Microbiology Time

This month, we bring you a new oral microbiota sampling method, a study on saliva and Long COVID, and yet another paper highlighting the importance of self-collection in the fight against cervical cancer.

  • This first study investigated the association between COVID-19 and Long COVID in children. The Italian researchers conducted a prospective study involving 167 pediatric patients hospitalized with confirmed acute SARS-CoV-2 infection, and collecting saliva samples with LolliSponge. A telephone survey was conducted at 3-6-12 months after discharge. Of the patients, 95.5% presented with symptoms upon admission. Regarding patients for whom it was feasible to determine the SARS-CoV-2 variant, the study identified the Delta variant in 21.6% and the Omicron variant in 78.4%. About 16.5% of patients reported symptoms indicative of Long COVID, such as weight loss, inappetence, chronic cough, fatigue, and others. Only 4 patients with Long COVID had a specific SARS-CoV-2 variant identified. The study emphasizes the significant concern of Long COVID in the pediatric population, highlighting the need for continuous monitoring and tailored symptom investigation based on age.
  • For the second study, we remain in Italy. Marianna Martinelli and colleagues assessed the accuracy of the BD Onclarity HPV assay on self-collected vaginal FLOQSwabs compared to cervical samples for detecting cervical intraepithelial neoplasia (CIN). Testing was conducted on two automated platforms, BD Viper LT and BD COR, and included 300 women. Self-sampling was performed with two vaginal swabs to assess, with the second one, the influence of freezing on the results. The results showed similar sensitivity for ≥CIN2 between vaginal and cervical samples, regardless of the platform used. Specificity was initially slightly lower for self-collected samples compared to cervical samples, but cut-off optimization for HPV positivity improved relative specificity without compromising sensitivity. No significant differences were observed between self-samples tested with the two platforms and between first- and second-collected (frozen) swabs. The study concludes that Onclarity assay on self-collected FLOQSwabs samples showed similar sensitivity and specificity (with cut-off optimization) to detect ≥CIN2 compared to cervical samples.
  • The third study addressed the challenge of standardizing oral microbiome analysis due to the variability in microbiota compositions across different oral habitats and the lack of standardized collection methods. The study proposes a standardized protocol for dental examination and material collection for next-generation sequencing (NGS) from various oral sites. The researchers involved 60 patients grouped into COVID-19 convalescents with and without antibiotics and healthy individuals. The collected biological samples were then used to conduct NGS (16S rRNA). Alpha and beta diversity analyses reveal notable differences in microbial communities, particularly in the supragingival plaque. The study emphasizes the importance of precise procedures during dental exams and material collection to avoid technical errors and contamination in NGS results. Dental indices like DMFT, D number, PI, and BOP are highlighted as valuable prognostic parameters for assessing oral health. The developed procedures are suggested for use in future studies by future studies.

Read the full studies: