A5059186047- Antibiotic Resistance in Bacteria
- Escherichia coli research studies
- Genomics and Phylogenetic Studies
- Vibrio bacteria research studies
- Bacterial Identification and Susceptibility Testing
- Enterobacteriaceae and Cronobacter Research
- Bacteriophages and microbial interactions
- Salmonella and Campylobacter epidemiology
- Bacterial Genetics and Biotechnology
- Antibiotic Use and Resistance
- Bacterial biofilms and quorum sensing
- Plant Pathogenic Bacteria Studies
- Clostridium difficile and Clostridium perfringens research
- Gut microbiota and health
- SARS-CoV-2 detection and testing
- Aquaculture disease management and microbiota
- Microbial Metabolic Engineering and Bioproduction
- SARS-CoV-2 and COVID-19 Research
- Biofuel production and bioconversion
- Evolution and Genetic Dynamics
- Identification and Quantification in Food
- COVID-19 diagnosis using AI
- Microbial Community Ecology and Physiology
- Pharmaceutical and Antibiotic Environmental Impacts
- Pneumonia and Respiratory Infections
Wellcome Sanger Institute
2019-2024
European Bioinformatics Institute
2019-2023
The University of Sydney
2015-2023
Westmead Hospital
2023
Wellcome Trust
2023
Leiden University Medical Center
2022
Brigham and Women's Hospital
2022
Universidade Federal do Rio de Janeiro
2022
National Institute for Public Health and the Environment
2022
Taronga Conservation Society Australia
2022
The open sharing of genomic data provides an incredibly rich resource for the study bacterial evolution and function even anthropogenic activities such as widespread use antimicrobials. However, these consist genomes assembled with different tools levels quality checking, large volumes completely unprocessed raw sequence data. In both cases, considerable computational effort is required before biological questions can be addressed. Here, we characterised 661,405 retrieved from European...
Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with (MSM). Multidrug resistance in S. common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant was reported the United Kingdom. Here, we aimed to identify genetic basis, evolutionary history, international...
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...
ABSTRACT The tet39 tetracycline resistance determinant and the macrolide genes msrE mphE were found in an 18.2-kb plasmid, pS30-1, recovered from a global clone 2 (GC2) Acinetobacter baumannii isolate Singapore, that conferred to erythromycin. pS30-1 also contains mobA mobC encoding MOB Q family proteins, but attempts mobilize utilizing coresident conjugative repAci6 plasmid unsuccessful. Eight p dif sites, consisting of inversely oriented binding sites for XerC XerD recombinases separated...
Escherichia coli is a highly diverse organism that includes range of commensal and pathogenic variants found across niches worldwide. In addition to causing severe intestinal extraintestinal disease, E. considered priority pathogen due high levels observed drug resistance. The diversity in the population driven by genome plasticity very large gene pool. All these have made one most well-studied organisms, as well commonly used laboratory strain. Today, there are thousands sequenced genomes...
To investigate the context of ribosomal RNA methyltransferase gene armA in carbapenem-resistant global clone 2 (GC2) Acinetobacter baumannii isolates from Singapore.Antibiotic resistance was determined using disc diffusion; PCR used to identify genes. Whole genome sequences were and contigs assembled ordered PCR. Resistance regions unsequenced mapped.Fifteen GC2 A. isolated at Singapore General Hospital over period 2004-11 found carry resistant carbapenems, third-generation cephalosporins,...
ABSTRACT A320, isolated in the Netherlands 1982 and also known as RUH134, is earliest available multiply antibiotic-resistant (MAR) Acinetobacter baumannii isolate belonging to global clone 2 (GC2) reference strain for this clone. The draft genome sequence of A320 was used investigate original location configuration IS 26 -bounded AbGRI2 resistance island found current GC2 isolates. PCR mapping sequencing were order contigs composing islands. contains two islands, AbGRI2-0a AbGRI2-0b, 7.8 kb...
Clear similarities between antibiotic resistance islands in the chromosomes of extensively antibiotic-resistant isolates from two dominant, globally distributed Acinetobacter baumannii clones, GC1 and GC2, suggest a common origin. A close relative likely progenitor both these regions was found R1215, conjugative IncM plasmid Serratia marcescens strain isolated prior to 1980. The 37.8-kb region R1215 lies within mucB gene includes aacC1, aadA1, aphA1b, bla TEM, catA1, sul1, tetA(A), genes...
