A solution to achieve sequencing from SARS-CoV-2 specimens with low viral loads: concatenation of reads from independent reactions.

BACKGROUND: During the pandemic, whole genome sequencing was critical to characterize SARS-CoV-2 for surveillance, clinical and therapeutical purposes. However, low viral loads in specimens often led to suboptimal sequencing, making lineage assignment and phylogenetic analysis difficult. We propose an alternative approach to sequencing these specimens that involves sequencing in triplicate and concatenation of the reads obtained using bioinformatics. This proposal is based on the hypothesis that the uncovered regions in each replicate differ and that concatenation would compensate for these gaps and recover a larger percentage of the sequenced genome. RESULTS: Whole genome sequencing was performed in triplicate on 30 samples with Ct > 32 and the benefit of replicate read concatenation was assessed. After concatenation: i) 28% of samples reached the standard quality coverage threshold (> 90% genome covered > 30x); ii) 39% of samples did not reach the coverage quality thresholds but coverage improved by more than 40%; and iii) SARS-CoV-2 lineage assignment was possible in 68.7% of samples where it had been impaired. CONCLUSIONS: Concatenation of reads from replicate sequencing reactions provides a simple way to access hidden information in the large proportion of SARS-CoV-2-positive specimens eliminated from analysis in standard sequencing schemes. This approach will enhance our potential to rule out involvement in outbreaks, to characterize reinfections and to identify lineages of concern for surveillance or therapeutical purposes.

Influence of diabetes and other risk factors on in-hospital mortality following kidney transplantation: an analysis of the Spanish National Hospital Discharge Database from 2016 to 2020.

INTRODUCTION: To assess time trends in incidence, clinical characteristics, complications, and hospital outcomes among patients with type 1 diabetes (T1D), with type 2 diabetes (T2D), and patients without diabetes who underwent kidney transplant (KT); to identify variables associated with in-hospital mortality (IHM); and to determine the impact of the COVID-19 pandemic. RESEARCH DESIGN AND METHODS: We used a nationwide discharge database to select KT recipients admitted to Spanish hospitals from 2016 to 2020. We stratified patients according to diabetes status. We used multivariable logistic regression to identify the variables associated with IHM. RESULTS: A total of 14 594 KTs were performed in Spain (T2D, 22.28%; T1D, 3.72%). The number of KTs rose between 2016 and 2019 and and decreased from 2019 to 2020 in all groups. In patients with T2D, the frequency of KT complications increased from 21.08% in 2016 to 34.17% in 2020 (p<0.001). Patients with T2D had significantly more comorbidity than patients with T1D and patients without diabetes (p<0.001). Patients with T1D experienced KT rejection significantly more frequently (8.09%) than patients with T2D (5.57%).COVID-19 was recorded in 26 out of the 2444 KTs performed in 2020, being found in 6 of the 39 patients deceased that year (15.38%) and in 0.83% of the survivors.The variables associated with IHM were comorbidity and complications of KT. The presence of T1D was associated with IHM (OR 2.6; 95% CI 1.36 to 5.16) when patients without diabetes were the reference category. However, T2D was not associated with a higher IHM (OR 0.86; 95% CI 0.61 to 1.2). CONCLUSIONS: The COVID-19 pandemic led to a decrease in the number of transplants. Patients with T1D have more rejection of the transplanted organ than patients with T2D. Fewer women with T2D undergo KT. The presence of T1D is a risk factor for IHM.

An Acute Infection due to Hepatitis E in the Context of a Patient with Rituximab and Methotrexate Therapy.

Background: This report presents the influence of immunosuppression by new rheumatological therapies on hepatitis E virus infection in a 54-year-old male patient with an anti-synthetase syndrome and treatment with methotrexate and rituximab. Case description: The patient arrived at the Emergency Department with epigastric pain, vomiting and dark urine. Initial examination revealed signs of inflammation and hepatic dysfunction. Subsequent laboratory tests and imaging confirmed acute hepatitis E infection in the context of recent initiation of rituximab therapy. Despite initial suspicion of pancreatitis, subsequent investigations ruled out pancreatic involvement. Treatment with ribavirin, along with supportive measures, led to significant clinical improvement with resolution of jaundice, ascites, and oedema. Conclusions: This case underscores the importance of considering hepatitis E in patients with autoimmune conditions, especially when initiating immunosuppressive therapies, a situation that is not well described in scientific literature and is increasingly common, necessitating proper recognition. LEARNING POINTS: Suspect hepatitis E virus infection in the presence of persistent liver failure of unknown cause.Recognise immunosuppression as a cause of increased risk of hepatitis E infection.Take into account the repercussions of immunosuppressive therapy such as rituximab regarding hepatitis E infections in immunocompromised patients.

