Acute respiratory infections (ARIs) remain a leading cause of global morbidity and mortality, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. Despite the availability of traditional diagnostic tools, including viral culture and highly elaborated PCR respiratory panels, many cases of ARI remain without an identified etiological agent. This is due to the vast diversity of viral agents that can be involved in cases of ARI, which represents a major limitation of the targeted diagnosis. In this context, viral metagenomics has emerged as a powerful, unbiased approach for detecting both known and novel pathogens directly from clinical samples. This review highlights the application of metagenomic next-generation sequencing for the investigation of etiological causes of ARIs, emphasizing its relevance in complex cases-particularly among immunocompromised patients-where standard methods might fail. We highlight the main viruses involved in respiratory infections, the strengths and limitations of metagenomic next-generation sequencing approaches, their role in genomic surveillance of respiratory viruses, and their potential to build public health responses to potentially emerging respiratory threats. Ultimately, integrating viral metagenomics into clinical and surveillance frameworks could enhance the early detection and control of respiratory viral diseases worldwide.

Global seroprevalence of SARS-CoV-2 in children and adolescents has risen to an estimated 56.6%. Limited data on children highlights the need for ongoing surveillance as recommended by the WHO. Understanding this need, in this study we carry out a feasibility study of a rapid lateral flow immunoassay test (LFIAT) and determine SARS-CoV-2 seroprevalence in children and adolescents. The method used in the paper included 202 children (1-18 years old) who were evaluated for SARS-CoV-2 IgG/IgM antibodies using the LFIAT. LFIAT provides results in 20 min. Demographic data was collected through questionnaires. As a result, SARS-CoV-2 antibody seroprevalence was 52.0% (n = 105). No gender differences were observed. Adolescents exhibited higher seroprevalence (63.0%) compared to children aged 1-5.9 (49.3%) and 6-11.9 years old (46.8%), without statistical significance (p > 0.05). The median age of seropositive children was 9 years, and 77.1% had a history of PCR-confirmed infection (p = 0.001). In conclusion, results are consistent with global data. It was observed that the LFIAT can be easily administered to children and parents had a positive outlook on the test. Findings suggest that LFIAT can be used to assess SARS-CoV-2 immunity, while providing the first seroprevalence estimate for SARS-CoV-2 among healthy children and adolescents in Turkey, utilizing the COVID-19 IgG/IgM Rapid Test-KitA.

Face masks are widely recognized as a key intervention to limit SARS-CoV-2 transmission, yet the distribution and persistence of viral RNA across different mask regions and layers remain poorly understood. To address this, we analyzed 185 masks collected from 60 SARS-CoV-2-positive individuals in Rio de Janeiro between December 2020 and September 2022. Masks were sectioned into anatomical regions (nose, mouth, sides) and structural layers (inner, middle, outer), and viral RNA was quantified using RT-qPCR. Samples with the highest viral loads were selected for partial sequencing of the spike gene, and paired analyses with swab samples were performed. Statistical comparisons included non-parametric tests and a linear mixed-effects model. Our results showed that the inner layer and nose region consistently harbored the highest viral RNA levels, with no significant differences between surgical and fabric masks. Viral load decreased by an estimated 39% per day, consistent with exponential decay. Sequencing confirmed identical viral genomes in masks and swabs and allowed identification of circulating variants, including Gamma and Omicron. These findings indicate that masks serve not only as effective physical barriers but also as non-invasive sources for genomic surveillance, providing insights into viral shedding patterns and informing strategies for monitoring and controlling SARS-CoV-2 transmission.

Post-acute sequelae of SARS-CoV-2 infection (PASC) frequently includes persistent fatigue and cognitive dysfunction, but the relationship between these symptoms remains poorly defined. In this prospective observational study at the Henry Ford St. John Long COVID Clinic (LCC) from July 2023 to March 2025, we assessed fatigue severity using the Fatigue Assessment Scale (FAS) and examined its relationship with depression and cognitive symptoms. New patients completed demographic and clinical questionnaires, Patient Health Questionnaire (PHQ)-9, and Montreal Cognitive Assessment (MoCA) at their first LCC visit. Among 41 patients, 35 (85.4%) met the inclusion criteria for fatigue (FAS ≥ 22), with 18 (51.5%) experiencing severe fatigue (FAS > 34). Severe fatigue was significantly associated with shortness of breath, chest pain, and depression. Patients experiencing severe fatigue had significantly higher median PHQ-9 scores (12.5) compared to those with mild to moderate fatigue (5.0, p < 0.001). However, there were no significant differences in MoCA scores between these groups. Our study suggests a strong relationship between fatigue and depression in patients with PASC, emphasizing the importance of integrated physical and psychological healthcare. Moreover, since cognitive performance does not vary with fatigue levels, all PASC patients with cognitive dysfunction should receive routine cognitive screenings, regardless of the severity of their fatigue.

