Ethics Guidance for Environmental Scientists Engaged in Surveillance of Wastewater for SARS-CoV-2.

The COVID-19 pandemic has given rise to rapid and widespread international pursuit of wastewater surveillance for genetic signals of SARS-CoV-2, the virus causing the pandemic. Environmental scientists and engineers familiar with the techniques required for this endeavor have responded. Many of the environmental scientists engaged in these investigations have not necessarily had experience with the ethical obligations associated with generating and handling human health data. The Canadian Water Network facilitated adoption of these surveillance methods by creating a national coalition, which included a public health advisory group that recognized a need for ethics guidance for the wastewater approach to public health surveillance. This Policy Analysis addresses that need and is based on a review of relevant ethics literature tightly focused on ethics applicable to public health surveillance. That review revealed that classical health bioethics governing clinical practice and general public health ethics guidance did not adequately address key issues in wastewater surveillance. The 2017 World Health Organization guidelines, directly based on a systematic literature review, specifically addressed ethical issues in public health surveillance. The application of relevant ethical guidance to wastewater surveillance is analyzed and summarized for environmental scientists.

Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations.

The ready availability of vast amounts of genomic sequence data has created the need to rethink comparative genomics algorithms using 'big data' approaches. Neptune is an efficient system for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches. Neptune's loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from non-targets using probabilistic models. Neptune uses parallel computing to efficiently identify and extract these loci from draft genome assemblies without requiring multiple sequence alignments or other computationally expensive comparative sequence analyses. Tests on simulated and real datasets showed that Neptune rapidly identifies regions that are both sensitive and specific. We demonstrate that this system can identify trait-specific loci from different bacterial lineages. Neptune is broadly applicable for comparative bacterial analyses, yet will particularly benefit pathogenomic applications, owing to efficient and sensitive discovery of differentially abundant genomic loci. The software is available for download at: http://github.com/phac-nml/neptune.

Where's the pump? Associating sporadic enteric disease with drinking water using a geographic information system, in British Columbia, Canada, 1996-2005.

We investigated whether risk of sporadic enteric disease differs by drinking water source and type using surveillance data and a geographic information system. We performed a cross-sectional analysis, at the individual level, that compared reported cases of enteric disease with drinking water source (surface or ground water) and type (municipal or private). We mapped 814 cases of campylobacteriosis, cryptosporidiosis, giardiasis, salmonellosis and verotoxigenic Escherichia coli infection, in a region of British Columbia, Canada, from 1996 to 2005, and determined the water source and type for each case's residence. Over the 10-year period, the risk of disease was 5.2 times higher for individuals living on land parcels serviced by private wells and 2.3 times higher for individuals living on land parcels serviced by the municipal surface/ground water mixed system, than the municipal ground water system. Rates of sporadic enteric disease potentially differ by drinking water source and type. Geographic information system technology and surveillance data are accessible to local public health authorities and used together are an efficient and affordable way to assess the role of drinking water in sporadic enteric disease.

Feasibility of self-collection of specimens for human papillomavirus testing in hard-to-reach women.

To study the feasibility of self-collected specimens for testing human papillomavirus (HPV) status among hard-to-reach women, outreach nurses recruited women in women's centres, shelters and alleys in Vancouver's Downtown Eastside. Of the 151 participants for whom samples were available, 43 (28.5%) tested positive for high-risk HPV. Outreach nurses were able to recontact 81.4% of the participants who tested positive and referred them for further testing. About 14% (21/151) of participants had never received a Papanicolaou smear in British Columbia, as compared with 8.3% (608/7336) of women in the BC general population (p < 0.05). This difference suggests that self-collection of specimens for HPV testing is a feasible method to reach women who have not previously participated in cervical cancer screening programs.

Usefulness of pulsed-field gel electrophoresis in tracking two outbreaks of invasive meningococcal disease serogroup C in British Columbia.

Two major outbreaks of invasive meningococcal disease serogroup C (IMD-C) were identified in British Columbia between 2000 and 2004. Pulsed-field gel electrophoresis (PFGE) and porA gene sequencing of all retained IMD-C isolates were used to assess correlations between genotypes and epidemiological patterns. PFGE patterns of IMD-C genotypes correlated with epidemiological patterns between 2000 and 2004 in British Columbia, and demonstrated that PFGE can identify outbreak-related cases. Both IMD-C outbreaks correlated with a respective PFGE pattern. PFGE analysis demonstrated that the 2004 British Columbia outbreak strain in men who have sex with men was closely related to the 2001 Abbotsford outbreak strain. PorA sequencing data indicated low diversity of class 1 outer membrane proteins in British Columbia, and did not correlate with epidemiological trends. There was a trend for outbreak-associated PFGE types to demonstrate higher case fatality rates.

Evaluation of a diagnostic polymerase chain reaction assay for Neisseria meningitidis in North America and field experience during an outbreak.

