Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021

Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.

Antimicrobial susceptibilities of Neisseria gonorrhoeae in Canada, 2021

Background

In Canada, gonorrhea is the second most prevalent bacterial sexually transmitted infection. The Gonococcal Antimicrobial Surveillance Programme (GASP - Canada), a passive surveillance system monitoring antimicrobial resistance in Neisseria gonorrhoeae in Canada since 1985, is the source for this summary of demographics, antimicrobial resistance and N. gonorrhoeae multi-antigen sequence typing (NG-MAST) of gonococcal isolates collected in Canada in 2021.

Methods

Provincial and territorial public health laboratories submitted N. gonorrhoeae cultures and data to the National Microbiology Laboratory in Winnipeg as part of the surveillance system. The antimicrobial resistance and molecular type of each isolate received were determined.

Results

In total, 3,439 N. gonorrhoeae cultures were received from laboratories across Canada in 2021, a 9.9% increase since 2020 (n=3,130). Decreased susceptibility to cefixime increased significantly (p<0.001) in 2021 (1.5%) compared to 2017 (0.6%). No significant change in decreased susceptibility to ceftriaxone was detected between 2017 and 2021 (0.6%) (p>0.001); however, one ceftriaxone-resistant isolate was identified. Azithromycin resistance decreased significantly (p<0.001) in 2021 (7.6%) compared to 2017 (11.7%); however, there was a significant increase (p<0.001) in the proportion of cultures with an azithromycin minimum inhibitory concentration of at least 1 mg/L (2017=22.2% to 2021=28.1%). In 2021, NG-MAST-19875 (15.3%) was the most prevalent sequence type in Canada; 20.3% of isolates with this sequence type were resistant to azithromycin.

Conclusion

The spread of antimicrobial-resistant gonorrhea is a significant public health concern. The continued regional and national surveillance of antimicrobial resistance in N. gonorrhoeae is essential in ensuring effective treatment therapies are recommended.

Nirmatrelvir-ritonavir use among adults hospitalized with COVID-19 during the Omicron phase of the COVID-19 pandemic, Canadian Nosocomial Infection Surveillance Program

Background

Recent studies have demonstrated the effectiveness of nirmatrelvir-ritonavir in reducing the risk of progression to severe disease among outpatients with mild to moderate coronavirus disease 2019 (COVID-19); however, data are limited regarding the use and role of nirmatrelvir-ritonavir among hospitalized patients. This study describes the use and outcomes of nirmatrelvir-ritonavir among adults hospitalized with COVID-19 in a sentinel network of Canadian acute care hospitals during the Omicron variant phase of the pandemic.

Methods

The Canadian Nosocomial Infection Surveillance Program conducts surveillance of hospitalized patients with COVID-19 in acute care hospitals across Canada. Demographic, clinical, treatment and 30-day outcome data were collected by chart review by trained infection control professionals using standardized questionnaires.

Results

From January 1 to December 31, 2022, 13% (n=490/3,731) of adult patients (18 years of age and older) hospitalized with COVID-19 in 40 acute care hospitals received nirmatrelvir-ritonavir either at admission or during hospitalization. Most inpatients who received nirmatrelvir-ritonavir, 79% of whom were fully vaccinated, had at least one pre-existing comorbidity (97%) and were of advanced age (median=79 years). Few were admitted to an intensive care unit (2.3%) and among the 490 nirmatrelvir-ritonavir treated inpatients, there were 13 (2.7%) deaths attributable to COVID-19.

Conclusion

These findings from a large sentinel network of Canadian acute-care hospitals suggest that nirmatrelvir-ritonavir is being used to treat adult COVID-19 patients at admission who are at risk of progression to severe disease or those who acquired COVID-19 in hospital. Additional research on the efficacy and indications for nirmatrelvir-ritonavir use in hospitalized patients is warranted to inform future policies and guidelines.

Trends in Clostridioides difficile infection rates in Canadian hospitals during the coronavirus disease 2019 (COVID-19) pandemic

The coronavirus disease 2019 (COVID-19) pandemic has placed significant burden on healthcare systems. We compared Clostridioides difficile infection (CDI) epidemiology before and during the pandemic across 71 hospitals participating in the Canadian Nosocomial Infection Surveillance Program. Using an interrupted time series analysis, we showed that CDI rates significantly increased during the COVID-19 pandemic.

Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-2020

OBJECTIVES

To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada.

METHODS

The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011-2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants.

RESULTS

Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants.

CONCLUSIONS

Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.

Trends in Severe Outcomes Among Adult and Pediatric Patients Hospitalized With COVID-19 in the Canadian Nosocomial Infection Surveillance Program, March 2020 to May 2022

Importance

Trends in COVID-19 severe outcomes have significant implications for the health care system and are key to informing public health measures. However, data summarizing trends in severe outcomes among patients hospitalized with COVID-19 in Canada are not well described.

Objective

To describe trends in severe outcomes among patients hospitalized with COVID-19 during the first 2 years of the COVID-19 pandemic.

Design, Setting, and Participants

Active prospective surveillance in this cohort study was conducted from March 15, 2020, to May 28, 2022, at a sentinel network of 155 acute care hospitals across Canada. Participants included adult (aged ≥18 years) and pediatric (aged 0-17 years) patients hospitalized with laboratory-confirmed COVID-19 at a Canadian Nosocomial Infection Surveillance Program (CNISP)-participating hospital.

Exposures

COVID-19 waves, COVID-19 vaccination status, and age group.

Main Outcomes and Measures

The CNISP collected weekly aggregate data on the following severe outcomes: hospitalization, admission to an intensive care unit (ICU), receipt of mechanical ventilation, receipt of extracorporeal membrane oxygenation, and all-cause in-hospital death.