Accelerating SARS-CoV-2 genomic surveillance in a routine clinical setting with nanopore sequencing.

BACKGROUND: SARS-CoV-2 genomic analysis has been key to the provision of valuable data to meet both epidemiological and clinical demands. High-throughput sequencing, generally Illumina-based, has been necessary to ensure the widest coverage in global variant tracking. However, a speedier response is needed for nosocomial outbreak analyses and rapid identification of patients infected by emerging VOCs. An alternative based on nanopore sequencing may be better suited to delivering a faster response when required; however, although there are several studies offering side-by-side comparisons of Illumina and nanopore sequencing, evaluations of the usefulness in the hospital routine of the faster availability of data provided by nanopore are still lacking. RESULTS: We performed a prospective 10-week nanopore-based sequencing in MinION in a routine laboratory setting, including 83 specimens where a faster response time was necessary. The specimens analyzed corresponded to i) international travellers in which lineages were assigned to determine the proper management/special isolation of the patients; ii) nosocomial infections and health-care-worker infections, where SNP-based comparisons were required to rule in/out epidemiological relationships and tailor specific interventions iii) sentinel cases and breakthrough infections to timely report to the Public Health authorities. MinION-based sequencing was compared with the standard procedures, supported on Illumina sequencing; MinION accelerated the delivery of results (anticipating results 1-12 days) and reduced costs per sample by 28€ compared to Illumina, without reducing accuracy in SNP calling. CONCLUSIONS: Parallel integration of Illumina and nanopore sequencing strategies is a suitable solution to ensure both high-throughput and rapid response to cope with accelerating the surveillance demands of SARS-CoV-2 while also maintaining accuracy.

Alternative molecular and genomic strategies to provide a rapid response to alerts concerning the introduction of new emerging SARS-CoV-2 variants: the Omicron alert.

During the COVID-19 pandemic, several SARS-CoV-2 variants of concern (VOCs) of particular relevance emerged. Early detection of VOCs entering a country is essential to control spread. The alert triggered by the first suspected case of the Omicron variant in Spain in a traveler arriving from South Africa in November 2021 provided a unique opportunity to evaluate four different methodological strategies tailored to rapid identification of Omicron. The different approaches were designed to respond to the different technical resources available in different settings. First, we used melting probes in RT-PCR to determine the presence of four Omicron signatures (K417N, E484A, P681H, and absence of L452R): three probes showed deviations in temperature (Tm) values relative to the reference codons (E484K-15.8°C, P681H-5.2°C, and L452R-7.2°C) and one maintained the reference value (K417N). The deviation in Tm of P681H suggested the presence of the characteristic Omicron N679K mutation in the probe hybridization region; these data pointed to the presence of Omicron alleles. Second, the presence of 29 of the 33 characteristic single nucleotide polymorphisms (SNPs) in the Omicron variant S-gene was identified by Sanger sequencing of nine amplicons. The final two strategies involved identification of 47 of the 50 non-synonymous and indel mutations attributed to Omicron by rapid nanopore whole genome sequencing (WGS) and by Illumina WGS technology. These strategies enabled us to pre-assign the first Omicron case in Spain with high certainty 2 h after receipt of RNA and to confirm it genomically 3 h later, so that the Public Health authorities could be rapidly notified. IMPORTANCE The study presents different experimental alternatives to identify new variants of concern (VOCs) of SARS-CoV-2 entering a certain population. Early detection of a new VOC is crucial for surveillance and control of spread. The objective is to provide laboratories with tools adapted to their resource capabilities that offer a sufficient level of resolution to rule out, confirm, or pre-assign the presence of a suspected VOC. The study describes four different techniques that were applied simultaneously to the first suspected Omicron case in Spain, highlighting the level of resolution and response time achieved in each case. These techniques are based on the detection of mutations in the S-gene of the virus that can easily adapt to potential emerging variants. The results of the study allow any laboratory to prepare for new alerts of SARS-CoV-2 VOCs.

