A5056617738- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Bacterial biofilms and quorum sensing
- Bacterial Genetics and Biotechnology
- Microbial infections and disease research
- Vibrio bacteria research studies
- Bacterial Identification and Susceptibility Testing
- Gut microbiota and health
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Microbial Community Ecology and Physiology
- Streptococcal Infections and Treatments
- Mollusks and Parasites Studies
- Evolution and Genetic Dynamics
- Neonatal and Maternal Infections
- Misinformation and Its Impacts
- Biosimilars and Bioanalytical Methods
- Machine Learning in Bioinformatics
- Identification and Quantification in Food
- Respiratory viral infections research
- Biosensors and Analytical Detection
- Monoclonal and Polyclonal Antibodies Research
- Neonatal Health and Biochemistry
- Viral gastroenteritis research and epidemiology
Wellcome Sanger Institute
2020-2025
European Bioinformatics Institute
2020-2023
Wellcome Trust
2022
University of Liverpool
2019-2020
Center for Research and Advanced Studies of the National Polytechnic Institute
2014-2017
Instituto Politécnico Nacional
2017
Abstract Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing characterise Pseudomonas aeruginosa MDR clinical isolates from hospital in Thailand. Using long-read sequence data obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays antibiotic genes located discrete, complex and dynamic regions, revealing evidence extensive duplication recombination events. A comprehensive pangenomic phylogenomic...
Naturally occurring plasmids come in different sizes. The smallest are less than a kilobase of DNA, while the largest can be over three orders magnitude larger. Historically, research has tended to focus on smaller that usually easier isolate, manipulate and sequence, but with improved genome assemblies made possible by long-read sequencing, there is increased appreciation very large plasmids—known as megaplasmids—are widespread, diverse, complex, often encode key traits biology their host...
The genus Serratia has been studied for over a century and includes clinically-important diverse environmental members. Despite this, there is paucity of genomic information across the robust whole genome-based phylogenetic framework lacking. Here, we have assembled analysed representative set 664 genomes from genus, including 215 historic isolates originally used in defining genus. Phylogenomic analysis reveals clearly-defined population structure which displays deep divisions aligns with...
Mobile genetic elements (MGEs) mediate the shuffling of genes among organisms. They contribute to spread virulence and antibiotic resistance (AMR) in human pathogens, such as particularly problematic group ESKAPE pathogens. Here, we performed first systematic analysis MGEs, including plasmids, prophages, integrative conjugative/mobilizable (ICEs/IMEs), across all We found that different MGE types are asymmetrically distributed these most horizontal gene transfer (HGT) events restricted by...
Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from patients 2018. Here, to characterize circulating genotypes, we analysed 260 sampled between 2018 and 2019. Eighty-four percent of V. were serogroup O1 belonging seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% non-toxigenic, divergent non-7PET lineages. Treatment severe with macrolides 2016 2019 coincided emergence...
Background Bacteriophage therapy is becoming part of mainstream Western medicine since antibiotics clinical use tend to fail. It involves applying lytic bacteriophages that self-replicate and induce cell lysis, thus killing their hosts. Nevertheless, bacterial promotes the selection resistant clones which sometimes may exhibit a decrease in virulence or antibiotic resistance. Methods In this work, we studied Pseudomonas aeruginosa phage φDCL-PA6 its variant φDCL-PA6α. Additionally,...
Phages and plasmids are discrete mobile genetic elements (MGEs) with critical roles in gene dissemination across bacteria but limited scope for exchanging DNA between them. By investigating recent gene-sharing events, Pfeifer Rocha describe how the hybrid phage-plasmids (P-Ps) promote flow MGE types evolve into new ones.
Nus-dependent Mexican Escherichia coli phages (mEp) were previously isolated from clinical samples of human feces. Approximately 50% corresponded to non-lambdoid temperate integrating a single immunity group, namely I (mEpimmI), and these as prevalent the lambdoid identified in such collection. In this work, we present structural functional characterization six representative mEpimmI (mEp010, mEp013, mEp021, mEp044, mEp515, mEp554). addition, searched for homologous prophages GenBank...
Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexible tails, bears genomes whose architecture replication mechanism, but not their nucleotide sequences, are like those coliphage Mu. By comparing genomic sequences this group P. phages one could draw conclusions about ontogeny evolution. Two newly isolated Mu-like described sequenced...
Phages are generally described as species specific or even strain specific, implying an inherent limitation for some to be maintained and spread in diverse bacterial communities. Moreover, phage isolation host range determination rarely consider the ecological context, likely biasing our notion on specificity. Here we isolated characterized a novel group of six promiscuous phages, named Atoyac, existing rivers sewage by using collection over 600 bacteria retrieved from same environments...
Quorum sensing (QS) in Pseudomonas aeruginosa coordinates the expression of virulence factors, some which are used as public goods. Since their production is a cooperative behavior, it susceptible to social cheating non-cooperative QS deficient mutants use resources without investing production. Nevertheless, functional systems abundant; hence, mechanisms regulating amount should exist. Evidence that demonstrates tight relationship between and susceptibility bacteria against attack lytic...
Abstract Plasmids are now the primary vectors of antimicrobial resistance, but our understanding how human industrialisation antibiotics influenced this is limited by a paucity data predating antibiotic era (PAE). By investigating plasmids from clinically relevant bacteria isolated between 1917 and 1954 comparing them to modern plasmids, we captured over 100 years evolution. We show that while all PAE were devoid resistance genes most never acquired them, small minority evolved drive global...
Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component microbiomes, as supported by virome surveys examples high genomic mosaicism. However, recent evidence suggests human gut is remarkably stable compared to other environments. Here we investigate origin, evolution, epidemiology crAssphage, a widespread virus. Through global collaboratory, obtained DNA sequences crAssphage from over one-third...
Previously, a collection of virulent phages infecting Pseudomonas aeruginosa was isolated from open water reservoirs and residual waters. Here, we described the comparative genomics set five related collection, physical structure genome, structural proteomics virion, transcriptional program archetypal phage PaMx41. The genomes were closely associated with each other those two P. phages, 119X PaP2, which previously filed in databases. Overall, approximately 43 kb, harboring 53 conserved...
If there is something we have learned from the antibiotic era, it that indiscriminate use of a therapeutic agent without clear understanding its long-term evolutionary impact can enormous health repercussions. This knowledge particularly relevant when agents are remarkably adaptable and diverse biological entities capable plethora interactions, most which remain largely unexplored. Although phage therapy (PT) undoubtedly holds potential to save lives, current efficacy in case studies recalls...
In this study, we describe seven vegetative phage genomes homologous to the historic B3 that infect Pseudomonas aeruginosa Like other groups, B3-like group contains conserved (core) and variable (accessory) open reading frames (ORFs) grouped at fixed regions in their genomes; however, either case, many ORFs remain without assigned functions. We constructed lysogens of phages strain Ps33 P. aeruginosa, a novel clinical isolate, assayed exclusion phenotype against variety temperate virulent...
Abstract Streptococcus agalactiae (or Group B , GBS) is a leading cause of neonatal sepsis and meningitis globally. To sense respond to variations in its environment, GBS possesses multiple two-component regulatory systems (TCSs) such as LytSR. Here, we aimed investigate the role LytSR pathogenicity. We generated an isogenic lytS knockout mutant clinical isolate used combination phenotypic vitro assays vivo murine models contribution colonisation invasive properties GBS. Deletion gene...
ABSTRACT Streptococcus agalactiae (or group B , GBS) is a leading cause of neonatal sepsis and meningitis globally. To sense respond to variations in its environment, GBS possesses multiple two-component regulatory systems (TCSs), such as LytSR. Here, we aimed investigate the role LytSR pathogenicity. We generated an isogenic lytS knockout mutant clinical isolate used combination phenotypic vitro assays vivo murine models contribution colonization invasive properties GBS. Deletion gene...