scholarly journals Development of a Mobile Laboratory for Sudden Onset Disasters

2019 ◽  
Vol 34 (s1) ◽  
pp. s24-s24
Author(s):  
Ian Marr ◽  
Dianne Stephens ◽  
Rob Baird ◽  
Josh Francis ◽  
David Read ◽  
...  
Keyword(s):  
Sudden Onset ◽  
Clinical Diagnostics ◽  
Cold Chain ◽  
Major Advance ◽  
Mobile Laboratory ◽  
Rt Pcr ◽  
Field Hospital ◽  
Diagnostic Laboratory ◽  
Pcr Multiplex ◽  
Timor Leste

Introduction:Clinical diagnostics in sudden-onset disasters (SOD) has historically been limited. With poor supply routes, lack of a cold chain, and challenging environmental conditions, many diagnostic platforms are unsuitable.Aim:We set out to design, implement, and evaluate a mobile diagnostic laboratory accompanying a type II emergency medical team (EMT) field hospital.Methods:Available diagnostic platforms were reviewed and selected against infield need. Platforms included HemoCue301/WBC DIFF, i-STAT, BioFire multiplex RT-PCR, Olympus BX53 microscopy, ABO/Rh Grouping, and specific rapid diagnostic tests (RDT). This equipment was trialed in Katherine, Australia and Dili, Timor-Leste.Results:During the initial deployment, validation of FilmArray rt-PCR multiplex tests was successful on blood culture, gastrointestinal, and respiratory panels. HemoCue301 (n = 20) haemoglobin values were compared on Sysmex XN 550 (r = 0.94). Analysis of HemoCue WBC DIFF samples had some variation when compared to Sysmex XN 550, (neutrophils r = 0.88, lymphocytes r = 0.49, monocytes r = 0.16, eosinophils r = 0.70, basophils r = 0.16). i-STAT showed non-significant differences for CHEM4 (n=10), CG8 (n = 10), and TnI (n = 5) against Vitros 250. A further trial of BioFire rt-PCR testing in Dili, Timor-Leste diagnosed 117 causative pathogens on 168 FilmArray test cartridges.Discussion:This mobile laboratory represents a major advance in SOD. Setup of the service was quick (<24hr) and transport to site rapidly. Training was simple and performance consistent. Future deployment in fragmented health systems after sudden onset disasters with EMT2 will now allow broader diagnostics.

Development of a Mobile Laboratory for Sudden Onset Disasters

2020 ◽  
pp. 1-11
Author(s):  
Ian Marr ◽  
Joshua R. Francis ◽  
Dianne P. Stephens ◽  
Kristy Marshall ◽  
David J. Read ◽  
...  
Keyword(s):  
Blood Culture ◽  
Sudden Onset ◽  
Clinical Diagnostics ◽  
Major Advance ◽  
Mobile Laboratory ◽  
Field Hospital ◽  
Diagnostic Laboratory ◽  
Timor Leste ◽  
Culture Identification

ABSTRACT Objectives: Clinical diagnostics in sudden onset disasters have historically been limited. We set out to design, implement, and evaluate a mobile diagnostic laboratory accompanying a type 2 emergency medical team (EMT) field hospital. Methods: Available diagnostic platforms were reviewed and selected against in field need. Platforms included HemoCue301/WBC DIFF, i-STAT, BIOFIRE FILMARRAY multiplex rt-PCR, Olympus BX53 microscopy, ABO/Rh grouping, and specific rapid diagnostic tests. This equipment was trialed in Katherine, Australia, and Dili, Timor-Leste. Results: During the initial deployment, an evaluation of FilmArray tests was successful using blood culture identification, gastrointestinal, and respiratory panels. HemoCue301 (n = 20) hemoglobin values were compared on Sysmex XN 550 (r = 0.94). HemoCue WBC DIFF had some variation, dependent on the cell, when compared with Sysmex XN 550 (r = 0.88-0.16). i-STAT showed nonsignificant differences against Vitros 250. Further evaluation of FilmArray in Dili, Timor-Leste, diagnosed 117 pathogens on 168 FilmArray pouches, including 25 separate organisms on blood culture and 4 separate cerebrospinal fluid pathogens. Conclusion: This mobile laboratory represents a major advance in sudden onset disaster. Setup of the service was quick (< 24 hr) and transport to site rapid. Future deployment in fragmented health systems after sudden onset disasters with EMT2 will now allow broader diagnostic capability.

