The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Prospective Cohort Study

Osteoclasts are specialized cells derived from the monocyte/macrophage haematopoietic lineage that develop and adhere to bone matrix, then secrete acid and lytic enzymes that degrade it in a specialized, extracellular compartment. Discovery of the RANK signalling pathway in the osteoclast has provided insight into the mechanisms of osteoclastogenesis and activation of bone resorption, and how hormonal signals impact bone structure and mass. Further study of this pathway is providing the molecular basis for developing therapeutics to treat osteoporosis and other diseases of bone loss.

Osteoclast differentiation and activation

The TNF and TNF receptor superfamilies: integrating mammalian biology.

Osteoporosis, a disease endemic in Western society, typically reflects an imbalance in skeletal turnover so that bone resorption exceeds bone formation. Bone resorption is the unique function of the osteoclast, and anti-osteoporosis therapy to date has targeted this cell. The osteoclast is a specialized macrophage polykaryon whose differentiation is principally regulated by macrophage colony-stimulating factor, RANK ligand, and osteoprotegerin. Reflecting integrin-mediated signals, the osteoclast develops a specialized cytoskeleton that permits it to establish an isolated microenvironment between itself and bone, wherein matrix degradation occurs by a process involving proton transport. Osteopetrotic mutants have provided a wealth of information about the genes that regulate the differentiation of osteoclasts and their capacity to resorb bone.

https://science.sciencemag.org/content/sci/289/5484/1504.full.pdf

Bone Resorption by Osteoclasts

Pendant les mois d’août et septembre dernier, l'entérovirus D68, un virus émergent causant une maladie respiratoire principalement chez les enfants, a été documenté au Canada, aux États-Unis de même que dans certaines régions de l'Europe et de l'Asie. Ce supplément offre le premier résumé épidémiologique des cas pédiatriques hospitalisés au Canada; il présente également des notions générales sur les entérovirus. Il contient également un lien vers le rapport traitant de deux cas de H7N9 au Canada, il fournit un aperçu de la situation de la grippe au Canada cette année, ainsi que deux résumés de l'estimation provisoire de l'efficacité du vaccin antigrippal de 2014-2015.

https://www.canada.ca/content/dam/phac-aspc/migration/phac-aspc/publicat/ccdr-rmtc/15vol41/dr-rm41s-1/assets/pdf/ccdrv41is1a01f-fra.pdf

Résumé de la surveillance des cas pédiatriques d'entérovirus D68 hospitalisés au Canada, septembre 2014

https://www.tandfonline.com/doi/pdf/10.1080/24745332.2022.2041328?needAccess=true

Chapter 12: An introductory guide to tuberculosis care to improve cultural competence for health care workers and public health professionals serving Indigenous Peoples of Canada

Rapid Real Time Surveillance and Monitoring of Pandemic Influenza Associated Pneumonia & Risk Factors Using Primary Care Electronic Medical Records (EMR)

BACKGROUND: In January 2001 we investigated an outbreak of Neisseria gonorrhoeae in a northern region of Alberta, Canada, and here we report on the epidemiology of the outbreak. GOAL: The goal was to examine the outbreak etiology and make recommendations for strengthening regional STD programs. STUDY DESIGN: Provincial STD notification forms were reviewed to identify cases, and a case-control study was undertaken to identify risk factors for infection. RESULTS: Gonorrhea was reported among 81 individuals, aged 15 to 60 years, between January 1999 and March 2001 in 8 neighboring communities. Attendance at a public bar in one community was associated with infection (P < 0.01). Cases were predominantly Aboriginal (96.3%) and aged less than 30 years (77.6%), and at least 39% of cases reported multiple sex partners. Casual partnering and extended sexual networks are believed to have influenced the spread of infection. CONCLUSION: This study emphasizes the importance of site-specific health interventions to effectively target at-risk individuals at high-risk locations, with preventive measures aimed at members of high-risk sexual networks. Effective interventions must ensure the availability of and access to appropriate health services for all residents of northern regions in Alberta.

Outbreak of Neisseria gonorrhoeae in Northern Alberta, Canada.

Background Edmonton is in the midst of a syphilis outbreak occurring largely in high risk and hard-to-reach populations. Point of care (POC) testing for syphilis and HIV offers the opportunity for immediate and rapid access to testing, and in the case of syphilis, immediate treatment. POC syphilis tests have not been previously evaluated in clinical settings in Canada. Methods Since 14 February 2011, treponemal syphilis (Bioline Syphilis 3.0) and HIV (INSTI HIV-1/HIV-2 Antibody Test) POC testing, using whole blood from a finger prick specimen, has been offered to outreach clients in Edmonton. POC results were compared to standard testing from simultaneously collected serum specimens. Baseline demographics, sexual and drug use risk behaviour information were collected. Age and gender were collected on individuals who refused POC testing. A descriptive analysis was performed on the characteristics and outcomes of participants and those who refused. Results As of 15 April 2011, 146 individuals had been offered POC testing; 85.6% (n=125) consented. Among participants, 59.2% (74) were male [vs 66.7% (14) of non-participants, p=0.5)] and the median age was 29 yrs (IQR 24–36 yrs) [vs non-participants median age 29 yrs (IQR 25–45 yrs), p=0.2)]. The majority of participants (83.2%; 104) were heterosexual, 59.2% (69) were Aboriginal, and 30.4% (38) reported injection drug use. Among females, 62.7% (32) reported sex trade involvement, while among males, 21.6% (16) reported sex with a sex trade worker. Of 121 syphilis treponemal POC tests, 5 (4.1%) were positive, all in old treated cases of syphilis that were asymptomatic for infectious syphilis at the time of testing. Two syphilis POC (1.7%) tests were falsely negative when compared to the standard screening test (Architect Syphilis TP Microparticles, Abbott Laboratories, Illinois, USA); both were in individuals previously treated for syphilis. Of 123 HIV POC tests, 2 (1.6%) were reactive, both newly diagnosed cases as confirmed by GS HIV-1 Western Blot (BioRad Laboratories, California, USA); both were negative by syphilis POC tests. Conclusion Preliminary results from Edmonton suggest that POC testing for syphilis and HIV is well accepted among high-risk populations in outreach settings in Edmonton. This ongoing study will assess the utility of these tests in mitigating the further spread of both syphilis and HIV through POC testing, and in the case of syphilis, POC treatment.

https://sti.bmj.com/content/sextrans/87/Suppl_1/A355.1.full.pdf

LBP-1.08 Preliminary report on experience with point of care syphilis and HIV testing in hard-to-reach populations in outreach settings in Edmonton, Canada

Tom Wong

Papers

Résumé de la surveillance des cas pédiatriques d'entérovirus D68 hospitalisés au Canada, septembre 2014

Chapter 12: An introductory guide to tuberculosis care to improve cultural competence for health care workers and public health professionals serving Indigenous Peoples of Canada

Rapid Real Time Surveillance and Monitoring of Pandemic Influenza Associated Pneumonia & Risk Factors Using Primary Care Electronic Medical Records (EMR)

Outbreak of Neisseria gonorrhoeae in Northern Alberta, Canada.

LBP-1.08 Preliminary report on experience with point of care syphilis and HIV testing in hard-to-reach populations in outreach settings in Edmonton, Canada