BMC Bioinformatics
November 2024
Background: Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid.
View Article and Find Full Text PDFTo compare the microbial communities inside hemodialysis catheters from symptomatic and asymptomatic patients to determine their differences. Catheters ( = 41) were removed from patients in the Saskatchewan Health Authority over an 18-month period. The catheter section inside the body was flushed and the contents were evaluated using culture-dependent and culture-independent analysis.
View Article and Find Full Text PDFMethods Mol Biol
June 2024
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach.
View Article and Find Full Text PDFBackground: Avian pathogenic Escherichia coli (APEC) are the causative agents of colibacillosis in chickens, a disease which has significant economic impact on the poultry industry. Large plasmids detected in APEC are known to contribute to strain diversity for pathogenicity and antimicrobial resistance, but there could be other plasmids that are missed in standard analysis. In this study, we determined the impact of sequencing and assembly factors for the detection of plasmids in an E.
View Article and Find Full Text PDFEscherichia coli infections in poultry cause significant morbidity and economic losses for producers each year. In a 3-year period, we collected and sequenced the whole genomes of E. coli disease isolates ( = 91), isolates from presumed healthy birds ( = 61), and isolates from 8 barn sites ( = 93) on broiler farms in Saskatchewan.
View Article and Find Full Text PDFis a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors and MGEs were profiled in a set of 1273 genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical and associated habitats.
View Article and Find Full Text PDFThis study evaluated the effect of combinations of feed-grade urea and slow-release urea (SRU) on fermentation and microbial protein synthesis within two artificial rumens (Rusitec) fed a finishing concentrate diet. The experiment was a completely randomized, dose-response design with SRU substituted at levels of 0% (control), 0.5%, 1%, or 1.
View Article and Find Full Text PDFRecent concerns over linkages between antimicrobial resistance in human pathogens and antimicrobial use in livestock have prompted researchers to investigate management strategies that reduce the current reliance on in-feed tylosin to control liver abscesses in feedlot cattle. A total of 7,576 crossbred yearlings were allocated to the study (~253 animals/pen, 10 replicate pens per treatment) and individually randomized to one of three treatments. Tylosin phosphate (11 ppm) was included in-feed (1) for the first 125 days on feed (DOF) (), (2) for DOF 41 to 161 (), or (3) for the entire feeding period (; day 0-161).
View Article and Find Full Text PDFBackground: Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water.
View Article and Find Full Text PDFWastewater treatment plants (WWTPs) are points of control for the environmental dissemination of antimicrobial resistant bacteria. Vancomycin-resistant enterococci (VRE) were used as indicators of antimicrobial resistance (AMR) in two WWTPs (biologically aerated filter (BAF) and conventional activated sludge (CAS)) in the same municipality. The removal and abundance of enterococci and VRE as well as the species and antimicrobial resistance profiles of VRE were assessed.
View Article and Find Full Text PDFThis study investigated the effect of treatment of wheat straw using ammonia fiber expansion (AFEX) and exogenous fibrolytic enzymes (Viscozyme) on fiber digestibility, rumen fermentation, microbial protein synthesis, and microbial populations in an artificial rumen system [Rumen Simulation Technique (RUSITEC)]. Four treatments were assigned to 16 vessels (4 per treatment) in 2 RUSITEC apparatuses in a randomized block design. Treatments were arranged as a 2 × 2 factorial using untreated or AFEX-treated wheat straw with or without exogenous fibrolytic enzymes [0 or 500 μg of protein/g straw dry matter (DM)].
View Article and Find Full Text PDFEnterococci species in wastewater including Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus and Enterococcus gallinarum isolates (n = 308) with low or high level vancomycin resistance were determined and compared using a phenotypic method (RapID™ STR system), 16S rRNA sequencing, and multi-locus (atpA, groESL, and pheS) sequence analysis (MLSA). Error rates for the RapID™ STR system were E. faecalis (15.
View Article and Find Full Text PDFThe objective of this study was to assess the prevalence of three serotypes, A1, A2, and A6 in 98 M. haemolytica isolates collected from clinical BRD cases in European cattle and assess their antimicrobial resistance profiles. Isolates were characterized by serotyping (plate agglutination and serotype specific PCR) and antimicrobial susceptibility testing.
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