Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Methods
2.2.1. DNA Isolation
2.2.2. MultiLocus Sequence Typing
2.2.3. Whole Genome Sequencing (WGS)
2.2.4. Data Analysis
2.2.5. Ethical Approval
3. Results
3.1. Prevalence of L. monocytogenes ST37
3.2. Genomic Analysis of the L. monocytogenes ST37 Isolates
3.2.1. Core Genome including 1748 Genes
3.2.2. Pan Genomic Studies of the ST37 Isolates
3.2.3. Prophages and Phages in the ST37 Isolates
3.2.4. The CRISPR System
3.2.5. Virulence Factors
3.2.6. Antibiotic Resistance
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Orsi, R.H.; den Bakker, H.C.; Wiedmann, M. Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics. Int. J. Med. Microbiol. 2011, 301, 79–96. [Google Scholar] [CrossRef]
- Moura, A.; Lefrancq, N.; Wirth, T.; Leclercq, A.; Borges, V.; Gilpin, B.; Dallman, T.J.; Frey, J.; Franz, E.; Nielsen, E.M.; et al. Emergence and global spread of Listeria monocytogenes main clinical clonal complex. Sci. Adv. 2021, 7, eabj9805. [Google Scholar] [CrossRef]
- Maury, M.M.; Bracq-Dieye, H.; Huang, L.; Vales, G.; Lavina, M.; Thouvenot, P.; Disson, O.; Leclercq, A.; Brisse, S.; Lecuit, M. Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products. Nat. Commun. 2019, 10, 2488. [Google Scholar] [CrossRef]
- Maury, M.M.; Tsai, Y.H.; Charlier, C.; Touchon, M.; Chenal-Francisque, V.; Leclercq, A.; Criscuolo, A.; Gaultier, C.; Roussel, S.; Brisabois, A.; et al. Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat. Genet. 2016, 48, 308–313. [Google Scholar] [CrossRef]
- Ragon, M.; Wirth, T.; Hollandt, F.; Lavenir, R.; Lecuit, M.; Le Monnier, A.; Brisse, S. A new perspective on Listeria monocytogenes evolution. PLoS Pathog. 2008, 4, e1000146. [Google Scholar] [CrossRef] [PubMed]
- Painset, A.; Björkman, J.T.; Kiil, K.; Guillier, L.; Mariet, J.F.; Félix, B.; Amar, C.; Rotariu, O.; Roussel, S.; Perez-Reche, F.; et al. LiSEQ-whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe. Microb. Genom. 2019, 5, e000257. [Google Scholar] [CrossRef]
- Linke, K.; Rückerl, I.; Brugger, K.; Karpiskova, R.; Walland, J.; Muri-Klinger, S.; Tichy, A.; Wagner, M.; Stessl, B. Reservoirs of listeria species in three environmental ecosystems. Appl. Environ. Microbiol. 2014, 80, 5583–5592. [Google Scholar] [CrossRef] [PubMed]
- Ho, A.J.; Ivanek, R.; Gröhn, Y.T.; Nightingale, K.K.; Wiedmann, M. Listeria monocytogenes fecal shedding in dairy cattle shows high levels of day-to-day variation and includes outbreaks and sporadic cases of shedding of specific L Monocytogenes Subtypes. Prev. Vet. Med. 2007, 80, 287–305. [Google Scholar] [CrossRef] [PubMed]
- Esteban, J.I.; Oporto, B.; Aduriz, G.; Juste, R.A.; Hurtado, A. Faecal shedding and strain diversity of Listeria monocytogenes in healthy ruminants and swine in Northern Spain. BMC Vet. Res. 2009, 5, 2. [Google Scholar] [CrossRef] [PubMed]
- Fredriksson-Ahomaa, M.; Sauvala, M.; Kurittu, P.; Heljanko, V.; Heikinheimo, A.; Paulsen, P. Characterisation of Listeria monocytogenes Isolates from Hunted Game and Game Meat from Finland. Foods 2022, 11, 3679. [Google Scholar] [CrossRef]
- Castro, H.; Douillard, F.P.; Korkeala, H.; Lindström, M. Mobile Elements Harboring Heavy Metal and Bacitracin Resistance Genes Are Common among Listeria monocytogenes Strains Persisting on Dairy Farms. mSphere 2021, 6, e0038321. [Google Scholar] [CrossRef] [PubMed]
