The nasal microbiome, a dynamic assemblage of commensals and opportunistic pathogens, is crucial to human health. Using cross-sectional data from 1,608 adults and longitudinal sampling of 149 individuals over 8–22 months, we identified nine nasal community state types (CSTs), defined by bacterial density and indicator taxa, with varying stability and transition patterns. Core taxa such as Staphylococcus epidermidis and Cutibacterium acnes were highly stable, while opportunistic pathogens like Staphylococcus aureus and Moraxella catarrhalis had shorter residence times. Interactions between Dolosigranulum pigrum and Corynebacterium pseudodiphtheriticum/propinquum were linked to reduced S. aureus colonization. Host factors, including age and biological sex, significantly shaped microbiome dynamics: men exhibited higher bacterial densities and pathogen colonization, while women showed more stable commensal-dominated CSTs. Aging was associated with shifts in CST frequencies, with declining S. aureus and increasing Enterobacterales. These findings reveal potential strategies by modulating nasal microbiome dynamics to reduce pathogen colonization and improve health.

BACKGROUND:Live attenuated influenza vaccine (LAIV) induces mucosal immunity through limited viral replication in the upper respiratory tract, but post-vaccination viral shedding dynamics and their clinical correlates remain incompletely characterized. METHODS:We evaluated 283 healthy adults (108 in 2023-2024, 175 during the 2024-2025 influenza seasons) following intranasal LAIV administration. Nasal swabs were collected on post-LAIV days 1, 2-4, and 5-7 to quantify influenza A and B RNA by RT-PCR. Viral detection, shedding duration and burden, clearance kinetics, and probability of detection were compared across seasons, vaccine strain compositions (quadrivalent vs. trivalent), and host factors. Respiratory symptoms were assessed. RESULTS:Early viral shedding was frequent: influenza A or B RNA was detected in 86.9% of participants on day 1, with co-detection in 52.7%. Probability of detection declined from 92% on day 1 to 9% on day 7. Influenza B had longer shedding duration (median, 2.0 vs. 1.0 days; p<0.001) and higher shedding burden (4.2 vs. 4.0 log₁₀ RNA copies/mL; p<0.001). Three clearance profiles - rapid (clearance ≤4 days), moderate (5-7 days), and slow (≥7 days) - were identified. Profiles were consistent across seasons but influenza B was disproportionately represented in slower-clearance groups (p<0.001). Total viral burden (p<0.01) and shedding duration (p=0.01) were associated with total symptom burden. CONCLUSIONS:LAIV replication begins within 24 hours and declines over the first week, with persistent shedding uncommon after day 7. Influenza B replicates more extensively and persists longer than influenza A. Symptom burden correlates with shedding duration and viral burden.

Abstract Background Accurate pubertal assessment is essential in pediatric endocrinology and adolescent health research. While Tanner staging remains the gold standard, its subjective nature and invasive genital examination limit feasibility and acceptability, especially in longitudinal studies and culturally sensitive settings. This study evaluated less intrusive pubertal assessment combinations that maintain discriminative accuracy. Methods We conducted a longitudinal study among 200 uncircumcised, sexually naïve males aged 15–17 years in Southwestern Uganda, with quarterly follow-up over three years. Clinicians assessed Tanner staging metrics (pubic hair, testicular volume, penile length, scrotal color), axillary hair, and serum testosterone. Markov transition models estimated Tanner stage progression. Ordinal logistic regression and area under the receiver operating characteristic curve (AUC) analyses quantified discriminative performance of individual and combined metrics. Results At baseline, participants were distributed across Tanner stages II (6.0%), III (13.5%), IV (55.0%), and V (25.5%). Among individual metrics, pubic hair distribution best predicted overall Tanner stage (AUC=0.867), while penile length was least predictive (AUC=0.833). The full four-metric Tanner model achieved high discrimination (AUC=0.993). However, a less intrusive combination of pubic hair and scrotal color achieved comparable discrimination (AUC=0.942), improving to AUC=0.953 with axillary hair and age. Markov modeling demonstrated frequent bidirectional transitions between Tanner stages IV and V, reflecting variability in longitudinal staging. Conclusions A minimally intrusive assessment combining pubic hair, scrotal color, axillary hair, and age reliably predicts pubertal stage, offering an acceptable alternative to traditional Tanner staging for research and surveillance contexts where genital manipulation is impractical or unethical.

