A5009040466- Reproductive tract infections research
- Bacterial Infections and Vaccines
- Syphilis Diagnosis and Treatment
- Legionella and Acanthamoeba research
- Mycobacterium research and diagnosis
- Tuberculosis Research and Epidemiology
- Vibrio bacteria research studies
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Evolution and Genetic Dynamics
- Salmonella and Campylobacter epidemiology
- Streptococcal Infections and Treatments
- Water Treatment and Disinfection
- Parasitic Infections and Diagnostics
- Antifungal resistance and susceptibility
- HIV, TB, and STIs Epidemiology
- Microbial infections and disease research
- Biosensors and Analytical Detection
- Gut microbiota and health
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Infectious Diseases and Tuberculosis
- Legume Nitrogen Fixing Symbiosis
- Antimicrobial Resistance in Staphylococcus
Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana
2013-2024
Universitat de València
2013-2024
Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública
2013-2024
Instituto de Salud Carlos III
2023-2024
Institute for Integrative Systems Biology
2023-2024
University of Oxford
2019-2022
Wellcome Sanger Institute
2016-2021
University of Zurich
2021
Open Data Institute
2019-2020
National Institute for Health Research
2020
Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist analyse predict a bacterial isolate from sequencing data. Here we present new tool, ARIBA, that identifies AMR-associated genes single nucleotide polymorphisms directly short reads, generates detailed customizable output. The accuracy advantages ARIBA over other are demonstrated on three datasets Gram-positive Gram-negative bacteria, with outperforming existing methods.
Gonorrhoea and MDR Neisseria gonorrhoeae remain public health concerns globally. Enhanced, quality-assured, gonococcal antimicrobial resistance (AMR) surveillance is essential worldwide. The WHO global Gonococcal Antimicrobial Surveillance Programme (GASP) was relaunched in 2009. We describe the phenotypic, genetic reference genome characteristics of 2016 strains intended for quality assurance GASP, other GASPs, diagnostics research
Traditional methods for molecular epidemiology of Neisseria gonorrhoeae are suboptimal. Whole-genome sequencing (WGS) offers ideal resolution to describe population dynamics and predict infer transmission antimicrobial resistance, can enhance infection control through linkage with epidemiological data. We used WGS, in conjunction linked phenotypic data, the gonococcal 20 European countries. aimed detail changes resistance levels (and reasons these changes) strain distribution (with a focus...
Human tuberculosis (TB) is caused by members of the Mycobacterium complex (MTBC). The MTBC comprises several human-adapted lineages known as M. sensu stricto, well two (L5 and L6) traditionally referred to africanum. Strains L5 L6 are largely limited West Africa for reasons unknown, little their genomic diversity, phylogeography evolution. Here, we analysed genomes 350 320 strains, isolated from patients 21 African countries, plus 5 related that had not been classified into any lineages. Our...
Abstract Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist analyse predict a bacterial isolate from sequencing data. Here we present new tool, ARIBA, that identifies AMR-associated genes single nucleotide polymorphisms directly short reads, generates detailed customisable output. The accuracy advantages ARIBA over other are demonstrated on three datasets Gram-positive Gram-negative bacteria, with outperforming...
Abstract As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access genomic public health on global scale. Here we present Pathogenwatch scheme Salmonella enterica serovar Typhi ( S . Typhi), web application enabling rapid identification markers antimicrobial...
Abstract Background Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant at least one of the two last-line antibiotics used in empiric therapy gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be identify new AMR clones transmission networks inform development point-of-care tests for antimicrobial susceptibility, novel antimicrobials vaccines. Community-driven tools that...
Multidrug-resistant Neisseria gonorrhoeae strains are prevalent, threatening gonorrhoea treatment globally, and understanding of emergence, evolution, spread antimicrobial resistance (AMR) in gonococci remains limited. We describe the genomic evolution their AMR, related to introduction therapies, examining isolates from 1928 (preantibiotic era) 2013 Denmark. This is, our knowledge, oldest gonococcal collection globally.Lyophilised were revived examined using Etest (18 antimicrobials)...
BackgroundGenomic surveillance using quality-assured whole-genome sequencing (WGS) together with epidemiological and antimicrobial resistance (AMR) data is essential to characterise the circulating Neisseria gonorrhoeae lineages their association patient groups (defined by demographic factors). In 2013, European gonococcal population was characterised genomically for first time. We describe in 2018 identify emerging or vanishing associated AMR characteristics of patients, elucidate recent...
