Walter Demczuk

Ceftiofur resistance in Salmonella enterica serovar Heidelberg from chicken meat and humans, Canada.

Use of this drug in chickens may limit effectiveness of cephalosporins in treating human infections.

Serotype distribution of invasive Streptococcus pneumoniae in Canada after the introduction of the 13-valent pneumococcal conjugate vaccine, 2010-2012.

The introduction of the 7-valent pneumococcal vaccine (PCV7) in Canada was very effective in reducing invasive pneumococcal disease (IPD) in children; however, increases of non-PCV7 serotypes have subsequently offset some of these reductions. A 13-valent pneumococcal vaccine (PCV13) targeting additional serotypes was implemented between 2010 and 2011, and in 2012 changes in the incidence of disease and the distribution of IPD serotypes began to emerge. The incidence of IPD in children <5 years of age declined from 18.0 to 14.2 cases per 100 000 population between 2010 and 2012; however, the incidence in ages ≥5 years remained relatively unchanged over the 3-year period, at about 9.7 cases per 100 000 population. From 2010 to 2012, PCV13 serotypes declined significantly from 66% (224/339) to 41% (101/244, p < 0.001) in children <5 years of age, and from 54% (1262/2360) to 43% (1006/2353, p < 0.001) in children ≥5 years of age. Serotypes 19A, 7F, 3, and 22F were the most common serotypes in 2012, with 19A decreasing from 19% (521/2727) to 14% (364/2620, p < 0.001), 7F decreasing from 14% (389/2727) to 12% (323/2620, p = 0.04), and 22F increasing from 7% (185/2727) to 11% (279/2620, p < 0.001) since 2010. Serotype 3 increased from 7% (23/339) to 10% (24/244) in <5-year-olds (p = 0.22) over the 3-year period. The highest rates of antimicrobial resistance were observed with clarithromycin (23%), penicillin using meningitis breakpoints (12%), clindamycin (8%), and trimethoprim-sulfamethoxazole (6%). Shifts in the distribution of IPD serotypes and reductions in the incidence of disease suggest that current immunization programs in Canada are effective in reducing the burden of IPD in children. While we acknowledge the limited data on the effectiveness of the PCV13 vaccine, to our knowledge, this study represents one of the first descriptions of the potential impact of the PCV13 vaccine in the Canadian population. Continued surveillance will be important to recognize replacement serotypes, to determine the extent of herd immunity effects in nonpaediatric populations, and to assess the overall effectiveness of PCV13 in reducing IPD in Canada.

Characterization of the First Extended-Spectrum Beta-Lactamase-Producing Salmonella Isolate Identified in Canada

ABSTRACT A single Salmonella enterica serovar Typhimurium isolate with an UT2 phage type producing an extended-spectrum beta-lactamase (ESBL) was identified in Canada in 2000. The isolate harbored two plasmids, one containing a blaTEM-1 gene and the other containing a blaSHV-2a gene. The ESBL gene was located on a 70-kb transferable plasmid which also carried tetracycline and trimethoprim resistance elements.

Phage-Based Typing Scheme for Salmonella enterica Serovar Heidelberg, a Causative Agent of Food Poisonings in Canada

ABSTRACT Salmonella enterica serovar Heidelberg is perhaps the second most frequent Salmonella serovar isolated from humans and the most common isolated from animals in Canada. This pathogen has shown increasing resistance to antimicrobial agents and mimics the multidrug resistance observed in S. enterica serovar Typhimurium strain DT 104. However, unlike for serovar Typhimurium, a rapid and inexpensive subtyping method has not been available for large-scale surveillance efforts. We developed a phage typing scheme and subtyped 2,523 strains of serovar Heidelberg from outbreaks, sporadic infections, and environmental sources in Canada between January 1991 and December 2000. All strains were sensitive to one or more phages and could be subdivided into 49 phage types. A total of 196 isolates from 13 major outbreaks could be subtyped into six phage types, while 86 strains from family outbreaks were assigned to seven phage types. All strains were typeable, and epidemiologically related strains isolated from patients and implicated foods had identical phage types, antibiograms, and pulsed-field gel electrophoresis (PFGE) patterns. Combining PFGE with phage typing increased the discriminatory power of the analysis beyond that of either method alone. We concluded that this phage typing scheme, in conjunction with PFGE, enhances subtyping of serovar Heidelberg strains. Furthermore, this phage typing scheme is a rapid, economical, stable, and reliable epidemiologic tool for tracing the origin of food-borne disease and for the surveillance of sporadic infections.

Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

ABSTRACT A large-scale, whole-genome comparison of Canadian Neisseria gonorrhoeae isolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While some N. gonorrhoeae multiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaic penA alleles, followed in 2000/2001 with the penA mosaic X allele and then in 2007 with ST1407 strains with the penA mosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated with penA mosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014

ABSTRACT The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZMr) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZMr strains. The genomes of 213 AZMr and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZMr (MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One isolate with high-level AZMr collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate levels of AZMr (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZMr was also associated with mtrR promoter mutations, including the −35A deletion and the presence of Neisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZMr strains arise independently and can then rapidly expand clonally in a region through local sexual networks.

