Bright A.T.,University of California at San Diego |
Manary M.J.,University of California at San Diego |
Tewhey R.,Scripps Research Institute |
Arango E.M.,University of Antioquia |
And 5 more authors.
PLoS Neglected Tropical Diseases | Year: 2014
Plasmodium vivax infects a hundred million people annually and endangers 40% of the world's population. Unlike Plasmodium falciparum, P. vivax parasites can persist as a dormant stage in the liver, known as the hypnozoite, and these dormant forms can cause malaria relapses months or years after the initial mosquito bite. Here we analyze whole genome sequencing data from parasites in the blood of a patient who experienced consecutive P. vivax relapses over 33 months in a non-endemic country. By analyzing patterns of identity, read coverage, and the presence or absence of minor alleles in the initial polyclonal and subsequent monoclonal infections, we show that the parasites in the three infections are likely meiotic siblings. We infer that these siblings are descended from a single tetrad-like form that developed in the infecting mosquito midgut shortly after fertilization. In this natural cross we find the recombination rate for P. vivax to be 10 kb per centimorgan and we further observe areas of disequilibrium surrounding major drug resistance genes. Our data provide new strategies for studying multiclonal infections, which are common in all types of infectious diseases, and for distinguishing P. vivax relapses from reinfections in malaria endemic regions. This work provides a theoretical foundation for studies that aim to determine if new or existing drugs can provide a radical cure of P. vivax malaria. © 2014 Bright et al.
Naidu P.,University of Alberta |
Yanow S.K.,Provincial Laboratory for Public Health |
Kowalewska-Grochowska K.T.,University of Alberta
Canadian Journal of Infectious Diseases and Medical Microbiology | Year: 2013
Background: Canada resettles 10,000 to 12,000 refugees annually. Despite this being a highly vulnerable population, there are little Canadian data on subclinical tropical diseases harboured in this population over the past 20 years. Objectives: To determine the seroprevalence and predictors of Strongyloides infection in refugees arriving in Edmonton, Alberta. Methods: A retrospective chart review of all refugees seen at the New Canadians Clinic between March 2009 and April 2010 was performed. Demographic, symptom and physical examination data were collected from the charts. Laboratory results were obtained from the electronic laboratory records. Results: A total of 350 subjects were studied. The overall seroprevalence of strongyloidiasis was 4.6%. Equivocal results were found in 6.3%. In the positive group, the majority were male (62.5%); 75% were born in Africa (P=0.004) and 81.2% lived in refugee camps in Africa (P=0.002). Eosinophilia was present in 25% of the positive subjects (P=0.05), in none of the equivocal group and in 8.7% of the negative group. Discussion: Persistent asymptomatic Strongyloides infection is maintained for years through autoinfection. Traditionally, eosinophilia was used as one of the key tools to diagnose chronic but stable diseases, but it was shown to have a poor predictive value for strongyloidiasis in returning expatriates as well as in those presenting with a disseminated form of the disease. It is important to raise awareness of the severe limitations of eosinophilia as a marker for strongyloidiasis when managing patients who either are immunocompromised, or about to start immunosuppressive therapy. Conclusions: The present study indicated that eosinophilia is a poor predictor of seropositivity and, thus, Strongyloides infection. Residence in Africa (birth/refugee camps) proved to be a significantly better predictor of Strongyloides seropositivity.
