terminal that lacks any riboflavin kinase (RFK) motif. This second protein is rare among bacteria and has been named FADS type II (LmFADS-2). Here we present a biochemical and biophysical study of LmFADS-1 and LmFADS-2 by integrating kinetic and thermodynamic data together with sequence and structural prediction methods to evaluate their occurrence in Listeria, as well as their function and molecular properties. Despite LmFADS-1 similarities to other type I FADSs, (i) its RFK activity has not riboflavin substrate inhibition and occurs under reducing and oxidizing conditions, (ii) its FMNAT activity requires strong reducing environment, and (iii) binding of reaction products, but not substrates, favors binding of the second ligand. LmFADS-2 produces FAD under oxidizing and reducing environments, but its C-terminus module function remains unknown. Listeria species conserve both FADSs, being sequence identity high within L. monocytogenes strains. Our data exemplify alternative strategies for FMN and FAD biosynthesis and homeostasis, envisaging that in Listeria two FADSs might be required to fulfill the supply of flavin cofactors under niches that can go from saprophytism to virulence. As FADSs are attractive antimicrobial targets, understanding of FADSs traits in different species is essential to help in the discovery of specific antimicrobials.
Collapse
Affiliation(s)
- Maria Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Arilla-Luna
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Jacques Bellalou
- Plateforme de Protéines Recombinantes, Institut Pasteur, CNRS-UMR 3528, Paris, France
| | - Inmaculada Yruela
- Estación Experimental de Aula Dei, National Spanish Research Council (CSIC), Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias and Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50009 Zaragoza, Spain; Group of Biochemistry, Biophysics and Computational Biology (BIFI-Unizar) Joint Unit to CSIC Spain.
| |
Collapse
|
4
|
Akgul A, Al-Janabi N, Das B, Lawrence M, Karsi A. Small molecules targeting LapB protein prevent Listeria attachment to catfish muscle. PLoS One 2017; 12:e0189809. [PMID: 29253892 PMCID: PMC5734760 DOI: 10.1371/journal.pone.0189809] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 12/01/2017] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes is a Gram-positive foodborne pathogen and the causative agent of listeriosis. L. monocytogenes lapB gene encodes a cell wall surface anchor protein, and mutation of this gene causes Listeria attenuation in mice. In this work, the potential role of Listeria LapB protein in catfish fillet attachment was investigated. To achieve this, boron-based small molecules designed to interfere with the active site of the L. monocytogenes LapB protein were developed, and their ability to prevent L. monocytogenes attachment to fish fillet was tested. Results indicated that seven out of nine different small molecules were effective in reducing the Listeria attachment to catfish fillets. Of these, three small molecules (SM3, SM5, and SM7) were highly effective in blocking Listeria attachment to catfish fillets. This study suggests an alternative strategy for reduction of L. monocytogenes contamination in fresh and frozen fish products.
Collapse
Affiliation(s)
- Ali Akgul
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Nawar Al-Janabi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Bhaskar Das
- Departments of Medicine and Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Mark Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, United States of America
| |
Collapse
|
5
|
Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes. Appl Environ Microbiol 2016; 82:6258-6272. [PMID: 27520821 PMCID: PMC5068157 DOI: 10.1128/aem.01532-16] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/09/2016] [Indexed: 12/16/2022] Open
Abstract
Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak.
IMPORTANCE Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST schemes can be used for the simultaneous identification of clonal groups and the differentiation of individual outbreak strains and epidemiologically unrelated strains of the same clonal group. We further developed lineage-specific cgMLST schemes that targeted more genomic regions than the species-specific cgMLST schemes. Our data revealed the genome-level diversity of clonal groups defined by classic MLST schemes. Our identification of U.S. and international outbreaks caused by major clonal groups can contribute to further understanding of the global epidemiology of L. monocytogenes.
Collapse
|
6
|
Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing. Appl Environ Microbiol 2015; 82:928-38. [PMID: 26590286 DOI: 10.1128/aem.02440-15] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/18/2015] [Indexed: 11/20/2022] Open
Abstract
We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.
