Improved Detection of Respiratory Pathogens by Use of High-Quality Sputum with TaqMan Array Card Technology

ABSTRACTNew diagnostic platforms often use nasopharyngeal or oropharyngeal (NP/OP) swabs for pathogen detection for patients hospitalized with community-acquired pneumonia (CAP). We applied multipathogen testing to high-quality sputum specimens to determine if more pathogens can be identified relative to NP/OP swabs. Children (<18 years old) and adults hospitalized with CAP were enrolled over 2.5 years through the Etiology of Pneumonia in the Community (EPIC) study. NP/OP specimens with matching high-quality sputum (defined as ≤10 epithelial cells/low-power field [lpf] and ≥25 white blood cells/lpf or a quality score [q-score] definition of 2+) were tested by TaqMan array card (TAC), a multipathogen real-time PCR detection platform. Among 236 patients with matched specimens, a higher proportion of sputum specimens had ≥1 pathogen detected compared with NP/OP specimens in children (93% versus 68%;P< 0.0001) and adults (88% versus 61%;P< 0.0001); for each pathogen targeted, crossing threshold (CT) values were earlier in sputum. Both bacterial (361 versus 294) and viral detections (245 versus 140) were more common in sputum versus NP/OP specimens, respectively, in both children and adults. When available, high-quality sputum may be useful for testing in hospitalized CAP patients.

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Utility of procalcitonin, C-reactive protein and white blood cells alone and in combination for the prediction of clinical outcomes in community-acquired pneumonia

Clinical Chemistry and Laboratory Medicine (CCLM) ◽

10.1515/cclm-2014-0456 ◽

2015 ◽

Vol 53 (4) ◽

Cited By ~ 37

Author(s):

Andriy Zhydkov ◽

Mirjam Christ-Crain ◽

Robert Thomann ◽

Claus Hoess ◽

Christoph Henzen ◽

...

Keyword(s):

Clinical Outcome ◽

Clinical Outcomes ◽

Blood Cells ◽

White Blood Cells ◽

Community Acquired Pneumonia ◽

Adverse Clinical Outcome ◽

C Reactive Protein ◽

Prognostic Information ◽

Reactive Protein

AbstractThe added value of biomarkers, such as procalcitonin (PCT), C-reactive protein (CRP), and white blood cells (WBC), as adjuncts to clinical risk scores for predicting the outcome of patients with community-acquired pneumonia (CAP) is in question. We investigated the prognostic accuracy of initial and follow-up levels of inflammatory biomarkers in predicting death and adverse clinical outcomes in a large and well-defined cohort of CAP patients.We measured PCT, CRP and WBC on days 1, 3, 5, and 7 and followed the patients over 30 days. We applied multivariate regression models and area under the curve (AUC) to investigate associations between these biomarkers, the clinical risk score CURB-65, and clinical outcomes [i.e., death and intensive care unit (ICU) admission].Of 925 patients with CAP, 50 patients died and 118 patients had an adverse clinical outcome. None of the initial biomarker levels significantly improved the CURB-65 score for mortality prediction. Follow-up biomarker levels showed significant independent association with mortality at days 3, 5, and 7 and with improvements in AUC. Initial PCT and CRP levels were independent prognostic predictors of adverse clinical outcome, and levels of all biomarkers during the course of disease provided additional prognostic information.This study provides robust insights into the added prognostic value of inflammatory markers in CAP. Procalcitonin, CRP, and to a lesser degree WBC provided some prognostic information on CAP outcomes, particularly when considering their kinetics at days 5 and 7 and when looking at adverse clinical outcomes instead of mortality alone.

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Estimation of Eosinophil Cells in Cord Blood with References Based on Blood in Adults via Bayesian Measurement Error Modeling

Bioinformatics ◽

10.1093/bioinformatics/btz839 ◽

2019 ◽

Cited By ~ 1

Author(s):

Yu Jiang ◽

Hongmei Zhang ◽

Shan V Andrews ◽

Hasan Arshad ◽

Susan Ewart ◽

...