Divis P.C.,University Malaysia Sarawak |
Shokoples S.E.,Provincial Laboratory for Public Health |
Singh B.,University Malaysia Sarawak |
Yanow S.K.,Provincial Laboratory for Public Health |
Yanow S.K.,University of Alberta
Malaria Journal | Year: 2010
Background: The misdiagnosis of Plasmodium knowlesi by microscopy has prompted a re-evaluation of the geographic distribution, prevalence and pathogenesis of this species using molecular diagnostic tools. In this report, a specific probe for P. knowlesi, that can be used in a previously described TaqMan real-time PCR assay for detection of Plasmodium spp., and Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae and Plasmodium ovale, was designed and validated against clinical samples. Methods. A hydrolysis probe for a real-time PCR assay was designed to recognize a specific DNA sequence within the P. knowlesi small subunit ribosomal RNA gene. The sensitivity, linearity and specificity of the assay were determined using plasmids containing P. knowlesi DNA and genomic DNA of P. falciparum, P. knowlesi, P. malariae, P. ovale and P. vivax isolated from clinical samples. DNA samples of the simian malaria parasites Plasmodium cynomolgi and Plasmodium inui that can infect humans under experimental conditions were also examined together with human DNA samples. Results. Analytical sensitivity of the P. knowlesi-specific assay was 10 copies/L and quantitation was linear over a range of 10-106 copies. The sensitivity of the assay is equivalent to nested PCR and P. knowlesi DNA was detected from all 40 clinical P. knowlesi specimens, including one from a patient with a parasitaemia of three parasites/L of blood. No cross-reactivity was observed with 67 Plasmodium DNA samples (31 P. falciparum, 23 P. vivax, six P. ovale, three P. malariae, one P. malariae/P. ovale, one P. falciparum/P. malariae, one P. inui and one P. cynomolgi) and four samples of human DNA. Conclusions. This test demonstrated excellent sensitivity and specificity, and adds P. knowlesi to the repertoire of Plasmodium targets for the clinical diagnosis of malaria by real-time PCR assays. Furthermore, quantitation of DNA copy number provides a useful advantage over other molecular assays to investigate the correlation between levels of infection and the spectrum of disease. © 2010 Divis et al; licensee BioMed Central Ltd.
Pang X.L.,Provincial Laboratory for Public Health |
Pang X.L.,University of Alberta |
Preiksaitis J.K.,University of Alberta |
Lee B.E.,University of Alberta
Journal of Medical Virology | Year: 2014
Viral gastroenteritis causes significant mortality and morbidity worldwide. Identifying the etiology of viral gastroenteritis is a challenge as most enteric viruses (EVs) are non-culturable. This study is to develop an EV testing panel using real-time PCR (EVPrtPCR) to simultaneously detect rotavirus, norovirus, sapovirus, astrovirus, and enteric adenovirus in stool samples. EVPrtPCR using universal amplification conditions was run in a single instrument run. EVPrtPCR was used to test 2,486 sporadic gastroenteritis samples submitted for EV testing using electron microscopy (EM) between July 2008 and July 2009. Retesting spiked negative stool samples and Salmon DNA as internal control were used to evaluate inhibition. EVPrtPCR detected viruses in significantly more samples: 748 (34%) as compared to 94 (3.8%) by EM. EM did not detect any norovirus, sapovirus, and mixed infection, and detected only 39% of rotavirus and 38.2% of enteric adenovirus positive samples. Four samples that tested positive for rotavirus and two for adenovirus and for small-round-structured viruses by EM were negative by EVPrtPCR. Norovirus was the most common virus detected (17.6%) with 92.4% as genogroup II, followed by rotavirus (6.8%), sapovirus (4.2%), astrovirus (2.0%), and enteric adenovirus (1.4%) with 9% samples positive for mixed infection. Overall, EV identification followed a U-shaped age distribution; positive samples were more common in children ≤5 years old and adults >60 years old. Norovirus, sapovirus and astrovirus showed winter predominance and rotavirus peaked in the spring. No inhibition was observed. Molecular technology significantly enhanced the identification of EV causing sporadic gastroenteritis in Alberta. © 2013 Wiley Periodicals, Inc.
Gharabaghi F.,Hospital for Sick Children |
Hawan A.,Armed Forces Hospital |
Drews S.J.,Provincial Laboratory for Public Health |
Drews S.J.,University of Calgary |
And 2 more authors.
Clinical Microbiology and Infection | Year: 2011
This study compares the performance of four commercial multiplex PCR assays (Resplex II Panel v2.0, Seeplex RV15, xTAG RVP and xTAG RVP Fast) and direct fluorescent antibody (DFA) staining and viral isolation. Seven hundred and fifty nasopharyngeal swabs were tested for 17 viral agents. In each assay, the sensitivity and specificity for each target were determined against a composite reference standard. Two hundred and eighty-eight out of 750 (38.4%) specimens were positive by DFA or viral isolation, while an additional 214 (28.5%) were positive by multiplex PCR, for a total positivity rate of 66.9%. Of 502 positive specimens, one virus was detected in 420 specimens (83.7%), two in 77 (15.3%), three in four (0.8%) and four in one case (0.2%). Compared with a composite reference standard, the inter-assay accuracy of the multiplex PCR assays varied, but all were superior to conventional diagnostic methods in detecting a broad range of respiratory viral agents in children. In addition, the sensitivity of two commercial assays, Resplex II Plus PRE and Seeplex Influenza A/B Subtyping, was determined relative to the Astra influenza Screen & Type assay for detection of influenza A viruses, including seasonal influenzas and pandemic H1N1 2009 influenza A virus. Using 75 positive and 55 negative nasopharyngeal swabs for influenza A by the Astra assay, the sensitivity of Seeplex and Resplex was 95.9% and 91.8%, respectively, with a specificity of 100% for both. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.
