Abstract
Listeria monocytogenes is a pathogenic bacterium which can live in adverse environments (low pH, high salinity, and low temperature). Even though there are various whole genome sequencing (WGS) data on L. monocytogenes, investigations on genetic differences between stress-resistant and -sensitive L. monocytogenes grown under stress environments have been not fully examined. This study aims to investigate and compare genetic characteristics between stress-resistant and -sensitive L. monocytogenes using whole genome sequencing (WGS). A total of 47 L. monocytogenes strains (43 stress-resistant and 4 stress-sensitive) were selected based on the stress-resistance tests under pH 3, 5% salt concentration, and 1 °C. The sequencing library for WGS was prepared and sequenced using an Illumina MiSeq. Genetic characteristics of two different L. monocytogenes groups were examined to analyze the pangenome, functionality, virulence, antibiotic resistance, core, and unique genes. The functionality of unique genes in the stress-resistant L. monocytogenes was distinct compared to the stress-sensitive L. monocytogenes, such as carbohydrate and nucleotide transport and metabolism. The lisR virulence gene was detected more in the stress-resistant L. monocytogenes than in the stress-sensitive group. Five stress-resistant L. monocytogenes strains possessed tet(M) antibiotic resistance gene. This is the first study suggesting that deep genomic characteristics of L. monocytogenes may have different resistance level under stress conditions. This new insight will aid in understanding the genetic relationship between stress-resistant and -sensitive L. monocytogenes strains isolated from diverse resources.
Key points
• Whole genomes of L. monocytogenes isolated from three different sources were analyzed.
• Differences in two L. monocytogenes groups were identified in functionality, virulence, and antibiotic resistance genes.
• This study first examines the association between resistances and whole genomes of stress-resistant and -sensitive L. monocytogenes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The whole genome sequences in this study are available at the GenBank of the National Center for Biotechnology Information (NCBI); PRJNA952623.
Change history
28 September 2023
A Correction to this paper has been published: https://doi.org/10.1007/s00253-023-12793-w
References
Abdelhamed H, Lawrence ML, Ramachandran R, Karsi A (2019) Validation of predicted virulence factors in Listeria monocytogenes identified using comparative genomics. Toxins 11(9):508. https://doi.org/10.3390/toxins11090508
Alcock BP, Raphenya AR, Lau TT, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen AV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48(D1):D517–D525. https://doi.org/10.1093/nar/gkz935
Arcari T, Feger ML, Guerreiro DN, Wu J, O’Byrne CP (2020) Comparative review of the responses of Listeria monocytogenes and Escherichia coli to low pH stress. Genes 11(11):1330. https://doi.org/10.3390/genes11111330
Bae D, Liu C, Zhang T, Jones M, Peterson SN, Wang C (2012) Global gene expression of Listeria monocytogenes to salt stress. J Food Prot 75(5):906–912
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
Bierne H, Cossart P (2007) Listeria monocytogenes surface proteins: from genome predictions to function. Microbiol Mol Biol Rev 71(2):377–397. https://doi.org/10.1128/MMBR.00039-06
Buchanan RL, Gorris LG, Hayman MM, Jackson TC, Whiting RC (2017) A review of Listeria monocytogenes: an update on outbreaks, virulence, dose-response, ecology, and risk assessments. Food Control 75:1–13. https://doi.org/10.1016/j.foodcont.2016.12.016
Bucur FI, Grigore-Gurgu L, Crauwels P, Riedel CU, Nicolau AI (2018) Resistance of Listeria monocytogenes to stress conditions encountered in food and food processing environments. Front Microbiol 9:2700. https://doi.org/10.3389/fmicb.2018.02700
