Oncogenic Kras drives invasion and maintains metastases in colorectal cancer.

Human colorectal cancer (CRC) is a major cause of cancer mortality and frequently harbors activating mutations in the KRAS gene. To understand the role of oncogenic KRAS in CRC, we engineered a mouse model of metastatic CRC that harbors an inducible oncogenic Kras allele (Krasmut ) and conditional null alleles of Apc and Trp53 (iKAP). The iKAP model recapitulates tumor progression from adenoma through metastases. Whole-exome sequencing revealed that the Krasmut allele was heterogenous in primary tumors yet homogenous in metastases, a pattern consistent with activated Krasmut signaling being a driver of progression to metastasis. System-level and functional analyses revealed the TGF-ß pathway as a key mediator of Krasmut -driven invasiveness. Genetic extinction of Krasmut resulted in specific elimination of the Krasmut subpopulation in primary and metastatic tumors, leading to apoptotic elimination of advanced invasive and metastatic disease. This faithful CRC model provides genetic evidence that Krasmut drives CRC invasion and maintenance of metastases.

Low prevalence of bacterial vaginosis in Kenyan adolescent girls and rapid incidence after first sex.

BACKGROUND: Bacterial vaginosis is a risk factor for sexually transmitted infections, including HIV. Adult African women have a high prevalence of bacterial vaginosis, but it is not known when first bacterial vaginosis occurs. OBJECTIVE: This study aimed to describe bacterial vaginosis in younger African women, before and after first sex, and to determine the incidence of bacterial vaginosis and significant correlates of bacterial vaginosis incidence and recurrence. STUDY DESIGN: In a prospective observational cohort study enrolling adolescents with limited sexual experience, young women aged 16 to 21 years were recruited in Thika, Kenya. Eligible participants were HIV and herpes simplex virus 2 seronegative and reported 0 or 1 lifetime sexual partner. The Nugent score was determined at quarterly visits from vaginal Gram stains. The trends in bacterial vaginosis were described over time; hazard ratios were calculated using Cox regression, and relative risk of bacterial vaginosis was estimated using generalized estimating equations and Poisson regression. RESULTS: A total of 400 participants with a median age of 18.6 years (interquartile range, 16-21) were enrolled. Of note, 322 participants (80.5%) reported no history of sex, whereas 78 participants (19.5%) reported sex with 1 partner. At enrollment, bacterial vaginosis (Nugent score of ≥7) was uncommon (21/375 [5.6%]). Overall, 144 participants had bacterial vaginosis at least once, for an incidence rate of 16.5 cases per 100 person-years. Before first sex, bacterial vaginosis was present at 2.8% of visits, compared with 13.7% of visits after first sex. An adjusted model of bacterial vaginosis incidence observed that first sex was associated with more than a 2-fold increased bacterial vaginosis risk (adjusted hazard ratio, 2.44; 95% confidence interval, 1.25-4.76; P=.009). Chlamydia diagnosis (adjusted hazard ratio, 1.73; 95% confidence interval, 1.1-2.8; P=.02), and herpes simplex virus 2 seropositivity (adjusted hazard ratio, 2.88; 95% confidence interval, 1.17-7.09; P=.021) were both associated with incident bacterial vaginosis. A multivariate generalized estimating equation model, including all episodes of bacterial vaginosis, demonstrated risk factors, including first sex, sexually transmitted infections, urban residence, recent sex, and no income; the most important risk factor was first sex (adjusted relative risk, 1.92; 95% confidence interval, 1.12-3.31; P=.018). The probability of bacterial vaginosis increased with each subsequent episode; mean Nugent scores increased after each bacterial vaginosis episode. CONCLUSION: Using detailed longitudinal observation, this study found that Kenyan adolescents have almost no bacterial vaginosis before first sex and that initiation of sexual activity was the strongest risk factor for both prevalent bacterial vaginosis and incident bacterial vaginosis.

