A novel anterior nasal swab to detect respiratory viruses: a prospective study of diagnostic accuracy.

Detection of respiratory viruses requires testing of the upper respiratory tract to obtain specimens for analysis. However, nasal and throat swabs can cause discomfort and procedural anxiety in children. Respiratory sampling methods which are accurate and less invasive are needed. We aim to determine the positive and negative percentage agreement of a novel anterior nasal swab (ANS) compared with the combined throat and anterior nasal swab (CTN), the reference standard, for detection of respiratory viruses. Children 5 - 18 years of age presenting to a tertiary paediatric hospital with respiratory symptoms were tested with both swabs in randomised order. Respiratory samples were tested on a multiplex RT-PCR panel. Viral detections, RT-PCR cycle-threshold values and child/parent/clinician experience of the swab were recorded. There were 157 viral detections from 249 participant CTN swabs. In comparison with the CTN, the overall positive and negative percentage agreement of ANS for detection of respiratory viruses was 96.2% (95% CI, 91.8-98.3%) and 99.8% (95% CI, 99.6-99.9%), respectively. The ANS was "extremely comfortable", or only a "little uncomfortable" for 90% of children compared with 48% for CTN. 202 children (84%) rated the ANS as the preferred swab, and 208 (87%) indicated they would prefer ANS for future testing. The ANS required additional laboratory handling processes compared to the CTN. The ANS has high positive percentage agreement and is comparable to the current standard of care. The high acceptability from the less invasive ANS provides a more comfortable method for respiratory virus testing in children.Trial registrationClinicalTrials.gov ID NCT05043623.

Stick with the nose Saliva rapid antigen testing is not a viable method for testing children under 5 years old.

AIM: Respiratory testing with rapid antigen tests (RATs) in children under 5 years of age may be uncomfortable and presents specific challenges to testing due to compliance and procedural distress. The aim of this study was to investigate sensitivity and feasibility of self-collected nasal and saliva RAT tests compared with a combined nose and throat (CTN) swab PCR in children under 5. METHODS: Children aged between 1 month and 5 years, with confirmed COVID-19 or who were a household contact within 7 days were included. A saliva RAT, nasal RAT and CTN swab were collected by the parent. SARS-CoV-2 cycle threshold (Ct) values for CTN tested by PCR were compared with saliva and nasal RAT results. Parent preference for method of sample was recorded. RESULTS: Forty-one children were recruited with median age of 1.5 (interquartile range 0.7-4.0) years. Only 22/41 (54%) of parents were able to successfully collect a saliva RAT from their child. Sensitivity of the nasal RAT and saliva RAT was 0.889 (95% confidence interval (CI) 0.739-0.969) and 0.158 (95% CI 0.034-0.396), respectively. Upper limit of nasal RAT detection by CTN Ct value was higher than saliva (36.05 vs. 27.29). While saliva RAT was rated most comfortable, nasal RAT was rated the preferred specimen by parents for future testing, due to saliva collection difficulties and time taken. CONCLUSIONS: Rapid antigen testing with nasal RAT is a more feasible and sensitive method for SARS-CoV-2 detection in young children compared with saliva RAT.

Virology and immune dynamics reveal high household transmission of ancestral SARS-CoV-2 strain.

BACKGROUND: Household studies are crucial for understanding the transmission of SARS-CoV-2 infection, which may be underestimated from PCR testing of respiratory samples alone. We aim to combine the assessment of household mitigation measures; nasopharyngeal, saliva, and stool PCR testing; along with mucosal and systemic SARS-CoV-2-specific antibodies, to comprehensively characterize SARS-CoV-2 infection and transmission in households. METHODS: Between March and September 2020, we obtained samples from 92 participants in 26 households in Melbourne, Australia, in a 4-week period following the onset of infection with ancestral SARS-CoV-2 variants. RESULTS: The secondary attack rate was 36% (24/66) when using nasopharyngeal swab (NPS) PCR positivity alone. However, when respiratory and nonrespiratory samples were combined with antibody responses in blood and saliva, the secondary attack rate was 76% (50/66). SARS-CoV-2 viral load of the index case and household isolation measures were key factors that determine secondary transmission. In 27% (7/26) of households, all family members tested positive by NPS for SARS-CoV-2 and were characterized by lower respiratory Ct values than low transmission families (Median 22.62 vs. 32.91; IQR 17.06-28.67 vs. 30.37-34.24). High transmission families were associated with enhanced plasma antibody responses to multiple SARS-CoV-2 antigens and the presence of neutralizing antibodies. Three distinguishing saliva SARS-CoV-2 antibody features were identified according to age (IgA1 to Spike 1, IgA1 to nucleocapsid protein (NP)), suggesting that adults and children generate distinct mucosal antibody responses during the acute phase of infection. CONCLUSION: Utilizing respiratory and nonrespiratory PCR testing, along with the measurement of SARS-CoV-2-specific local and systemic antibodies, provides a more accurate assessment of infection within households and highlights some of the immunological differences in response between children and adults.