Limited genetic diversity in Salmonella enterica Serovar Enteritidis PT13

BackgroundSalmonella enterica serovar Enteritidis has emerged as a significant foodborne pathogen throughout the world and is commonly characterized by phage typing. In Canada phage types (PT) 4, 8 and 13 predominate and in 2005 a large foodborne PT13 outbreak occurred in the province of Ontario. The ability to link strains during this outbreak was difficult due to the apparent clonality of PT13 isolates in Canada, as there was a single dominant pulsed-field gel electrophoresis (PFGE) profile amongst epidemiologically linked human and food isolates as well as concurrent sporadic strains. The aim of this study was to perform comparative genomic hybridization (CGH), DNA sequence-based typing (SBT) genomic analyses, plasmid analyses, and automated repetitive sequence-based PCR (rep-PCR) to identify epidemiologically significant traits capable of subtyping S. Enteritidis PT13.ResultsCGH using an oligonucleotide array based upon chromosomal coding sequences of S. enterica serovar Typhimurium strain LT2 and the Salmonella genomic island 1 successfully determined major genetic differences between S. Typhimurium and S. Enteritidis PT13, but no significant strain-to-strain differences were observed between S. Enteritidis PT13 isolates. Individual loci (safA and fliC) that were identified as potentially divergent in the CGH data set were sequenced in a panel of S. Enteritidis strains, and no differences were detected between the PT13 strains. Additional sequence-based typing was performed at the fimA, mdh, manB, cyaA, citT, caiC, dmsA, ratA and STM0660 loci. Similarly, no diversity was observed amongst PT13 strains. Variation in plasmid content between PT13 strains was observed, but macrorestriction with Bgl II did not identify further differences. Automated rep-PCR patterns were variable between serovars, but S. Enteritidis PT13 strains could not be differentiated.ConclusionNone of the methods identified any significant variation between PT13 strains. Greater than 11,300 base pairs of sequence for each of seven S. Enteritidis PT13 strains were analyzed without detecting a single polymorphic site, although diversity between different phage types of S. Enteritidis was observed. These data suggest that Canadian S. Enteritidis PT13 strains are highly related genetically.

Trends in asymptomatic nasopharyngeal colonization with streptococcus pneumoniae after introduction of the 13-valent pneumococcal conjugate vaccine in Calgary, Canada.

Background: We previously reported serotype-specific trends in pneumococcal nasopharyngeal colonization soon after introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in mid-2002. Our current aim is to describe later trends after PCV7 and early trends after PCV13 vaccine introduction in 2010. Methods: The Calgary Area Streptococcus pneumoniae Epidemiology Research team conducted 10 point-prevalence surveys of pneumococcal nasopharyngeal colonization in healthy children aged 12 and 18 months and 4.5 years biannually from 2003 to 2005 (previously reported) and annually in 2006, 2010, 2011 and 2012. Results: For surveys conducted during 2010–2012, the proportion colonized was 13.2% compared with 19.9% in surveys conducted during 2003–2006 (P < 0.001). Vaccination with 2 or more doses of PCV7 or PCV13, older age and recent antibiotic use reduced the odds of colonization with any pneumococcus. By 2012, 94% of all isolates were nonvaccine serotypes with 11A, 15A/B/C, 22F, 23A/B and 35B/F representing 75% of all isolates. Conclusions: Pneumococcal nasopharyngeal colonization has changed profoundly since the introduction of conjugate vaccines and overall colonization by pneumococcus has declined in recent years. By 2012, nonvaccine serotypes have nearly completely replaced vaccine serotypes. The impact on clinical disease remains to be seen.

Population Structure and Antimicrobial Resistance of Invasive Serotype IV Group B Streptococcus, Toronto, Ontario, Canada

Conjugate vaccines should include polysaccharide or virulence proteins of this serotype to provide complete protection.

Assessment of multidrug resistance, clonality and virulence in non-PCV-13 Streptococcus pneumoniae serotypes in Canada, 2011–13

OBJECTIVES Serotype replacement in Streptococcus pneumoniae following the implementation of a new vaccine has been associated with the emergence of non-vaccine serotypes as prominent causes of invasive pneumococcal disease (IPD). The aim of this study was to characterize specific non-PCV-13 serotypes 15A, 22F, 33F and 35B from IPD, isolated in Canada post-PCV-13 introduction in 2010. METHODS Of 3802 IPD isolates collected from across Canada in 2011-13, 18.4% were found to be serotypes 15A, 22F, 33F and 35B. These 699 isolates were subjected to antimicrobial susceptibility testing, PFGE, MLST, molecular detection of pneumococcal pili and comparison with Pneumococcal Molecular Epidemiology Network (PMEN) clones. RESULTS This study demonstrated clonal spread of specific STs, including MDR ST63 and its Sweden(15A)-25-related variants, the increasingly common ST433 and a variant of piliated, penicillin-non-susceptible ST558, related to PMEN clone Utah(35B)-24 (ST377). New STs of serotype 33F were identified. Several potential capsular switching events were identified within these serotypes. CONCLUSIONS Non-PCV-13 serotype 22F is increasing in Canada through the rapid clonal expansion of ST433. Numerous new STs associated with serotype 33F indicate the potential divergence of the serotype. Serotypes 15A and 35B in Canada are related to international clones of S. pneumoniae.