Significant Patient Impact Observed Upon Implementation of Point-of-Care Early Infant Diagnosis Technologies in an Observational Study in Malawi.

Background: In Malawi in 2014, <20% of human immunodeficiency virus (HIV)-exposed infants received an early infant diagnosis (EID) test in the first 2 months of life and only 30% of HIV-infected children were on antiretroviral therapy (ART). We sought to understand the potential patient impact of improving timely infant diagnosis and treatment initiation through implementation of point-of-care (POC) EID technologies in Malawi. Methods: In this observational study, POC EID technologies were introduced into routine services at 7 health facilities across Malawi in September 2015. The primary outcome was the proportion of HIV-infected infants initiating ART within 60 days of sample collection in the POC arm compared to the baseline arm with conventional laboratory-based EID testing. Results: The time from sample collection to result received by the patient decreased significantly from 56 days (interquartile range [IQR], 30-81 days) in the baseline arm to <1 day in the POC arm (P < .001). Of the HIV-infected infants, the time between sample collection and ART initiation was reduced from 38 days (IQR, 30-54 days) in the baseline arm to <1 day (IQR, 0-1 day) in the POC arm (P = .019). Furthermore, the proportion of HIV-infected infants initiated on ART within 60 days of sample collection increased significantly from 41.9% to 91.1% after the introduction of POC (adjusted risk ratio, 2.28; P < .001). Conclusions: ART initiation rates were significantly improved with the implementation of same-day POC EID testing compared with referred, longer-turnaround laboratory-based testing.

Repression of Salmonella Host Cell Invasion by Aromatic Small Molecules from the Human Fecal Metabolome.

The human microbiome is a collection of microorganisms that inhabit every surface of the body that is exposed to the environment, generally coexisting peacefully with their host. These microbes have important functions, such as producing vitamins, aiding in maturation of the immune system, and protecting against pathogens. We have previously shown that a small-molecule extract from the human fecal microbiome has a strong repressive effect on Salmonella enterica serovar Typhimurium host cell invasion by modulating the expression of genes involved in this process. Here, we describe the characterization of this biological activity. Using a series of purification methods, we obtained fractions with biological activity and characterized them by mass spectrometry. These experiments revealed an abundance of aromatic compounds in the bioactive fraction. Selected compounds were obtained from commercial sources and tested with respect to their ability to repress the expression of hilA, the gene encoding the master regulator of invasion genes in Salmonella We found that the aromatic compound 3,4-dimethylbenzoic acid acts as a strong inhibitor of hilA expression and of invasion of cultured host cells by Salmonella Future studies should reveal the molecular details of this phenomenon, such as the signaling cascades involved in sensing this bioactive molecule.IMPORTANCE Microbes constantly sense and adapt to their environment. Often, this is achieved through the production and sensing of small extracellular molecules. The human body is colonized by complex communities of microbes, and, given their biological and chemical diversity, these ecosystems represent a platform where the production and sensing of molecules occur. In previous work, we showed that small molecules produced by microbes from the human gut can significantly impair the virulence of the enteric pathogen Salmonella enterica Here, we describe a specific compound from the human gut that produces this same effect. The results from this work not only shed light on an important biological phenomenon occurring in our bodies but also may represent an opportunity to develop drugs that can target these small-molecule interactions to protect us from enteric infections and other diseases.

A Systematic Review on the Potential of Aspirin to Reduce Cardiovascular Risk in Schizophrenia.

Cardiovascular disease (CVD), including heart disease and stroke, continues to be the leading cause of death worldwide. Patients with mental health disorders, including schizophrenia (SCZ) are known to have an increased risk for CVD. Given the association with metabolic syndrome, patients with SCZ are often prescribed metformin and statins but its impact remains unsatisfactory. The use of aspirin (ASA) to decrease cardiovascular risk in the general population has been thoroughly investigated and clear guidelines are currently in place. Since adjuvant treatment with ASA could possibly decrease CVD risk and mortality in SCZ, we conducted a systematic review of the literature to determine the state of the current literature on this subject. Our systematic review points to gaps in the literature on CVD prevention in SCZ and illustrates an obvious need for further research. Although several studies have shown increased CVD risk in SCZ, to date, no research has been conducted on the utilization of CVD preventative treatment such as ASA for SCZ.

