UNLABELLED: Listeria monocytogenes presents a significant concern for the food industry due to its ability to persist in the food processing environment. One of the factors contributing to its persistence is decreased sensitivity to disinfectants. Our objective was to assess the diversity of L. monocytogenes sensitivity to food industry disinfectants by testing the response of 1,671 L. monocytogenes isolates to quaternary ammonium compounds (QACs) and 414 isolates to peracetic acid (PAA) using broth microdilution and growth curve analysis assays, respectively, and to categorize the isolates into sensitive and tolerant. A high phenotype-genotype concordance (95%) regarding tolerance to QACs was obtained by screening the genomes for the presence of QAC tolerance-associated genes bcrABC, emrE, emrC, and qacH. Based on this high concordance, we assessed the QAC genes' dissemination among publicly available L. monocytogenes genomes (n = 39,196). Overall, QAC genes were found in 23% and 28% of the L. monocytogenes collection in this study and in the global data set, respectively. bcrABC and qacH were the most prevalent genes, with bcrABC being the most detected QAC gene in the USA, while qacH dominated in Europe. No significant differences (P > 0.05) in the PAA tolerance were detected among isolates belonging to different lineages, serogroups, clonal complexes, or isolation sources, highlighting limited variation in the L. monocytogenes sensitivity to this disinfectant. The present work represents the largest testing of L. monocytogenes sensitivity to important food industry disinfectants at the phenotypic and genomic level, revealing diversity in the tolerance to QACs while all isolates showed similar sensitivity to PAA. IMPORTANCE: Contamination of Listeria monocytogenes within food processing environments is of great concern to the food industry due to challenges in eradicating the isolates once they become established and persistent in the environment. Genetic markers associated with increased tolerance to certain disinfectants have been identified, which alongside other biotic and abiotic factors can favor the persistence of L. monocytogenes in the food production environment. By employing a comprehensive large-scale phenotypic testing and genomic analysis, this study significantly enhances the understanding of the L. monocytogenes tolerance to quaternary ammonium compounds (QACs) and the genetic determinants associated with the increased tolerance. We provide a global overview of the QAC genes prevalence among public L. monocytogenes sequences and their distribution among clonal complexes, isolation sources, and geographical locations. Additionally, our comprehensive screening of the peracetic acid (PAA) sensitivity shows that this disinfectant can be used in the food industry as the lack of variation in sensitivity indicates reliable effect and no apparent possibility for the emergence of tolerance.

Arla Innovation Center Arla Foods amba Aarhus N Denmark

Austrian Agency for Health and Food Safety Institute of Medical Microbiology and Hygiene National Reference Laboratory for Listeria monocytogenes Graz Austria

Chair for Food Safety and Analytics Ludwig Maximilians University Munich Munich Germany

Department of Public Health Masaryk University Medical Faculty Brno Czech Republic

Food Innovation Center Oregon State University Portland Oregon USA

German Federal Institute for Risk Assessment Berlin Germany

Institute for Food Safety and Hygiene Vetsuisse Faculty University of Zurich Zurich Switzerland

Institute of Microbiology and Parasitology Veterinary Faculty University of Ljubljana Ljubljana Slovenia

Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G Caporale Giuseppe Caporale Teramo Italy

Listeriosis Reference Service Food Directorate Bureau of Microbial Hazards Ottawa Ontario Canada

Nofima The Norwegian Institute of Food Fisheries and Aquaculture Research Ås Norway

North Carolina State University Raleigh North Carolina USA

Public Health England National Infection Service London United Kingdom

Research Group for Food Microbiology and Hygiene National Food Institute Technical University of Denmark Kgs Lyngby Denmark

Research Group for Genomic Epidemiology National Food Institute Technical University of Denmark Kgs Lyngby Denmark

Unit for Food Microbiology Institute for Food Safety Food Technology and Veterinary Public Health University of Veterinary Medicine Vienna Austria

University of Vermont Burlington Vermont USA

University of Wisconsin Madison Madison Wisconsin USA

University of Zaragoza Zaragoza Spain

Zobrazit více v PubMed

Radoshevich L, Cossart P. 2018. Listeria monocytogenes: towards a complete picture of its physiology and pathogenesis. Nat Rev Microbiol 16:32–46. doi:10.1038/nrmicro.2017.126 PubMed DOI