scholarly journals Computer-Aided Medical Microbiology Monitoring Tool: A Strategy to Adapt to the SARS-CoV-2 Epidemic and That Highlights RT-PCR Consistency

2021 ◽  
Vol 11 ◽  
Author(s):  
Linda Mueller ◽  
Valentin Scherz ◽  
Gilbert Greub ◽  
Katia Jaton ◽  
Onya Opota
Keyword(s):  
Turnaround Time ◽  
Quality Monitoring ◽  
Rt Pcr ◽  
Monitoring Tool ◽  
Diagnostic Laboratory ◽  
Important Health ◽  
Polymerase Chain ◽  
Automated Processes ◽  
Regulatory Decisions ◽  
Case Validation

Since the beginning of the COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in the number of SARS-CoV-2 RT-PCR. To maintain a rapid turnaround time, we moved from a case-by-case validation of RT-PCR results to an automated validation and immediate results transmission to clinicians. A quality-monitoring tool based on a homemade algorithm coded in R was developed, to preserve high quality and to track aberrant results. We present the results of this quality-monitoring tool applied to 35,137 RT-PCR results. Patients tested several times led to 4,939 pairwise comparisons: 88% concordant and 12% discrepant. The algorithm automatically solved 428 out of 573 discrepancies. The most likely explanation for these 573 discrepancies was related for 44.9% of the situations to the clinical evolution of the disease, 27.9% to preanalytical factors, and 25.3% to stochasticity of the assay. Finally, 11 discrepant results could not be explained, including 8 for which clinical data was not available. For patients repeatedly tested on the same day, the second result confirmed a first negative or positive result in 99.2% or 88.9% of cases, respectively. The implemented quality-monitoring strategy allowed to: i) assist the investigation of discrepant results ii) focus the attention of medical microbiologists onto results requiring a specific expertise and iii) maintain an acceptable turnaround time. This work highlights the high RT-PCR consistency for the detection of SARS-CoV-2 and the necessity for automated processes to handle a huge number of microbiological results while preserving quality.

Recent advances in the laboratory diagnosis of peste des petits ruminants

2021 ◽  
Vol 77 (05) ◽  
pp. 226-231
Author(s):  
WIESŁAW NIEDBALSKI ◽  
ANDRZEJ FITZNER ◽  
KRZYSZTOF BULENGER ◽  
ANDRZEJ KĘSY
Keyword(s):  
Reverse Transcription ◽  
Animal Health ◽  
Clinical Signs ◽  
Small Ruminants ◽  
Clinical Diagnostics ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Peste Des Petits Ruminants ◽  
Rt Pcr ◽  
Agar Gel

Peste des petits ruminants (PPR) is a highly contagious and economically important, viral disease of small ruminants caused by the peste des petits ruminants virus (PPRV), which belongs to the genus Morbilivirus in the family Paramyxoviridae. PPR control is achieved mostly through vaccination and/or slaughter of susceptible animals coupled with clinical or laboratory-based diagnosis. Since clinical signs of PPR are not disease-specific and clinical diagnostics is not reliable, it should be confirmed by laboratory testing. Laboratory confirmation of clinical suspicions is made by detection of PPRV in blood, swabs or post-mortem tissues through classical virus isolation (VI), agar gel immunodiffusion (AGID)/agar gel precipitation test (AGPT), counter-immunoelectrophoresis (CIE), immunoperoxidase test (IPT) or enzyme-linked immunosorbent (ELISA) assays. However, these conventional methods have been superseded by more rapid, sensitive and accurate molecular diagnostic techniques based on the amplification of parts of either nucleocapsid (N) or fusion (F) protein gene, such as RT-PCR, real-time RT-PCR, reverse transcription loop-mediated isothermal amplification (RT-LAMP), reverse transcription recombinase polymerase amplification (RT-RPA) and Oxford nanopore MinION technology. Although these molecular diagnostic assays are accurate, rapid and sensitive, they have to be performed in laboratory settings, and samples must be transported under appropriate conditions from the field to the laboratory, which can delay the confirmation of PPRV infection. The recently developed immunochromatographic lateral flow device (IC-LFD) assay can be used in the field (“pen-side”) without the need for expensive equipment, so a well-established laboratory is not required. The control and eventual eradication of PPR is now one of the top priorities for the Food and Agriculture Organization (FAO) and the World Organization for Animal Health (OIE). In 2015, the international community agreed on a global strategy for PPR eradication, setting 2030 as a target date for elimination of the disease

scholarly journals Olfactory and Gustatory Dysfunctions as a Clinical Manifestation of Coronavirus Disease 2019 in a Malaysian Tertiary Center

