Genexpert

Manufactured by Cepheid

Sourced in United States, Germany

The GeneXpert is a compact, automated system for molecular diagnostic testing. It is designed to perform rapid, real-time PCR (Polymerase Chain Reaction) analysis to detect the presence of specific nucleic acid sequences. The GeneXpert system integrates sample preparation, nucleic acid amplification, and detection in a single fully-automated process.

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95 protocols using genexpert

Pulmonary Tuberculosis Case Recruitment Protocol

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Recruitment of pulmonary TB cases began in May 2013 and concluded in
February 2017. Eligible for recruitment as cases were all patients, aged
18–70, with newly diagnosed active pulmonary TB by chest x-ray and sputum
smear positivity (at least one of two sputum specimens positive for acidfast
bacilli by microscopy), using methods recommended by the World Health
Organization(Getahun et al. 2007 (link)).
Later in the study, cases diagnosed using GeneXpert (Cepheid Inc.) were included
after the TB Center acquired a GeneXpert device. Excluded as cases were:

Anyone with known immunosuppressive conditions or taking
immunosuppressive drugs (e.g., corticosteroids, cancer chemotherapy)
to minimize effect modification, as exploration of this was not an
objective of the investigation.

Anyone with a history of TB.

Although informed consent was obtained at the time of diagnosis,
collection of data for the study did not begin until at least 4 weeks of
treatment had occurred, as a precautionary measure for the field staff.
Although the original intention had been to collect all cases mainly
from Kaski District, where the WRTC, is located, towards the end of the field
data collection, since recruitment of cases from the WRTC was slower than
anticipated, cases were also obtained from TB diagnostic centers in districts
neighboring Kaski, namely Tanahun, Syanja and Parbat.

Bates M.N., Pope K., Sijali T.R., Pokhrel A.K., Pillarisetti A., Lam N.L, & Verma S.C. (2018). Household fuel use and pulmonary tuberculosis in western Nepal: A case-control study. Environmental research, 168, 193-205.

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Structured Questionnaire and Sputum Analysis for TB Diagnosis

Cited 1 time

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After written consent was obtained from all study participants, a structured
questionnaire adapted from a previous study conducted in Kenya²⁷ and Ethiopia^{17 (link)} was used to collect the socio-demographic, behavioral, environmental, and
treatment-related characteristics. The questions were presented to the study
participants by face-to-face interview (Supplement material).
Participants were instructed to bring a sputum specimen in a clean, sterile, and
screw-cupped container. The sputum specimens were examined using GeneXpert (Cepheid).²⁸ Briefly, 1 mL of sputum was mixed with 2 mL of a buffered reagent to
liquefy the sputum and incubated at room temperature for 10 min. After
incubation, 2 mL was transferred to a cartridge in order to release the target
DNA, and then the cartridge was loaded into GeneXpert (Cepheid) machines. The
result was displayed on the computer screen after 2 h of processing.

Andarge D.B., Anticho T.L., Jara G.M, & Ali M.M. (2021). Prevalence of Mycobacterium tuberculosis infection and rifampicin resistance among presumptive tuberculosis cases visiting tuberculosis clinic of Adare General Hospital, Southern Ethiopia. SAGE Open Medicine, 9, 20503121211045541.

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Evaluating Antibiotic Trials for Diagnosing PTB

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We will include studies in any language published after 1993 that recruited adults being investigated for PTB and performed and reported outcomes of both trial-of-antibiotics and mycobacteriology investigations as part of their diagnostics work up. We will define mycobacteriology tests as any laboratory test that identifies evidence of MTB from a sputum sample. There is no defined reference mycobacteriology diagnostic test for MTB; each of the available tests has considerable flaws. Considering the time period of the review, we expect smear microscopy, smear microscopy using a fluorescent microscope, Cepheid GeneXpert, and mycobacterial culture. The guiding PIRO (population, index test, reference test and Outcome) framework for the research question is as presented in Table 1 below.Table 1

Research question

Population	Adult patients with respiratory symptoms
Index test	Trial-of-antibiotics (any course of broad-spectrum antimicrobial given with the goal of ruling out TB in a symptomatic adult)
Reference test	Any mycobacteriology test (we expect smear microscopy, smear microscopy using a fluorescent microscope, Cepheid GeneXpert, and mycobacterial culture)
Outcome	Proportion of mycobacteriology-positive or mycobacteriology-negative participants correctly identified by trial-of-antibiotics (sensitivity and specificity)
Design	Cross-sectional, cohort, and randomised controlled studies

Divala T.H., Fielding K.L., Nliwasa M., Sloan D.J., Gupta-Wright A, & Corbett E.L. (2018). Sensitivity and specificity of using trial-of-antibiotics versus sputum mycobacteriology for diagnosis of tuberculosis: protocol for a systematic literature review. Systematic Reviews, 7, 141.

