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Lagarde J, Feurer C, Denis M, Douarre PE, Piveteau P, Roussel S. Listeria monocytogenes prevalence and genomic diversity along the pig and pork production chain. Food Microbiol 2024; 119:104430. [PMID: 38225039 DOI: 10.1016/j.fm.2023.104430] [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: 04/07/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 01/17/2024]
Abstract
The facultative intracellular bacterium Listeria monocytogenes (L. monocytogenes) is the causative agent of listeriosis, a severe invasive illness. This ubiquitous species is widely distributed in the environment, but infection occurs almost exclusively through ingestion of contaminated food. The pork production sector has been heavily affected by a series of L. monocytogenes-related foodborne outbreaks in the past around the world. Ready-to-eat (RTE) pork products represent one of the main food sources for strong-evidence listeriosis outbreaks. This pathogen is known to be present throughout the entire pig and pork production chain. Some studies hypothesized that the main source of contamination in final pork products was either living pigs or the food-processing environment. A detailed genomic picture of L. monocytogenes can provide a renewed understanding of the routes of contamination from pig farms to the final products. This review provides an overview of the prevalence, the genomic diversity and the genetic background linked to virulence of L. monocytogenes along the entire pig and pork production chain, from farm to fork.
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Affiliation(s)
- Jean Lagarde
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France; INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Carole Feurer
- IFIP, The French Pig and Pork Institute, Department of Fresh and Processed Meat, La Motte au Vicomte, 35650, Le Rheu, France
| | - Martine Denis
- ANSES, Unit of Hygiene and Quality of Poultry and Pork Products (UHQPAP), Ploufragan-Plouzané-Niort Laboratory, 31 rue des fusillés, 22440, Ploufragan, France
| | - Pierre-Emmanuel Douarre
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France
| | - Pascal Piveteau
- INRAE, Unit of Process Optimisation in Food, Agriculture and the Environment (UR OPAALE), 17 avenue de Cucillé, 35000, Rennes, France
| | - Sophie Roussel
- ANSES, Salmonella and Listeria Unit (USEL), University of Paris-Est, Maisons-Alfort Laboratory for Food Safety, 14 rue Pierre et Marie Curie, 94700, Maisons-Alfort, France.
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Osek J, Wieczorek K. Why does Listeria monocytogenes survive in food and food-production environments? J Vet Res 2023; 67:537-544. [PMID: 38130454 PMCID: PMC10730553 DOI: 10.2478/jvetres-2023-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Listeria monocytogenes is one of the most dangerous food-borne pathogens and is responsible for human listeriosis, a severe disease with a high mortality rate, especially among the elderly, pregnant women and newborns. Therefore, this bacterium has an important impact on food safety and public health. It is able to survive and even grow in a temperature range from -0.4°C to 45°C, a broad pH range from 4.6 to 9.5 and at a relatively low water activity (aW < 0.90), and tolerates salt content up to 20%. It is also resistant to ultraviolet light, biocides and heavy metals and forms biofilm structures on a variety of surfaces in food-production environments. These features make it difficult to remove and allow it to persist for a long time, increasing the risk of contamination of food-production facilities and ultimately of food. In the present review, the key mechanisms of the pathogen's survival and stress adaptation have been presented. This information may grant better understanding of bacterial adaptation to food environmental conditions.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal Origin, National Veterinary Research Institute, 24-100Puławy, Poland
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Angelidis AS, Grammenou AS, Kotzamanidis C, Giadinis ND, Zdragas AG, Sergelidis D. Prevalence, Serotypes, Antimicrobial Resistance and Biofilm-Forming Ability of Listeria monocytogenes Isolated from Bulk-Tank Bovine Milk in Northern Greece. Pathogens 2023; 12:837. [PMID: 37375527 DOI: 10.3390/pathogens12060837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
The prevalence of Listeria monocytogenes in bovine bulk-tank milk (BTM) in Greece has not been previously investigated. The aim of the study was to estimate the prevalence of L. monocytogenes in bovine BTM in Greece and to characterize the isolates in terms of carriage of genes encoding for pathogenic determinants, assess the isolates' biofilm-forming ability and determine their susceptibility against 12 antimicrobials. Samples (n = 138) of bovine BTM were obtained from farms located throughout Northern Greece and were analyzed qualitatively and quantitatively for L. monocytogenes. Five samples (3.6%) tested positive for L. monocytogenes. The pathogen's populations in these positive samples were below 5 CFU/mL. Most isolates belonged to the molecular serogroup "1/2a, 3a". All isolates carried the virulence genes inlA, inlC, inlJ, iap, plcA and hlyA, but actA was detected in only three isolates. The isolates displayed weak to moderate biofilm-forming ability and distinct antimicrobial resistance profiles. All isolates were characterized as multidrug resistant, with resistance to penicillin and clindamycin being a common feature. Considering that L. monocytogenes constitutes a serious public health threat, the key findings of the study, related to the carriage of virulence genes and multidrug resistance, highlight the importance of continued monitoring of the pathogen in farm animals.
