scholarly journals Implementation of Sample Pooling Procedure Using a Rapid SARS-CoV-2 Diagnostic Real-Time PCR Test Performed Prior to Hospital Admission of People with Intellectual Disabilities

2021 ◽  
Vol 18 (17) ◽  
pp. 9317
Author(s):  
Antonino Musumeci ◽  
Mirella Vinci ◽  
Francesca L’Episcopo ◽  
Alda Ragalmuto ◽  
Vincenzo Neri ◽  
...  
Keyword(s):  
Hospital Admission ◽  
Response Times ◽  
Health Management ◽  
Diagnostic Testing ◽  
High Risk Group ◽  
Sample Collection ◽  
Health Maintenance ◽  
Personnel Costs ◽  
Viral Spread ◽  
Sample Pooling

Reliability, accuracy, and timeliness of diagnostic testing for SARS-CoV-2 infection have allowed adequate public health management of the disease, thus notably helping the timely mapping of viral spread within the community. Furthermore, the most vulnerable populations, such as people with intellectual disability and dementia, represent a high-risk group across multiple dimensions, including a higher prevalence of pre-existing conditions, lower health maintenance, and a propensity for rapid community spread. This led to an urgent need for reliable in-house rapid testing to be performed prior to hospital admission. In the present study, we describe a pooling procedure in which oropharyngeal and nasopharyngeal swabs for SARS-CoV-2 detection (performed prior to hospital admission using rapid RT-PCR assay) are pooled together at the time of sample collection. Sample pooling (groups of 2–4 samples per tube) allowed us to significantly reduce response times, consumables, and personnel costs while maintaining the same test sensitivity.

scholarly journals Longitudinal sampling is required to maximize detection of intrahost A/H3N2 virus variants

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
B F Koel ◽  
R M Vigeveno ◽  
M Pater ◽  
S M Koekkoek ◽  
A X Han ◽  
...  
Keyword(s):  
Neutralizing Antibodies ◽  
De Novo ◽  
Diagnostic Testing ◽  
Influenza Viruses ◽  
Surface Proteins ◽  
H3n2 Virus ◽  
Virus Population ◽  
Sample Collection ◽  
Routine Surveillance ◽  
H3n2 Influenza

Abstract Seasonal human influenza viruses continually change antigenically to escape from neutralizing antibodies. It remains unclear how genetic variation in the intrahost virus population and selection at the level of individual hosts translates to the fast-paced evolution observed at the global level because emerging intrahost antigenic variants are rarely detected. We tracked intrahost variants in the hemagglutinin and neuraminidase surface proteins using longitudinally collected samples from 52 patients infected by A/H3N2 influenza virus, mostly young children, who received oseltamivir treatment. We identified emerging putative antigenic variants and oseltamivir-resistant variants, most of which remained detectable in samples collected at subsequent days, and identified variants that emerged intrahost immediately prior to increases in global rates. In contrast to most putative antigenic variants, oseltamivir-resistant variants rapidly increased to high frequencies in the virus population. Importantly, the majority of putative antigenic variants and oseltamivir-resistant variants were first detectable four or more days after onset of symptoms or start of treatment, respectively. Our observations demonstrate that de novo variants emerge, and may be positively selected, during the course of infection. Additionally, based on the 4–7 days post-treatment delay in emergence of oseltamivir-resistant variants in six out of the eight individuals with such variants, we find that limiting sample collection for routine surveillance and diagnostic testing to early timepoints after onset of symptoms can potentially preclude detection of emerging, positively selected variants.

scholarly journals The Laboratory Diagnosis ofHaemophilus ducreyi

2005 ◽  
Vol 16 (1) ◽  
pp. 31-34 ◽  
Author(s):  
Michelle Alfa
Keyword(s):  
Diagnostic Testing ◽  
Laboratory Diagnosis ◽  
Primary Method ◽  
Sample Collection ◽  
Culture Methods ◽  
Transmitted Infection ◽  
Diagnostic Laboratory ◽  
Sexually Transmitted ◽  
Alternative Approaches ◽  
Genetic Amplification