Center for Disease Control and Prevention (2022) Listeria (Listeriosis). Atlanta: CDC Retrieved from https://www.cdc.gov/listeria/
Chan YC, Hu Y, Chaturongakul S, Files KD, Bowen BM, Boor KJ, Wiedmann M (2008) Contributions of two-component regulatory systems, alternative σ factors, and negative regulators to Listeria monocytogenes cold adaptation and cold growth. J Food Prot 71(2):420–425
Cotter PD, Emerson N, Gahan CG, Hill C (1999) Identification and disruption of lisRK, a genetic locus encoding a two-component signal transduction system involved in stress tolerance and virulence in Listeria monocytogenes. J Bacteriol 181(21):6840–6843. https://doi.org/10.1128/JB.181.21.6840-6843.1999
De Noordhout CM, Devleesschauwer B, Angulo FJ, Verbeke G, Haagsma J, Kirk M, Havelaar A, Speybroeck N (2014) The global burden of listeriosis: a systematic review and meta-analysis. The Lancet Infect Dis 14(11):1073–1082. https://doi.org/10.1016/S1473-3099(14)70870-9
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. Peer J 3:e1319. https://doi.org/10.7717/peerj.1319
Halbedel S, Prager R, Fuchs S, Trost E, Werner G, Flieger A (2018) Whole-genome sequencing of recent Listeria monocytogenes isolates from Germany reveals population structure and disease clusters. J Clin Microbiol 56(6):e00119-e218. https://doi.org/10.1128/JCM.00119-18
Hurley D, Luque-Sastre L, Parker CT, Huynh S, Eshwar AK, Nguyen SV, Andrews N, Fanning S (2019) Whole-genome sequencing-based characterization of 100 Listeria monocytogenes isolates collected from food processing environments over a four-year period. Msphere 4(4):e00252-e319. https://doi.org/10.1128/mSphere.00252-19
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11(1):1–11. https://doi.org/10.1186/1471-2105-11-119
Jung YM, Lee JN, Shin HD, Lee YH (2004) Role of tktA gene in pentose phosphate pathway on odd-ball biosynthesis of poly-β-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon. J Biosci Bioeng 98(3):224–227. https://doi.org/10.1016/S1389-1723(04)00272-5
Kim E, Yang SM, Cho EJ, Kim HY (2020) Novel real-time PCR assay for Lactobacillus casei group species using comparative genomics. Food Microbiol 90:103485. https://doi.org/10.1016/j.fm.2020.103485
Kim E, Yang SM, Kim D, Kim HY (2022) Complete genome sequencing and comparative genomics of three potential probiotic strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8. Front Microbiol 12:4135. https://doi.org/10.3389/fmicb.2021.794315
Liu Y, Ceruso M, Jiang Y, Datta AR, Carter L, Strain E, Pepe T, Fratamico P (2013) Construction of Listeria monocytogenes mutants with in-frame deletions in the phosphotransferase transport system (PTS) and analysis of their growth under stress conditions. J Food Sci 78(9):M1392–M1398. https://doi.org/10.1111/1750-3841.12181
Luth S, Kleta S, Al Dahouk S (2018) Whole genome sequencing as a typing tool for foodborne pathogens like Listeria monocytogenes–the way towards global harmonisation and data exchange. Trends Food Sci Technol 73:67–75. https://doi.org/10.1016/j.tifs.2018.01.008
Morvan A, Moubareck C, Leclercq A, Hervé-Bazin M, Bremont S, Lecuit M, Courvalin P, Le Monnier A (2010) Antimicrobial resistance of Listeria monocytogenes strains isolated from humans in France. Antimicrob Agents Chemother 54(6):2728–2731. https://doi.org/10.1128/AAC.01557-09
O’Driscoll B, Gahan CG, Hill C (1996) Adaptive acid tolerance response in Listeria monocytogenes: isolation of an acid-tolerant mutant which demonstrates increased virulence. Appl Environ Microbiol 62(5):1693–1698. https://doi.org/10.1128/aem.62.5.1693-1698.1996
Park SY, Choi JW, Yeon J, Lee MJ, Chung DH, Kim MG, Lee KH, Kim KS, Bahk GJ, Kim KY, Kim CH (2005) Predictive modeling for the growth of Listeria monocytogenes as a function of temperature, NaCl, and pH. J Microbiol Biotechnol 15(6):1323–1329
Parra-Flores J, Holý O, Bustamante F, Lepuschitz S, Pietzka A, Contreras-Fernández A, Ruppitsch W (2021) Virulence and antibiotic resistance genes in Listeria monocytogenes strains isolated from ready-to-eat foods in Chile. Front Microbiol 12:4163. https://doi.org/10.3389/fmicb.2021.796040
