Abstract:
:An outbreak of coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) began in Wuhan, Hubei, China, in December 2019 and spread rapidly worldwide. The response by the Alberta Precision Laboratories, Public Health Laboratory (ProvLab), AB, Canada, included the development and implementation of nucleic acid detection-based assays and dynamic changes in testing protocols for the identification of cases as the epidemic curve increased exponentially. This rapid response was essential to slow down and contain transmission and provide valuable time to the local health authorities to prepare appropriate response strategies. As of May 24, 2020, 236,077 specimens were tested, with 6,475 (2.74%) positives detected in the province of Alberta, Canada. Several commercial assays are now available; however, the response from commercial vendors to develop and market validated tests is a time-consuming process. In addition, the massive global demand made it difficult to secure a reliable commercial supply of testing kits and reagents. A public health laboratory serves a unique and important role in the delivery of health care. One of its functions is to anticipate and prepare for novel emerging pathogens with a plan for pandemic preparedness. Here, we outline the response that involved the development and deployment of testing methodologies that evolved as SARS-CoV-2 spread worldwide, the challenges encountered, and mitigation strategies. We also provide insight into the organizational structure of how a public health response is coordinated in Alberta, Canada, and its benefits.
journal_name
J Clin Microbioljournal_title
Journal of clinical microbiologyauthors
Pabbaraju K,Wong AA,Douesnard M,Ma R,Gill K,Dieu P,Fonseca K,Zelyas N,Tipples GAdoi
10.1128/JCM.01110-20subject
Has Abstractpub_date
2020-07-23 00:00:00issue
8eissn
0095-1137issn
1098-660Xpii
JCM.01110-20journal_volume
58pub_type
杂志文章abstract::Members of the genus Exophiala are often difficult to identify to the species level because of their variable morphological appearances. This paper describes the methods used to identify Exophiala mesophila and provides salient differential features for distinguishing other mesophilic members of the genus. ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.8.3885-3889.2003
更新日期:2003-08-01 00:00:00
abstract::Two group A, subgroup I, rotavirus strains possessing "super short" RNA patterns were adapted to growth in MA-104 cells. Both produced marked cytopathic effect in primary culture. Reciprocal cross-neutralization titers, polypeptide analysis, and the serum neutralizing antibody response of an infected child suggested t...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.1.183-185.1987
更新日期:1987-01-01 00:00:00
abstract::The distribution of EDL 933 O island 122 (OI-122) was investigated in 70 strains of Verocytotoxin-producing Escherichia coli (VTEC) of multiple serotypes that were classified into five "seropathotypes" (A through E) based on the reported occurrence of serotypes in human disease, in outbreaks, and/or in the hemolytic-u...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.11.4930-4940.2003
更新日期:2003-11-01 00:00:00
abstract::Blood culture records from 1994 to 1995 from five U.S. medical centers all using the Difco ESP continuous monitoring blood culture system were reviewed retrospectively. Among a total of 7,362 isolates of bacteria and yeasts, only 0.1% of possibly significant isolates would have been missed had blood cultures been rout...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.35.5.1290-1292.1997
更新日期:1997-05-01 00:00:00
abstract::To evaluate the ability of the Amplicor MTB Assay to detect Mycobacterium tuberculosis complex (MTBC) organisms in BACTEC 12B broth cultures, 249 cultures with a growth index (GI) of > or = 20 from 160 patients were tested retrospectively. Specimens were processed by standard methods, and then BACTEC 12B vials and Mid...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.35.4.900-902.1997
更新日期:1997-04-01 00:00:00
abstract::The rapid identification of blood culture isolates and antimicrobial susceptibility test (AST) results play critical roles for the optimal treatment of patients with bloodstream infections. Whereas others have looked at the time to detection in automated culture systems, we examined the overall time from specimen coll...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.00500-18
更新日期:2018-11-27 00:00:00
abstract::Nocardia identification required laborious and time-consuming phenotypic and chemotaxonomic methods until molecular methods were developed in the mid-1990s. Here we reassessed the capacity of PCR-restriction enzyme pattern analysis (PRA) of the hsp65 gene to differentiate Nocardia species, including 36 new species. Ou...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.44.2.536-546.2006
