scholarly journals Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay

2021 ◽  
Vol 15 (12) ◽  
pp. e0010025
Author(s):  
Yun Wu ◽  
Fei Wang ◽  
Chaoyue Wang ◽  
Xinming Tang ◽  
Xianyong Liu ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Large Scale ◽  
Clinical Symptoms ◽  
Pneumocystis Pneumonia ◽  
Pneumocystis Jirovecii ◽  
Clinical Samples ◽  
Pcr Diagnosis ◽  
Clinical Surveillance ◽  
Pulmonary Toxoplasmosis ◽  
Immune Defects

Pneumocystis pneumonia (PCP) and pulmonary toxoplasmosis (PT) are caused by Pneumocystis jirovecii and Toxoplasma gondii. The clinical symptoms and imaging of PCP and PT are indistinguishable. A duplex qPCR was developed to differentiate between these two pathogens. In testing 92 clinical samples to validate the performance of this method for P. jirovecii detection, it identified 31 positive samples for P. jirovecii infection, consistent with clinical diagnosis. Among the remainder of the 61 clinical samples with suspected PCP, yet showing as negative by the conventional PCR diagnosis approach, 6 of them proved positive using our new assay. Our new approach also produced similar results in identification of T. gondii infections, giving a result of 2 positive and 20 negative in clinical samples. An investigation was undertaken on the prevalence of P. jirovecii and T. gondii infections using 113 samples from lung infection patients. 9% (10/113) were shown to be positive with infections of P. jirovecii, 2% with T. gondii (2/113) and 5% (6/113) were co-infected with both pathogens. Although this duplex qPCR can detect individual P. jirovecii and T. gondii infection, and co-infection of both pathogens, further large-scale investigations are needed to validate its performance, especially in T. gondii detection. Our assay provides a rapid and accurate tool for PCP and PT diagnosis in immunocompromised population and clinical surveillance of these infections in patients with no immune defects.

scholarly journals Molecular Serotyping and Resistance of Clinical Strains of Haemophilus (Glaesserella) Parasuis in Chinese Pig Farms From 2016 to 2018.

2021 ◽  
Author(s):  
Jinjin Liu ◽  
Long Guo ◽  
Yi Yuan ◽  
Wenbo Song ◽  
Qianqian Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Symptoms ◽  
Inhibitory Effect ◽  
Diffusion Method ◽  
Economic Losses ◽  
Clinical Samples ◽  
Peptide Antibiotics ◽  
Disk Diffusion Method ◽  
Positive Role ◽  
Pig Farms

Abstract Haemophilus parasuis (H. parasuis) is the etiological agent of Glässer's disease and brings great economic losses to the pig industry. The goal of our research is to reveal the serotypes of H. parasuis isolated from large-scale pig farms in China from 2016 to 2018. From 2016 to 2018, 8153 H. parasuis field strains were isolated from 14610 clinical samples of sick pigs with clinical symptoms from 26 provinces and cities of China. Among them, 1386 strains were identified as H. parasuis by PCR, and the isolation rate was 9.49%. Through multiplex PCR, we showed that type 5/12 and type 4 strains had the highest separation rate, followed by type 13 and type 14 strains. Using disk diffusion method, we found cephalosporin antibiotics and peptide antibiotics all had good inhibitory effect on H. parasuis. Our conclusion may play a positive role in the prevention and treatment of H. parasuis.

scholarly journals Large-scale silane bead-based SARS-CoV-2 testing of a nursing home in Spain identifies a viral reservoir during lockdown period

2021 ◽  
Author(s):  
Nicholas D. Weber ◽  
Ainhoa Goñi-Salaverri ◽  
Jose A. Rodríguez ◽  
Juan Pablo Unfried ◽  
Daniel Alameda ◽  
...  
Keyword(s):  
Nursing Home ◽  
Nursing Homes ◽  
Large Scale ◽  
Magnetic Beads ◽  
Rna Extraction ◽  
Academic Research ◽  
High Sensitivity ◽  
Viral Reservoir ◽  
Clinical Samples ◽  
Clinical Surveillance