2020 ◽  
pp. 000348942096316 ◽  
Author(s):  
Kuganathan Ramasamy ◽  
Jeyasakthy Saniasiaya ◽  
Norhaslinda Abdul Gani
Keyword(s):  
Nasal Obstruction ◽  
Telephone Interview ◽  
Complete Recovery ◽  
Sudden Onset ◽  
Olfactory Dysfunction ◽  
Rt Pcr ◽  
Younger Age ◽  
Tertiary Center ◽  
The Mean ◽  
Polymerase Chain

Objective: To investigate the prevalence of olfactory and gustatory dysfunction among patients with COVID-19 infection and the recovery rate. Methods: Adult patients (≥18 years) tested positive for COVID-19 via reverse transcription-polymerase chain reaction (RT-PCR) and admitted in Hospital Tuanku Ja’afar Seremban, Malaysia, were recruited in this study. Patients completed a questionnaire via telephone interview comprising the following details: age, sex, ethnicity, comorbidities, general and otorhinolaryngological symptoms, onset and duration of olfactory and gustatory dysfunction. Patients with persistent olfactory and gustatory dysfunction at the time of the initial interview were followed-up every 3 to 5 days till resolution. Results: A total of 145 patients were included in our study. The mean age of patients was 43.0 ± 17.7 (range: 18-86). Fever (44.1%) and cough (39.3%) were the most prevalent general symptoms. Thirty-one patients (21.4%) reported olfactory dysfunction and 34 (23.4%) reported dysgeusia. There was a significant association between both olfactory and gustatory dysfunction ( P < .001). Altered sense of smell or taste occurred before other symptoms in 7 (15.9%); concomitant in 16 (36.4%) and after in 15 (34.1%). Six patients (13.6%) reported isolated sudden-onset anosmia. The median duration of olfactory and gustatory dysfunctions was 7 days. Complete recovery was achieved for 70.5% of the patients within 7 days of symptom onset. Only 6 (19.4%) of the 31 patients with olfactory dysfunction experienced nasal obstruction or rhinorrhea. Olfactory dysfunction was not significantly associated with nasal obstruction or rhinorrhea. Olfactory dysfunction was significantly associated with younger age ( P = .002), female ( P = .011), and hyperlipidemia ( P = .012). Gustatory dysfunction was significantly associated with fever ( P = .019) and cough ( P = .039). Conclusion: Olfactory and gustatory dysfunction is a pertinent manifestation of COVID-19. Most of the affected patients achieve rapid and complete recovery. Sudden onset of olfactory and gustatory dysfunction should be recognized as a major symptom of COVID-19 as we implore to contain this pandemic.

scholarly journals Lyophilized Matrix Containing Ready-to-Use Primers and Probe Solutions for Standardization of Real-Time PCR and RT-qPCR Diagnostics

Proceedings ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 7
Author(s):  
Remi N Charrel ◽  
Laurence Thirion
Keyword(s):  
Real Time ◽  
Molecular Techniques ◽  
Cold Chain ◽  
Rt Pcr ◽  
Emerging Viruses ◽  
Valley Fever ◽  
Term Stability ◽  
E Gene ◽  
Long Term Stability

Real-time molecular techniques have become the reference methods for the direct diagnosis of pathogens. The reduction of steps is a key factor in order to decrease the risk of human errors resulting in invalid series and delayed results. We describe here a process involving the preparation of oligonucleotide primers and a hydrolysis probe in a single tube at predefined optimized concentrations that are stabilized via lyophilization (Lyoph-P&P). Lyoph-P&P was compared to the classic protocol using extemporaneously prepared liquid reagents, assaying (i) sensitivity, (ii) long-term stability at 4 °C, and (iii) long-term stability at 37 °C, mimicking transportation without a cold chain. Two previously published molecular assays were selected for this study. They target two emerging viruses that are listed on the blueprint of the WHO to be considered for preparedness and response actions: chikungunya virus (CHIKV) and Rift Valley fever phlebovirus (RVFV). The results of our study demonstrate that (i) Lyoph-P&P is stable for at least four days at 37 °C, supporting shipping without the need of a cold chain, (ii) Lyoph-P&P rehydrated solution is stable at 4 °C for at least two weeks, (iii) the sensitivity observed with Lyoph-P&P is at least equal to, and often better than, that observed with liquid formulation, and (iv) the validation of results observed with low-copy specimens is rendered easier by higher fluorescence levels. In conclusion, Lyoph-P&P holds several advantages over extemporaneously prepared liquid formulations and merits consideration as a novel real-time molecular assay for implementation into a laboratory with routine diagnostic activity. Since the meeting, this concept has been applied to the COVID-19 situation: two diagnostic assays (E gene and RdRp) have been developed and can be ordered on the European Virus Archive catalog (https://www.european-virus-archive.com/detection-kit/lyophilized-primers-and-probe-rt-pcr-2019-ncov-e-gene; https://www.european-virus-archive.com/detection-kit/lyophilized-primers-and-probe-rt-pcr-sars-cov-2-rdrp-gene).

