Equal performance of self-collected and health care worker-collected pharyngeal swabs for group a streptococcus testing by PCR

Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study

BACKGROUND

The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories. Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing, expand testing capacity, and reduce opportunities for exposure of health professionals in the context of a pandemic.

OBJECTIVE

We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff.

METHODS

Each adult participant collected 1 nasal swab, sampling both nares with the single swab, after which they collected 1 nasal swab from 1 child. After all the participant samples were collected for the household, the research staff member collected a separate single duplicate sample from each individual. Immediately after the sample collection, the adult participants completed a questionnaire about the acceptability of the sampling procedures. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis.

RESULTS

In total, 21 households participated in the study, each with 1 adult and 1 child, yielding 42 individuals with paired samples. Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by RNA sequencing demonstrated that adequate collection technique was achieved by brief instructions.

CONCLUSIONS

Our results support the feasibility of a scalable and convenient means for the identification of respiratory viruses and implementation in pandemic preparedness for novel respiratory pathogens.

Adolescents may accurately self-collect pharyngeal and rectal clinical specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae infection

Background

The COVID-19 pandemic illuminated the benefits of telemedicine. Self-collected specimens are a promising alternative to clinician-collected specimens when in-person testing is not feasible. In this study, we assessed the adequacy of self-collected pharyngeal and rectal specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae among individuals undergoing chlamydia and gonorrhea screening.

Methods

We used data from a large cohort study that included male and female adolescents between the ages of 12–24 years. We considered self-collected specimens adequate for clinical use if the human synthase gene (a control target of the assay) was detected in the specimen.

Results

In total, 2,458 specimens were included in the analysis. The human synthase gene was detected in 99.2% (2,439/2,458) of all self-collected specimens, 99.5% (1,108/1,114) of the pharyngeal specimens, and 99.0% (1,331/1,344) of the rectal specimens.

Conclusion

Self-collected pharyngeal and rectal specimens demonstrated a very high proportion of human gene presence, suggesting that self-collection was accurate. A limitation of this study is that the sample adequacy control detects the presence or absence of the human hydroxymethylbilane synthase gene, but it does not indicate the specific anatomic origin of the human hydroxymethylbilane synthase gene. Self-collected specimens may be an appropriate alternative to clinician-collected specimens.

A Systematic Review and Meta-analysis of Upper Airway Swab Collection for Detection of Viral and Bacterial Pathogens by Individuals or Caregivers Compared to Health Care Workers

Self- or caregiver collection of upper airway swabs reduces infectious exposures of health care workers (HCWs) and the need to redeploy clinical staff to testing roles. We aimed to determine whether self- or caregiver collection has adequate diagnostic performance for detection of viral and bacterial upper airway pathogens. We did a systematic review and meta-analysis of studies comparing diagnostic accuracy of self- or caregiver-collected upper airway swabs collected by patients or caregivers compared to HCWs. All study types except case reports and series were included if sufficient data were presented to calculate sensitivity, specificity, and Cohen's kappa. Studies published from 1946 to 17 August 2020 were included in the search. We did a meta-analysis to assess pooled sensitivity and specificity. Twenty studies were included in the systematic review and 15 in the meta-analysis. The overall sensitivity of swabs collected by patients or caregivers compared to HCWs was 91% (95% confidence interval [CI], 87 to 94), and specificity was 98% (95% CI, 96 to 99). Sensitivity ranged from 65% to 100% and specificity from 73% to 100% across the studies. All but one study concluded that self- or caregiver-collected swabs were acceptable for detection of upper airway pathogens. Self- and caregiver collection of upper airway swabs had reassuring diagnostic performance for multiple pathogens. There are numerous potential benefits of self- and caregiver-collected swabs for patients, families, researchers, and health systems. Further research to optimize implementation of sample collection by patients and caregivers is warranted.