Results

Among 1 513 065 admissions, the proportion of adult (n = 51 679) and pediatric (n = 4035) patients hospitalized with laboratory-confirmed COVID-19 was highest in waves 5 and 6 of the pandemic compared with waves 1 to 4 (77.3 vs 24.7 per 1000 patient admissions). Despite this, the proportion of patients with positive test results for COVID-19 who were admitted to an ICU, received mechanical ventilation, received extracorporeal membrane oxygenation, and died were each significantly lower in waves 5 and 6 when compared with waves 1 through 4. Admission to the ICU and in-hospital all-cause death rates were significantly higher among those who were unvaccinated against COVID-19 when compared with those who were fully vaccinated (incidence rate ratio, 4.3 and 3.9, respectively) or fully vaccinated with an additional dose (incidence rate ratio, 12.2 and 15.1, respectively).

Conclusions and Relevance

The findings of this cohort study of patients hospitalized with laboratory-confirmed COVID-19 suggest that COVID-19 vaccination is important to reduce the burden on the Canadian health care system as well as severe outcomes associated with COVID-19.

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.

Antimicrobial susceptibilities of Neisseria gonorrhoeae in Canada, 2020

Background

The Gonococcal Antimicrobial Surveillance Programme is a passive surveillance system that has monitored antimicrobial resistance in Neisseria gonorrhoeae in Canada since the 1980s. This article summarizes the demographics, antimicrobial resistances and NG-MAST (N. gonorrhoeae multiantigen sequence typing) for cultures collected in 2020.

Methods

The National Microbiology Laboratory (NML) in Winnipeg received resistant N. gonorrhoeae cultures from provincial and territorial public health laboratories. Agar dilution was used to determine the minimum inhibitory concentrations to ten antimicrobials for all cultures received at NML, according to Clinical and Laboratory Standards Institute guidelines. The NG-MAST typing was also determined for each culture.

Results

A total of 3,130 N. gonorrhoeae cases were cultured across Canada in 2020; a 36% decrease from 2019 (n=4,859). The level of decreased susceptibility to cefixime increased significantly between 2016 and 2020 to 2.8% (p=0.0054). Decreased susceptibility to ceftriaxone declined significantly between 2016 (1.8%) and 2020 to 0.9% (p=0.001), and there was no significant change with azithromycin between 2016 (7.2%) and 2020 (6.1%). The proportion of cultures with an azithromycin minimum inhibitory concentrations of ≥1 mg/L increased significantly from 11.6% in 2016 to 15.3% in 2020 (p=0.0017). The most common NG-MAST type in Canada for 2020 was sequence type (ST)-11461, while ST-12302 was most commonly associated with azithromycin resistance and ST-16639 with cephalosporin decreased susceptibility.

Conclusion

Antimicrobial resistance in N. gonorrhoeae remains an important public health concern and continued surveillance is imperative to monitor trends to ensure the recommended therapies will be the most effective.

Invasive pneumococcal disease surveillance in Canada, 2020

Background

Invasive pneumococcal disease (IPD), which is caused by Streptococcus pneumoniae, has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has markedly decreased the incidence of IPD in Canada; however, the distribution of serotypes has shifted in favour of non-vaccine types. This report summarizes the demographics, serotypes and antimicrobial resistance of IPD infections in Canada in 2020.

Methods

The Public Health Agency of Canada's National Microbiology Laboratory (Winnipeg, Manitoba) collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. A total of 2,108 IPD isolates were reported in 2020. Serotyping was performed by Quellung reaction and antimicrobial susceptibilities were determined in collaboration with the University of Manitoba/Canadian Antimicrobial Resistance Alliance. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System.

Results

Overall incidence of IPD in Canada decreased significantly from 11.5 (95% confidence interval [CI]: 10.1-13.1) to 6.0 (95% CI: 5.0-7.2), and from 10.0 (95% CI: 9.7-10.3) to 5.9 (95% CI: 5.7-6.2) cases per 100,000 from 2019 to 2020; in those younger than five years and those five years and older, respectively. The most common serotypes overall were 4 (11.2%, n=237), 3 (10.9%, n=229) and 8 (7.2%, n=151). From 2016 to 2020, serotypes with increasing trends (p<0.05) included 4 (6.4%-11.2%), 3 (9.5%-10.9%), 8 (5.2%-7.2%) and 12F (3.6%-5.7%). The overall prevalence of PCV13 serotypes increased over the same period (30.3%-34.9%, p<0.05). Antimicrobial resistance rates in 2020 included 23.0% clarithromycin and 9.9% penicillin (IV meningitis breakpoints). Multidrug-resistant IPD has significantly increased since 2016 (4.2%-9.5%, p<0.05).

Conclusion

Though the incidence of IPD decreased in 2020 in comparison to previous years across all age groups, disease due to PCV13 serotypes 3 and 4, as well as non-PCV13 serotypes such as 8 and 12F, increased in prevalence. Continued surveillance of IPD is imperative to monitor shifts in serotype distribution and antimicrobial resistance.

Invasive group A streptococcal disease surveillance in Canada, 2020

Background

Invasive group A streptococcal (iGAS) disease (caused by Streptococcus pyogenes) has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, emm types and antimicrobial resistance of iGAS infections in Canada in 2020.

Methods

The Public Health Agency of Canada's National Microbiology Laboratory (Winnipeg, Manitoba) collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive S. pyogenes. Emm typing was performed on all isolates using the Centers for Disease Control and Prevention emm sequencing protocol. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines. Population-based iGAS disease incidence rates up to 2019 were obtained through the Canadian Notifiable Disease Surveillance System.

Results

Overall, the incidence of iGAS disease in Canada has increased from 4.0 to 8.1 cases per 100,000 population from 2009 to 2019. The 2019 incidence represents a slight decrease from the 2018 rate of 8.6 cases per 100,000 population. A total of 2,867 invasive S. pyogenes isolates that were collected during 2020 are included in this report, representing a decrease from 2019 (n=3,194). The most common emm types in 2020 were emm49 (16.8%, n=483) and emm76 (15.0%, n=429), both increasing significantly in prevalence since 2016 (p<0.001). The former most prevalent type, emm1, decreased to 7.6% (n=217) in 2020 from 15.4% (n=325) in 2016. Antimicrobial resistance rates in 2020 included 11.5% resistance to erythromycin, 3.2% resistance to clindamycin and 1.6% nonsusceptibility to chloramphenicol.