scholarly journals Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis

2005 ◽  
Vol 109 (4) ◽  
pp. 365-379 ◽  
Author(s):  
Stephen A. Bustin ◽  
Reinhold Mueller
Keyword(s):  
Real Time ◽  
Reverse Transcription ◽  
Therapy Monitoring ◽  
Clinical Diagnostics ◽  
Clinical Diagnostic Laboratory ◽  
Diagnostic Laboratory ◽  
Qrt Pcr ◽  
Reverse Transcription Pcr ◽  
Clinical Diagnostic ◽  
Pcr Assays

qRT-PCR (real-time reverse transcription-PCR) has become the benchmark for the detection and quantification of RNA targets and is being utilized increasingly in novel clinical diagnostic assays. Quantitative results obtained by this technology are not only more informative than qualitative data, but simplify assay standardization and quality management. qRT-PCR assays are most established for the detection of viral load and therapy monitoring, and the development of SARS (severe acute respiratory syndrome)-associated coronavirus qRT-PCR assays provide a textbook example of the value of this technology for clinical diagnostics. The widespread use of qRT-PCR assays for diagnosis and the detection of disease-specific prognostic markers in leukaemia patients provide further examples of their usefulness. Their value for the detection of disease-associated mRNA expressed by circulating tumour cells in patients with solid malignancies is far less apparent, and the clinical significance of results obtained from such tests remains unclear. This is because of conceptual reservations as well as technical limitations that can interfere with the diagnostic specificity of qRT-PCR assays. Therefore, although it is evident that qRT-PCR assay has become a useful and important technology in the clinical diagnostic laboratory, it must be used appropriately and it is essential to be aware of its limitations if it is to fulfil its potential.

A polymer lab-on-a-chip for reverse transcription (RT)-PCR based point-of-care clinical diagnostics

Lab on a Chip ◽  
2008 ◽  
Vol 8 (12) ◽  
pp. 2121 ◽  
Author(s):  
Soo Hyun Lee ◽  
Sung-Woo Kim ◽  
Ji Yoon Kang ◽  
Chong H. Ahn
Keyword(s):  
Reverse Transcription ◽  
Point Of Care ◽  
Lab On A Chip ◽  
Clinical Diagnostics ◽  
Rt Pcr

scholarly journals Molecular characteristics of rotavirus genotypes circulating in the south of Benin, 2016-2018

2020 ◽  
Author(s):  
Jijoho Michel Agbla ◽  
Mathew D Esona ◽  
Alidéhou Jerrold Agbankpé ◽  
Annick Capo-Chichi ◽  
Rashi Gautam ◽  
...  
Keyword(s):  
World Health ◽  
Molecular Characteristics ◽  
Rt Pcr ◽  
Predominant Genotype ◽  
Pcr Multiplex ◽  
One Step ◽  
Stool Samples ◽  
Pcr Method ◽  
Health Organization ◽  
P Type

Abstract Objective: Rotavirus remains the main causative agent of gastroenteritis in young children in countries that have not yet introduced the vaccine. In Benin, rotavirus vaccine was introduced late December 2019 into the EPI. This study aims to provide pre-vaccination era rotavirus genotyping data in Benin. These data can supplement data from the surveillance system of Ministry of Health of Benin which is supported by the World Health Organization (WHO).Results: Of the 420 diarrheal stool samples, actively collected in southern Benin from July 2016 through November 2018 from children under five years old and suffering from gastroenteritis, 167 (39.8%) samples were rotavirus EIA positive. 186 (44.3%) samples contained amplifiable rotavirus RNA detected by qRT-PCR method and were genotyped using one-step RT-PCR multiplex genotyping method. G1P[8] represents the predominant genotype (32%) followed by the G2P[4] (26%), G3P[6] (16%), G12P[8] (13%) and mixed G and P types (1%). Four samples (2%) could not be assigned both G and P type specificity.

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