The vaginal microbiota has importance in preserving vaginal health and defending the host against disease. The advent of new molecular techniques and computer science has allowed researchers to discover microbial composition in depth and associate the structure of vaginal microbial communities. There is a consensus that vaginal flora is grouped into a restricted number of communities, although the structure of the community is constantly changing. Certain Community-State Types (CSTs) are more associated with poor reproductive outcomes and sexually transmitted diseases (STDs) meanwhile, CSTs dominated by Lactobacillus species—particularly Lactobacillus crispatus—are more related to vaginal health. In this work, we have reviewed how modifiable and non-modifiable factors may affect normal vaginal microbiota homeostasis—including sexual behavior, race or ethnicity, and hygiene. Special interest has been given to how the use of probiotics, diet intake, and use of hormone replacement therapies (HRTs) can potentially impact vaginal microbiota composition.

Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act as regional hubs within their respective health districts. Sequencing is performed at three reference laboratories, with downstream data analysis and reporting centralized at a bioinformatics platform. From 2021 to 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision making. This surveillance framework at a regional granularity demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats.

The aim of our study is to describe the characteristics of patients infected by MPXV in our setting, determine the prevalence of MPXV in samples which are classically used for diagnosing sexually transmitted infections (STIs) such as anal, urethral, pharyngeal and urine, and assess the prevalence of coinfection with STIs in the same samples. A cross-sectional study was conducted, collecting all confirmed cases of MPXV between June and July 2022 using polymerase chain reaction (PCR). Sociodemographic data, HIV and other STIs status, prevalence of MPXV and STIs in urethral, anal, pharyngeal or urine samples, were collected. Data from 22 patients were extracted, all of whom were MSM and 54,5% were previously HIV positive. The median age was 43 years. All the skin samples were positive for MPXV, followed by anal samples (n = 10) (45,5%). MPXV was isolated in 2 or more samples simultaneously in 12 (54%) cases. 9 (41%) patients were positive for an STI and 4 of them had more than one STI (18,2%). Human monkeypox has been epidemiologically significant among MSM. MPXV should be investigated not only in skin lesions but also in samples classically used for STI. MPXV, like other STIs, share ways of transmission and coinfection may be underdiagnosed.

Background: Limited data are available regarding the susceptibility of the reverse transcriptase V106 polymorphism to doravirine. Methods: Doravirine susceptibility was measured in site-directed mutants (SDMs) containing V106I, V106A, V106M, and Y188L mutations in subtype B (NL4-3, HXB2) and CRF02_AG background and in recombinant viruses with RT harboring V106I alone derived from 50 people with HIV. Results: HIV-1 B subtype was detected in 1523 of 2705 cases. Prevalence of V106I was 3.2% in B and 2.5% in non-B subtypes, and was higher in subtype F (8.1%) and D (14.3%). Fold-changes (FC) in susceptibility for SDMs were below doravirine biological cutoff (3.0) for V106I, but not for V106A, V106M, and Y188L. Clinically derived viruses tested included 22 B (median FC, 1.2; interquartile range [IQR], 0.9–1.6) and 28 non-B subtypes (median FC, 1.8; IQR, 0.9–3.0). Nine (18%) viruses showed FC values equal or higher than the doravirine biological FC cutoff. Conclusions: The prevalence of the HIV-1 RT V106I polymorphism in MeditRes HIV consortium remains low, but significantly more prevalent in subtypes D and F. V106I minimally decreased the susceptibility to doravirine in SDMs and most clinical isolates. Reduced susceptibility seems to occur at increased frequency in subtype F1; however, the clinical impact remains to be investigated. Clinical Trials Registration: NCT04894357.

Importance: The actual demand on SARS-CoV-2 diagnosis is a current challenge for clinical laboratories. Sample pooling may help to ameliorate workload in clinical laboratories. Objective: to evaluate the efficacy of sample pooling compared to the individual analysis for the diagnosis of CoVID-19, by using different commercial platforms for nucleic acid extraction and amplification. Design and settings: observational, prospective, multicentre study across 9 Spanish clinical microbiology laboratories including SARS-CoV-2 RNA testing performed in April 2020, during the first three days after acceptance to participate. Participants and Methods: 3519 naso-oro-pharyngeal samples received at the participating laboratories were processed individually and in pools (351 pools) according to the existing methodology in each of the centres. Results: We found that 253 pools (2519 samples) were negative, and 99 pools (990 samples) were positive; with 241 positive samples (6.85%), our pooling strategy would have saved 2167 PCR tests. For 29 pools (made out of 290 samples) we found discordant results when compared to their correspondent individual samples: in 24/29 pools (30 samples), minor discordances were found; for five pools (5 samples), we found major discordances. Sensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988. As a result of the sample dilution effect of pooling, a loss of 2-3 Cts was observed for E, N or RdRP genes. Conclusion: we show a high efficiency of pooling strategies for SARS-CoV-2 RNA testing, across different RNA extraction and amplification platforms, with excellent performance in terms of sensitivity, specificity, and positive and negative predictive values. We believe that our results may help clinical laboratories to respond to the actual demand and clinical need on SARS-CoV-2 testing, especially for the screening of low prevalence populations. Key points: Question: May clinical laboratories implement sample pooling as an efficient and safe strategy for SARS-COV-2 RT-PCR screening? Findings: Sensitivity, specificity, positive and negative predictive values for pooling were 97.93%, 100%, 100% and 99.85% respectively; accuracy was 99.86% and kappa concordant coefficient was 0.988. Meaning: Sample pooling can be used safely at clinical laboratories, especially for the screening of low prevalence populations.

Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative integrates sample collection from 27 hospitals, with sequencing performed at three reference laboratories and a centralized bioinformatics platform for data analysis and reporting. Between 2021 and 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision-making. This surveillance framework demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats.