Dental plaque microbiota sequence counts for microbial profiling and resistance genes detection.

Shotgun metagenomics sequencing experiments are finding a wide range of applications. Nonetheless, there are still limited guidelines regarding the number of sequences needed to acquire meaningful information for taxonomic profiling and antimicrobial resistance gene (ARG) identification. In this study, we explored this issue in the context of oral microbiota by sequencing with a very high number of sequences (~ 100 million), four human plaque samples, and one microbial community standard and by evaluating the performance of microbial identification and ARGs detection through a downsampling procedure. When investigating the impact of a decreasing number of sequences on quantitative taxonomic profiling in the microbial community standard datasets, we found some discrepancies in the identified microbial species and their abundances when compared to the expected ones. Such differences were consistent throughout downsampling, suggesting their link to taxonomic profiling methods limitations. Overall, results showed that the number of sequences has a great impact on metagenomic samples at the qualitative (i.e., presence/absence) level in terms of loss of information, especially in experiments having less than 40 million reads, whereas abundance estimation was minimally affected, with only slight variations observed in low-abundance species. The presence of ARGs was also assessed: a total of 133 ARGs were identified. Notably, 23% of them inconsistently resulted as present or absent across downsampling datasets of the same sample. Moreover, over half of ARGs were lost in datasets having less than 20 million reads. This study highlights the importance of carefully considering sequencing aspects and suggests some guidelines for designing shotgun metagenomics experiments with the final goal of maximizing oral microbiome analyses. Our findings suggest varying optimized sequence numbers according to different study aims: 40 million for microbiota profiling, 50 million for low-abundance species detection, and 20 million for ARG identification. KEY POINTS: • Forty million sequences are a cost-efficient solution for microbiota profiling • Fifty million sequences allow low-abundance species detection • Twenty million sequences are recommended for ARG identification.

To Get Vaccinated or Not? The Vaccination Decision-Making by Healthcare Professionals Working in Haematology: A Qualitative Study.

Haematological patients are more susceptible to infections. Vaccination has always been the most effective primary prevention strategy, even during the COVID-19 pandemic. However, the efficacy of vaccines for some haematological patients is low. Although vaccination of Healthcare Workers (HCWs) could protect patients from vaccine-preventable diseases, there is evidence of a high level of hesitation among healthcare workers in Italy. The aim of this study was to explore the attitudes towards vaccination of HCWs caring for haematology patients. Qualitative descriptive design was conducted. Twenty-one HCWs were interviewed. Content analysis was applied to the qualitative data. The following themes were generated from the analysis: "Trust", "Decision-making process focusing on individual health", "Decision-making process focusing on community health", "Changing opinion", and "Two sides of vaccination commitment". The most hesitant HCWs were oriented towards individual health. They perceived a lack of benefit from vaccines, feared side effects, or were influenced by negative experiences of others. In contrast, community-health-oriented HCWs showed more positive attitudes towards vaccination. Some hesitant HCWs changed their opinion on vaccination because they began to reflect on the importance of vaccination for the community. The change in opinion of some HCWs interviewed provided insight into the importance of focusing organisational efforts on collective responsibility.