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Affiliation(s)
- Apostolos S Angelidis
- Laboratory of Safety and Quality of Milk and Dairy Products, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Afroditi S Grammenou
- Laboratory of Hygiene of Foods of Animal Origin-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Charalampos Kotzamanidis
- Hellenic Agricultural Organization-DIMITRA, Veterinary Research Institute of Thessaloniki, 57001 Thermi, Greece
| | - Nektarios D Giadinis
- Clinic of Farm Animals, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54627 Thessaloniki, Greece
| | - Antonios G Zdragas
- Hellenic Agricultural Organization-DIMITRA, Veterinary Research Institute of Thessaloniki, 57001 Thermi, Greece
| | - Daniel Sergelidis
- Laboratory of Hygiene of Foods of Animal Origin-Veterinary Public Health, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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Matle I, Mafuna T, Madoroba E, Mbatha KR, Magwedere K, Pierneef R. Population Structure of Non-ST6 Listeria monocytogenes Isolated in the Red Meat and Poultry Value Chain in South Africa. Microorganisms 2020; 8:microorganisms8081152. [PMID: 32751410 PMCID: PMC7464360 DOI: 10.3390/microorganisms8081152] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/22/2020] [Accepted: 06/28/2020] [Indexed: 12/17/2022] Open
Abstract
Meat products have been implicated in many listeriosis outbreaks globally, however there is a dearth of information on the diversity of L. monocytogenes isolates circulating in food products in South Africa. The aim of this study was to investigate the population structure of L. monocytogenes isolated in the meat value chain within the South African market. Based on whole-genome sequence analysis, a total of 217 isolates were classified into two main lineage groupings namely lineages I (n = 97; 44.7%) and II (n = 120; 55.3%). The lineage groups were further differentiated into IIa (n = 95, 43.8%), IVb (n = 69, 31.8%), IIb (n = 28, 12.9%), and IIc (n = 25, 11.5%) sero-groups. The most abundant sequence types (STs) were ST204 (n = 32, 14.7%), ST2 (n = 30, 13.8%), ST1 (n = 25, 11.5%), ST9 (n = 24, 11.1%), and ST321 (n = 21, 9.7%). In addition, 14 clonal complex (CCs) were identified with over-representation of CC1, CC3, and CC121 in "Processed Meat-Beef", "RTE-Poultry", and "Raw-Lamb" meat categories, respectively. Listeria pathogenic islands were present in 7.4% (LIPI-1), 21.7% (LIPI-3), and 1.8% (LIPI-4) of the isolates. Mutation leading to premature stop codons was detected in inlA virulence genes across isolates identified as ST121 and ST321. The findings of this study demonstrated a high-level of genomic diversity among L. monocytogenes isolates recovered across the meat value chain control points in South Africa.
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Affiliation(s)
- Itumeleng Matle
- Bacteriology Division, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort 0110, South Africa;
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Florida 1709, South Africa;
| | - Thendo Mafuna
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa;
- Biotechnology Platform, Agricultural Research Council-Onderstepoort Veterinary Research, Private Bag X 05, Onderstepoort 0110, Pretoria, South Africa
| | - Evelyn Madoroba
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, KwaDlangezwa 3886, South Africa;
| | - Khanyisile R. Mbatha
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Florida 1709, South Africa;
| | - Kudakwashe Magwedere
- Directorate of Veterinary Public Health, Department of Agriculture, Land Reform and Rural Development, Pretoria 0001, South Africa;
| | - Rian Pierneef
- Biotechnology Platform, Agricultural Research Council-Onderstepoort Veterinary Research, Private Bag X 05, Onderstepoort 0110, Pretoria, South Africa
- Correspondence: ; Tel.: +27-12-5299-356
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Tamburro M, Sammarco ML, Fanelli I, Ripabelli G. Characterization of Listeria monocytogenes serovar 1/2a, 1/2b, 1/2c and 4b by high resolution melting analysis for epidemiological investigations. Int J Food Microbiol 2019; 310:108289. [DOI: 10.1016/j.ijfoodmicro.2019.108289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/24/2019] [Accepted: 08/04/2019] [Indexed: 02/07/2023]
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Poimenidou SV, Dalmasso M, Papadimitriou K, Fox EM, Skandamis PN, Jordan K. Virulence Gene Sequencing Highlights Similarities and Differences in Sequences in Listeria monocytogenes Serotype 1/2a and 4b Strains of Clinical and Food Origin From 3 Different Geographic Locations. Front Microbiol 2018; 9:1103. [PMID: 29922249 PMCID: PMC5996115 DOI: 10.3389/fmicb.2018.01103] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
The prfA-virulence gene cluster (pVGC) is the main pathogenicity island in Listeria monocytogenes, comprising the prfA, plcA, hly, mpl, actA, and plcB genes. In this study, the pVGC of 36 L. monocytogenes isolates with respect to different serotypes (1/2a or 4b), geographical origin (Australia, Greece or Ireland) and isolation source (food-associated or clinical) was characterized. The most conserved genes were prfA and hly, with the lowest nucleotide diversity (π) among all genes (P < 0.05), and the lowest number of alleles, substitutions and non-synonymous substitutions for prfA. Conversely, the most diverse gene was actA, which presented the highest number of alleles (n = 20) and showed the highest nucleotide diversity. Grouping by serotype had a significantly lower π value (P < 0.0001) compared to isolation source or geographical origin, suggesting a distinct and well-defined unit compared to other groupings. Among all tested genes, only hly and mpl were those with lower nucleotide diversity in 1/2a serotype than 4b serotype, reflecting a high within-1/2a serotype divergence compared to 4b serotype. Geographical divergence was noted with respect to the hly gene, where serotype 4b Irish strains were distinct from Greek and Australian strains. Australian strains showed less diversity in plcB and mpl relative to Irish or Greek strains. Notable differences regarding sequence mutations were identified between food-associated and clinical isolates in prfA, actA, and plcB sequences. Overall, these results indicate that virulence genes follow different evolutionary pathways, which are affected by a strain's origin and serotype and may influence virulence and/or epidemiological dominance of certain subgroups.
