Optimizing next-generation sequencing efficiency in clinical settings: analysis of read length impact on cost and performance.

BACKGROUND: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification. RESULTS: Our findings revealed that moving from 75 bp to 150 bp read length approximately doubles both the cost and sequencing time. Opting for 300 bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75 bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75 bp reads to 100% with 150-300 bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75 bp, 95% with 150 bp, and 97% with 300 bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa. CONCLUSIONS: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75 bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability.

Impact of high-concentrate diets with cottonseed associated with calcium lignosulfonate on the metabolic, productive, and carcass characteristics of feedlot lambs.

This study aimed to evaluate the metabolic, productive, and carcass parameters of feedlot lambs fed high-concentrate diets with cottonseed associated with calcium lignosulfonate. Treatments consisted of diets including whole cottonseed, crushed cottonseed, whole cottonseed with lignosulfonate (100 g/kg), crushed cottonseed with lignosulfonate (100 g/kg), and a control diet without cottonseed. Thirty ½ Dorper ½ Santa Inês, non-castrated male lambs with an average live weight of 24.9 ± 3.6 kg and an average age of 3.5 months were evaluated in a completely randomized design. There was no effect (P > 0.05) on the intakes of dry matter, organic matter, crude protein, and non-fibrous carbohydrates. The crushing of cottonseed and association with lignosulfonate increased (P < 0.01) the intake and digestibility of ether extract. No effect was observed (P > 0.05) for the concentrations of urine and plasma urea N, which averaged 616.2 and 108.6 mg/dL, respectively. There was a change (P < 0.01) in nitrogen balance for digested N in g/day. There was no effect (P > 0.05) on the urinary concentration of purine derivatives, except for uric acid excretions (P < 0.05). Lignosulfonate associated with cottonseed provided an average daily gain of 0.293 kg/day, which was higher than the 0.226 kg/day obtained without lignosulfonate, but lower than control (0.302 kg/day), which also showed higher values of carcass yield. High-concentrate diets formulated without cottonseed improve lamb production performance. The use of high-concentrate diets with cottonseed associated with calcium lignosulfonate provides greater weight gains in lambs.

Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.

OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment. RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.

Effect of high-concentrate diets with calcium lignosulfonate and cottonseed processing method on quantitative traits and non-carcass components of feedlot cull ewes.

This study examined the effects of cottonseed processing form and the inclusion of calcium lignosulfonate in high-concentrate diets for feedlot cull ewes on carcass traits and non-carcass components. Thirty Santa Inês cull ewes with an average body weight of 44.2  ±  5.2 kg and an average age of 50 months were distributed into collective stalls in a completely randomized design. The treatments consisted of diets including whole cottonseed, crushed cottonseed, whole cottonseed treated with lignosulfonate (100 g/kg, as fed), crushed cottonseed treated with lignosulfonate (100 g/kg, as fed), and a control diet without cottonseed. The experimental diets did not influence ( P > 0.05 ) average daily weight gain (0.195 kg/day), slaughter weight (51.74 kg), or in vivo biometric and on-carcass measurements. There was no difference ( P > 0.05 ) in loin-eye area or subcutaneous fat thickness as evaluated in vivo by ultrasound. There was no diet effect on hot carcass weight and yield (24.8 kg and 47.8 %), cold carcass weight and yield (24.2 kg and 46.8 %), or chilling loss (2.1 %). Non-carcass components did not differ in response to the diets ( P > 0.05 ). Dietary inclusion of calcium lignosulfonate increases the proportions of udder and liver relative to empty body weight ( P < 0.05 ). Neither the cottonseed processing method nor the inclusion of calcium lignosulfonate in high-concentrate diets for cull ewes affects their performance, biometric or morphometric measurements, non-carcass components, or qualitative traits of their carcass.

Medium- and long-term survival after pacemaker implant: Improved survival with right ventricular outflow tract pacing.