Escherichia coli clonal complex 38 (CC38) is a genetically diverse lineage increasingly linked to antimicrobial resistance and extraintestinal infections in humans. Despite its clinical and epidemiological relevance, its population structure, zoonotic potential, and ecological associations remain poorly understood. We analyzed 242 human E. coli CC38 bloodstream isolates collected through Danish national surveillance, 83 isolates from food and production animals, and 2313 international genomes to investigate host associations and transmission dynamics. Phylogenetic reconstruction, Bayesian host prediction based on mobile genetic elements, and statistical testing of plasmid–host associations were used to delineate population structure and identify potential host-associated markers. Here we show that Danish CC38 isolates belong to multiple sub-lineages, with no evidence of foodborne outbreaks and limited hospital transmission. Bayesian host prediction supports a poultry origin for several distinct human sub-lineages. Global analyses of 2638 genomes reveal two major clusters: a poultry-associated Cluster I and a predominantly human-associated Cluster II, which subdivides into eight sub-lineages with distinct host, resistance, and virulence profiles. Two small plasmids, ColRNAI and Col(MG828), are strongly enriched in poultry and livestock isolates but largely absent from human-associated sub-clusters, indicating their value as host-associated genetic markers. Our findings refine the phylogenetic structure of E. coli CC38 and identify plasmid markers that may enhance genomic surveillance of zoonotic transmission. These results highlight the importance of a One Health approach to monitor antimicrobial resistance across human, food, and animal reservoirs. Together, these insights support data-driven One Health surveillance and intervention strategies. Antibiotic-resistant bacteria are a growing concern for both human and animal health. This study examined a specific group of E. coli bacteria, which can cause serious infections. By comparing the genomes of bacteria, isolated from people, food, and animals in Denmark and around the world, the researchers mapped how different lineages are related and where they are most likely to come from. The results show that some strains found in humans may have originated in poultry. The study also identified two small DNA elements strongly linked to bacteria from poultry and livestock. These elements could help trace how resistant bacteria move between animals and humans, supporting more effective disease surveillance and antibiotic resistance prevention. Roer et al. analyze genomes of Escherichia coli clonal complex 38 from humans, animals, and food to investigate its spread and host associations. They find distinct human and poultry lineages and identify plasmid markers linked to animal adaptation and zoonotic transmission.

Specific anaerobic species within the penile microbiome - Bacteria Associated with Seroconversion, Inflammation and Immune Cells (BASIC) - have been linked to increased HIV-1 susceptibility. These bacteria can directly disrupt epithelial integrity and are believed to increase local inflammation, resulting in an increased density of HIV-susceptible T cells in the inner foreskin. It is currently unknown whether other immune cells bearing the HIV entry receptors, CD4 and CCR5, are also elevated in individuals with a high abundance of BASIC species. Using inner foreskin tissues and penile swabs from males undergoing voluntary medical male circumcision, we performed a retrospective cross-sectional study to assess the relationship between BASIC species and the tissue density of such immune cells, including CD68+ macrophages, CD11c+ dendritic cells, and CD207+ Langerhans cells. The most abundant cells in the inner foreskin expressing the HIV co-receptors were CD11c+ dendritic cells (48.6% of CD4+/CCR5+ cells), followed by CD68+ macrophages (28.6%), CD3+ T cells (18.8%), and CD207+ Langerhans-like (8.8%) cells. The absolute abundance of BASIC species was associated with elevated tissue densities of both CD4+/CCR5+ T cells (as previously reported) and a heterogeneous population of CD3-/CD4+/CCR5+ cells of myeloid origin. In the dermis, BASIC species abundance was linked to elevated densities of cells expressing CD11c, CD68, and CD207, as well as those co-expressing CD11c and CD207; furthermore, CD11c+ and CD207+ cells were farther from the basement membrane in participants with a high abundance of BASIC species. Myeloid cells were not elevated in participants with a high abundance of control taxa. In an integrated analysis including previously published data from this same cohort, myeloid-cell densities clustered tightly together, positively correlated with BASIC species and pro-inflammatory cytokines, and had trends to negative correlations with control taxa (significant for CD207+ cell density). Overall, our findings suggest that BASIC species are associated with a broader foreskin immune phenotype marked by increased densities of HIV-susceptible myeloid and T cells, alongside epithelial disruption.

