One Health Genomic Analysis of Extended-Spectrum ß-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016.

Extended-spectrum ß-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012-2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.

A One-Health Genomic Investigation of Gentamicin Resistance in Salmonella from Human and Chicken Sources in Canada, 2014 to 2017.

We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Genr) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Genr Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Genr serovars were Salmonella enterica serovars Heidelberg (n = 93; 31.5%), 4,[5],12:i:- (n = 42; 14.2%), Kentucky (n = 37; 12.5%), Infantis (n = 33; 11.2%), and Typhimurium (n = 23; 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3'')-Ia, respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.

Brevibacterium massiliense (Roux and Raoult 2009) is a later heterotypic synonym of Brevibacterium ravenspurgense (Mages, Frodl, Bernard and Funke 2009), using whole-genome sequence analysis as a comparative tool.

A patient strain derived from urine was found by 16S rRNA gene sequencing to be closely related (99.6 % identity) to sequences derived from both Brevibacterium ravenspurgense CCUG 56047T and Brevibacterium massilienseCCUG 53855T. Those species had been described during the same 11 month period in 2008-2009. Further characterization revealed that those isolates could not be readily distinguished from each other biochemically, by cellular fatty acids, antimicrobial susceptibility, MALDI-TOF MS, 16S rRNA gene sequencing or by whole-genome sequence (WGS) analyses. By WGS comparison, these isolates had an aerage nucleotide identity using blastn (ANIb) scores of 95.7 % or higher to each other, DNA G+C content in the range of 62.3 mol%-62.4 mol%, with genome sizes ranging from 2.28×106 to 2.41×106 bases. Based on these data, we propose that the name B. massiliense is a later heterotypic synonym of B. ravenspurgense and provide an emended description of B. ravenspurgense.

Early diagnosis of monomicrobial Clostridioides difficile bacteremia in a patient without colitis.

Bacteremia is a rare finding among Clostridioides difficile infections. We describe a case of a 67-year-old man with resected colorectal cancer with colostomy who presented with small bowel obstruction and was admitted for lysis of adhesions. On day 8 of admission, he developed leukocytosis and raised inflammatory markers with isolation of Gram-positive bacilli in several blood cultures, which was presumptively identified through blood culture pelleting and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) as C. difficile. The diagnosis was confirmed with conventional culture and reference lab identification and the patient demonstrated clinical response with parenteral then oral vancomycin that briefly worsened when therapy was switched to parenteral metronidazole and then improved once oral vancomycin was resumed. Our case was notable in that the combination of pelleting and MALDI-TOF offered early diagnosis in this patient whose positive blood cultures were suspicious for contamination and in whom there was an absence of diarrheal illness or features of colitis on abdominal imaging. Early diagnosis is critical for the timely initiation of therapy, implementation of infection prevention and control measures and in selection of appropriate therapy for antimicrobial stewardship.

La bactériémie est rare lors d'une infection à Clostridioides difficile. Les auteurs décrivent le cas d'un homme de 67 ans ayant une colostomie découlant de la résection d'un cancer colorectal, qui a consulté à cause d'une occlusion du grêle et a été hospitalisé pour traiter des adhésiolyses. Le huitième jour de l'hospitalisation, il a présenté une leucocytose et une augmentation des marqueurs inflammatoires, des bacilles à Gram positif ont été isolés dans plusieurs hémocultures, et un diagnostic provisoire de C. difficile a été posé par culot de sang et désorption/ionisation laser assistée par matrice par temps de vol (MALDI-TOF). Le diagnostic a été confirmé par une culture classique et par le laboratoire de référence, et le patient a affiché une réponse clinique à la vancomycine par voie parentérale, puis par voie orale. Son état s'est brièvement aggravé lors du passage au métronidazole par voie parentérale, puis s'est amélioré à la reprise de la vancomycine par voie orale. Le cas était remarquable parce que la combinaison du culot et de la MALDI-TOF a permis d'obtenir un diagnostic rapide chez ce patient dont les hémocultures positives ont suggéré une contamination dont l'imagerie abdominale ne révélait pas de maladie diarrhéique ni de caractéristiques de colite. Il est essentiel de poser un diagnostic précoce pour entreprendre le traitement rapidement, adopter des mesures de prévention et de contrôle des infections et sélectionner le traitement approprié à la gouvernance antimicrobienne.