Conclusion

Though the number of collected invasive S. pyogenes isolates decreased slightly in 2020 in comparison to previous years, iGAS disease remains an important public health concern. The emm distribution in Canada has been subtly shifting over the past five years, away from common and well-known emm1 and towards emm49 and emm76. It is important to continue surveillance of S. pyogenes in Canada to monitor expanding replacement emm types, as well as outbreak clones and antimicrobial resistance.

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

Extended-spectrum β-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 bla_SHV-2 and bla_CTX-M-1 IncI1 plasmids_, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-bla_SHV-2 plasmid differed by only 1–7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying bla_CTX-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.

Characterization of Healthcare-Associated and Community-Associated Clostridioides difficile Infections among Adults, Canada, 2015-2019

We investigated epidemiologic and molecular characteristics of healthcare-associated (HA) and community-associated (CA) Clostridioides difficile infection (CDI) among adult patients in Canadian Nosocomial Infection Surveillance Program hospitals during 2015–2019. The study encompassed 18,455 CDI cases, 13,735 (74.4%) HA and 4,720 (25.6%) CA. During 2015–2019, HA CDI rates decreased by 23.8%, whereas CA decreased by 18.8%. HA CDI was significantly associated with increased 30-day all-cause mortality as compared with CA CDI (p<0.01). Of 2,506 isolates analyzed, the most common ribotypes (RTs) were RT027, RT106, RT014, and RT020. RT027 was more often associated with CDI-attributable death than was non-RT027, regardless of acquisition type. Overall resistance C. difficile rates were similar for all drugs tested except moxifloxacin. Adult HA and CA CDI rates have declined, coinciding with changes in prevalence of RT027 and RT106. Infection prevention and control and continued national surveillance are integral to clarifying CDI epidemiology, investigation, and control.

An outbreak of COVID-19 associated with a fitness centre in Saskatchewan: Lessons for prevention

BACKGROUND

An outbreak of the coronavirus disease 2019 (COVID-19) occurred in Saskatchewan from September 12 to October 20, 2020. The index event, attendance at a local gym, seeded six additional clusters/outbreaks in multiple settings. These included a high school, a hospital, three workplaces (A, B and C) and several households. The overall cluster comprised 63 cases, 27 gym members and an additional 36 second, third and fourth generation cases.

METHODS

All outbreak-related, laboratory-confirmed cases of COVID-19 were included in the analysis. Local public health authorities interviewed all cases and contacts and conducted environmental investigations of the fitness facility. We used descriptive epidemiological methods to understand transmission dynamics of the gym-associated cluster using case investigation, contact investigation and laboratory data, including whole genome sequencing.

RESULTS

Sequencing data confirmed the unique lineage of cluster-related cases (n=32 sequenced; severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2] lineage B.1.1.72). In addition to gym attendance, infectious cases attended high school and were involved in other activities. Despite ongoing transmission in the fitness facility, no secondary cases were identified in the high school where four student belonging to the cluster attended class during their infectious period.

CONCLUSION

We describe an outbreak of COVID-19 where the index case(s) attended a fitness facility, and further spread occurred for 38 days despite active-case finding and isolation of positive cases over this period. Due to gym attendance over time, short-term closing and cleaning may not interrupt chains of transmission. Targeted, preventive public health action in fitness facilities may be warranted. Control measures worked to limit in-school acquisition.

High Prevalence of Macrolide and Fluoroquinolone Resistance-Mediating Mutations in Mycoplasma genitalium-Positive Urine Specimens From Saskatchewan

BACKGROUND

Mycoplasma genitalium is an emerging, sexually transmitted infection, which is more prevalent than Chlamydia trachomatis in some regions. An increase in antibiotic resistance, that is, azithromycin and moxifloxacin, recommended for treating M. genitalium infections has been noted. This is the first detailed report on the prevalence of M. genitalium and its antimicrobial resistance in Saskatchewan, Canada.

METHODS

Aptima urine specimens (n = 1977), collected for the diagnosis of C. trachomatis/Neisseria gonorrhoeae, were tested for M. genitalium using the Aptima M. genitalium assay (MG-TMA). Antimicrobial resistance was ascertained using polymerase chain reaction and DNA sequencing of 23S rRNA (azithromycin) and parC (moxifloxacin) from Aptima M. genitalium assay-positive specimens; mutations predictive of resistance were noted.

RESULTS

The prevalence of M. genitalium was 9.6% (189/1977). Predicted resistance to azithromycin (substitutions at positions 2058/2059 in 23S rRNA) was observed in 63.6% (70/110) of the specimens tested, whereas resistance to moxifloxacin (S83I in ParC) was observed in 10.6% (9/85) of the specimens. Mutations in both 23S rRNA and ParC were observed in 2.12% (4/189) of the specimens. Women aged 20 to 24 years had the highest prevalence (18.3%, P < 0.001), and in females, M. genitalium was significantly associated with C. trachomatis or N. gonorrhoeae/C. trachomatis (P < 0.001) coinfection. The prevalence of M. genitalium (9.6%) in the province of Saskatchewan was higher than that of the other 2 bacterial sexually transmitted infections (N. gonorrhoeae (3.09%) and C. trachomatis (6.85%).

CONCLUSIONS

The prevalence of M. genitalium (9.6%) and associated resistance to azithromycin (63.6%) in Saskatchewan high, suggesting that empiric azithromycin therapy may not be adequate for treating M. genitalium infections.

Evaluation of Adjunctive Azithromycin Prophylaxis in Women Undergoing Cesarean Delivery in a Setting With Low Baseline Incidence of Surgical Site Infection

OBJECTIVE

The purpose of this quality improvement study was to determine the effect of adding azithromycin to standard antibiotic prophylaxis on the rates surgical site infection (SSI) in women undergoing both elective and non-elective cesarean deliveries at our centre.

METHODS

A before-and-after quality improvement study was conducted at the Regina General Hospital in Regina, Saskatchewan. Data collected from 989 women who had a caesarean delivery between June 1, 2016 and June 30, 2017 were compared with those from 1033 women who had a caesarean delivery between August 1, 2017 and July 31, 2018, after the introduction of adjunctive azithromycin prophylaxis. The primary outcome measure was the change in the incidence of SSI up to 30 days following surgery. Secondary outcome measures included timing of azithromycin prophylaxis and the number of women who did not receive azithromycin.