Keyword(s):

Measurement Error ◽

Cord Blood ◽

Blood Cells ◽

White Blood Cells ◽

Error Modeling ◽

Supplementary Information ◽

Estimation Accuracy ◽

Bioconductor Package ◽

High Quality ◽

Eosinophil Cell

Abstract Motivation Eosinophils are phagocytic white blood cells with a variety of roles in the immune system. In situations where actual counts are not available, high quality approximations of their cell proportions using indirect markers are critical. Results We develop a Bayesian measurement error model to estimate proportions of eosinophils in cord blood, using the cord blood DNA methylation profiles, based on markers of eosinophil cell heterogeneity in blood of adults. The proposed method can be directly extended to other cells across different reference panels. We demonstrate the method’s estimation accuracy using B cells and show that the findings support the proposed approach. The method has been incorporated into the estimateCellCounts function in the minfi package to estimate eosinophil cells proportions in cord blood. Availability estimateCellCounts function is implemented and available in Bioconductor package minfi. Supplementary information Supplementary data are available at Bioinformatics online.

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CELL DEATH MODES OF WHITE BLOOD CELLS IN PATIENTS WITH COMMUNITY-ACQUIRED PNEUMONIA AND PULMONARY TUBERCULOSIS

10.1183/13993003.congress-2021.pa2468 ◽

2021 ◽

Author(s):

Olga Hovardovska ◽

Olga Schevchenko ◽

Oksana Nakonechna ◽

Yuliia Kalashnyk-Vakulenko ◽

Anton Tkachenko ◽

...

Keyword(s):

Cell Death ◽

Pulmonary Tuberculosis ◽

Blood Cells ◽

White Blood Cells ◽

Community Acquired Pneumonia

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Invited response to definition of hormesis (EJ Calabrese and LA Baldwin)

Human & Experimental Toxicology ◽

10.1191/0960327102ht221oa ◽

2002 ◽

Vol 21 (2) ◽

pp. 107-109 ◽

Cited By ~ 4

Author(s):

J A Pickrell ◽

F W Oehme

Keyword(s):

Blood Cells ◽

Radiation Injury ◽

White Blood Cells ◽

Essential Element ◽

Pulmonary Injury ◽

Final Phase ◽

Disparate Data ◽

Definition Of

Calabrese and Baldwin have proposed the Theory of Hormesis to explain a variety of disparate data. We evaluated the explanation using examples of pulmonary injury, radiation injury to white blood cells and selenium as an essential element, reducer of carcinogenesis and a potential toxicant. Calabrese and Baldwin have fulfilled many of the criteria allowing generalizability of their theory. They have gathered data extensively. These data were logically consistent with their experiences. They needed to examine critically the theory and any theories competing with it. At this point, each theory must be proved, disproved or its limitations clearly stated. It is in this phase that most work is still being accomplished. This examination is important because it provides referents for vigorous outside criticism, the final phase. Calabrese and Baldwin are to be complimented on seeking outside comment. Considerable refinement of the theory has taken place with time.

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Methodology for detecting trace amounts of microchimeric DNA from peripheral murine white blood cells by real-time PCR

Biological Procedures Online ◽

10.1251/bpo51 ◽

2003 ◽

Vol 5 (1) ◽

pp. 103-107 ◽

Cited By ~ 1

Author(s):

Carol M. Artlett ◽

C. Gennaro Dito ◽

Paul J. Christner

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Blood Cells ◽

White Blood Cells

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Identification of Bacterial and Viral Codetections With Mycoplasma pneumoniae Using the TaqMan Array Card in Patients Hospitalized With Community-Acquired Pneumonia

Open Forum Infectious Diseases ◽

10.1093/ofid/ofw071 ◽

2016 ◽

Vol 3 (2) ◽

Cited By ~ 10

Author(s):

Maureen H. Diaz ◽

Kristen E. Cross ◽

Alvaro J. Benitez ◽

Lauri A. Hicks ◽

Preeta Kutty ◽

...