Systematic genomic analysis of SARS-CoV-2 co-infections throughout the pandemic and segregation of the strains involved.

BACKGROUND: SARS-CoV-2 recombinants involving the divergent Delta and Omicron lineages have been described, and one of them, "Kraken" (XBB.1.5), has recently been a matter of concern. Recombination requires the coexistence of two SARS-CoV-2 strains in the same individual. Only a limited number of studies have focused on the identification of co-infections and are restricted to co-infections involving the Delta/Omicron lineages. METHODS: We performed a systematic identification of SARS-CoV-2 co-infections throughout the pandemic (7609 different patients sequenced), not biassed towards the involvement of highly divergent lineages. Through a comprehensive set of validations based on the distribution of allelic frequencies, phylogenetic consistency, re-sequencing, host genetic analysis and contextual epidemiological analysis, these co-infections were robustly assigned. RESULTS: Fourteen (0.18%) co-infections with ≥ 8 heterozygous calls (8-85 HZs) were identified. Co-infections were identified throughout the pandemic and involved an equal proportion of strains from different lineages/sublineages (including pre-Alpha variants, Delta and Omicron) or strains from the same lineage. Co-infected cases were mainly unvaccinated, with mild or asymptomatic clinical presentation, and most were at risk of overexposure associated with the healthcare environment. Strain segregation enabled integration of sequences to clarify nosocomial outbreaks where analysis had been impaired due to co-infection. CONCLUSIONS: Co-infection cases were identified throughout the pandemic, not just in the time periods when highly divergent lineages were co-circulating. Co-infections involving different lineages or strains from the same lineage were occurring in the same proportion. Most cases were mild, did not require medical assistance and were not vaccinated, and a large proportion were associated with the hospital environment.

Early SARS-CoV-2 Reinfections Involving the Same or Different Genomic Lineages, Spain.

Centers for Disease Control and Prevention guidelines consider SARS-CoV-2 reinfection when sequential COVID-19 episodes occur >90 days apart. However, genomic diversity acquired over recent COVID-19 waves could mean previous infection provides insufficient cross-protection. We used genomic analysis to assess the percentage of early reinfections in a sample of 26 patients with 2 COVID-19 episodes separated by 20-45 days. Among sampled patients, 11 (42%) had reinfections involving different SARS-CoV-2 variants or subvariants. Another 4 cases were probable reinfections; 3 involved different strains from the same lineage or sublineage. Host genomic analysis confirmed the 2 sequential specimens belonged to the same patient. Among all reinfections, 36.4% involved non-Omicron, then Omicron lineages. Early reinfections showed no specific clinical patterns; 45% were among unvaccinated or incompletely vaccinated persons, 27% were among persons <18 years of age, and 64% of patients had no risk factors. Time between sequential positive SARS-CoV-2 PCRs to consider reinfection should be re-evaluated.

A One Health approach revealed the long-term role of Mycobacterium caprae as the hidden cause of human tuberculosis in a region of Spain, 2003 to 2022.

IntroductionMycobacterium caprae is a member of the Mycobacterium tuberculosis complex (MTBC) not routinely identified to species level. It lacks specific clinical features of presentation and may therefore not be identified as the causative agent of tuberculosis. Use of whole genome sequencing (WGS) in the investigation of a family microepidemic of tuberculosis in Almería, Spain, unexpectedly identified the involvement of M. caprae.AimWe aimed to evaluate the presence of additional unidentified M. caprae cases and to determine the magnitude of this occurrence.MethodsFirst-line characterisation of the MTBC isolates was done by MIRU-VNTR, followed by WGS. Human and animal M. caprae isolates were integrated in the analysis.ResultsA comprehensive One Health strategy allowed us to (i) detect other 11 M. caprae infections in humans in a period of 18 years, (ii) systematically analyse M. caprae infections on an epidemiologically related goat farm and (iii) geographically expand the study by including 16 M. caprae isolates from other provinces. Integrative genomic analysis of 41 human and animal M. caprae isolates showed a high diversity of strains. The animal isolates' diversity was compatible with long-term infection, and close genomic relationships existed between isolates from goats on the farm and recent cases of M. caprae infection in humans.DiscussionZoonotic circulation of M. caprae strains had gone unnoticed for 18 years. Systematic characterisation of MTBC at species level and/or extended investigation of the possible sources of exposure in all tuberculosis cases would minimise the risk of overlooking similar zoonotic events.