INTRODUCTION: Long-term prognosis after pacemaker implant depends on numerous variables, particularly structural heart disease. There is evidence that apical stimulation could favor the development of heart failure and, therefore, influence mortality. Other right ventricular pacing sites have been studied, for example the outflow tract, but no reports regarding long-term clinical outcome are available. OBJECTIVE: Compare all-cause mortality between two different sites of stimulation in the right ventricle. METHODS: We retrospectively analyzed 150 consecutive patients who underwent pacemaker implantation because of complete AV block (spontaneous or after AV node ablation), symptomatic second-degree AV block, and symptomatic atrial fibrillation with slow ventricular response. All patients were implanted at the same institution with the standard technique. Apical stimulation was performed with a passive or active fixation lead and outflow tract pacing with an active fixation lead. Data collection period began in July 1999 and ended on December 2004. All patients included were greater than 70% ventricular paced during pacemaker follow-up. Patients older than 85 years were excluded from the analysis. Age, pacemaker mode, sex, ejection fraction, diabetes, and structural cardiac disease were analyzed. Mean age was 72+/-7 years (median 74 years, range 27-85 years), 101 (67%) were male, 56 had implanted a VVI PM, and 94 patients a DDD PM. Patients were divided into two groups: outflow tract (55 patients) and apical pacing (95 patients). Mean follow-up was 1,231+/-642 days (median 1,158 days, range 9 to 2,694 days), which ended on July 2007. Total mortality was examined with the Kaplan-Meier method to construct overall survival curves. Multivariate Cox proportional hazards regression models were performed. RESULTS: All patients or relatives were contacted personally or by phone. There were no major statistical differences in patient background between the two groups. During follow-up, 18 patients (32%) died in the outflow tract group and 49 (51%) in the apical group (log-rank p=0.02). Cox regression multivariate analysis showed that outflow tract pacing and a low left ventricular ejection fraction (<40%) were the only independent variables with significant correlation with survival (p=0.006 and 0.003, respectively). CONCLUSIONS: Outflow tract pacing appears to improve medium- and long-term survival. Prospective randomized trials with a greater amount of patients are necessary to confirm the findings of this study.

Wide complex irregularly regular tachycardia with QRS alternation.

A 44-year-old white man was referred to our service because of a history of symptomatic rapid palpitations that had begun on January 2007. He had no previous history of syncope or family history of sudden cardiac death. The patient was otherwise well and had not been taking any medications. The electrocardiogram (ECG) recorded during sinus rhythm was within normal limits. A 12-lead ECG was performed during the last episode on July 2007 while he was working at his office. An irregular wide complex tachycardia with varying QRS morphology (left bundle-branch block with an alternating pattern) was documented. The differential diagnoses based on the 12-lead electrocardiogram (ECG) were supraventricular tachycardia with aberrant conduction and QRS alternans, atrial tachycardia with anterograde conduction over an accessory pathway, or ventricular tachycardia. An electrophysiology study was performed and the results are discussed.

Effect of calcium lignosulfonate supplementation on metabolic profiles of confined lambs.

This study aimed to evaluate the effect of calcium lignosulfonate associated with whole cottonseed in high-concentrate diets for sheep. Eight Dorper crossbred sheep with an average live weight of 42.5 ± 1.70 kg were assigned to two 4 × 4 Latin squares. The following experimental diets were evaluated: control diet (without calcium lignosulfonate) and diets with inclusion of 50, 100, and 150 g of calcium lignosulfonate/kg fresh matter. Diets were composed of soybean meal, ground corn, and whole cottonseed. Feed intake, digestibility, metabolic characteristics, and feeding behavior were evaluated. The intake of nutritional components did not show significant differences as a function of the lignosulfonate levels in the diet; however, the increase in calcium lignosulfonate levels linearly decreased the dry matter digestibility. Rumen ammonia nitrogen concentrations decreased linearly as the lignosulfonate levels in the diets were increased. There was no effect of lignosulfonate levels on blood parameters or feeding behavior of the animals. The use of lignosulfonate associated with cottonseed decreases the digestibility of dry matter and the concentration of rumen ammonia nitrogen, but does not change the intake of nutritional components, the blood parameters, or the feeding behavior of sheep.