Collapse
|
7
|
Pightling AW, Petronella N, Pagotto F. The Listeria monocytogenes Core-Genome Sequence Typer (LmCGST): a bioinformatic pipeline for molecular characterization with next-generation sequence data. BMC Microbiol 2015; 15:224. [PMID: 26490433 PMCID: PMC4618880 DOI: 10.1186/s12866-015-0526-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/21/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Next-generation sequencing provides a powerful means of molecular characterization. However, methods such as single-nucleotide polymorphism detection or whole-chromosome sequence analysis are computationally expensive, prone to errors, and are still less accessible than traditional typing methods. Here, we present the Listeria monocytogenes core-genome sequence typing method for molecular characterization. This method uses a high-confidence core (HCC) genome, calculated to ensure accurate identification of orthologs. We also developed an evolutionarily relevant nomenclature based upon phylogenetic analysis of HCC genomes. Finally, we created a pipeline (LmCGST; https://sourceforge.net/projects/lmcgst/files/) that takes in raw next-generation sequencing reads, calculates a subject HCC profile, compares it to an expandable database, assigns a sequence type, and performs a phylogenetic analysis. RESULTS We analyzed 29 high-quality, closed Listeria monocytogenes chromosome sequences and identified loci that are reliable targets for automated molecular characterization methods. We identified 1013 open-reading frames that comprise our high-confidence core (HCC) genome. We then populated a database with HCC profiles from 114 taxa. We sequenced 84 randomly selected isolates from the Listeriosis Reference Service for Canada's collection and analysed them with the LmCGST pipeline. In addition, we generated pulsed-field gel electrophoresis, ribotyping, and in silico multi-locus sequence typing (MLST) data for the 84 isolates and compared the results to those obtained using the CGST method. We found that all of the methods yielded results that are generally congruent. However, due to the increased numbers of categories, the CGST method provides much greater discriminatory power than the other methods tested here. CONCLUSIONS We show that the CGST method provides increased discriminatory power relative to typing methods such as pulsed-field gel electrophoresis, ribotyping, and multi-locus sequence typing while it addresses several shortcomings of other methods of molecular characterization with next-generation sequence data. It uses discrete, well-defined groupings (types) of organisms that are phylogenetically relevant and easily interpreted. In addition, the CGST scheme can be expanded to include additional loci and HCC profiles in the future. In total, the CGST method provides an approach to the molecular characterization of Listeria monocytogenes with next-generation sequence data that is highly reproducible, easily standardized, portable, and accessible.
Collapse
Affiliation(s)
- Arthur W Pightling
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD, 20740, USA.
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Products and Food Branch, Health Canada, 251 Sir Frederick Banting Driveway, Ottawa, K1A 0K9, ON, Canada.
| | - Franco Pagotto
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD, 20740, USA.
| |
Collapse
|
8
|
Tan MF, Siow CC, Dutta A, Mutha NV, Wee WY, Heydari H, Tan SY, Ang MY, Wong GJ, Choo SW. Development of ListeriaBase and comparative analysis of Listeria monocytogenes. BMC Genomics 2015; 16:755. [PMID: 26444974 PMCID: PMC4595109 DOI: 10.1186/s12864-015-1959-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background Listeria consists of both pathogenic and non-pathogenic species. Reports of similarities between the genomic content between some pathogenic and non-pathogenic species necessitates the investigation of these species at the genomic level to understand the evolution of virulence-associated genes. With Listeria genome data growing exponentially, comparative genomic analysis may give better insights into evolution, genetics and phylogeny of Listeria spp., leading to better management of the diseases caused by them. Description With this motivation, we have developed ListeriaBase, a web Listeria genomic resource and analysis platform to facilitate comparative analysis of Listeria spp. ListeriaBase currently houses 850,402 protein-coding genes, 18,113 RNAs and 15,576 tRNAs from 285 genome sequences of different Listeria strains. An AJAX-based real time search system implemented in ListeriaBase facilitates searching of this huge genomic data. Our in-house designed comparative analysis tools such as Pairwise Genome Comparison (PGC) tool allowing comparison between two genomes, Pathogenomics Profiling Tool (PathoProT) for comparing the virulence genes, and ListeriaTree for phylogenic classification, were customized and incorporated in ListeriaBase facilitating comparative genomic analysis of Listeria spp. Interestingly, we identified a unique genomic feature in the L. monocytogenes genomes in our analysis. The Auto protein sequences of the serotype 4 and the non-serotype 4 strains of L. monocytogenes possessed unique sequence signatures that can differentiate the two groups. We propose that the aut gene may be a potential gene marker for differentiating the serotype 4 strains from other serotypes of L. monocytogenes. Conclusions ListeriaBase is a useful resource and analysis platform that can facilitate comparative analysis of Listeria for the scientific communities. We have successfully demonstrated some key utilities of ListeriaBase. The knowledge that we obtained in the analyses of L. monocytogenes may be important for functional works of this human pathogen in future. ListeriaBase is currently available at http://listeria.um.edu.my. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1959-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mui Fern Tan
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Avirup Dutta
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Naresh Vr Mutha
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Hamed Heydari
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Computer Science and Engineering Department, University of Nebraska-Lincoln, Lincoln, NE, 1468588-0115, USA.
