scholarly journals Toward health technology assessment of whole-genome sequencing diagnostic tests: challenges and solutions

2017 ◽  
Vol 14 (3) ◽  
pp. 235-247 ◽  
Author(s):  
Katherine Payne ◽  
Martin Eden ◽  
Niall Davison ◽  
Egbert Bakker
2017 ◽  
Vol 33 (S1) ◽  
pp. 19-20
Author(s):  
Jean-Charles Lafarge ◽  
Denis-Jean David ◽  
Michèle Morin-Surroca

INTRODUCTION:The increase in travelers and refugees combined with global warming may soon lead to the development of tropical diseases such as Schistosoma or Strongyloides infections in some European countries.Those intestinal parasites may persist for decades with subclinical infections or low-grade disease with nonspecific manifestations. In the presence of immunosuppression, strongyloidiasis can rapidly evolve into life-threatening disseminated disease, whereas chronic schistosomiasis can lead to complications causing future morbidity and death.Currently in France, an update of diagnostic tests reimbursed for those tropical diseases is ongoing to fully cover diagnostic needs.Our aim was to assess the clinical relevance of tests used in schistosomiasis’ or strongyloidiasis’ diagnosis and include the most relevant in the national list of reimbursed tests.METHODS:The assessment involves a critical analysis of national and international guidelines identified by a systematic literature search, and stakeholders’ views.RESULTS:This work identifies several autochthonous outbreaks of those diseases in France; such as urogenital schistosomiasis that occurred in Corsica, in summer 2013. Also it enlightens the increase of strongyloides serological tests performed in the past years. Those facts prove the potential development of those infections in Europe.It underlines that, serology is the first diagnostic test line for most cases and is more sensitive than stool microscopy which represents however the final diagnostic investigation to confirm the intestinal infection.It confirms the main indications of those two diagnostic tools.It relies on a tropical infectious disease expert network including the French army health service. They have brought further clarification of diagnostic tests clinical relevance for travelers or autochthonous cases.CONCLUSIONS:This new use of Health Technology Assessment has allowed updating and listing the relevant diagnostic tools which might be crucial to better follow those diseases and it may help the health system to face the increase of tropical infections.


2017 ◽  
Vol 38 (4) ◽  
pp. 179
Author(s):  
Ben Polkinghorne ◽  
Anthony Draper ◽  
Michelle Harlock ◽  
Robyn Leader

OzFoodNet is Australia's national enhanced foodborne disease surveillance network. OzFoodNet is currently evolving in order to meet the most significant challenges faced since it commenced in 2000: the transition to culture independent diagnostic tests and the introduction of whole genome sequencing for typing of enteric pathogens. This has changed the nature of foodborne disease surveillance and outbreak investigation in Australia.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan B. Parr ◽  
Eddy Kieto ◽  
Fernandine Phanzu ◽  
Paul Mansiangi ◽  
Kashamuka Mwandagalirwa ◽  
...  

AbstractThe majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a bead-based immunoassay for Plasmodium antigens; and/or whole-genome sequencing. Among 3627 symptomatic subjects, 427 (11.8%) had RDT-/microscopy + results. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. 56.8% of subjects had PCR-confirmed malaria. Non-falciparum co-infection with P. falciparum was common (13.2%). Agreement between PCR and HRP2-based RDTs was satisfactory (Cohen’s kappa = 0.66) and superior to microscopy (0.33). Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.


2020 ◽  
Author(s):  
Jonathan B Parr ◽  
Eddy Kieto ◽  
Fernandine Phanzu ◽  
Paul Masiangi ◽  
Kashamuka Mwandagalirwa ◽  
...  

Background The majority of Plasmodium falciparum malaria diagnoses in Africa are made using rapid diagnostic tests (RDTs) that detect histidine-rich protein 2. Increasing reports of false-negative RDT results due to parasites with deletions of the pfhrp2 and/or pfhrp3 genes (pfhrp2/3) raise concern about existing malaria diagnostic strategies. We previously identified pfhrp2-negative parasites among asymptomatic children in the Democratic Republic of the Congo (DRC), but their impact on diagnosis of symptomatic malaria is unknown. Methods We performed a cross-sectional study of false-negative RDTs in symptomatic subjects in 2017. Parasites were characterized by microscopy; RDT; pfhrp2/3 genotyping and species-specific PCR assays; a multiplex bead-based immunoassay; and/or whole-genome sequencing. Results Among 3,627 symptomatic subjects, we identified 427 (11.8%) RDT-/microscopy+ cases. Parasites from eight (0.2%) samples were initially classified as putative pfhrp2/3 deletions by PCR, but antigen testing and whole-genome sequencing confirmed the presence of intact genes. Malaria prevalence was high (57%) and non-falciparum co-infection common (15%). HRP2-based RDT performance was satisfactory and superior to microscopy. Conclusions Symptomatic malaria due to pfhrp2/3-deleted P. falciparum was not observed in the DRC. Ongoing HRP2-based RDT use is appropriate for the detection of falciparum malaria in the DRC.


