One-year survival of patients admitted for sepsis to intensive care units in Colombia.

BACKGROUND: Sepsis is a frequent cause of admission to intensive care units (ICUs). High mortality rates are estimated globally, and in our country, few studies have reported one-year survival. The objective of this study is to determine one-year survival in patients with sepsis admitted to the ICU in Colombia, compared with the survival of patients admitted for other conditions. METHODS: Retrospective cohort study using administrative databases from the Ministry of Health of Colombia. One-year survival and the adjusted hazard ratio for survival, adjusted for comorbidities included in the Charlson Index, were determined using a Cox proportional hazards model for patients admitted for other causes as well as for those admitted for sepsis. This was then compared with an inverse propensity score weighting model. RESULTS: A total of 116.407 patients were initially admitted to the ICUs, with 12.056 (10.36%) diagnosed with sepsis. Within the first year, 4.428 (36.73%) patients died due to sepsis. Age and male gender were associated with an increased risk of death from sepsis, and the covariates associated with one-year mortality were as follows: age over 80 years with HR 9.91 (95% CI: 9.22-10.65), renal disease with HR 3.16 (95% CI: 3.03-3.29), primary tumoral disease with HR 2.07 (95% CI: 1.92-2.23), liver disease with HR 2.27 (95% CI: 2.07-2.50), and metastatic solid tumor with HR 2.03 (95% CI: 1.92-2.15). CONCLUSION: This study revealed a high one-year sepsis mortality rate in the population, associated with variables such as age over 80 years, the presence of renal disease, liver disease, connective tissue diseases, and cancer. Men exhibited higher mortality compared to women.

Effect of Biomass Torrefaction on the Syngas Quality Produced by Chemical Looping Gasification at 20 kWth Scale.

The innovative Biomass Chemical Looping Gasification (BCLG) process uses two reactors (fuel and air reactors) to generate nitrogen-free syngas with low tar content under autothermal conditions. A solid oxygen carrier supplies the oxygen for partial oxidation of the fuel. This study investigated the BCLG process, conducted over 25 h of continuous operation at 20 kWth scale, using ilmenite as the oxygen carrier and wheat straw pellets as fuel (WSP). The effect of using torrefied wheat straw pellets (T-WSP) on the syngas quality was assessed. In addition, the impact of several operational variables on the overall process performance and syngas yield was analyzed. The primary factors influencing the syngas yield were the char conversion through gasification and the oxygen-to-fuel ratio. Higher temperatures, extended residence times of solids in the fuel reactor, and using a secondary gasifier led to increased char conversion, enhancing H2 and CO production. Optimizing the air reactor design could enhance the CO2 capture potential by inhibiting the combustion of bypassed char. While char conversion and syngas yield with T-WSP were lower than those with WSP at temperatures below 900 °C, T-WSP achieved a higher syngas yield under conditions favoring high char conversion. The presence of CH4 and light hydrocarbons showed minimal sensitivity to operating conditions variation, limiting the theoretical syngas yield. Overall, the CLG unit operated smoothly without any agglomeration issues.

How to Sample Dozens of Substitutions per Site with λ Dynamics.

Alchemical free energy methods are useful in computer-aided drug design and computational protein design because they provide rigorous statistical mechanics-based estimates of free energy differences from molecular dynamics simulations. λ dynamics is a free energy method with the ability to characterize combinatorial chemical spaces spanning thousands of related systems within a single simulation, which gives it a distinct advantage over other alchemical free energy methods that are mostly limited to pairwise comparisons. Recently developed methods have improved the scalability of λ dynamics to perturbations at many sites; however, the size of chemical space that can be explored at each individual site has previously been limited to fewer than ten substituents. As the number of substituents increases, the volume of alchemical space corresponding to nonphysical alchemical intermediates grows exponentially relative to the size corresponding to the physical states of interest. Beyond nine substituents, λ dynamics simulations become lost in an alchemical morass of intermediate states. In this work, we introduce new biasing potentials that circumvent excessive sampling of intermediate states by favoring sampling of physical end points relative to alchemical intermediates. Additionally, we present a more scalable adaptive landscape flattening algorithm for these larger alchemical spaces. Finally, we show that this potential enables more efficient sampling in both protein and drug design test systems with up to 24 substituents per site, enabling, for the first time, simultaneous simulation of all 20 amino acids.