Huang C, Lu TL, Yang Y. 2023. Mortality risk factors related to Listeriosis - a meta-analysis. J Infect Public Health 16:771–783. doi:10.1016/j.jiph.2023.03.013 PubMed DOI

Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernández Escámez PS, Girones R, Herman L, Koutsoumanis K, Nørrung B, et al. . 2018. Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU. EFSA J 16:e05134. doi:10.2903/j.efsa.2018.5134 PubMed DOI PMC

Belias A, Sullivan G, Wiedmann M, Ivanek R. 2022. Factors that contribute to persistent Listeria in food processing facilities and relevant interventions: a rapid review. Food Control 133:108579. doi:10.1016/j.foodcont.2021.108579 DOI

Orsi RH, Borowsky ML, Lauer P, Young SK, Nusbaum C, Galagan JE, Birren BW, Ivy RA, Sun Q, Graves LM, Swaminathan B, Wiedmann M. 2008. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9:539. doi:10.1186/1471-2164-9-539 PubMed DOI PMC

Fagerlund A, Møretrø T, Heir E, Briandet R, Langsrud S. 2017. Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces. Appl Environ Microbiol 83:e01046-17. doi:10.1128/AEM.01046-17 PubMed DOI PMC

Bland R, Brown SRB, Waite-Cusic J, Kovacevic J. 2022. Probing antimicrobial resistance and sanitizer tolerance themes and their implications for the food industry through the Listeria monocytogenes lens. Compr Rev Food Sci Food Saf 21:1777–1802. doi:10.1111/1541-4337.12910 PubMed DOI

Fagerlund A, Heir E, Møretrø T, Langsrud S. 2020. Listeria monocytogenes biofilm removal using different commercial cleaning agents. Molecules 25:792. doi:10.3390/molecules25040792 PubMed DOI PMC

McDonnell G, Russell AD. 1999. Antiseptics and disinfectants: activity, action, and resistance. Clin Microbiol Rev 12:147–179. doi:10.1128/CMR.12.1.147 PubMed DOI PMC

Gilbert P, Moore LE. 2005. Cationic antiseptics: diversity of action under a common epithet. J Appl Microbiol 99:703–715. doi:10.1111/j.1365-2672.2005.02664.x PubMed DOI

Gerba CP. 2015. Quaternary ammonium biocides: efficacy in application. Appl Environ Microbiol 81:464–469. doi:10.1128/AEM.02633-14 PubMed DOI PMC

Jia Y, Lu H, Zhu L. 2022. Molecular mechanism of antibiotic resistance induced by mono- and twin-chained quaternary ammonium compounds. Sci Total Environ 832:155090. doi:10.1016/j.scitotenv.2022.155090 PubMed DOI PMC

He Y, Xu T, Li S, Mann DA, Britton B, Oliver HF, den Bakker HC, Deng X. 2022. Integrative assessment of reduced Listeria monocytogenes susceptibility to benzalkonium chloride in produce processing environments. Appl Environ Microbiol 88:e0126922. doi:10.1128/aem.01269-22 PubMed DOI PMC

Dutta V, Elhanafi D, Kathariou S. 2013. Conservation and distribution of the benzalkonium chloride resistance cassette bcrABC in Listeria monocytogenes. Appl Environ Microbiol 79:6067–6074. doi:10.1128/AEM.01751-13 PubMed DOI PMC

Müller A, Rychli K, Muhterem-Uyar M, Zaiser A, Stessl B, Guinane CM, Cotter PD, Wagner M, Schmitz-Esser S. 2013. Tn6188 - a novel transposon in Listeria monocytogenes responsible for tolerance to benzalkonium chloride. PLoS ONE 8:e76835. doi:10.1371/journal.pone.0076835 PubMed DOI PMC

Chmielowska C, Korsak D, Szuplewska M, Grzelecka M, Maćkiw E, Stasiak M, Macion A, Skowron K, Bartosik D. 2021. Benzalkonium chloride and heavy metal resistance profiles of Listeria monocytogenes strains isolated from fish, fish products and food-producing factories in Poland. Food Microbiol 98:103756. doi:10.1016/j.fm.2021.103756 PubMed DOI