Chancroid is a sexually transmitted infection caused byHaemophilus ducreyi. This fastidious, Gram-negative coccobacilli dies rapidly outside the human host, making diagnostic testing using culture methods difficult. This genital ulcer infection is not common in Canada and, therefore, can often be misdiagnosed. The objective of the present paper is to provide practical approaches for the diagnosis of chancroid in Canadian patients where the prevalence of this infection is low. Issues related to sample collection, sample transport and available diagnostic tests are reviewed, and several alternative approaches are outlined. Although antigen detection, serology and genetic amplification methods have all been reported forH ducreyi, none are commercially available. Culture is still the primary method available to most laboratories. However, the special media necessary for direct bedside inoculation is often not available; therefore, communication with the diagnostic laboratory and rapid specimen transport are essential when chancroid is suspected

Public health impacts of culture independent diagnostic testing in Australia

2017 ◽  
Vol 38 (4) ◽  
pp. 162
Author(s):  
Fiona J May
Keyword(s):  
Public Health ◽  
Health Management ◽  
Diagnostic Testing ◽  
Primary Source ◽  
Outbreak Detection ◽  
Surveillance Systems ◽  
Advantages And Disadvantages ◽  
Testing Protocol ◽  
Culture Independent ◽  
The Impact

Culture independent diagnostic tests (CIDT) for detection of pathogens in clinical specimens have become widely adopted in Australian pathology laboratories. Pathology laboratories are the primary source of notification of pathogens to state and territory surveillance systems. Monitoring and analysis of surveillance data is integral to guiding public health actions to reduce the incidence of disease and respond to outbreaks. As with any change in testing protocol, the advantages and disadvantages of the change from culture based testing to culture independent testing need to be weighed up and the impact on surveillance and outbreak detection assessed. This article discusses the effect of this change in testing on surveillance and public health management of pathogens in Australia, with specific focus on gastrointestinal pathogens.

scholarly journals The Ageing Population and the Challenges of Health Management: A Study of Retirees of Public Institutions in South East Nigeria

2020 ◽  
Vol 7 (1) ◽  
pp. 31
Author(s):  
Samuel O. Okafor ◽  
Christopher O. Ugwuibe
Keyword(s):  
Public Health ◽  
Health Policy ◽  
Public Health Policy ◽  
Health Management ◽  
Survey Design ◽  
Public Institutions ◽  
Health Facilities ◽  
Ageing Population ◽  
Health Maintenance ◽  
Public Health Facilities

While life expectancy will continue to improve owing to the domestic humanitarian improvement, proxy-policy influence on the sub-Saharan African nations [Nigeria included] by the United Nations and other developed nations, the ageing population will continue to increase making it more or less policy imperative among the nations within this region. Among other things, public health policy occupies the most important position in the web of policy approach to the needs and care for the aged. In the light of the above, the present paper investigated the realities of public health policy outcome [1988 to 2016], as it affects the ageing populations via public health facilities and health packages for the aged. 600 retirees of public institutions from southeast Nigeria were involved in the study, which adopted survey design and modified random sampling techniques. In view of the substantive issues of the study, less than 25% of the respondents go for regular medical checkups and self-health maintenance, more than 80% depended on self-support for medical upkeep; the regression model adopted in the study proved [p< .05], the factors affecting regular health upkeep and satisfaction with services at the public health facilities among the retirees.

scholarly journals Seed quality and mycoflora associated with chickpea (Cicer arientinum L.) seed in Ethiopia

2020 ◽  
Vol 20 (06) ◽  
pp. 16761-16778
Author(s):  
Gezahegne Getaneh ◽  
◽  
T Tefera ◽  
F Lemmessa ◽  
S Ahmed ◽  
...  
Keyword(s):  
Relative Density ◽  
Infection Rate ◽  
Seed Quality ◽  
Health Management ◽  
Agricultural Research ◽  
Infection Frequency ◽  
Sample Collection ◽  
Storage Container ◽  
Seed Sources ◽  
Seed Health