| | - Shi Yang Tan
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Mia Yang Ang
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia. .,Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, Kuala Lumpur, 50603, Malaysia.
| |
Collapse
|
9
|
Abdelhamed H, Lawrence ML, Karsi A. A novel suicide plasmid for efficient gene mutation in Listeria monocytogenes. Plasmid 2015; 81:1-8. [PMID: 26038185 DOI: 10.1016/j.plasmid.2015.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 10/23/2022]
Abstract
Although several plasmids have been used in Listeria monocytogenes for generating mutants by allelic exchange, construction of L. monocytogenes mutants has been inefficient due to lack of effective selection markers for first and second recombination events. To address this problem, we have developed a new suicide plasmid, pHoss1, by using the pMAD plasmid backbone and anhydrotetracycline selection marker (secY antisense RNA) driven by an inducible Pxyl/tetO promoter. Expression of the secY antisense RNA eliminates merodiploids and selects for the loss of plasmid via a second allelic exchange, which enriches the number of mutants with deleted genes. To assess the effectiveness of pHoss1 for the generation of stable in-frame deletion mutations, we deleted the ispG and ispH genes of L. monocytogenes serotype 4b strain F2365. Results showed that identification of the second allelic exchange mutants was very efficient with 80-100% of the colonies yielding desired deletion mutants. L. monocytogenes' intestinal cell attachment was not altered when ispG and ispH genes were deleted. We expect that this new plasmid will be very useful for construction of marker-free deletion mutants in L. monocytogenes and in other Gram-positive bacteria, including Staphylococcus aureus and Bacillus cereus.
Collapse
Affiliation(s)
- Hossam Abdelhamed
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA.
| |
Collapse
|
10
|
Kyoui D, Takahashi H, Miya S, Kuda T, Igimi S, Kimura B. Genetic distance in the whole-genome perspective on Listeria monocytogenes strains F2-382 and NIHS-28 that show similar subtyping results. BMC Microbiol 2014; 14:309. [PMID: 25492229 PMCID: PMC4269915 DOI: 10.1186/s12866-014-0309-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/24/2014] [Indexed: 11/17/2022] Open
Abstract
Background Genome subtyping approaches could provide useful epidemiological information regarding food pathogens. However, the full genomic diversity of strains that show similar subtyping results has not yet been completely explored. Most subtyping methods are based on the differences of only a portion of the genome. We investigated two draft genome sequences of Listeria monocytogenes strain F2-382 and NIHS-28, which have been identified as closely related strains by subtyping (identical multi-virulence-locus sequence typing and multiple-locus variable number tandem repeat analysis sequence types and very similar pulsed-field gel electrophoresis patterns), despite their different sources. Results Two closely related strains were compared by genome structure analysis, recombination analysis, and single nucleotide polymorphism (SNP) analysis. Both genome structure analysis and recombination analysis showed that these two strains are more closely related than other strains, from a whole-genome perspective. However, the analysis of SNPs indicated that the two strains differ at the single nucleotide level. Conclusion We show the relationship between the results of genome subtyping and whole-genome sequencing. It appears that the relationships among strains indicated by genome subtyping methods are in accord with the relationships indicated by whole-genome analysis. However, our results also indicate that the genetic distance between the closely related strains is greater than that between clonal strains. Our results demonstrate that subtyping methods using a part of the genome are reliable in assessing the genetic distance of the strains. Furthermore, the genetic differences in the same subtype strains may provide useful information to distinguish the bacterial strains. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0309-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Daisuke Kyoui
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan.
| | - Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan.
| | - Satoko Miya
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan.
| | - Takashi Kuda
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan.
| | - Shizunobu Igimi
- Division of Biomedical Food Research, National Institute of Health Science, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Bon Kimura
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo, 108-8477, Japan.