- Terentjeva, M.; Šteingolde, Ž.; Meistere, I.; Elferts, D.; Avsejenko, J.; Streikiša, M.; Gradovska, S.; Alksne, L.; Ķibilds, J.; Bērziņš, A. Prevalence, Genetic Diversity and Factors Associated with Distribution of Listeria monocytogenes and Other Listeria spp. in Cattle Farms in Latvia. Pathogens 2021, 10, 851. [Google Scholar] [CrossRef] [PubMed]
- Kubicová, Z.; Roussel, S.; Félix, B.; Cabanová, L. Genomic diversity of Listeria monocytogenes isolates from Slovakia (2010 to 2020). Front. Microbiol. 2021, 12, 729050. [Google Scholar] [CrossRef]
- Roedel, A.; Dieckmann, R.; Brendebach, H.; Hammerl, J.A.; Kleta, S.; Noll, M.; Al Dahouk, S.; Vincze, S. Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics. Appl. Environ. Microbiol. 2019, 85, e01253-19. [Google Scholar] [CrossRef] [PubMed]
- Stessl, B.; Szakmary-Brändle, K.; Vorberg, U.; Schoder, D.; Wagner, M. Temporal analysis of the Listeria monocytogenes population structure in floor drains during reconstruction and expansion of a meat processing plant. Int. J. Food Microbiol. 2020, 314, 108360. [Google Scholar] [CrossRef]
- Alvarez-Molina, A.; Cobo-Díaz, J.F.; López, M.; Prieto, M.; de Toro, M.; Alvarez-Ordóñez, A. Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing. Int. J. Food Microbiol. 2021, 340, 109043. [Google Scholar] [CrossRef]
- Psareva, E.K.; Liskova, E.A.; Razheva, I.V.; Yushina, Y.K.; Grudistova, M.A.; Gladkova, N.A.; Potemkin, E.A.; Zhurilov, P.A.; Sokolova, E.V.; Andriyanov, P.A.; et al. Diversity of Listeria monocytogenes strains isolated from food products in the Central European part of Russia in 2000–2005 and 2019–2020. Foods 2021, 10, 2790. [Google Scholar] [CrossRef]
- Voronina, O.L.; Kunda, M.S.; Ryzhova, N.N.; Aksenova, E.I.; Kutuzova, A.V.; Tikulmina, A.N.; Karpova, T.I.; Melkumyan, A.R.; Klimova, E.A.; Gruzdeva, O.A.; et al. Genomic characteristics of listeria that caused invasive listeriosis during the COVID-19 pandemic. Lond. J. Res. Sci. Nat. Form. (LJRS) 2023, 23, 33–61. [Google Scholar] [CrossRef]
- Grant, J.R.; Stothard, P. The CGView Server: A comparative genomics tool for circular genomes. Nucleic Acids Res. 2008, 36, W181–W184. [Google Scholar] [CrossRef]
- Brettin, T.; Davis, J.J.; Disz, T.; Edwards, R.A.; Gerdes, S.; Olsen, G.J.; Olson, R.; Overbeek, R.; Parrello, B.; Pusch, G.D.; et al. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 2015, 5, 8365. [Google Scholar] [CrossRef]
- Li, W.; O’Neill, K.R.; Haft, D.H.; DiCuccio, M.; Chetvernin, V.; Badretdin, A.; Coulouris, G.; Chitsaz, F.; Derbyshire, M.K.; Durkin, A.S.; et al. RefSeq: Expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res. 2021, 49, D1020–D1028. [Google Scholar] [CrossRef] [PubMed]
- Arndt, D.; Grant, J.R.; Marcu, A.; Sajed, T.; Pon, A.; Liang, Y.; Wishart, D.S. PHASTER: A better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016, 44, W16–W21. [Google Scholar] [CrossRef] [PubMed]
- Moura, A.; Criscuolo, A.; Pouseele, H.; Maury, M.M.; Leclercq, A.; Tarr, C.; Björkman, J.T.; Dallman, T.; Reimer, A.; Enouf, V.; et al. Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes. Nat. Microbiol. 2016, 2, 16185. [Google Scholar] [CrossRef] [PubMed]
- Zhang, Z.; Schwartz, S.; Wagner, L.; Miller, W. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 2000, 7, 203–214. [Google Scholar] [CrossRef]
- Kumar, S.; Stecher, G.; Tamura, K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 2016, 33, 1870–1874. [Google Scholar] [CrossRef]
