Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.

To investigate the levels of MDR in the predominant serotypes of invasive Streptococcus pneumoniae isolated in Canada over a 10 year period. All isolates were serotyped and had antimicrobial susceptibility testing performed, in accordance with CLSI guidelines (M07-11 Ed., 2018). Complete susceptibility profiles were available for 13 712 isolates. MDR was defined as resistance to three or more classes of antimicrobial agents (penicillin MIC ≥2 mg/L defined as resistant). Serotypes were determined by Quellung reaction. In total, 14 138 invasive isolates of S. pneumoniae were tested in the SAVE study (S. pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada), a collaboration between the Canadian Antimicrobial Resistance Alliance and Public Health Agency of Canada—National Microbiology Laboratory. The rate of MDR S. pneumoniae in SAVE was 6.6% (902/13 712). Annual rates of MDR S. pneumoniae decreased between 2011 and 2015 (8.5% to 5.7%) and increased between 2016 and 2020 (3.9% to 9.4%). Serotypes 19A and 15A were the most common serotypes demonstrating MDR (25.4% and 23.5% of the MDR isolates, respectively); however, the serotype diversity index increased from 0.7 in 2011 to 0.9 in 2020 with a statistically significant linear increasing trend (P < 0.001). In 2020, MDR isolates were frequently serotypes 4 and 12F in addition to serotypes 15A and 19A. In 2020, 27.3%, 45.5%, 50.5%, 65.7% and 68.7% of invasive MDR S. pneumoniae were serotypes included in the PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccines, respectively. Although current vaccine coverage of MDR S. pneumoniae in Canada is high, the increasing diversity of serotypes observed among the MDR isolates highlights the ability of S. pneumoniae to rapidly evolve.

Phenotypic susceptibility testing of the Mycobacterium tuberculosis complex (MTBC) isolate requires culture growth, which can delay rapid detection of resistant cases. Whole genome sequencing (WGS) and data analysis pipelines can assist in predicting resistance to antimicrobials used in the treatment of tuberculosis (TB). This study compared phenotypic susceptibility testing results and WGS-based predictions of antimicrobial resistance (AMR) to four first-line antimicrobials—isoniazid, rifampin, ethambutol, and pyrazinamide—for MTBC isolates tested between the years 2018–2022. For this 5-year retrospective analysis, the WGS sensitivity for predicting resistance for isoniazid, rifampin, ethambutol, and pyrazinamide using Mykrobe was 86.7%, 100.0%, 100.0%, and 47.8%, respectively, and the specificity was 99.4%, 99.5%, 98.7%, and 99.9%, respectively. The predictive values improved slightly using Mykrobe corrections applied using TB Profiler, i.e., the WGS sensitivity for isoniazid, rifampin, ethambutol, and pyrazinamide was 92.31%, 100%, 100%, and 57.78%, respectively, and the specificity was 99.63%. 99.45%, 98.93%, and 99.93%, respectively. The utilization of WGS-based testing addresses concerns regarding test turnaround time and enables analysis for MTBC member identification, antimicrobial resistance prediction, detection of mixed cultures, and strain genotyping, all through a single laboratory test. WGS enables rapid resistance detection compared to traditional phenotypic susceptibility testing methods using the WHO TB mutation catalog, providing an insight into lesser-known mutations, which should be added to prediction databases as high-confidence mutations are recognized. The WGS-based methods can support TB elimination efforts in Canada and globally by ensuring the early start of appropriate treatment, rapidly limiting the spread of TB outbreaks.

We assessed the pharmacodynamic activity of ertapenem against Escherichia coli with reduced susceptibility (MIC 0.12-0.5 mg/L), intermediate resistance (MIC 1.0 mg/L) or resistance (MIC ≥ 2 mg/L) to ertapenem using an in vitro model. Fifteen extended-spectrum β-lactamase- or carbapenemase-producing E. coli were studied. The in vitro pharmacodynamic model was inoculated with ∼1 × 10(6) cfu/mL and ertapenem was dosed once daily at 0 and 24 h to simulate free (ƒ) Cmax and t½ obtained after either 1 g or 2 g intravenous once-daily doses in healthy volunteers (1 g: ƒCmax 15 mg/L, t½ 4 h). Sampling was performed over 48 h to assess viable growth and resistance selection. An ertapenem T> MIC ≥ 75.4% (ertapenem MICs ≤ 0.5 mg/L) resulted in bactericidal (≥ 3 log10 killing) activity against all strains. An ertapenem T>MIC of 61% was bactericidal at 6 and 12 h but regrowth at 24 and 48 h occurred in some strains. An ertapenem T>MIC of 13%-43% was bactericidal at 6 h but regrowth (with MIC increases) occurred. No inhibition of an NDM strain with an ertapenem T>MIC of 0% (ertapenem MIC 256 mg/L) occurred at any timepoint. Once-daily dosing with 1 g of ertapenem was bactericidal against ESBL-producing E. coli with ertapenem MICs ≤ 0.5 mg/L and was bactericidal against strains with MICs of 1.0 mg/L, with regrowth in some strains. Ertapenem MICs of 2-8 mg/L resulted in early bactericidal activity followed by regrowth. Once-daily dosing with 2 g of ertapenem was bactericidal against strains with an MIC of 1.0 mg/L, but regrowth occurred in some strains with an ertapenem MIC of 2 mg/L.

Objectives: VRE resistant to potential therapeutic agents such as linezolid are an increasing concern in Canada and worldwide. Infections produced by these isolates have limited treatment options and are associated with poor clinical outcomes. We report an isolate of vancomycin-resistant Enterococcus faecium (VREfm); identified through the Canadian surveillance program, CANWARD, which exhibited linezolid resistance (LVREfm); and carried the optrA and cfr(D) genes on a linear plasmid. Methods: Antimicrobial susceptibility testing was performed by broth microdilution and MICs were interpreted by 2025 CLSI breakpoints. WGS was performed to characterize resistance determinants and the associated plasmid. Results: In 2021, a single LVREfm isolate was recovered from a blood culture of a 67-year-old male patient admitted to an ICU. The isolate was XDR but remained susceptible dose dependent to daptomycin (MIC = 2 mg/L). MLST identified the isolate as ST817, a sequence type not commonly found in our national collection. Vancomycin resistance was mediated by the vanA gene cluster, while linezolid resistance determinants included optrA, cfr(D) and the 23S rRNA gene mutation, G2576T. Vancomycin and linezolid resistance genes were co-located on a linear plasmid that exhibited over 94% sequence identity to previously described linear plasmids from India and the USA. Notably, the plasmid also encoded four toxin–antitoxin systems, potentially contributing to its stability and persistence. Conclusions: This case highlights the appearance of linezolid resistance in VRE mediated by linear plasmids in Canada and underscores the importance of ongoing genomic surveillance to track the dissemination of MDR determinants in clinical settings.