| |
Collapse
|
11
|
Paul D, Steele C, Donaldson JR, Banes MM, Kumar R, Bridges SM, Arick M, Lawrence ML. Genome comparison of Listeria monocytogenes serotype 4a strain HCC23 with selected lineage I and lineage II L. monocytogenes strains and other Listeria strains. GENOMICS DATA 2014; 2:219-25. [PMID: 26484097 PMCID: PMC4536003 DOI: 10.1016/j.gdata.2014.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/30/2014] [Accepted: 06/11/2014] [Indexed: 11/18/2022]
Abstract
More than 98% of reported human listeriosis cases are caused by specific serotypes within genetic lineages I and II. The genome sequence of Listeria monocytogenes lineage III strain HCC23 (serotype 4a) enables whole genomic comparisons across all three L. monocytogenes lineages. Protein cluster analysis indicated that strain HCC23 has the most unique protein pairs with nonpathogenic species Listeria innocua. Orthology analysis of the genome sequences of representative strains from the three L. monocytogenes genetic lineages and L. innocua (CLIP11262) identified 319 proteins unique to nonpathogenic strains HCC23 and CLIP11262 and 58 proteins unique to pathogenic strains F2365 and EGD-e. BLAST comparison of these proteins with all the sequenced L. monocytogenes and L. innocua revealed 126 proteins unique to serotype 4a and/or L. innocua; 14 proteins were only found in pathogenic serotypes. Some of the 58 proteins unique to pathogenic strains F2365 and EGD-e were previously published and are already known to contribute to listerial virulence.
Collapse
Affiliation(s)
- Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Chelsea Steele
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Janet R Donaldson
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Michelle M Banes
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Ranjit Kumar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| | - Susan M Bridges
- Department of Computer Sciences and Engineering, Mississippi State University, Mississippi State, MS, USA
| | - Mark Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - Mark L Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, USA
| |
Collapse
|
12
|
Lin TH, Hu YN, Shaw GC. Two enzymes, TilS and HprT, can form a complex to function as a transcriptional activator for the cell division protease gene ftsH in Bacillus subtilis. J Biochem 2013; 155:5-16. [PMID: 24001521 DOI: 10.1093/jb/mvt081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The FtsH protein is an ATP-dependent cytoplasmic membrane protease involved in the control of membrane protein quality, cell division and heat shock response in Bacillus subtilis and many other bacteria. TilS, the tRNA(Ile2) lysidine synthetase, is a tRNA-binding protein that can modify pre-tRNA(Ile2). HprT, the hypoxanthine-guanine phosphoribosyltransferase, is implicated in purine salvage. Both tilS and hprT are essential for cell viability of B. subtilis. In this report, by co-purification experiments and gel filtration analyses, we show that there is complex formation between co-expressed TilS and HprT. Electrophoretic mobility shift assays and in vitro transcription analyses demonstrated that the TilS/HprT complex functions as a specific DNA-binding protein that can stimulate ftsH transcription in vitro. Two regions located upstream of the ftsH promoter have been identified as the TilS/HprT-binding sites and shown to be required for TilS/HprT-dependent ftsH transcription in vitro and in vivo. Results from gel supershift assays support the notion that the TilS/HprT complex likely employs its distinct segments for interaction with these two distinct TilS/HprT-binding sites, respectively. In conclusion, we present the first evidence that bi-functional TilS and HprT can form a complex to function as a transcriptional activator to stimulate ftsH transcription.
Collapse
Affiliation(s)
- Ta-Hui Lin
- Institute of Biochemistry and Molecular Biology, School of Life Science, National Yang-Ming University, Taipei 112, Taiwan, People's Republic of China
| | | | | |
Collapse
|
13
|
den Bakker HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q, Young SK, Kodira CD, Yandava C, Hepburn TA, Haas BJ, Birren BW, Wiedmann M. Evolutionary dynamics of the accessory genome of Listeria monocytogenes. PLoS One 2013; 8:e67511. [PMID: 23825666 PMCID: PMC3692452 DOI: 10.1371/journal.pone.0067511] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 05/23/2013] [Indexed: 11/18/2022] Open
Abstract
Listeria monocytogenes, a foodborne bacterial pathogen, is comprised of four phylogenetic lineages that vary with regard to their serotypes and distribution among sources. In order to characterize lineage-specific genomic diversity within L. monocytogenes, we sequenced the genomes of eight strains from several lineages and serotypes, and characterized the accessory genome, which was hypothesized to contribute to phenotypic differences across lineages. The eight L. monocytogenes genomes sequenced range in size from 2.85-3.14 Mb, encode 2,822-3,187 genes, and include the first publicly available sequenced representatives of serotypes 1/2c, 3a and 4c. Mapping of the distribution of accessory genes revealed two distinct regions of the L. monocytogenes chromosome: an accessory-rich region in the first 65° adjacent to the origin of replication and a more stable region in the remaining 295°. This pattern of genome organization is distinct from that of related bacteria Staphylococcus aureus and Bacillus cereus. The accessory genome of all lineages is enriched for cell surface-related genes and phosphotransferase systems, and transcriptional regulators, highlighting the selective pressures faced by contemporary strains from their hosts, other microbes, and their environment. Phylogenetic analysis of O-antigen genes and gene clusters predicts that serotype 4 was ancestral in L. monocytogenes and serotype 1/2 associated gene clusters were putatively introduced through horizontal gene transfer in the ancestral population of L. monocytogenes lineage I and II.