- Chaudhari, N.M.; Gupta, V.K.; Dutta, C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci. Rep. 2016, 6, 24373. [Google Scholar] [CrossRef]
- Zhou, Y.; Liang, Y.; Lynch, K.H.; Dennis, J.J.; Wishart, D.S. PHAST: A fast phage search tool. Nucleic Acids Res. 2011, 39, W347–W352. [Google Scholar] [CrossRef]
- Couvin, D.; Bernheim, A.; Toffano-Nioche, C.; Touchon, M.; Michalik, J.; Néron, B.; Rocha, E.P.C.; Vergnaud, G.; Gautheret, D.; Pourcel, C. CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins. Nucleic Acids Res. 2018, 46, W246–W251. [Google Scholar] [CrossRef]
- Chen, L.; Yang, J.; Yu, J.; Yao, Z.; Sun, L.; Shen, Y.; Jin, Q. VFDB: A reference database for bacterial virulence factors. Nucleic Acids Res. 2005, 33 (Suppl. S1), D325–D328. [Google Scholar] [CrossRef]
- Alcock, B.P.; Huynh, W.; Chalil, R.; Smith, K.W.; Raphenya, A.R.; Wlodarski, M.A.; Edalatmand, A.; Petkau, A.; Syed, S.A.; Tsang, K.K.; et al. CARD 2023: Expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023, 51, D690–D699. [Google Scholar] [CrossRef]
- Kuenne, C.; Billion, A.; Mraheil, M.A.; Strittmatter, A.; Daniel, R.; Goesmann, A.; Barbuddhe, S.; Hain, T.; Chakraborty, T. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC Genom. 2013, 14, 47. [Google Scholar] [CrossRef] [PubMed]
- Hain, T.; Steinweg, C.; Kuenne, C.T.; Billion, A.; Ghai, R.; Chatterjee, S.S.; Domann, E.; Kärst, U.; Goesmann, A.; Bekel, T.; et al. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J. Bacteriol. 2006, 188, 7405–7415. [Google Scholar] [CrossRef] [PubMed]
- Fox, E.M.; Allnutt, T.; Bradbury, M.I.; Fanning, S.; Chandry, P.S. Comparative Genomics of the Listeria monocytogenes ST204 Subgroup. Front. Microbiol. 2016, 7, 2057. [Google Scholar] [CrossRef] [PubMed]
- Dorscht, J.; Klumpp, J.; Bielmann, R.; Schmelcher, M.; Born, Y.; Zimmer, M.; Calendar, R.; Loessner, M.J. Comparative genome analysis of Listeria bacteriophages reveals extensive mosaicism, programmed translational frameshifting, and a novel prophage insertion site. J. Bacteriol. 2009, 191, 7206–7215. [Google Scholar] [CrossRef]
- Ripp, S.; Miller, R.V. The role of pseudolysogeny in bacteriophage-host interactions in a natural freshwater environment. Microbiology 1997, 143, 2065–2070. [Google Scholar] [CrossRef]
- Ripp, S.; Miller, R.V. Dynamics of the pseudolysogenic response in slowly growing cells of Pseudomonas aeruginosa. Microbiology (Reading) 1998, 144 Pt 8, 2225–2232. [Google Scholar] [CrossRef]
- Mäntynen, S.; Laanto, E.; Oksanen, H.M.; Poranen, M.M.; Díaz-Muñoz, S.L. Black box of phage-bacterium interactions: Exploring alternative phage infection strategies. Open Biol. 2021, 11, 210188. [Google Scholar] [CrossRef]
- Hof, H.; Nichterlein, T.; Kretschmar, M. Management of listeriosis. Clin. Microbiol. Rev. 1997, 10, 345–357. [Google Scholar] [CrossRef]
- Espenhain, L.; Takeuchi-Storm, N.; Munch, P.K.; Hansen, L.T.; Nielsen, N.L.; Andersen, J.K.; Schjørring, S. Listeria monocytogenes. In Annual Report on Zoonoses in Denmark 2022; Lassen, B., Olsen, A., Sandberg, M., Müller, L., Torpdahl, M., Petersen, C.K., Eds.; Annual Report on Zoonoses in Denmark; National Food Institute, Technical University of Denmark: Kongens Lyngby, Denmark, 2023; pp. 10–14. [Google Scholar]
- European Centre for Disease Prevention and Control. Listeriosis. In ECDC. Annual Epidemiological Report for 2021; ECDC: Stockholm, Sweden, 2022. [Google Scholar]