Rapid Identification of Relevant Microbial Strains by Identifying Multiple Marker Single Nucleotide Polymorphisms via Amplicon Sequencing: Epidemic Monkeypox Virus as a Proof of Concept.

Despite the proven value of applying genomic data for epidemiological purposes, commonly used high-throughput sequencing formats are not adapted to the response times required to intervene and finally control outbreaks. In this study, we propose a fast alternative to whole-genome sequencing (WGS) to track relevant microbiological strains: nanopore sequencing of multiple amplicons including strain marker single nucleotide polymorphisms (SNPs). As a proof a concept, we evaluated the performance of our approach to offer a rapid response to the most recent public health global alarm, the monkeypox virus (MPXV) global outbreak. Through a multisequence alignment, a list of 42 SNPs were extracted as signature makers for this outbreak. Twenty primer pairs were designed to amplify in a multiplex PCR the regions including 22 of these SNPs. Amplicon pools were sequenced in a MinION device, and SNPs were called in real time by an in-house bioinformatic pipeline. A total of 120 specimens (95 MPXV-PCR positive, Ct values from 14 to 39) were selected. In 67.37% of the positive subset, all 22 SNPs were called. After excluding low viral load specimens, in 92% of samples ≥11 outbreak SNPs were called. No false positives were observed in any of the 25 negative specimens. The total turnaround time required for this strategy was 5 hours, and the cost per sample was 14 euros. Nanopore sequencing of multiple amplicons harboring signature SNPs escapes the targeting limitations of strain-specific PCRs and offers a powerful alternative to systematic WGS, paving the way to real-time genomic epidemiology and making immediate intervention possible to finally optimize transmission control. IMPORTANCE Nanopore sequencing of multiple amplicons harboring signature single nucleotide polymorphisms (SNPs) escapes the targeting limitations of strain-specific PCRs and offers a powerful alternative to systematic whole-genome analysis, paving the way to real-time genomic epidemiology and making immediate intervention possible to finally optimize transmission control.

Association of blood-based biomarkers with radiologic markers and cognitive decline in atrial fibrillation patients.

BACKGROUND: Atrial fibrillation (AF) has been associated with an increased risk of silent brain infarcts (SBI) and cognitive impairment, even in patients with low embolic risk. We aimed to test the association between 11 blood-biomarkers representing different AF-related pathways, and SBI, white matter hyperintensities (WMH), and cognitive decline in patients with AF and low embolic risk. METHODS: The present study followed a cross-sectional design. 70 patients with a history of AF and CHADS2 score ≤1, and 10 controls with neither AF nor SBI were included. All patients underwent a 3T brain MRI. Cortical and large subcortical ischemic lesions were considered presumed embolic origin lesions. White matter hyperintensities (WMH) were measured according to the Fazekas scale. A subset of patients underwent cognitive evaluation with the MoCA test. Circulating proteins were measured under blind conditions in a laboratory at Roche Diagnostics, Germany. RESULTS: 45 patients presented SBI in the MRI, and 25 did not. Ang-2, FGF-23, and BMP-10 were increased in patients with SBI. Ang-2 was elevated only in patients with embolic infarcts, whereas FGF-23 and BMP-10 tended to be elevated in patients with both types of infarcts. Ang-2 (OR = 1.56 [0.94-2.59], p = 0.087), and BMP-10 (OR = 4.83 [0.99-23.60], p = 0.052) were the biomarkers that showed the highest association with SBI when entered in a multivariable logistic regression model corrected by age. No biomarker was found associated with WMH or mild cognitive impairment. CONCLUSIONS: BMP-10, and Ang-2 were increased in patients with SBI. Its usefulness to detect SBI in AF patients should be further explored.

Sex Differences in COVID-19 Hospitalization and Hospital Mortality among Patients with COPD in Spain: A Retrospective Cohort Study.