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Affiliation(s)
- Sofia V. Poimenidou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Marion Dalmasso
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
| | - Konstantinos Papadimitriou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Edward M. Fox
- CSIRO Agriculture and Food, Werribee, VIC, Australia
| | - Panagiotis N. Skandamis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Athens, Greece
| | - Kieran Jordan
- Teagasc Food Research Centre, Moorepark, Fermoy, Co., Cork, Ireland
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Hadjilouka A, Paramithiotis S, Drosinos EH. Genetic Analysis of the Listeria Pathogenicity Island 1 of Listeria monocytogenes 1/2a and 4b Isolates. Curr Microbiol 2018; 75:857-865. [PMID: 29468304 DOI: 10.1007/s00284-018-1458-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 02/19/2018] [Indexed: 12/22/2022]
Abstract
The aim of the present study was to apply descriptive, phylogenetic, recombination, and selection analyses on alignments of the Listeria Pathogenicity Island 1 (LIPI-1) of 1/2a and 4b Listeria monocytogenes isolates of different origin in order to gain insights into the evolution of this virulence gene cluster. For that purpose, a total of 19 L. monocytogenes isolates (9 meat isolates, serotype 1/2a; 5 meat isolates, serotype 4b; 5 strawberry isolates, serotype 4b) that have been previously separated at strain level were subjected to sequencing of their LIPI-1. Descriptive analysis revealed extensive nucleotide diversity mostly in the intragenic regions. The actA gene of 1/2a and 4b meat isolates and the hly gene of the 4b strawberry isolates exhibited the higher diversity; limited diversity was observed in prfA and plcA genes of the 4b isolates and mpl gene of the 1/2a isolates. Phylogenetic analysis of the complete island resulted in two major clusters that were consistent with serotype assignment of the isolates. Moreover, effective discrimination between serotypes was obtained by plcA, plcB, mpl, actA and the intergenic regions plcA-prfA and plcA-hly. In all cases but plcB and plcA-prfA 4b isolates were also differentiated according to their source of isolation as well. Selection analysis revealed that the island consisted of randomly evolving DNA with the exception of prfA gene of 1/2a isolates and actA gene of 4b meat isolates for which purifying selection or population expansion was indicated. Finally, no statistically significant evidence for recombination has been observed.
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Affiliation(s)
- Agni Hadjilouka
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
| | - Spiros Paramithiotis
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece.
| | - Eleftherios H Drosinos
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55, Athens, Greece
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Liu Y, Orsi RH, Boor KJ, Wiedmann M, Guariglia-Oropeza V. Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σ B. Front Microbiol 2017; 8:1910. [PMID: 29075236 PMCID: PMC5641562 DOI: 10.3389/fmicb.2017.01910] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 09/19/2017] [Indexed: 11/13/2022] Open
Abstract
Among Listeria monocytogenes' four alternative σ factors, σB controls the largest regulon. As σB-dependent transcription of some genes may be masked by overlaps among regulons, and as some σB-dependent genes are expressed only under very specific conditions, we hypothesized that the σB regulon is not yet fully defined. To further extend our understanding of the σB regulon, we used RNA-seq to identify σB-dependent genes in an L. monocytogenes strain that expresses σB following rhamnose induction, and in which genes encoding the other alternative sigma factors have been deleted. Analysis of RNA-seq data with multiple bioinformatics approaches, including a sliding window method that detects differentially transcribed 5' untranslated regions (UTRs), identified 105 σB-dependent transcription units (TUs) comprising 201 genes preceded by σB-dependent promoters. Of these 105 TUs, 7 TUs comprising 15 genes had not been identified previously as σB-dependent. An additional 23 genes not reported previously as σB-dependent were identified in 9 previously recognized σB-dependent TUs. Overall, 38 of these 201 genes had not been identified previously as members of the L. monocytogenes σB regulon. These newly identified σB-dependent genes encode proteins annotated as being involved in transcriptional regulation, oxidative and osmotic stress response, and in metabolism of energy, carbon and nucleotides. In total, 18 putative σB-dependent promoters were newly identified. Interestingly, a number of genes previously identified as σB-dependent did not show significant evidence for σB-dependent transcription in our experiments. Based on promoter analyses, a number of these genes showed evidence for co-regulation by σB and other transcriptional factors, suggesting that some σB-dependent genes require additional transcriptional regulators along with σB for transcription. Over-expression of a single alternative sigma factor in the absence of all other alternative sigma factors allowed us to: (i) identify new σB-dependent functions in L. monocytogenes, such as regulation of genes involved in 1,2-propanediol utilization (LMRG_00594-LMRG_00611) and biosynthesis of pyrimidine nucleotides (LMRG_00978-LMRG_00985); and (ii) identify new σB-dependent genes involved in stress response and pathogenesis functions. These data further support that σB not only regulates stress response functions, but also plays a broad role in L. monocytogenes homeostasis and resilience.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Kathryn J Boor
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
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Rojas TCG, Lobo FP, Hongo JA, Vicentini R, Verma R, Maluta RP, da Silveira WD. Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains. Foodborne Pathog Dis 2017; 14:245-252. [PMID: 28398866 DOI: 10.1089/fpd.2016.2219] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The ability to obtain bacterial genomes from the same host has allowed for comparative studies that help in the understanding of the molecular evolution of specific pathotypes. Avian pathogenic Escherichia coli (APEC) is a group of extraintestinal strains responsible for causing colibacillosis in birds. APEC is also suggested to possess a role as a zoonotic agent. Despite its importance, APEC pathogenesis still has several cryptic pathogenic processes that need to be better understood. In this work, a genome-wide survey of eight APEC strains for genes with evidence of recombination revealed that ∼14% of the homologous groups evaluated present signs of recombination. Enrichment analyses revealed that nine Gene Ontology (GO) terms were significantly more represented in recombinant genes. Among these GO terms, several were noted to be ATP-related categories. The search for positive selection in these APEC genomes revealed 32 groups of homologous genes with evidence of positive selection. Among these groups, we found several related to cell metabolism, as well as several uncharacterized genes, beyond the well-known virulence factors ompC, lamB, waaW, waaL, and fliC. A GO term enrichment test showed a prevalence of terms related to bacterial cell contact with the external environment (e.g., viral entry into host cell, detection of virus, pore complex, bacterial-type flagellum filament C, and porin activity). Finally, the genes with evidence of positive selection were retrieved from genomes of non-APEC strains and tested as were done for APEC strains. The result revealed that none of the groups of genes presented evidence of positive selection, confirming that the analysis was effective in inferring positive selection for APEC and not for E. coli in general, which means that the study of the genes with evidence of positive selection identified in this study can contribute for the better understanding of APEC pathogenesis processes.