The study was conducted at Ethiopian Institute of Agricultural Research, Haramaya University and Jimma University, Ethiopia. Crop yield is directly associated with the physical and biological quality of planting material or seed. Ninety-nine (99) chickpea seed lot samples were collected for physical purity,seed health and germination tests from major chickpea growing areas in Ethiopia in the 2016/17 cropping season to assess the status of chickpea seed health and quality among subsistence farmers,research stations and seed growers.The seed lots were grouped as researcher saved, farmers saved and seed growers’ saved seed. The maximum physical purity of 97.5% was recorded for the researcher saved seed lots, 90.8% for the seed growers and 87.4 % for the farmers saved seeds. Foreign matters and broken seeds were the most contaminants found in the seed lots. The seed germination percentages were in the range of 96.3% to 98.5% for all seed sources and there were no significant differences among the seed lot samples. A total of seventeen (17) fungi species were isolated from all seed sources with different frequency and amount. These are Fusarium spp., Aspergillus sp., A. niger, A. flavus, A. nidulans, A. candidus, A. fumigatus, Penicillium sp., Rhizopus sp., Verticillium sp., Rhizoctonia sp., Pythium sp.,Alternaria sp., Helminthosporium sp. Phylostica sp., Cladosporium sp., Negrospora sp.Aspergillus flavus was found the most dominant with recovery(Relative Density=21.53%, Infection rate=10.36%, and Infection Frequency=25.59 %)from all seed lots. There were high variations in relative density, Infection rate, and Infection frequency among isolated fungi. Ascochyta rabieithe most important chickpea disease was not found in this study. This might relate to the incidence and prevalence of sample collection season/cropping year which was low in expected areas.The current study concluded that there are seed qualities and seed health management issues with regards to different seed sources (farmers, research and private sectors); this entails strong seed quality control and growers’ awareness creation on storage sanitation, seed health test before sowing, and production of healthy crops. To keep the seed health in a better condition, seed growers should keep a wider interval of rotation, develop use of the healthy improved seed, after some generation (4-5), seed grading to avoid loss of physical purity, use of appropriate storage container (ventilated and clean), seed dressing with safe pesticides, and appropriate moisture level for storage(about 14%)should have to keep.Longer storage also gives a chance to contaminate the whole seed and can expose to decay.

scholarly journals Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S139-S139
Author(s):  
J C Lownik ◽  
J S Farrar ◽  
G Way ◽  
R K Martin
Keyword(s):  
Supply Chain ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Virus Detection ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Sample Collection ◽  
Rt Pcr ◽  
Hydrolysis Probe ◽  
Time Requirements

Abstract Introduction/Objective Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler. Methods/Case Report We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler. Results (if a Case Study enter NA) This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes. Conclusion We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.

scholarly journals Evaluation of pool-based testing approaches to enable population-wide screening for COVID-19

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243692
Author(s):  
Timo de Wolff ◽  
Dirk Pflüger ◽  
Michael Rehme ◽  
Janin Heuer ◽  
Martin-Immanuel Bittner
Keyword(s):  
Infection Rate ◽  
Primary Study ◽  
Viral Spread ◽  
Test Characteristics ◽  
Testing Strategies ◽  
Resource Limited ◽  
Input Parameters ◽  
Sample Pooling ◽  
Broad Variety ◽  
The Uk

Objective Rapid testing is paramount during a pandemic to prevent continued viral spread and excess morbidity and mortality. This study investigates whether testing strategies based on sample pooling can increase the speed and throughput of screening for SARS-CoV-2, especially in resource-limited settings. Methods In a mathematical modelling approach conducted in May 2020, six different testing strategies were simulated based on key input parameters such as infection rate, test characteristics, population size, and testing capacity. The situations in five countries were simulated, reflecting a broad variety of population sizes and testing capacities. The primary study outcome measurements were time and number of tests required, number of cases identified, and number of false positives. Findings The performance of all tested methods depends on the input parameters, i.e. the specific circumstances of a screening campaign. To screen one tenth of each country’s population at an infection rate of 1%, realistic optimised testing strategies enable such a campaign to be completed in ca. 29 days in the US, 71 in the UK, 25 in Singapore, 17 in Italy, and 10 in Germany. This is ca. eight times faster compared to individual testing. When infection rates are lower, or when employing an optimal, yet more complex pooling method, the gains are more pronounced. Pool-based approaches also reduce the number of false positive diagnoses by a factor of up to 100. Conclusions The results of this study provide a rationale for adoption of pool-based testing strategies to increase speed and throughput of testing for SARS-CoV-2, hence saving time and resources compared with individual testing.

