Impact of a pulmonary embolism response team (PERT) in the prognosis of patients with acute symptomatic pulmonary embolism

BACKGROUND

The effect of a pulmonary embolism response team (PERT) in the short-term prognosis of patients with acute symptomatic pulmonary embolism (PE) lacks clarity. We therefore aimed at evaluating the effect of a PERT team on short-term mortality among patients with acute PE.

METHODS

We retrospectively reviewed consecutive patients with acute symptomatic PE enrolled in a single-center registry between 2007 and 2022. We used propensity score matching to compare treatment effects for patients with similar predicted probabilities of receiving management by the PERT team. The primary outcome was all-cause mortality within 30 days following the diagnosis of PE. The secondary outcome was 30-day PE-related mortality.

RESULTS

Of the 2,902 eligible patients who had acute symptomatic PE, 223 (7.7%; 95% confidence interval [CI], 6.7%-8.7%) were managed by the PERT team. Two hundred and seven patients who were treated by the PERT were matched with 207 patients who were not. Matched pairs did not show a statistically significant lower all-cause (odds ratio [OR], 1.09; 95% CI, 0.63-1.89) or PE-related death (OR, 1.30; 95% CI, 0.47-3.62) for PERT management compared with no PERT management through 30 days after diagnosis of PE.

CONCLUSIONS

Our results suggest that multidisciplinary care of patients with acute symptomatic PE by a PERT team is not associated with a significant reduction in short-term all-cause or PE-related mortality.

Exploring the inhibitory potential of the antiarrhythmic drug amiodarone against Clostridioides difficile toxins TcdA and TcdB

The intestinal pathogen Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in humans. The symptoms of C. difficile-associated diseases (CDADs) are directly associated with the pathogen's toxins TcdA and TcdB, which enter host cells and inactivate Rho and/or Ras GTPases by glucosylation. Membrane cholesterol is crucial during the intoxication process of TcdA and TcdB, and likely involved during pore formation of both toxins in endosomal membranes, a key step after cellular uptake for the translocation of the glucosyltransferase domain of both toxins from endosomes into the host cell cytosol. The licensed drug amiodarone, a multichannel blocker commonly used in the treatment of cardiac dysrhythmias, is also capable of inhibiting endosomal acidification and, as shown recently, cholesterol biosynthesis. Thus, we were keen to investigate in vitro with cultured cells and human intestinal organoids, whether amiodarone preincubation protects from TcdA and/or TcdB intoxication. Amiodarone conferred protection against both toxins independently and in combination as well as against toxin variants from the clinically relevant, epidemic C. difficile strain NAP1/027. Further mechanistic studies suggested that amiodarone's mode-of-inhibition involves also interference with the translocation pore of both toxins. Our study opens the possibility of repurposing the licensed drug amiodarone as a novel pan-variant antitoxin therapeutic in the context of CDADs.

Tumor ablation and vertebral augmentation in the treatment of vertebral metastases: A multicenter study

INTRODUCTION

Treatment of metastatic vertebral fractures without neural compression is performed with percutaneous cementation techniques. The increase in intratumoral pressure by these techniques can send tumor cells into the bloodstream. To prevent this dissemination and improve pain treatment, ablation techniques have been introduced that would allow the creation of a cavity in the tumor prior to cementation or directly necrosing the metastasis when its size is small.

MATERIAL

We present the experience with ablation of two hospitals and two different ablation techniques. The first group used radiofrequency ablation (A) in 14 patients (26 vertebrae), 4 of whom underwent vertebral arthrodesis. The second group used microwave ablation (B) in 93 patients (129 lesions) without associated vertebral instrumentation.

RESULTS

In group A pain improvement in VAS was 7.7-2.6 at 6 weeks. There were no complications derived from the ablation. In most cases cementation was associated. In the group B pain improvement in VAS went from 6.8-1.7 at 6 weeks. Cementation was associated in all cases. There were no complications derived from the ablation.

CONCLUSION

The association of ablation techniques with vertebral cementation is a safe technique that significantly improves the patient's pain and can help control the disease.

[Translated article] Tumor ablation and vertebral augmentation in the treatment of vertebral metastases: A multicenter study

INTRODUCTION

Treatment of metastatic vertebral fractures without neural compression is performed with percutaneous cementation techniques. The increase in intratumoral pressure by these techniques can send tumor cells into the bloodstream. To prevent this dissemination and improve pain treatment, ablation techniques have been introduced that would allow the creation of a cavity in the tumor prior to cementation or directly necrosing the metastasis when its size is small.

MATERIAL

We present the experience with ablation of two hospitals and two different ablation techniques. The first group used radiofrequency ablation (A) in 14 patients (26 vertebrae), 4 of whom underwent vertebral arthrodesis. The second group used microwave ablation (B) in 93 patients (129 lesions) without associated vertebral instrumentation.

RESULTS

In group A pain improvement in VAS was 7.7-2.6 at 6 weeks. There were no complications derived from the ablation. In most cases cementation was associated. In the group B pain improvement in VAS went from 6.8 to 1.7 at 6 weeks. Cementation was associated in all cases. There were no complications derived from the ablation.

CONCLUSION

The association of ablation techniques with vertebral cementation is a safe technique that significantly improves the patient's pain and can help control the disease.

Operando DRIFT-MS for studying the oxidative steam reforming of ethanol (OSRE) reaction

An operando DRIFT-MS system (Diffuse Reflectance Infrared Fourier Transform Spectroscopy coupled with Mass Spectrometry) was designed and set up to study the oxidative steam reforming of ethanol reaction (OSRE). This reaction involves the mixture of water, ethanol and oxygen to produce mainly hydrogen, which is a rather attractive energy carrier. Spectroscopic monitoring of the process is a key tool to contribute to the understanding of: i) the dynamics on the catalyst surface, ii) the reaction mechanism and iii) the effect of the solid's properties on the catalytic process. In this sense, this document sets forth the experimental design that allows to carry out the study under operando DRIFT-MS conditions through time for the OSRE reaction. Selection criteria for parameters, materials, configuration, and experimental conditions are included, particularly optimizing the parameters of particle size and the dilution factor with KBr as well as the temperature and flow conditions for carrying out the reaction.•Clear signals of the adsorbed species in IR that do not present interference by water in the reaction atmosphere.•Simple assembly and online product detection by MS that allow to follow the change in the products of the OSRE reaction according to the temperature.•Controlled entry of gases and quantification by loop injection.

