Performance of a Molecular Test for Group A Streptococcus Pharyngitis.

We performed a prospective study to determine if the pretest probability of a positive loop-mediated isothermal amplification test is greater when there are more signs and symptoms of GAS pharyngitis. Patients were enrolled if a clinician obtained a GAS RADT. The McIsaac score was calculated. The prevalence of positive LAMP and RADT results increased as the McIsaac score increased. The calculated sensitivity of LAMP was superior to RADT.

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study.

BACKGROUND: Faecal shedding of SARS-CoV-2 has raised concerns about transmission through faecal microbiota transplantation procedures. Validation parameters of authorised tests for SARS-CoV-2 RNA detection in respiratory samples are described in product labelling, whereas the published methods for SARS-CoV-2 detection from faecal samples have not permitted a robust description of the assay parameters. We aimed to develop and validate a test specifically for detection of SARS-CoV-2 in human stool. METHODS: In this validation study, we evaluated performance characteristics of a reverse transcriptase real-time PCR (RT-rtPCR) test for detection of SARS-CoV-2 in human stool specimens by spiking stool with inactivated SARS-CoV-2 material. A modified version of the US Centers for Disease Control and Prevention RT-rtPCR SARS-CoV-2 test was used for detection of viral RNA. Analytical sensitivity was evaluated in freshly spiked stool by testing two-fold dilutions in replicates of 20. Masked samples were tested by a second laboratory to evaluate interlaboratory reproducibility. Short-term (7-day) stability of viral RNA in stool samples was assessed with four different stool storage buffers (phosphate-buffered saline, Cary-Blair medium, Stool Transport and Recovery [STAR] buffer, and DNA/RNA Shield) kept at -80°C, 4°C, and ambient temperature (approximately 21°C). We also tested clinical stool and anal swab specimens from patients who were SARS-CoV-2 positive by nasopharyngeal testing. FINDINGS: The lower limit of detection of the assay was found to be 3000 viral RNA copies per g of original stool sample, with 100% detection across 20 replicates assessed at this concentration. Analytical sensitivity was diminished by approximately two times after a single freeze-thaw cycle at -80°C. At 100 times the limit of detection, spiked samples were generally stable in all four stool storage buffers tested for up to 7 days, with maximum changes in mean threshold cycle values observed at -80°C storage in Cary-Blair medium (from 29·4 [SD 0·27] at baseline to 30·8 [0·17] at day 7; p<0·0001), at 4°C storage in DNA/RNA Shield (from 28·5 [0·15] to 29·8 [0·09]; p=0·0019), and at ambient temperature in STAR buffer (from 30·4 [0·24] to 32·4 [0·62]; p=0·0083). 30 contrived SARS-CoV-2 samples were tested by a second laboratory and were correctly identified as positive or negative in at least one of two rounds of testing. Additionally, SARS-CoV-2 RNA was detected using this assay in the stool and anal swab specimens of 11 of 23 individuals known to be positive for SARS-CoV-2. INTERPRETATION: This is a sensitive and reproducible assay for detection of SARS-CoV-2 RNA in human stool, with potential uses in faecal microbiota transplantation donor screening, sewage monitoring, and further research into the effects of faecal shedding on the epidemiology of the COVID-19 pandemic. FUNDING: National Institute of Allergy and Infectious Diseases, US National Institutes of Health; Center for Biologics Evaluation and Research, US Food and Drug Administration.

Severe Acute Respiratory Syndrome Coronavirus 2 Point Prevalence Among Asymptomatic Hospitalized Children and Subsequent Healthcare Worker Evaluation.

Asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carriage among hospitalized children and risk of transmission to healthcare workers (HCWs) was evaluated by point prevalence survey. We estimated 1-2% prevalence of SARS-CoV-2 among children without coronavirus disease 2019 symptoms. There was no secondary transmission among HCWs exposed to these patients.

Highly Sensitive Molecular Assay for Group A Streptococci Over-identifies Carriers and May Impact Outpatient Antimicrobial Stewardship.