Vedolizumab and ART in recent HIV-1 infection unveil the role of α4ß7 in reservoir size.

We evaluated the safety and viral rebound, after analytical treatment interruption (ATI), of vedolizumab and ART in recent HIV-1 infection. We used this model to analyze the impact of α4ß7 on the HIV-1 reservoir size. Participants started ART with monthly Vedolizumab infusions and ATI was performed at week 24. Biopsies were obtained from ileum and caecum at baseline and week 24. Vedolizumab levels, HIV-1 reservoir, flow cytometry and cell-sorting and antibody competition experiments were assayed. Vedolizumab was safe and well-tolerated. No participant achieved undetectable viremia off ART 24 weeks after ATI. Only a modest effect on the time to achieve >1000 HIV-RNA copies/mL and the proportion of participants off ART was observed, being higher compared to historical controls. Just before ATI, α4ß7 expression was associated with HIV-1 DNA and RNA in peripheral blood and with PD1 and TIGIT levels. Importantly, a complete blocking of α4ß7 was observed on peripheral CD4+ T-cells but not in gut (ileum and caecum), where α4ß7 blockade and vedolizumab levels were inversely associated with HIV-1 DNA. Our findings support α4ß7 as an important determinant in HIV-1 reservoir size, suggesting the complete α4ß7 blockade in tissue as a promising tool for HIV-cure combination strategies.

Adsorption Mechanism and Characteristic Temperatures of the Monolayer Adsorption of CO2 on Graphite: The Role of Graphene Dimensions.

Although simulation results for gaseous adsorption on a surface of infinite extent, modeled with periodic conditions at the boundaries of the simulation box, agree with experimental data at high temperatures, simulated isotherms at temperatures below the triple point temperature show unphysical substeps because of the compromise of interactions within the box and interactions between the box and its mirror image boxes. This has been alleviated with surfaces of finite dimensions (Loi, Q. K.; Colloids Surf., A 2021, 622, 126690 and Castaño Plaza, O.; Langmuir 2023, 39 (21), 7456-7468) to account for free boundaries at the adsorbate patch on the surface, and the critical parameter of this model substrate is the size of the finite surface. If it is too small, the adsorbate patch does not model the physical reality; however, if it is too large, the computation time is excessive, making the simulation impractical. In this study, we used carbon dioxide/graphite as the model system to explore the effects of finite dimensions on the description of experimental data of Terlain, A.; Larher, Y. Surf. Sci. 1983, 125 (1), 304-311, especially for temperatures below the bulk triple point temperature. With the appropriate choice of graphene size, we derived the 2D triple point and 2D critical point temperatures of the monolayer, and most importantly, for temperatures below the 2D critical point temperature, the adsorption mechanism for the formation of the monolayer is due to the interplay between the boundary growth process and the vacancy filling. The extent of this interplay is found to depend on the fractional coverage of the surface.

Chloroplast Isolation in Agavaceas.

Chloroplast isolation protocols have been extensively developed for various species of plants, particularly model organisms with easily manipulable physical characteristics. However, succulent plants, such as Agave angustifolia Haw., which possess adaptations for arid environments like the Crassulacean acid metabolism (CAM) and a thicker cuticle, have received less attention, resulting in a potential knowledge gap. This chapter presents a specialized protocol focusing on isolating chloroplast from A. angustifolia, a species exhibiting adaptations to arid conditions and holding ecological and economic significance due to its role in producing bacanora and mezcal beverages. By successfully isolating chloroplast from A. angustifolia plant growth in ex vitro and in vitro conditions, this protocol enables comprehensive future analyses to elucidate metabolic processes and explore potential applications in related species. Consequently, this research aims to bridge this knowledge gap in chloroplast isolation for succulent plants, providing new insights for future investigations in the field.

The Global Experience of Laryngeal Transplantation: Series of Eleven Patients in Three Continents.