In the post-pandemic era, respiratory viruses continue to cause substantial morbidity and mortality among hospitalized adults. SARS-CoV-2 and influenza remain the most common pathogens, while RSV and rhinovirus have re-emerged as relevant causes of severe illness. This study compared the characteristics and outcomes of virus-specific infections detected by multiplex real-time PCR over two consecutive seasons.

This retrospective cohort study was conducted at a 1010-bed tertiary-care hospital in Türkiye between June 2022 and June 2024. Adults hospitalized with at least one respiratory virus detected by MRT-PCR were included. Demographic, clinical, and laboratory data were analyzed. Pathogen-specific comparisons were limited to monoinfections, and predictors of in-hospital mortality were identified using multivariable logistic regression.

Among 518 admissions, influenza (33.6%) and SARS-CoV-2 (29.3%) were the predominant pathogens, followed by rhinovirus (11.2%), RSV (6.6%), and other respiratory viruses (19.6%). Overall in-hospital mortality was 26.6%. Mortality differed across virus groups in unadjusted analyses, being highest in SARS-CoV-2 and RSV and lowest in rhinovirus. Non-survivors were older, more comorbid, more often immunosuppressed, and more likely to require oxygen therapy or ICU care at sampling. In multivariable analysis, independent predictors of mortality were ICU location at sampling (aOR 5.52), oxygen requirement (aOR 3.39), immunosuppression (aOR 3.67), older age (per 10-year increase: aOR 1.25), and secondary bacterial infection (aOR 7.00). Viral etiology, including SARS-CoV-2, was not independently associated with mortality after adjustment.

Among hospitalized adults, mortality was driven primarily by host-related factors and secondary bacterial infection rather than by viral etiology. These findings highlight the need for strengthened adult immunization programs, reliable respiratory virus surveillance, the prevention of bacterial superinfection, and the development of and equitable access to effective vaccines and antiviral therapies to reduce severe outcomes in high-risk adults.

Viral respiratory infections (VRIs) remain a leading cause of global morbidity and mortality. In Djibouti, diagnostic capacity for respiratory viruses is extremely limited, and little is known about the epidemiology of VRIs in the country. To address this gap, we conducted a prospective study aimed at monitoring and describing the epidemiological and virological features of VRIs over a two-year period in Djibouti. The study was carried out between January 2023 and December 2024 in seven healthcare centers. Nasopharyngeal and/or oropharyngeal swabs were collected from consenting patients presenting with influenza-like illness (ILI) or acute respiratory infections (ARI). VRIs were diagnosed using a multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assay targeting 16 respiratory viruses. Among the 647 samples tested, at least one respiratory virus was detected in 133 (20.6%). Influenza (6.6%), rhinovirus (5.9%), and SARS-CoV-2 (3.4%) were the most frequently detected pathogens. Adult aged 26-50 years (40.8%) were the most affected, followed by those aged 15-25 years (30.4%). None of the respiratory viruses displayed a clear seasonal pattern. These findings demonstrate the co-circulation of multiple respiratory viruses among ILI/ARI patients in Djibouti and provide the first baseline data to inform national surveillance strategies. The results underscore the need to strengthen routine laboratory-based surveillance, enhance diagnostic capacity, and integrate molecular monitoring into national public health policies for better preparedness against emerging respiratory threats.