RESULTS

Surgical site infection rates decreased from 3.5% to 2.9% after adjunctive azithromycin prophylaxis was introduced. The absolute reduction in SSIs of 0.6% was not statistically significant (P = 0.42). There were no differences in SSI rates between the elective and non-elective subgroups.

CONCLUSION

Adding azithromycin to the standard antibiotic prophylaxis for cesarean delivery showed no statistically significant reduction in SSI rates in a population with low baseline rates of SSI.

Characterization of antimicrobial resistance genes from Neisseria gonorrhoeae positive remnant Aptima urine specimens

Aim: To ascertain the antimicrobial resistance and strain types (STs) of Neisseria gonorrhoeae from 50 remnant Aptima urine specimens using molecular methods. Methods: Mutations predictive of resistance to six antibiotics were identified in eight genes. STs were determined using NG-MAST and NG-STAR. Results: All eight antimicrobial resistance genes could be characterized in 36 specimens. A total of 17 specimens were predicted to be susceptible to all antibiotics, including ceftriaxone. Decreased susceptibility to cefixime and ciprofloxacin resistance was predicted in 11 specimens (PBP2 type 34.001). Overall, 38/50 specimens were predicted to be ciprofloxacin susceptible; three were azithromycin resistant. Nineteen NG-MAST and 21 NG-STAR STs were noted. Conclusion: Molecular analysis of remnant Aptima specimens enabled the prediction of emerging gonococcal cefixime and azithromycin resistance which would otherwise have been undetected.

Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada

This study examined the phylogenetic structure of serotype a Haemophilus influenzae (Hia) isolates recovered from patients in Canada. Hia isolates from 490 separate patients and an American Type Culture Collection (ATCC) strain were analyzed by multilocus sequence typing (MLST), with 18 different sequence types (STs) identified. Most (85.7%) Hia patient isolates were typed as ST-23 and another 12.7% belonged to 14 different STs with 6, 5, or 4 MLST gene loci related to ST-23 (ST-23 complex). Core genome single-nucleotide variation phylogeny (SNVPhyl) on whole genome sequence (WGS) data of 121 Hia patient isolates representing all identified STs and the ATCC strain revealed 2 phylogenetic populations, with all the ST-23 complex isolates within 1 population. The other phylogenetic population contained only the ATCC strain and 3 patient isolates. Concatenated hitABC sequences retrieved from WGS data and analyzed by MEGA (Molecular Evolutionary Genetic Analysis) alignment confirmed the phylogeny obtained by SNVPhyl. The sodC gene was found only in isolates in the minor phylogenetic population. The 2 phylogenetic populations of the Canadian Hia isolates are similar to the 2 clonal divisions described for serotype b H. influenzae. Combining MLST, core SNVPhyl, and hitABC gene sequence alignment showed that most (99.4%) Canadian Hia patient isolates belonged to 1 major phylogenetic population.

The evolving epidemiology of Clostridium difficile infection in Canadian hospitals during a postepidemic period (2009-2015)

BACKGROUND

The clinical and molecular epidemiology of health care-associated Clostridium difficile infection in nonepidemic settings across Canada has evolved since the first report of the virulent North American pulsed-field gel electrophoresis type 1 (NAP1) strain more than 15 years ago. The objective of this national, multicentre study was to describe the evolving epidemiology and molecular characteristics of health care-associated C. difficile infection in Canada during a post-NAP1-epidemic period, particularly patient outcomes associated with the NAP1 strain.

METHODS

Adult inpatients with C. difficile infection were prospectively identified, using a standard definition, between 2009 and 2015 through the Canadian Nosocomial Infection Surveillance Program (CNISP), a network of 64 acute care hospitals. Patient demographic characteristics, severity of infection and outcomes were reviewed. Molecular testing was performed on isolates, and strain types were analyzed against outcomes and epidemiologic trends.

RESULTS

Over a 7-year period, 20 623 adult patients admitted to hospital with health care-associated C. difficile infection were reported to CNISP, and microbiological data were available for 2690 patients. From 2009 to 2015, the national rate of health care-associated C. difficile infection decreased from 5.9 to 4.3 per 10 000 patient-days. NAP1 remained the dominant strain type, but infection with this strain has significantly decreased over time, followed by an increasing trend of infection with NAP4 and NAP11 strains. The NAP1 strain was significantly associated with a higher rate of death attributable to C. difficile infection compared with non-NAP1 strains (odds ratio 1.91, 95% confidence interval [CI] 1.29-2.82). Isolates were universally susceptible to metronidazole; one was nonsusceptible to vancomycin. The proportion of NAP1 strains within individual centres predicted their rates of health care-associated C. difficile infection; for every 10% increase in the proportion of NAP1 strains, the rate of health care-associated C. difficile infection increased by 3.3% (95% CI 1.7%-4.9%).

INTERPRETATION

Rates of health care-associated C. difficile infection have decreased across Canada. In nonepidemic settings, NAP4 has emerged as a common strain type, but NAP1, although decreasing, continues to be the predominant circulating strain and remains significantly associated with higher attributable mortality.

Increase in ST-11 serogroup W Neisseria meningitidis invasive meningococcal disease in Canada, 2016-2018

BACKGROUND

Many countries have experienced increases in invasive meningococcal disease (IMD) due to a serogroup W Neisseria meningitidis (MenW) strain of the multilocus sequence type (ST)-11 clonal complex (CC). MenW ST-11 was first reported in Ontario, Canada, in 2014. By 2016, this strain caused IMD in five provinces and was responsible for 18.8% of the IMD cases in Canada.

OBJECTIVE

To provide an update on invasive MenW disease in Canada including the strain characteristics, specimen source of isolates, age, sex and geographic distribution of cases.