Adaptation culturally and linguistically to the Chilean population and validation the Dry Eye Questionnaire 5

BACKGROUND AND OBJECTIVE

There are different methods for evaluating dry eye disease (DID), including questionnaires that analyze different aspects of its symptoms, which are important for its better understanding and therapeutic management. The Dry Eye Questionnaire 5 (DEQ-5), is unique in its kind, because in addition to its simplicity, it measures symptoms in 4 dimensions. the aim of this study is to adapt culturally and linguistically and validate this instrument to the Chilean population.

MATERIAL AND METHODS

for the adaptation, the translation and retro-translation of the original version was carried out, its linguistic analysis, the pilot test and the expert panel review (which included a linguistics specialist) were used. For the validation, a psychometric analysis of reliability and validity of the construct was incorporated. The sample in which it was validated was constituted by 205 people with dry eye disease.

RESULTS

141 (69%) of the respondents were women, the mean of age was 48 years ± 16,7, and the median of the total score DEQ-5 was 13 points (R.I 8 - 15 points). The adapted version resulted in a Cronbach alpha of 0.8085, scoring that classified it as good.

DISCUSSION

the questionnaire DEQ-5, which was adapted and validated, was a good instrument to be used in populations with similar characteristics of those in the study. More so, the factor analysis enriched comprehension of the way in which people with dry eye disease relate their symptoms and which questions relate more between them, representing in a better way the aspects evaluated of the symptomatology of this disease.

XAIRE: An ensemble-based methodology for determining the relative importance of variables in regression tasks. Application to a hospital emergency department

Nowadays it is increasingly important in many applications to understand how different factors influence a variable of interest in a predictive modeling process. This task becomes particularly important in the context of Explainable Artificial Intelligence. Knowing the relative impact of each variable on the output allows us to acquire more information about the problem and about the output provided by a model. This paper proposes a new methodology, XAIRE, that determines the relative importance of input variables in a prediction environment, considering multiple prediction models in order to increase generality and avoid bias inherent in a particular learning algorithm. Concretely, we present an ensemble-based methodology that promotes the aggregation of results from several prediction methods to obtain a relative importance ranking. Also, statistical tests are considered in the methodology in order to reveal significant differences between the relative importance of the predictor variables. As a case study, XAIRE is applied to the arrival of patients in a Hospital Emergency Department, which has resulted in one of the largest sets of different predictor variables in the literature. Results show the extracted knowledge related to the relative importance of the predictors involved in the case study.

Non-Toxigenic Clostridioides difficile Strain E4 (NTCD-E4) Prevents Establishment of Primary C. difficile Infection by Epidemic PCR Ribotype 027 in an In Vitro Human Gut Model

Clostridioides difficile infection (CDI) remains a significant healthcare burden. Non-toxigenic C. difficile (NTCD) strains have shown a benefit in preventing porcine enteritis and in human recurrent CDI. In this study, we evaluated the efficacy of metronidazole-resistant NTCD-E4 in preventing CDI facilitated by a range of antimicrobials in an in vitro human gut model. NTCD-E4 spores (at a dose of 107) were instilled 7 days before a clinical ribotype (RT) 027 (at the same dose) strain (210). In separate experiments, four different antimicrobials were used to perturb gut microbiotas; bacterial populations and cytotoxin production were determined using viable counting and Vero cell cytotoxicity, respectively. RT027 and NTCD-E4 proliferated in the in vitro model when inoculated singly, with RT027 demonstrating high-level cytotoxin (3-5-log10-relative units) production. In experiments where the gut model was pre-inoculated with NTCD-E4, RT027 was remained quiescent and failed to produce cytotoxins. NTCD-E4 showed mutations in hsmA and a gene homologous to CD196-1331, previously linked to medium-dependent metronidazole resistance, but lacked other metronidazole resistance determinants. This study showed that RT027 was unable to elicit simulated infection in the presence of NTCD-E4 following stimulation by four different antimicrobials. These data complement animal and clinical studies in suggesting NTCD offer prophylactic potential in the management of human CDI.

Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants

Toxin B (TcdB) is a major exotoxin responsible for diseases associated with Clostridioides difficile infection. Its sequence variations among clinical isolates may contribute to the difficulty in developing effective therapeutics. Here, we investigate receptor-binding specificity of major TcdB subtypes (TcdB1 to TcdB12). We find that representative members of subtypes 2, 4, 7, 10, 11, and 12 do not recognize the established host receptor, frizzled proteins (FZDs). Using a genome-wide CRISPR-Cas9-mediated screen, we identify tissue factor pathway inhibitor (TFPI) as a host receptor for TcdB4. TFPI is recognized by a region in TcdB4 that is homologous to the FZD-binding site in TcdB1. Analysis of 206 TcdB variant sequences reveals a set of six residues within this receptor-binding site that defines a TFPI binding-associated haplotype (designated B4/B7) that is present in all TcdB4 members, a subset of TcdB7, and one member of TcdB2. Intragenic micro-recombination (IR) events have occurred around this receptor-binding region in TcdB7 and TcdB2 members, resulting in either TFPI- or FZD-binding capabilities. Introduction of B4/B7-haplotype residues into TcdB1 enables dual recognition of TFPI and FZDs. Finally, TcdB10 also recognizes TFPI, although it does not belong to the B4/B7 haplotype, and shows species selectivity: it recognizes TFPI of chicken and to a lesser degree mouse, but not human, dog, or cattle versions. These findings identify TFPI as a TcdB receptor and reveal IR-driven changes on receptor-specificity among TcdB variants.

Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential

Clostridium perfringens is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of C. perfringens; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 C. perfringens genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. In silico MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the C. perfringens genomes found in publicly available databases were derived from food (n = 85) and bird (n = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%). The most frequently found virulence factors based on > 70% coverage and 99.95% identity were plc (100%), nanH (99%), ccp (99%), and colA (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while tetA (39.5%) and tetB (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of C. perfringens is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of C. perfringens as a one of the most common causes of foodborne illness.