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Detecting Carbapenemase-Producing Strains

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The presence of carbapenemase was confirmed using a real-time polymerase chain reaction (RT-PCR) method, GeneXpert (Cepheid, Sunnyvale, CA, EUA), which allows identification of KPC-encoding, NDM-encoding, VIM-encoding, OXA-48-encoding, and IMP-encoding genes.
ASCs were performed using rectal samples collected by dry swabs and swabs with transport medium. Dry swabs were used to investigate the presence of the carbapenemase gene using the RT-PCR method, GeneXpert (Cepheid). The swabs with transport medium were used, in PCR positive cases, to perform the cultural examination for microorganism identification, as mentioned above.
The carbapenemase-producing strains were subjected to pulsed-field gel electrophoresis (PFGE) at the National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal, as previously described.^{31 (link)}

Peres D., Figueiredo P., Andrade P., Rocha-Pereira N., Carvalho C., Ferraz R., Duro R., Dias A., Gomes A., Pereira C., Braga G., Pereira V., Azevedo L., Moniz E., Ribeiro M., Ferreira E., Manageiro V., Teixeira J., Guimarães T., Caniça M, & Alves C. (2022). Outbreak of KPC-producing Klebsiella pneumoniae at a Portuguese university hospital: Epidemiological characterization and containment measures. Porto Biomedical Journal, 7(6), e186.

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PET/CT Imaging for Tuberculosis Biomarkers

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This is a report on the 18 F-FDG PET/CT imaging component of a prospective study evaluating imaging patterns from 18 F-FDG PET/CT scans, transcriptomic and proteomic biosignatures, cell subset analysis, cytokine and chemokine patterns, and other nonspecific inflammatory markers as potential biomarkers of successful eradication of tuberculous disease and infection and for predicting the risk of persistence or relapse after treatment completion. We recruited patients who completed a standard 6-mo regimen of ATT for confirmed DS-PTB in clinics within Tshwane District. Participants were identified from the AitaHealth database managed by the Department of Family Health at the University of Pretoria. The primary care doctors at the participating clinics determined that prospective participants had completed a full course of treatment for DS-PTB as per South African guidelines (18). Inclusion criteria were known HIV infection status, age 18-65 y, GeneXpert (Cepheid)-positive at the start of treatment and culture-confirmed susceptible to first-line tuberculosis drugs, available pretreatment isolate, completion of the full course of treatment for DS-PTB and needing no further treatment (as deemed by the primary care physician), and residence in a household recorded on the AitaHealth database.

Lawal I.O., Fourie B.P., Mathebula M., Moagi I., Lengana T., Moeketsi N., Nchabeleng M., Hatherill M, & Sathekge M.M. (2020). ¹⁸F-FDG PET/CT as a Noninvasive Biomarker for Assessing Adequacy of Treatment and Predicting Relapse in Patients Treated for Pulmonary Tuberculosis. Journal of nuclear medicine : official publication, Society of Nuclear Medicine, 61(3).

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Defining COVID-19 and Tuberculosis Severity

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According to China’s Novel Coronavirus Pneumonia Diagnosis and Treatment Plan (Seventh Edition) [15 ], the clinical classifications are mild, moderate, severe and critical. Mild type: the clinical symptoms are mild, with no manifestations of pneumonia on imaging. Moderate type: the patients have fever, respiratory tract symptoms, and other symptoms; imaging can show signs of pneumonia. Severe COVID-19 patients were defined as having oxygen saturation <93% on room air, dyspnea, respiratory rate ≥30/min, arterial oxygen partial pressure/fraction of inspired oxygen ratio <300 mmHg, and/or lung infiltrates >50% within 24–48 h. Critical COVID-19 patients were defined as having respiratory failure, septic shock, and/or multiple organ dysfunction or failure.
Bacteriologically confirmed tuberculosis was defined as TB diagnosed in a biological specimen by a nucleic acid amplification test (GeneXpert, Cepheid), smear microscopy, or culture.
Clinically diagnosed tuberculosis was defined as the lack of bacteriological confirmation and the presence of at least 2 of the following:

Symptoms/signs suggestive of tuberculosis;

Chest radiograph consistent with tuberculosis;

Close tuberculosis exposure or immunologic evidence of mycobacterium tuberculosis infection;

Positive response to tuberculosis treatment.

