Highlights from infectious disease genomics
Genome Medicine Collection
- RESEARCH
Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom
Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare...Genome Medicine 2017 9:70Published on: 25 July 2017 - RESEARCH
High-dimensional assessment of B-cell responses to quadrivalent meningococcal conjugate and plain polysaccharide vaccine
Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A...Genome Medicine 2017 9:11Published on: 30 January 2017 - RESEARCH
The variability and reproducibility of whole genome sequencing technology for detecting resistance to anti-tuberculous drugs
The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resis...Genome Medicine 2016 8:132Published on: 22 December 2016 - RESEARCH
Next-generation sequencing diagnostics of bacteremia in septic patients
Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitiv...Genome Medicine 2016 8:73Published on: 1 July 2016 - RESEARCH
B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation
A diverse B-cell repertoire is essential for recognition and response to infectious and vaccine antigens. High-throughput sequencing of B-cell receptor (BCR) genes can now be used to study the B-cell repertoir...Genome Medicine 2016 8:68Published on: 16 June 2016 - RESEARCH
Statistical inference of a convergent antibody repertoire response to influenza vaccine
Vaccines dramatically affect an individual’s adaptive immune system and thus provide an excellent means to study human immunity. Upon vaccination, the B cells that express antibodies (Abs) that happen to bind ...Genome Medicine 2016 8:60Published on: 3 June 2016 - RESEARCH
Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection
Recurrent Clostridium difficile infection (CDI) remains problematic, with up to 30 % of individuals diagnosed with primary CDI experiencing at least one episode of recurrence. The success of microbial-based thera...Genome Medicine 2016 8:47Published on: 27 April 2016 - REVIEW
Microbiome mediation of infections in the cancer setting
Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic bar...Genome Medicine 2016 8:40Published on: 18 April 2016 - SOFTWARE
SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads
SpoTyping is a fast and accurate program for in silico spoligotyping of Mycobacterium tuberculosis isolates from next-generation sequencing reads. This novel method achieves high accuracy...Genome Medicine 2016 8:19Published on: 17 February 2016 - RESEARCH
Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected...Genome Medicine 2016 8:18Published on: 13 February 2016 - RESEARCH
Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network
Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmiss...Genome Medicine 2016 8:4Published on: 12 January 2016 - RESEARCH
Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain
Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against...Genome Medicine 2015 7:124Published on: 25 November 2015 - METHOD
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, ...Genome Medicine 2015 7:99Published on: 29 September 2015 - METHOD
Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences
Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequenci...Genome Medicine 2015 7:51Published on: 27 May 2015 - RESEARCH
Transcriptional profiling defines dynamics of parasite tissue sequestration during malaria infection
During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and orga...Genome Medicine 2015 7:19Published on: 27 February 2015 - RESEARCH
Plasmodium falciparumgene expression measured directly from tissue during human infection
During the latter half of the natural 48-h intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium of tissues, away from the spleen and inaccessible to perip...Genome Medicine 2014 6:110Published on: 29 November 2014 - REVIEW
Virus-host interactomics: new insights and opportunities for antiviral drug discovery
The current therapeutic arsenal against viral infections remains limited, with often poor efficacy and incomplete coverage, and appears inadequate to face the emergence of drug resistance. Our understanding of...Genome Medicine 2014 6:115Published on: 29 November 2014 - METHOD
Systematic identification and quantification of phase variation in commensal and pathogenic Escherichia coli
Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting ge...Genome Medicine 2014 6:112Published on: 28 November 2014 - RESEARCH
Next generation sequencing analysis of nine Corynebacterium ulcerans isolates reveals zoonotic transmission and a novel putative diphtheria toxin-encoding pathogenicity island
Toxigenic Corynebacterium ulcerans can cause a diphtheria-like illness in humans and have been found in domestic animals, which were suspected to serve as reservoirs for a zoonotic transmission. Additionally, tox...Genome Medicine 2014 6:113Published on: 28 November 2014 - RESEARCH
An integrated transcriptome and expressed variant analysis of sepsis survival and death
Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor o...Genome Medicine 2014 6:111Published on: 26 November 2014 - RESEARCH
Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments
Dendritic cells localize throughout the body, where they can sense and capture invading pathogens to induce protective immunity. Hence, harnessing the biology of tissue-resident dendritic cells is fundamental ...Genome Medicine 2014 6:98Published on: 25 November 2014 - SOFTWARE
SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significa...Genome Medicine 2014 6:90Published on: 20 November 2014 - METHOD
A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens
Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little ...Genome Medicine 2014 6:101Published on: 15 November 2014
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