Oxford Nanopore long-read sequencing offers advantages over Illumina short-reads for the identifi... more Oxford Nanopore long-read sequencing offers advantages over Illumina short-reads for the identification and characterization of bacterial pathogens for outbreak detection and surveillance activities within a diagnostic public health laboratory context. Compared to Illumina, Nanopore is more cost-effective for small batches, has a lower capital costs, and has a faster turnaround times, in addition to the ability to assemble complete bacterial genomes. The quantity and quality of DNA required for Nanopore sequencing is higher than Illumina, and DNA extraction methods recommended for obtaining high molecular weight DNA are different from those typically used in diagnostic laboratories. Using a Salmonella isolate with a previously closed PacBio genome as a model Enterobacteriaceae organism, we evaluated the quantity, quality, and fragmentation of five commercial DNA extraction kits. Nanopore sequencing performance was evaluated for the top three methods: Qiagen EZ1 DNA Tissue, Qiagen DN...
Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica sub... more Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:– from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.
Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Man... more Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied.
Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antib... more Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antibiotic resistance genes (ARGs) in the gut microbiota. The gut microbiota often suffers from various disturbances. It is not clear whether and how disturbed microbiota may affect ARG mobility under antibiotic treatments. For proof of concept, in the presence or absence of streptomycin pre-treatment, mice were inoculated orally with a β-lactam-susceptible Salmonella enterica serovar Heidelberg clinical isolate (recipient) and a β-lactam resistant Escherichia coli O80:H26 isolate (donor) carrying a blaCMY-2 gene on an IncI2 plasmid. Immediately following inoculation, mice were treated with or without ampicillin in drinking water for 7 days. Faeces were sampled, donor, recipient and transconjugant were enumerated, blaCMY-2 abundance was determined by quantitative PCR, faecal microbial community composition was determined by 16S rRNA amplicon sequencing and cecal samples were observed histolog...
We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmo... more We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmonella. These genome sequences will provide useful references for understanding the genetic variation within Salmonella enterica serotypes, particularly as references to aid in comparative genomics studies, as well as providing information for improving in silico serotyping accuracy.
Oxford Nanopore long-read sequencing offers advantages over Illumina short-reads for the identifi... more Oxford Nanopore long-read sequencing offers advantages over Illumina short-reads for the identification and characterization of bacterial pathogens for outbreak detection and surveillance activities within a diagnostic public health laboratory context. Compared to Illumina, Nanopore is more cost-effective for small batches, has a lower capital costs, and has a faster turnaround times, in addition to the ability to assemble complete bacterial genomes. The quantity and quality of DNA required for Nanopore sequencing is higher than Illumina, and DNA extraction methods recommended for obtaining high molecular weight DNA are different from those typically used in diagnostic laboratories. Using a Salmonella isolate with a previously closed PacBio genome as a model Enterobacteriaceae organism, we evaluated the quantity, quality, and fragmentation of five commercial DNA extraction kits. Nanopore sequencing performance was evaluated for the top three methods: Qiagen EZ1 DNA Tissue, Qiagen DN...
Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica sub... more Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:– from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.
Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Man... more Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied.
Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antib... more Ingestion of food- or waterborne antibiotic-resistant bacteria may lead to dissemination of antibiotic resistance genes (ARGs) in the gut microbiota. The gut microbiota often suffers from various disturbances. It is not clear whether and how disturbed microbiota may affect ARG mobility under antibiotic treatments. For proof of concept, in the presence or absence of streptomycin pre-treatment, mice were inoculated orally with a β-lactam-susceptible Salmonella enterica serovar Heidelberg clinical isolate (recipient) and a β-lactam resistant Escherichia coli O80:H26 isolate (donor) carrying a blaCMY-2 gene on an IncI2 plasmid. Immediately following inoculation, mice were treated with or without ampicillin in drinking water for 7 days. Faeces were sampled, donor, recipient and transconjugant were enumerated, blaCMY-2 abundance was determined by quantitative PCR, faecal microbial community composition was determined by 16S rRNA amplicon sequencing and cecal samples were observed histolog...
We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmo... more We report here 32 completed closed genome sequences of strains representing 30 serotypes of Salmonella. These genome sequences will provide useful references for understanding the genetic variation within Salmonella enterica serotypes, particularly as references to aid in comparative genomics studies, as well as providing information for improving in silico serotyping accuracy.
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