COVID-19 testing in a UK dental practice - results of a pilot study

Objective In December 2019, a novel coronavirus (SARS-CoV-2) caused a disease outbreak that soon became a global pandemic. Dentists are potentially exposed to infectious microorganisms, including SARS-CoV-2, by virtue of the transmission routes and work environment. This study aims to determine the infection load in a dental healthcare setting during the onset of the pandemic in the UK, as well as to evaluate the effectiveness of recommended test regimens in order to estimate potential risks for caregivers and patients in a dynamically changing pandemic environment.Methods Twenty-four persons (dental personnel of one dental office and family contacts) were included in this pilot study, and their infection load was determined between March and May 2020 using antigen and antibody tests.Results Of the 24 subjects, three tested positive for SARS-CoV-2 and were quarantined accordingly. After six weeks, they tested negative for the virus, had built antibodies and had no remaining symptoms, enabling an efficient return to work.Conclusion This paper outlines the results of COVID-19 testing in a dental practice during the onset of the pandemic, and discusses possible strategies and protocols to gain certainty in the dental practice, assessing possible testing scenarios that can be performed in a primary healthcare setting.

Evolution of Specimen Self-Collection in the COVID-19 Era: Implications for Population Health Management of Infectious Disease

Laboratory testing is an important component in the diagnosis of respiratory tract infections such as with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, specimen collection not only risks exposure of health care workers and other patients to infection, but also necessitates use of personal protective equipment that may be in short supply during periods of heightened disease activity. Self-collection of nasal or oropharyngeal swabs offers an alternative to address these drawbacks. Although studies in the past decade have demonstrated the utility of this approach for respiratory infections, it has not been widely adopted in routine clinical practice. The rapid spread of coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has focused attention on the need for safe, convenient, timely, and scalable methods for collecting upper respiratory specimens for testing. The goals of this article are to highlight the literature regarding self-collected nasal or oropharyngeal specimens for respiratory pathogen testing; discuss the role of self-collection in helping prevent the spread of the COVID-19 disease from infected patients and facilitating a shift toward “virtual” medicine or telemedicine; and describe the current and future state of self-collection for infectious agents, and the impacts these approaches can have on population health management and disease diagnosis and prevention.

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.

Diagnostic accuracy of an app-guided, self-administered test for influenza among individuals presenting to general practice with influenza-like illness: study protocol

INTRODUCTION

Diagnostic tests for influenza in Australia are currently only authorised for use in clinical settings. At-home diagnostic testing for influenza could reduce the need for patient contact with healthcare services, which potentially could contribute to symptomatic improvement and reduced spread of influenza. We aim to determine the accuracy of an app-guided nasal self-swab combined with a lateral flow immunoassay for influenza conducted by individuals with influenza-like illness (ILI).

METHODS AND ANALYSIS

Adults (≥18 years) presenting with ILI will be recruited by general practitioners (GP) participating in Australian Sentinel Practices Research Network. Eligible participants will have a nasal swab obtained by their GP for verification of influenza A/B status using reverse transcription polymerase chain reaction (RT-PCR) test at an accredited laboratory. Participants will receive an influenza test kit and will download an app that collects self-reported symptoms and influenza risk factors, then instructs them in obtaining a low-nasal self-swab, running a QuickVue influenza A+B lateral flow immunoassay (Quidel Corporation) and interpreting the results. Participants will also interpret an enhanced image of the test strip in the app. The primary outcome will be the accuracy of participants' test interpretation compared with the laboratory RT-PCR reference standard. Secondary analyses will include accuracy of the enhanced test strip image, accuracy of an automatic test strip reader algorithm and validation of prediction rules for influenza based on self-reported symptoms. A post-test survey will be used to obtain participant feedback on self-test procedures.

ETHICS AND DISSEMINATION

The study was approved by the Human Research and Ethic Committee (HREC) at the University of Adelaide (H-2019-116). Protocol details and any amendments will be reported to https://www.tga.gov.au/. Results will be published in the peer-reviewed literature, and shared with stakeholders in the primary care and diagnostics communities.

TRIAL REGISTRATION NUMBER

Australia New Zealand Clinical Trial Registry (U1111-1237-0688).

Who fails to return within 30 days after being tested positive for HIV/STI in a free testing centre?

Background

Some patients who test positive for sexually transmitted infections (STIs) fail to return for results and treatment. To target improvement actions, we need to find out who these patients are. This study aimed to explore factors associated with failure to return within 30 days (FTR30) after testing among patients with positive results in a free STI testing centre in Paris.

Methods

All patients with at least one positive result between October 2016 and May 2017 and who completed a self-administered questionnaire were included in this cross-sectional study (n = 214). The questionnaire included sociodemographic factors, sexual behaviour and history of testing. Factors associated with FTR30 were assessed using logistic regression models.