(1) Background: We aimed to assess the effect of COPD in the incidence of hospital admissions for COVID-19 and on the in-hospital mortality (IHM) according to sex. (2) Methods: We used national hospital discharge data to select persons aged ≥40 years admitted to a hospital with a diagnosis of COVID-19 in 2020 in Spain. (3) Results: The study population included 218,301 patients. Age-adjusted incidence rates of COVID-19 hospitalizations for men with and without COPD were 10.66 and 9.27 per 1000 persons, respectively (IRR 1.14; 95% CI 1.08−1.20; p < 0.001). The IHM was higher in men than in women regardless of the history of COPD. The COPD was associated with higher IHM among women (OR 1.09; 95% CI 1.01−1.22) but not among men. The COPD men had a 25% higher risk of dying in the hospital with COVID-19 than women with COPD (OR 1.25, 95% CI 1.1−1.42). (4) Conclusions: Sex differences seem to exist in the effect of COPD among patients suffering COVID-19. The history of COPD increased the risk of hospitalization among men but not among women, and COPD was only identified as a risk factor for IHM among women. In any case, we observed that COPD men had a higher mortality than COPD women. Understanding the mechanisms underlying these sex differences could help predict the patient outcomes and inform clinical decision making to facilitate early treatment and disposition decisions.

Angiosarcoma of the aorta diagnosed via endoscopic ultrasound.

A 54-year-old man consulted for low back pain of 5 weeks of evolution, refractory to regular analgesics, and significant weight loss. The PET-CT revealed a retroperitoneal mass in contact with the anterior wall of the abdominal aorta. After consulting with the Endoscopy Unit, an endoscopic ultrasound-guided FNAP was performed due to the accessibility of the lesion and the less invasive nature of these procedures. The anatomopathological result was angiosarcoma of the aorta.

Non-alcoholic beverage and fast-food consumption, among first- and fourth-year nursing students in Madrid

Sugar-sweetened beverages and fast-food consumption have been associated with non-communicable diseases. Objective. Was to analyze consumption of non-alcoholic beverage and fast-food consumption among first- and fourth-year nursing students. Materials and methods. A questionnaire-based survey was conducted among first-and fourth-year nursing students in Madrid, Spain. Anthropometric data (weight and height) and demographic data were collected, as were data on consumption of specific foods and beverages. Results. The survey was completed by 436 students. Mean (SD) age was 22.0 (6.8) years, 84.1 % of were women.26.2 % of the students were underweight; 6.3 % were overweight. Consumption of sugar-sweetened beverages and diet drinks was moderate. Slightly more than three-quarters of the students (75.5 %) purchased fast food in the previous month. Burger bars were the most frequently visited fast-food outlet (77.2 %). A direct relationship was observed between BMI and fast-food consumption (rho = 0.099; p = 0.042) and between BMI and consumption of diet cola or carbonated drinks (rho = 0.120; p = 0.013). Conclusion. We provide new epidemiological data from a specific university population that could be useful to promote more studies that help design appropriate strategies to increase a healthy lifestyle(AU)

Las bebidas azucaradas y el consumo de comida rápida se han asociado con enfermedades no transmisibles. Objetivo. Analizar el consumo de bebidas no alcohólicas y el consumo de comida rápida entre estudiantes universitarios de primer y cuarto curso de enfermería. Materiales y métodos. Cuestionario validado entre estudiantes de enfermería de primer y cuarto año en Madrid, España. Se recopilaron datos antropométricos (peso y altura) y demográficos, así como datos sobre consumo de alimentos y bebidas específicos. Resultados. La encuesta fue completada por 436 estudiantes. La edad media (DE) fue de 22,0 (6,8) años, el 84,1 % eran mujeres; el 26,2 % de los estudiantes tenían bajo peso y el 6,3% mostraban sobrepeso. El consumo de bebidas azucaradas y bebidas dietéticas fue moderado. Más de tres cuartas partes de estudiantes (75,5%) compraron comida rápida en el mes anterior. Las hamburgueserías fueron el restaurante de comida rápida más visitado (77,2%). Se observó una relación directa entre el IMC y el consumo de comida rápida (rho = 0,099; p = 0,042) y entre el IMC y el consumo de refrescos dietéticos o bebidas gaseosas (rho = 0,120; p = 0,013). Conclusión. Aportamos nuevos datos epidemiológicos de una población universitaria concreta, que podrían ser de utilidad para promover más estudios que ayuden a diseñar estrategias adecuadas para incrementar un estilo de vida saludable(AU)

Nosocomial Transmission of SARS-CoV-2 Involving Vaccinated Health Care Workers.