- Cabal, A.; Pietzka, A.; Huhulescu, S.; Allerberger, F.; Ruppitsch, W.; Schmid, D. Isolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria. Front. Microbiol. 2019, 10, 2282. [Google Scholar] [CrossRef]
- Maćkiw, E.; Korsak, D.; Kowalska, J.; Felix, B.; Stasiak, M.; Kucharek, K.; Antoszewska, A.; Postupolski, J. Genetic diversity of Listeria monocytogenes isolated from ready-to-eat food products in retail in Poland. Int. J. Food Microbiol. 2021, 358, 109397. [Google Scholar] [CrossRef] [PubMed]
- Hain, T.; Ghai, R.; Billion, A.; Kuenne, C.T.; Steinweg, C.; Izar, B.; Mohamed, W.; Mraheil, M.A.; Domann, E.; Schaffrath, S.; et al. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genom. 2012, 13, 144. [Google Scholar] [CrossRef] [PubMed]
- Rabinovich, L.; Sigal, N.; Borovok, I.; Nir-Paz, R.; Herskovits, A.A. Prophage excision activates Listeria competence genes that promote phagosomal escape and virulence. Cell 2012, 150, 792–802. [Google Scholar] [CrossRef] [PubMed]
Groups of the COGs | Genes | ||
---|---|---|---|
Unique | Accessory | Core | |
Cellular processes and signaling | 28% | 22% | 17% |
Information storage and processing | 30% | 32% | 14% |
Metabolism | 14% | 14% | 40% |
Poorly characterized | 28% | 32% | 22% |
Source | Strain | Prophage | Bacteriophage | |||||||
---|---|---|---|---|---|---|---|---|---|---|
lmo0112 | tRNA-Ser(cga) | tRNA-Arg(tct) | tRNA-Leu(gag) | comK | tRNA-Arg(ccg) | tRNA-Thr(ggt) | Total | Class: Caudoviricetes | ||
FPE | GIMC2026:LmcBD14 | √ | √ | √ | 3 | |||||
FPE | GIMC2027:LmcBD15 | √ | √ | √ | 3 | |||||
Meat | GIMC2054:Lmc6888 | √ | √ | √ | 3 | |||||
Meat | GIMC2071:Lmc9864 | √ | √ | √ | 3 | |||||
Meat | GIMC2106:Lmc10704 | √ | √ | √ | √ | 4 | ||||
Meat | GIMC2107:Lmc11363 | √ | √ | √ | √ | 4 | ||||
Fish | GIMC2053:Lmc6646 | √ | √ | √ | 3 | |||||
Fish | GIMC2103:Lmc6942 | √ | √ | √ | 3 | |||||
Fish | GIMC2105:Lmc10258 | √ | √ | √ | 3 | |||||
Clin | GIMC2063:LmcUH21 | √ | √ | 2 | ||||||
Clin | GIMC2082:LmcIH1-5 | √ | √ | √ | 3 | |||||
Clin | GIMC2094:LmcH67_7 | √ | √ | √ | 3 | |||||
Clin | GIMC2123:LmcUH37 | √ | √ | 2 | ||||||
Clin | GIMC2134:LmcEH-7 | √ | √ | √ | 3 | |||||
Clin | GIMC2112:LmcIH1-8 | √ | √ | √ | 3 | √ | ||||
Clin | GIMC2113:LmcIH1-9 | √ | √ | √ | 3 | √ |
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Voronina, O.L.; Kunda, M.S.; Ryzhova, N.N.; Aksenova, E.I.; Kustova, M.A.; Karpova, T.I.; Melkumyan, A.R.; Klimova, E.A.; Gruzdeva, O.A.; Tartakovsky, I.S. Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates. Life 2023, 13, 2167. https://doi.org/10.3390/life13112167
Voronina OL, Kunda MS, Ryzhova NN, Aksenova EI, Kustova MA, Karpova TI, Melkumyan AR, Klimova EA, Gruzdeva OA, Tartakovsky IS. Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates. Life. 2023; 13(11):2167. https://doi.org/10.3390/life13112167
Chicago/Turabian StyleVoronina, Olga L., Marina S. Kunda, Natalia N. Ryzhova, Ekaterina I. Aksenova, Margarita A. Kustova, Tatiana I. Karpova, Alina R. Melkumyan, Elena A. Klimova, Olga A. Gruzdeva, and Igor S. Tartakovsky. 2023. "Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates" Life 13, no. 11: 2167. https://doi.org/10.3390/life13112167
APA StyleVoronina, O. L., Kunda, M. S., Ryzhova, N. N., Aksenova, E. I., Kustova, M. A., Karpova, T. I., Melkumyan, A. R., Klimova, E. A., Gruzdeva, O. A., & Tartakovsky, I. S. (2023). Listeria monocytogenes ST37 Distribution in the Moscow Region and Properties of Clinical and Foodborne Isolates. Life, 13(11), 2167. https://doi.org/10.3390/life13112167