LAMBDR: Long-range amplification and Nanopore sequencing of Mycobacterium bovis direct-repeat region. A novel method for in-silico spoligotyping of M. bovis directly from badger faeces.
James, R. S.; Travis, E. R.; Hewlett, P. C.; Wellington, E.; Kravar-Garde, L.
Show abstract
The environment is an overlooked source of Mycobacterium bovis, the causative agent of bovine TB. Long read, end to end sequencing of variable repeat regions across the M. bovis genome was evaluated as a method of acquiring rapid strain level resolution directly from environmental samples. Eight samples of M. bovis, two BCG strains (Danish and Pasteur), and a single M. tuberculosis type culture (NCTC 13144) were used to generate data for this method. Long range PCR amplification of the direct repeat region was used to synthesize [~]5kb template DNA for onward sequence analysis. This has permitted culture independent identification of M. bovis spoligotypes present in the environment. Sequence level analysis of the direct repeat region showed that spoligotyping may underestimate strain diversity due to the inability to identify both SNPs and primer binding mutations using a biotinylated hybridisation approach.
Matching journals
The top 11 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Environmental risk factors associated with the presence of Mycobacterium ulcerans in Victoria, Australia 93%
- Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence Typing 92%
- DNA Extraction Protocols for Animal Fecal Material on Blood Spot Cards 92%
Similar papers in this journal
- Genomic reconstruction of Bacillus anthracis from complex environmental samples enables high throughput identification and lineage assignment in Pakistan 94%
- Evidence of a novel sublineage of Streptococcus agalactiae in elephants from zoo populations in Germany 93%
- Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections 92%
Similar papers in this journal
- MagnaExtract, a novel magnetic bead-based extraction method for the molecular detection of antimicrobial resistance genes in fresh water. 95%
- Prevalence of antimicrobial resistance phenotypes and genes in stable fly- and manure-derived bacterial isolates from clinically relevant taxa in dairy settings 93%
- An evaluation of screening methods for the detection of extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae in environmental samples from healthcare settings 92%
Similar papers in this journal
- Development of a multiplex real-time PCR assay for BCG and validation in a clinical laboratory 93%
- Nested PCR to optimize rpoB metabarcoding for low-concentration and host-associated bacterial DNA 92%
- Validation of selective agars for detection and quantification of Escherichia coli resistant to critically important antimicrobials 92%
Similar papers in this journal
- Reduced antibacterial drug resistance and blaCTX-M β-lactamase gene carriage in cattle-associated Escherichia coli at low temperatures, at sites dominated by older animals and on pastureland: implications for surveillance. 92%
- Can genomics and meteorology predict outbreaks of legionellosis in urban settings? 92%
- intI1 primer selection for class 1 integron integrase gene and transcript quantification - validation and application for monitoring intl1 gene abundance within septic tanks in Thailand 92%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.