BACKGROUND: The loss of laryngeal function affects breathing, swallowing, and voice, thus severely compromises quality of life. Laryngeal transplantation has long been suggested as a solution for selected highly affected patients with complete laryngeal function loss. OBJECTIVE: To obtain insights regarding the advantages, weaknesses, and limitations of this procedure and facilitate future advances, we collected uniform data from all known laryngeal transplants reported internationally. METHODOLOGY: A case series. Patients were enrolled retrospectively by each institutional hospital or clinic. Eleven patients with complete loss of laryngeal function undergoing total laryngeal transplantation between 1998 and 2018 were recruited. RESULTS: After a minimum of 24 months follow-up, three patients had died (27%), and there were two graft explants in survivors, one total and one partial, due to chronic rejection. In the remaining cases, voice was functional in 62.5% and 50% achieved decannulation. Swallowing was initially restricted, but only one patient was gastrostomy-dependent by 6 months and all had normal or near-normal swallowing by the end of year two after transplantation. Median follow-up was 73 months. Functional (voice, swallowing, airway) recovery peaked between 12 and 24 months. CONCLUSIONS: Laryngeal transplantation is a complex procedure with significant morbidity. Significant improvements in quality of life are possible for highly selected individuals with end-stage laryngeal disorders, including laryngeal neoplasia, but further technical and pharmacological developments are required if the technique is to be more widely applicable. An international registry should be created to provide better quality pooled data for analysis of outcomes of any future laryngeal transplants. LEVEL OF EVIDENCE: IV Laryngoscope, 2024.

A Feeding Trial to Investigate Strategies to Mitigate the Impacts of Pimelea Poisoning in Australian Cattle.

Pimelea poisoning of cattle causes distinct symptoms and frequently death, attributable to the toxin simplexin. Pimelea poisoning was induced via addition of ground Pimelea trichostachya plant to the daily feed in a three-month trial with Droughtmaster steers. The trial tested four potential mitigation treatments, namely, biochar, activated biochar, bentonite, and a bacterial inoculum, and incorporated negative and positive control groups. All treatments tested were unable to prevent the development of simplexin poisoning effects. However, steers consuming a bentonite adsorbent together with Pimelea showed lesser rates-of-decline for body weight (P < 0.05) and four hematological parameters (P < 0.02), compared to the positive control group fed Pimelea only. Microbiome analysis revealed that despite displaying poisoning symptoms, the rumen microbial populations of animals receiving Pimelea were very resilient, with dominant bacterial populations maintained over time. Unexpectedly, clinical edema developed in some animals up to 2 weeks after Pimelea dosing was ceased.

Fiberoptic Endoscopy Evaluation of Swallowing (FEES) Findings Associated with High Pneumonia Risk in a Cohort of Patients at Risk of Dysphagia.

Aspiration detected in the fiberoptic endoscopy evaluation of swallowing (FEES) has been inconsistently associated with pneumonia, with no evidence of the risk of pneumonia from other alterations in swallowing safety detected in FEES. We conducted a dynamic, ambidirectional cohort study involving 148 subjects at risk of dysphagia in a tertiary university hospital. Our aim was to determine the risk of pneumonia attributed to alterations in swallowing safety detected during FEES. We used multivariate negative binomial regression models to adjust for potential confounders. The incidence density rate (IR) of pneumonia in patients with tracheal aspiration of any consistency was 26.6/100 people-years (RR 7.25; 95% CI: 3.50-14.98; P < 0.001). The IR was 19.7/100 people-years (RR 7.85; 95% CI: 3.34-18.47; P < 0.001) in those with laryngeal penetration of any consistency and 18.1/100 people-years (RR 6.24; 95% CI: 2.58-15.09; P < 0.001) in those with pharyngeal residue of any consistency. When adjusted for aspiration, the association of residue and penetration with pneumonia disappeared, suggesting that their risk of pneumonia is dependent on the presence of aspiration and that only aspiration is independently associated with pneumonia. This increased risk of pneumonia was significant in uni- and multivariate negative binomial regression models. We found an independently increased risk of pneumonia among patients with dysphagia and aspiration detected during FEES. Alterations in the oral and pharyngeal phases of swallowing, without aspiration, did not increase the risk of pneumonia.

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter.

Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.

A targeted likelihood estimation comparing cefepime and piperacillin/tazobactam in critically ill patients with community-acquired pneumonia (CAP).