Fagerlund A, Wagner E, Møretrø T, Heir E, Moen B, Rychli K, Langsrud S. 2022. Pervasive Listeria monocytogenes is common in the norwegian food system and is associated with increased prevalence of stress survival and resistance determinants. Appl Environ Microbiol 88:e0086122. doi:10.1128/aem.00861-22 PubMed DOI PMC

Jiang X, Yu T, Xu Y, Wang H, Korkeala H, Shi L. 2019. MdrL, a major facilitator superfamily efflux pump of Listeria monocytogenes involved in tolerance to benzalkonium chloride. Appl Microbiol Biotechnol 103:1339–1350. doi:10.1007/s00253-018-9551-y PubMed DOI

Romanova NA, Wolffs PFG, Brovko LY, Griffiths MW. 2006. Role of efflux pumps in adaptation and resistance of Listeria monocytogenes to benzalkonium chloride. Appl Environ Microbiol 72:3498–3503. doi:10.1128/AEM.72.5.3498-3503.2006 PubMed DOI PMC

Schulz LM, Dreier F, de Sousa Miranda LM, Rismondo J. 2023. Adaptation mechanisms of Listeria monocytogenes to quaternary ammonium compounds. Microbiol Spectr 11:e0144123. doi:10.1128/spectrum.01441-23 PubMed DOI PMC

Jiang X, Ren S, Geng Y, Yu T, Li Y, Liu L, Liu G, Wang H, Shi L. 2020. The sug operon involves in resistance to quaternary ammonium compounds in Listeria monocytogenes EGD-e. Appl Microbiol Biotechnol 104:7093–7104. doi:10.1007/s00253-020-10741-6 PubMed DOI

Bechtel TD, Hershelman J, Ghoshal M, McLandsborough L, Gibbons JG. 2024. Chemical mutagenesis of Listeria monocytogenes for increased tolerance to benzalkonium chloride shows independent genetic underpinnings and off-target antibiotic resistance. PLOS ONE 19:e0305663. doi:10.1371/journal.pone.0305663 PubMed DOI PMC

Møretrø T, Schirmer BCT, Heir E, Fagerlund A, Hjemli P, Langsrud S. 2017. Tolerance to quaternary ammonium compound disinfectants may enhance growth of Listeria monocytogenes in the food industry. Int J Food Microbiol 241:215–224. doi:10.1016/j.ijfoodmicro.2016.10.025 PubMed DOI

Manso B, Melero B, Stessl B, Jaime I, Wagner M, Rovira J, Rodríguez-Lázaro D. 2020. The response to oxidative stress in Listeria monocytogenes is temperature dependent. Microorganisms 8:521. doi:10.3390/microorganisms8040521 PubMed DOI PMC

Palma F, Radomski N, Guérin A, Sévellec Y, Félix B, Bridier A, Soumet C, Roussel S, Guillier L. 2022. Genomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches. Food Microbiol 106:103757. doi:10.1016/j.fm.2021.103757 PubMed DOI

Wessels S, Ingmer H. 2013. Modes of action of three disinfectant active substances: a review. Regul Toxicol Pharmacol 67:456–467. doi:10.1016/j.yrtph.2013.09.006 PubMed DOI

Kragh ML, Ivanova M, Dalgaard P, Leekitcharoenphon P, Truelstrup Hansen L. 2024. Sensitivity of 240 Listeria monocytogenes isolates to common industrial biocides is more dependent on the presence of residual organic matter or biofilm than on genetic determinants. Food Control 158:110244. doi:10.1016/j.foodcont.2023.110244 DOI

Wiedmann M. 2022. Listeria develops reduced sanitizer sensitivity but not resistance at recommended sanitizer use levels. Center for Produce Safety, Woodland, CA. Available from: https://www.centerforproducesafety.org/amass/documents/researchproject/454/CPS

Elhanafi D, Dutta V, Kathariou S. 2010. Genetic characterization of plasmid-associated benzalkonium chloride resistance determinants in a Listeria monocytogenes strain from the 1998-1999 outbreak. Appl Environ Microbiol 76:8231–8238. doi:10.1128/AEM.02056-10 PubMed DOI PMC

