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A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission.
Genome Med
January 2025
Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
Background: Mixed infection with multiple strains of the same pathogen in a single host can present clinical and analytical challenges. Whole genome sequence (WGS) data can identify signals of multiple strains in samples, though the precision of previous methods can be improved. Here, we present MixInfect2, a new tool to accurately detect mixed samples from Mycobacterium tuberculosis short-read WGS data.
View Article and Find Full Text PDFUsing machine learning to forecast peak health care service demand in real-time during the 2022-23 winter season: A pilot in England, UK.
PLoS One
January 2025
Real-time Syndromic Surveillance Team, Field Services, Health Protection Operations, UK Health Security Agency, Birmingham, United Kingdom.
During winter months, there is increased pressure on health care systems in temperature climates due to seasonal increases in respiratory illnesses. Providing real-time short-term forecasts of the demand for health care services helps managers plan their services. During the Winter of 2022-23 we piloted a new forecasting pipeline, using existing surveillance indicators which are sensitive to increases in respiratory syncytial virus (RSV).
View Article and Find Full Text PDFEvaluation of nationwide analysis surveillance for methicillin-resistant within Genomic Medicine Sweden.
Microb Genom
January 2025
Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, rebro University, rebro, Sweden.
National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach. A national methicillin-resistant (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS.
View Article and Find Full Text PDFFecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.
Int J Mol Sci
January 2025
Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University, 28040 Madrid, Spain.
Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC.
View Article and Find Full Text PDFIntegration of 168,000 samples reveals global patterns of the human gut microbiome.
Cell
January 2025
Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA. Electronic address:
The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline.
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