whole-genome sequencing
Research Article | Host-Microbe BiologyGenomic Epidemiology and Evolution of Escherichia coli in Wild Animals in MexicoEscherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals.
Research Article | Molecular Biology and PhysiologyAnalysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome SequencingFew studies have focused on the reasons for the low cure rate of multidrug-resistant tuberculosis in China and within-host evolution during treatment, which is of great significance for improving clinical treatment regimens. Acquired resistance events were common during the ineffective treatment, among which resistance to amikacin and high-level moxifloxacin were the most common.
Observation | Ecological and Evolutionary ScienceNovel Effective Bacillus cereus Group Species “Bacillus clarus” Is Represented by Antibiotic-Producing Strain ATCC 21929 Isolated from SoilThe B. cereus group comprises numerous closely related lineages with various degrees of pathogenic potential and industrial relevance. Species-level taxonomic classification of B. cereus group strains is important for risk evaluation and communication but remains challenging. Biochemical and...
Research Article | Clinical Science and EpidemiologyPhylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing...
Research Article | Clinical Science and EpidemiologyHorizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in TanzaniaHorizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed...
Research Article | Clinical Science and EpidemiologyIMP-38-Producing High-Risk Sequence Type 307 Klebsiella pneumoniae Strains from a Neonatal Unit in ChinaWe described the genome and resistome characterization of a carbapenem-resistant Klebsiella pneumoniae ST307 strain carrying blaIMP-38 in China. This report highlights that the high-risk ST307 clone continues to acquire different antimicrobial resistance genes, posing significant challenges to clinical practice, and should be closely monitored....
Research Article | Host-Microbe BiologyAn Avirulence Gene Cluster in the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Identified through Genetic Mapping and Whole-Genome Sequencing of a Sexual PopulationStripe rust is a destructive disease of wheat worldwide. Growing resistant cultivars is the most effective, easy-to-use, economical, and environmentally friendly strategy for the control of the disease. However, P. striiformis f. sp. tritici can produce new virulent races that may circumvent race-specific resistance. Therefore, understanding the genetic basis...
Research Article | Host-Microbe BiologyCombining Whole-Genome Sequencing and Multimodel Phenotyping To Identify Genetic Predictors of Salmonella VirulenceSalmonella species are bacteria that are a major source of foodborne disease through contamination of a diversity of foods, including meat, eggs, fruits, nuts, and vegetables. More than 2,600 different Salmonella enterica serovars have been identified, and only a few of them are associated with illness in humans. Despite the fact that they are genetically...
Research Article | Host-Microbe BiologyInsights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. UniversitiesU.S. university students are at a higher risk of invasive meningococcal disease than the general population. The responsible pathogen, Neisseria meningitidis, can be carried asymptomatically in the oropharynx; the dynamics of meningococcal carriage and the genetic features that distinguish carriage versus disease states are not completely understood. Through our...
Observation | Host-Microbe BiologyNatural Transmission of Helicobacter saguini Causes Multigenerational Inflammatory Bowel Disease in C57/129 IL-10−/− MiceWhile family history is a significant risk factor for developing inflammatory bowel disease (IBD), it is unclear whether the microbiome from parents is a transmissible influence on disease in their offspring. Furthermore, it is unknown whether IBD-associated microbes undergo genomic adaptations during multigenerational transmission and chronic colonization in their hosts. Herein, we show that a single bacterial species,...