CONTEXT: Meningococcal infection has a high public profile because of its dramatic presentation, high fatality rate, and propensity to occur in outbreaks and clusters of cases. Use of a diagnostic polymerase chain reaction (PCR) assay could enhance laboratory confirmation of cases and guide the public health response in North America. OBJECTIVE: To assess the performance of a PCR assay for the diagnosis of meningococcal disease after its implementation in a North American setting and to evaluate sensitivity and specificity of the assay for the detection of prevalent bacterial isolates. DESIGN: Laboratory evaluation of the sensitivity and specificity of a PCR assay for Neisseria meningitidis and observational study of a series of cases comparing molecular diagnosis against the criterion standard of conventional laboratory diagnostic tests. SETTING: A Canadian province with a population of 4 million people. PATIENTS: Children and adults presenting with suspected meningococcal disease in British Columbia. MAIN OUTCOME MEASURES: The sensitivity and specificity of the PCR assay when compared against standard laboratory methods. RESULTS: The PCR assay correctly identified all of 38 Canadian isolates of Neisseria meningitidis and correctly assigned the serogroup to each isolate. None of 57 other gram-positive or gram-negative bacteria or yeasts were detected by the PCR assay. In a clinical evaluation, for diagnosis of meningococcal disease, the PCR assay had a sensitivity and specificity of 91% and 76%, respectively, against conventional methods of diagnosis. Use of the PCR assay increased the laboratory confirmation of clinically suspected cases by 36%. During an outbreak, the PCR assay allowed serogroup determination in 3 of 7 cases, aiding in the public health decision to launch an immunization campaign. CONCLUSIONS: The PCR assay is more sensitive than conventional methods for the diagnosis of meningococcal disease, and enhanced surveillance may help direct the public health response to the changing epidemiology of disease in North America.

Epidemiology, antibiotic susceptibility, and serotype distribution of Streptococcus pneumoniae associated with invasive pneumococcal disease in British Columbia - A call to strengthen public health pneumococcal immunization programs.

BACKGROUND: This study examined the epidemiology, antibiotic susceptibility and serotype distribution of Streptococcus pneumoniae associated with invasive pneumococcal disease (IPD) in British Columbia. METHODS: Six hospitals and one private laboratory network participated in a prospective, sentinel laboratory based surveillance study of IPD, between October 1999 and October 2000. At each site, S pneumoniae isolates were collected and epidemiological data were gathered using a structured questionnaire, for all cases of IPD meeting the study case definition. Isolates were serotyped and tested for antimicrobial susceptibility. Bivariate associations were analyzed and multivariate logistic regression was used to identify independent risk factors associated with hospitalization or death. RESULTS: One hundred three reports and isolates were collected. Seventy-nine per cent of cases were community-acquired, 64% required hospitalization and 5% died. Cases with one or more assessed risk factor for IPD and of female sex were independent variables associated with hospitalization or death. One-third of isolates had reduced penicillin susceptibility and 96% of these represented serotypes contained in the 23-valent pneumococcal polysaccharide vaccine (PPV-23). Overall, 89% of serotypes identified are included in the PPV-23 vaccine and 88% of isolates from children under five years of age are found in the 7-valent pneumococcal conjugate vaccine (PCV-7). Forty-one per cent of cases qualified for publicly funded pneumococcal vaccine and 34% of eligible persons were vaccinated. CONCLUSIONS: Overall, pneumococcal serotypes associated with IPD in this study closely matched serotypes included in PPV-23 products currently licensed in Canada. Most serotypes associated with IPD in children under five years of age are included in a recently licenced PCV-7. One third of isolates demonstrated reduced penicillin susceptibility, most involving serotypes included in PPV-23. Effective delivery of current public health immunization programs using PPV-23 and extending protection to infants and young children using the PCV-7 will prevent many cases of IPD.

Low pertussis toxin antibody levels in two regional cohorts of Canadian pregnant women.

Infants under 6 months of age are at greatest risk of mortality and severe morbidity from pertussis disease. Interventions that increase pertussis protection in newborns are therefore a clear public health imperative. The objective of this study was to assess maternal pertussis toxin antibody (anti-PT) level as a potential source of mother-to-child transfer of pertussis-associated antibodies that may reduce neonatal risk of pertussis disease. Anti-PT level was assessed in a 2013 cohort of pregnant women from two regions in two Canadian provinces, British Columbia and Nova Scotia. Basic demographics, health, and pertussis immunization history were collected, along with blood specimens. Anti-PT levels were compared for self-reported vaccination status and prior pertussis disease. To assess secular trend, a parallel analysis was also undertaken, using anonymized residual sera from a 1996-1997 cohort of pregnant women in British Columbia. A total of 169 pregnant women participated in the study - 50 from Nova Scotia and 119 from British Columbia. The mean and median age of participants from both sites was 31 years of age (range 16-42 years). The lower limit of quantification of the anti-PT assay was 10 ELISA units per milliliter (EU/ml). Overall, 59% of women had anti-PT levels less than 10 EU/ml and anti-PT level did not differ with time since last self-reported pertussis vaccination (χ(2)(2)=3.166, p=0.205). Among a 1996-1997 cohort of pregnant women in British Columbia, 101 of 200 (51%) had anti-PT levels less than 10 EU/ml. Our study found that most pregnant women in two geographically disparate health regions in Canada have low residual anti-PT levels, may be vulnerable to pertussis infection themselves, and would unlikely be a source of passive ante- or postnatal transfer of anti-PT to their newborn.