Phage Therapy in the Management of Urinary Tract Infections: A Comprehensive Systematic Review.

Urinary tract infections (UTIs) are a problem worldwide, affecting almost half a billion people each year. Increasing antibiotic resistance and limited therapeutic options have led to the exploration of alternative therapies for UTIs, including bacteriophage (phage) therapy. This systematic review aims at evaluating the efficacy of phage therapy in treating UTIs. We employed a comprehensive search strategy for any language, any animal, and any publication date. A total of 55 in vivo and clinical studies were included. Of the studies, 22% were published in a non-English language, 32.7% were before the year 1996, and the rest were after 2005. The results of this review suggest that phage therapy for UTIs can be effective; more than 72% of the included articles reported microbiological and clinical improvements. On the other hand, only 5 randomized controlled trials have been completed, and case reports and case series information were frequently incomplete for analysis. Overall, this comprehensive systematic review identifies preliminary evidence supporting the potential of phage therapy as a safe and viable option for the treatment of UTIs.

Canadian SARS-CoV-2 serological survey using antenatal serum samples: a retrospective seroprevalence study.

BACKGROUND: Insufficient data on the rate and distribution of SARS-CoV-2 infection in Canada has presented a substantial challenge to the public health response to the COVID-19 pandemic. Our objective was to assess SARS-CoV-2 seroprevalence in a representative sample of pregnant people throughout Canada, across multiple time points over 2 years of the pandemic, to describe the seroprevalence and show the ability of this process to provide prevalence estimates. METHODS: This Canadian retrospective serological surveillance study used existing serological prenatal samples across 10 provinces over multiple time periods: Feb. 3-21, 2020; Aug. 24-Sept. 11, 2020; Nov. 16-Dec. 4, 2020; Nov. 15-Dec. 3, 2021; and results from the province of British Columbia during a period in which the SARS-CoV-2 B.1.1.529 (Omicron) variant was predominant, from Nov. 15, 2021, to June 11, 2022. Age and postal code administrative data allowed for comparison with concurrent polymerase chain reactivity (PCR)-positive results collected by Statistics Canada and the Canadian Surveillance of COVID-19 in Pregnancy (CANCOVID-Preg) project. RESULTS: Seropositivity in antenatal serum as early as February 2020 indicates SARS-CoV-2 transmission before the World Health Organization's declaration of the pandemic. Seroprevalence in our sample of pregnant people was 1.84 to 8.90 times higher than the recorded concurrent PCR-positive prevalence recorded among females aged 20-49 years in November-December 2020. Overall seropositivity in our sample of pregnant people was low at the end of 2020, increasing to 15% in 1 province by the end of 2021. Seroprevalence among pregnant people in BC during the Omicron period increased from 5.8% to 43% from November 2021 to June 2022. INTERPRETATION: These results indicate widespread vulnerability to SARS-CoV-2 infection before vaccine availability in Canada. During the time periods sampled, public health tracking systems were under-reporting infections, and seroprevalence results during the Omicron period indicate extensive community spread of SARS-CoV-2 infection.

A four specimen-pooling scheme reliably detects SARS-CoV-2 and influenza viruses using the BioFire FilmArray Respiratory Panel 2.1.