AbstractBackgroundSpain is one of the countries most heavily affected by the COVID-19 pandemic. As in other countries such as UK and USA, nursing homes have been an important human reservoir for the virus and the population with the highest mortality worldwide. The presence of asymptomatic carriers within nursing homes is one of the factors that could provoke new outbreaks during the relaxing of lockdown measures.MethodsWe developed a high-throughput protocol for RNA extraction of patient samples based on silane magnetic beads in multi-well plates. The sensitivity, specificity and reproducibility rates were assessed using positive and negative clinical samples from the Clinica Universidad de Navarra, Spain. We utilized the protocol to test a pilot cohort of 138 residents and 87 staff from a nursing home in Northern Navarre, Spain.FindingsOur protocol showed high sensitivity (100%), specificity (96·0%) and linear correlation with PCR cycle threshold values obtained with a standard testing kit (R2 = 0·807, p=3E-05). Testing of 225 individuals from the nursing home revealed 63 residents (46%) and 14 staff (16%) positive for SARS-CoV-2. Only 18 of the positive residents (28·6%) were symptomatic at time of testing. During follow-up, 6 PCR-negative symptomatic residents were retested and resulted positive. One-month mortality among positive residents was higher than in negative residents (15·9% vs 1·3%), regardless of age or comorbidities.InterpretationRapid silane bead-based RNA extraction expanded the testing capabilities and COVID-19 patients were promptly identified. Personal and public health measures were enacted to avoid spreading and tighten clinical surveillance. The ability to easily adapt the technical capabilities of academic research centers to large-scale testing for SARS-CoV-2 could provide an invaluable tool for ensuring a safe lifting of lockdown in countries with high numbers of cases.FundingEuropean Molecular Biology Organization and Genomics Unit, Cima Universidad de Navarra.

scholarly journals Detection of Pneumocystis jirovecii in Hospitalized Children Less Than 3 Years of Age

2021 ◽  
Vol 7 (7) ◽  
pp. 546
Author(s):  
Estelle Menu ◽  
Jean-Sélim Driouich ◽  
Léa Luciani ◽  
Aurélie Morand ◽  
Stéphane Ranque ◽  
...  
Keyword(s):  
Severe Combined Immunodeficiency ◽  
Hyaline Membrane Disease ◽  
Relevant Information ◽  
Underlying Disease ◽  
Pneumocystis Pneumonia ◽  
Pneumocystis Jirovecii ◽  
Respiratory Pathogens ◽  
Respiratory Sample ◽  
Few Data ◽  
Underlying Diseases

Few data are available in the literature regarding Pneumocystis jirovecii infection in children under 3 years old. This retrospective cohort study aimed to describe medically relevant information among them. All children under 3 years old treated in the same medical units from April 2014 to August 2020 and in whom a P. jirovecii evaluation was undertaken were enrolled in the study. A positive case was defined as a child presenting at least one positive PCR for P. jirovecii in a respiratory sample. Medically relevant information such as demographical characteristics, clinical presentation, microbiological co-infections, and treatments were collected. The objectives were to describe the characteristics of these children with P. jirovecii colonization/infection to determine the key underlying diseases and risk factors, and to identify viral respiratory pathogens associated. The PCR was positive for P. jirovecii in 32 children. Cardiopulmonary pathologies (21.9%) were the most common underlying disease in them, followed by severe combined immunodeficiency (SCID) (18.8%), hyaline membrane disease (15.6%), asthma (9.4%) and acute leukaemia (6.3%). All SCID children were diagnosed with pneumocystis pneumonia. Co-infection with Pj/Rhinovirus (34.4%) was not significant. Overall mortality was 18.8%. Paediatric pneumocystis is not restricted to patients with HIV or SCID and should be considered in pneumonia in children under 3 years old.