Kovacevic J, Ziegler J, Wałecka-Zacharska E, Reimer A, Kitts DD, Gilmour MW. 2016. Tolerance of Listeria monocytogenes to quaternary ammonium sanitizers is mediated by a novel efflux pump encoded by emrE. Appl Environ Microbiol 82:939–953. doi:10.1128/AEM.03741-15 PubMed DOI PMC

Kremer PHC, Lees JA, Koopmans MM, Ferwerda B, Arends AWM, Feller MM, Schipper K, Valls Seron M, van der Ende A, Brouwer MC, van de Beek D, Bentley SD. 2017. Benzalkonium tolerance genes and outcome in Listeria monocytogenes meningitis. Clin Microbiol Infect 23:265. doi:10.1016/j.cmi.2016.12.008 PubMed DOI PMC

Bland RN, Johnson JD, Waite-Cusic JG, Weisberg AJ, Riutta ER, Chang JH, Kovacevic J. 2021. Application of whole genome sequencing to understand diversity and presence of genes associated with sanitizer tolerance in Listeria monocytogenes from produce handling sources. Foods 10:10. doi:10.3390/foods10102454 PubMed DOI PMC

Bolten S, Harrand AS, Skeens J, Wiedmann M. 2022. Nonsynonymous mutations in fepR Are associated with adaptation of Listeria monocytogenes and other Listeria spp. to low concentrations of benzalkonium chloride but do not increase survival of L. monocytogenes and Other Listeria spp. after exposure to benzalkonium chloride concentrations recommended for use in food processing environments. Appl Environ Microbiol 88:e0048622. doi:10.1128/aem.00486-22 PubMed DOI PMC

Douarre PE, Sévellec Y, Le Grandois P, Soumet C, Bridier A, Roussel S. 2022. FepR as a central genetic target in the adaptation to quaternary ammonium compounds and cross-resistance to ciprofloxacin in Listeria monocytogenes. Front Microbiol 13:864576. doi:10.3389/fmicb.2022.864576 PubMed DOI PMC

Jiang X, Yu T, Xu P, Xu X, Ji S, Gao W, Shi L. 2018. Role of efflux pumps in the in vitro development of ciprofloxacin resistance in Listeria monocytogenes. Front Microbiol 9:2350. doi:10.3389/fmicb.2018.02350 PubMed DOI PMC

Tezel U, Pavlostathis SG. 2015. Quaternary ammonium disinfectants: microbial adaptation, degradation and ecology. Curr Opin Biotechnol 33:296–304. doi:10.1016/j.copbio.2015.03.018 PubMed DOI

Guidi F, Orsini M, Chiaverini A, Torresi M, Centorame P, Acciari VA, Salini R, Palombo B, Brandi G, Amagliani G, Schiavano GF, Massacci FR, Fisichella S, Domenico MD, Ancora M, Pasquale AD, Duranti A, Cammà C, Pomilio F, Blasi G. 2021. Hypo- and hyper-virulent Listeria monocytogenes clones persisting in two different food processing plants of central italy. Microorganisms 9:376. doi:10.3390/microorganisms9020376 PubMed DOI PMC

Roedel A, Dieckmann R, Brendebach H, Hammerl JA, Kleta S, Noll M, Al Dahouk S, Vincze S. 2019. Biocide-tolerant Listeria monocytogenes isolates from german food production plants do not show cross-resistance to clinically relevant antibiotics. Appl Environ Microbiol 85:e01253-19. doi:10.1128/AEM.01253-19 PubMed DOI PMC

Luque-Sastre L, Fox EM, Jordan K, Fanning S. 2018. A comparative study of the susceptibility of Listeria species to sanitizer treatments when grown under planktonic and biofilm conditions. J Food Prot 81:1481–1490. doi:10.4315/0362-028X.JFP-17-466 PubMed DOI

Gelbicova T, Florianova M, Hluchanova L, Kalova A, Korena K, Strakova N, Karpiskova R. 2020. Comparative analysis of genetic determinants encoding cadmium, arsenic, and benzalkonium chloride resistance in Listeria monocytogenes of human, food, and environmental origin. Front Microbiol 11:599882. doi:10.3389/fmicb.2020.599882 PubMed DOI PMC