METHODS

N. meningitidis from culture-positive IMD cases are routinely submitted to the National Microbiology Laboratory (NML) for serogroup, serotype, serosubtype and sequence type analysis. The data from January 1, 2016 to December 31, 2018 were analyzed by calculating the proportion of IMD cases caused by MenW compared with other serogroups. In addition, trends based on age, sex and geographic distribution of cases and specimen source of isolates were analyzed based on information on specimen requisition forms.

RESULTS

Over the 3-year period, 292 individual IMD case isolates were analyzed. The percentage of IMD case isolates typed as MenW more than doubled from 19% (n=15) to 44% (n=51) in 2018 when MenW became the most common serogroup, exceeded the number of MenB, MenC or MenY. In total, 93 MenW case isolates were identified, 91% (n=85) belonged to the ST-11 CC. The increase in MenW affected all age groups (but was most common in those older than 60) and both sexes, and occurred across the country but most prevalent in western Canada. The most common specimen source was blood.

CONCLUSION

In 2018, MenW was the most common serogroup for isolates received by the NML from culture-positive IMD cases in Canada. Over 90% of the MenW serogroup isolates belonged to the ST-11 CC. The quadrivalent ACWY meningococcal conjugate vaccine protects against IMD caused by strains in the A, C, W or Y serogroups and therefore may protect against IMD caused by the new MenW ST-11 strain; however, more research is needed. The emergence of variant strains highlight the importance of strain characterization in IMD surveillance and research.

Multidrug-resistant and extensively drug-resistant Neisseria gonorrhoeae in Canada, 2012-2016

BACKGROUND

Neisseria gonorrhoeae have acquired resistance to many antimicrobials, including third generation cephalosporins and azithromycin, which are the current gonococcal combination therapy recommended by the Canadian Guidelines on Sexually Transmitted Infections.

OBJECTIVE

To describe antimicrobial susceptibilities for N. gonorrhoeae circulating in Canada between 2012 and 2016.

METHODS

Antimicrobial resistance profiles were determined using agar dilution of N. gonorrhoeae isolated in Canada 2012-2016 (n=10,167) following Clinical Laboratory Standards Institute guidelines. Data were analyzed by applying multidrug-resistant gonococci (MDR-GC) and extensively drug-resistant gonococci (XDR-GC) definitions.

RESULTS

Between 2012 and 2016, the proportion of MDR-GC increased from 6.2% to 8.9% and a total of 19 cases of XDR-GC were identified in Canada (0.1%, 19/18,768). The proportion of isolates with decreased susceptibility to cephalosporins declined between 2012 and 2016 from 5.9% to 2.0% while azithromycin resistance increased from 0.8% to 7.2% in the same period.

CONCLUSION

While XDR-GC are currently rare in Canada, MDR-GC have increased over the last five years. Azithromycin resistance in N. gonorrhoeae is established and spreading in Canada, exceeding the 5% level at which the World Health Organization states an antimicrobial should be reviewed as an appropriate treatment. Continued surveillance of antimicrobial susceptibilities of N. gonorrhoeae is necessary to inform treatment guidelines and mitigate the impact of resistant gonorrhea.

Blastomycosis in Southern Saskatchewan 2000-2015: Unique presentations and disease characteristics

In the literature, cases of blastomycosis in Canada have been documented in provinces bordering the Great Lakes, including Ontario and Quebec, as well as Manitoba. This is the first study to our knowledge reporting cases of mycosis seen in southern Saskatchewan suggesting a broader area of endemicity. We searched the Regina Qu'Appelle Health Region (RQHR) Microbiology Laboratory for all culture-confirmed cases of Blastomyces from January 2000 to December 2015 and identified 15 cases. Thirteen cases were reviewed, identifying common presenting symptoms, misdiagnosis, comorbidities, travel history, time from presentation to diagnosis, diagnostic specimen, treatment, and clinical outcome. Nine patients had no travel to areas known to be endemic to environmental blastomycosis. Eight patients presented with respiratory symptoms, four with skin lesions, four with constitutional symptoms, and one presented with chest pain after a fall. Initial misdiagnosis occurred in nine (69%) of the 13 cases, and all six patients that died of the disease were misdiagnosed. These six patients (46%) were acutely ill with refractory disseminated disease, leading to respiratory failure. It is probable that Blastomyces is present as an endemic fungus in the soil of southern Saskatchewan. Possibly due to a lack of awareness of this pathogen in the area, initial misdiagnoses were common and likely contributed to significant morbidity and mortality.

Disseminated Exophiala dermatitidis causing septic arthritis and osteomyelitis

Background

Exophiala dermatitidis is a melanized fungus isolated from many environmental sources. Infections caused by Exophiala species are typically seen in immunocompromised hosts and manifest most commonly as cutaneous or subcutaneous disease. Systemic infections are exceedingly rare and associated with significant morbidity and mortality

Case presentation

A 28-year-old female originally from India presented with fevers, chills, weight loss and increasing back pain. She had a recent diffuse maculopapular rash that resulted in skin biopsy and a tentative diagnosis of sarcoidosis, leading to administration of azathioprine and prednisone. An MRI of her spine revealed a large paraspinal abscess requiring surgical intervention and hardware placement. Cultures from the paraspinal abscess grew a colony of dark pigmented mold. Microscopy of the culture revealed a melanized fungus, identified as Exophiala dermatitidis. Voriconazole was initially utilized, but due to relapse of infection involving the right iliac crest and left proximal humerus, she received a prolonged course of amphotericin B and posaconazole in combination and required 7 separate surgical interventions. Prolonged disease stability following discontinuation of therapy was achieved.

Conclusions

Described is the first identified case of disseminated Exophiala dermatitidis causing osteomyelitis and septic arthritis in a patient on immunosuppressive therapy. A positive outcome was achieved through aggressive surgical intervention and prolonged treatment with broad-spectrum antifungal agents.

Cinnamomum zeylanicum bark essential oil induces cell wall remodelling and spindle defects in Candida albicans

Background

Cinnamon (Cinnamomum zeylanicum) bark extract exhibits potent inhibitory activity against Candida albicans but the antifungal mechanisms of this essential oil remain largely unexplored.