The COVID-19 pandemic required increased testing capacity, enabling rapid case identification and effective contract tracing to reduce transmission of disease. The BioFire FilmArray is a fully automated nucleic acid amplification test system providing specificity and sensitivity associated with gold standard molecular methods. The FilmArray Respiratory Panel 2.1 targets 22 viral and bacterial pathogens, including SARS-CoV-2 and influenza virus. While each panel provides a robust output of information regarding pathogen detection, the specimen throughput is low. This study evaluates the FilmArray Respiratory Panel 2.1 using 33 pools of contrived nasal samples and 22 pools of clinical nasopharyngeal specimens to determine the feasibility of increasing testing capacity, while maintaining detection of both SARS-CoV-2 and influenza virus. We observed 100% detection and 90% positive agreement for SARS-CoV-2 and 98% detection and 95% positive agreement for influenza viruses with pools of contrived or clinical specimens, respectively. While discordant results were mainly attributed to loss in sensitivity, the sensitivity of the pooling assay was well within accepted limits of detection for a nucleic acid amplification test. Overall, this study provides evidence supporting the use of pooling patient specimens, one in four with the FilmArray Respiratory Panel 2.1 for the detection of SARS-CoV-2 and influenza virus.

Overview of Canada's Antimicrobial Resistance Network (AMRNet): A data-driven One Health approach to antimicrobial resistance surveillance.

The Antimicrobial Resistance Network (AMRNet) is a laboratory-based antimicrobial resistance (AMR) surveillance system under development at the Public Health Agency of Canada's (PHAC's) National Microbiology Laboratory. The AMRNet surveillance system captures information on antimicrobial susceptibility testing from clinical and veterinary laboratories including both public and private facilities. In the future, the AMRNet system will also capture relevant data from existing PHAC surveillance systems for AMR including the Canadian Integrated Program for Antimicrobial Resistance Surveillance, the Canadian Nosocomial Infection Surveillance Program and the Enhanced Surveillance of Antimicrobial-Resistant Gonorrhea program, and contribute to the Canadian Antimicrobial Resistance Surveillance System. AMRNet's integrated "One Health" approach will allow health professionals and researchers to take a multi-dimensional perspective of AMR in both human and animal health in Canada and will make Canada a leader in AMR surveillance. AMRNet is a collaboration between PHAC, provincial and territorial public health organizations as well as clinical and veterinary laboratories across the country. As part of a phased rollout, AMRNet is now collecting human clinical data from three provinces, from both inpatients and outpatients. Ultimately, AMRNet aims to capture all antimicrobial susceptibility testing results from all bacterial and fungal pathogens across Canada. This article describes the AMRNet surveillance system, including program objectives, system structure and the data collected. The integration of human and animal data in AMRNet will inform One Health responses to AMR issues. The capacity to collect and to disseminate data to stakeholders in real time is a critical step to addressing emerging AMR issues in Canada.

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.

Whole genome sequencing (WGS) of Salmonella supports both molecular typing and detection of antimicrobial resistance (AMR). Here, we evaluated the correlation between phenotypic antimicrobial susceptibility testing (AST) and in silico prediction of AMR from WGS in Salmonella enterica (n = 1321) isolated from human infections in Canada. Phenotypic AMR results from broth microdilution testing were used as the gold standard. To facilitate high-throughput prediction of AMR from genome assemblies, we created a tool called Staramr, which incorporates the ResFinder and PointFinder databases and a custom gene-drug key for antibiogram prediction. Overall, there was 99% concordance between phenotypic and genotypic detection of categorical resistance for 14 antimicrobials in 1321 isolates (18,305 of 18,494 results in agreement). We observed an average sensitivity of 91.2% (range 80.5-100%), a specificity of 99.7% (98.6-100%), a positive predictive value of 95.4% (68.2-100%), and a negative predictive value of 99.1% (95.6-100%). The positive predictive value of gentamicin was 68%, due to seven isolates that carried aac(3)-IVa, which conferred MICs just below the breakpoint of resistance. Genetic mechanisms of resistance in these 1321 isolates included 64 unique acquired alleles and mutations in three chromosomal genes. In general, in silico prediction of AMR in Salmonella was reliable compared to the gold standard of broth microdilution. WGS can provide higher-resolution data on the epidemiology of resistance mechanisms and the emergence of new resistance alleles.