Epidemiologia e fatores de riscos relacionados à intoxicação alimentar causada por Clostridium Botulinum: uma revisão narrativa / Epidemiology and risk factors related to food intoxication caused by Clostridium Botulinum: a narrative review

O botulismo é uma doença resultante da ação de uma toxina produzida pelo Clostridium botulinum. Devido à sua gravidade e alta mortalidade é considerado um problema de saúde pública. Nesta revisão apresentamos os principais fatores de riscos associados à intoxicação alimentar provocada pelo Clostridium botulinum, bem como realizamos um levantamento epidemiológico sobre o botulismo alimentar e infantil. A busca bibliográfica considerou as bases de dados Scielo, Medline, Lilacs e PubMed. Foram selecionados artigos originais e relatos de caso publicados em inglês, espanhol e português, incluindo publicações dos últimos dez anos. A partir das análises dos títulos, resumos e artigos, um total de 26 artigos foram incluídos nesta revisão. Verificou-se predomínio de 54% dos casos referentes ao botulismo alimentar, dos quais aproximadamente 58% confirmaram a ocorrência da toxina tipo A; e 35% referente ao botulismo infantil. Na literatura consultada os principais sintomas, relacionados ao botulismo alimentar, identificados foram: visão turva, vômito, paralisia flácida, náuseas, tontura, diplopia, dificuldade respiratória, disatria, disfagia, fraqueza muscular, boca seca, ptose e cefaleia. Dentre as principais fontes de contaminação, 65% das publicações selecionadas identificaram as conservas como principal causa do botulismo alimentar. Embora o mel (42%) seja a única fonte registrada de alimento veiculador do agente causador do botulismo infantil, alguns relatos na literatura (25%) associaram à doença com a inalação de poeira contendo esporos do Clostridium botulinum, bem como o uso de plantas medicinais (25%). Os sintomas mais comuns observados na literatura foram: constipação dificuldade respiratória e dificuldade de sucção. Apesar de vários relatos na literatura acerca das duas doenças, o botulismo ainda é muito subnotificado dado ao diagnóstico muitas vezes equivocado, ressaltando-se a importância do diagnóstico precoce no tratamento da doença pelos profissionais de saúde, bem como a disponibilidade de informações relevantes para a investigação epidemiológica de doenças de notificação compulsória. Os dados apresentados também demonstram a importância de sensibilizar a população dos principais riscos e medidas de prevenção, já que a maioria dos casos relatados está relacionada a práticas inadequadas de preparo dos alimentos. (AU)

Botulism is a disease resulting from the action of a toxin produced by Clostridium botulinum. Because of its severity and high mortality, it is considered a public health problem. In this review, we present the main risk factors associated with food poisoning caused by Clostridium botulinum, as well as an epidemiological survey on foodborne and infant botulism. A bibliographic search was conducted in SciELO, MEDLINE, LILACS and PubMed databases. Original articles and case reports published in English, Spanish and Portuguese in the past ten years were selected. After analyzing titles, abstracts and articles, 26 articles were used in this review. In total, 54% of the cases were related to foodborne botulism, of which approximately 58% had confirmed type A botulism, and 35% were related to infant botulism. In the literature consulted, the main symptoms related to foodborne botulism were blurred vision, vomiting, flaccid paralysis, nausea, dizziness, diplopia, respiratory distress, dysarthria, dysphagia, muscle weakness, dry mouth, ptosis and headache. Among the sources of contamination, 65% of the published studies reported home-canned foods as the main cause of foodborne botulism. Although honey (42%) is the only reported food source for the agent causing infant botulism, some reports in the literature (25%) associated the disease with inhalation of dust containing Clostridium botulinum spores, as well as use of medicinal plants (25%). The most common symptoms observed in the literature were constipation, difficulty breathing and difficulty suckling. Although several reports on the two forms of the disease exist, botulism remains under-reported because of often incorrect diagnosis. Thus, early diagnosis is important for an adequate treatment provided by health professionals, as well as availability of relevant information for the epidemiological investigation of notifiable diseases. The data presented in this study also demonstrate the importance of raising people's awareness to main risks and prevention measures, as most reported cases were related to inadequate food preparation practices. (AU)

Vias fascículo ventriculares: una rareza electrofisiológica / Ventricular fascicle pathways: an electrophysiological rarity / Vias fascículo-ventriculares: uma raridade eletrofisiológica

Las vias fascículo ventriculares (FV) sustentan una forma rara de preexcitation en la que la morfologia ECG recuerda a la de las vias paraseptales superiores, pero no participan en mecanismos de taquicardia ni requieren tratamiento específico. Algumas diferencias electrocardiográficas, la respuesta a la adenosina intravenosa y, sobre todo el estudio electrofisiológico sientam el diagnóstico diferencial. Se presentan los dos casos con vias FV de una serie consectiva de 62 pacientes con vias accesorias patentes remitidos a nuestro laboratorio para ablación con radiofrecuencia. En uno no se indujeron arritmias y en otro se indujo una taquicardia por reentrada nodal, que se sometió a ablación con êxito y que permitió el diagnóstico de inserción infrahisiana de la via accessoria FC.