Pelvic inflammatory disease (PID), although traditionally viewed as a sexually transmitted infection (STI), can also result from non-sexually transmitted microorganisms that display distinct epidemiologic and clinical characteristics. Unlike STI-related PID, these infections are less influenced by sexual behavior, often show a bimodal age distribution, and are linked to bacterial vaginosis (BV)-associated dysbiosis, iatrogenic uterine procedures, postpartum states, or inadequate access to timely screening and care. Non-STI-related PID is usually polymicrobial, predominantly involving BV-associated vaginal, enteric, or urinary commensals that ascend into the upper genital tract, while respiratory tract organisms, mycobacteria, and biofilm-associated pathogens may also play a role. Pathophysiological mechanisms include disruption of the endocervical barrier, mucus degradation, biofilm formation, hematogenous or iatrogenic seeding, and chronic cytokine-mediated inflammation and fibrosis. Clinical manifestations range from asymptomatic/subclinical disease to acute pelvic pain and tubo-ovarian abscess (TOA) and can progress to systemic infection and sepsis. Diagnosing non-STI PID is challenging due to nonspecific symptoms, negative STI tests, and inconclusive imaging findings, while management relies on broad-spectrum antimicrobials with surgery as needed. Given these complexities, this review aims to synthesize current knowledge on non-STI-related PID, clarify key considerations for its diagnosis, management, and prevention, and outline future perspectives to improve clinical outcomes.

Antibiotic resistance can be considered one of the major bacterial pathogenesis factors, and its increase is an important public health concern. Among resistant bacteria, staphylococci can express high levels of resistance, representing some of the most common human pathogens that are important causes of infection at any level. This paper aims to assess the burden of staphylococcal infections, in light of the growing phenomenon of antibiotic resistance, in a high-risk hospital setting. We carried out a cross-sectional study on data obtained from clinical specimens from an Italian healthcare facility particularly specialised in orthopaedics and traumatology. Specifically, we evaluated the trends in the Staphylococcus spp. detection rates and antibiotic resistance in the ten-year period of 2012-2024. The number of specimens increased over time but remarkably decreased during the COVID-19 pandemic. Despite this, the detection rate of Staphylococcus spp. remained quite constant, confirming the common circulation of these pathogens in such nosocomial environments. Antibiotic resistance concomitantly decreased, but a novel increase was found in recent years. Our findings highlight the importance of continuous monitoring of the antibiotic resistance rates of staphylococci due to the importance of these pathogens in human pathology and their ability to cause life-threatening antibiotic-resistant infections.

Acute Respiratory Infections are a common reason for Pediatric Emergency Department (PED) visits. Differentiating bacterial and viral infections may be challenging and might result in incorrect antibiotic prescriptions and exacerbation of antimicrobial resistance. This study evaluated the impact of new diagnostic tests in PED.

A retrospective cohort of 4882 acute febrile respiratory infection cases presenting to the PED was analyzed, comparing two periods: Period 1 (October 2016-March 2017, n = 2181) and Period 2 (October 2023-March 2024, n = 2701). During Period 1, Group A Streptococcus and Respiratory Syncytial Virus rapid antigen detection tests were available. During Period 2, new point-of-care tests (POCTs), including rapid C-reactive protein and rapid antigen detection for Influenza A, Influenza B, and SARS-CoV-2, and a multiplex PCR nasal swab, were introduced.

In Period 2, antibiotic prescriptions decreased by 28.4%, along with a reduction in broad-spectrum antibiotic use. A significant correlation was observed between reduced antibiotic prescription and the use of new POCTs and multiplex PCR tests. Performance of blood tests and chest radiographs also decreased.

Implementing novel diagnostic tests in PED helps clinicians select more appropriate management options with an impact on reduced stress and radiation exposure and antibiotic prescription.

Acute Diarrheal Disease (ADD) remains a major global health concern, with rotavirus A (RVA) and human adenovirus (HAdV) as key viral agents. This study evaluated the positivity rate and molecular characterization of RVA and HAdV in fecal samples from 114 children (0-5 years) in Goiás, Brazil, between January 2022 and December 2023, following the COVID-19 public health emergency. RVA was detected in 13.1% of samples (genotypes G1 and G6 associated with P[8]) and HAdV in 15.8% (genotypes A31, B3, C1, and C6), with two coinfection cases also being detected (1.7%). RVA predominated in unvaccinated 0-to-6-month-old children, while most asymptomatic cases occurred among vaccinated children. HAdV was also mainly identified in this age group, including asymptomatic children. Viral positivity was more common among children without access to treated water. In conclusion, this study underscores the ongoing circulation and genetic diversity of RVA and HAdV among children in Goiás in the post-pandemic period. The findings highlight the influence of vaccination coverage and sanitation on viral positivity, emphasizing the need for integrated public health strategies. Continuous molecular surveillance remains essential to detect emerging genotypes and guide effective prevention and control measures against ADD.