Delivery of Community-based Antiretroviral Therapy to Maintain Viral Suppression and Retention in Care in South Africa.

BACKGROUND: To determine whether the Centralized Chronic Medication Dispensing and Distribution (CCMDD) program in South Africa's differentiated ART delivery model affects clinical outcomes, we assessed viral load (VL) suppression and retention in care between patients participating in the program and those receiving the clinic-based standard of care. METHODS: Clinically stable people living with HIV (PLHIV) eligible for differentiated care were referred to the national CCMDD program and followed up for up to 6 months. In this secondary analysis of trial cohort data, we estimated the association between routine patient participation in the CCMDD program and their clinical outcomes of viral suppression (<200 copies/mL) and retention in care. RESULTS: Among 390 PLHIV, 236 (61%) were assessed for CCMDD eligibility; 144 (37%) were eligible, and 116 (30%) participated in the CCMDD program. Participants obtained their ART in a timely manner at 93% (265/286) of CCMDD visits. VL suppression and retention in care was very similar among CCMDD-eligible patients who participated in the program compared with patients who did not participate in the program (aRR: 1.03; 95% CI: 0.94-1.12). VL suppression alone (aRR: 1.02; 95% CI: 0.97-1.08) and retention in care alone (aRR: 1.03; 95% CI: 0.95-1.12) were also similar between CCMDD-eligible PLHIV who participated in the program and those who did not. CONCLUSION: The CCMDD program successfully facilitated differentiated care among clinically stable participants. PLHIV participating in the CCMDD program maintained a high proportion of viral suppression and retention in care, indicating that community-based ART delivery model did not negatively affect their HIV care outcomes.

Adolescent Girls and Young Women in Kenya Demonstrate Rapid STI Incidence Following First Sex: Data From a Longitudinal Cohort.

PURPOSE: Adolescent girls and young women (AGYW) are disproportionately affected by STIs. Observation of life course events can describe behavioral and biological factors associated with STI risk. METHODS: Sexually inexperienced AGYW aged 16-20 years in Kenya were followed for five years. Quarterly visits assessed for C. trachomatis (CT), N. gonorrhea (GC), and T. vaginalis (TV), bacterial vaginosis (BV), HSV-2, and HIV. Sexual activity was self-reported but amended if incongruent with results from STI, pregnancy, or any other testing. Cox regression and Generalized Estimating Equation models were used to determine hazard ratios (HRs) and relative risks (RRs) of STI. RESULTS: During follow-up, 293 of 400 participants reported sex, 163 AGYW experienced an STI, and 72 participants had multiple STIs. Among 163 participants that experienced an STI, there were a total of 259 visits where STIs were detected, 78% (n = 201) of which included CT. Cox regression found participants with BV had over two-fold higher risk of first STI acquisition (adjusted hazard ratio (aHR): 2.35; 95% confidence interval (CI) 1.43-3.88; p = .001). Increased risk for first STI episode was associated with a new partner (aHR: 3.16; 95% CI 1.59-6.28; p = .001). AGYW who did not disclose sexual activity had the highest risk (aHR: 3.60; 95% CI 1.93-6.70; p < .001). Condom use was low, with 21% reporting condom use with sex. GEE analysis of all STIs including incident, prevalent, and recurrent, confirmed these risk factors. DISCUSSION: During the critical years after first sex, AGYW with BV, new sexual partners, and those who did not disclose sexual activity were at highest risk for STI events, especially CT.

Longitudinal assessment of bacterial vaginosis prior to and during incident pregnancy: an observational study in Kenyan adolescent girls and young women.