AB0569 FRECUENCY, TYPE AND DETERMINANTS OF COGNITIVE DEFICIT IN A COLOMBIAN COHORT OF PATIENTS WITH SLE

Background

Cognitive deficit is part of the neuropsychiatric syndromes associated with systemic lupus erythematosus (SLE) (1). SLE patiens have 2.8 times more risk to develop cognitive deficit (2) and the prevalence is unknown among this population, with variable data from 5% to 80% (3). ACR (American Collegue of Rheumathology) recomends a specific neuropsychological battery (4), but many of the published studies uses variables diagnostic tests. Cardiovascular comorbidities and the use of certain immunosuppressive are involved in the development of cognitive deficit and may be confusors at the time of diagnosis (5). Cognitive deficit affects the quality of life and predisposes to the development of dementia (6). In our setting, the frequency of cognitive deficit as a manifestation of neuropsychiatric SLE is unknown. Determining conditions of it are unknown as well.

Objectives

1.To define the frequency and degree of cognitive deficit in a cohort of patients with SLE

2.To describe associated factors (including quality of life and depression).

Methods

This was a cross-sectional observational study with 94 patients with SLE. The presence of cognitive deficit was established through a screening test (MoCA test). The diagnosis was confirmed through a battery of specific neuropsychological tests that were performed to patients with abnormal MoCA test. Quality of life was assessed using the LupusCol questionnaire wich is a validated scale for for measuring quality of life in SLE Colombian population. To measure the presence of depression we use the Beck inventory, this scale is also validated in SLE population. An exploratory analysis of the variables was performed and differences were established. A multivariate analysis was performed to find the variables associated with the cognitive deficit.

Results

Of the 94 patients, 90 (95.7%) were women. Of the 94 patients, 43 (51.2%) presented some degree of depression. The median for the loss of quality of life was VIII 21.03% (IQ 10.2 - 40.3). 35 (37.2%) patients had abnormal screening test. Specific neuropsychological tests were applied to 31 (90%) and of those, 11 patients (12.2%) presented a cognitive deficit. An association between cognitive deficit with a greater deterioration in quality of life was found (OR 1.05, 95% CI 1.01,1.09).

Conclusion

The frequency of cognitive deficit is important. There is an association of cognitive deficit with worse scores in quality of life. In addition, it was found that half of the patients presented some degree of depression. The comprehensive assessment of patients with SLE should include the evaluation of cognitive deficit and depression, because of their impact in quality of life, among other clinical aspects.

References

[1]Liang MH, Corzillius M, Bae SC, Lew RA, Fortin PR, Gordon C, et al. The American College of Rheumatology nomenclature and case definitions for neuropsychiatric lupus syndromes. Arthritis Rheum. 1999;42(4):599–608

[2]Rayes H Al, Tani C, Kwan A, Marzouk S, Colosimo K, Medina-Rosas J, et al. What is the prevalence of cognitive impairment in lupus and which instruments are used to measure it? A systematic review and meta-analysis. Vol. 48, Seminars in Arthritis and Rheumatism. 2018. p. 240–55.

[3]Kello N, Anderson E, Diamond B. Cognitive Dysfunction in SLE : a case for initiating trials. Arthritis Rheumatol. 2019;71(9):1413–25

[4]Kozora E, Ellison MC, West S. Reliability and validity of the proposed American College of Rheumatology neuropsychological battery for systemic lupus erythematosus. Arthritis Care Res. 2004;51(5):810–8.

[5]Waterloo K, Omdal R, Mellgren SI, Husby G. Neuropsychological functions in systemic lupus erythematosus: A comparison with chronic whiplash patients. Eur J Neurol. 1997;4(2):171–7.

[6]Kanapathy A, Nik Jaafar NR, Shaharir SS, Chan LF, Rozita M, Ch’ng SS. Prevalence of cognitive impairment using the Montreal Cognitive Assessment questionnaire among patients with systemic lupus erythematosus: a cross-sectional 53 study at two tertiary centres in Malaysia. Lupus. 2019;28(7):854–61.

Disclosure of Interests

None declared

A new analytical model for the response curve in megavoltage photon beams of the radiochromic EBT3 films measured with flatbed scanners

Purpose

The aim of this work is to study a new analytical model which describes the dose–response curve in megavoltage photon beams of the radiochromic EBT3 film measured with two commercially available flatbed scanners. This model takes into account the different increase of the number of two types of absorbents in the film with absorbed dose and it allows to identify parameters that depend on the flatbed scanner and the film model, and parameters that exclusively depend on the production lot. In addition, the new model is also compared with other models commonly used in the literature in terms of its performance in reducing systematic calibration uncertainties.

Methods and materials

The new analytical model consists on a linear combination of two saturating exponential functions for every color channel. The exponents modeling the growing of each kind of absorbent are film model and scanner model‐dependent, but they do not depend on the manufacturing lot. The proposed model considers the different dose kinetics of each absorbent and the apparent effective behavior of one of the absorbents in the red color channel of the scanner.

The dose–response curve has been measured using EBT3 films, a percentage depth dose (PDD) calibration method in a dose range between 0.5 and 25 Gy, and two flatbed scanners: a Microtek 1000 XL and an EPSON 11000 XL. The PDD calibration method allows to obtain a dense collection of calibration points which have been fitted to the proposed response curve model and to other published models. The fit residuals were used to evaluate the performance of each model compared with the new analytical model.

Results

The model presented here does not introduce any systematic deviations up to the degree of accuracy reached in this work. The residual distribution is normally shaped and with lower variance than the distributions of the other published models. The model separates the parameters reflecting specific characteristics of the dosimetry system from the linear parameters which depend only on the production lot and are related to the relative abundance of each type of absorbent. The calibration uncertainty is reduced by a mean factor of two by using this model compared with the other studied models.

Conclusions

The proposed model reduces the calibration uncertainty related to systematic deviations introduced by the response curve. In addition, it separates parameters depending on the flatbed scanner and the film model from those depending on the production lot exclusively and therefore provides a better characterization of the dosimetry system and increases its reliability.

Water security determines social attitudes about dams and reservoirs in South Europe

River barriers affect river dynamics and aquatic biota, altering the entire ecosystem. Nevertheless, dams and reservoirs provide goods like water supply and low-carbon energy that are becoming increasingly critical under current climate change. To know to what extent dams and reservoirs are important to the population, we explored social attitudes towards dams and reservoirs using a face-to-face questionnaire in two regions of contrasting climate and water security in Spain, a country with one of highest densities of dams in Europe. Results (N = 613) revealed a higher support for dams, mediated by the recognition of the services they provide, in the drier Mediterranean Malaga province (Andalusia), than in the wetter Atlantic Asturias province (Bay of Biscay), where water shortages are rare. Awareness of the impacts of the dams was more pronounced in Malaga, coupled with a higher willingness to pay for reconnecting rivers. Social awareness of both impacts and services provided by dams and reservoirs may depend on local climate and water security; different dam acceptance emphasizes the need to involve local citizens in the decision-making processes about water management.