BACKGROUND: Timely, accurate diagnosis of group A streptococci (GAS) pharyngitis prevents acute rheumatic fever and limits antibiotic overuse. The illumigene group A Streptococcus assay (Meridian Bioscience, Cincinnati, OH) is a molecular test for GAS pharyngitis with high sensitivity and specificity. We sought to determine whether the illumigene test is more likely than throat culture to be positive in patients without pharyngeal symptoms and explore the limits of detection of the test. METHODS: Patients 3-17 years of age were eligible if they had no history of pharyngitis or use of antibiotics within the previous 2 weeks; there were no upper respiratory infection symptoms, sore throat or fever and no signs of infection. Culture and illumigene were performed on duplicate throat swabs. Excess lysate from a subset of illumigene tests was evaluated by real-time polymerase chain reaction. Institutional Review Board approval was obtained. RESULTS: We enrolled 385 patients from February 2016 to October 2017; mean age was 10 yr; 51% were male. Most visits were for health supervision (69%). Significantly more illumigene tests (78/385, 20.3%) than throat cultures (48/385, 12.5%) were positive (χ; P =0.0035). Illumigene was "indeterminate" for 3 patients, leaving 382 pairs of swabs for analysis. Results were discordant for 32 of 382 pairs (8.4%); 31 of 32 (97%) were illumigene-positive/culture-negative (McNemar test; P < 0.000001). Real-time polymerase chain reaction was negative in 4 of 13 (31%) tested illumigene-positive lysates; the paired culture had been negative in all four. The limit of detection for the illumigene test was 55 colony forming units/mL. CONCLUSIONS: The illumigene test is significantly more likely than throat culture to yield positive results in patients without GAS pharyngitis. Failure to appropriately select patients for testing may negatively impact antimicrobial stewardship efforts without benefit to patients.

Seven-year surveillance of north american pediatric group a streptococcal pharyngitis isolates.

BACKGROUND: Pharyngeal group A streptococcal (GAS) emm type surveillance enhances understanding of the epidemiology of pharyngitis and invasive GAS disease and formulation of multivalent type-specific vaccines. In addition, such surveillance provides pre-GAS vaccine baseline data. We assessed geographic and temporal trends in GAS emm-type distribution among pediatric pharyngeal isolates collected systematically in the United States and Canada from 2000 to 2007. METHODS: We collected approximately 100 acute GAS pharyngitis isolates from each of 13 widely scattered sites (10 in the United States and 3 in Canada) annually for 7 seasons (2000-2007) from 3- to 18-year-old children. We assessed emm type and subtype by DNA sequencing and analyzed temporal and geographic trends. RESULTS: A total of 7040 US and 1434 Canadian GAS isolates were studied. The 6 most prevalent emm types (in descending order) were 1, 12, 28, 4, 3, and 2 in the United States and 12, 1, 28, 4, 3, 2, and 77 in Canada, constituting 70%-71% of isolates in each country; 10 emm types constituted 87%-89% total. Fifty-six emm types were identified in the United States, including 8 new types, and 33 types in Canada. Although a few types predominated nationally, marked variability among individual sites and at individual sites from year to year was observed. US-Canadian differences in type distribution were apparent. Twenty percent of isolates represented emm subtypes that differed slightly from reference types; 110 new subtypes were identified. An experimental 26-valent M protein vaccine covers 85% of pharyngitis isolates. CONCLUSIONS: Although overall US and Canadian emm type distribution was consistent and relatively few types dominated nationally, striking intersite and temporal variations within individual sites in prevalent emm types of GAS occurred. These results have important implications for the development and formulation of type-specific GAS vaccines.

Performance of a rapid antigen-detection test and throat culture in community pediatric offices: implications for management of pharyngitis.

