Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States

A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents.

[1]  V. Sintchenko,et al.  It Is Not All about Single Nucleotide Polymorphisms: Comparison of Mobile Genetic Elements and Deletions in Listeria monocytogenes Genomes Links Cases of Hospital-Acquired Listeriosis to the Environmental Source , 2015, Journal of Clinical Microbiology.

[2]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[3]  S. Knabel,et al.  Prophages in Listeria monocytogenes Contain Single-Nucleotide Polymorphisms That Differentiate Outbreak Clones within Epidemic Clones , 2008, Journal of Clinical Microbiology.

[4]  D. A. A. Mossel,et al.  Detection and enumeration of Listeria monocytogenes in foods , 2003 .

[5]  Yan Luo,et al.  CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data , 2015, PeerJ Comput. Sci..

[6]  D Raoult,et al.  Whole genome sequencing as a tool to investigate a cluster of seven cases of listeriosis in Austria and Germany, 2011–2013 , 2014, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[7]  A. Goesmann,et al.  Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome , 2013, BMC Genomics.

[8]  David S. Wishart,et al.  PHASTER: a better, faster version of the PHAST phage search tool , 2016, Nucleic Acids Res..

[9]  Mikhail Pachkov,et al.  Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads , 2014, Molecular biology and evolution.

[10]  J. Marimón,et al.  Two Outbreaks of Listeria monocytogenes Infection, Northern Spain , 2014, Emerging infectious diseases.

[11]  A. Datta,et al.  Comparative evaluation of direct plating and most probable number for enumeration of low levels of Listeria monocytogenes in naturally contaminated ice cream products. , 2017, International journal of food microbiology.

[12]  Errol Strain,et al.  High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach , 2012, BMC Genomics.

[13]  C. Buchrieser,et al.  Differentiation of the Major Listeria monocytogenes Serovars by Multiplex PCR , 2004, Journal of Clinical Microbiology.

[14]  M. Allard,et al.  Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes , 2016, Applied and Environmental Microbiology.

[15]  L. Gram,et al.  Bias in the Listeria monocytogenes Enrichment Procedure: Lineage 2 Strains Outcompete Lineage 1 Strains in University of Vermont Selective Enrichments , 2005, Applied and Environmental Microbiology.

[16]  B. Birren,et al.  Short-term genome evolution of Listeria monocytogenes in a non-controlled environment , 2008, BMC Genomics.

[17]  J. R. Gorny,et al.  Multistate outbreak of listeriosis associated with cantaloupe. , 2013, The New England journal of medicine.

[18]  S. Brisse,et al.  A New Perspective on Listeria monocytogenes Evolution , 2008, PLoS pathogens.

[19]  Sophia Kathariou,et al.  Listeria monocytogenes virulence and pathogenicity, a food safety perspective. , 2002, Journal of food protection.

[20]  T. Hammack,et al.  Recovery and Growth Potential of Listeria monocytogenes in Temperature Abused Milkshakes Prepared from Naturally Contaminated Ice Cream Linked to a Listeriosis Outbreak , 2016, Front. Microbiol..

[21]  Eduardo P C Rocha,et al.  Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes , 2016, Nature Microbiology.

[22]  P. Gerner-Smidt,et al.  Novel Epidemic Clones of Listeria monocytogenes, United States, 2011 , 2013, Emerging infectious diseases.

[23]  A. Datta,et al.  Prevalence and Level of Listeria monocytogenes in Ice Cream Linked to a Listeriosis Outbreak in the United States. , 2016, Journal of food protection.

[24]  Steen Ethelberg,et al.  Whole-genome Sequencing Used to Investigate a Nationwide Outbreak of Listeriosis Caused by Ready-to-eat Delicatessen Meat, Denmark, 2014. , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[25]  Ruth Timme,et al.  Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database , 2016, Journal of Clinical Microbiology.

[26]  M. Wagner,et al.  Genomes of sequence type 121 Listeria monocytogenes strains harbor highly conserved plasmids and prophages , 2015, Front. Microbiol..

[27]  Yi Chen,et al.  Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation. , 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[28]  S. Kathariou,et al.  comK Prophage Junction Fragments as Markers for Listeria monocytogenes Genotypes Unique to Individual Meat and Poultry Processing Plants and a Model for Rapid Niche-Specific Adaptation, Biofilm Formation, and Persistence , 2011, Applied and Environmental Microbiology.

[29]  Derrick J. Zwickl Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , 2006 .

[30]  N. Petronella,et al.  Choice of reference-guided sequence assembler and SNP caller for analysis of Listeria monocytogenes short-read sequence data greatly influences rates of error , 2015, BMC Research Notes.

[31]  R. Mandrell,et al.  Competitive Fitness of Listeria monocytogenes Serotype 1/2a and 4b Strains in Mixed Cultures with and without Food in the U.S. Food and Drug Administration Enrichment Protocol , 2006, Applied and Environmental Microbiology.

[32]  Lee S. Katz,et al.  Notes from the field: listeriosis associated with stone fruit--United States, 2014. , 2015 .

[33]  David S. Wishart,et al.  PHAST: A Fast Phage Search Tool , 2011, Nucleic Acids Res..

[34]  Ken Chen,et al.  VarScan: variant detection in massively parallel sequencing of individual and pooled samples , 2009, Bioinform..

[35]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[36]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[37]  D. Ussery,et al.  Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart , 2013, Applied and Environmental Microbiology.

[38]  Yi Chen,et al.  Distributed under Creative Commons Cc-by 4.0 an Evaluation of Alternative Methods for Constructing Phylogenies from Whole Genome Sequence Data: a Case Study with Salmonella Background , 2022 .

[39]  Yi Chen,et al.  Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing , 2016, Applied and Environmental Microbiology.

[40]  E. Mavrogonatou,et al.  Listeria monocytogenes Strains Underrepresented during Selective Enrichment with an ISO Method Might Dominate during Passage through Simulated Gastric Fluid and In Vitro Infection of Caco-2 Cells , 2016, Applied and Environmental Microbiology.

[41]  M. Wiedmann,et al.  FSL J1-208, a Virulent Uncommon Phylogenetic Lineage IV Listeria monocytogenes Strain with a Small Chromosome Size and a Putative Virulence Plasmid Carrying Internalin-Like Genes , 2012, Applied and Environmental Microbiology.