更新日期:2006-02-01 00:00:00
abstract::Enteroaggregative Escherichia coli (EAEC) is an emerging enteric pathogen that causes acute and chronic diarrhea among children, human immunodeficiency virus-infected patients, and travelers to developing regions of the world. The pathogenesis of EAEC strains involves the production of biofilm. In this study, we deter...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01128-06
更新日期:2007-01-01 00:00:00
abstract::We evaluated the use of mannitol salt agar with oxacillin for use as a primary screening medium for the simultaneous detection and identification of methicillin-resistant Staphylococcus aureus in clinical surveillance specimens. Oxacillin agar dilution susceptibility tests with mannitol salt agar and Mueller-Hinton ag...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.22.4.501-504.1985
更新日期:1985-10-01 00:00:00
abstract::Enteroviral meningoencephalitis was diagnosed in a patient with an immunodeficiency syndrome acquired after treatment with rituximab for a relapsed primary B-cell lymphoma. A second meningoencephalitic episode was diagnosed 6 months later and was successfully treated with a combination of immunoglobulins and pleconari...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.10.4605-4610.2003
更新日期:2003-10-01 00:00:00
abstract::Saksenaea is a monotypic genus belonging to the order Mucorales and capable of producing severe human infections. Through a polyphasic study based on analysis of the sequences of the internal transcribed spacer (ITS) region, domains D1 and D2 of the 28S rRNA gene, and the elongation factor 1α (EF-1α) gene, as well as ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.01646-10
更新日期:2010-12-01 00:00:00
abstract::Coagulase-negative staphylococci obtained from patients with continuous ambulatory peritoneal dialysis-related peritonitis were cultured in nutrient broth in an atmosphere of air containing 5% carbon dioxide (reflecting the CO2 tension found in freshly used dialysate). Significant differences were observed between the...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.28.8.1813-1817.1990
更新日期:1990-08-01 00:00:00
abstract::Neisseria meningitidis is the causative agent of meningococcal sepsis and meningitis. Neisseria polysaccharea is a nonpathogenic species. N. polysaccharea is able to use sucrose to produce amylopectin, a starch-like polysaccharide, which distinguishes it biochemically from the pathogenic species N. meningitidis. The d...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.1.273-278.2003
更新日期:2003-01-01 00:00:00
abstract::VlsE, the variable surface antigen of Borrelia burgdorferi, contains an immunodominant conserved region named IR(6). In the present study, the diagnostic performance of a peptide enzyme-linked immunosorbent assay (ELISA) based on a 26-mer synthetic peptide (C(6)) with the IR(6) sequence was explored. Sensitivity was a...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.37.12.3990-3996.1999
更新日期:1999-12-01 00:00:00
abstract::Two types of commercially available microdilution trays were inoculated with log-phase cultures, stationary-phase cultures, and direct suspensions of 18- to 24-h colonies, with essentially comparable results. Direct pick-up of colonies was also tested with two Prompt inoculation systems (3M Co.); they were found to be...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.18.3.645-651.1983
更新日期:1983-09-01 00:00:00
abstract::The effectiveness of antiretroviral therapy may be limited by the development of human immunodeficiency virus type 1 (HIV-1) resistance. Monitoring for resistance will perhaps allow changes in therapy prior to deterioration in the patient's clinical or immunologic status. Our objective was to develop a rapid, specific...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.33.2.342-347.1995
更新日期:1995-02-01 00:00:00
abstract::Fluorescence of sensitized bacterial suspensions, reactive with either fluorescein-labeled or rhodamine-labeled antiglobulins, could be quantitatively distinguished in dual-labeled preparations by fluorescence immunoassay. ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:
更新日期:1978-09-01 00:00:00
abstract::By serological methods, all 83 known types of Streptococcus pneumoniae could be shown to possess C polysaccharide and F antigen. Cross-reactions due to these two antigens between pneumococci and a broad range of most other commonly encountered streptococci were examined. The presence of an antigen closely similar or i...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.25.10.1854-1859.1987
更新日期:1987-10-01 00:00:00
abstract::We have developed a sensitive assay for Treponema pallidum subsp. pallidum (T. pallidum), the agent of veneral syphilis, based upon the polymerase chain reaction (PCR). A 658-bp portion of the gene encoding the 47-kDa membrane immunogen was amplified, and the PCR products were probed by DNA-DNA hybridization with a 49...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.29.1.62-69.1991