BackgroundRegular quality-assured whole-genome sequencing linked to antimicrobial resistance (AMR) and patient metadata is imperative elucidate the shifting gonorrhoea epidemiology, both nationally internationally. We aimed examine gonococcal population in European Economic Area (EEA) 2020, emerging disappearing lineages associated with AMR metadata, compare 2013 2018 data, explain changes epidemiology.MethodsIn this retrospective genomic surveillance study, we analysed consecutive isolates...
Emergence and global success of tuberculosis involve core pathogenesis functions under selection in epidemiological settings.
Abstract Neisseria gonorrhoeae is an urgent public health threat due to rapidly increasing incidence and antibiotic resistance. In contrast with the trend of resistance, clinical isolates that have reverted susceptibility regularly appear, prompting questions about which pressures compete antibiotics shape gonococcal evolution. Here, we used genome-wide association identify loss-of-function (LOF) mutations in efflux pump mtrCDE operon as a mechanism increased demonstrate these are...
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, support identification investigation outbreaks nearly real-time. Whole-genome sequencing ideal for emergence dissemination determinants, predicting AMR, the gonococcal population spread human population. The novel, rapid revolutionary long-read sequencer MinION a small hand-held device...
Abstract The emergence of resistance to azithromycin complicates treatment Neisseria gonorrhoeae , the etiologic agent gonorrhea. Substantial remains unexplained after accounting for known mutations. Bacterial genome-wide association studies (GWAS) can identify novel genes but must control genetic confounders while maintaining power. Here, we show that compared single-locus GWAS, conducting GWAS conditioned on mutations reduces number false positives and identifies a G70D mutation in RplD...
Abstract Objectives Novel antimicrobials for treatment of gonorrhoea are imperative. The first-in-class spiropyrimidinetrione zoliflodacin is promising and currently in an international Phase 3 randomized controlled clinical trial (RCT) uncomplicated gonorrhoea. We evaluated the vitro activity genetic conservation target (GyrB) other potential resistance determinants among 1209 consecutive Neisseria gonorrhoeae isolates obtained from 25 EU/European Economic Area (EEA) countries 2018 compared...
MDR and XDR Neisseria gonorrhoeae strains remain major public health concerns internationally, quality-assured global gonococcal antimicrobial resistance (AMR) surveillance is imperative. The WHO Gonococcal Antimicrobial Surveillance Programme (GASP) Enhanced GASP (EGASP), including metadata WGS, are expanding internationally. We present the phenotypic, genetic reference genome characteristics of 2024 (n = 15) for quality assurance worldwide. All superseded 14) were identically characterized.
Legionella pneumophila is an environmental bacterium and the causative agent of Legionnaires' disease. Previous genomic studies have shown that recombination accounts for a high proportion (>96%) diversity within several major disease-associated sequence types (STs) L. pneumophila. This suggests represents potentially important force shaping adaptation virulence. Despite this, little known about biological effects in pneumophila, particularly with regards to homologous (whereby genes are...
Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling the level covariation alleles across chromosome and model-free testing dependencies between pairs have been shown to successfully uncover patterns selection bacterial populations. Here we introduce a method, SpydrPick, whose computational efficiency enables analysis at scale pan-genomes many bacteria. SpydrPick...
Abstract Objectives Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global threat and novel treatment alternatives are imperative. Herein, susceptibility to the antimicrobial zoliflodacin, currently Phase 3 randomized controlled clinical trial for gonorrhoea treatment, was investigated by screening zoliflodacin GyrB target mutations publicly available gonococcal genomes and, where feasible, determination of associated MIC. Methods The European Nucleotide Archive queried using...
Abstract Mycobacterium africanum ( Maf) causes a substantial proportion of human tuberculosis in some countries West Africa, but little is known on this pathogen. We compared the genomes 253 Maf clinical isolates from Ghana, including N = 175 Lineage 5 (L5) and 78 6 (L6). found that genomic diversity L6 was higher than L5 despite smaller sample size. Regulatory proteins appeared to evolve neutrally under purifying selection L6. Even though over 90% T cell epitopes were conserved both...