Cefepime and piperacillin/tazobactam are antimicrobials recommended by IDSA/ATS guidelines for the empirical management of patients admitted to the intensive care unit (ICU) with community-acquired pneumonia (CAP). Concerns have been raised about which should be used in clinical practice. This study aims to compare the effect of cefepime and piperacillin/tazobactam in critically ill CAP patients through a targeted maximum likelihood estimation (TMLE). A total of 2026 ICU-admitted patients with CAP were included. Among them, (47%) presented respiratory failure, and (27%) developed septic shock. A total of (68%) received cefepime and (32%) piperacillin/tazobactam-based treatment. After running the TMLE, we found that cefepime and piperacillin/tazobactam-based treatments have comparable 28-day, hospital, and ICU mortality. Additionally, age, PTT, serum potassium and temperature were associated with preferring cefepime over piperacillin/tazobactam (OR 1.14 95% CI [1.01-1.27], p = 0.03), (OR 1.14 95% CI [1.03-1.26], p = 0.009), (OR 1.1 95% CI [1.01-1.22], p = 0.039) and (OR 1.13 95% CI [1.03-1.24], p = 0.014)]. Our study found a similar mortality rate among ICU-admitted CAP patients treated with cefepime and piperacillin/tazobactam. Clinicians may consider factors such as availability and safety profiles when making treatment decisions.

A Solar to Chemical Strategy: Green Hydrogen as a Means, Not an End.

Green hydrogen is the key to the chemical industry achieving net zero emissions. The chemical industry is responsible for almost 2% of all CO2 emissions, with half of it coming from the production of simple commodity chemicals, such as NH3, H2O2, methanol, and aniline. Despite electrolysis driven by renewable power sources emerging as the most promising way to supply all the green hydrogen required in the production chain of these chemicals, in this review, it is worth noting that the photocatalytic route may be underestimated and can hold a bright future for this topic. In fact, the production of H2 by photocatalysis still faces important challenges in terms of activity, engineering, and economic feasibility. However, photocatalytic systems can be tailored to directly convert sunlight and water (or other renewable proton sources) directly into chemicals, enabling a solar-to-chemical strategy. Here, a series of recent examples are presented, demonstrating that photocatalysis can be successfully employed to produce the most important commodity chemicals, especially on NH3, H2O2, and chemicals produced by reduction reactions. The replacement of fossil-derived H2 in the synthesis of these chemicals can be disruptive, essentially safeguarding the transition of the chemical industry to a low-carbon economy.

Contrast-induced encephalopathy in patients with advanced chronic kidney disease: What the nephrologist needs to know.

Contrast-induced encephalopathy is a neurological complication related to contrast used in endovascular procedures or computed tomography (CT). The main risk factors are arterial hypertension, diabetes mellitus, chronic kidney disease (CKD), hyperosmolar contrasts, the amount of infused contrast and its direct infusion in the posterior cerebral territory, or pathologies with blood-brain barrier damage. Symptomatology is non-specific and may present as altered level of consciousness, neurological focality or seizures. Diagnosis is done by exclusion after ischemic or hemorrhagic stroke has been ruled out; CT or MRI are useful for differentiation. Generally, it appears shortly after exposure and the symptoms lasts 48-72h with complete recovery, although cases with persistence of symptoms or longer duration have been described. Treatment consists of monitoring, supportive measures and kidney replacement therapy (KRT) with hemodialysis (HD) in patients in chronic KRT program. It is important for the nephrologist to be aware of this entity given the susceptibility of the patient on HD as well as its potential therapeutic role in these patients.

Tumor-Infiltrating T Cells in Skin Basal Cell Carcinomas and Squamous Cell Carcinomas: Global Th1 Preponderance with Th17 Enrichment-A Cross-Sectional Study.

Basal cell carcinomas (BCCs) and squamous cell carcinomas (SCCs) are high-incidence, non-melanoma skin cancers (NMSCs). The success of immune-targeted therapies in advanced NMSCs led us to anticipate that NMSCs harbored significant populations of tumor-infiltrating lymphocytes with potential anti-tumor activity. The main aim of this study was to characterize T cells infiltrating NMSCs. Flow cytometry and immunohistochemistry were used to assess, respectively, the proportions and densities of T cell subpopulations in BCCs (n = 118), SCCs (n = 33), and normal skin (NS, n = 30). CD8+ T cells, CD4+ T cell subsets, namely, Th1, Th2, Th17, Th9, and regulatory T cells (Tregs), CD8+ and CD4+ memory T cells, and γδ T cells were compared between NMSCs and NS samples. Remarkably, both BCCs and SCCs featured a significantly higher Th1/Th2 ratio (~four-fold) and an enrichment for Th17 cells. NMSCs also showed a significant enrichment for IFN-γ-producing CD8+T cells, and a depletion of γδ T cells. Using immunohistochemistry, NMSCs featured denser T cell infiltrates (CD4+, CD8+, and Tregs) than NS. Overall, these data favor a Th1-predominant response in BCCs and SCCs, providing support for immune-based treatments in NMSCs. Th17-mediated inflammation may play a role in the progression of NMSCs and thus become a potential therapeutic target in NMSCs.