scholarly journals LncGSEA: a versatile tool to infer lncRNA associated pathways from large-scale cancer transcriptome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanan Ren ◽  
Ting-You Wang ◽  
Leah C. Anderton ◽  
Qi Cao ◽  
Rendong Yang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Clinical Samples ◽  
Sequencing Data ◽  
Multiple Cancer ◽  
Regulatory Pathways ◽  
Cancer Transcriptome ◽  
Versatile Tool

Abstract Background Long non-coding RNAs (lncRNAs) are a growing focus in cancer research. Deciphering pathways influenced by lncRNAs is important to understand their role in cancer. Although knock-down or overexpression of lncRNAs followed by gene expression profiling in cancer cell lines are established approaches to address this problem, these experimental data are not available for a majority of the annotated lncRNAs. Results As a surrogate, we present lncGSEA, a convenient tool to predict the lncRNA associated pathways through Gene Set Enrichment Analysis of gene expression profiles from large-scale cancer patient samples. We demonstrate that lncGSEA is able to recapitulate lncRNA associated pathways supported by literature and experimental validations in multiple cancer types. Conclusions LncGSEA allows researchers to infer lncRNA regulatory pathways directly from clinical samples in oncology. LncGSEA is written in R, and is freely accessible at https://github.com/ylab-hi/lncGSEA.

scholarly journals Cervical Cat Scratch Disease Lymphadenitis in a Patient with Immunoglobulin M Antibodies to Toxoplasma gondii

2002 ◽  
Vol 9 (2) ◽  
pp. 496-498
Author(s):  
Mardjan Arvand ◽  
Ilkay Kazak ◽  
Sergije Jovanovic ◽  
Hans-Dieter Foss ◽  
Oliver Liesenfeld
Keyword(s):  
Toxoplasma Gondii ◽  
Clinical Symptoms ◽  
Bartonella Henselae ◽  
Cervical Lymphadenopathy ◽  
Immunoglobulin M ◽  
Cat Scratch Disease ◽  
Specific Immunoglobulin ◽  
Acute Toxoplasmosis

ABSTRACT We report on a young patient with chronic cervical lymphadenopathy and serological and histological evidence for infection with Bartonella henselae and Toxoplasma gondii. Serological follow-up studies, including testing for avidity of Toxoplasma-specific immunoglobulin G antibodies, assisted in the determination of the cause of the acute lymphadenitis. Our results suggest that the clinical symptoms were most likely due to cat scratch disease rather than to acute toxoplasmosis.

scholarly journals Identification of a Third Human Polyomavirus

2007 ◽  
Vol 81 (8) ◽  
pp. 4130-4136 ◽  
Author(s):  
Tobias Allander ◽  
Kalle Andreasson ◽  
Shawon Gupta ◽  
Annelie Bjerkner ◽  
Gordana Bogdanovic ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Large Scale ◽  
Severe Disease ◽  
Amino Acid Identity ◽  
Human Polyomavirus ◽  
Clinical Samples ◽  
Human Pathogens ◽  
Human Respiratory Tract ◽  
Ki Polyomavirus ◽  
Virus Screening

ABSTRACT We have previously reported on a system for large-scale molecular virus screening of clinical samples. As part of an effort to systematically search for unrecognized human pathogens, the technology was applied for virus screening of human respiratory tract samples. This resulted in the identification of a previously unknown polyomavirus provisionally named KI polyomavirus. The virus is phylogenetically related to other primate polyomaviruses in the early region of the genome but has very little homology (<30% amino acid identity) to known polyomaviruses in the late region. The virus was found by PCR in 6 (1%) of 637 nasopharyngeal aspirates and in 1 (0.5%) of 192 fecal samples but was not detected in sets of urine and blood samples. Since polyomaviruses have oncogenic potential and may produce severe disease in immunosuppressed individuals, continued searching for the virus in different medical contexts is important. This finding further illustrates how unbiased screening of respiratory tract samples can be used for the discovery of diverse virus types.