Clostridioides difficile in Latin America: A comprehensive review of literature (1984-2021)

This narrative review summarizes literature on C. difficile and C. difficile infections (CDI) that emerged from Latin America (LA) between 1984 and 2021. The revised information includes papers in English, Spanish, or Portuguese that were retrieved from the databases Pubmed, Scopus, Web of Science, Google Scholar, Scielo, and Lilacs. Information is presented chronologically and segregated in subregions, focusing on clinical presentation, risk factors, detection and typing methods, prevalence and incidence rates, circulating strains, and, when available, phenotypic traits, such as antimicrobial susceptibility patterns. Studies dealing with cases, clinical aspects of CDI, and performance evaluations of diagnostic methods predominated. However, they showed substantial differences in case definitions, measuring units, populations, and experimental designs. Although a handful of autochthonous strains were identified, predominantly in Brazil and Costa Rica, the presentation and epidemiology of CDI in LA were highly comparable to what has been reported in other regions of the world. Few laboratories isolate and type this bacterium and even less generate whole genome sequences or perform basic science on C. difficile. Less than ten countries lead academic productivity on C. difficile or CDI-related topics, and information from various countries in Central America and the Caribbean is still lacking. The review ends with a global interpretation of the data and recommendations to further develop and consolidate this discipline in LA.

The Compound U18666A Inhibits the Intoxication of Cells by Clostridioides difficile Toxins TcdA and TcdB

The intestinal pathogen Clostridioides (C.) difficile is a major cause of diarrhea both in hospitals and outpatient in industrialized countries. This bacterium produces two large exotoxins, toxin A (TcdA) and toxin B (TcdB), which are directly responsible for the onset of clinical symptoms of C. difficile-associated diseases (CDADs), such as antibiotics-associated diarrhea and the severe, life-threatening pseudomembranous colitis. Both toxins are multidomain proteins and taken up into host eukaryotic cells via receptor-mediated endocytosis. Within the cell, TcdA and TcdB inactivate Rho and/or Ras protein family members by glucosylation, which eventually results in cell death. The cytotoxic mode of action of the toxins is the main reason for the disease. Thus, compounds capable of inhibiting the cellular uptake and/or mode-of-action of both toxins are of high therapeutic interest. Recently, we found that the sterol regulatory element-binding protein 2 (SREBP-2) pathway, which regulates cholesterol content in membranes, is crucial for the intoxication of cells by TcdA and TcdB. Furthermore, it has been shown that membrane cholesterol is required for TcdA- as well as TcdB-mediated pore formation in endosomal membranes, which is a key step during the translocation of the glucosyltransferase domain of both toxins from endocytic vesicles into the cytosol of host cells. In the current study, we demonstrate that intoxication by TcdA and TcdB is diminished in cultured cells preincubated with the compound U18666A, an established inhibitor of cholesterol biosynthesis and/or intracellular transport. U18666A-pretreated cells were also less sensitive against TcdA and TcdB variants from the epidemic NAP1/027 C. difficile strain. Our study corroborates the crucial role of membrane cholesterol for cell entry of TcdA and TcdB, thus providing a valuable basis for the development of novel antitoxin strategies in the context of CDADs.

FastMLST: A Multi-core Tool for Multilocus Sequence Typing of Draft Genome Assemblies

Multilocus Sequence Typing (MLST) is a precise microbial typing approach at the intra-species level for epidemiologic and evolutionary purposes. It operates by assigning a sequence type (ST) identifier to each specimen, based on a combination of alleles of multiple housekeeping genes included in a defined scheme. The use of MLST has multiplied due to the availability of large numbers of genomic sequences and epidemiologic data in public repositories. However, data processing speed has become problematic due to the massive size of modern datasets. Here, we present FastMLST, a tool that is designed to perform PubMLST searches using BLASTn and a divide-and-conquer approach that processes each genome assembly in parallel. The output offered by FastMLST includes a table with the ST, allelic profile, and clonal complex or clade (when available), detected for a query, as well as a multi-FASTA file or a series of FASTA files with the concatenated or single allele sequences detected, respectively. FastMLST was validated with 91 different species, with a wide range of guanine-cytosine content (%GC), genome sizes, and fragmentation levels, and a speed test was performed on 3 datasets with varying genome sizes. Compared with other tools such as mlst, CGE/MLST, MLSTar, and PubMLST, FastMLST takes advantage of multiple processors to simultaneously type up to 28 000 genomes in less than 10 minutes, reducing processing times by at least 3-fold with 100% concordance to PubMLST, if contaminated genomes are excluded from the analysis. The source code, installation instructions, and documentation of FastMLST are available at https://github.com/EnzoAndree/FastMLST

A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile

Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile. Of the 10 330 C. difficile genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (P<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3 %), 4 (81.5 %) and 5 (64.8 %) compared to other clades (collectively 26.9 %) (P<0.0001). MDR prevalence was highest in clade 4 (61.6 %) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3 %). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (P<0.0001), ST11 (clade 5) with tetracycline resistance (various tet-family genes) (P<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLS_B) resistance (mainly ermB) (P<0.0001) and MDR (P<0.0001). A novel and previously overlooked tetM-positive transposon designated Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may aid in the early detection of drug-resistant C. difficile strains, and prevention of their dissemination worldwide.

[Effectiveness, adherence and usability of a teleneurorehabilitation programme to ensure continuity of care for patients with acquired brain injury during the COVID-19 pandemic]

INTRODUCTION

The health pandemic brought about by SARS-CoV-2 (COVID-19) has limited access to neurorehabilitation programmes for many patients who have suffered stroke, traumatic brain injury or acquired brain damage due to some other cause. As telerehabilitation allows for the provision of care in situations of social distancing, it may mitigate the negative effects of confinement. The aim of this study was to determine the efficacy, adherence and usability of a teleneurorehabilitation intervention for patients with acquired brain injury.

PATIENTS AND METHODS

All patients included in a face-to-face neurorehabilitation programme at the time of the declaration of the state of alarm in Spain due to COVID-19 and who agreed to participate in the study were included in a teleneurorehabilitation programme. The effectiveness of the programme, understood as an improvement in independence, was quantified with the Barthel index. Adherence to the programme and usability of the tool were explored through questionnaires.