Results

We analyzed the impact of cinnamon bark oil on C. albicans RSY150, and clinical strains isolated from patients with candidemia and candidiasis. The viability of RSY150 was significantly compromised in a dose dependent manner when exposed to cinnamon bark oil, with extensive cell surface remodelling at sub inhibitory levels (62.5 μg/mL). Atomic force microscopy revealed cell surface exfoliation, altered ultrastructure and reduced cell wall integrity for both RSY150 and clinical isolates exposed to cinnamon bark oil. Cell wall damage induced by cinnamon bark oil was confirmed by exposure to stressors and the sensitivity of cell wall mutants involved in cell wall organization, biogenesis, and morphogenesis. The essential oil triggered cell cycle arrest by disrupting beta tubulin distribution, which led to mitotic spindle defects, ultimately compromising the cell membrane and allowing leakage of cellular components. The multiple targets of cinnamon bark oil can be attributed to its components, including cinnamaldehyde (74%), and minor components (< 6%) such as linalool (3.9%), cinamyl acetate (3.8%), α-caryophyllene (5.3%) and limonene (2%). Complete inhibition of the mitotic spindle assembly was observed in C. albicans treated with cinnamaldehyde at MIC (112 μg/mL).

Conclusions

Since cinnamaldehyde disrupts both the cell wall and tubulin polymerization, it may serve as an effective antifungal, either by chemical modification to improve its specificity and efficacy or in combination with other antifungal drugs.

Electronic supplementary material

The online version of this article (10.1186/s40694-018-0046-5) contains supplementary material, which is available to authorized users.

Hematospermia in a returned traveler

Hematospermia is a common complaint among patients seen in outpatient urology clinics. The differential diagnosis is broad and includes inflammatory, infectious, neoplastic, structural, systemic, and traumatic causes. The most common infectious causes are uropathogens and sexually transmitted infections. However, with increasing global travel, physicians must maintain a high clinical suspicion for pathogens not endemic to their region, including Echinococcus, Mycobacterium tuberculosis, and Schistosoma.1 We present a case of hematospermia in a traveler returning from Eastern Africa with exposure to Lake Malawi. The patient's microscopic analysis of semen was positive for Schistosoma haematobium, revealing a rare presentation of S. haematobium infection.

Multidrug and extensively drug-resistant tuberculosis in Canada 1997-2008: demographic and disease characteristics

Setting

Nationwide Canadian public health surveillance.

Objective

Description of demographic features and disease characteristics of drug-resistant tuberculosis (TB) in Canada over a 12 year period.

Design

Continuous surveillance of all cases of culture-confirmed TB in Canada. Demographic and microbiologic features were analyzed and comparisons between drug-susceptible, multidrug-resistant (MDR), and drug-resistant not-MDR were made. Cases of extensively drug resistant TB are described.

Results

15,993 cases of culture-confirmed TB were reported during the study period. There were 5 cases of XDR-TB, 177 cases of MDR-TB, and 1,234 cases of first-line drug resistance not-MDR. The majority of drug-resistant cases were reported in foreign-born individuals, with drug-resistant cases diagnosed earlier post-arrival in Canada compared to drug-susceptible cases. In MDR-TB isolates, there was a high rate of drug-resistance to other first- and second-line drugs, making reliable empiric therapeutic recommendations for MDR-TB difficult. There was a statistically significant association between both MDR and drug-resistance not-MDR, and the risk of a negative treatment outcome (defined as treatment failure, absconded, or treatment ongoing >3 yrs).

Conclusion

Drug-resistance complicates TB management even in developed nations with well-established TB control programs. The predominantly international origin of drug-resistant cases highlights the need for global strategies to combat TB.

An updated systematic review and meta-analysis on the treatment of active tuberculosis in patients with HIV infection

BACKGROUND

Human immunodeficiency virus (HIV) infection increases the risk of poor outcomes in active tuberculosis. We updated a systematic review and meta-analysis assessing the effects of duration of rifamycins, schedule of dosing, and antiretroviral therapy (ART) on failure, relapse, death during treatment, and acquired drug resistance (ADR) in patients with HIV and active tuberculosis.

METHODS

We searched for randomized control trials (RCTs) and observational studies published between January 2008 and November 2011. We pooled risk differences (RD) from RCTs comparing rifampin for ≥9 months and 6 months. Within strata of the 3 treatment covariates, we calculated pooled risks and adjusted odds ratios (aORs) using outcomes from RCTs and observational studies.

RESULTS

After screening 2293 citations, 7 studies were added in the update. Risk of relapse was lowered with rifampin treatment for ≥9 months compared with 6 months (pooled RD = -9.1%; 95% CI, -16.5, -1.8). Odds of relapse were higher with shorter durations of rifamycins (aOR 2 vs ≥8 months = 5.0 [1.9, 13.2]; 6 vs ≥8 months = 2.4 [1.2, 5.0]) and in the absence of ART (aOR = 14.3, [2.1, 97.8]). Post hoc meta-regression restricted to arms with ART demonstrated no associations between rifamycin duration, dosing schedule, and outcomes.

CONCLUSIONS

In patients with HIV and active tuberculosis, ART reduces the risk of TB relapse. Use of rifamycins for ≥8 months and daily dosing in the intensive phase also improve TB treatment outcomes; however, a paucity of evidence makes their importance less clear for patients on ART. There is an urgent need to increase the number of coinfected patients receiving ART.

Accuracy of rapid influenza diagnostic tests: a meta-analysis

BACKGROUND

Timely diagnosis of influenza can help clinical management.

PURPOSE

To examine the accuracy of rapid influenza diagnostic tests (RIDTs) in adults and children with influenza-like illness and evaluate factors associated with higher accuracy.

DATA SOURCES

PubMed and EMBASE through December 2011; BIOSIS and Web of Science through March 2010; and citations of articles, guidelines, reviews, and manufacturers.

STUDY SELECTION

Studies that compared RIDTs with a reference standard of either reverse transcriptase polymerase chain reaction (first choice) or viral culture.

DATA EXTRACTION

Reviewers abstracted study data by using a standardized form and assessed quality by using Quality Assessment of Diagnostic Accuracy Studies criteria.