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Affiliation(s)
- Thaís Cabrera Galvão Rojas
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Francisco Pereira Lobo
- 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil
| | - Jorge Augusto Hongo
- 2 Laboratório Multiusuário de Bioinformática, Embrapa Informática Agropecuária , Campinas, Brazil
| | - Renato Vicentini
- 3 Systems Biology Laboratory, Centre for Molecular Biology and Genetic Engineering, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Renu Verma
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Renato Pariz Maluta
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
| | - Wanderley Dias da Silveira
- 1 Department of Genetics, Evolution and Bioagents, Institute of Biology, State University of Campinas (UNICAMP) , Campinas, Brazil
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Liu Y, Orsi RH, Boor KJ, Wiedmann M, Guariglia-Oropeza V. An advanced bioinformatics approach for analyzing RNA-seq data reveals sigma H-dependent regulation of competence genes in Listeria monocytogenes. BMC Genomics 2016; 17:115. [PMID: 26880300 PMCID: PMC4754846 DOI: 10.1186/s12864-016-2432-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/03/2016] [Indexed: 11/14/2022] Open
Abstract
Background Alternative σ factors are important transcriptional regulators in bacteria. While σB has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σH has not yet been well defined in Listeria, even though σH controls a large regulon in the closely related non-pathogenic Bacillus subtilis. Results Using RNA-seq characterization of a L. monocytogenes strain with deletions of all 4 genes encoding alternative σ factors (ΔBCHL), which was further modified to overexpress sigH (ΔBCHL::Prha-sigH), we identified 6 transcription units (TUs) that are transcribed from σH-dependent promoters. Five of these TUs had not been previously identified. Identification of these promoters was facilitated by use of a bio-informatics approach that compared normalized RNA-seq coverage (NRC), between ΔBCHL::Prha-sigH and a ΔBCHL control, using sliding windows of 51 nt along the whole genome rather than comparing NRC calculated only for whole genes. Interestingly, we found that three operons that encode competence genes (comGABCDEFG, comEABC, coiA) are transcribed from σH-dependent promoters. While these promoters were highly conserved in L. monocytogenes, none of them were found in all Listeria spp. and coiA and its σH-dependent promoter were only found in L. monocytogenes. Conclusions Our data indicate that a number of L. monocytogenes competence genes are regulated by σH. This σH-dependent regulation of competence related genes is conserved in the pathogen L. monocytogenes, but not in other non-pathogenic Listeria strains. Combined with prior data that indicated a role of σH in virulence in a mouse model, this suggests a possible novel role of σH-dependent competence genes in L. monocytogenes virulence. Development and implementation of a sliding window approach to identify differential transcription using RNA-seq data, not only allowed for identification of σH-dependent promoters, but also provides a general approach for sensitive identification of differentially transcribed promoters and genes, particularly for genes that are transcribed from multiple promoter elements only some of which show differential transcription. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2432-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yichang Liu
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Renato Hohl Orsi
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Kathryn Jean Boor
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, 14853, USA.
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Nyarko EB, Donnelly CW. Listeria monocytogenes: Strain Heterogeneity, Methods, and Challenges of Subtyping. J Food Sci 2015; 80:M2868-78. [PMID: 26588067 DOI: 10.1111/1750-3841.13133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 10/02/2015] [Indexed: 12/28/2022]
Abstract
Listeria monocytogenes is a food-borne bacterial pathogen that is associated with 20% to 30% case fatality rate. L. monocytogenes is a genetically heterogeneous species, with a small fraction of strains (serotypes 1/2a, 1/2b, 4b) implicated in human listeriosis. Monitoring and source tracking of L. monocytogenes involve the use of subtyping methods, with the performance of genetic-based methods found to be superior to phenotypic-based ones. Various methods have been used to subtype L. monocytogenes isolates, with the pulsed-field gel electrophoresis (PFGE) being the gold standard. Although PFGE has had a massive impact on food safety through the establishment of the PulseNet, there is no doubt that whole genome sequence (WGS) typing is accurate, has a discriminatory power superior to any known method, and allows genome-wide differences between strains to be quantified through the comparison of nucleotide sequences. This review focuses on the different techniques that have been used to type L. monocytogenes strains, their performance challenges, and the tremendous impact WGS typing could have on the food safety landscape.