RESULTS

Altogether, 46 patients, accounting for 70.6% of the total, participated in the study. Participants significantly improved their independence and showed an improvement in the Barthel index between the start (77.3 ± 28.6) and the end of the programme (82.3 ± 26). Adherence to the intervention was very high (8.1 ± 2.2 out of 10) and the online sessions were the most highly rated content. The tool used showed a high usability (50.1 ± 9.9 out of 60) and could be used without assistance by more than half the participants.

CONCLUSION

The teleneurorehabilitation intervention was found to be effective in improving patients' independence, and promoted a high degree of adherence and usability.

Avances de la bioinformática en Costa Rica: vista retrospectiva y perspectivas

Introducción: La disciplina científica de la bioinformática tiene aplicaciones innovadoras para las sociedades humanas. Costa Rica, pequeña en tamaño y población en comparación con otros países de América Latina, ha ido adoptando la disciplina de manera progresiva. Reconocer los avances puede ayudarnos a determinar hacia dónde queremos ir como país, así como también cómo podemos contribuir a la región latinoamericana. Objetivos: Este manuscrito revisa el impacto de la investigación bioinformática en Costa Rica, la aplicación de la ciencia, los desafíos y oportunidades en su desarrollo y su potencial contribución a la sociedad. Métodos: Evaluamos los avances en este campo de investigación, por lo que buscamos datos de publicaciones y repositorios de secuencias, así como información de actividades de capacitación, redes, infraestructura, páginas web y fuentes de financiamiento. Resultados: Observamos avances importantes desde el año 2010, incluyendo un aumento en oportunidades de entrenamiento y número de publicaciones, aportes significativos a las bases de datos de secuencias y conexiones por medio de redes. Sin embargo, ciertas áreas, como la masa crítica, el mapeo de grupos de investigación y la financiación requieren más atención. Conclusiones: Sugerimos que para beneficiarse de las aplicaciones de la bioinformática se deben fortalecer tres aspectos clave: la comunidad científica, la infraestructura de investigación y las oportunidades de financiamiento. La comunidad científica y sus patrocinadores deben promover la investigación basada en bioinformática, invertir en la formación de estudiantes de posgrado, aumentar la formación de profesionales, crear oportunidades laborales para carreras en bioinformática y promover colaboraciones internacionales a través de redes. El impacto de tal inversión sería el desarrollo de proyectos ambiciosos pero factibles y colaboraciones extendidas dentro de la región latinoamericana. Esto permitiría realizar contribuciones significativas para abordar los desafíos globales y la aplicación de nuevos enfoques de investigación, innovación y transferencia de conocimiento para el desarrollo de la economía, siempre considerando la ética de la investigación.

Reverse transcriptase and protease inhibitors mutational viral load in HIV infected pregnant women with transmitted drug resistance in Argentina

Objective

Argentina has reported high levels of transmitted drug resistance (TDR), in HIV-infected pregnant women by population sequencing. We aimed to describe, in patients with TDR, the percentage of quasispecies harboring resistance mutations (RAMs) and mutational load (ML).

Patients and Methods

Retrospective study in a cohort of 40 naïve HIV-infected pregnant women, whose pretreatment samples had been genotyped by TRUGENE (period 2008-2014). Samples were re-sequenced with Ultra-deep Sequencing and ML was calculated considering baseline HIV-1 RNA load multiplied by the frequency of quasispecies harboring RAMs.

Results

TDR for NNRTIs, NRTIs and PIs was 17.5% (n=7 patients), 10% (n=4), 12.5% (n=5) respectively. Predominant NNRTI RAMs were K103N (n=4; 10%) and G190A/E/S (n=3; 7.5%). For NNRTIs, 78% of RAMs were present in >93.5% of viral population and ML was >1000 copies/mL (c/mL) for 89%, with a median (IQR) of 8330 c/ml (7738-29796). The following NRTI RAMs were described (per patient: % of quasispecies, ML): T215I (99.7%, 11014 c/ml); D67G (1.28%, 502 c/mL); M41L (79.8%, 88578 c/mL) and M184I (1.02%, 173 c/mL). Most frequent PI-RAMs were I85V, M46I, I50V and L90M (n=2, 5% each). For PIs, quasispecies with RAMs were <2.3% of viral population and ML was <350 c/mL for 77.8% of them.

Conclusion

NNRTI-RAMs are predominant within the viral population, usually exceeding the threshold of 1000 c/mL, indicating potential higher risk of perinatal transmission. Conversely, PI mutations appear mostly as minority variants, with potential lower risk of transmission. Among NRTI, quasispecies harboring RAMs and ML values were variable.

Resistance of Clostridioides difficile spores (Clostridiales: Peptostreptococcaceae) to sodium dichloroisocyanurate

Clostridioides difficile is a significant cause of diarrhea in hospitals and the community. This bacterial pathogen is transmitted through the ingestion of endospores, which are challenging to eliminate due to intrinsic resistance to a variety of chemical disinfection agents. The well-characterized laboratory strain CD630 displays low virulence, has not caused outbreaks, and is highly susceptible to disinfectants. Nonetheless, a closely related strain termed NAPCR1 caused outbreaks in Costa Rica and later became endemic in many hospitals from this country. This strain causes disease through unusual mechanisms and is genotypically distinct from CD630. Consequently, its epidemic potential could be influenced by as yet unknown spore phenotypes, such as increased resistance to disinfectants. Objective: To determine whether the NAPCR1 strain is more resistant to a conventional and highly effective C. difficile sporicidal agent than strain CD630 and to identify potential explanatory mechanisms at the genomic level. Methods: We used an in vitro dilution-neutralization method to calculate the sporicidal activity of sodium dichloroisocyanurate (DCC) against purified spores from three subtypes of NAPCR1 isolates (LIBA-2945, LIBA-5761, and LIBA-6276), CD630, and a representative of the highly virulent and epidemic NAP1 strain (LIBA-5758). This phenotypic characterization was complemented with a genomics-steered search of polymorphisms in 15 spore- or sporulation-related genes. Results: Whereas DCC at a final concentration of 0.1 % (w/v) eradicated CD630 endospores with high efficacy (log10 reduction factor (LFR) ≥ 5), it only partially inactivated NAPCR1 (average LFR range: = 1.77-3.37) and NAP1 endospores (average LRF = 3.58). As hypothesized, the three NAPCR1 subtypes tested were more resistant to DCC than strain CD630 (ANOVA, P < 0.05), with LIBA-5761 showing the highest level of DCC resistance overall (ANOVA, P < 0.05). All three NAPCR1 isolates showed large deletions in bclA1. Besides, isolates LIBA-5761 and LIBA-6276 had deletions in bclA2. Conclusions: Our in vitro tests revealed a differential resistance of spores from the C. difficile NAPCR1 strain to DCC. They highlight the importance of continuously evaluating the efficacy of deployed disinfection agents against circulating strains and hint to a potential role of structural proteins from the exosporium in resistance to disinfectants in C. difficile.