Antidiabetic Effect of Passiflora ligularis Leaves in High Fat-Diet/Streptozotocin-Induced Diabetic Mice.

Type 2 diabetes mellitus (T2DM) is a major global public health concern, prompting the ongoing search for new treatment options. Medicinal plants have emerged as one such alternative. Our objective was to evaluate the antidiabetic effect of an extract from the leaves of Passiflora ligularis (P. ligularis). For this purpose, T2DM was first induced in mice using a high-fat diet and low doses of streptozotocin. Subsequently, an aqueous extract or an ethanolic extract of P. ligularis leaves was administered for 21 days. The following relevant results were found: fasting blood glucose levels were reduced by up to 41%, and by 29% after an oral glucose overload. The homeostasis model assessment of insulin resistance (HOMA-IR) was reduced by 59%. Histopathologically, better preservation of pancreatic tissue was observed. Regarding oxidative stress parameters, there was an increase of up to 48% in superoxide dismutase (SOD), an increase in catalase (CAT) activity by 35% to 80%, and a decrease in lipid peroxidation (MDA) by 35% to 80% in the liver, kidney, or pancreas. Lastly, regarding the lipid profile, triglycerides (TG) were reduced by up to 30%, total cholesterol (TC) by 35%, and low-density lipoproteins (LDL) by up to 32%, while treatments increased high-density lipoproteins (HDL) by up to 35%. With all the above, we can conclude that P. ligularis leaves showed antihyperglycemic, hypolipidemic, and antioxidant effects, making this species promising for the treatment of T2DM.

Curve-Modelling and Machine Learning for a Better COPD Diagnosis.

Background: Development of new tools in artificial intelligence has an outstanding performance in the recognition of multidimensional patterns, which is why they have proven to be useful in the diagnosis of Chronic Obstructive Pulmonary Disease (COPD). Methods: This was an observational analytical single-centre study in patients with spirometry performed in outpatient medical care. The segment that goes from the peak expiratory flow to the forced vital capacity was modelled with quadratic polynomials, the coefficients obtained were used to train and test neural networks in the task of classifying patients with COPD. Results: A total of 695 patient records were included in the analysis. The COPD group was significantly older than the No COPD group. The pre-bronchodilator (Pre BD) and post-bronchodilator (Post BD) spirometric curves were modelled with a quadratic polynomial, and the coefficients obtained were used to feed three neural networks (Pre BD, Post BD and all coefficients). The best neural network was the one that used the post-bronchodilator coefficients, which has an input layer of 3 neurons and three hidden layers with sigmoid activation function and two neurons in the output layer with softmax activation function. This system had an accuracy of 92.9% accuracy, a sensitivity of 88.2% and a specificity of 94.3% when assessed using expert judgment as the reference test. It also showed better performance than the current gold standard, especially in specificity and negative predictive value. Conclusion: Artificial Neural Networks fed with coefficients obtained from quadratic and cubic polynomials have interesting potential of emulating the clinical diagnostic process and can become an important aid in primary care to help diagnose COPD in an early stage.

Lytic transglycosylase Slt of Pseudomonas aeruginosa as a periplasmic hub protein.

Peptidoglycan is a major constituent of the bacterial cell wall. Its integrity as a polymeric edifice is critical for bacterial survival and, as such, it is a preeminent target for antibiotics. The peptidoglycan is a dynamic crosslinked polymer that undergoes constant biosynthesis and turnover. The soluble lytic transglycosylase (Slt) of Pseudomonas aeruginosa is a periplasmic enzyme involved in this dynamic turnover. Using amber-codon-suppression methodology in live bacteria, we incorporated a fluorescent chromophore into the structure of Slt. Fluorescent microscopy shows that Slt populates the length of the periplasmic space and concentrates at the sites of septation in daughter cells. This concentration persists after separation of the cells. Amber-codon-suppression methodology was also used to incorporate a photoaffinity amino acid for the capture of partner proteins. Mass-spectrometry-based proteomics identified 12 partners for Slt in vivo. These proteomics experiments were complemented with in vitro pulldown analyses. Twenty additional partners were identified. We cloned the genes and purified to homogeneity 22 identified partners. Biophysical characterization confirmed all as bona fide Slt binders. The identities of the protein partners of Slt span disparate periplasmic protein families, inclusive of several proteins known to be present in the divisome. Notable periplasmic partners (KD < 0.5 µM) include PBPs (PBP1a, KD = 0.07 µM; PBP5 = 0.4 µM); other lytic transglycosylases (SltB2, KD = 0.09 µM; RlpA, KD = 0.4 µM); a type VI secretion system effector (Tse5, KD = 0.3 µM); and a regulatory protease for alginate biosynthesis (AlgO, KD < 0.4 µM). In light of the functional breadth of its interactome, Slt is conceptualized as a hub protein within the periplasm.