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Affiliation(s)
- Esmond B Nyarko
- Dept. of Animal and Food Science, Univ. of Delaware, 044 Townsend Hall, 531 S. College Avenue, Newark, Del., 19716, U.S.A
| | - Catherine W Donnelly
- Dept. of Nutrition and Food Science, Univ. of Vermont, 109 Carrigan Drive, 256 Carrigan Wing, Burlington, Vt., 05405, U.S.A
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Role of sigB and osmolytes in desiccation survival of Listeria monocytogenes in simulated food soils on the surface of food grade stainless steel. Food Microbiol 2015; 46:443-451. [DOI: 10.1016/j.fm.2014.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/05/2014] [Accepted: 09/12/2014] [Indexed: 11/24/2022]
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Rupp S, Aguilar-Bultet L, Jagannathan V, Guldimann C, Drögemüller C, Pfarrer C, Vidondo B, Seuberlich T, Frey J, Oevermann A. A naturally occurring prfA truncation in a Listeria monocytogenes field strain contributes to reduced replication and cell-to-cell spread. Vet Microbiol 2015; 179:91-101. [PMID: 25813546 DOI: 10.1016/j.vetmic.2015.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/27/2015] [Accepted: 03/03/2015] [Indexed: 12/23/2022]
Abstract
Listeria (L.) monocytogenes is an environmental bacterium that may become an intracellular pathogen upon ingestion to cause gastroenteritis, septicaemia, abortions, and/or fatal infections of the central nervous system. We here describe a L. monocytogenes field strain (JF5171) isolated from a bovine placenta in the context of abortion, which exhibited attenuation in bovine brain-slice cultures. The whole genome of strain JF5171 was sequenced, and the invasion, replication, and intercellular spread of JF5171 were further analyzed by quantification of colony forming units and immunofluorescence studies. Phospholipase and hemolysis activity of JF5171 were also quantified along with transcription levels of actA, hly and prfA. The data obtained were compared to those of the widely used L. monocytogenes reference strain, EGD-e. JF5171 exhibited reduced replication and lower levels of phospholipase and hemolysis activity. Invasion and cell-to-cell spread was strongly decreased compared to EGD-e, and actin polymerization was absent. A frame shift deletion was identified in the JF5171 coding region of the major regulator for virulence, prfA. This resulted in a truncated C-terminus sequence (WEN* vs. WGKLN*). In addition, a point mutation resulted in a lysine to arginine substitution at amino acid position 197. Complementation with prfA from EGD-e and with (EGD-e) prfA-K197N increased the replication and spread efficiency of JF5171. In contrast, complementation with the truncated version of prfA had no effect. Taken together, these results suggest that the truncated C-terminus of prfA considerably contributes to the strongly attenuated phenotype observed in vitro.
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Affiliation(s)
- Sebastian Rupp
- Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern CH-3012, Switzerland
| | - Lisandra Aguilar-Bultet
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern CH-3001, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Claudia Guldimann
- Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Cord Drögemüller
- Institute of Genetics, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Christiane Pfarrer
- Department of Anatomy, University of Veterinary Medicine Hannover, Hannover D-30173, Germany
| | - Beatriz Vidondo
- Veterinary Public Health Institute, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3097, Switzerland
| | - Torsten Seuberlich
- Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, University of Bern, Bern CH-3001, Switzerland
| | - Anna Oevermann
- Division of Neurological Sciences, Department of Clinical Research and Veterinary Public Health, Vetsuisse Faculty, University of Bern, Bern CH-3001, Switzerland.
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Ribeiro VB, Destro MT. Listeria monocytogenes serotype 1/2b and 4b isolates from human clinical cases and foods show differences in tolerance to refrigeration and salt stress. J Food Prot 2014; 77:1519-26. [PMID: 25198843 DOI: 10.4315/0362-028x.jfp-13-548] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Control of Listeria monocytogenes in food processing facilities is a difficult issue because of the ability of this microorganism to form biofilms and adapt to adverse environmental conditions. Survival at high concentrations of sodium chloride and growth at refrigeration temperatures are two other important characteristics of L. monocytogenes isolates. The aim of this study was to compare the growth characteristics under stress conditions at different temperatures of L. monocytogenes serotypes responsible for the majority of clinical cases from different sources. Twenty-two L. monocytogenes isolates, 12 from clinical cases (8 serotype 4b and 4 serotype 1/2a) and 10 from food (6 serotype 4b and 4 serotype 1/2a), and an L. monocytogenes Scott A (serotype 4b) reference strain were analyzed for the ability to grow in brain heart infusion broth plus 1.9 M NaCl (11%) at 4, 10, and 25°C for 73, 42, and 15 days, respectively. The majority of L. monocytogenes strains was viable or even grew at 4°C and under the high osmotic conditions usually used to control pathogens in the food industry. At 10°C, most strains could adapt and grow; however, no significant difference (P > 0.05) was found for lag-phase duration, maximum growth rate, and maximum cell density. At 25°C, all strains were able to grow, and populations increased by up 5 log CFU/ml. Clinical strains had a significantly longer lag phase and lower maximum cell density (P < 0.05) than did food strains. Regarding virulence potential, no significant differences in hemolytic activity were found among serotypes; however, serotype 4b strains were more invasive in Caco-2 cells than were serotype 1/2a strains (P < 0.05). The global tendency of decreasing NaCl concentrations in processed foods for health reasons may facilitate L. monocytogenes survival and growth in these products. Therefore, food companies must consider additional microbial growth barriers to assure product safety.
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Affiliation(s)
- V B Ribeiro
- Department of Food and Experimental Nutrition, University of São Paulo, São Paulo 05508000, Brazil.
| | - M T Destro
- Department of Food and Experimental Nutrition, University of São Paulo, São Paulo 05508000, Brazil
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15
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Ribeiro VB, Mujahid S, Orsi RH, Bergholz TM, Wiedmann M, Boor KJ, Destro MT. Contributions of σ(B) and PrfA to Listeria monocytogenes salt stress under food relevant conditions. Int J Food Microbiol 2014; 177:98-108. [PMID: 24631633 DOI: 10.1016/j.ijfoodmicro.2014.02.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 02/13/2014] [Accepted: 02/22/2014] [Indexed: 01/22/2023]
Abstract
Listeria monocytogenes is well known to survive and grow under several stress conditions, including salt stress, which is important for growth in certain foods as well as for host infection. To characterize the contributions, to salt stress response, of transcriptional regulators important for stress response and virulence (i.e., σ(B) and PrfA), we analyzed three L. monocytogenes parent strains and isogenic mutants (ΔsigB, ΔprfA, and ΔsigBΔprfA), representing different serotypes and lineages, for their ability to grow, at 25°C, in BHI with 1.9 M NaCl. With regard to growth rate, only the lineage IV strain presented a significant difference between the parent strain and both of its respective mutants lacking prfA (ΔprfA and ΔsigBΔprfA). Conversely, the lineage I and II parent strains showed significantly shorter lag phase in comparison to their respective ΔsigB mutant strains. Intestinal epithelial cell invasion assay and hemolytic activity assays showed a significant role for σ(B) in the former and for PrfA in the latter. To explore the mechanism that may contribute to the extended lag phase in the ΔsigB mutant strain and survival and growth of the parent strain upon salt shock, whole genome transcription profiling was performed to compare transcript levels between the lineage I, serotype 1/2b, parent strain and its isogenic ΔsigB mutant after 30 min of lag phase growth at 25°C in the presence of 1.9M NaCl (salt shock) without aeration. Microarray data showed significantly higher transcript levels for 173 genes in the parent strain as compared to the ΔsigB strain. Overall, 102 of the 173 σ(B) up-regulated genes had been identified in previous studies, indicating that 71 genes were newly identified as being up-regulated by σ(B) in this study. We hypothesize that, among these genes newly identified as σ(B) up-regulated, four genes (lmo2174, lmo0530, lmo0527 and lmo0529) may play a major role in response to salt stress. Lmo2174 contains domains that facilitate sensing and producing a transduction signal in the form of cyclic di-GMP, which may activate the enzymes Lmo0527, Lmo0529 and Lmo0530, which encode proteins similar to those responsible for synthesis of exopolysaccharides that may protect the cell by changing the cell wall structure during salt stress. Overall, our data showed that σ(B), but not PrfA, contributes to growth under salt stress. Moreover, we show that the σ(B) regulon of a L. monocytogenes lineage I strain challenged with salt shock includes salt stress-specific as well as previously unidentified σ(B) up-regulated genes.
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Affiliation(s)
- V B Ribeiro
- Departamento de Alimentos e Nutrição Experimental, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - S Mujahid
- Department of Food Science, Cornell University, Ithaca, NY, USA.
| | - R H Orsi
- Department of Food Science, Cornell University, Ithaca, NY, USA.
| | - T M Bergholz
- Department of Food Science, Cornell University, Ithaca, NY, USA.
| | - M Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, USA.
| | - K J Boor
- Department of Food Science, Cornell University, Ithaca, NY, USA.
| | - M T Destro
- Departamento de Alimentos e Nutrição Experimental, Universidade de São Paulo, São Paulo, SP, Brazil.
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Tsai YHL, Maron SB, McGann P, Nightingale KK, Wiedmann M, Orsi RH. Recombination and positive selection contributed to the evolution of Listeria monocytogenes lineages III and IV, two distinct and well supported uncommon L. monocytogenes lineages. INFECTION GENETICS AND EVOLUTION 2011; 11:1881-90. [PMID: 21854875 DOI: 10.1016/j.meegid.2011.08.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 10/17/2022]
Abstract
Listeriamonocytogenes lineages III and IV represent two uncommon lineages of the human and animal pathogen L. monocytogenes, characterized by occurrence of unusual phenotypic and genetic characteristics that differentiate them from the common lineages I and II. To gain further insights into the evolution of lineages III and IV, we amplified and sequenced housekeeping genes (i.e., gap, prs, purM, ribC, and sigB), internalin genes (i.e., inlA, inlB, inlC, inlG, inlC2, inlD, inlE, inlF, and inlH) and the virulence gene cluster containing prfA, plcA, hly, mpl, actA, and plcB for lineages III (n = 7) and IV (n = 4) isolates. Phylogenetic analyses of the sequences obtained along with previously reported sequence data for 40 isolates representing lineages I (n = 18), II (n = 21), and III (n = 1), showed that lineages III and IV represent divergent and monophyletic lineages. The virulence gene cluster as well as the inlAB operon were present in all isolates, with inlF absent from all lineages III and IV isolates. While all lineage IV isolates contained only inlC (in addition to inlAB), lineage III isolates showed considerable diversity with regard to internalin gene presence, including presence of (i) only inlC (n = 2), (ii) inlC and inlGC2DE (n = 3), (iii) only inlGC2DE (n = 2), and (iv) inlC and inlC2DE (n = 1). In addition to evidence for horizontal gene transfer events, among lineages III and IV isolates, in prs, actA, plcB, mpl, inlA, inlB, inlG, inlD, and inlE, we also found significant evidence for positive selection in the hly promoter region and, along the lineages III and IV branches, for actA (including in sites recognized for interactions with proteins involved in actin tail polymerization). In conclusion, lineages III and IV represent two distinct monophyletic groups with contributions of intragenic recombination to the evolution of their internalin genes as well as contributions of positive selection to evolution of the virulence genes island.