Putative Conjugative Plasmids with tcdB and cdtAB Genes in Clostridioides difficile

The major toxins of Clostridioides difficile (TcdA, TcdB, CDT) are chromosomally encoded in nearly all known strains. Following up on previous findings, we identified 5 examples of a family of putative conjugative plasmids with tcdB and cdtAB in clinical C. difficile isolates from multilocus sequence typing clades C-I, 2, and 4.

Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy

Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.

Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review

Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.

Interaction between three stress-related gene polymorphisms and food addiction increases the risk to develop obesity in a sample of Mexican people attending a nutrition clinic

Chronic stress exposure impacts negatively in individuals leading to food addiction, overweight or obesity. Stress-genes and their translation products are responsible for the responses of humans to adverse environments. Alterations in stress-genes expression or protein function may induce behaviors as compulsive eating of high-energy containing food, which decreases stress-induced negative feelings. However, chronic stress is not assessed in Mexican population. We analyzed here the association between polymorphisms of CRH, CRHR2 and glucocorticoids (GR, NR3C1) receptor genes with food addiction and obesity and overweight in Mexican patients of a Nutrition Clinic. We recruited 508 individuals of both genders, who accepted to participate in the study at their first visit to the clinic, obtaining their fat mass percentage and a blood sample for the genetic analysis. Participants answered the Yale's food addiction scale and were subjected to a Trier social test, as an acute stressful stimulus. Pre and post-test saliva samples were obtained to evaluate cortisol levels and adrenal axis' response to the acute stress. The 63% of participants classified as stressed (S); 6.5% of normal-weight individuals showed food-addiction, whereas 63% of participants with food-addiction were also stressed. The fat mass percentage was greater in stress-addiction than in stressed non-addiction participants. The best interaction model for obesity development risk comprehended the presence of polymorphisms of the three genes that in combination with food addiction increased the risk for developing obesity 2.8-4-fold. Thus, frequent stress exposure favors food-addiction, which along with genetic susceptibility seems to add up to Mexican obesity/overweight rates.

Efficacy of Bifidobacterium breve CECT7263 for infantile colic treatment: an open-label, parallel, randomised, controlled trial

Infantile colic is a prevalent condition characterised by excessive crying with no effective treatment available. We aimed to evaluate the efficacy of Bifidobacterium breve CECT7263 and a combination of this and Lactobacillus fermentum CECT5716 versus simethicone in reducing the daily time spent crying in colicky infants. A multicentre randomised, open-label, parallel, controlled trial of 28 days was performed in 150 infants who were diagnosed with colic according to the Rome III criteria and who randomly received simethicone (80 mg/day; Simethicone group), B. breve CECT7263 (2×10⁸ cfu/day, Bb group), or a combination of L. fermentum CECT5716 and B. breve CECT7263 (1×10⁸ cfu/day per strain, Bb+Lf group). The main outcomes were minutes of crying per day and the percentage of reduction in daily crying from baseline. Data were analysed per intention to treat. All treatments significantly decreased the daily crying time at the end of the intervention (P-time <0.001). However, the infants in the Bb group had significantly decreased crying time from the first week of the study (P<0.05), whereas the Bb+Lf group and the simethicone group had significantly decreased crying time from the second week (P<0.05). The percentage of reduction in the minutes of crying from baseline in the Bb group was significantly higher than that in the Simethicone group every week of the intervention (-40.3 vs -27.6% at 1-week; -59.2 vs -43.2% at 2-weeks; -64.5 vs -53.5% at 3-week and -68.5 vs -59.5% at 4-weeks, P<0.05). Additionally, in the Bb group, infants had better night sleep, and parents reported a more positive mood at the end of the intervention. All the products used in the study were safe and well tolerated. In conclusion, the breastmilk-isolated probiotic strain B. breve CECT7263 is a safe and effective treatment for infantile colic, presenting an earlier and more robust effect than the reference prescribed drug, simethicone.

A new approach to radiochromic film dosimetry based on non-local means

Radiochromic film in conjunction with flatbed scanners are frequently employed as dosimeters for advanced techniques in radiotherapy. Their strengths are as follows: light element composition, low energy dependence, near biological tissue equivalence and high spatial resolution. However, they have some weaknesses as well: non-uniformities, read out noise, and scanning artifacts. Several processing protocols have been proposed intending to correct the perturbations these weaknesses produce. The aim of this paper is to present a new processing protocol for radiochromic film dosimetry based on a non-local means denoising algorithm. Three dose distributions of open square fields and a spatial combination of these fields using different angles of incidence and monitor units have been employed to validate the protocol. The dose distributions are traceable to ionization chamber measurements. Additionally, a real dose distribution of a treatment was used to simulate scanning data with noise and scanning lateral artifact, and to study how the protocol behaves under these perturbations. The same measured raw data have been processed by means of an implementation of the multichannel protocol (multigaussian method). It has been found that the proposed protocol reduces dose uncertainty even though it uses fewer scans than the multichannel protocol.

MICROBIOTA INSIGHTS IN CLOSTRIDIUM DIFFICILE INFECTION AND INFLAMMATORY BOWEL DISEASE

Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation that includes Crohn´s disease (CD) and ulcerative colitis (UC). Although the etiology is still unknown, some specific factors have been directly related to IBD, including genetic factors, abnormal intestinal immunity, and/or gut microbiota modifications. Recent findings highlight the primary role of the gut microbiota closely associated with a persistent inappropriate inflammatory response. This gut environment of dysbiosis in a susceptible IBD host can increasingly worsen and lead to colonization and infection with some opportunistic pathogens, especially Clostridium difficile. C. difficile is an intestinal pathogen considered the main cause of antibiotic-associated diarrhea and colitis and an important complication of IBD, which can trigger or worsen an IBD flare. Recent findings have highlighted the loss of bacterial cooperation in the gut ecosystem, as well as the pronounced intestinal dysbiosis, in patients suffering from IBD and concomitant C. difficile infection (CDI). The results of intestinal microbiota studies are still limited and often difficult to compare because of the variety of disease conditions. However, these data provide important clues regarding the main modifications and interrelations in the complicated gut ecosystem to better understand both diseases and to take advantage of the development of new therapeutic strategies. In this review, we analyze in depth the gut microbiota changes associated with both forms of IBD and CDI and their similarity with the dysbiosis that occurs in CDI. We also discuss the metabolic pathways that favor the proliferation or decrease in several important taxa directly related to the disease.