COVID-19 vaccination has proven to be effective at preventing symptomatic disease but there are scarce data to fully understand whether vaccinated individuals can still behave as SARS-CoV-2 transmission vectors. Based on viral genome sequencing and detailed epidemiological interviews, we report a nosocomial transmission event involving two vaccinated health care-workers (HCWs) and four patients, one of them with fatal outcome. Strict transmission control measures, as during the prevaccination period, must be kept between HCWs and HCWs-patients in nosocomial settings. IMPORTANCE COVID-19 vaccination has proven to be effective at preventing symptomatic disease. Although some transmission events involving vaccinated cases have also been reported, scarce information is still available to fully understand whether vaccinated individuals may still behave as vectors in SARS-CoV-2 transmission events. Here, we report a SARS-CoV-2 nosocomial transmission event, supported on whole genome sequencing, in early March 2021 involving two vaccinated HCWs and four patients in our institution. Strict transmission control measures between HCWs and HCWs - patients in nosocomial settings must not be relaxed, and should be kept as strictly as during the prevaccination period.

Recurrences of multidrug-resistant tuberculosis: Strains involved, within-host diversity, and fine-tuned allocation of reinfections.

Recurrent tuberculosis occurs due to exogenous reinfection or reactivation/persistence. We analysed 90 sequential MDR Mtb isolates obtained in Argentina from 27 patients with previously diagnosed MDR-TB that recurred in 2018 (1-10 years, 2-10 isolates per patient). Three long-term predominant strains were responsible for 63% of all MDR-TB recurrences. Most of the remaining patients were infected by strains different from each other. Reactivation/persistence of the same strain caused all but one recurrence, which was due to a reinfection with a predominant strain. One of the prevalent strains showed marked stability in the recurrences, while in another strain higher SNP-based diversity was observed. Comparisons of intra- versus inter-patient SNP distances identified two possible reinfections with closely related variants circulating in the community. Our results show a complex scenario of MDR-TB infections in settings with predominant MDR Mtb strains.

Overlapping prison/community tuberculosis outbreaks in Costa Rica revealed by alternative analysis of suboptimal material.

Costa Rica has a low incidence of tuberculosis. Thus, identifying transmission hotspots is key to implement interventions. A tuberculosis outbreak was suspected in a prison in Costa Rica. Given the suboptimal quality of the samples received in our laboratory in Madrid, we applied alternative schemes for their analysis. In the first scheme, we bypassed the standard approach of applying systematic mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and used a strain-specific polymerase chain reaction (PCR) that allowed identifying a cluster involving six cases (C1). The second scheme followed the canonical MIRU-VNTR path coupled with a whole-genomic amplification step, by which a second unsuspected overlapping cluster (C2), was detected in the same prison. These findings justified the implementation of a surveillance programme adapted to local resources based on a tailored multiplex allele-specific oligonucleotide (ASO)-PCR targeting C1 and C2. Presence of the C2 strain at a different prison was determined. ASO-PCR was applied extensively and alerted to the active circulation of one of the strains within and beyond prisons. Our study shows that alternative methodological strategies may provide useful data in settings with lack of resources for performing systematic standard molecular epidemiology programmes and/or with suboptimal material for analysis.

SARS-CoV-2 superinfection and reinfection with three different strains.

We report a corona virus disease (COVID-19) case with unprecedented viral complexity. In the first severe episode, two different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains (superinfection) were identified within a week. Three months after discharge, the patient was readmitted and was infected in a nosocomial outbreak with a different strain, suffering a second milder COVID-19 episode.

Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy.