Results

More than two-thirds of patients were men (72%), and the median age of patients was 27 years. Most patients were born in metropolitan France (56%) or in sub-Saharan Africa (22%). Men who had sex with men represented 36% of the study population. The FTR30 rate was 14% (95% CI [10–19%]). In multivariate analysis, previous HIV testing in younger persons (aOR: 3.36, 95% CI [1.27–8.84]), being accompanied by another person at the pretest consultation (aOR: 3.45, 95% CI [1.36–8.91]), and lower self-perceived risk of HIV infection (aOR: 2.79, 95% CI [1.07–7.30]) were associated with a higher FTR30. Testing for chlamydia/gonorrhoea without presumptive treatment was associated with a lower FTR30 (aOR: 0.21, 95% CI [0.07–0.59]).

Conclusions

These factors that affect failure to return are related to the patient’s representations and involvement in the STI screening process. Increasing health literacy and patient empowerment could help to decrease failure to return after being tested positive for HIV/STI.

Trial registration

Not applicable.

Detection of Group A Streptococcus in the Saliva of Children Presenting With Pharyngitis Using the cobas Liat PCR System

Rapid turnaround real-time polymerase chain reaction (PCR) has recently become available as a point-of-care test for group A Streptococcus (GAS) in children presenting with pharyngitis. Our aim in this pilot study was to determine if GAS can be detected in the saliva of children with sore throat using swabs inoculated by children sucking on them as they would a lollipop. Twenty children with positive rapid antigen detection tests for GAS from pharyngeal swabs were enrolled. Pharyngeal and lollipop samples underwent PCR testing using the cobas Liat system. All 20 pharyngeal swabs were positive; 19 of 20 lollipop samples were positive. The increased sensitivity of the new PCR kits for GAS may permit use of less invasive and more comfortable sampling techniques for diagnosis.

Changing from Clinician-Collected to Self-Collected Throat Swabs for Oropharyngeal Gonorrhea and Chlamydia Screening among Men Who Have Sex with Men

The coronavirus disease 2019 (COVID-19) pandemic has led many clinics to move from clinician-collected to self-collected oropharyngeal swabs for the detection of sexually transmitted infections (STIs). Before this change, however, self-collection was used primarily for genital and anorectal infections, with only limited studies on the performance of self-collection of oropharyngeal swabs for oropharyngeal STI detection. The Melbourne Sexual Health Centre (MSHC) changed from clinician-collected to self-collected oropharyngeal swabs for oropharyngeal gonorrhea and chlamydia screening on 16 March 2020 in order to reduce health care worker risk during the COVID-19 pandemic. We compared the proportions of valid and positive samples for gonorrhea and chlamydia among men who have sex with men (MSM) in two time periods; the clinician collection period, between 20 January and 15 March 2020, and the self-collection period, between 16 March and 8 May 2020. A total of 4,097 oropharyngeal swabs were included. The proportion of oropharyngeal swabs with equivocal or invalid results for Neisseria gonorrhoeae was higher in the self-collection period (1.6% [24/1,497]) than in the clinician collection period (0.9% [23/2,600]) (P = 0.038), but the proportions did not differ for the detection of Chlamydia trachomatis The positivity rates of oropharyngeal N. gonorrhoeae (adjusted prevalence ratio [PR], 1.07 [95% confidence interval {CI}, 0.85 to 1.34]) (P = 0.583) and oropharyngeal C. trachomatis (adjusted PR, 0.84 [95% CI, 0.51 to 1.39]) (P = 0.504) specimens did not differ between the two periods. Self-collected oropharyngeal swabs for the detection of N. gonorrhoeae and C. trachomatis have acceptable performance characteristics and, importantly, reduce health care worker exposure to respiratory infections.

Self-collection: An appropriate alternative during the SARS-CoV-2 pandemic

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First study providing evidence of equivalence of self-collection for SARS-CoV-2.

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Self-collection has potential to increase accessibility and detection of SARS-CoV-2.

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Self-collection has potential to preserve PPE supplies.

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Self-collection has potential to reduce exposure to others.

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Self-collection was easy to perform and preferred by the majority of participants.

Objectives

To evaluate the reliability of self-collection for SARS-CoV-2 and other respiratory viruses because swab collections for SARS-CoV-2 put health workers at risk of infection and require use of personal protective equipment (PPE).