The nasal mucosa is the primary entry site for many respiratory viruses, and immune molecules present at the time of exposure may dictate if infection occurs. However, the baseline immune state in healthy adults – and how it influences susceptibility to viruses – remains poorly defined. Levels of 16 immune molecules were measured in nasal secretions from two independent cohorts of healthy adults (total n = 166, Luminex). Participants were clustered based on normalized concentrations of immune analytes to identify profiles. An in vitro organotypic model of the nasal epithelium was used to examine the effect of immune profiles on SARS-CoV-2 infection: primary human nasal epithelial cells (n = 9 donors) were grown at air-liquid interface to induce mucociliary differentiation (42 days), treated with recombinant human cytokines (72 h), and then challenged with wildtype SARS-CoV-2 Omicron BA.1 (24 h). SARS-CoV-2 entry factor expression (post-cytokines, pre-challenge) and viral infection (N gene) were measured by qRT-PCR. In both cohorts, a unique cluster was observed, characterized by distinctly high levels of antiviral interferons – particularly IFN-λ3 – with comparatively low levels of inflammatory chemokines and cytokines. In contrast, individuals with high overall levels of inflammatory mediators had absent IFN-λ3. In vitro, pretreatment with IFN-λ3 and IFN-α2, but not with pro-inflammatory cytokines, significantly reduced SARS-CoV-2 replication in differentiated nasal epithelial cultures, despite upregulating ACE2 expression. Healthy adults exhibit distinct nasal immune profiles, with an exogenous IFN-λ3–dominant, low-inflammatory state conferring resistance to SARS-CoV-2 in an in vitro primary nasal epithelial model. The nasal immune milieu may influence susceptibility to respiratory viruses and the efficacy of mucosally administered vaccines.

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-producing E. coli) pose a growing global health threat. Although Latin America has been identified as a global hotspot of antimicrobial resistance, the zoonotic contribution to drug-resistant infections in the region remains poorly defined. We analyzed 137 clinical ESBL-producing E. coli isolates from urinary tract infections (UTIs) in Quito, Ecuador, applying a Bayesian latent class model informed by host-associated mobile genetic elements to estimate the fraction of infections attributable to food-animal sources. We estimated that 25.5% (35/137) of UTI isolates were putative zoonotic cases. This proportion rose to 42.5% after excluding ST131-H30, a human-associated pandemic lineage. Putative zoonotic isolates were enriched for animal-associated β-lactamase genes (e.g., blaTEM-1B, blaCTX-M-65), lacked human-associated markers such as blaOXA-1, and exhibited diverse antimicrobial resistance gene profiles resembling those observed among food-animal isolates. These isolates were also enriched for ColV-associated virulence genes typically linked to avian pathogenic E. coli. Putative zoonotic strains contributed substantially to third-generation cephalosporin-resistant UTIs in Quito, Ecuador, challenging assumptions derived from high-income settings that such infections are driven predominantly by human-to-human transmission. These findings highlight the importance of integrated One Health surveillance and mitigation, particularly in low- and middle-income countries where gaps in water, sanitation, and hygiene (WASH) may interact with antimicrobial use in food production to amplify antimicrobial resistance transmission.IMPORTANCEESBL-producing E. coli have rapidly emerged as a major global antimicrobial resistance threat. In Latin America, cephalosporins are commonly used in food-animal production, fueling the emergence of ESBL-producing E. coli. In low- and middle-income countries, excessive antimicrobial use driven by poorly regulated over-the-counter sales, combined with inadequate water, sanitation, and hygiene (WASH) infrastructure, can facilitate antimicrobial-resistant pathogen transmission from food animals to humans. Using a novel statistical-genomic approach, we found that over one in four cephalosporin-resistant UTIs in Quito, Ecuador, may be caused by E. coli strains originating from food animals. Our findings highlight the public health risks associated with antimicrobial use in food-animal production and the role of environmental and infrastructure-related vulnerabilities. As global demand for animal protein continues rising in middle-income countries, controlling zoonotic antimicrobial resistance transmission becomes increasingly urgent for protecting human health through integrated One Health strategies.