OBJECTIVE: To determine bacterial vaginosis (BV) status at multiple time points among adolescent girls and young women (AGYW) and assess the impact of pregnancy on their BV status. DESIGN: Longitudinal cohort study. SETTING: Thika, Kenya. PARTICIPANTS: AGYW aged 16-20 years enrolled prior to first sex or reporting only a single lifetime partner. MAIN OUTCOME MEASURES: The primary outcome was relative risk (RR) of BV during pregnancy compared with before pregnancy by analysing longitudinal trends in BV over time. BV risk was estimated using Poisson regression models. RESULTS: A total of 121 AGYW became pregnant in the parent cohort and had BV results before, during or after pregnancy. Point prevalence of BV was 11.0% at visits >12 months pre-pregnancy, 13.0% at 3-12 months pre-pregnancy, 22.1% at <3 months pre-pregnancy and 13.4% during pregnancy. Compared with visits during pregnancy, RR of BV was 1.65 (95% CI: 1.00 to 2.71; p=0.05) at visits <3 months pre-pregnancy, 0.97 (95% CI: 0.62 to 1.52; p=0.90) at visits 3-12 months pre-pregnancy and 0.82 (95% CI: 0.44 to 1.53; p=0.53) at visits 12 months pre-pregnancy. An adjusted analysis including age, income, residence, date of first sex, recent sexual activity and positive sexually transmitted infection test resulted in small changes in risk estimates, with adjusted RR of BV of 1.66 (95% CI: 1.04 to 2.67; p=0.04) at visits <3 months pre-pregnancy compared with visits during pregnancy. CONCLUSIONS: BV risk during pregnancy was lower than during the immediate pre-pregnancy period. Hormonal changes in pregnancy may reduce BV.

Size-Induced Ferroelectricity in Antiferroelectric Oxide Membranes.

Despite extensive studies on size effects in ferroelectrics, how structures and properties evolve in antiferroelectrics with reduced dimensions still remains elusive. Given the enormous potential of utilizing antiferroelectrics for high-energy-density storage applications, understanding their size effects will provide key information for optimizing device performances at small scales. Here, the fundamental intrinsic size dependence of antiferroelectricity in lead-free NaNbO3 membranes is investigated. Via a wide range of experimental and theoretical approaches, an intriguing antiferroelectric-to-ferroelectric transition upon reducing membrane thickness is probed. This size effect leads to a ferroelectric single-phase below 40 nm, as well as a mixed-phase state with ferroelectric and antiferroelectric orders coexisting above this critical thickness. Furthermore, it is shown that the antiferroelectric and ferroelectric orders are electrically switchable. First-principle calculations further reveal that the observed transition is driven by the structural distortion arising from the membrane surface. This work provides direct experimental evidence for intrinsic size-driven scaling in antiferroelectrics and demonstrates enormous potential of utilizing size effects to drive emergent properties in environmentally benign lead-free oxides with the membrane platform.

Repression of Salmonella enterica phoP expression by small molecules from physiological bile.

Infection with Salmonella enterica serovar Typhi in humans causes the life-threatening disease typhoid fever. In the laboratory, typhoid fever can be modeled through the inoculation of susceptible mice with Salmonella enterica serovar Typhimurium. Using this murine model, we previously characterized the interactions between Salmonella Typhimurium and host cells in the gallbladder and showed that this pathogen can successfully invade gallbladder epithelial cells and proliferate. Additionally, we showed that Salmonella Typhimurium can use bile phospholipids to grow at high rates. These abilities are likely important for quick colonization of the gallbladder during typhoid fever and further pathogen dissemination through fecal shedding. To further characterize the interactions between Salmonella and the gallbladder environment, we compared the transcriptomes of Salmonella cultures grown in LB broth or physiological murine bile. Our data showed that many genes involved in bacterial central metabolism are affected by bile, with the citric acid cycle being repressed and alternative respiratory systems being activated. Additionally, our study revealed a new aspect of Salmonella interactions with bile through the identification of the global regulator phoP as a bile-responsive gene. Repression of phoP expression could also be achieved using physiological, but not commercial, bovine bile. The biological activity does not involve PhoPQ sensing of a bile component and is not caused by bile acids, the most abundant organic components of bile. Bioactivity-guided purification allowed the identification of a subset of small molecules from bile that can elicit full activity; however, a single compound with phoP inhibitory activity could not be isolated, suggesting that multiple molecules may act in synergy to achieve this effect. Due to the critical role of phoP in Salmonella virulence, further studies in this area will likely reveal aspects of the interaction between Salmonella and bile that are relevant to disease.