Ventricular fascicle connections are an unusual form of pre-excitation. The 12-lead surface ECG during sinus rhythm is similar to the ECG of patients with anteroseptal and midseptal bypass tracts. These fibers do not participate in the tachycardia circuit or need any treatment. Electrocardiographic differences, the response to adenosine and particularly, the electrophysiologicstudy will guide to the correct diagnosis. We present two cases of ventricular fascicle connections in a consecutive series of 62 patients with accessory pathways referred to our service for evaluation and ablation. In one patient, no arrhythmias were induced, and in another patient an atrio-ventricular reentrant nodal tachycardia was induced, which was successfully ablated. The study also revealed theinfra-Hisian insertion of the ventricular fascicle connection.

As vias fascículo-ventriculares (FV) sustentam uma forma rara de pré-excitação em que a morfologia ECG recorda a das vias paraseptais superiores, mas não participam dos mecanismos de taquicardia nem requerem tratamento específico. Algumas diferenças eletrocardiográficas, a resposta à adenosina intravenosa e, sobretudo, o estudo eletrofisiológico estabelecem o diagnóstico diferencial. Apresentam-se os dois casos com vias FV de uma série consecutiva de 62 pacientes com viasacessórias patentes encaminhados ao nosso laboratório para ablação com radiofrequência. Em um não foram induzidas arritmias e no outro foi induzida uma taquicardia por reentrada nodal, que foi submetida à ablação com sucesso e que permitiu o diagnóstico de inserção infra-hissiana da via acessória FV.

Artefactos y seudoartefactos en el electrocardiograma / Artifacts and pseudo artifacts in the electrocardiogram

El examen minucioso del electrocardiograma es fundamental para establecer un correcto diagnóstico y tratamiento. La presencia de artefactos o un análisis superficial del electrocardiograma puede generar errores diagnósticos. Presentamos seis pacientes con registros electrocardiográficos complejos que llevaron a un diagnóstico inicial falso. El análisis cuidadoso de los electrocardiogramas fue decisivo para establecer el diagnóstico definitivo, evitando tratamientos inapropiados.

¿Se puede predecir el riesgo de muerte súbita luego de sufrir un infarto de miocardio? / Can sudden death be predicted after myocardial infarcts?

La muerte súbita es responsable de más de la mitad de las muertes debidas a causas cardíacas. Nuestra habilidad para reconocer a los pacientes de alto riesgo de muerte súbita se ha incrementado, pero 90 por ciento de las muertes ocurren en sujetos sin factores de riesgo identificables. Además, sabemos que la mayoría tiene enfermedad coronaria preexistente y que la muerte súbita cardíaca es fundamentalmente un problema extrahospitalario. Una población de alta mortalidad y fácil de detectar es la que ya ha sufrido un infarto de miocardio. La mortalidad posinfarto de miocardio oscila entre 5 por ciento a 11 por ciento, dentro de los seis a 12 meses luego del alta y 20 por ciento a los cinco años. Numerosos marcadores se han identificado, pero su valor predictivo positivo es relativamente bajo. El más importante es la disfunción ventricular izquierda. Otras variables: clínicas, basadas en imágenes, autonómicas, electrocardiográficas, además de algunos biomarcadores, métodos invasivos y combinación de variables, se han descripto para estratificar el riesgo y se comentan en este trabajo. Desafortunadamente, aún desconocemos cuál es la combinación que tiene la capacidad predictiva más poderosa. Actualmente, la estratificación del riesgo de muerte súbita se lleva a cabo utilizando solamente la historia clínica, la clase funcional y la fracción de eyección ventricular izquierda (FEVI). En principio, los pacientes de alto riesgo deben recibir betabloqueantes, inhibidores de la enzima convertidora, espironolactona y antitrombóticos. En casos seleccionados se deberá considerar el implante de un cardiodesfibrilador. Otras variables se incorporarán para identificar mejor a los grupos de mayor riesgo.