Multicenter Evaluation of the Xpert Norovirus Assay for Detection of Norovirus Genogroups I and II in Fecal Specimens

Norovirus is the most common cause of sporadic gastroenteritis and outbreaks worldwide. The rapid identification of norovirus has important implications for infection prevention measures and may reduce the need for additional diagnostic testing. The Xpert Norovirus assay recently received FDA clearance for the detection and differentiation of norovirus genogroups I and II (GI and GII), which account for the vast majority of infections. In this study, we evaluated the performance of the Xpert Norovirus assay with both fresh, prospectively collected (n= 914) and frozen, archived (n= 489) fecal specimens. A Centers for Disease Control and Prevention (CDC) composite reference method was used as the gold standard for comparison. For both prospective and frozen specimens, the Xpert Norovirus assay showed positive percent agreement (PPA) and negative percent agreement (NPA) values of 98.3% and 98.1% for GI and of 99.4% and 98.2% for GII, respectively. Norovirus prevalence in the prospective specimens (collected from March to May of 2014) was 9.9% (n= 90), with the majority of positives caused by genogroup II (82%,n= 74). The positive predictive value (PPV) of the Xpert Norovirus assay was 75% for GI-positive specimens, whereas it was 86.5% for GII-positive specimens. The negative predictive values (NPV) for GI and GII were 100% and 99.9%, respectively.

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Urea-Fibrinogen Slide Coagulase Test – A Simple Alternative Method for the Rapid Identification of Staphylococcus aureus

Journal of Gandaki Medical College-Nepal ◽

10.3126/jgmcn.v10i1.17903 ◽

2017 ◽

Vol 10 (1) ◽

pp. 5-10

Author(s):

Binita Koirala Sharma ◽

S Gokhale ◽

K Sharma

Keyword(s):

Staphylococcus Aureus ◽

Sensitivity And Specificity ◽

Reference Method ◽

Cost Effective ◽

Rapid Identification ◽

Accurate Identification ◽

Predictive Values ◽

Negative Results ◽

Animal Pathogens ◽

Sensitivity Specificity

Introduction: The accurate identification of Staphylococcus aureus clinical isolates requires a series of tests. Morphological features and slide coagulase test are two criteria on which S. aureus are identified. Resort to tube coagulase test is sought when results of slide coagulase test are equivocal or doubtful. Both coagulase tests detect the enzymes that convert fibrinogen into fibrin. Human, rabbit or sheep pooled plasma is used as substrate for both tests. Slide coagulase test is simpler and faster as compared to tube coagulase test. The plasma could be carrier of many human and animal pathogens like HIV, HBV, HCV etc. Storage of plasma for longer duration is fraught with chances of contamination. Improperly stored plasma can lead to false positive or negative results. Citrated plasma may be unsuitable for this test if contaminated with citrate utilizing bacteria. Considering the role of S. aureus as a common etiological agent in nosocomial and community infections, there is a need of implementing rapid, easy and cost-effective phenotypic test.Objectives: Considering the disadvantages and risks associated with fresh plasma, this study aims to launch for safer, more reliable substitute with longer shelf life that may provide reliable results for prompt identification of S. aureus by slide coagulase test.Methods: The present work evaluates slide coagulase test (SCT), and urea fibrinogen slide coagulase test (UF-SCT) for S. aureus detection considering Tube coagulase test (TCT) as the reference method. Sensitivity, specificity, positive predictive value and negative predictive values of SCT and UF-SCT were calculated using TCT as gold standard. Results: A total of 150 staphylococcal isolates from different clinical specimens ere selected for the evaluation of coagulase tests. All the specimens were subjected to SCT, UF-SCT and TCT. The UF-SCT showed better sensitivity (95.04%), specificity (100%), PPV (100%), and NPV (82.85%) with reference to TCT. UF-SCT showed similar sensitivity and specificity to SCT. None of the isolates were negative in UF-SCT and positive in SCT. Since UF-SCT does not incorporate plasma directly and at the same time has a very good sensitivity and specificity, it is recommended that UF-SCT could replace SCT for identification of S. aureus.Conclusion: The findings of present study shall encourage laboratories to use the urea-fibrinogen slide coagulase test routinely for the rapid identification of S aureus.Journal of Gandaki Medical College Vol. 10, No. 1, 2017, Page: 5-10

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Simultaneous Evaluation of Diagnostic Assays for Pharyngeal and Rectal Neisseria gonorrhoeae and Chlamydia trachomatis Using a Master Protocol

Clinical Infectious Diseases ◽

10.1093/cid/ciz1105 ◽

2019 ◽

Cited By ~ 3

Author(s):

Sarah B Doernberg ◽

Lauren Komarow ◽

Thuy Tien T Tran ◽

Zoe Sund ◽

Mark W Pandori ◽

...