Schwering M.,University of Calgary |
Song J.,University of Calgary |
Louie M.,Provincial Laboratory for Public Health |
Turner R.J.,University of Calgary |
Ceri H.,University of Calgary
Biofouling | Year: 2013
A model biofilm, formed of multiple species from environmental drinking water, including opportunistic pathogens, was created to explore the tolerance of multi-species biofilms to chlorine levels typical of water-distribution systems. All species, when grown planktonically, were killed by concentrations of chlorine within the World Health Organization guidelines (0.2-5.0 mg l-1). Higher concentrations (1.6-40-fold) of chlorine were required to eradicate biofilm populations of these strains, ∼70% of biofilms tested were not eradicated by 5.0 mg l-1 chlorine. Pathogenic bacteria within the model multi-species biofilms had an even more substantial increase in chlorine tolerance; on average ∼700-1100 mg l-1 chlorine was required to eliminate pathogens from the biofilm, 50-300-fold higher than for biofilms comprising single species. Confocal laser scanning microscopy of biofilms showed distinct 3D structures and multiple cell morphologies and arrangements. Overall, this study showed a substantial increase in the chlorine tolerance of individual species with co-colonization in a multi-species biofilm that was far beyond that expected as a result of biofilm growth on its own. © 2013 Taylor & Francis.
Manage D.P.,University of Alberta |
Lauzon J.,University of Alberta |
Atrazhev A.,University of Alberta |
Pang X.,University of Alberta |
And 2 more authors.
Lab on a Chip - Miniaturisation for Chemistry and Biology | Year: 2013
Testing of whole blood in miniaturized PCR is compromised by the opaque nature of whole blood that leads to physical masking of a fluorescent signal. We demonstrate a method to perform real-time PCR with whole blood that avoids interference from the opacity of whole blood. © The Royal Society of Chemistry 2013.
Singh A.E.,University of Alberta |
Plitt S.S.,Public Health Agency of Canada |
Osiowy C.,National Microbiology Laboratory |
Surynicz K.,National Microbiology Laboratory |
And 3 more authors.
Journal of Viral Hepatitis | Year: 2011
Mother-to-child transmission of hepatitis B virus (HBV) continues to occur despite immunoprophylaxis. We examined maternal factors contributing to transmission in infants receiving adequate immunoprophylaxis in Alberta, Canada. Prenatal specimens from HBsAg-positive women whose babies developed HBV infection despite immunoprophylaxis (cases) and HBsAg-positive mothers whose babies did not (controls) were tested for HBsAg, HBeAg and HBV DNA. Specimens with detectable DNA underwent HBV genotyping. Routinely collected surveillance data and laboratory test results were compared between cases and controls. Twelve cases and 52 controls were selected from a provincial registry from 2000 to 2005. At the time of prenatal screening, median maternal age was 31 years [interquartile range (IQR): 27.5-34.5], and median gestational age was 12 weeks (IQR 10.0-15.5). Cases were more likely than controls to test positive for HBeAg (77.8%vs 23.1%; P < 0.05). Of all mothers with detectable viral load (n = 51), cases had a significantly higher median viral load than did controls (5.6 × 10 8 IU/mL vs 1750 IU/mL, P < 0.0001). Of the two cases who were HBeAg negative, one had an undetectable viral load 8 months prior to delivery and a sP120T mutation. The viral load in the other case was 14 000 IU/mL. The majority of isolates were genotype B (31.3%) and C (31.3%) with no significant differences in genotype between cases or controls. In this case-control study, transmission of HBV to infants was more likely to occur in mothers positive for HBeAg and with high HBV DNA. © 2010 Blackwell Publishing Ltd.