Collapse
Affiliation(s)
- Henk C den Bakker
- Department of Food Science, Cornell University, Ithaca, New York, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Holch A, Webb K, Lukjancenko O, Ussery D, Rosenthal BM, Gram L. Genome sequencing identifies two nearly unchanged strains of persistent Listeria monocytogenes isolated at two different fish processing plants sampled 6 years apart. Appl Environ Microbiol 2013; 79:2944-51. [PMID: 23435887 PMCID: PMC3623136 DOI: 10.1128/aem.03715-12] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/16/2013] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a food-borne human-pathogenic bacterium that can cause infections with a high mortality rate. It has a remarkable ability to persist in food processing facilities. Here we report the genome sequences for two L. monocytogenes strains (N53-1 and La111) that were isolated 6 years apart from two different Danish fish processers. Both strains are of serotype 1/2a and belong to a highly persistent DNA subtype (random amplified polymorphic DNA [RAPD] type 9). We demonstrate using in silico analyses that both strains belong to the multilocus sequence typing (MLST) type ST121 that has been isolated as a persistent subtype in several European countries. The purpose of this study was to use genome analyses to identify genes or proteins that could contribute to persistence. In a genome comparison, the two persistent strains were extremely similar and collectively differed from the reference lineage II strain, EGD-e. Also, they differed markedly from a lineage I strain (F2365). On the proteome level, the two strains were almost identical, with a predicted protein homology of 99.94%, differing at only 2 proteins. No single-nucleotide polymorphism (SNP) differences were seen between the two strains; in contrast, N53-1 and La111 differed from the EGD-e reference strain by 3,942 and 3,471 SNPs, respectively. We included a persistent L. monocytogenes strain from the United States (F6854) in our comparisons. Compared to nonpersistent strains, all three persistent strains were distinguished by two genome deletions: one, of 2,472 bp, typically contains the gene for inlF, and the other, of 3,017 bp, includes three genes potentially related to bacteriocin production and transport (lmo2774, lmo2775, and the 3'-terminal part of lmo2776). Further studies of highly persistent strains are required to determine if the absence of these genes promotes persistence. While the genome comparison did not point to a clear physiological explanation of the persistent phenotype, the remarkable similarity between the two strains indicates that subtypes with specific traits are selected for in the food processing environment and that particular genetic and physiological factors are responsible for the persistent phenotype.
Collapse
Affiliation(s)
- Anne Holch
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kristen Webb
- Department of Biology, Allegheny College, Meadville, Pennsylvania, USA
| | - Oksana Lukjancenko
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Ussery
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Benjamin M. Rosenthal
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland, USA
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
15
|
Warner SL, Boggs J, Lee JK, Reddy S, Banes M, Cooley J. Clinical, pathological, and genetic characterization of Listeria monocytogenes causing sepsis and necrotizing typhlocolitis and hepatitis in a foal. J Vet Diagn Invest 2012; 24:581-6. [PMID: 22529130 DOI: 10.1177/1040638711436245] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Listeria monocytogenes was isolated from the blood, lungs, and liver of a 5-week-old American Quarter Horse filly that presented with a 2-day history of fever, lethargy, ataxia, and seizure activity. The foal was born on a well-managed breeding facility to a multiparous mare with no periparturient complications. At 8 hr of age, the foal had an adequate passive transfer of immunity (immunoglobulin G > 2,000 mg/dl). Since the time of birth, the foal reportedly had mild, intermittent diarrhea that responded to gastrointestinal protectants and probiotics. Despite prompt and aggressive treatment after hospital referral, the foal's condition deteriorated, and the foal was humanely euthanized. Postmortem gross and histopathologic examination revealed severe hepatitis with necrosis and fibrinonecrotic typhlitis and colitis. In addition to a positive blood culture for L. monocytogenes, immunohistochemistry confirmed the presence of this bacterium in the liver, cecum, and colon. Furthermore, a multiplex polymerase chain reaction identified the etiologic organism as a virulent L. monocytogenes strain.