DATA SYNTHESIS

159 studies evaluated 26 RIDTs, and 35% were conducted during the H1N1 pandemic. Failure to report whether results were assessed in a blinded manner and the basis for patient recruitment were important quality concerns. The pooled sensitivity and specificity were 62.3% (95% CI, 57.9% to 66.6%) and 98.2% (CI, 97.5% to 98.7%), respectively. The positive and negative likelihood ratios were 34.5 (CI, 23.8 to 45.2) and 0.38 (CI, 0.34 to 0.43), respectively. Sensitivity estimates were highly heterogeneous, which was partially explained by lower sensitivity in adults (53.9% [CI, 47.9% to 59.8%]) than in children (66.6% [CI, 61.6% to 71.7%]) and a higher sensitivity for influenza A (64.6% [CI, 59.0% to 70.1%) than for influenza B (52.2% [CI, 45.0% to 59.3%).

LIMITATION

Incomplete reporting limited the ability to assess the effect of important factors, such as specimen type and duration of influenza symptoms, on diagnostic accuracy.

CONCLUSION

Influenza can be ruled in but not ruled out through the use of RIDTs. Sensitivity varies across populations, but it is higher in children than in adults and for influenza A than for influenza B.

PRIMARY FUNDING SOURCE

Canadian Institutes of Health Research.

Microcolony culture techniques for tuberculosis diagnosis: a systematic review

BACKGROUND

There is considerable demand for quicker and more affordable yet accurate diagnostic tools for tuberculosis (TB). The microscopic observation drug susceptibility (MODS) assay and the thin-layer agar (TLA) assay are inexpensive, rapid microcolony-based culture methods.

METHODS

A systematic review and meta-analysis was performed to assess the accuracy and other test characteristics of MODS and TLA compared to a reference standard of traditional solid or liquid culture. Pooled estimates of sensitivity and specificity and their 95% confidence intervals were estimated with an exact binomial likelihood random effects meta-analysis.

RESULTS

A total of 21 eligible studies were identified, 12 that evaluated MODS, seven that evaluated TLA and two that evaluated both. The overall pooled sensitivity and specificity of MODS were respectively 92% (95%CI 87-97) and 96% (90-100), and for TLA they were respectively 87% (95%CI 79-94) and 98% (95%CI 94-100), although there was considerable heterogeneity of results. When the studies were restricted to those assessing accuracy of MODS in sputum samples only, the sensitivity was 96% (95%CI 94-98) and the specificity 96% (95%CI 89-100). The mean intervals from reception of specimens to results were 9.2 days with MODS and 11.5 days with TLA; contamination rates averaged 6.6% with MODS and 12.3% with TLA; materials and supplies costs averaged US$1.48 for MODS and US$2.42 for TLA.

CONCLUSIONS

MODS and TLA appear to be accurate and rapid yet inexpensive diagnostic tools for active TB. However, this review did not find sufficient evidence on the feasibility and costs of implementation of these tests, nor on the impact of these tests on patient outcomes.

Comparison of LED and conventional fluorescence microscopy for detection of acid fast bacilli in a low-incidence setting

INTRODUCTION

Light emitting diode fluorescence microscopes have many practical advantages over conventional mercury vapour fluorescence microscopes, which would make them the preferred choice for laboratories in both low- and high-resource settings, provided performance is equivalent.

METHODS

In a nested case-control study, we compared diagnostic accuracy and time required to read slides with the Zeiss PrimoStar iLED, LW Scientific Lumin, and a conventional fluorescence microscope (Leica DMLS). Mycobacterial culture was used as the reference standard, and subgroup analysis by specimen source and organism isolated were performed.

RESULTS

There was no difference in sensitivity or specificity between the three microscopes, and agreement was high for all comparisons and subgroups. The Lumin and the conventional fluorescence microscope were equivalent with respect to time required to read smears, but the Zeiss iLED was significantly time saving compared to both.

CONCLUSIONS

Light emitting diode microscopy should be considered by all tuberculosis diagnostic laboratories, including those in high income countries, as a replacement for conventional fluorescence microscopes. Our findings provide support to the recent World Health Organization policy recommending that conventional fluorescence microscopy be replaced by light emitting diode microscopy using auramine staining in all settings where fluorescence microscopy is currently used.

Evaluation of light emitting diode-based fluorescence microscopy for the detection of mycobacteria in a tuberculosis-endemic region

OBJECTIVES

To evaluate fluorescence microscopy (FM) using light emitting diode (LED) technology for the detection of acid-fast bacilli at a tertiary referral centre in Mumbai, India, a tuberculosis-endemic country.

DESIGN

LED FM was introduced into a laboratory experienced with Ziehl-Neelsen (ZN) microscopy but unfamiliar with FM. It was evaluated in parallel with routine ZN microscopy services and compared with mycobacterial culture as a reference standard.

RESULTS

A total of 1357 pulmonary and 917 extra-pulmonary specimens were examined during the study. LED FM had 78.3% sensitivity and 92.0% specificity against mycobacterial culture when using pulmonary specimens, and 34.0% sensitivity and 88.8% specificity for extra-pulmonary specimens. The mean time per smear examination was 2.48 min for ZN vs. 1.41 min for LED FM. Several biases in study design and operation identified during analysis, which are likely to lead to underestimates of LED FM accuracy, are discussed in the context of future LED FM evaluations.

CONCLUSIONS

Although LED FM has significant benefits over both ZN microscopy and conventional FM, its implementation and validation may be prone to difficulties which could hamper evaluation of its performance. Adequate training and detailed standard operating procedures are important to maximise accuracy.