The vaginal and penile coronal sulcus microbiome influence reproductive health outcomes and susceptibility to multiple sexually transmitted infections including HIV. There is evidence that genital bacteria are shared between heterosexual partners during sex, but the dynamics of this microbiota exchange remain poorly understood. Using microbiome characterization from established heterosexual couples, we found that condomless penile-vaginal sex dramatically altered the coronal sulcus microbiome, with transient dominance by Lactobacillus spp. Conversely, condom-protected penile-vaginal sex did not result in significant shifts in overall composition (p = 0.63). Significant changes were observed in the female partner’s genital microbiome, including increased Corynebacterium spp. and increased abundance of Bacteria Associated with Seroconversion, Inflammation, and Cells (BASICs) (Prevotella bivia, Peptostreptococcus anaerobius, Dialister micraerophilus, Prevotella disiens, Dialister propionicifaciens, Dialister succinatiphilus) in individuals with a colonized male partner. By 72 h post-coitus L. iners cell-normalized abundance remained elevated in the penile microbiome, but other taxa returned to baseline levels. Causal mediation analysis indicated a pH-mediated increase in vaginal Gardnerella at 72 h. Condom-protected penile-vaginal sex was associated with minimal genital microbiome changes, whereas condomless penile-vaginal sex among established couples led to extensive exchange of genital microbiota. Most disruptions to the microbiome resolved within 2–3 days, although changes in vaginal pH were associated with longer-lasting increases in Gardnerella abundance.

OBJECTIVES:Decolonization treatment of asymptomatic methicillin-resistant Staphylococcus aureus (MRSA) carriage is recommended as a preventive measure in several countries, including Denmark. This study aimed to investigate the temporal dynamics of the nasal and throat microbiota in MRSA carriers undergoing decolonization treatment and to assess bacterial changes associated with treatment success. METHODS:Adults with asymptomatic nasal MRSA carriage (n = 34) were included in this prospective observational study. Participants underwent a 5-day decolonization regimen consisting of 2% mupirocin nasal ointment and daily skin cleansing with 4% chlorhexidine soap. Nasal and throat samples were collected at multiple time points from baseline to 6 months after treatment and analysed by 16S rRNA gene sequencing. A reference group of untreated community-dwelling adults (n = 116) served as comparison. RESULTS:At 1-month follow-up, 21 of 34 participants (62%) were successfully decolonized, whereas 13 (38%) remained MRSA positive at one or more body sites. At baseline, no nasal bacterial taxa were significantly associated with nasal MRSA decolonization outcome. The nasal bacterial community changed significantly within the first 2 days of treatment and remained distinct from the baseline composition for 30 days, both among those with successful decolonization and those who remained colonized with MRSA. Nasal community state types characterized by S. aureus, coagulase-negative staphylococci, Moraxella, and Dolosigranulum became less prevalent during treatment, whereas community state types dominated by Corynebacterium and Cutibacterium increased in prevalence. Among successfully decolonized participants, the nasal microbiota at 3 and 6 months after treatment continued to differ from baseline and from the reference group, mainly because of a sustained depletion of Dolosigranulum and Moraxella. In contrast, the throat microbiota showed only short-term compositional changes. CONCLUSIONS:Decolonization treatment significantly alters the nasal microbiota, with both short-term and persistent effects. Future strategies could consider supplementation with beneficial nasal commensals, such as Dolosigranulum, after treatment to promote microbiome recovery.

