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Applied and Environmental Microbiology
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whole-genome sequencing

  • Open Access
    Genomic Insights into Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> <em>spa</em> Type t899 Isolates Belonging to Different Sequence Types
    Evolutionary and Genomic Microbiology
    Genomic Insights into Methicillin-Resistant Staphylococcus aureus spa Type t899 Isolates Belonging to Different Sequence Types

    This study showed the genetic diversity and population structure of S. aureus presenting the same spa type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using spa typing only.

    Henok Ayalew Tegegne, Ivana Koláčková, Martina Florianová, Pierre Wattiau, Tereza Gelbíčová, Cécile Boland, Jean-Yves Madec, Marisa Haenni, Renáta Karpíšková
  • Open Access
    Using Land Runoff To Survey the Distribution and Genetic Diversity of <span class="named-content genus-species" id="named-content-1">Burkholderia pseudomallei</span> Strains in Vientiane, Laos
    Public and Environmental Health Microbiology
    Using Land Runoff To Survey the Distribution and Genetic Diversity of Burkholderia pseudomallei Strains in Vientiane, Laos

    The environmental bacterium B. pseudomallei is the etiological agent of melioidosis, a tropical disease with one model estimating a global annual incidence of 165,000 cases and 89,000 deaths. In the Lao People’s Democratic Republic (Laos), the environmental distribution and population structure of B....

    Audrey Rachlin, Manophab Luangraj, Mirjam Kaestli, Sayaphet Rattanavong, Phonelavanh Phoumin, Jessica R. Webb, Mark Mayo, Bart J. Currie, David A. B. Dance
  • Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination
    Evolutionary and Genomic Microbiology | Spotlight
    Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination

    Identifying selection from SNP data obtained from whole-genome sequencing studies is challenging. Some current measures used to identify and quantify selection acting on genomes rely on fixed differences; thus, these are inappropriate for SNP data where variants are not fixed. With the increase in whole-genome sequencing studies, it is important to consider SNP data in the context of evolutionary processes. How SNPs are counted and...

    Sara L. Loo, Anna Ong, Wunna Kyaw, Loïc M. Thibaut, Ruiting Lan, Mark M. Tanaka
  • High-Level Antibiotic Tolerance of a Clinically Isolated <span class="named-content genus-species" id="named-content-1">Enterococcus faecalis</span> Strain
    Public and Environmental Health Microbiology
    High-Level Antibiotic Tolerance of a Clinically Isolated Enterococcus faecalis Strain

    Enterococcus faecalis represents a major group of pathogens causing nosocomial infections that are resistant to multiple classes of antibiotics. An important challenge associated with E. faecalis infection is the emergence of multidrug-tolerant strains, which have normal MICs but do not respond to...

    Huan Gu, Sweta Roy, Xiaohui Zheng, Tian Gao, Huilin Ma, Zafer Soultan, Christopher Fortner, Shikha Nangia, Dacheng Ren
  • F4- and F18-Positive Enterotoxigenic <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Isolates from Diarrhea of Postweaning Pigs: Genomic Characterization
    Genetics and Molecular Biology
    F4- and F18-Positive Enterotoxigenic Escherichia coli Isolates from Diarrhea of Postweaning Pigs: Genomic Characterization

    Diarrhea in the postweaning period due to enterotoxigenic E. coli (ETEC) is an economically relevant disease in pig production worldwide. In Denmark, prevention is mainly achieved by zinc oxide administration (to be discontinued by 2022). In addition, a breeding program has been implemented that aims to reduce the prevalence of this illness. Treatment with...

    Vanesa García, Michela Gambino, Karl Pedersen, Svend Haugegaard, John Elmerdahl Olsen, Ana Herrero-Fresno
  • Reply to Li et al., “GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect <em>Salmonella</em> Serotype Prediction Using SeqSero2”
    Letter to the Editor
    Reply to Li et al., “GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2”
    Laura Uelze, Maria Borowiak, Carlus Deneke, István Szabó, Jennie Fischer, Simon H. Tausch, Burkhard Malorny
  • Prevalence of Cefotaxime-Resistant <span class="named-content genus-species" id="named-content-1">Escherichia coli</span> Isolates from Healthy Cattle and Sheep in Northern Spain: Phenotypic and Genome-Based Characterization of Antimicrobial Susceptibility
    Public and Environmental Health Microbiology
    Prevalence of Cefotaxime-Resistant Escherichia coli Isolates from Healthy Cattle and Sheep in Northern Spain: Phenotypic and Genome-Based Characterization of Antimicrobial Susceptibility

    Extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)-producing E. coli isolates have emerged in recent years as some of the fastest spreading antimicrobial resistance determinants in humans and food-producing animals, becoming a concern for animal and public health. This study provided insight into the prevalence of cefotaxime-resistant...

    Maitane Tello, Medelin Ocejo, Beatriz Oporto, Ana Hurtado
  • Open Access
    In-Depth Longitudinal Study of <span class="named-content genus-species" id="named-content-1">Listeria monocytogenes</span> ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing
    Food Microbiology
    In-Depth Longitudinal Study of Listeria monocytogenes ST9 Isolates from the Meat Processing Industry: Resolving Diversity and Transmission Patterns Using Whole-Genome Sequencing

    Listeria monocytogenes is a deadly foodborne pathogen that is widespread in the environment, and certain types can be established in food factories. The sequence type ST9 dominates in meat processing environments, and this work was undertaken to obtain data needed for the tracking of this subtype. By using whole-genome sequencing (WGS), we revealed the presence of...

    Annette Fagerlund, Solveig Langsrud, Trond Møretrø
  • Local and Transboundary Transmissions of Methicillin-Resistant <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Sequence Type 398 through Pig Trading
    Public and Environmental Health Microbiology
    Local and Transboundary Transmissions of Methicillin-Resistant Staphylococcus aureus Sequence Type 398 through Pig Trading

    Over the past decade, livestock-associated methicillin-resistant Staphylococcus aureus sequence type 398 (LA-MRSA ST398) has spread among pig holdings throughout Europe, in parallel with the increased incidence of infections among humans, especially in intensive pig farming regions. Despite the growing prevalence of LA-MRSA ST398 in Italian pig farms, the transmission...

    Mattia Pirolo, Raphael N. Sieber, Arshnee Moodley, Daniela Visaggio, Irene Artuso, Angela Gioffrè, Francesco Casalinuovo, Giovanna Spatari, Luca Guardabassi, Marc Stegger, Paolo Visca
  • Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the <span class="named-content genus-species" id="named-content-1">Stenotrophomonas maltophilia</span> Complex
    Public and Environmental Health Microbiology
    Comparative Whole-Genome Phylogeny of Animal, Environmental, and Human Strains Confirms the Genogroup Organization and Diversity of the Stenotrophomonas maltophilia Complex

    Given its naturally large antimicrobial resistance profile, the Stenotrophomonas maltophilia complex (Smc) is a set of emerging pathogens of immunosuppressed and cystic fibrosis patients. As it is group of environmental microorganisms, this adaptation to humans is an opportunity to understand the genetic and metabolic selective mechanisms involved in this process. The...

    Mélanie Mercier-Darty, Guilhem Royer, Brigitte Lamy, Chadly Charron, Olivier Lemenand, Camille Gomart, Frédéric Fourreau, Jean-Yves Madec, Estelle Jumas-Bilak, Jean-Winoc Decousser
    and the Resapath Network, the ColBVH Network

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