OBJECTIVES: The goals were to establish performance characteristics of a rapid antigen-detection test and blood agar plate culture performed and interpreted in community pediatric offices and to assess the effect of the pretest likelihood of group A streptococcus pharyngitis on test performance (spectrum bias). METHODS: Two throat swabs were collected from 1848 children 3 to 18 years of age who were evaluated for acute pharyngitis between November 15, 2004, and May 15, 2005, in 6 community pediatric offices. One swab was used to perform the rapid antigen-detection test and a blood agar plate culture in the office and the other was sent to our laboratory for blood agar plate culture. Clinical findings were used to calculate the McIsaac score for each patient. The sensitivities of the office tests were calculated, with the hospital laboratory culture results as the criterion standard. RESULTS: Thirty percent of laboratory blood agar plate cultures yielded group A streptococcus (range among sites: 21%-36%). Rapid antigen-detection test sensitivity was 70% (range: 61%-80%). Office culture sensitivity was significantly greater, 81% (range: 71%-91%). Rapid antigen-detection test specificity was 98% (range: 98%-99.5%), and office culture specificity was 97% (range: 94%-99%), a difference that was not statistically significant. The sensitivity of a combined approach using the rapid antigen-detection test and back-up office culture was 85%. Among patients with McIsaac scores of >2, rapid antigen-detection test sensitivity was 78%, office culture sensitivity was 87%, and combined approach sensitivity was 91%. Positive diagnostic test results were significantly associated with McIsaac scores of >2. CONCLUSIONS: The sensitivity of the office culture was significantly greater than the sensitivity of the rapid antigen-detection test, but neither test was highly sensitive. The sensitivities of each diagnostic modality and the recommended combined approach were best among patients with greater pretest likelihood of group A streptococcus pharyngitis.

Macrolide resistance and emm type distribution of invasive pediatric group A streptococcal isolates: three-year prospective surveillance from a children's hospital.

OBJECTIVE: Macrolide-resistant group A streptococci (GAS) have been suggested to have more invasive potential. An M protein-based GAS vaccine is currently in development. We sought to define the GAS emm types and macrolide resistance rates among pediatric invasive GAS isolates collected prospectively during a recent 40-month period at our children's hospital. PATIENTS AND METHODS: We prospectively identified and collected GAS isolates from patients with invasive GAS disease (isolates from normally sterile sites). Susceptibility assays for erythromycin and clindamycin were performed by E-test. emm typing was performed by the Centers for Disease Control and Prevention. Clinical characteristics of patients were identified by chart review. RESULTS: A total of 37 patient isolates were identified, of which 35 isolates were able to be characterized. Four patients had underlying illness. No macrolide resistance was detected among the isolates. The most common emm types causing invasive disease were emm 1.0 (43%) and emm 12.0 (11.1%). CONCLUSIONS: In this group of 35 invasive GAS isolates, no cases of macrolide resistance were found. emm type 1 accounted for the highest percentage of invasive disease, followed by emm type 12. The type-specific GAS M protein-based vaccine currently in development includes the emm types of 33 of 35 (94%) of the invasive emm types in this series.

Community-based surveillance in the united states of macrolide-resistant pediatric pharyngeal group A streptococci during 3 respiratory disease seasons.

BACKGROUND: In 2001, a total of 48% of pharyngeal group A streptococci (GAS) from Pittsburgh children were macrolide resistant. We assessed macrolide resistance, resistance genes, and emm types among GAS in the United States. METHODS: In prospective, multicenter, community-based surveillance of pharyngeal GAS recovered from children 3-18 years old during 3 respiratory seasons (the 2000-2001 season, the 2001-2002 season, and the 2002-2003 season), GAS were tested for macrolide resistance and underwent emm gene sequencing. Macrolide-resistant GAS were tested for resistance to clindamycin, and resistance genes were determined. RESULTS: Erythromycin resistance was observed in 4.4% of isolates from the 2000-2001 season, 4.3% from the 2001-2002 season, and 3.8% from the 2002-2003 season (P=.80). Clindamycin resistance was found in 1.04% of isolates; annual rates of clindamycin resistance were stable (P=.75). The predominant resistance genotype each year was mef A (65%-76.9%; overall, 70.3%). Resistant isolates included strains representing 8-11 different emm types each year. Heterogeneity of emm subtypes, resistance genes, and clindamycin resistance was evident among resistant isolates within some emm types. Geographic variability in resistance rates was present each year. CONCLUSIONS: The macrolide resistance rate among pharyngeal GAS was <5% and was stable over the 3 seasons. However, rates varied among sites each year. There was no evidence of spread of a specific resistant clone, increasing clindamycin resistance, or escalation in median erythromycin MICs.