Keyword(s):

Chlamydia Trachomatis ◽

Neisseria Gonorrhoeae ◽

Reference Method ◽

Likelihood Ratios ◽

Anatomic Site ◽

Transmitted Infection ◽

Cross Sectional ◽

Predictive Values ◽

Sexually Transmitted ◽

Percent Agreement

Abstract Background Pharyngeal and rectal Neisseria gonorrhoeae and Chlamydia trachomatis play important roles in infection and antibacterial resistance transmission, but no US Food and Drug Administration (FDA)–cleared assays for detection at these sites existed prior to this study. The objective was to estimate performance of assays to detect those infections in pharyngeal and rectal specimens to support regulatory submission. Methods We performed a cross-sectional, single-visit study of adults seeking sexually transmitted infection testing at 9 clinics in 7 states. We collected pharyngeal and rectal swabs from participants. The primary outcome was positive and negative percent agreement for detection of N. gonorrhoeae and C. trachomatis for 3 investigational assays compared to a composite reference. Secondary outcomes included positivity as well as positive and negative predictive values and likelihood ratios. Subgroup analyses included outcomes by symptom status and sex. Results A total of 2598 participants (79% male) underwent testing. We observed N. gonorrhoeae positivity of 8.1% in the pharynx and 7.9% in the rectum and C. trachomatis positivity of 2.0% in the pharynx and 8.7% in the rectum. Positive percent agreement ranged from 84.8% to 96.5% for different anatomic site infection combinations, whereas negative percent agreement was 98.8% to 99.6%. Conclusions This study utilized a Master Protocol to generate diagnostic performance data for multiple assays from different manufacturers in a single study population, which ultimately supported first-in-class FDA clearance for extragenital assays. We observed very good positive percent agreement when compared to a composite reference method for the detection of both pharyngeal and rectal N. gonorrhoeae and C. trachomatis. Clinical Trials Registration NCT02870101.

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Simultaneous Detection of Bluetongue Virus Serotypes Using xMAP Technology

Microorganisms ◽

10.3390/microorganisms8101564 ◽

2020 ◽

Vol 8 (10) ◽

pp. 1564

Author(s):

Martin Ashby ◽

Paulina Rajko-Nenow ◽

Carrie Batten ◽

John Flannery

Keyword(s):

Bluetongue Virus ◽

Rapid Assessment ◽

Simultaneous Detection ◽

Rapid Identification ◽

Prevention Measures ◽

Control And Prevention ◽

Reference Strains ◽

Testing Reference ◽

Important Disease ◽

Xmap Technology

Bluetongue is an economically important disease of ruminants caused by the bluetongue virus (BTV). BTV is serologically diverse, which complicates vaccination strategies. Rapid identification of the causative BTV serotypes is critical, however, real-time PCR (RT-qPCR) can be costly and time consuming to perform when the circulating serotypes are unknown. The Luminex xMAP technology is a high-throughput platform that uses fluorescent beads to detect multiple targets simultaneously. We utilized existing BTV serotyping RT-qPCR assays for BTV-1 to BTV-24 and adapted them for use with the xMAP platform. The xMAP assay specifically detected all 24 BTV serotypes when testing reference strains. In all BTV-positive samples, the sensitivity of the BTV xMAP was 87.55% whereas the sensitivity of the serotype-specific RT-qPCR was 79.85%. The BTV xMAP assay allowed for the specific detection of BTV serotypes 1–24 at a lower cost than current RT-qPCR assays. Overall, the assay provides a useful novel diagnostic tool, particularly when analyzing large sample sets. The use of the BTV xMAP assay will allow for the rapid assessment of BTV epidemiology and may inform decision-making related to control and prevention measures.

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Local hospital experience of emergency management in the response to SARS (Preprint)

10.2196/preprints.20287 ◽

2020 ◽

Author(s):

Ying Yan

Keyword(s):

Emergency Management ◽

Infection Prevention ◽

Public Health Emergency ◽

The Novel ◽

Prevention Measures ◽

Hospital Emergency ◽

Local Hospital ◽

Referral Network ◽

Novel Coronavirus ◽

Hospital Transmission

UNSTRUCTURED The ongoing outbreak of SARS-CoV-2 infection was first identified in Wuhan, China at the late of 2019. Following the acceleration of the novel coronavirus spreading, person-person transmissions in family residences, hospitals and other public environments have led to a major public hazard in China. Currently, the SARS-CoV-2 outbreak has been further developed into a public health emergency of international concern. In response to an occurring pandemic, hospitals need an emergency strategy and plan to manage their space, staff, and other essential resources, therefore, to provide optimum care to patients involved. In addition, infection prevention measures urgently need to be implemented to reduce in-hospital transmission and avoid the occurrence of virus super-spreading. For hospitals without capacity to manage severe patients, a referral network is often needed. We present our successful field experience regarding hospital emergency management and local hospitals network model in response to SARS-CoV-2 emerging epidemic.