The 2018 Global Point Prevalence Survey of antimicrobial consumption and resistance in 47 Canadian hospitals: a cross-sectional survey.

BACKGROUND: Patient-level surveillance of antimicrobial use (AMU) in Canadian hospitals empowers the reduction of inappropriate AMU and was piloted in 2017 among 14 hospitals in Canada. We aimed to describe AMU on the basis of patient-level data in Canadian hospitals in 2018 in terms of antimicrobial prescribing prevalence and proportions, antimicrobial indications, and agent selection in medical, surgical and intensive care wards. METHODS: Canadian adult, pediatric and neonatal hospitals were invited to participate in the standardized web-based cross-sectional Global Point Prevalence Survey of Antimicrobial Consumption and Resistance (Global-PPS) conducted in 2018. An identified site administrator assigned all wards admitting inpatients to specific surveyors. A physician, pharmacist or nurse with infectious disease training performed the survey. The primary outcomes were point prevalence rates for AMU over the study period regarding prescriptions, indications and agent selection in medical, surgical and intensive care wards. The secondary outcomes were AMU for resistant organisms and practice appropriateness evaluated on the basis of quality indicators. Antimicrobial consumption is presented in terms of prevalence and proportions. RESULTS: Forty-seven of 118 (39.8%) hospitals participated in the survey; 9 hospitals were primary care centres, 15 were secondary care centres and 23 were tertiary or specialized care centres. Of 13 272 patients included, 33.5% (n = 4447) received a total of 6525 antimicrobials. Overall, 74.1% (4832/6525) of antimicrobials were for therapeutic use, 12.6% (n = 825) were for medical prophylaxis, 8.9% (n = 578) were for surgical prophylaxis, 2.2% (n = 143) were for other use and 2.3% (n = 147) were for unidentified reasons. A diagnosis or indication was documented in the patient's file at the initiation for 87.3% (n = 5699) of antimicrobials; 62.9% (n = 4106) of antimicrobials had a stop or review date; and 72.0% (n = 4697) of prescriptions were guided by local guidelines. INTERPRETATION: Overall, three-quarters of AMU was for therapeutic use across participating hospitals. Canadian hospitals should be further incentivized to create and adapt local guidelines on the basis of recent antimicrobial resistance data.

The 2017 global point prevalence survey of antimicrobial consumption and resistance in Canadian hospitals.

BACKGROUND: Patient-level surveillance (indication, appropriate choice, dosing, route, duration) of antimicrobial use in Canadian hospitals is needed to reduce antimicrobial overuse and misuse. Patient-level surveillance has not been performed on a national level in Canada. The Global Point Prevalence Survey of Antimicrobial Consumption and Resistance (Global-PPS) is an international collaborative to monitor antimicrobial use and resistance in hospitals worldwide. Global-PPS locally documents on a single day patient-level antimicrobial prescribing practices. This article presents the results of the 2017 Global-PPS in Canadian hospitals with established antimicrobial stewardship programs. METHODS: Hospitals part of the Canadian Nosocomial Infection Surveillance Program were invited to participate. Surveys could be performed any time in the 2017 calendar year. All in-patient wards in each hospital were surveyed by a physician, pharmacist or nurse with infectious disease training. RESULTS: Fourteen Canadian hospitals participated in the survey. Of 4118 patients, 1400 patients (34.0%) received a total of 2041 antimicrobials. Overall, 73.1% (n = 1493) of antimicrobials were for therapeutic use, 14.2% (n = 288) were for medical prophylaxis, 8.3% (n = 170) were for surgical prophylaxis, 1.8% (n = 37) were for other reasons, and 0.2% (n = 3) were used as prokinetic agents. Only 2.5% (n = 50) were for unknown reasons. For antimicrobials for therapeutic use, 29.9% of patients were treated for lower respiratory tract (343/1147), 10.5% for intra-abdominal (120/1147), 9.3% for skin and soft tissue (107/1147) and 7.5% for gastro-intestinal (86/1147) infections. CONCLUSIONS: Standardized methodology amongst Global-PPSs allows the comparison of our results to the 2015 Global-PPS. The prevalence of antimicrobial use on medical, surgical, and intensive care wards are similar to those previously observed in North America. Indication of antimicrobials has not been previously reported on such a large scale in Canadian hospitals. This report serves as a comparison for further point prevalence surveys that are currently underway. It will be used for identifying opportunities and benchmarking in antibiotic stewardship.