Stoller A, Stevens MJA, Stephan R, Guldimann C. 2019. Characteristics of Listeria Monocytogenes strains persisting in a meat processing facility over a 4-year period. Pathogens 8:32. doi:10.3390/pathogens8010032 PubMed DOI PMC

Conficoni D, Losasso C, Cortini E, Di Cesare A, Cibin V, Giaccone V, Corno G, Ricci A. 2016. Resistance to biocides in Listeria monocytogenes collected in meat-processing environments. Front Microbiol 7:1627. doi:10.3389/fmicb.2016.01627 PubMed DOI PMC

Kropac AC, Eshwar AK, Stephan R, Tasara T. 2019. New insights on the role of the pLMST6 plasmid in Listeria monocytogenes biocide tolerance and virulence. Front Microbiol 10:1538. doi:10.3389/fmicb.2019.01538 PubMed DOI PMC

Wiegand I, Hilpert K, Hancock REW. 2008. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat Protoc 3:163–175. doi:10.1038/nprot.2007.521 PubMed DOI

Meier AB, Guldimann C, Markkula A, Pöntinen A, Korkeala H, Tasara T. 2017. Comparative phenotypic and genotypic analysis of swiss and finnish Listeria monocytogenes isolates with respect to benzalkonium chloride resistance. Front Microbiol 8:397. doi:10.3389/fmicb.2017.00397 PubMed DOI PMC

Karlsmose AK, Ivanova M, Kragh ML, Kjeldgaard JS, Otani S, Svendsen CA, Papić B, Zdovc I, Tasara T, Stephan R, Heir E, Langsrud S, Møretrø T, Dalgaard P, Fagerlund A, Hansen LT, Aarestrup FM, Leekitcharoenphon P. 2024. A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities. Infect Genet Evol 119:105582. doi:10.1016/j.meegid.2024.105582 PubMed DOI

Castro H, Douillard FP, Korkeala H, Lindström M. 2021. Mobile elements harboring heavy metal and bacitracin resistance genes are common among Listeria monocytogenes strains persisting on dairy farms. mSphere 6:e0038321. doi:10.1128/mSphere.00383-21 PubMed DOI PMC

Schmitz-Esser S, Anast JM, Cortes BW. 2021. A large-scale sequencing-based survey of plasmids in Listeria monocytogenes reveals global dissemination of plasmids. Front Microbiol 12:653155. doi:10.3389/fmicb.2021.653155 PubMed DOI PMC

Harter E, Wagner EM, Zaiser A, Halecker S, Wagner M, Rychli K. 2017. Stress survival islet 2, predominantly present in Listeria monocytogenes strains of sequence type 121, is involved in the alkaline and oxidative stress responses. Appl Environ Microbiol 83:e00827-17. doi:10.1128/AEM.00827-17 PubMed DOI PMC

Daeschel D, Pettengill JB, Wang Y, Chen Y, Allard M, Snyder AB. 2022. Genomic analysis of Listeria monocytogenes from US food processing environments reveals a high prevalence of QAC efflux genes but limited evidence of their contribution to environmental persistence. BMC Genomics 23:488. doi:10.1186/s12864-022-08695-2 PubMed DOI PMC

Painset A, Björkman JT, Kiil K, Guillier L, Mariet JF, Félix B, Amar C, Rotariu O, Roussel S, Perez-Reche F, Brisse S, Moura A, Lecuit M, Forbes K, Strachan N, Grant K, Møller-Nielsen E, Dallman TJ. 2019. 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 5:e000257. doi:10.1099/mgen.0.000257 PubMed DOI PMC

Ebner R, Stephan R, Althaus D, Brisse S, Maury M, Tasara T. 2015. Phenotypic and genotypic characteristics of Listeria monocytogenes strains isolated during 2011–2014 from different food matrices in Switzerland. Food Control 57:321–326. doi:10.1016/j.foodcont.2015.04.030 DOI

Cooper AL, Carrillo CD, DeschÊnes M, Blais BW. 2021. Genomic markers for quaternary ammonium compound resistance as a persistence indicator for Listeria monocytogenes contamination in food manufacturing environments. J Food Prot 84:389–398. doi:10.4315/JFP-20-328 PubMed DOI

Maury MM, Bracq-Dieye H, Huang L, Vales G, Lavina M, Thouvenot P, Disson O, Leclercq A, Brisse S, Lecuit M. 2019. Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products. Nat Commun 10:2488. doi:10.1038/s41467-019-10380-0 PubMed DOI PMC