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of urinary tract infections (UTIs) worldwide and may be transmitted from food animals to humans via contaminated meat. However, the contribution of zoonotic ExPEC strains to UTIs in metropolitan areas remains unclear. We estimated the proportion of UTIs attributable to zoonotic ExPEC across eight Southern California counties. Between 2017 and 2021, we collected 12,616 E. coli isolates from retail meat and 23,483 from UTI patients, sequencing a representative subset of 5,728 isolates. Using a Bayesian latent class model trained with 17 host-associated genetic markers, we inferred the host origin of each isolate. Demographic, clinical, and antimicrobial resistance profiles were compared between meat isolates and clinical isolates inferred to be of human or food-animal origin. Most UTI patients were female (88%), with a median age of 50 years; 37% were Hispanic and 31% non-Hispanic white. Zoonotic ExPEC strains accounted for 18% of UTIs overall, rising to 21.5% in high-poverty neighborhoods. Women had a higher zoonotic proportion than men (19.7% vs 8.5%, P < 0.001). Among men, those with zoonotic infections were older than those with non-zoonotic infections (median 73.0 vs 65.0 years, P = 0.028). These findings underscore the contribution of zoonotic ExPEC to the UTI burden in Southern California and the need for targeted interventions to reduce risk in vulnerable communities.IMPORTANCEUrinary tract infections (UTIs) are among the most common bacterial infections worldwide and are primarily caused by Escherichia coli. While E. coli is known to colonize both humans and food-producing animals, the extent to which zoonotic strains impact human disease remains poorly understood. Emerging evidence suggests that food animals may serve as an underrecognized reservoir for extraintestinal pathogenic E. coli (ExPEC). In this study, we used a genomic attribution model to quantify the contribution of zoonotic strains to UTIs in Southern California. We found that approximately 18% of E. coli UTIs were likely attributable to food animals. Individuals living in high-poverty neighborhoods had a 1.6-fold increased risk of zoonotic UTIs compared to those in low-poverty areas. These findings highlight zoonotic transmission as an important driver of UTIs and suggest that reducing ExPEC in food-animal reservoirs could help lower disease burden and address health disparities.

Importance:Accurate species identification and antifungal susceptibility testing are essential for effective aspergillosis treatment. However, non-Aspergillus fumigatus species, such as Aspergillus tubingensis, are often misidentified and understudied, potentially compromising proper prognosis and treatment. Objective:To examine the species and prevalence of triazole resistance among clinical Aspergillus isolates in Southern California. Design, Setting, and Participants:This cross-sectional study collected clinical Aspergillus cultures from September 1, 2019, to June 30, 2023, at Kaiser Permanente Southern California, an integrated health system serving a diverse regional population. Triazole susceptibility testing and whole genome sequencing were performed on selected isolates. A total of 2421 consecutive Aspergillus cultures were included. Eighty putative Aspergillus niger isolates were selected for sequencing, including 44 with positive growth in the presence of at least one clinically relevant triazole. Main Outcomes and Measures:The primary outcome was the genome-based species identification of A tubingensis. The secondary outcome was triazole susceptibility above the A niger epidemiological cut-off values. The hypothesis that A tubingensis is a prevalent, underrecognized, triazole-resistant pathogen was developed during data collection. Results:Of 2421 cultures, 1835 were successfully cultured for Aspergillus. After purification and deduplication, 1505 isolates were screened for triazole resistance. A substantial fraction of putative A niger isolates grew at the A niger epidemiological cut-off for itraconazole (110 of 664 [15.1%]). DNA sequencing revealed that 59 of 80 putative A niger isolates (73.8%) were actually A tubingensis. Elevated triazole minimum inhibitory concentrations were not strongly associated with any known cyp51 mutations among the A tubingensis isolates. Conclusions and Relevance:In this cross-sectional study of Aspergillus isolates from Kaiser Permanente Southern California, A tubingensis was a prevalent but underrecognized cause of aspergillosis in Southern California. Its frequent misidentification, association with invasive infections, and triazole resistance underscore the need for improved diagnostics and species-specific epidemiological investigations.