Adding saliva testing to oropharyngeal and deep nasal swab testing increases PCR detection of SARS-CoV-2 in primary care and children.

OBJECTIVE: To compare the concordance and acceptability of saliva testing with standard-of-care oropharyngeal and bilateral deep nasal swab testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in children and in general practice. DESIGN: Prospective multicentre diagnostic validation study. SETTING: Royal Children's Hospital, and two general practices (cohealth, West Melbourne; Cirqit Health, Altona North) in Melbourne, July-October 2020. PARTICIPANTS: 1050 people who provided paired saliva and oropharyngeal-nasal swabs for SARS-CoV-2 testing. MAIN OUTCOME MEASURES: Numbers of cases in which SARS-CoV-2 was detected in either specimen type by real-time polymerase chain reaction; concordance of results for paired specimens; positive percent agreement (PPA) for virus detection, by specimen type. RESULTS: SARS-CoV-2 was detected in 54 of 1050 people with assessable specimens (5%), including 19 cases (35%) in which both specimens were positive. The overall PPA was 72% (95% CI, 58-84%) for saliva and 63% (95% CI, 49-76%) for oropharyngeal-nasal swabs. For the 35 positive specimens from people aged 10 years or more, PPA was 86% (95% CI, 70-95%) for saliva and 63% (95% CI, 45-79%) for oropharyngeal-nasal swabs. Adding saliva testing to standard-of-care oropharyngeal-nasal swab testing increased overall case detection by 59% (95% CI, 29-95%). Providing saliva was preferred to an oropharyngeal-nasal swab by most participants (75%), including 141 of 153 children under 10 years of age (92%). CONCLUSION: In children over 10 years of age and adults, saliva testing alone may be suitable for SARS-CoV-2 detection, while for children under 10, saliva testing may be suitable as an adjunct to oropharyngeal-nasal swab testing for increasing case detection.

COVID-19 public health measures and respiratory viruses in children in Melbourne.

AIM: To describe the epidemiology of respiratory viruses in children before and during the 2020 SARS-CoV-2 pandemic and the relationship to public health measures instituted by the Victorian government. METHODS: Retrospective audit of respiratory viruses at a tertiary paediatric hospital in Melbourne from January 2015 up to week 47, 2020 in children under 18 years of age. The proportion of positive cases in weeks 1-47 in 2015-2019 (period 1) were compared to weeks 1-47, 2020 (period 2), and reviewed in the context of public health restrictions in Victoria. RESULTS: An annual average of 4636 tests were performed in period 1 compared to 3659 tests in period 2. Proportions of positive influenza A virus, influenza B virus, respiratory syncytial virus (RSV) and human parainfluenza virus were significantly reduced in period 2 compared to period 1: 77.3, 89.4, 68.6 and 66.9% reductions, respectively (all P < 0.001). From week 12-47, 2020, 28 893 SARS-CoV-2 tests were performed with a 0.64% positivity rate. Influenza viruses were not detected after week 17, RSV was not detected after week 35. CONCLUSIONS: Strict public health measures and border closures were successful in eliminating community transmission of SARS-CoV-2 in Melbourne. This was associated with a significant reduction in other respiratory virus infections in children. Identifying sustainable and effective ongoing public health interventions to reduce transmission of RSV and influenza could result in reduced morbidity and mortality in children and requires further research.

Compliance with screening for and recommended management of maternal group B streptococcus carriage in pregnancy.