Methods

In a prospective study, patients from two states in Australia attending dedicated COVID-19 collection clinics were offered the option to first self-collect (SC) nasal and throat swabs (SCNT) prior to health worker collect (HC) using throat and nasal swabs (Site 1) or throat and nasopharyngeal swabs (Site 2). Samples were analysed for SARS-CoV-2 as well as common respiratory viruses. Concordance of results between methods was assessed using Cohen's kappa (κ) and Cycle threshold (Ct) values were recorded for all positive results as a surrogate measure for viral load.

Results

Of 236 patients sampled by HC and SC, 25 had SARS-CoV-2 (24 by HC and 25 by SC) and 63 had other respiratory viruses (56 by HC and 58 by SC). SC was highly concordant with HC (κ = 0.890) for all viruses including SARS-CoV-2 and more concordant than HC to positive results by any method (κ = 0.959 vs 0.933). Mean SARS-CoV-2 E-gene and N-gene, rhinovirus and parainfluenza Ct values did not differ between HC and SCNT.

Conclusions

Self-collection of nasal and throat swabs offers a reliable alternative to health worker collection for the diagnosis of SARS-CoV-2 and other respiratory viruses and provides patients with easier access to testing, reduces exposure of the community and health workers to those being tested and reduces requirement for PPE.

Development of a Laboratory-safe and Low-cost Detection Protocol for SARS-CoV-2 of the Coronavirus Disease 2019 (COVID-19)

The severe acute respiratory coronavirus 2 (SARS-CoV-2), which emerged in December 2019 in Wuhan, China, has spread rapidly to over a dozen countries. Especially, the spike of case numbers in South Korea sparks pandemic worries. This virus is reported to spread mainly through person-to-person contact via respiratory droplets generated by coughing and sneezing, or possibly through surface contaminated by people coughing or sneezing on them. More critically, there have been reports about the possibility of this virus to transmit even before a virus-carrying person to show symptoms. Therefore, a low-cost, easy-access protocol for early detection of this virus is desperately needed. Here, we have established a real-time reverse-transcription PCR (rtPCR)-based assay protocol composed of easy specimen self-collection from a subject via pharyngeal swab, Trizol-based RNA purification, and SYBR Green-based rtPCR. This protocol shows an accuracy and sensitivity limit of 1-10 virus particles as we tested with a known lentivirus. The cost for each sample is estimated to be less than 15 US dollars. Overall time it takes for an entire protocol is estimated to be less than 4 hours. We propose a cost-effective, quick-and-easy method for early detection of SARS-CoV-2 at any conventional Biosafety Level II laboratories that are equipped with a rtPCR machine. Our newly developed protocol should be helpful for a first-hand screening of the asymptomatic virus-carriers for further prevention of transmission and early intervention and treatment for the rapidly propagating virus.

Acceptability and Feasibility of Self-Collecting Biological Specimens for HIV, Sexually Transmitted Infection, and Adherence Testing Among High-Risk Populations (Project Caboodle!): Protocol for an Exploratory Mixed-Methods Study

BACKGROUND

Men who have sex with men (MSM) in the United States experience a disproportionate burden of HIV and bacterial sexually transmitted infections (STIs), such as gonorrhea and chlamydia. Screening levels among MSM remain inadequate owing to barriers to testing such as stigma, privacy and confidentiality concerns, transportation issues, insufficient clinic time, and limited access to health care. Self-collection of specimens at home and their return by mail for HIV and bacterial STI testing, as well as pre-exposure prophylaxis (PrEP) adherence monitoring, could be a resource-efficient option that might mitigate some of these barriers.

OBJECTIVE

Project Caboodle! is a mixed-methods study that explores the acceptability and feasibility of self-collecting and returning a bundle of 5 different specimens for HIV and bacterial STI testing, as well as PrEP adherence monitoring, among sexually active HIV-negative or unknown status MSM in the United States aged 18 to 34 years.

METHODS

Participants will be recruited using age, race, and ethnicity varied advertising on social networking websites and mobile gay dating apps. In Phase 1, we will send 100 participants a box containing materials for self-collecting and potentially returning a finger-stick blood sample (for HIV testing), pharyngeal swab, rectal swab, and urine specimen (for gonorrhea and chlamydia testing), and hair sample (to assess adequacy for potential PrEP adherence monitoring). Specimen return will not be incentivized, and participants can choose to mail back all, some, or none of the specimens. Test results will be delivered back to participants by trained counselors over the phone. In Phase 2, we will conduct individual in-depth interviews using a video-based teleconferencing software (VSee) with 32 participants from Phase 1 (half who returned all specimens and half who returned some or no specimens) to examine attitudes toward and barriers to completing various study activities.