Gorski L, Cooley MB, Oryang D, Carychao D, Nguyen K, Luo Y, Weinstein L, Brown E, Allard M, Mandrell RE, Chen Y. 2022. Prevalence and clonal diversity of over 1,200 Listeria monocytogenes isolates collected from public access waters near produce production areas on the central California coast during 2011 to 2016. Appl Environ Microbiol 88:e0035722. doi:10.1128/aem.00357-22 PubMed DOI PMC

Cheng Y, Mousavi ZE, Pennone V, Hurley D, Butler F. 2023. Association between the presence of resistance genes and sanitiser resistance of Listeria monocytogenes isolates recovered from different food-processing facilities. Microorganisms 11:2989. doi:10.3390/microorganisms11122989 PubMed DOI PMC

Merchel Piovesan Pereira B, Wang X, Tagkopoulos I. 2020. Short- and long-term transcriptomic responses of Escherichia coli to biocides: a systems analysis. Appl Environ Microbiol 86:e00708-20. doi:10.1128/AEM.00708-20 PubMed DOI PMC

Kastbjerg VG, Gram L. 2012. Industrial disinfectants do not select for resistance in Listeria monocytogenes following long term exposure. Int J Food Microbiol 160:11–15. doi:10.1016/j.ijfoodmicro.2012.09.009 PubMed DOI

Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics 70:e102. doi:10.1002/cpbi.102 PubMed DOI

Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi:10.1093/bioinformatics/btt086 PubMed DOI PMC

Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. 2014. Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52:1529–1539. doi:10.1128/JCM.02981-13 PubMed DOI PMC

Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi:10.1093/bioinformatics/btu153 PubMed DOI

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. 2015. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31:3691–3693. doi:10.1093/bioinformatics/btv421 PubMed DOI PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. doi:10.1093/bioinformatics/btp348 PubMed DOI PMC

Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32:268–274. doi:10.1093/molbev/msu300 PubMed DOI PMC

Letunic I, Bork P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 47:W256–W259. doi:10.1093/nar/gkz239 PubMed DOI PMC

Wambui J, Eshwar AK, Aalto-Araneda M, Pöntinen A, Stevens MJA, Njage PMK, Tasara T. 2020. The analysis of field strains isolated from food, animal and clinical sources uncovers natural mutations in Listeria monocytogenes nisin resistance genes. Front Microbiol 11:549531. doi:10.3389/fmicb.2020.549531 PubMed DOI PMC

Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Göker M. 2013. Opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics 29:1823–1824. doi:10.1093/bioinformatics/btt291 PubMed DOI

Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842. doi:10.1093/bioinformatics/btq033 PubMed DOI PMC

Blackwell GA, Hunt M, Malone KM, Lima L, Horesh G, Alako BTF, Thomson NR, Iqbal Z. 2021. Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences. PLOS Biol 19:e3001421. doi:10.1371/journal.pbio.3001421 PubMed DOI PMC

Clausen PTLC, Aarestrup FM, Lund O. 2018. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 19:307. doi:10.1186/s12859-018-2336-6 PubMed DOI PMC

Gupta A, Jordan IK, Rishishwar L. 2017. stringMLST: a fast k-mer based tool for multilocus sequence typing. Bioinformatics 33:119–121. doi:10.1093/bioinformatics/btw586 PubMed DOI

DerSimonian R, Laird N. 1986. Meta-analysis in clinical trials. Control Clin Trials 7:177–188. doi:10.1016/0197-2456(86)90046-2 PubMed DOI

R Core Team . 2024. R: a language and environment for statistical computing. Available from: https://www.R-project.org/

Wickham H. 2016. Ggplot2: Elegant graphics for data analysis. Springer-Verlag, New York.

South A. 2011. Rworldmap : A new R package for mapping global data. R J 3:35. doi:10.32614/RJ-2011-006 DOI

Allaire JJ, Ellis P, Gandrud C, Kuo K, Lewis BW, Owen J, Russell K, Rogers J, Sese C, Yetman CJ. 2017. NetworkD3: D3 JavaScript Network Graphs from R. https://cran.r-project.org/web/packages/networkD3/.