更新日期:1991-01-01 00:00:00
abstract::Specimens submitted for diagnosis of herpes simplex virus infections were inoculated into shell vials and conventional culture tubes. Inoculated culture tubes were incubated with rolling at 96 rpm. Immunoperoxidase (IP) staining and cytopathic effects (CPE) were used to detect positive cultures. At 24 h, 42 (53%) of t...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.27.12.2884-2886.1989
更新日期:1989-12-01 00:00:00
abstract::A procedure using the Smart Cycler instrument and a fluorescence quencher (FQ) probe for the specific identification of Mycobacterium tuberculosis complex (MTB) was used to detect organisms in 366 acid-fast bacillus smear-positive respiratory specimens. It was compared to culture and the AMPLICOR M. tuberculosis PCR t...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/jcm.41.10.4783-4786.2003
更新日期:2003-10-01 00:00:00
abstract::Gram-negative, non-saccharolytic, brown- or black-pigment-forming, nonmotile anaerboic coccobacilli, capable of decomposing hydrogen peroxide and identified as Bacteroides asaccharolyticus (B. melaninogenicus subsp. asaccharolyticus), were isolated from the supra- and subgingival plaques of beagle dogs with gingivitis...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.11.5.522-526.1980
更新日期:1980-05-01 00:00:00
abstract::Campylobacter jejuni isolates from stool samples of patients with domestically acquired sporadic infections and from chicken from retail shops were studied during seasonal peaks from June to September over a 3-year period from 1996 to 1998. A large number of pulsed-field gel electrophoresis (PFGE) genotypes (a combine...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.38.5.1998-2000.2000
更新日期:2000-05-01 00:00:00
abstract::Seven commercial rotavirus antigen assays were compared with in-house PCR methods for detecting rotavirus in stool specimens. The assay sensitivities were 80% to 100%, while the specificities were 54.3% for one commercial immunochromatographic (ICT) method and 99.4% to 100% for other assays. Thus, except for one comme...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.02251-14
更新日期:2015-01-01 00:00:00
abstract::Seventy-nine methicillin-resistant Staphylococcus aureus (MRSA) strains, isolated during 1980 to 1990, were classified as MRSA Aggl- (14 strains) and MRSA Aggl+ (65 strains) strains on the basis of test results in slide agglutination assays designed to detect fibrinogen-binding protein (clumping factor) and protein A ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.32.1.143-147.1994
更新日期:1994-01-01 00:00:00
abstract::Visceral and cutaneous leishmaniases are heterogenous entities. The Leishmania species that a given patient harbors usually cannot be determined clinically, and this identification is essential to prescribe the best species-specific therapeutic regimen. Our diagnosis procedure includes a real-time PCR assay targeted a...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.02555-06
更新日期:2007-07-01 00:00:00
abstract::Clostridium difficile is a major cause of antibiotic-associated gastrointestinal illness. Recently, an increased incidence of hospital-acquired infections with severe outcomes has been reported in North America and Europe. Current molecular-typing methods for detection of outbreaks and nosocomial transmission are labo...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.02364-05
更新日期:2006-07-01 00:00:00
abstract::Screening of blood for human T-cell lymphotropic virus type 1 and type 2 (HTLV-1 and -2, respectively) is important to diagnose and prevent infection and ensure the safety of blood supplies. The Elecsys HTLV-I/II assay is a newly developed, electrochemiluminescence screening assay for the detection of HTLV-1/2 infecti...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章,多中心研究
doi:10.1128/JCM.00169-17
更新日期:2017-07-01 00:00:00
abstract::An enzyme-linked immunosorbent assay was developed to study the subclass distribution of immunoglobulin G (IgG) specific to the core glycolipid (CGL) of the Re mutant of Salmonella minnesota R595 in serum samples from individuals with an IgG response toward these antigens. In a group of healthy blood donors, we detect...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.26.5.857-862.1988
更新日期:1988-05-01 00:00:00
abstract::A micro enzyme-linked immunosorbent assay was used to detect the presence of amoebic antigen in polyethylene-glycol-precipitated circulating immune complexes (CIC). A cutoff dilution of greater than 1:160 for the precipitates was taken to be of clinical significance. Among the patients with amoebic liver abscess, 93% ...
journal_title:Journal of clinical microbiology
pub_type: 杂志文章
doi:10.1128/JCM.23.6.1088-1090.1986
更新日期:1986-06-01 00:00:00