Antibiotic resistant strains of Acinetobacter baumannii are responsible for a large and increasing burden nosocomial infections in Thailand other countries Southeast Asia. New approaches to their control treatment urgently needed we actively seeking biological agents that remove the polysaccharide capsules protect these pathogens from host's immune system. To examine phylogenetic relationships, distribution capsule chemotypes, acquired antibiotic resistance determinants, susceptibility...
Healthcare-associated infections (HCAIs) affect the most vulnerable people in society and are increasingly difficult to treat face of mounting antimicrobial resistance (AMR). Routine surveillance represents an effective way understanding circulation burden bacterial transmission hospital settings. Here, we used whole-genome sequencing (WGS) retrospectively analyse carbapenemase-producing Gram-negative bacteria from a single UK over 6 years (n=165). We found that vast majority isolates were...
Abstract Enterotoxigenic Escherichia coli (ETEC) is an enteric pathogen responsible for the majority of diarrheal cases worldwide. ETEC infections are estimated to cause 80,000 deaths annually, with highest rates burden, ca 75 million per year, amongst children under 5 years age in resource-poor countries. It also leading diarrhoea travellers. Previous large-scale sequencing studies have found seven major lineages currently circulation We used PacBio long-read combined Illumina create...
We examined 185 complete, publicly available FII-33 plasmid sequences, characterizing their backbone and various insertions. The variable characteristic insertions facilitated evolutionary reconstruction for this group, beginning with the acquisition of a primary resistance region (PRR) over 10 years ago. plasmids have evolved by acquiring additional genes in PRR via translocatable elements forming cointegrates other types. In all cases, IS26 is suspected to mediated cointegration. Plasmid...
Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success different AMR during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella (pKSR100 and pAPR100) that circulated in same transmission network had starkly contrasting epidemiological outcomes to identify plasmid features may contributed...
To understand the acquisition of resistance genes by a non-GC1, non-GC2 Acinetobacter baumannii strain responsible for 4 year outbreak at Sydney hospital.Representative isolates were screened to antibiotics. Three subjected WGS using Illumina HiSeq. One genome was completed with MinION long reads. Resistance regions compared known sequences bioinformatics.Isolates resistant third-generation cephalosporins, gentamicin and tobramycin, sulfamethoxazole erythromycin. Sequenced ST49 (Institut...
ABSTRACT The open sharing of genomic data provides an incredibly rich resource for the study bacterial evolution and function, even anthropogenic activities such as widespread use antimicrobials. Whilst these archives are in data, considerable processing is required before biological questions can be addressed. Here, we assembled characterised 661,405 genomes using a uniform standardised approach, retrieved from European Nucleotide Archive (ENA) November 2018. A searchable COBS index has...
The plasmid pCD-METRO confers metronidazole resistance in Clostridioides difficile. We showed high sequence similarity among plasmids from different isolates and identified associated metronidazole-resistant clinical veterinary reservoirs the Americas. recommend using PCR or genomic assays to detect C.
Genomic surveillance of SARS-CoV-2 has been essential to inform public health response outbreaks. The high incidence infection resulted in a smaller proportion cases undergoing whole genome sequencing due finite resources. We present framework for estimating the impact reduced depths genomic on resolution outbreaks, based clustering approach using pairwise genetic and temporal distances. apply simulated outbreak data show that outbreaks are detected less frequently when fewer subjected...
Here, this report presents two genomes of Vibrio cholerae O1 serotype Ogawa, recovered from cholera cases in Australia linked to travel Pakistan 2022. Their multidrug-resistant genotype represents the current activity within seventh pandemic. One genome sequences was assembled using both short- and long-read sequences.
A rehydratable dry-film plating method for Escherichia coli, the Petrifilm E. coli/Coliform (EC) Count Plate in foods, has been compared with AOAC INTERNATIONAL most probable number (MPN) method. Eleven laboratories participated collaborative study. Three coli levels 8 samples each of frozen raw ground turkey, beef, and cooked fish were tested duplicate. Mean log counts plate procedure not significantly different from those MPN inoculated low or high inocula levels, turkey at medium level,...
Transposons are mobile genetic elements (MGE) that can carry additional cargo nonessential for their own transposition. This include antibiotic or heavy metal resistance genes those increasing metabolic plasticity. In addition to transposing across between the chromosome and other replicons in a single cell, they transfer bacteria as passengers on conjugative plasmids capable of intercellular transfer. be grouped mechanisms movement by lengths bounding inverted repeats target site...