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A comparative evaluation of two chromogenic media for surveillance of carbapenem-resistant Enterobacterales with non-carbapenemase-producing or carbapenemase-producing strains other than blaKPC: blaGES-5, blaNDM-1 or blaVIM-2

Journal of Laboratory Medicine ◽

10.1515/labmed-2018-0139 ◽

2019 ◽

Vol 43 (3) ◽

pp. 173-176

Author(s):

Chang-Hun Park

Keyword(s):

Rapid Detection ◽

Comparative Evaluation ◽

Susceptibility Testing ◽

Rapid Identification ◽

Surveillance Program ◽

Contact Precaution ◽

Chain Reaction ◽

Carbapenem Resistant ◽

Control And Prevention ◽

Polymerase Chain

Abstract Background Infections caused by carbapenem-resistant Enterobacterales (CREs) are an emerging problem associated with high rates of morbidity and mortality. CREs are divided into two categories (carbapenemase-producing [CP] CRE and non-CP CRE). The most prevalent carbapenemase produced by Enterobacterales is Klebsiella pneumoniae carbapenemase (KPC) in Korea. Rapid identification of CREs is clinically important in infection control precaution. We compared the performance of two chromogenic media (chromID CARBA agar and CHROMagar KPC agar) for non-CP CREs or CP CREs with blaGES-5, blaNDM-1 or blaVIM-2 in a Korean hospital. Methods The study was carried out during a 3-month period from April to June 2017 during the surveillance program for CRE colonization. Antimicrobial susceptibility testing (AST) and polymerase chain reaction (PCR) were performed at the Korean Centers for Disease Control and Prevention. Results A total of 45 rectal swabs from 42 hospitalized patients were examined. Sensitivity of both chromID CARBA and CHROMagar KPC were 100% for CP CREs; and 50% and 100% for non-CP CREs, respectively. Specificity of chromID CARBA and CHROMagar KPC were 89.2% and 70.3% for CP CRE, respectively; and 76.9% and 66.7% for non-CP CRE, respectively. Conclusions The CHROMagar KPC is useful to monitor non-CP and CP CREs. The chromID CARBA is efficient for rapid detection of CP CREs requiring high contact precaution.

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The Science Behind Safe School Re-Opening: Leveraging the Pillars of Infection Control to Support Safe Elementary and Secondary Education During the COVID-19 Pandemic

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab134 ◽

2021 ◽

Author(s):

Elissa M Schechter-Perkins ◽

Polly van den Berg ◽

Westyn Branch-Elliman

Keyword(s):

Infection Control ◽

Infection Prevention ◽

Diagnostic Testing ◽

Current Evidence ◽

Implementation Barriers ◽

Safe School ◽

Elementary And Secondary Education ◽

School Settings ◽

Environmental Controls ◽

Prevention Interventions

Abstract There are limited tools for adapting COVID-19 infection control plans to school settings. We present an infection prevention model for optimizing safe re-opening for elementary and secondary schools during the global COVID-19 pandemic and review the current evidence behind various infection prevention interventions in school settings. The model is adapted from the Centers for Disease Control and Prevention fundamental pillars for infection prevention, and includes four categories of intervention: epidemiologic controls (town prevalence metrics, diagnostic testing, quarantine strategies), administrative controls (state vaccination policies, alternative school models, symptom screens, quarantine breaks), engineering/environmental controls (distancing, outdoor space, ventilation), and personal protective equipment (PPE)/Hand hygiene (face coverings, hand sanitizing). The adapted infection control pillars model utilizes implementation-science informed considerations to maximize pragmatism and adherence by leveraging evidence-based strategies. It highlights the necessity of redundant infection prevention interventions, acknowledges the importance of community buy-in to achieve real-world effectiveness, and addresses tactics to overcome implementation barriers. Recommendations are grounded in the Dynamic Sustainability Framework and include suggestions to maintain infection prevention effectiveness over time to ensure ongoing safety.

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425. The Utility of Paired Upper and Lower COVID-19 Sampling in Patients with Artificial Airways

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.619 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S279-S279

Author(s):

Eimear Kitt ◽

Julia S Sammons ◽

Kathleen Chiotos ◽

Susan E Coffin ◽

...