BACKGROUND: Universal screening of pregnant women at 35-37 weeks gestation is recommended for detection of anogenital group B streptococcus carriage. Intrapartum chemoprophylaxis is prescribed to carriers to prevent transmission to babies, reducing early-onset neonatal group B streptococcal sepsis. AIMS: To review compliance with, and the effects of education on group B streptococcus screening and intrapartum chemoprophylaxis practices at The Royal Women's Hospital, Melbourne, Australia. MATERIALS AND METHODS: A retrospective audit of women delivering in February 2016 and February-March 2017 was conducted. In February 2017, updated early-onset group B streptococcal disease prevention guidelines were released and promoted with targeted education of clinical staff. Compliance was considered appropriate if practices followed up-to-date local protocols. RESULTS: Screening rate for group B streptococcus was 84.4% (599/710) and carriage rate 19.5% (109/558), while intrapartum antibiotic prophylaxis was optimal in 83% of those labouring greater than four hours (39/47). There was no significant difference in compliance between 2016 and 2017. Of 113 women with unknown group B streptococcal status at delivery, only five of 33 (15%) with clinical risk factors for early-onset neonatal disease received intrapartum prophylaxis. CONCLUSIONS: Compliance remained stable, with no change during or after implementation of new protocols. Compliance with protocols was low for cases with unknown group B streptococcal status at delivery but with the presence of one or more clinical risk factors for early-onset group B streptococcal sepsis.

Manipulating the baby biome: What are the issues?

Establishing a baby biome through the controversial practice of 'vaginal seeding' has generated interest among the general public and healthcare providers alike. We discuss the potential risks of this practice and offer a harm minimisation approach to managing women requesting vaginal microbiome transfer after delivery by caesarean section.

Rapid time to results and high sensitivity of the CarbaNP test on early cultures.

For rapid results, we adapted the CarbaNP test by using 5-hour-old cultures; the sensitivity and specificity for detection of carbapenemase production were 100% for non-OXA-producing organisms. The sensitivity from early cultures was 94% for detection of carbapenemase production in Enterobacteriaceae strains. Utilizing younger cultures allows the test to be incorporated into a single day's workflow, facilitating timely patient care and antimicrobial stewardship.

Clinical and Health System Impact of Biofire Filmarray Meningitis/Encephalitis Routine Testing of CSF in a Pediatric Hospital: An Observational Study.

BACKGROUND: Rapid cartridge-based molecular test panels targeting multiple pathogens are increasingly available, improve pathogen detection and reduce turn-around-time but are more expensive than standard testing. Confirmation that these test panels contribute to improved patient or health service outcomes is required. METHODS: In March 2021, our pediatric hospital laboratory implemented the BioFire Filmarray™ meningitis/encephalitis (M/E) panel as an additional routine test for all cerebrospinal fluid (CSF) samples collected from infants <90 days or from any patient in the emergency department. A retrospective chart review was done to ascertain changes in clinical outcomes, antimicrobial prescribing practices, and hospital length of stay, comparing two discrete 6-month periods: preimplementation (March-August 2019) and postimplementation (March-August 2021). RESULTS: Both pre- and postimplementation groups were similar at baseline, except the preimplementation group had a higher proportion of infants with enterovirus and parechovirus meningitis. There was no significant difference between the groups in terms of median length of stay (2.94 vs 3.47 days, p = 0.41), duration of antibiotic treatment (2.0 vs 2.3 days, p = 0.25), need for central venous access (12.9% vs 17%, p = 0.38) or hospital-in-the-home admission (9.4% vs 9%, p = 0.92). A similar proportion of infants received aciclovir (33% vs 31%), however, a reduction in duration was observed (1.36 vs 0.90 days, p = 0.03) in the postimplementation period. CONCLUSIONS: Introduction of the Biofire Filmarray™ M/E panel for routine testing of CSF samples reduced the duration of antiviral prescribing but had only a minor impact on antibiotic prescribing practices or health service outcomes in our pediatric hospital. The introduction of new laboratory testing needs to be supported by a comprehensive stewardship program to see optimal outcomes from new testing platforms.

Antimicrobial resistance and its detection in Staphylococcus saprophyticus urinary isolates.