scholarly journals Immediate pools of malaria infections at diagnosis combined with targeted deep sequencing accurately quantifies frequency of drug resistance mutations

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11794
Author(s):  
Ozkan Aydemir ◽  
Benedicta Mensah ◽  
Patrick W. Marsh ◽  
Benjamin Abuaku ◽  
James Leslie Myers-Hansen ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Diagnostic Testing ◽  
Resistance Mutation ◽  
Drug Resistance Mutation ◽  
Sub Saharan Africa ◽  
Resistance Mutations ◽  
Drug Resistance Mutations ◽  
Antimalarial Resistance ◽  
Sample Pooling ◽  
Sub Saharan

Antimalarial resistance surveillance in sub-Saharan Africa is often constrained by logistical and financial challenges limiting its breadth and frequency. At two sites in Ghana, we have piloted a streamlined sample pooling process created immediately by sequential addition of positive malaria cases at the time of diagnostic testing. This streamlined process involving a single tube minimized clinical and laboratory work and provided accurate frequencies of all known drug resistance mutations after high-throughput targeted sequencing using molecular inversion probes. Our study validates this method as a cost-efficient, accurate and highly-scalable approach for drug resistance mutation monitoring that can potentially be applied to other infectious diseases such as tuberculosis.

scholarly journals SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance

2020 ◽  
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Sudha Ananth ◽  
Allan Njau ◽  
Pankaj Ahluwali ◽  
...  
Keyword(s):  
Clinical Sample ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Community Setting ◽  
Absolute Quantification ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Direct Pcr ◽  
Sample Pooling ◽  
Saliva Collection

BackgroundThe limitations of widespread current COVID-19 diagnostic testing lie at both pre-analytical and analytical stages. Collection of nasopharyngeal swabs is invasive and is associated with exposure risk, high cost, and supply-chain constraints. Additionally, the RNA extraction in the analytical stage is the most significant rate-limiting step in the entire testing process. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction free RT-PCR test using any of the commercially available RT-PCR kits.MethodsWe optimized saliva collection devices, heat-shock treatment and homogenization. The effect of homogenization on saliva samples for extraction-free RT-PCR assay was determined by evaluating samples with and without homogenization and preforming viscosity measurements. Saliva samples (872) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. Further, a five-sample pooling strategy was evaluated as per FDA guidelines using the SalivaSTAT protocol.ResultsThe saliva collection (done without any media) performed comparable to the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95°C for 30-minutes and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreement (NPA) of 95.8% and 100%, respectively. The LoD was established as ∼20-60 copies/ml by absolute quantification. Further, a five-sample pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively.ConclusionWe have optimized an extraction-free direct RT-PCR assay for saliva samples that demonstrated comparable performance to FDA-EUA assay (Extraction and RT-PCR). The SalivaSTAT protocol is a rapid, sensitive, and cost-effective method that can be adopted globally, and has the potential to meet testing needs and may play a significant role in management of the current pandemic.

Laboratory Testing for Microbial Detection

2016 ◽  
Author(s):  
Michael Arce
Keyword(s):  
Laboratory Testing ◽  
Disease Burden ◽  
Diagnostic Testing ◽  
Sample Collection ◽  
Microbial Detection ◽  
Microbial Infections ◽  
Future Care ◽  
Missed Diagnosis ◽  
Clinically Significant ◽  
Selection Of

The approach to microbial detection in patients who present to acute settings should be focused and should aim to result in clinically significant findings while minimizing the chances of a missed diagnosis or missed complications related to a patient’s existing disease burden. Judicious selection of laboratory tests, efficient sample collection, and laboratory reporting are all important considerations. This chapter provides general guidelines for the initial evaluation of potential microbial infections in patients presenting to the Emergency Department (ED). In some cases, the diagnosis will remain uncertain during the patient’s stay, but diagnostic testing initiated in the ED may be beneficial for the inpatient or outpatient team and the future care of the patient.

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