Perez F, Granger BE (2007) IPython: a system for interactive scientific computing. Comput Sci Eng 9(3):21–29. https://doi.org/10.1109/MCSE.2007.53
Quereda JJ, Morón-García A, Palacios-Gorba C, Dessaux C, García-del Portillo F, Pucciarelli MG, Ortega AD (2021) Pathogenicity and virulence of Listeria monocytogenes: a trip from environmental to medical microbiology. Virulence 12(1):2509–2545. https://doi.org/10.1080/21505594.2021.1975526
Rismondo J, Schulz LM (2021) Not just transporters: alternative functions of ABC transporters in Bacillus subtilis and Listeria monocytogenes. Microorganisms 9(1):163. https://doi.org/10.3390/microorganisms9010163
Sun Y, Wilkinson BJ, Standiford TJ, Akinbi HT, O’Riordan MX (2012) Fatty acids regulate stress resistance and virulence factor production for Listeria monocytogenes. J Bacteriol 194(19):5274–5284. https://doi.org/10.1128/JB.00045-12
Tasara T, Stephan R (2006) Cold stress tolerance of Listeria monocytogenes: a review of molecular adaptive mechanisms and food safety implications. J Food Prot 69(6):1473–1484. https://doi.org/10.4315/0362-028X-69.6.1473
Thedieck K, Hain T, Mohamed W, Tindall BJ, Nimtz M, Chakraborty T, Wehland J, Jänsch L (2006) The MprF protein is required for lysinylation of phospholipids in listerial membranes and confers resistance to cationic antimicrobial peptides (CAMPs) on Listeria monocytogenes. Mol Microbiol 62(5):1325–1339. https://doi.org/10.1111/j.1365-2958.2006.05452.x
Wemekamp-Kamphuis HH, Wouters JA, de Leeuw PP, Hain T, Chakraborty T, Abee T (2004) Identification of sigma factor σB-controlled genes and their impact on acid stress, high hydrostatic pressure, and freeze survival in Listeria monocytogenes EGD-e. Appl Environ Microbiol 70(6):3457–3466. https://doi.org/10.1128/AEM.70.6.3457-3466.2004
Zhang Y, Zhang J, Chang X, Qin S, Song Y, Tian J, Ma A (2022) Analysis of 90 Listeria monocytogenes contaminated in poultry and livestock meat through whole-genome sequencing. Food Res Int 159:111641. https://doi.org/10.1016/j.foodres.2022.111641
Zhu X, Long F, Chen Y, Knøchel S, She Q, Shi X (2008) A putative ABC transporter is involved in negative regulation of biofilm formation by Listeria monocytogenes. Appl Environ Microbiol 74(24):7675–7683. https://doi.org/10.1128/AEM.01229-08
Acknowledgements
The authors would like to thank Dr. Hyun Jung Kim, a research of the Korea Food Research Institute for funding, and Dr. Hae Yeong Kim, Sang Do Ha, and Michael Rothrock for sharing strains.
Funding
This research was supported by Korean Food Research Institute funds awarded to Si Hong Park (grant number: E0210702-01).
Author information
Authors and Affiliations
Contributions
S. P. and H.K. conceived and designed research. E. K., S. Y., and H. H. conducted experiments and collected samples. H. H., E. K., S. Y., and S. P. analyzed the data and H. H. and S. P. drafted the manuscript. H. H. and S. P. wrote and critically reviewed the manuscript. All authors read and approved the manuscript.
Corresponding author
Ethics declarations
Ethics approval and consent to participate
This article does not contain any studies with human participants or animals performed by any of the authors.
Consent to participate
Not applicable.
Consent for publication
All co-authors agreed to publish data in the scientific journal.
Competing interests
The authors declare no competing interests.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The original version of this article was revised. The Figures 1 and 3 are now corrected.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Hong, H., Yang, S.M., Kim, E. et al. Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes. Appl Microbiol Biotechnol 107, 6047–6056 (2023). https://doi.org/10.1007/s00253-023-12693-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-023-12693-z