Mechanical nanolattices printed using nanocluster-based photoresists.

Natural materials exhibit emergent mechanical properties as a result of their nanoarchitected, nanocomposite structures with optimized hierarchy, anisotropy, and nanoporosity. Fabrication of such complex systems is currently challenging because high-quality three-dimensional (3D) nanoprinting is mostly limited to simple, homogeneous materials. We report a strategy for the rapid nanoprinting of complex structural nanocomposites using metal nanoclusters. These ultrasmall, quantum-confined nanoclusters function as highly sensitive two-photon activators and simultaneously serve as precursors for mechanical reinforcements and nanoscale porogens. Nanocomposites with complex 3D architectures are printed, as well as structures with tunable, hierarchical, and anisotropic nanoporosity. Nanocluster-polymer nanolattices exhibit high specific strength, energy absorption, deformability, and recoverability. This framework provides a generalizable, versatile approach for the use of photoactive nanomaterials in additive manufacturing of complex systems with emergent mechanical properties.

High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer.

Changes in DNA methylation patterns are an important characteristic of human cancer. Tumors have reduced levels of genomic DNA methylation and contain hypermethylated CpG islands, but the full extent and sequence context of DNA hypomethylation and hypermethylation is unknown. Here, we used methylated CpG island recovery assay-assisted high-resolution genomic tiling and CpG island arrays to analyze methylation patterns in lung squamous cell carcinomas and matched normal lung tissue. Normal tissues from different individuals showed overall very similar DNA methylation patterns. Each tumor contained several hundred hypermethylated CpG islands. We identified and confirmed 11 CpG islands that were methylated in 80-100% of the SCC tumors, and many hold promise as effective biomarkers for early detection of lung cancer. In addition, we find that extensive DNA hypomethylation in tumors occurs specifically at repetitive sequences, including short and long interspersed nuclear elements and LTR elements, segmental duplications, and subtelomeric regions, but single-copy sequences rarely become demethylated. The results are consistent with a specific defect in methylation of repetitive DNA sequences in human cancer.

A Rapid, High-Sensitivity SARS-CoV-2 Nucleocapsid Immunoassay to Aid Diagnosis of Acute COVID-19 at the Point of Care: A Clinical Performance Study.

INTRODUCTION: The LumiraDx severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen test, which uses a high-sensitivity, microfluidic immunoassay to detect the nucleocapsid protein of SARS-CoV-2, was evaluated for diagnosing acute coronavirus disease 2019 (COVID-19) in adults and children across point-of-care settings (NCT04557046). METHODS: Two paired anterior nasal swabs or two paired nasopharyngeal swabs were collected from each participant. Swabs were tested by the LumiraDx SARS-CoV-2 antigen test and compared with real-time polymerase chain reaction (rt-PCR; Roche cobas 6800 platform). Sensitivity, specificity and likelihood ratios were calculated. Results were stratified on the basis of gender, age, duration of symptoms, and rt-PCR cycle threshold. RESULTS: Out of the 512 participants, aged 0-90 years, of this prospective validation study, 414 (81%) were symptomatic for COVID-19 and 123 (24%) swabs were positive for SARS-CoV-2 based on rt-PCR testing. Compared with rt-PCR, the 12-min nasal swab test had 97.6% sensitivity and 96.6% specificity, and nasopharyngeal swab had 97.5% sensitivity and 97.7% specificity, within 12 days of symptom onset, representing the period of infectivity. All (100%) samples detected within 33 rt-PCR cycles were also identified using the antigen test. Results were consistent across age and gender. The user error rate of the test system when used by minimally trained operators was 0.7% (95% confidence interval [CI] 0.1-3.7%). CONCLUSION: The rapid, high-sensitivity assay using nasopharyngeal or anterior nasal sampling may offer significant improvements for diagnosing acute SARS-CoV-2 infection in clinic- and community-based settings.