A point-of-care diagnostic for differentiating Ebola from endemic febrile diseases

2018 ◽  
Vol 10 (471) ◽  
pp. eaat0944 ◽  
Author(s):  
David Sebba ◽  
Alexander G. Lastovich ◽  
Melody Kuroda ◽  
Eric Fallows ◽  
Joshua Johnson ◽  
...  
Keyword(s):  
Ebola Virus ◽  
Clinical Symptoms ◽  
Point Of Care ◽  
Hemorrhagic Fever ◽  
Diagnostic Methods ◽  
Outbreak Detection ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Live Virus ◽  
And Control

Hemorrhagic fever outbreaks such as Ebola are difficult to detect and control because of the lack of low-cost, easily deployable diagnostics and because initial clinical symptoms mimic other endemic diseases such as malaria. Current molecular diagnostic methods such as polymerase chain reaction require trained personnel and laboratory infrastructure, hindering diagnostics at the point of need. Although rapid tests such as lateral flow can be broadly deployed, they are typically not well-suited for differentiating among multiple diseases presenting with similar symptoms. Early detection and control of Ebola outbreaks require simple, easy-to-use assays that can detect and differentiate infection with Ebola virus from other more common febrile diseases. Here, we developed and tested an immunoassay technology that uses surface-enhanced Raman scattering (SERS) tags to simultaneously detect antigens from Ebola, Lassa, and malaria within a single blood sample. Results are provided in <30 min for individual or batched samples. Using 190 clinical samples collected from the 2014 West African Ebola outbreak, along with 163 malaria positives and 233 negative controls, we demonstrated Ebola detection with 90.0% sensitivity and 97.9% specificity and malaria detection with 100.0% sensitivity and 99.6% specificity. These results, along with corresponding live virus and nonhuman primate testing of an Ebola, Lassa, and malaria 3-plex assay, indicate the potential of the SERS technology as an important tool for outbreak detection and clinical triage in low-resource settings.

scholarly journals Development and evaluation of duplex TaqMan real-time PCR assay for detection and differentiation of wide-type and MGF505-2R gene-deleted African swine fever viruses

2020 ◽  
Author(s):  
zhenhua Guo ◽  
Kunpeng Li ◽  
Songlin Qiao ◽  
Xinxin Chen ◽  
Ruiguang Deng ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Large Scale ◽  
Limit Of Detection ◽  
African Swine Fever ◽  
Economic Losses ◽  
Clinical Samples ◽  
Diagnosis Method ◽  
Pcr Method ◽  
And Control

Abstract Background: African swine fever (ASF) is the most important disease to the pigs and cause serious economic losses to the countries with large-scale swine production. Vaccines are recognized as the most useful tool to prevent and control ASF virus (ASFV) infection. Currently, the MGF505 and MGF360 gene-deleted ASFVs or combined with CD2v deletion were confirmed to be the most promising vaccine candidates. Thus, it is essential to develop a diagnosis method to discriminate wide-type strain from the vaccines used.Results: In this study, we established a duplex TaqMan real-time PCR based on the B646L gene and MGF505-2R gene. The sequence alignment showed that the targeted regions of primers and probes are highly conserved in the genotype II ASFVs. The duplex real-time assay can specifically detect B646L and MGF505-2R gene single or simultaneously without cross-reaction with other porcine viruses tested. The limit of detection was 5.8 copies and 3.0 copies for the standard plasmids containing B646L and MGF505-2R genes, respectively. Clinical samples were tested in parallel by duplex real-time PCR and a commercial ASFV detection kit. The detection results of these two assays against B646L gene were well consistent.Conclusion: We successfully developed and evaluated a duplex TaqMan real-time PCR method which can effectively distinguish the wide type and MGF505 gene-deleted ASFVs. It would be a useful tool for the clinical diagnosis and control of ASF.