Objective: Successfully educating urgent care patients on appropriate use and risks of antibiotics can be challenging. We assessed the conscious and subconscious impact various educational materials (informational handout, priming poster, and commitment poster) had on urgent care patients' knowledge and expectations regarding antibiotics.Design: Stratified Block Randomized Control Trial.Setting: Urgent care centers (UCCs) in Colorado, Florida, Georgia, and New Jersey.Participants: Urgent care patients.Methods: We randomized 29 UCCs across six study arms to display specific educational materials (informational handout, priming poster, and commitment poster). The primary intention-to-treat (ITT) analysis evaluated whether the materials impacted patient knowledge or expectations of antibiotic prescribing by assigned study arm. The secondary as-treated analysis evaluated the same outcome comparing patients who recalled seeing the assigned educational material and patients who either did not recall seeing an assigned material or were in the control arm.Results: Twenty-seven centers returned 2,919 questionnaires across six study arms. Only 27.2% of participants in the intervention arms recalled seeing any educational materials. In our primary ITT analysis, no difference in knowledge or expectations of antibiotic prescribing was noted between groups. However, in the as-treated analysis, the handout and commitment poster were associated with higher antibiotic knowledge scores.Conclusions: Educational materials in UCCs are associated with increased antibiotic-related knowledge among patients when they are seen and recalled; however, most patients do not recall passively displayed materials. More emphasis should be placed on creating and drawing attention to memorable patient educational materials.

Specific anaerobic taxa within the penile microbiome-the Bacteria Associated with Seroconversion, Inflammation and Immune Cells (BASIC) species-enhance HIV-1 susceptibility, in part by recruiting susceptible cells to the inner foreskin. However, their effect on epithelial barrier integrity has not been described. Using foreskin tissues and penile swabs from 116 males undergoing voluntary medical male circumcision, we assessed the relationship between BASIC species and foreskin epithelial thickness, junction protein expression, and cellular proliferation. The absolute abundance of BASIC species was associated with reduced tissue expression of the epithelial junction proteins claudin-1 and E-cadherin, and with elevated soluble E-cadherin in penile secretions, suggesting proteolytic cleavage. These effects were not seen in participants with a high abundance of control taxa without high levels of BASIC species. The BASIC species Prevotella bivia, but not Peptostreptococcus anaerobius or Dialister micraerophilus, was shown to directly degrade recombinant human E-cadherin and to increase the release of soluble E-cadherin from foreskin epithelial cells in vitro. In vivo BASIC species absolute abundance was also linked to a thicker nucleated epithelium and increased keratinocyte proliferation, with no change in stratum corneum thickness. Therefore, BASIC species may enhance penile HIV susceptibility by directly disrupting epithelial integrity, in addition to previously described target cell recruitment.

Genital inflammation increases HIV susceptibility and is associated with the density of pro-inflammatory anaerobes in the vagina and coronal sulcus. The penile urethra is a critical site of HIV acquisition, although correlates of urethral HIV acquisition are largely unknown. While Streptococcus mitis is a consistent component of the urethral flora, the presence of Gardnerella vaginalis has been linked with prior penile-vaginal sex and urethral inflammation. Here, we use a flow cytometry-based bacterial assay to quantify urethral IgA and IgG that bind G. vaginalis and S. mitis in a cross-sectional cohort of 45 uncircumcised Ugandan men and to evaluate their association with the urethral microbiome and local soluble immune factors. Urethral antibodies binding both bacterial species were readily detectable, with G. vaginalis predominantly bound by IgA, and S. mitis equivalently by IgA and IgG. Gardnerella vaginalis-binding IgA was elevated in participants with detectable urethral Gardnerella, with the latter only present in participants who reported prior penile-vaginal sex. In contrast, detectable urethral S. mitis was not associated with sexual history or levels of S. mitis-binding IgA/IgG. The time from the last penile-vaginal sex was inversely correlated with the urethral concentrations of total IgA, G. vaginalis-binding IgA, and chemokines IL-8 and MIP-1β; these inflammatory chemokines were independently associated with higher total IgA concentration, but not with G. vaginalis-binding IgA. This first description of microbe-binding antibodies in the penile urethra suggests that urethral colonization by Gardnerella after penile-vaginal sex specifically induces a G. vaginalis-binding IgA response. Prospective studies of the host-microbe relationship in the urethra may have implications for the development of vaccines against sexually-transmitted bacteria.