Diagnosing tuberculosis with urine lipoarabinomannan: systematic review and meta-analysis

Lipoarabinomannan (LAM) is a potential marker of active tuberculosis (TB). We performed a systematic review and meta-analysis regarding use of urinary LAM assays for diagnosing active TB. We systematically searched for published and unpublished studies that evaluated urinary LAM for active TB diagnosis. Extracted data were pooled using bivariate random effects models and hierarchical summary receiver operating characteristic curves. Heterogeneity was explored through subgroup analysis and meta-regression. Quality was assessed according to standardised QUADAS (Quality Assessment of Diagnostic Accuracy Studies) criteria. In seven studies that assessed test accuracy in microbiologically confirmed cases only, estimates of sensitivity ranged from 13% to 93%, while specificity ranged from 87% to 99%. In five studies that assessed accuracy in clinical and confirmed TB cases, sensitivity ranged from 8% to 80%, while specificity ranged from 88% to 99%. In five studies with results stratified by HIV status, sensitivity was 3-53% higher in HIV-positive than HIV-negative subgroups; sensitivity was highest with advanced immunosuppression. The LAM urinary assay has several characteristics that make it attractive for diagnosing active TB, but has suboptimal sensitivity for routine clinical use. Further studies are needed to evaluate the potential value of the LAM assay in individuals with advanced HIV or for diagnosis of paediatric TB.

Microscopic-observation drug susceptibility and thin layer agar assays for the detection of drug resistant tuberculosis: a systematic review and meta-analysis

BACKGROUND

Simple, rapid, and affordable tests are needed to detect drug resistance in Mycobacterium tuberculosis. We did a systematic review and meta-analysis to investigate the accuracy of microscopic-observation drug susceptibility (MODS) and thin layer agar (TLA) assays for rapid screening of patients at risk of drug-resistant tuberculosis.

METHODS

In accordance with protocols and methods recommended by the Cochrane Diagnostic Test Accuracy Working Group, we systematically searched PubMed, Embase, and Biosis for reports published between January, 1990, and February, 2009. We included studies investigating detection of drug resistance in M tuberculosis with the MODS or TLA assay, and in which an accepted reference standard was used. Data extracted from the studies were combined by use of bivariate random-effects regression models and hierarchical summary receiver operating characteristic curves to estimate sensitivity and specificity for detection of resistance to specific drugs.

FINDINGS

We identified 12 studies, of which nine investigated the MODS assay and three investigated the TLA assay. For the MODS assay of rifampicin resistance, pooled estimates were 98·0% (95% CI 94·5-99·3) for sensitivity and 99·4% (95·7-99·9) for specificity. For the MODS assay of isoniazid resistance with a 0·1 μg/mL cutoff, pooled sensitivity was 97·7% (94·4-99·1) and pooled specificity was 95·8% (88·1-98·6), but with a 0·4 μg/mL cutoff, sensitivity decreased to 90·0% (84·5-93·7) and specificity increased to 98·6% (96·9-99·4). All assessments of rifampicin and isoniazid resistance with the TLA assay yielded 100% accuracy. Mean turnaround time was 9·9 days (95% CI 4·1-15·8) for the MODS assay and 11·1 days (10·1-12·0) for the TLA assay.

INTERPRETATION

MODS and TLA assays are inexpensive, rapid alternatives to conventional methods for drug susceptibility testing of M tuberculosis. Our data and expert opinion informed WHO's recommendation for use of selected non-commercial drug susceptibility tests, including MODS, as an interim solution until capacity for genotypic or automated liquid culture drug susceptibility testing is developed.

FUNDING

Stop TB Department of WHO.

Bacteriophage assays for rifampicin resistance detection in Mycobacterium tuberculosis: updated meta-analysis

OBJECTIVE

To update a previously reported meta-analysis of evidence regarding the diagnostic accuracy and performance characteristics of commercial and non-commercial phage-based assays for the detection of rifampicin (RMP) resistant tuberculosis (TB). DESIGN AND OUTCOMES: We conducted a systematic review and meta-analysis of test accuracy using bivariate random effects regression and hierarchical summary receiver operating characteristics (HSROC) analysis. Tests included the commercial FASTPlaque assays, luciferase reporter phage (LRP) assays, and in-house phage amplification tests. Sensitivity and specificity for RMP resistance were the main outcomes.

RESULTS

By updating previous literature searches, a total of 31 studies (with 3085 specimens) were included in this meta-analysis. Evaluations of commercial phage amplification assays yielded more variable estimates of sensitivity (range 81-100%) and specificity (range 73-100%) compared to evaluations of in-house amplification assays (sensitivity range 88-100%, specificity range 84-100%). LRP evaluations yielded the most consistent estimates of diagnostic accuracy, with seven of eight studies reporting 100% sensitivity and four of eight reporting 100% specificity. Estimates of accuracy failed to capture a major failing of the commercial assay, i.e., the rate of contaminated and indeterminate results. These ranged from 3% to 36% in studies looking at direct detection of RMP resistance from patient specimens (mean 20%).

CONCLUSION

Phage-based assays will require further development to maximise interpretable results and reduce technical failures. Once technical issues are resolved, impact on patient-important outcomes and cost-effectiveness need to be determined to inform policy for widespread use.

Serotypes and antimicrobial susceptibilities of invasive Streptococcus pneumoniae pre- and post-seven valent pneumococcal conjugate vaccine introduction in Alberta, Canada, 2000-2006

Alberta, Canada introduced the Streptococcus pneumoniae seven valent conjugate vaccine (PCV7) program for children less than 2 years of age in September 2002. We determined the rates of invasive pneumococcal disease in Alberta, Canada 2 years pre- and 4 years post-PCV7 introduction (2000-2006) as well as the rates of antibiotic resistance and serotype distribution in this same time period. Overall, PCV7 serotypes decreased 61% from 2000 to 2006. The greatest decrease in incidence of invasive pneumococcal disease occurred in children less than 2 years of age declining from a high of 96.7/100,000 (2000) to 25.8/100,000 (2006) (P<0.0001). Non-susceptibility of S. pneumoniae isolates to penicillin dropped significantly from 14% in 2000 to 4.6% in 2006 (P<0.0001). Non-susceptible erythromycin isolates also decreased from 8.8% (2000) to 5.8% (2006) (P=0.13). The introduction of PCV7 in Alberta, Canada has decreased the incidence of invasive pneumococcal disease in Alberta as well as resulting in a decrease in antibiotic resistance over this same time frame, principally for penicillin resistance.