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Van Stelten A, Simpson JM, Chen Y, Scott VN, Whiting RC, Ross WH, Nightingale KK. Significant shift in median guinea pig infectious dose shown by an outbreak-associated Listeria monocytogenes epidemic clone strain and a strain carrying a premature stop codon mutation in inlA. Appl Environ Microbiol 2011; 77:2479-87. [PMID: 21296943 PMCID: PMC3067448 DOI: 10.1128/aem.02626-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 01/28/2011] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes contains (i) epidemic clone (EC) strains, which have been linked to the majority of listeriosis outbreaks worldwide and are overrepresented among sporadic cases in the United States, and (ii) strains commonly isolated from ready-to-eat foods that carry a mutation leading to a premature stop codon (PMSC) in inlA, which encodes the key virulence factor internalin A (InlA). Internalin A binds certain isoforms of the cellular receptor E-cadherin to facilitate crossing the intestinal barrier during the initial stages of an L. monocytogenes infection. Juvenile guinea pigs, which express the human isoform of E-cadherin that binds InlA, were intragastrically challenged with a range of doses of (i) an EC strain associated with a listeriosis outbreak or (ii) a strain carrying a PMSC mutation in inlA. Recovery of L. monocytogenes from tissues (i.e., liver, spleen, mesenteric lymph nodes, and ileum) was used to develop strain-specific dose-response curves on the basis of individual and combined organ data. Modeling of individual and combined organ data revealed an approximate 1.2 to 1.3 log(10) increase in the median infectious dose for the strain carrying a PMSC in inlA relative to that for the EC strain. Inclusion of the strain parameter significantly improved the goodness of fit for individual and combined organ models, indicating a significant shift in median infectious dose for guinea pigs challenged with an inlA PMSC strain compared to that for guinea pigs challenged with an EC strain. Results from this work provide evidence that the L. monocytogenes dose-response relationship is strain specific and will provide critical data for enhancement of current risk assessments and development of future risk assessments.
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Affiliation(s)
- A. Van Stelten
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - J. M. Simpson
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - Y. Chen
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - V. N. Scott
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - R. C. Whiting
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - W. H. Ross
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
| | - K. K. Nightingale
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado 80523, Grocery Manufacturers Association, Washington, DC 20005, United States Food and Drug Administration, College Park, Maryland 20740, Exponent, Bowie, Maryland 20715, Health Canada, Ottawa, Ontario K1A OJ0, Canada
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18
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Stress survival islet 1 (SSI-1) survey in Listeria monocytogenes reveals an insert common to listeria innocua in sequence type 121 L. monocytogenes strains. Appl Environ Microbiol 2011; 77:2169-73. [PMID: 21239547 DOI: 10.1128/aem.02159-10] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes strains (n = 117) were screened for the presence of stress survival islet 1 (SSI-1). SSI-1(+) strains (32.5%) belonged mainly to serotypes 1/2c, 3b, and 3c. All sequence type 121 (ST-121) strains included (n = 7) possessed homologues to Listeria innocua genes lin0464 and lin0465 instead of SSI-1.
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19
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Shen XL, Li SZ, Li YQ, Chen X. Episodic sitewise positive selection on the signal recognition particle protein Ffh in Actinobacteria. FEBS Lett 2010; 584:3975-8. [DOI: 10.1016/j.febslet.2010.07.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 07/29/2010] [Indexed: 11/30/2022]
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20
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Lucas Stelling CR, Orsi RH, Wiedmann M. Complementation of Listeria monocytogenes null mutants with selected Listeria seeligeri virulence genes suggests functional adaptation of Hly and PrfA and considerable diversification of prfA regulation in L. seeligeri. Appl Environ Microbiol 2010; 76:5124-39. [PMID: 20543041 PMCID: PMC2916458 DOI: 10.1128/aem.03107-09] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/30/2010] [Indexed: 11/20/2022] Open
Abstract
While Listeria seeligeri and L. monocytogenes contain the main Listeria virulence gene cluster, only L. monocytogenes is considered an intracellular pathogen. Initial evolutionary analyses showed that the virulence genes prfA, hly, and plcA are conserved in L. seeligeri, with specific Hly and PrfA amino acid residues showing evidence for positive selection in L. seeligeri. Our data also show that temperature-dependent transcript patterns for prfA, which encodes a transcriptional regulator of virulence genes, differed between L. monocytogenes and L. seeligeri. To further investigate the divergence of virulence gene function and regulation, L. seeligeri prfA (prfA(LS)), hly (hly(LS)), and plcA (plcA(LS)), as well as prfA(LS) constructs with different prfA promoter regions, were introduced into appropriate L. monocytogenes null mutants. Only when prfA(LS) was under the control of the L. monocytogenes prfA promoters (P1- and P2prfA) (P1P2(LM) prfA(LS)) was prfA(LS) able to fully complement the Delta prfA(LM) deletion. hly(LS) introduced into an L. monocytogenes background under its native promoter showed transcript levels similar to those of hly(LM) and was able to partially restore L. monocytogenes wild-type-level hemolysis and intracellular growth, even though Hly(LM) and Hly(LS) showed distinct patterns of cell- and supernatant-associated hemolytic activities. Our data indicate that (i) regulation of prfA expression differs between L. monocytogenes and L. seeligeri, although hly transcription is temperature dependent in both species, and (ii) PrfA and Hly functions are largely, but not fully, conserved between L. seeligeri and L. monocytogenes. Virulence gene homologues and their expression thus appear to have adapted to distinct but possibly related functions in these two species.