scholarly journals Efficacy of the new β-D-glucan measurement kit for diagnosing invasive fungal infections, as compared with that of four conventional kits

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255172
Author(s):  
Yuuki Bamba ◽  
Kei Nagano ◽  
Hiroshi Moro ◽  
Hideyuki Ogata ◽  
Mariko Hakamata ◽  
...  
Keyword(s):  
Measurement Method ◽  
Diagnostic Performance ◽  
Fungal Infections ◽  
Pneumocystis Pneumonia ◽  
Invasive Fungal Infections ◽  
Clinical Samples ◽  
Clinical Diagnoses ◽  
European Regulations ◽  
Pre Treatment ◽  
Positive Results

Background Each of the currently available (1→3)-β-D-glucan (BDG) measurement kits follows a different measurement method and cut-off value. Comparisons of diagnostic performance for invasive fungal infections (IFIs) are desirable. Additionally, ecological considerations are becoming increasingly important in the development of new measurement kits. Methods The plasma BDG levels in clinical samples were measured using the following currently available kits: the Fungitec G test MKII, the Fungitec G test ES, Fungitell, the β-Glucan test Wako, and the newly developed Wako kit (Wako-Eu). Wako-Eu uses a pre-treatment solution that conforms to European regulations for the registration, evaluation, authorisation, and restriction of chemicals. The values obtained for the samples using each kit were studied and compared. Results Of the 165 patients evaluated, 12 had IFIs, including pneumocystis pneumonia, aspergillosis, and candidiasis. BDG values obtained using the kits were moderately correlated with each other. Clinical diagnoses of the evaluated cases indicated that 21 false positives were diagnosed by at least one kit. The sensitivity of the Fungitell kit was relatively low, but those of the other four were over 90%. The specificity was above 90% for all kits. For positive predictive value, the Wako and the Wako-Eu methods were superior to the others owing to fewer false positive results. Conclusions The newly developed Wako-Eu method, which considers ecological concerns, shows diagnostic performance equivalent to that of its predecessor. To improve the diagnostic accuracy of IFIs, it is necessary to interpret the results carefully, giving due consideration to the characteristics of each measurement kit.

scholarly journals Performance of 2 Polymerization Protocols Targeting Cloned Toxoplasma Parasites

2018 ◽  
Vol 6 (9) ◽  
pp. 1577-1580
Author(s):  
Nihal A. Hanafy ◽  
Mohamed S. Badr ◽  
Ghada M. Nasr
Keyword(s):  
Toxoplasma Gondii ◽  
Real Time ◽  
Parasitic Infection ◽  
Clinical Samples ◽  
Molecular Assays ◽  
Low Concentrations ◽  
Target Dna ◽  
Primer Sets ◽  
Amplification Failure ◽  
Reference Samples

BACKGROUND: Toxoplasma gondii is a common parasitic infection of humans. Infection is usually mild. Serious complications can occur in pregnant and immunocompromised patients. AIM: The present study aims to investigate the performance of 2 different PCR protocols; real-time quantitative molecular assays (qPCR) and conventional molecular assays (cPCR), using 2 different sets of primers and by using cloned purified Toxoplasma genomic substances to be evaluated as reference samples. METHODS: The target DNA was provided in 8 different quantities. RESULTS: Amplification failure was reported only with the cPCR in samples of low concentrations using both primer sets. Quantitative PCR detected the 8 different dilutions of the purified Toxoplasma gondii using the 2 sets of primers while cPCR was sensitive to detect only 6 different dilutions. CONCLUSION: Generally real-time quantitative molecular assays, is easy to use method compared to conventional PCR assay and produces more reliable results within only one hour time but still the possible application of qPCRs in routine diagnosis necessitates analysis of a large number of clinical samples in further studies to make the proper choice.

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