Kaisu Rantakokko-Jalava

Our aim was to study the detection of group A streptococcus (GAS) with different diagnostic methods in paediatric pharyngitis patients with and without a confirmed viral infection. In this prospective observational study, throat swabs and blood samples were collected from children (age 1–16 years) presenting to the emergency department with febrile pharyngitis. A confirmed viral infection was defined as a positive virus diagnostic test (nucleic acid amplification test [NAAT] and/or serology) together with an antiviral immune response of the host demonstrated by elevated (≥ 175 µg/L) myxovirus resistance protein A (MxA) blood concentration. Testing for GAS was performed by a throat culture, by 2 rapid antigen detection tests (StrepTop and mariPOC) and by 2 NAATs (Simplexa and Illumigene). Altogether, 83 children were recruited of whom 48 had samples available for GAS testing. Confirmed viral infection was diagnosed in 30/48 (63%) children with febrile pharyngitis. Enteroviruses 11/30 (37%), adenoviruses 9/30 (30%) and rhinoviruses 9/30 (30%) were the most common viruses detected. GAS was detected by throat culture in 5/30 (17%) with and in 6/18 (33%) patients without a confirmed viral infection. Respectively, GAS was detected in 4/30 (13%) and 6/18 (33%) by StrepTop, 13/30 (43%) and 10/18 (56%) by mariPOC, 6/30 (20%) and 9/18 (50%) by Simplexa, and 5/30 (17%) and 6/18 (30%) patients by Illumigene.Conclusion: GAS was frequently detected also in paediatric pharyngitis patients with a confirmed viral infection. The presence of antiviral host response and increased GAS detection by sensitive methods suggest incidental throat carriage of GAS in viral pharyngitis. What is Known:•The frequency and significance of GAS-virus co-detection are poorly characterised in children with pharyngitis.•Detection of a virus and the antiviral host response likely indicates symptomatic infection. What is New:•Group A streptococcus (GAS) was detected in 17–43% of the children with confirmed viral pharyngitis depending on the GAS diagnostic method.•Our results emphasize the risk of detecting and treating incidental pharyngeal carriage of GAS in children with viral pharyngitis.

In 2019, more than 200 cases of Chlamydia trachomatis negative/equivocal by the Aptima Combo 2 assay (AC2, target: 23S rRNA) with slightly elevated relative light units (RLUs), but positive by the Aptima Chlamydia trachomatis assay (ACT, target: 16S rRNA) have been detected in Finland To identify the cause of the AC2 CT false-negative specimens, we sequenced parts of the CT 23S rRNA gene in 40 specimens that were AC2 negative/equivocal but ACT positive. A single nucleotide polymorphism (SNP; C1515T in the C. trachomatis 23S rRNA gene) was revealed in 39 AC2/ACT discordant specimens. No decrease in the number of mandatorily notified C. trachomatis cases was observed nationally in Finland in 2010–2019. When RLUs obtained for AC2 negative specimens were retrospectively evaluated in 2011–2019, a continuous increase in the proportion of samples with RLUs 10–19 was observed since 2014, and a slight increase in the proportion of samples with RLUs 20–84 in 2017–2019, indicating that the Finnish new variant of C. trachomatis might have been spreading nationally for several years. This emphasizes that careful surveillance of epidemiology, positivity rate and test performance are mandatory to detect any changes affecting detection of infections.

Since February 2019, over 160 Chlamydia trachomatis (CT) cases testing negative or equivocal by Aptima Combo 2 (AC2) but positive by Aptima CT test run with Panther instruments occurred in Finland. The AC2 test targets chlamydial 23S rRNA while the CT test targets 16S rRNA. Sequencing of 10 strains revealed a nucleotide substitution in 23S rRNA. The significance of this for the failure of the AC2 test to detect the variant is not yet known.

Three hundred and fifty-three consecutive urine cultures growing Enterobacteriaceae, Pseudomonas aeruginosa or enterococci were subjected to parallel identification (ID) and antimicrobial susceptibility testing (AST) by Vitek 2 and routine methods, including simple screening tests or API 20 E for ID and standardized disc diffusion for AST. Accuracy of results, technician hands-on time required by both methods and time to results were compared. Vitek 2 correctly identified 322 (94.7%) of the 340 gram-negative isolates and 17 (81%) of the 21 Enterococcus faecalis strains. AST by Vitek 2 and disc diffusion gave category agreement for 4,058 (95.5%) of 4,248 organism-antimicrobial agent combinations. With MIC determination by E-test as reference, AST by Vitek 2 and disc diffusion produced 15 and 3 very major errors, respectively. Six (40%) of the fifteen very major errors by Vitek 2 were associated with trimethoprim-sulfamethoxazole. With an average of 22 specimens processed per day, use of Vitek 2 saved 80 min per day of technician hands-on time as compared to routine methods. Regarding the cost of hands-on worktime and consumables, use of Vitek 2 for identification of Escherichia coli-screened Enterobacteriaceae saved 0.70 p per sample in comparison to API 20 E. More than 80% of Enterobacteriaceae introduced to Vitek 2 in the morning could be reported by 16:00.