Keyword(s):

Prospective Study ◽

Mycoplasma Pneumoniae ◽

Community Acquired Pneumonia ◽

Respiratory Pathogens ◽

Number Of Patients ◽

Taqman Array ◽

Respiratory Specimens

Abstract Mycoplasma pneumoniae was detected in a number of patients with community-acquired pneumonia in a recent prospective study. To assess whether other pathogens were also detected in these patients, TaqMan Array Cards were used to test 216 M pneumoniae-positive respiratory specimens for 25 additional viral and bacterial respiratory pathogens. It is interesting to note that 1 or more codetections, predominantly bacterial, were identified in approximately 60% of specimens, with codetections being more common in children.

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A novel real-time PCR assay panel for detection of common respiratory pathogens in a convenient, strip-tube array format

10.1101/455568 ◽

2018 ◽

Author(s):

Mohammad Rubayet Hasan ◽

Hassan Al Mana ◽

Virginia Young ◽

Patrick Tang ◽

Eva Thomas ◽

...

Keyword(s):

Real Time ◽

Real Time Pcr ◽

Pathogen Detection ◽

Respiratory Infections ◽

Simultaneous Detection ◽

Respiratory Pathogens ◽

Routine Manner ◽

Pcr Assays ◽

Sensitivity Specificity ◽

Array Format

AbstractCommercial multiplex assays, built on different chemistries and platforms are widely available for simultaneous detection of pathogens that cause respiratory infections. However, these tests are often difficult to implement in a resource limited setting because of high cost. In this study, we developed and validated a method for simultaneous testing of common respiratory pathogens (Respanel) by real-time PCR in a convenient, strip-tube array format. Primers and probes for sixteen PCR assays were selected from the literature or newly designed. Following optimization of individual PCR assays, strip-tube arrays were prepared by dispensing primer-probe mixes (PPM) into two sets of 8-tube strips. Nucleic acid extracts from specimens were mixed with PCR master mix, and dispensed column-wise into 2X8-wells of a 96-well plate. PPMs from strip-tubes were then added to the wells using a multichannel pipette for real-time PCR. Individual PCR assays were optimized using previously known specimens (n=397) with 91%-100% concordance with culture, DFA or PCR results. Respanel was then tested in a routine manner at two different sites using specimens (n=147) previously tested by Qiagen Resplex I&II or Fast-Track Diagnostics Respiratory Pathogens 21 assays. The sensitivity, specificity and accuracy of Respanel were 94%, 95% and 95%, respectively, against Resplex and 88%, 100% and 99%, respectively, against FTDRP21. Respanel detected 48% more pathogens (p<0.05) than Resplex but the rate of pathogen detection was not significantly different from FTDRP21. Respanel is a convenient and inexpensive assay that is more sensitive than Resplex and comparable to FTDRP21 for the detection of common respiratory pathogens.

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Evaluating the use of a 22-pathogen TaqMan array card for rapid diagnosis of respiratory pathogens in intensive care

Journal of Medical Microbiology ◽

10.1099/jmm.0.001218 ◽

2020 ◽

Vol 69 (7) ◽

pp. 971-978

Author(s):

Nick K. Jones ◽

Andrew Conway Morris ◽

Martin D. Curran ◽

Surendra Parmar ◽

Olajumoke Sule ◽

...