In vivo animal models confirm an increased virulence potential and pathogenicity of the NAP1/RT027/ST01 genotype within the Clostridium difficile MLST Clade 2

Background

Based on MLST analyses the global population of C. difficile is distributed in eight clades, of which Clade 2 includes the “hypervirulent” NAP1/RT027/ST01 strain along with various unexplored sequence types (STs).

Methods

To clarify whether this clinically relevant phenotype is a widespread feature of C. difficile Clade 2, we used the murine ileal loop model to compare the in vivo pro-inflammatory (TNF-α, IL-1β, IL-6) and oxidative stress activities (MPO) of five Clade 2 clinical C. difficile isolates from sequence types (STs) 01, 41, 67, and 252. Besides, we infected Golden Syrian hamsters with spores from these strains to determine their lethality, and obtain a histological evaluation of tissue damage, WBC counts, and serum injury biomarkers (LDH, ALT, AST, albumin, BUN, creatinine, Na⁺, and Cl⁻). Genomic distances were calculated using Mash and FastANI to explore whether the responses were dictated by phylogeny.

Results

The ST01 isolate tested ranked first in all assays, as it induced the highest overall levels of pro-inflammatory cytokines, MPO activity, epithelial damage, biochemical markers, and mortality measured in both animal models. Statistically indistinguishable or rather similar outputs were obtained for a ST67 isolate in tests such as tissue damage, neutrophils count, and lethal activity. The results recorded for the two ST41 isolates tested were of intermediate magnitude and the ST252 isolate displayed the lowest pathogenic potential in all animal experiments. This ordering matched the genomic distance of the ST01 isolate to the non-ST01 isolates.

Conclusions

Despite their close phylogenic relatedness, our results demonstrate differences in pathogenicity and virulence levels in Clade 2 C. difficile strains, confirm the high severity of infections caused by the NAP1/RT027/ST01 strain, and highlight the importance of C. difficile typing.

Experimental studies of boron neutron capture therapy (BNCT) using histone deacetylase inhibitor (HDACI) sodium butyrate, as a complementary drug for the treatment of poorly differentiated thyroid cancer (PDTC)

PURPOSE

The present study analyzed different protocols of administration of boronophenylalanine (BPA) and sodium butyrate (NaB) to increase the BNCT efficacy for poorly differentiated thyroid cancer (PDTC).

MATERIALS AND METHODS

Nude mice implanted with human PDTC cells (WRO) were distributed into four protocols: 1) BPA; 2) BPA + ip NaB; 3) BPA + oral NaB; 4) Control. Biodistribution and histologic studies were performed. LAT (BPA transporter) isoforms gene expression was assessed by RT-PCR.

RESULTS

Tumor growth delay was observed in animals of the Protocol #3 (p < 0.05). NaB (Protocol #2) increased tumor boron uptake 2-h post BPA injection (p < 0.05). On the other hand, NaB upregulated the expression of all the isoforms of the LAT transporter in vitro. Histologic studies showed a significant decrease of mitotic activity and an increase of vacuoles in tumors of Protocol #3. Neutrons alone or combined with NaB caused some tumor growth delay (p < 0.05), while in the BNCT and BNCT + NaB groups, there was a halt in tumor growth in 70 and 80% of the animals, respectively.

CONCLUSIONS

Intraperitoneally administration of NaB increased boron uptake while oral administration for a longer period of time induced tumor growth delay previous to BPA administration. The use of NaB via ip would optimize the irradiation results.

Epigenetic regulation of TLR2-mediated periapical inflammation

AIM

To determine the methylation pattern of TLR2 gene promoter and its association with the transcriptional regulation of periapical inflammatory and angiogenic responses in symptomatic and asymptomatic forms of apical periodontitis.

METHODOLOGY

In this cross-sectional study, apical lesions were obtained from volunteers with asymptomatic apical periodontitis (AAP) (n = 17) and symptomatic apical periodontitis (SAP) (n = 17) scheduled for tooth extraction, and both total RNA and DNA were extracted. DNA was bisulfite-treated, a region of CpG island within the TLR2 gene was amplified by qPCR and the products were sequenced. Additionally, the mRNA expression of TLR2, TLR4, IL-6, IL-12, TNFalpha, IL-23, IL-10, TGFbeta, VEGFA and CDH5 was analysed by qPCR. The data were analysed with chi-square tests, Mann-Whitney or unpaired t-tests, and Spearman´s correlation; variable adjustments were performed using multiple linear regression (P < 0.05).

RESULTS

TLR2 depicted a hypomethylated DNA profile at the CpG island in SAP when compared with AAP, along with upregulated expression of TLR2, with pro-inflammatory cytokines IL-6 and IL-23, and the angiogenesis marker CDH5 (P < 0.05). TLR2 methylation percentage negatively correlated with mRNA levels of IL-23 and CDH5 in apical periodontitis. Lower methylation frequencies of single CpG dinucleotides -8 and -10 localized in close proximity to nuclear factor κB (NFκB) binding within the TLR2 promoter were identified in SAP versus AAP (P < 0.05). Finally, unmethylated -10 and -8 single sites demonstrated up-regulation of IL-23, IL-10 and CDH5 transcripts compared to their methylated counterparts (P < 0.05).

CONCLUSIONS

TLR2 gene promoter hypomethylation was linked to transcriptional activity of pro-inflammatory cytokines and angiogenic markers in exacerbated periapical inflammation. Moreover, unmethylated single sites in close proximity to NFκB binding were involved in active transcription of IL-23, IL-10 and CDH5.

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico

Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.