2019 ◽  
Vol 8 (41) ◽  
Author(s):  
Rebecca L. Tallmadge ◽  
Patrick K. Mitchell ◽  
Renee Anderson ◽  
Rebecca Franklin-Guild ◽  
Laura B. Goodman

Whole-genome sequencing of Mycoplasma mucosicanis type strain 1642 was performed to support efforts to better understand the clinical significance of Mycoplasma infection in canine health. The availability of this sequence will also further the development of highly specific diagnostic tests.


2020 ◽  
Vol 24 (42) ◽  
pp. 1-122
Author(s):  
Amanda L Lewis ◽  
Grace J Young ◽  
Lucy E Selman ◽  
Caoimhe Rice ◽  
Clare Clement ◽  
...  

Background Lower urinary tract symptoms (LUTS) in men may indicate bladder outlet obstruction (BOO) or weakness, known as detrusor underactivity (DU). Severe bothersome LUTS are a common indication for surgery. The diagnostic tests may include urodynamics (UDS) to confirm whether BOO or DU is the cause, potentially reducing the number of people receiving (inappropriate) surgery. Objectives The primary objective was to determine whether a care pathway including UDS is no worse for symptom outcome than one in which it is omitted, at 18 months after randomisation. Rates of surgery was the key secondary outcome. Design This was a pragmatic, multicentre, two-arm (unblinded) randomised controlled trial, incorporating a health economic analysis and qualitative research. Setting Urology departments of 26 NHS hospitals in England. Participants Men (aged ≥ 18 years) seeking further treatment, potentially including surgery, for bothersome LUTS. Exclusion criteria were as follows: unable to pass urine without a catheter, having a relevant neurological disease, currently undergoing treatment for prostate or bladder cancer, previously had prostate surgery, not medically fit for surgery and/or unwilling to be randomised. Interventions Men were randomised to a care pathway based on non-invasive routine tests (control) or routine care plus invasive UDS (intervention arm). Main outcome measures The primary outcome was International Prostate Symptom Score (IPSS) at 18 months after randomisation and the key secondary outcome was rates of surgery. Additional secondary outcomes included adverse events (AEs), quality of life, urinary and sexual symptoms, UDS satisfaction, maximum urinary flow rate and cost-effectiveness. Results A total of 820 men were randomised (UDS, 427; routine care, 393). Sixty-seven men withdrew before 18 months and 11 died (unrelated to trial procedures). UDS was non-inferior to routine care for IPSS 18 months after randomisation, with a confidence interval (CI) within the margin of 1 point (–0.33, 95% CI –1.47 to 0.80). A lower surgery rate in the UDS arm was not found (38% and 36% for UDS and routine care, respectively), with overall rates lower than expected. AEs were similar between the arms at 43–44%. There were more cases of acute urinary retention in the routine care arm. Patient-reported outcomes for LUTS improved in both arms and satisfaction with UDS was high in men who received it. UDS was more expensive than routine care. From a secondary care perspective, UDS cost an additional £216 over an 18-month time horizon. Quality-adjusted life-years (QALYs) were similar, with a QALY difference of 0.006 in favour of UDS over 18 months. It was established that UDS was acceptable to patients, and valued by both patients and clinicians for its perceived additional insight into the cause and probable best treatment of LUTS. Limitations The trial met its predefined recruitment target, but surgery rates were lower than anticipated. Conclusions Inclusion of UDS in the diagnostic tests results in a symptom outcome that is non-inferior to a routine care pathway, but does not affect surgical rates for treating BOO. Results do not support the routine use of UDS in men undergoing investigation of LUTS. Future work Focus should be placed on indications for selective utilisation of UDS in individual cases and long-term outcomes of diagnosis and therapy. Trial registration Current Controlled Trials ISRCTN56164274. Funding This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 42. See the NIHR Journals Library website for further project information.


2008 ◽  
Vol 19 (4) ◽  
pp. 253-269 ◽  
Author(s):  
Sabine Heel ◽  
Sonja Fischer ◽  
Stefan Fischer ◽  
Tobias Grässer ◽  
Ellen Hämmerling ◽  
...  

Zunächst führt dieser Artikel in die wesentlichen Begrifflichkeiten und Zielstellungen der Versorgungsforschung ein. Er befasst sich dann mit der Frage, wie die einzelnen Teildisziplinen der Versorgungsforschung, (1) die Bedarfsforschung, (2) die Inanspruchnahmeforschung, (3) die Organisationsforschung, (4) das Health Technology Assessment, (5) die Versorgungsökonomie, (6) die Qualitätsforschung und zuletzt (7) die Versorgungsepidemiologie konzeptionell zu fassen sind, und wie sie für neuropsychologische Anliegen ausformuliert werden müssen. In diesem Zusammenhang werden die in den einzelnen Bereichen jeweils vorliegenden versorgungsrelevanten Studienergebnisse referiert. Soweit es zulässig ist, werden Bedarfe für die Versorgungsforschung und Versorgungspraxis in der Neurorehabilitation daraus abgeleitet und Anregungen für die weitere empirische Forschung formuliert. Der Artikel bezieht sich – entsprechend seines Anliegens – ausschließlich auf Studien, die sich mit der Situation der deutschen Neurorehabilitation befassen.


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