Collapse
Affiliation(s)
- Shayna L Warner
- Department of Clinical Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA
| | | | | | | | | | | |
Collapse
|
16
|
Payne A, Schmidt TB, Nanduri B, Pendarvis K, Pittman JR, Thornton JA, Grissett J, Donaldson JR. Proteomic analysis of the response of Listeria monocytogenes to bile salts under anaerobic conditions. J Med Microbiol 2012; 62:25-35. [PMID: 22977076 DOI: 10.1099/jmm.0.049742-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Listeria monocytogenes is a food-borne pathogen responsible for the disease listeriosis. The infectious process depends on survival in the high bile-salt conditions encountered throughout the gastrointestinal tract, including the gallbladder. However, it is not clear how bile-salt resistance mechanisms are induced, especially under physiologically relevant conditions. This study sought to determine how the L. monocytogenes strains EGDe (serovar 1/2a), F2365 (serovar 4a) and HCC23 (serovar 4b) respond to bile salts under anaerobic conditions. Changes in the expressed proteome were analysed using multidimensional protein identification technology coupled with electrospray ionization tandem mass spectrometry. In general, the response to bile salts among the strains tested involved significant alterations in the presence of cell-wall-associated proteins, DNA repair proteins, protein folding chaperones and oxidative stress-response proteins. Strain viability correlated with an initial osmotic stress response, yet continued survival for EGDe and F2365 involved different mechanisms. Specifically, proteins associated with biofilm formation in EGDe and transmembrane efflux pumps in F2365 were expressed, suggesting that variations exist in how virulent strains respond and adapt to high bile-salt environments. These results indicate that the bile-salt response varies among these serovars and that further research is needed to elucidate how the response to bile salts correlates with colonization potential in vivo.
Collapse
Affiliation(s)
- Angela Payne
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ty B Schmidt
- Animal Sciences Department, University of Nebraska, Lincoln, NE 68588, USA
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ken Pendarvis
- Life Sciences and Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762, USA
| | - Joseph R Pittman
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Justin A Thornton
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jessica Grissett
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| | - Janet R Donaldson
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA
| |
Collapse
|
17
|
Hain T, Ghai R, Billion A, Kuenne CT, Steinweg C, Izar B, Mohamed W, Mraheil MA, Domann E, Schaffrath S, Kärst U, Goesmann A, Oehm S, Pühler A, Merkl R, Vorwerk S, Glaser P, Garrido P, Rusniok C, Buchrieser C, Goebel W, Chakraborty T. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics 2012; 13:144. [PMID: 22530965 PMCID: PMC3464598 DOI: 10.1186/1471-2164-13-144] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 04/12/2012] [Indexed: 12/13/2022] Open
Abstract
Background Listeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans. Results The genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model. Conclusion Comparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.
Collapse
Affiliation(s)
- Torsten Hain
- Institute of Medical Microbiology, Justus-Liebig-University, Schubertstrasse 81, Giessen, D-35392, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
FSL J1-208, a virulent uncommon phylogenetic lineage IV Listeria monocytogenes strain with a small chromosome size and a putative virulence plasmid carrying internalin-like genes. Appl Environ Microbiol 2012; 78:1876-89. [PMID: 22247147 DOI: 10.1128/aem.06969-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial genus Listeria contains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential of L. welshimeri and L. seeligeri. In this paper we present data on the genome of L. monocytogenes strain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallest Listeria chromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such as inlA, inlB, and inlC and the full prfA gene cluster. The small genome size is mainly caused by the absence of prophages in the genome of L. monocytogenes FSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genus Listeria. L. monocytogenes FSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genus Listeria.
Collapse
|
19
|
Genome sequence of the nonpathogenic Listeria monocytogenes serovar 4a strain M7. J Bacteriol 2011; 193:5019-20. [PMID: 21742872 DOI: 10.1128/jb.05501-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report presents the complete and annotated genome sequence of the naturally nonpathogenic Listeria monocytogenes serovar 4a strain M7, isolated from cow's milk in Zhejiang province, China.
Collapse
|
20
|
Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| |
Collapse
|