Detection of mixed Mycobacterium tuberculosis (MTB) infections is essential, particularly when resistance mutations are present in minority bacterial populations that may affect patients' disease evolution and treatment. Whole-genome sequencing (WGS) has extended the amount of key information available for the diagnosis of MTB infection, including the identification of mixed infections. Having genomic information at diagnosis for early intervention requires carrying out WGS directly on the clinical samples. However, few studies have been successful with this approach due to the low representation of MTB DNA in sputa. In this study, we evaluated the ability of a strategy based on specific MTB DNA enrichment by using a newly designed capture platform (MycoCap) to detect minority variants and mixed infections by WGS on controlled mixtures of MTB DNAs in a simulated sputum genetic background. A pilot study was carried out with 12 samples containing 98% of a DNA pool from sputa of patients without MTB infection and 2% of MTB DNA mixtures at different proportions. Our strategy allowed us to generate sequences with a quality equivalent to those obtained from culture: 62.5× depth coverage and 95% breadth coverage (for at least 20× reads). Assessment of minority variant detection was carried out by manual analysis and allowed us to identify heterozygous positions up to a 95:5 ratio. The strategy also automatically distinguished mixed infections up to a 90:10 proportion. Our strategy efficiently captures MTB DNA in a nonspecific genetic background, allows detection of minority variants and mixed infections, and is a promising tool for performing WGS directly on clinical samples. IMPORTANCE We present a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by whole-genome sequencing. The objective of the strategy is the direct detection in patient sputum; in this way, minority populations of resistant strains can be identified at the time of diagnosis, facilitating identification of the most appropriate treatment for the patient from the first moment. For this, a platform for capturing M. tuberculosis-specific DNA was designed to enrich the clinical sample and obtain quality sequences.

Sex Differences in Hospital-Acquired Pneumonia among Patients with Type 2 Diabetes Mellitus Patients: Retrospective Cohort Study using Hospital Discharge Data in Spain (2016-2019).

(1) Background: To analyze the incidence, clinical characteristics, use of procedures, and in-hospital outcomes in patients who developed pneumonia during their hospital admission according to sex and to the presence of type 2 diabetes mellitus (T2DM). (2) Methods: Retrospective cohort study using data from the Spanish National Hospital Discharge Database. Hospital-acquired pneumonia (HAP) was classed as non-ventilator HAP and ventilator-associated pneumonia (VAP). Separate analyses were performed for men and women with and without T2DM. Population subgroups were compared using propensity score matching. (3) Results: HAP was identified in 38,814 patients (24.07% with T2DM). The adjusted incidence of HAP was higher in patients with T2DM (both sexes) (IRR 1.28; 95% CI 1.25-1.31). The incidence of HAP was higher in men with T2DM than in women with T2DM (adjusted-IR 1.47; 95% CI 1.41-1.53). The incidence of HAP among T2DM patients increased over time. In-hospital mortality (IHM) was around 28% irrespective of T2DM status and sex. After adjusting for confounders and sex, VAP was associated to higher IHM among patients with T2DM (OR 2.09; 95% CI 1.7-2.57). (4) Conclusions: T2DM is associated with a higher risk of HAP, whose incidence increased over time. Men with T2DM have an almost 50% higher risk of HAP than women with T2DM. The probability of dying in the hospital was not associated with sex or T2DM.

Community-Acquired Pneumonia among Patients with COPD in Spain from 2016 to 2019. Cohort Study Assessing Sex Differences in the Incidence and Outcomes Using Hospital Discharge Data.

BACKGROUND: To describe and analyze the incidence and hospital outcomes of patients admitted with community-acquired pneumonia (CAP) according to Chronic Obstructive Pulmonary Disease (COPD) status and sex in Spanish hospitals from 2016 to 2019. METHODS: We conducted a cohort study using national hospital discharge data of all patients ≥40 years with CAP. RESULTS: A total of 500,833 patients (59.0% men) was identified. Incidence of CAP increased over time. Age-adjusted incidence was 4.42-times higher in COPD patients. In-hospital mortality (IHM) was lower in men and women with COPD than in those without COPD (14.41% vs. 10.70% in men; 11.12% vs. 8.58%. in women; p < 0.001). The risk of dying in hospital increased with age, presence of several comorbidities (excluding T2DM that was a protective factor), and need for mechanical ventilation (non-invasive and invasive) during admission, irrespective of sex. Over time, the IHM decreased significantly in men and women with COPD. Men with COPD were significantly more likely to die in hospital than were COPD women (OR 1.13; 95% CI 1.07-1.21). CONCLUSIONS: Incidence of CAP was higher among subjects with COPD, although the effect of COPD was higher in men than in women. By contrast, IHM was lower in COPD patients, but men with COPD were significantly more likely to die in hospital than were COPD women.