Feasibility and impact of near-point-of-care integrated tuberculosis/HIV testing in Malawi and Zimbabwe.

OBJECTIVES: Near-point-of-care (POC) testing for early infant diagnosis (EID) and viral load expedites clinical action and improves outcomes but requires capital investment. We assessed whether excess capacity on existing near-POC devices used for TB diagnosis could be leveraged to increase near-POC HIV molecular testing, termed integrated testing, without compromising TB services. DESIGN: Preimplementation/postimplementation studies in 10 health facilities in Malawi and 8 in Zimbabwe. METHODS: Timeliness of EID and viral load test results and clinical action were compared between centralized and near-POC testing using Somers' D tests (continuous indicators) and risk ratios (RR, binary indicators); TB testing/treatment rates and timeliness were analyzed preintegration/postintegration. RESULTS: With integration, average device utilization increased but did not exceed 55%. Despite the addition of HIV testing, TB test volumes, timeliness, and treatment initiations were maintained. Although few HIV-positive infants were identified, near-POC EID testing improved treatment initiation within 1 month by 57% compared with centralized EID [Malawi RR: 1.57, 95% confidence interval (CI) 0.98-2.52], and near-POC viral load testing significantly increased the proportion of patients with elevated viral load receiving clinical action within 1 month (Zimbabwe RR: 5.26, 95% CI 3.38-8.20; Malawi RR: 3.90, 95% CI 2.58-5.91). CONCLUSION: Integrating TB/HIV testing using existing multidisease platforms is feasible and enables increased access to rapid diagnostics without disrupting existing TB services. Our results serve as an example of a novel, efficient implementation model that can increase access to critical testing services across disease silos and should be considered for additional clinical applications.

Point-of-care testing can achieve same-day diagnosis for infants and rapid ART initiation: results from government programmes across six African countries.

INTRODUCTION: Point-of-care (POC) early infant diagnosis (EID) testing has been shown to dramatically decrease turnaround times from sample collection to caregiver result receipt and time to ART initiation for HIV-positive infants compared to centralized laboratory testing. As governments in sub-Saharan Africa implement POC EID technologies, we report on the feasibility and effectiveness of POC EID testing and the impact of same-day result delivery on rapid ART initiation within national programmes across six countries. METHODS: This pre-/post-evaluation compared centralized laboratory-based (pre) with POC (post) EID testing in 52 facilities across Cameroon, Democratic Republic of Congo, Ethiopia, Kenya, Senegal and Zimbabwe between April 2017 and October 2019 (country-dependent). Data were collected retrospectively from routine records at health facilities for all infants tested under two years of age. Hazard ratios and 95% confidence intervals were calculated to compare time-to-event outcomes, visualized with Kaplan-Meier curves, and the Somers' D test was used to compare continuous outcomes. RESULTS: Data were collected for 2892 EID tests conducted on centralized laboratory-based platforms and 4610 EID tests on POC devices with 127 (4%) and 192 (4%) HIV-positive infants identified, respectively. POC EID significantly reduced the time from sample collection to caregiver result receipt (POC median: 0 days, IQR: 0 to 0 vs. centralized: 35 days, IQR: 26 to 56) and time from sample collection to ART initiation for HIV-positive infants (POC median: 1 day, IQR: 0 to 7 vs. centralized: 39 days, IQR: 26 to 57). With POC testing, 72% of infants received results on the same day as sample collection; HIV-positive infants with a same-day diagnosis had six times the rate of ART initiation compared to those diagnosed one or more days after sample collection (HR: 6.39; 95% CI: 3.44 to 11.85). CONCLUSIONS: Same-day diagnosis and treatment initiation for infants is possible with POC EID within routine government-led and -supported public sector healthcare facilities in resource-limited settings. Given that POC EID allows for rapid ART initiation, aligning to the World Health Organization's recommendation of ART initiation within seven days, its use in public sector programmes has the potential to reduce overall mortality for infants with HIV through early treatment initiation.