BACKGROUND:The nasal microbiome may influence host risk for COVID-19 by modulating the expression of key proteins that facilitate SARS-CoV-2 entry, including angiotensin-converting enzyme 2 (ACE2), which binds the virus, and transmembrane serine protease 2 (TMPRSS2), which activates viral entry into nasal epithelial cells. This study examined whether the expression levels of ACE2 and TMPRSS2 in the nasal cavity predict the risk of SARS-CoV-2 infection and whether the host nasal microbiome modulates their expression. METHODS:Using 1548 self-collected nasal swabs from a population-based surveillance testing of community-dwelling adults in Washington D.C., we conducted two retrospective case-control studies (cross-sectional: n = 111 cases and 343 controls; longitudinal: n = 97 cases, 286 controls) and a nasal microbiome study (n = 428). Cases, defined as individuals with a positive SARS-CoV-2 test, were matched with controls based on age and test date. Pre-infection samples were analysed. We measured nasal ACE2/TMPRSS2 expression using RT-qPCR and characterized the nasal microbiome using 16S rRNA gene-based qPCR and sequencing. We used machine learning and regression analysis to determine if nasal ACE2/TMPRSS2 expression predicts SARS-CoV-2 infection and whether the nasal microbiome influences their expression. FINDINGS:Elevated nasal ACE2/TMPRSS2 expression was associated with 3.6-fold increased risk of contracting COVID-19 (95% CI = 1.71-7.47) compared to those with no detectable levels of ACE2 or TMPRSS2. Before testing positive for SARS-CoV-2, cases also had significantly higher and more unstable ACE2/TMPRSS2 expression in their nasal cavity than controls. Having high densities of Staphylococcus aureus, Haemophilus influenzae, or Moraxella catarrhalis/nonliquefaciens was linked to increased nasal ACE2/TMPRSS2 expression. In contrast, having high densities of Dolosigranulum pigrum was associated with decreased nasal ACE2/TMPRSS2 expression. INTERPRETATION:These results suggest that natural variation in the nasal microbiome significantly impacts ACE2/TMPRSS2 expression in the nasal cavity and the near-term risk of SARS-CoV-2 infection in adults. Modifying the nasal microbiome could potentially reduce COVID-19 risk. FUNDING:Research reported in this article was supported by the Milken Institute School of Public Health, the George Washington University and the National Institute of Allergy and Infectious Diseases, National Institutes of Health under award number R01AI168182. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Objective: Urgent care centers (UCCs) have reported high rates of antibiotic prescribing for acute respiratory tract infections. Prior UCC studies have generally been limited to single networks. Broadly generalizable stewardship efforts targeting common diagnoses are needed. This study examines the effectiveness of an antibiotic stewardship intervention in reducing inappropriate prescribing for bronchitis and viral upper respiratory tract infections (URTIs) in UCCs. Design: A quality improvement study comparing inappropriate antibiotic prescribing rates in UCCs after the introduction of an antibiotic stewardship intervention. Setting: Forty-nine UCCs in 27 different networks from 18 states, including 1 telemedicine site. Participants: Urgent care clinicians from a national collaborative of UCCs, all members of the Urgent Care Association. Methods: The intervention included signing a commitment statement and selecting from 5 different intervention options during 3 plan-do-study-act cycles. The primary outcome was the percentage of urgent care encounters for viral URTIs or bronchitis with inappropriate prescribing, stratified by clinician engagement and diagnosis. A 3-month baseline and 9-month intervention period were compared using a regression model using a generalized estimating equation. Results: Among 15,385 encounters, the intervention was associated with decreases in inappropriate antibiotic prescribing for bronchitis (48% relative decrease, aOR = 0.52; 95% CI, 0.33-0.83) and viral URTIs (33%, aOR = 0.67; 95% CI, 0.55-0.82) among actively engaged clinicians compared to baseline. The intervention did not result in significant changes for clinicians not actively engaged. Conclusions: This intervention was associated with reductions in inappropriate prescribing among actively engaged clinicians. Implementing stewardship interventions in UCCs may reduce inappropriate antibiotic prescriptions for common diagnoses; however, active clinician engagement may be necessary.