Keyword(s):

Intensive Care ◽

Type Species ◽

Pathogen Detection ◽

Laboratory Diagnosis ◽

Fungal Culture ◽

Respiratory Pathogens ◽

Content Type ◽

Chain Reactions ◽

Link Type ◽

Taqman Array

Introduction. Pneumonia is highly prevalent in intensive care units (ICUs), with high associated mortality. Empirical treatment prioritizes breadth of coverage while awaiting laboratory diagnosis, often at the expense of antimicrobial stewardship. Microarrays use multiple parallel polymerase chain reactions to enable a rapid syndromic approach to laboratory diagnosis. Aim. To evaluate the clinical and laboratory implications of introducing a bespoke 22-pathogen TaqMan Array Card (TAC) for rapid pathogen detection in deep respiratory samples from adult ICUs. Methodology. TAC results from all ICU patients prospectively tested over a 9-month period at Cambridge’s Clinical Microbiology and Public Health Laboratory were compared to those of corresponding conventional microbiological assays (culture-, PCR- or serology-based) in terms of result agreement and time-to-result availability. Clinical impact was assessed by retrospective review of medical records. Results. Seventy-one patients were included [45 (63 %) male, median age 59). Overall result agreement was 94 %, with TAC detecting more pathogens than conventional methods. TAC detected Streptococcus pneumoniae more readily than culture (7 vs 0 cases; P=0.02). TAC did not detect Aspergillus spp. in eight culture- or galactomannan-positive cases. The median turnaround time (1 day) was significantly shorter than that of bacterial/fungal culture, Pneumocystis jirovecii PCR and galactomannan testing (each 3 days; P<0.001), atypical bacteria serology (13 days; P<0.001) and Mycobacterium tuberculosis culture (46 days; P<0.001). Earlier result availability prompted discontinuation of unnecessary antimicrobials in 15/71 (21 %) cases, but had no bearing on patient isolation/deisolation. Conclusion. TAC provided greater overall yield of pathogen detection and faster turnaround times, permitting earlier discontinuation of unnecessary antimicrobials.

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Pathogens detected using a syndromic molecular diagnostic platform in patients hospitalized with severe respiratory illness in South Africa in 2017

10.1101/2021.11.10.21266173 ◽

2021 ◽

Author(s):

Malefu Moleleki ◽

Mignon du Plessis ◽

Kedibone Ndlangisa ◽

Cayla Reddy ◽

Anne von Gottberg ◽

...

Keyword(s):

South Africa ◽

Pathogen Detection ◽

Respiratory Illness ◽

Molecular Diagnostic ◽

Respiratory Pathogens ◽

Individual Level ◽

Chi Squared ◽

Syncytial Virus ◽

Taqman Array ◽

Severe Respiratory Illness

Background Pneumonia continues to be a leading cause of death globally; however, in >50% of cases, an etiological agent is not identified. We describe the use of a multi-pathogen platform, TaqMan array card (TAC) real-time PCR, for the detection of pathogens in patients hospitalized with severe respiratory illness (SRI). Methods We conducted prospective hospital-based surveillance for SRI among patients at two sentinel sites in South Africa between January and December 2017. Patients were included in this study if a blood specimen and at least one respiratory specimen (naso- and oro-pharyngeal (NP/OP) swabs and/or sputum) were available for testing. We tested respiratory specimens for 21 respiratory pathogens and blood samples for nine bacteria using TAC. Pathogen detection was compared by age group and HIV status using the chi-squared test. Results During 2017, 956 patients were enrolled in SRI surveillance, and of these, 637 (67%) patients were included in this study (637 blood, 487 NP/OP and 411 sputum specimens tested). At least one pathogen was detected in 83% (527/637) of patients. Common pathogens detected included H. influenzae (225/637; 35%), S. pneumoniae (224/637; 35%), rhinovirus (144/637; 23%), S. aureus (129/637; 20%), K. pneumoniae (85/637; 13%), M. tuberculosis (75/637; 12%), and respiratory syncytial virus (57/637; 9%). Multiple pathogens (≥2) were co-detected in 57% (364/637) of patients. Conclusion While use of a multi-pathogen platform was useful in the detection of a pathogen in the majority of the patients, pathogen co-detections were common and would need clinical assessment for usefulness in individual-level treatment and management decisions.

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