RESULTS

Project Caboodle! was funded in May 2018, and participant recruitment began in March 2019. The processes of designing a study logo, creating advertisements, programming Web-based surveys, and finalizing step-by-step written instructions accompanied by color images for specimen self-collection have been completed. The boxes containing 5 self-collection kits affixed with unique identification stickers are being assembled, and shipping procedures (for mailing out boxes to participants and for specimen return by participants using prepaid shipping envelopes) and payment procedures for completing the surveys and in-depth interviews are being finalized.

CONCLUSIONS

Self-collection of biological specimens at home and their return by mail for HIV and bacterial STI testing, as well as PrEP adherence monitoring, might offer a practical and convenient solution to improve comprehensive prevention efforts for high-risk MSM. The potentially reduced time, expense, and travel associated with this approach could facilitate a wider implementation of screening algorithms and remote monitoring strategies.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/13647.

Advances Afoot in Microbiology

In 2016, the American Academy of Microbiology convened a colloquium to examine point-of-care (POC) microbiology testing and to evaluate its effects on clinical microbiology. Colloquium participants included representatives from clinical microbiology laboratories, industry, and the government, who together made recommendations regarding the implementation, oversight, and evaluation of POC microbiology testing. The colloquium report is timely and well written (V. Dolen et al., Changing Diagnostic Paradigms for Microbiology, 2017, https://www.asm.org/index.php/colloquium-reports/item/6421-changing-diagnostic-paradigms-for-microbiology?utm_source=Commentary&utm_medium=referral&utm_campaign=diagnostics). Emerging POC microbiology tests, especially nucleic acid amplification tests, have the potential to advance medical care.

New Developments in Clinical Bacteriology Laboratories

There are a number of changes underway in modern clinical bacteriology laboratories. Panel-based molecular diagnostics are now available for numerous applications, including, but not limited to, detection of bacteria and select antibacterial resistance markers in positive blood culture bottles, detection of acute gastroenteritis pathogens in stool, and detection of selected causes of acute meningitis and encephalitis in the cerebrospinal fluid. Today, rapid point-of-care nucleic acid amplification tests are bringing the accuracy of sophisticated molecular diagnostics closer to patients. A proteomic technology, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, is enabling rapid, accurate, and cost-effective identification of bacteria, as well as fungi, recovered in cultures. Laboratory automation, common in chemistry laboratories, is now available for clinical bacteriology laboratories. Finally, there are several technologies under development, such as rapid phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis for the detection of bacteria in clinical specimens. It is helpful for clinicians to be aware of the pace of new development in their bacteriology laboratory to enable appropriate test ordering, to enable test interpretation, and to work with their laboratories and antimicrobial stewardship programs to ensure that new technology is implemented to optimally improve patient care.

Point-Counterpoint: A Nucleic Acid Amplification Test for Streptococcus pyogenes Should Replace Antigen Detection and Culture for Detection of Bacterial Pharyngitis

Nucleic acid amplification tests (NAATs) have frequently been the standard diagnostic approach when specific infectious agents are sought in a clinic specimen. They can be applied for specific agents such as S. pyogenes, or commercial multiplex NAATs for detection of a variety of pathogens in gastrointestinal, bloodstream, and respiratory infections may be used. NAATs are both rapid and sensitive. For many years, S. pyogenes testing algorithms used a rapid and specific group A streptococcal antigen test to screen throat specimens, followed, in some clinical settings, by a throat culture for S. pyogenes to increase the sensitivity of its detection. Now S. pyogenes NAATs are being used with increasing frequency. Given their accuracy, rapidity, and ease of use, should they replace antigen detection and culture for the detection of bacterial pharyngitis? Bobbi Pritt and Robin Patel of the Mayo Clinic, where S. pyogenes NAATs have been used for well over a decade with great success, will explain the advantages of this approach, while Richard (Tom) Thomson and Tom Kirn of the NorthShore University HealthSystem will discuss their concerns about this approach to diagnosing bacterial pharyngitis.