Unraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing

Strain Variability of Listeria monocytogenes under NaCl Stress Elucidated by a High-Throughput Microbial Growth Data Assembly and Analysis Protocol

(2020) Mariella Aalto-Araneda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of Benzalkonium Chloride Resistance and Potential Virulence of Listeria monocytogenes Isolates Obtained from Different Stages of a Poultry Production Chain in Spain

(2020) VICTORIA LÓPEZ-ALONSO et al.   JOURNAL OF FOOD PROTECTION

Ecogenetics of antibiotic resistance in Listeria monocytogenes

(2020) Fernando Baquero et al.   MOLECULAR MICROBIOLOGY

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Plasmids contribute to food processing environment–associated stress survival in three Listeria monocytogenes ST121, ST8, and ST5 strains

(2019) Annabel L. Naditz et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Hypervirulent Listeria monocytogenes clones’ adaption to mammalian gut accounts for their association with dairy products

(2019) Mylène M. Maury et al.   Nature Communications

New Insights on the Role of the pLMST6 Plasmid in Listeria monocytogenes Biocide Tolerance and Virulence

(2019) Alexandra C. Kropac et al.   Frontiers in Microbiology

Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates

(2019) Michael Feldgarden et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Biocide-Tolerant Listeria monocytogenes Isolates from German Food Production Plants Do Not Show Cross-Resistance to Clinically Relevant Antibiotics

(2019) A. Roedel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The ability of Listeria monocytogenes to form biofilm on surfaces relevant to the mushroom production environment

(2019) Lionel Kenneth Dygico et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Prevalence and persistence of Listeria monocytogenes in premises and products of small food business operators in Northern Ireland

(2018) Robert H. Madden et al.   FOOD CONTROL

Listeria monocytogenes Sequence Types 121 and 14 Repeatedly Isolated Within One Year of Sampling in a Rabbit Meat Processing Plant: Persistence and Ecophysiology

(2018) Frédérique Pasquali et al.   Frontiers in Microbiology

Risk Factors and Level of Listeria monocytogenes Contamination of Raw Pork in Retail Markets in China

(2018) Hua Li et al.   Frontiers in Microbiology

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

(2018) Elena Oniciuc et al.   Genes

Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015

(2018) Ivo Van Walle et al.   Eurosurveillance

Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes

(2018) Tamazight Cherifi et al.   BMC MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Resistance of Listeria monocytogenes to Stress Conditions Encountered in Food and Food Processing Environments

(2018) Florentina Ionela Bucur et al.   Frontiers in Microbiology

Detection of premature stop codons leading to truncated internalin A among food and clinical strains of Listeria monocytogenes

(2017) Margarida Ferreira da Silva et al.   FOOD MICROBIOLOGY

Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept

(2017) Ivan Nastasijevic et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

(2016) Brendan R. Jackson et al.   CLINICAL INFECTIOUS DISEASES

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment

(2016) Monika Dzieciol et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity

(2016) Mylène M Maury et al.   NATURE GENETICS

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

The Role of Stress and Stress Adaptations in Determining the Fate of the Bacterial Pathogen Listeria monocytogenes in the Food Chain

(2016) Kerrie NicAogáin et al.   Frontiers in Microbiology

Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes

(2016) Alexandra Moura et al.   Nature Microbiology

Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains

(2016) Annette Fagerlund et al.   PLoS One

Tolerance of Listeria monocytogenes to Quaternary Ammonium Sanitizers Is Mediated by a Novel Efflux Pump Encoded by emrE

(2015) Jovana Kovacevic et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Connection between Persistent, Disinfectant-Resistant Listeria monocytogenes Strains from Two Geographically Separate Iberian Pork Processing Plants: Evidence from Comparative Genome Analysis

(2015) Sagrario Ortiz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes

(2015) Werner Ruppitsch et al.   JOURNAL OF CLINICAL MICROBIOLOGY

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Diversity and distribution of Listeria monocytogenes in meat processing plants

(2014) Belén Martín et al.   FOOD MICROBIOLOGY

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Overexpression offetA(ybbL) andfetB(ybbM), Encoding an Iron Exporter, Enhances Resistance to Oxidative Stress in Escherichia coli

(2013) Sergios A. Nicolaou et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Conservation and Distribution of the Benzalkonium Chloride Resistance CassettebcrABCin Listeria monocytogenes

(2013) Vikrant Dutta et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The ubiquitous nature ofListeria monocytogenesclones: a large-scale Multilocus Sequence Typing study

(2013) Jana K. Haase et al.   ENVIRONMENTAL MICROBIOLOGY

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

Tn6188 - A Novel Transposon in Listeria monocytogenes Responsible for Tolerance to Benzalkonium Chloride

(2013) Anneliese Müller et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Life History Trade-Offs and Relaxed Selection Can Decrease Bacterial Virulence in Environmental Reservoirs

(2012) Lauri Mikonranta et al.   PLoS One

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Prevalence, Distribution, and Diversity of Listeria monocytogenes in Retail Environments, Focusing on Small Establishments and Establishments with a History of Failed Inspections

(2011) KARIN HOELZER et al.   JOURNAL OF FOOD PROTECTION

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Genetic Characterization of Plasmid-Associated Benzalkonium Chloride Resistance Determinants in a Listeria monocytogenes Strain from the 1998-1999 Outbreak

(2010) D. Elhanafi et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics

(2010) Renato H. Orsi et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Re-evaluation, Optimization, and Multilaboratory Validation of the PulseNet-Standardized Pulsed-Field Gel Electrophoresis Protocol for Listeria monocytogenes

(2009) Jessica L. Halpin et al.   Foodborne Pathogens and Disease

Typing ofListeria monocytogenesstrains isolated in Italy byinlA gene characterization and evaluation of a new cost-effective approach to antisera selection for serotyping

(2009) M. Tamburro et al.   JOURNAL OF APPLIED MICROBIOLOGY

Rapid Identification and Typing of Listeria Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

(2008) S. B. Barbuddhe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A New Perspective on Listeria monocytogenes Evolution

(2008) Marie Ragon et al.   PLoS Pathogens