Huang W., Liu P., Yan B., Zheng F., Yang Y., Xi X., Xia L, & Shen Y. (2024). Impact of Tuberculosis on Disease Severity and Viral Shedding Duration in COVID-19 Patients. Viruses, 16(2), 260.

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Rapid Antigen and PCR Testing for Influenza

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Different rapid antigen detection kits were used across the different seasons. These included: Rapid FLU virus test kit Capilia™ Tauns, Japan; Quick-Ex flu A/B rapid influenza test Denka Seiken, Japan; Quick-Ex flu A/B & RSV rapid influenza test Denka Seiken, Japan; and BD Directigen™ EZ Flu A + B (Becton Dickinson, Cockeysville, Md.). Testing was performed following the manufacturer’s instructions.

Polymerase chain reaction: real-time reverse-transcriptase (RT) polymerase chain reaction (PCR) using the GENEXPERT (Cepheid) platform was used at AUBMC Clinical Molecular Biology Laboratory [33 (link)].

Only 2 patients were diagnosed by serology testing (Influenza A IgG titers cutoff < 1:10, our patients had a titer level of 1:5120). This was during the 2009 influenza pandemic.

Assaf-Casals A., Saleh Z., Khafaja S., Fayad D., Ezzeddine H., Saleh M., Chamseddine S., Sayegh R., Sharara S.L., Chmaisse A., Kanj S.S., Kanafani Z., Hanna-Wakim R., Araj G.F., Mahfouz R., Saito R., Suzuki H., Zaraket H, & Dbaibo G.S. (2020). The burden of laboratory-confirmed influenza infection in Lebanon between 2008 and 2016: a single tertiary care center experience. BMC Infectious Diseases, 20, 339.

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SARS-CoV-2 Detection in Biological Samples

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Samples were tested using the Cepheid GeneXpert. Plasma samples were processed according to the manufacturer’s instructions and semen samples were processed as described previously [20 (link)]. Samples with a failed internal control (SAC, sample adequacy control), but passing internal controls (CIC, Cepheid internal control), were considered negative due to limited cross-reactivity with human and nonhuman primate housekeeping genes.

Bennett R.S., Logue J., Liu D.X., Reeder R.J., Janosko K.B., Perry D.L., Cooper T.K., Byrum R., Ragland D., St. Claire M., Adams R., Burdette T.L., Brady T.M., Hadley K., Waters M.C., Shim R., Dowling W., Qin J., Crozier I., Jahrling P.B, & Hensley L.E. (2020). Kikwit Ebola Virus Disease Progression in the Rhesus Monkey Animal Model. Viruses, 12(7), 753.

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Clostridium Difficile Infection Surveillance

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Patient characteristics (age, sex, type of surgery, International Classification of Disease, Ninth or Tenth Revision documentation of Crohn’s disease or ulcerative colitis) and treatment information (prophylactic antibiotics, cancer therapy) were extracted from existing hospital databases following institutional review board approval. The CDI cases were obtained from the institution’s infection control surveillance database, which includes CDI diagnoses occurring in any inpatient or outpatient facility affiliated with the cancer center (~600 annually) and CDI diagnoses in cancer center patients reported by outside facilities. CDI testing across all affiliated sites is performed on a single-step polymerase chain reaction (PCR) platform (GeneXpert, Cepheid, Sunnyvale, CA) with subsequent molecular fingerprinting by multilocus sequence typing.^{5 (link)} Only diarrheal stool samples are tested.

Cohen B., Levine M, & Kamboj M. (2019). Clostridium difficile infection following outpatient cancer surgery. Infection control and hospital epidemiology, 40(12), 1440-1441.

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Carbapenemase Detection and Genetic Relatedness

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Bacterial colonies suspicious for the production of carbapenemases

Molecular characterization was performed using the Xpert Carba-R Assay on the GeneXpert® system (Cepheid, Sunnyvale, California, USA). Colonies considered as suspicious for the production of carbapenemases but with a negative result on the GeneXpert®, were send to the NRC of CPE to exclude resistance.

Genetic relatedness

To confirm genetic relatedness between isolates from patients and environmental samples, pulsed-field gel electrophoresis (PFGE) was performed.

De Geyter D., Blommaert L., Verbraeken N., Sevenois M., Huyghens L., Martini H., Covens L., Piérard D, & Wybo I. (2017). The sink as a potential source of transmission of carbapenemase-producing Enterobacteriaceae in the intensive care unit. Antimicrobial Resistance and Infection Control, 6, 24.

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