Inter- and intra-host sequence diversity reveal the emergence of viral variants during an overwintering epidemic caused by dengue virus serotype 2 in southern Taiwan.

Purifying selection during dengue viral infection has been suggested as the driving force of viral evolution and the higher complexity of the intra-host quasi-species is thought to offer an adaptive advantage for arboviruses as they cycle between arthropod and vertebrate hosts. However, very few studies have been performed to investigate the viral genetic changes within (intra-host) and between (inter-host) humans in a spatio-temporal scale. Viruses of different serotypes from various countries imported to Taiwan cause annual outbreaks. During 2001-2003, two consecutive outbreaks were caused by dengue virus serotype 2 (DENV-2) and resulted in a larger-scale epidemic with more severe dengue cases in the following year. Phylogenetic analyses showed that the viruses from both events were similar and related to the 2001 DENV-2 isolate from the Philippines. We comprehensively analyzed viral sequences from representative dengue patients and identified three consensus genetic variants, group Ia, Ib and II, with different spatio-temporal population dynamics. The phylodynamic analysis suggested group Ib variants, characterized by lower genetic diversity, transmission rate, and intra-host variant numbers, might play the role of maintenance variants. The residential locations among the patients infected by group Ib variants were in the outer rim of case clusters throughout the 2001-2003 period whereas group Ia and II variants were located in the centers of case clusters, suggesting that group Ib viruses might serve as "sheltered overwintering" variants in an undefined ecological niche. Further deep sequencing of the viral envelope (E) gene directly from individual patient serum samples confirmed the emergence of variants belonging to three quasi-species (group Ia, Ib, and II) and the ancestral role of the viral variants in the latter phase of the 2001 outbreak contributed to the later, larger-scale epidemic beginning in 2002. These findings enhanced our understanding of increasing epidemic severity over time in the same epidemic area. It also highlights the importance of combining phylodynamic and deep sequencing analysis as surveillance tools for detecting dynamic changes in viral variants, particularly searching for and monitoring any specific viral subpopulation. Such subpopulations might have selection advantages in both fitness and transmissibility leading to increased epidemic severity.

Antivirulence activity of the human gut metabolome.

The mammalian gut contains a complex assembly of commensal microbes termed microbiota. Although much has been learned about the role of these microbes in health, the mechanisms underlying these functions are ill defined. We have recently shown that the mammalian gut contains thousands of small molecules, most of which are currently unidentified. Therefore, we hypothesized that these molecules function as chemical cues used by hosts and microbes during their interactions in health and disease. Thus, a search was initiated to identify molecules produced by the microbiota that are sensed by pathogens. We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion. It has been known for decades that the microbiota protects its hosts from invading pathogens, and these data suggest that chemical sensing may be involved in this phenomenon. Further investigations should reveal the exact biological role of this molecule as well as its therapeutic potential. Importance: Microbes can communicate through the production and sensing of small molecules. Within the complex ecosystem formed by commensal microbes living in and on the human body, it is likely that these molecular messages are used extensively during the interactions between different microbial species as well as with host cells. Deciphering such a molecular dialect will be fundamental to our understanding of host-microbe interactions in health and disease and may prove useful for the design of new therapeutic strategies that target these mechanisms of communication.