Abstract Background Urgent care centers (UCCs) have previously been associated with high rates of inappropriate antibiotic prescribing without supporting appropriate diagnoses. Prior antibiotic stewardship studies in urgent care settings have generally been limited to pediatric clinics and diagnoses or conducted within single urgent care networks. Broadly generalizable stewardship efforts targeting common diagnoses across ages are needed. Methods This quality improvement study's participants were UCC clinicians from a national collaborative of 49 UCCs in 27 networks across 18 states within the United States. Stewardship interventions included signing of a commitment statement, and a choice of intervention options to implement during two plan-do-study-act (PDSA) cycles during the intervention period. The primary outcome was the percent of urgent care encounters (from randomly selected patient charts) for viral illness or bronchitis diagnoses with inappropriate antibiotic prescribing, stratified by whether the clinician was a direct participant in the quality improvement study and by diagnosis. A 3-month baseline and 9-month intervention period were compared using an interrupted time series with a generalized estimating equation model. Results 15,588 patient encounters were included with a diagnosis of bronchitis or viral illness. The intervention was associated with a 39% relative decrease in inappropriate antibiotic prescribing (aOR=0.61, 95%CI 0.48-0.77) among participating clinicians compared to baseline. The intervention did not result in a significant change in inappropriate antibiotic prescribing (aOR=1.08, p=0.54) for clinicians who did not directly participate. Conclusion This antibiotic stewardship intervention was associated with significant reductions in inappropriate prescribing among clinicians who directly participated. Implementing stewardship interventions in UCCs may reduce inappropriate antibiotic prescriptions for common diagnoses; however, direct clinician participation may be necessary, especially in settings with high rates of clinician turnover. Disclosures All Authors: No reported disclosures

Background The World Health Organization (WHO) clinical case definitions for pneumonia were designed to prioritize sensitivity over specificity. In sub-Saharan Africa, the disease that is most likely to be misclassified as pneumonia is Plasmodium falciparum malaria. Methods By using chest X-ray positivity as an indicator for pneumonia, we estimated the extent of pneumonia misclassification due to malaria in the Pneumonia Etiology Research for Child Health (PERCH) study. Additionally, we developed a simple model to predict the proportion of pneumonia cases as defined by the WHO that could be attributed to malaria in settings with varying levels of malaria parasitaemia prevalence. Results In the PERCH study, the prevalence of malaria parasitaemia was low (4.7% among WHO pneumonia cases and 1.4% among controls) and we estimate that only 2.5% of WHO pneumonia cases were misclassified. However, when assuming a prevalence of malaria parasitaemia of 24%, corresponding to the average for malaria-endemic areas in Africa, we estimate that 28% of WHO pneumonia cases are misclassified. Among malaria-slide-positive WHO pneumonia cases in PERCH, lower chest wall indrawing [adjusted odds ratio (aOR) =18.1, 95% confidence interval (95% CI): 1.9, 175.8, P = 0.012], crackles on chest auscultation (aOR = 13.1, 95% CI: 1.4, 127.4, P = 0.027), and nasal flaring (aOR = 5.9, 95% CI: 1.1, 32.8, P = 0.041) were associated with chest X-ray positivity. Conclusion In settings that are typical of sub-Saharan Africa, we predict that one-quarter of WHO-defined pneumonia cases are malaria rather than pneumonia. Among children with WHO pneumonia who also test positive for malaria parasitaemia, clinical features that favour pneumonia include lower chest wall indrawing, nasal flaring, and crackles on chest auscultation.