The aim of this study was to describe the antibiotic susceptibility of clinical Staphylococcus saprophyticus isolates collected prospectively from urine specimens over a 2-month period from September to October 2022 at a single centre in Melbourne, Australia. Species identification was performed by MALDI-TOF MS. All isolates underwent phenotypic antibiotic susceptibility testing by disc diffusion using European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) guidelines and VITEK2, and mecA polymerase chain reaction. A total of 302 S. saprophyticus isolates from 298 patients were included in this study. Most specimens (91.1%) were referred by community general practitioners from non-hospitalised patients. Antimicrobial resistance to non-ß-lactam antibiotics was uncommon; trimethoprim susceptibility was 97%; trimethoprim/sulfamethoxazole, 98%; nitrofurantoin, 100%; and ciprofloxacin, 100% (100% ciprofloxacin susceptible, increased exposure by EUCAST breakpoints). Methicillin resistance (by mecA detection) was the most common form of urinary antibiotic resistance at 5.6%. VITEK2 susceptibility testing for methicillin resistance had a poor specificity of 61.8% (95% CI 55.8-67.4%) compared to mecA detection. These findings indicate that empiric antibiotic recommendations of trimethoprim, trimethoprim/sulfamethoxazole, and nitrofurantoin for treatment of urinary S. saprophyticus remain appropriate.

A case report describing the immune response of an infant with congenital heart disease and severe COVID-19.

Background: Children with SARS-CoV-2 infection generally present with milder symptoms or are asymptomatic in comparison with adults, however severe disease occurs in a subset of children. To date, the immune correlates of severe COVID-19 in young children have been poorly characterised. Methods: We report the kinetics of immune responses in relation to clinical and virological features in an infant with acute severe COVID-19 using high-dimensional flow cytometry and multiplex cytokine analysis. Results: Systemic cellular and cytokine profiling show an initial increase in neutrophils and monocytes with depletion of lymphoid cell populations (particularly CD8 + T and NK cells) and elevated inflammatory cytokines. Expansion of memory CD4 + T (but not CD8 + T) cells occurred over time, with a predominant Th2 bias. Marked activation of T cell populations observed during the acute infection gradually resolved as the child recovered. Substantial in vitro activation of T-cell populations and robust cytokine production, in response to inactivated SARS-CoV-2 stimulation, was observed 3 months after infection indicating durable, long-lived cellular immune memory. Conclusions: These findings provide important insights into the immune response of a young infant with severe COVID-19 and will help to inform future research into therapeutic targets for high-risk groups.

Can colony-forming unit testing be used to extend the shelf life of BCG vaccines?

A recent shortage in supply of Bacille Calmette-Guérin (BCG), the live attenuated vaccine given to protect against tuberculosis (TB) caused major disruption to global vaccination programs. In this study, we assessed whether quantification of viable bacteria, could be used to inform the use of the BCG vaccine beyond its manufacturer-assigned expiration date. The viability of a single batch of BCG-Denmark was tested in three independent laboratories. There was high inter-vial and inter-laboratory variability in viability counts, however all three laboratories detected a decrease in BCG viability over time. Despite this, there was no difference in the rate of BCG scar formation in infants who were vaccinated with this batch of BCG before and after its manufacturer-assigned expiration date. This study demonstrates the potential for using BCG viability counts to guide the use of BCG vaccine beyond the manufacturer-assigned expiration date.

Human papillomavirus vaccination: the population impact.

We currently have the knowledge and experience to prevent much of human papillomavirus (HPV)-related disease burden globally. In many countries where prophylactic HPV vaccination programs have been adopted as highly effective public health programs with good vaccine coverage, we are already seeing, in real-world settings, reduction of vaccine-related HPV-type infections, genital warts and cervical pre-cancers with potential reductions in vulvar, vaginal and anal pre-cancers. Moreover, we are seeing a change in cervical screening paradigms, as HPV-based screening programs now have strong evidence to support their use as more sensitive ways to detect underlying cervical abnormalities, as compared with conventional cervical cytology. This article describes the impact of prophylactic vaccination on these outcomes and in settings where these vaccines have been implemented in national immunisation programs. Given the successes seen to date and the availability of essential tools, there has been a global push to ensure that every woman has access to effective cervical screening and every girl has the opportunity for primary prevention through vaccination. A gender-neutral approach by offering vaccination to young boys has also been adopted by some countries and is worthy of consideration given that HPV-related cancers also affect males. Furthermore, vaccination of young boys has the advantage of reducing the risk of HPV transmission to sexual partners, lowering the infectious pool of HPV in the general population and ultimately HPV-related diseases for both genders. Therefore, it is appropriate that all countries consider and promote national guidelines and programs to prevent HPV-related diseases.