Keyword(s):

Respiratory Tract ◽

Lower Respiratory Tract ◽

Diagnostic Testing ◽

Cross Sectional Study ◽

Upper Respiratory Tract ◽

Cross Sectional ◽

Mechanically Ventilated ◽

Paired Samples ◽

Control And Prevention ◽

Polymerase Chain

Abstract Background The Centers for Disease Control and Prevention (CDC) recommends upper respiratory tract (URT) polymerase chain reaction (PCR) testing as the initial diagnostic test for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Lower respiratory tract (LRT) testing for patients requiring mechanical ventilation is also recommended. The goal of this study was to evaluate concordance between paired URT and LRT specimens in children undergoing pre-admission/procedure screening or diagnostic testing. We hypothesized that < 10% of paired tests would have discordant results. Methods Single center cross-sectional study including children with artificial airways who had paired URT and LRT SARS-CoV-2 PCR testing between 4/1/2020 and 6/8/2020. URT specimens included nasopharyngeal (NP) swabs and aspirates. LRT specimens included tracheal aspirates and bronchoalveolar lavages. URT and LRT specimens were classified as paired if the two specimens were collected within 24 hours. Artificial airways included tracheostomies and endotracheal tubes. Tests were classified as diagnostic versus screening based on the indication selected in the order. Results 102 paired specimens were obtained during the study period. Fifty-nine were performed for screening and 43 were performed for diagnosis of suspected SARS-CoV-2. Overall, 94 specimens (92%) were concordant, including 89 negative from both sources and 5 positive from both sources. Eight specimens (8%) were discordant, all of which were positive from the URT and negative from the LRT (Figure 1). Among patients undergoing screening, 3 of 4 positive tests were discordant and among symptomatic patients, 5 of 9 positive tests were discordant. There were no instances of a positive LRT specimen with a negative URT specimen. Figure 1. Performance of upper and lower respiratory tract SARS-CoV-2 PCR testing in children with artificial airways Conclusion Overall, most paired samples from the URT and LRT yielded concordant results with no pairs positive from the LRT and negative from the URT. These data support the CDC recommendation that URT specimens are the preferred initial SARS-CoV-2 test, while LRT specimens should be collected only from mechanically ventilated with suspected SARS-CoV-2. Disclosures All Authors: No reported disclosures

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Evaluation of SARS-CoV-2 antigen-based rapid diagnostic kits in Pakistan: formulation of COVID-19 national testing strategy

Virology Journal ◽

10.1186/s12985-021-01505-3 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Umar Saeed ◽

Sara Rizwan Uppal ◽

Zahra Zahid Piracha ◽

Azhar Rasheed ◽

Zubair Aftab ◽

...

Keyword(s):

Gold Standard ◽

Injection Drug Users ◽

Drug Users ◽

Diagnostic Testing ◽

False Negative ◽

Cross Sectional Study ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Cross Sectional ◽

Negative Results

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.

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On the robustness of latent class models for diagnostic testing with no gold standard

Statistics in Medicine ◽

10.1002/sim.8999 ◽

2021 ◽

Author(s):

Matthew R. Schofield ◽

Michael J. Maze ◽

John A. Crump ◽

Matthew P. Rubach ◽

Renee Galloway ◽

...

Keyword(s):

Gold Standard ◽

Latent Class ◽

Diagnostic Testing ◽

Latent Class Models ◽

No Gold Standard ◽

Class Models

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Universal Masking to Control Healthcare-Associated Transmission of SARS-CoV-2

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2021.127 ◽

2021 ◽

pp. 1-24

Author(s):

Eliza R. Thompson ◽

Faith S. Williams ◽

Pat A. Giacin ◽

Shay Drummond ◽

Eric Brown ◽

...

Keyword(s):

Large Scale ◽

Infection Prevention ◽

Index Patient ◽

Field Investigation ◽

Point Prevalence ◽

Control Measures ◽

Prevention Measures ◽

Infection Control Measures ◽

Va Health Care System ◽

Healthcare Associated

Abstract Objective: To assess extent of a healthcare-associated outbreak of SARS-CoV-2 and evaluate effectiveness of infection control measures, including universal masking Design: Outbreak investigation including 4 large-scale point-prevalence surveys Setting: Integrated VA Health Care System with 2 facilities and 330 beds Participants: Index patient and 250 exposed patients and staff Methods: We identified exposed patients and staff and classified them as probable and confirmed cases based on symptoms and testing. We performed a field investigation and assessment of patient and staff interactions to develop probable transmission routes. Infection prevention interventions implemented included droplet and contact precautions, employee quarantine, and universal masking with medical and cloth facemasks. Four point-prevalence surveys of patient and staff subsets were conducted using real-time reverse-transcriptase polymerase chain reaction for SARS-CoV-2. Results: Among 250 potentially exposed patients and staff, 14 confirmed cases of Covid-19 were identified. Patient roommates and staff with prolonged patient contact were most likely to be infected. The last potential date of transmission from staff to patient was day 22, the day universal masking was implemented. Subsequent point-prevalence surveys in 126 patients and 234 staff identified 0 patient cases and 5 staff cases of Covid-19, without evidence of healthcare-associated transmission. Conclusions: Universal masking with medical facemasks was effective in preventing further spread of SARS-CoV-2 in our facility in conjunction with other traditional infection prevention measures.

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