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Browse normalized, publication-ready research with direct links to its evidence and source.
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Readable research linked to original sources
Browse normalized, publication-ready research with direct links to its evidence and source.
Loading articles data…
Readable research linked to original sources
Browse normalized, publication-ready research with direct links to its evidence and source.
16 articles
Newest firstDraft genome sequences of seven Bacillus strains isolated from Chelidonium majus seeds and six Pseudomonas strains isolated from Cannabis sativa roots and stems are reported. These genome sequences provide a foundation for functional and comparative genomic analyses to unravel potential traits associated with plant growth promotion and protection.
Open article record in new tab ↗BackgroundAntibiotic resistance is a global priority in healthcare. Leveraging thousands of whole-genome sequences, here we reveal the core resistance determinants of oral streptococci, focusing on assessing pattern variability and gene exchange across commensals and pathogens. MethodsGenomic information was obtained from the National Center for Biotechnology Information. Determinants of antibiotic resistance were…
ObjectiveWhole genome sequencing (WGS) is increasingly being used to guide infection prevention and control measures. However, the value of regional prospective WGS surveillance for vancomycin-resistant Enterococcus faecium (VREfm) remains uncertain. The objective of this study is to investigate the value of routine centralised multicentre WGS in regional outbreak detection and analysis of transmission of VREfm wi…
Wastewater surveillance at healthcare facilities for carbapenem-resistant (CR) bacteria harboring carbapenemase genes could result in earlier detection of circulating or emerging antimicrobial resistance (AR) threats. However, knowledge gaps exist regarding the CR bacterial community and carbapenemase genes present in facility wastewater and plumbing, which need to be addressed. Wastewater effluent samples from th…
Candida auris emerged in Chicago, IL, USA in 2016 and has since become endemic. We used whole genome sequencing (WGS) of 494 isolates, epidemiologic metadata, and patient transfer data to describe the transmission of C. auris among Chicago healthcare facilities between 2016 - 2021. 99% of isolates formed a single clade IV phylogenetic lineage, suggesting a single introduction. Isolates were grouped into genomic cl…
BackgroundThe rising antimicrobial resistance in Salmonella Typhi presents a critical public health challenge by limiting effective treatment options. This highlights the importance of sustained genomic surveillance of the high-risk lineages and antimicrobial resistance determinants of S. Typhi to inform and support the implementation of typhoid vaccination programs, especially in endemic regions. In this context,…
Open article record in new tab ↗BackgroundGene editing techniques have been identified as potential tools to combat antimicrobial resistance (AMR). Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and associated sequences (Cas) can be key players in this process. Their presence in bacteria can impact the success of this technology in combating AMR. The aim of this study is to investigate whether CRISPR loci are associated by mu…
Open article record in new tab ↗S. aureus is a common cause of skin and soft tissue infections (SSTIs) and has recently become the most common cause of bloodstream infections (BSIs), but whether the strains causing these two clinical syndromes overlap has not been studied adequately. USA300/500 (clonal complex [CC] 8-ST8) and USA100 (CC5-ST5) have dominated among methicillin-resistant S. aureus (MRSA) strains in the U.S. since the early 2000s. W…
Antimicrobial resistance is one of the greatest current threats to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing is typically conducted, requiring 48-72 h to identify appropriate antibiotics for treatment.…
Open article record in new tab ↗Structured summaryO_ST_ABSBackgroundC_ST_ABSWhole genome sequencing (WGS) for managing healthcare associated infections (HCAIs) has developed considerably through experiences with SARS-CoV-2. We interviewed various healthcare professionals (HCPs) with direct experience of using WGS in hospitals (within the COG-UK Hospital Onset COVID-19 Infection (HOCI) study) to explore its acceptability and future use. MethodAn…
Plasmids are infectious double stranded DNA molecules that are found within bacteria. Horizontal gene transfer promotes successful spread of different types of plasmids within or among bacteria species, making their detection an important task for guiding clinical treatment. We used whole genome sequenced data to determine the prevalence of plasmid replicons in clinical bacterial isolates, the presence of resistan…
Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals - the time between symptom onset in an infector and infectee - are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals contacts and exposures (who infec…
Abaca (Musa textilis Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Abuab was sequenced using Illumina Novaseq 6000 and Pacific Biosciences Single-Molecule Real-Time Sequel. The genome size of Abua…
Increasing evidence of regional pathogen transmission networks highlights the importance of investigating the dissemination of multidrug-resistant organisms (MDROs) across a region to identify where transmission is occurring and how pathogens move across regions. We developed a framework for investigating MDRO regional transmission dynamics using whole-genome sequencing data and created regentrans, an easy-to-use,…
Open article record in new tab ↗Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare transmission, and that the primary sites of C. difficile transmission may be strain dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs.…
Canine leukoencephalomyelopathy (LEMP) is a juvenile-onset neurodegenerative disorder of the CNS white matter currently described in Rottweiler and Leonberger dogs. Genome-wide association study (GWAS) allowed us to map LEMP in a Leonberger cohort to dog chromosome 18. Subsequent whole genome re-sequencing of a Leonberger case enabled the identification of a single private homozygous non-synonymous missense varian…
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