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Affiliation(s)
| | - Renato H. Orsi
- Graduate Field of Microbiology, Department of Food Science, Cornell University, Ithaca, New York 14853
| | - Martin Wiedmann
- Graduate Field of Microbiology, Department of Food Science, Cornell University, Ithaca, New York 14853
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21
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Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak. BMC Genomics 2010; 11:120. [PMID: 20167121 PMCID: PMC2834635 DOI: 10.1186/1471-2164-11-120] [Citation(s) in RCA: 240] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE) revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. RESULTS The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs) and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. CONCLUSIONS High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.
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Affiliation(s)
- Matthew W Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
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22
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Graves LM, Helsel LO, Steigerwalt AG, Morey RE, Daneshvar MI, Roof SE, Orsi RH, Fortes ED, Milillo SR, den Bakker HC, Wiedmann M, Swaminathan B, Sauders BD. Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest. Int J Syst Evol Microbiol 2009; 60:1280-1288. [PMID: 19667380 DOI: 10.1099/ijs.0.014118-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four isolates (FSL S4-120(T), FSL S4-696, FSL S4-710, and FSL S4-965) of Gram-positive, motile, facultatively anaerobic, non-spore-forming bacilli that were phenotypically similar to species of the genus Listeria were isolated from soil, standing water and flowing water samples obtained from the natural environment in the Finger Lakes National Forest, New York, USA. The four isolates were closely related to one another and were determined to be the same species by whole genome DNA-DNA hybridization studies (>82 % relatedness at 55 degrees C and >76 % relatedness at 70 degrees C with 0.0-0.5 % divergence). 16S rRNA gene sequence analysis confirmed their close phylogenetic relatedness to Listeria monocytogenes and Listeria innocua and more distant relatedness to Listeria welshimeri, L. seeligeri, L. ivanovii and L. grayi. Phylogenetic analysis of partial sequences for sigB, gap, and prs showed that these isolates form a well-supported sistergroup to L. monocytogenes. The four isolates were sufficiently different from L. monocytogenes and L. innocua by DNA-DNA hybridization to warrant their designation as a new species of the genus Listeria. The four isolates yielded positive reactions in the AccuProbe test that is purported to be specific for L. monocytogenes, did not ferment L-rhamnose, were non-haemolytic on blood agar media, and did not contain a homologue of the L. monocytogenes virulence gene island. On the basis of their phenotypic characteristics and their genotypic distinctiveness from L. monocytogenes and L. innocua, the four isolates should be classified as a new species within the genus Listeria, for which the name Listeria marthii sp. nov. is proposed. The type strain of L. marthii is FSL S4-120(T) (=ATCC BAA-1595(T) =BEIR NR 9579(T) =CCUG 56148(T)). L. marthii has not been associated with human or animal disease at this time.
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Affiliation(s)
- Lewis M Graves
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Leta O Helsel
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Arnold G Steigerwalt
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Roger E Morey
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Maryam I Daneshvar
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Sherry E Roof
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Esther D Fortes
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sara R Milillo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Henk C den Bakker
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Balasubramanian Swaminathan
- Enteric Diseases Laboratory Branch and Bacterial Zoonoses Branch, Division of Foodborne, Bacterial, and Mycotic Diseases, National Center for Zoonotic, Vector-borne and Enteric Diseases, Coordinating Center for Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Brian D Sauders
- New York State Department of Agriculture and Markets Food Laboratory Division, Albany, NY 12235, USA
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23
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Vos M. Why do bacteria engage in homologous recombination? Trends Microbiol 2009; 17:226-32. [PMID: 19464181 DOI: 10.1016/j.tim.2009.03.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 03/15/2009] [Accepted: 03/20/2009] [Indexed: 11/27/2022]
Abstract
Microbiologists have long recognized that the uptake and incorporation of homologous DNA from outside the cell is a common feature of bacteria, with important implications for their evolution. However, the exact reasons why bacteria engage in homologous recombination remain elusive. This Opinion article aims to reinvigorate the debate by examining the costs and benefits that homologous recombination could engender in natural populations of bacteria. It specifically focuses on the hypothesis that homologous recombination is selectively maintained because the genetic variation it generates improves the response of bacterial populations to natural selection, analogous to sex in eukaryotes.
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Affiliation(s)
- Michiel Vos
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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24
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Lefébure T, Stanhope MJ. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res 2009; 19:1224-32. [PMID: 19304960 DOI: 10.1101/gr.089250.108] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core genome loci under positive selection in at least one lineage and the same gene frequently under positive selection in multiple lineages. Tests are provided that reject recombination, saturation, and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome-wide adaptive evolution may result from a Red Queen macroevolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus, as reported by the authors in an earlier work, may be a consequence of these taxa inhabiting less species-rich habitats, and more unique niches. Despite many common loci under positive selection in multiple Campylobacter lineages, we found no evidence for molecular adaptive convergence at the level of the same or adjacent codons, or even protein domains. Taken collectively, these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency toward a common gastrointestinal habitat.
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Affiliation(s)
- Tristan Lefébure
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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