Mbonye A.K.,Makerere University |
Birungi J.,Uganda Virus Research Institute |
Yanow S.,Provincial Laboratory for Public Health |
Magnussen P.,Copenhagen University
BMC Infectious Diseases | Year: 2013
Background: Malaria is a public health problem in Uganda; affecting mainly women and children. Effective treatment has been hampered by over-diagnosis and over-treatment with anti-malarial drugs among patients presenting with fever. In order to understand the effect of drug pressure on sulfadoxine-pyrimethamine (SP) resistance in pregnancy, a sample of pregnant women presenting with fever in out-patient clinics was studied. The main objective was to assess prescription patterns and drug use in pregnancy especially SP; and draw implications on the efficacy of SP for intermittent preventive treatment of malaria in pregnancy (IPTp).Methods: A total of 998 pregnant women with a history of fever were interviewed and blood samples taken for diagnosis of malaria and HIV infections. Data were captured on the drugs prescribed for the current febrile episode and previous use of drugs especially SP, anti-retroviral drugs (ARVs) and cotrimoxazole.Results: Few pregnant women, 128 (12.8%) were parasitaemic for P.falciparum; and of these, 72 (56.3%) received first-line treatment with Artemether-lumefantrine (Coartem®) 14 (10.9%) SP and 33 (25.8%) quinine. Of the parasite negative patients (non-malarial fevers), 186 (21.4%) received Coartem, 423 (48.6%) SP and 19 (2.1%) cotrimoxazole. Overall, malaria was appropriately treated in 35.5% of cases. Almost all febrile pregnant women, 91.1%, were sleeping under a mosquito net. The majority of them, 911 (91.3%), accepted to have an HIV test done and 92 (9.2%) were HIV positive. Of the HIV positive women, 23 (25.0%) were on ARVs, 10 (10.9%) on cotrimoxazole and 30 (32.6%) on SP. A significant proportion of women, 40 (43.5%), were on both SP and cotrimoxazole. Age and occupation were associated with diagnosis and treatment of malaria and HIV infections.Conclusion: There is inappropriate treatment of malaria and non-malarial fevers among pregnant women in these facilities. This is due to non-adherence to the guidelines. Over-prescription and use of anti-malarial drugs, especially SP may have implications on resistance against SP for malaria prevention in pregnancy. The policy implications of these findings are to evaluate SP efficacy as IPTp; and the need to enforce adherence to the current clinical treatment guidelines. © 2013 Mbonye et al.; licensee BioMed Central Ltd.
Peirano G.,University of Calgary |
Ahmed-Bentley J.,University of Alberta |
Fuller J.,University of Alberta |
Fuller J.,Provincial Laboratory for Public Health |
And 3 more authors.
Journal of Clinical Microbiology | Year: 2014
We describe here the characteristics of Alberta, Canada, patients with infections or colonizations with carbapenemase-producing Gram-negative bacteria during 2010 to 2013 that were linked to recent travel outside Canada. Antimicrobial susceptibility was determined by broth microdilution, and isolates were characterized using PCR, sequencing, and multilocus sequencing typing. A broth mating study was used to assess the transferability of resistance plasmids, which were subsequently characterized. All the patients (n=12) included in our study had contact with a health care system while abroad. Most of the patients presented with urinary tract infections (UTIs) and were admitted to hospitals within weeks after their return to Alberta. Secondary spread occurred in 1 case, resulting in the death of another patient. The carbapenemase-producing bacteria (n=17) consisted of Escherichia coli (sequence type 101 [ST101], ST365, ST405, and ST410) with NDM-1, Klebsiella pneumoniae (ST15, ST16, ST147, ST258, ST340, ST512, and ST972) with NDM-1, OXA-181, KPC-2, and KPC-3, Acinetobacter baumannii with OXA-23, Providencia rettgeri with NDM-1, Enterobacter cloacae with KPC-2, and Citrobacter freundii with NDM-1. The blaNDM-1 gene was associated with various narrow-(i.e., IncF) and broad-(i.e., IncA/C and IncL/M) host-range plasmids with different addiction factors. Our results show that NDM-producing K. pneumoniae, belonging to a variety of sequence types with different plasmid scaffolds, are regularly imported from India into Alberta. Clinical microbiology laboratories should remain vigilant in detecting bacteria with carbapenemases. Copyright © 2014, American Society for Microbiology. All Rights Reserved.