Clinical utility of rapid shallow breathing index in predicting successful weaning: secondary analysis of the COBRE-US trial.

OBJECTIVE: To assess the predictive capacity of the Rapid Shallow Breathing Index (RSBI) for success in spontaneous breathing trials (SBT) and extubation in critically ill patients. We evaluated the association between RSBI, duration of mechanical ventilation, and ventilator-free time at 28 days. DESIGN: Prospective multicenter observational study. Secondary analysis of the COBRE-US study. SETTING: Intensive care unit (ICU). PATIENTS OR PARTICIPANTS: 367 patients in the ICU receiving invasive mechanical ventilation. INTERVENTIONS: Assessment of RSBI at the end of SBT. MAIN VARIABLES OF INTEREST: RSBI, SBT, duration of mechanical ventilation, and ventilator-free time at 28 days were evaluated. RESULTS: 367 patients in the ICU under invasive mechanical ventilation were evaluated, of whom 59.7% were male with a median age of 61 years (IQR: 49-72). A total of 456 SBT were conducted with a success rate of 76.5%. RSBI had a ROC-curve of 0.53 for SBT success and a ROC-curve of 0.48 for extubation. The Spearman correlation coefficient between RSBI and duration of ventilation was 0.117 (p = 0.026), while for ventilator-free time at 28 days, it was -0.116 (p = 0.028). CONCLUSIONS: RSBI was not associated with success in SBT or extubation, regardless of the cutoff point used. Correlation analyses showed weak associations between RSBI and both the duration of ventilation and ventilator-free time at 28 days.

Dynamics and features of transmission clusters of HIV-1 subtypes in the state of São Paulo, Brazil.

Background: Molecular epidemiology techniques allow us to track the HIV-1 transmission dynamics. Herein, we combined genetic, clinical and epidemiological data collected during routine clinical treatment to evaluate the dynamics and characteristics of transmission clusters of the most prevalent HIV-1 subtypes in the state of São Paulo, Brazil. Methods: This was a cross-sectional study conducted with 2,518 persons living with HIV (PLWH) from 53 cities in São Paulo state between Jan 2004 to Feb 2015. The phylogenetic tree of protease/reverse transcriptase (PR/RT) regions was reconstructed by PhyML and ClusterPicker used to infer the transmission clusters based on Shimodaira-Hasegawa (SH) greater than 90% (phylogenetic support) and genetic distance less than 6%. Results: Of a total of 2,518 sequences, 2,260 were pure subtypes at the PR/RT region, being B (88%), F1 (8.1%), and C (4%). About 21.2% were naïve with a transmitted drug resistance (TDR) rate of 11.8%. A total of 414 (18.3%) of the sequences clustered. These clusters were less evident in subtype B (17.7%) and F1 (15.1%) than in subtype C (40.2%). Clustered sequences were from PLWH at least 5 years younger than non-clustered among subtypes B (p < 0.001) and C (p = 0.037). Men who have sex with men (MSM) predominated the cluster in subtype B (51%), C (85.7%), and F1 (63.6%; p < 0.05). The TDR rate in clustered patients was 15.4, 13.6, and 3.1% for subtypes B, F1, and C, respectively. Most of the infections in subtypes B (80%), C (64%), and F1 (59%) occurred within the state of São Paulo. The metropolitan area of São Paulo presented a high level of endogenous clustering for subtypes B and C. The São Paulo city had 46% endogenous clusters of subtype C. Conclusion: Our findings showed that MSM, antiretroviral therapy in Treatment-Naive (ART-naïve) patients, and HIV1-C, played an important role in the HIV epidemic in the São Paulo state. Further studies in transmission clusters are needed to guide the prevention intervention.