Sentinel surveillance of Lyme disease risk in Canada, 2019: Results from the first year of the Canadian Lyme Sentinel Network (CaLSeN).

BACKGROUND: Lyme disease is an emerging vector-borne zoonotic disease of increasing public health importance in Canada. As part of its mandate, the Canadian Lyme Disease Research Network (CLyDRN) launched a pan-Canadian sentinel surveillance initiative, the Canadian Lyme Sentinel Network (CaLSeN), in 2019. OBJECTIVES: To create a standardized, national sentinel surveillance network providing a real-time portrait of the evolving environmental risk of Lyme disease in each province. METHODS: A multicriteria decision analysis (MCDA) approach was used in the selection of sentinel regions. Within each sentinel region, a systematic drag sampling protocol was performed in selected sampling sites. Ticks collected during these active surveillance visits were identified to species, and Ixodes spp. ticks were tested for infection with Borrelia burgdorferi, Borrelia miyamotoi, Anaplasma phagocytophilum, Babesia microti and Powassan virus. RESULTS: In 2019, a total of 567 Ixodes spp. ticks (I. scapularis [n=550]; I. pacificus [n=10]; and I. angustus [n=7]) were collected in seven provinces: British Columbia, Manitoba, Ontario, Québec, New Brunswick, Nova Scotia and Prince Edward Island. The highest mean tick densities (nymphs/100 m2) were found in sentinel regions of Lunenburg (0.45), Montréal (0.43) and Granby (0.38). Overall, the Borrelia burgdorferi prevalence in ticks was 25.2% (0%-45.0%). One I. angustus nymph from British Columbia was positive for Babesia microti, a first for the province. The deer tick lineage of Powassan virus was detected in one adult I. scapularis in Nova Scotia. CONCLUSION: CaLSeN provides the first coordinated national active surveillance initiative for tick-borne disease in Canada. Through multidisciplinary collaborations between experts in each province, the pilot year was successful in establishing a baseline for Lyme disease risk across the country, allowing future trends to be detected and studied.

Roles of Lsr2 in colony morphology and biofilm formation of Mycobacterium smegmatis.

The lipid-rich cell wall is a defining feature of Mycobacterium species. Individual cell wall components affect diverse mycobacterial phenotypes including colony morphology, biofilm formation, antibiotic resistance, and virulence. In this study, we describe a transposon insertion mutant of Mycobacterium smegmatis mc2 155 that exhibits altered colony morphology and defects in biofilm formation. The mutation was localized to the lsr2 gene. First identified as an immunodominant T-cell antigen of Mycobacterium leprae, lsr2 orthologs have been identified in all sequenced mycobacterial genomes, and homologs are found in many actinomycetes. Although its precise function remains unknown, localization experiments indicate that Lsr2 is a cytosolic protein, and cross-linking experiments demonstrate that it exists as a dimer. Characterization of cell wall lipid components reveals that the M. smegmatis lsr2 mutant lacks two previously unidentified apolar lipids. Characterization by mass spectrometry and thin-layer chromatography indicate that these two apolar lipids are novel mycolate-containing compounds, called mycolyl-diacylglycerols (MDAGs), in which a mycolic acid (alpha- or alpha'-mycolate) molecule is esterified to a glycerol. Upon complementation with an intact lsr2 gene, the mutant reverts to the parental phenotypes and MDAG production is restored. This study demonstrates that due to its impact on the biosynthesis of the hydrophobic MDAGs, Lsr2 plays an important role in the colony morphology and biofilm formation of M. smegmatis.