Development of a 64 SNV panel for breed authentication in Iberian pigs and their derived meat products

Spanish legislation regulates the labelling of Iberian pig meat and dry-cured products, which are labelled as "Ibérico" or "100% Ibérico" when they come from Duroc x Iberian crossbred or Iberian purebred pigs. Although the analytical authentication of breed origin is not mandatory, a genetic diagnostic tool is demanded by producers and consumers. We have designed a 64 Single Nucleotide Variant genotyping panel displaying extreme allelic frequencies between Duroc and Iberian purebred samples. Average proportions of Iberian alleles of 0.99, 0.01, 0.77 and 0.48 were estimated by admixture clustering analysis of known origin samples, for Iberian and Duroc purebred, 75% Iberian and 50% Iberian classes, respectively. A supervised analysis with 1419 samples showed some overlapping between contiguous classes, but the calculated degrees of separability ranged from 0.800 to 0.996, exceeding the threshold value (0.70) for considering suitable for prediction. Therefore, this panel is a useful genetic tool to infer purebred or crossbred Iberian origin of live animals, meat and dry-cured products.

High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Genotyping methods and genome sequencing are indispensable to reveal genomic structure of bacterial species displaying high level of genome plasticity. However, reconstruction of genome or assembly is not straightforward due to data complexity, including repeats, mobile and accessory genetic elements of bacterial genomes. Moreover, since the solution to this problem is strongly influenced by sequencing technology, bioinformatics pipelines, and selection criteria to assess assemblers, there is no systematic way to select a priori the optimal assembler and parameter settings. To assembly the genome of Pseudomonas aeruginosa strain AG1 (PaeAG1), short reads (Illumina) and long reads (Oxford Nanopore) sequencing data were used in 13 different non-hybrid and hybrid approaches. PaeAG1 is a multiresistant high-risk sequence type 111 (ST-111) clone that was isolated from a Costa Rican hospital and it was the first report of an isolate of P. aeruginosa carrying both blaVIM-2 and blaIMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes. To assess the assemblies, multiple metrics regard to contiguity, correctness and completeness (3C criterion, as we define here) were used for benchmarking the 13 approaches and select a definitive assembly. In addition, annotation was done to identify genes (coding and RNA regions) and to describe the genomic content of PaeAG1. Whereas long reads and hybrid approaches showed better performances in terms of contiguity, higher correctness and completeness metrics were obtained for short read only and hybrid approaches. A manually curated and polished hybrid assembly gave rise to a single circular sequence with 100% of core genes and known regions identified, >98% of reads mapped back, no gaps, and uniform coverage. The strategy followed to obtain this high-quality 3C assembly is detailed in the manuscript and we provide readers with an all-in-one script to replicate our results or to apply it to other troublesome cases. The final 3C assembly revealed that the PaeAG1 genome has 7,190,208 bp, a 65.7% GC content and 6,709 genes (6,620 coding sequences), many of which are included in multiple mobile genomic elements, such as 57 genomic islands, six prophages, and two complete integrons with blaVIM-2 and blaIMP-18 MBL genes. Up to 250 and 60 of the predicted genes are anticipated to play a role in virulence (adherence, quorum sensing and secretion) or antibiotic resistance (β-lactamases, efflux pumps, etc). Altogether, the assembly and annotation of the PaeAG1 genome provide new perspectives to continue studying the genomic diversity and gene content of this important human pathogen.

Symbolic Partial-Order Execution for Testing Multi-Threaded Programs

We describe a technique for systematic testing of multi-threaded programs. We combine Quasi-Optimal Partial-Order Reduction, a state-of-the-art technique that tackles path explosion due to interleaving non-determinism, with symbolic execution to handle data non-determinism. Our technique iteratively and exhaustively finds all executions of the program. It represents program executions using partial orders and finds the next execution using an underlying unfolding semantics. We avoid the exploration of redundant program traces using cutoff events. We implemented our technique as an extension of KLEE and evaluated it on a set of large multi-threaded C programs. Our experiments found several previously undiscovered bugs and undefined behaviors in memcached and GNU sort, showing that the new method is capable of finding bugs in industrial-size benchmarks.

Hospital environment hygiene nurse: a key player to reduce healthcare associated infections by multi-resistant organisms

Background

Multi-Resistant Organisms (MRO) healthcare-associated infections (HAI) are closely associated with contamination of surfaces. Outsourced companies are usually in charge of both hospital hygiene and environmental hygiene personnel (EHP) supervision, which can result in bias.

Methods

A quasi-experimental study. The intervention was to add the "Hospital Environment Hygiene Nurse" (HEHN). MRO acquired infection rate and MRO acquired colonized rate were calculated, pre and post intervention. Confounding variables: MRO carriage rate upon admission and hospitalisation days median (HDM) were calculated.

Results

Median length of stay: 5 days (p=0.85, interquartile range=6 days). Carriage rate upon admission: 4.3% for pre-intervention vs 5.3% post-intervention, dif. (CI 95%): 1% (-1% to 2.9%) p=0.33. MRO acquired infection rate: 4.3% for pre-intervention vs. 2% post-intervention, Standardized Infection Ratio (SIR) (CI 95%): 0.47 (0.25 to 0.87). MRO acquired colonization rate:10.4% for pre-intervention vs. 7.9% post-intervention, SIR (CI 95%): 0.75 (0.53 to 1.07).

Conclusions

As a reinforcement to standard infection control (IC) measures in place, the incorporation of an exclusive, full-time HEHN was significantly useful to reduce MRO HAI.

A collection of three integration-free iPSCs derived from old male and female healthy subjects

Here, we present the characterization of three iPSC lines derived from dermal fibroblasts of old healthy subjects. Fibroblasts were reprogrammed using Sendai viral vectors encoding OCT4, SOX2, KLF4 and c-MYC. The iPSCs expressed endogenous pluripotency markers, could generate the three germ layers (ectoderm, mesoderm and endoderm), maintained a stable karyotype, and were free from Sendai vectors and reprogramming factors. These integration-free iPSCs can serve for establishing control cell cultures in studies searching for phenotypes and mechanisms that could potentially be dysregulated in degenerative diseases.

An integration-free iPSC line, ICCSICi007-A, derived from a female Alzheimer's disease patient with the APOE-ε4/ε4 alleles

The epsilon4 (ε4) allele of the APOE gene, which encodes the apolipoprotein E4 (ApoE4), is the strongest genetic risk factor known for late-onset Alzheimer´s disease (LOAD). Here, we present the characterization of an iPSC line generated from dermal fibroblasts of a female AD patient using Sendai viral vectors encoding the transcription factors OCT4, SOX2, KLF4 and c-MYC. The iPSCs maintained the original genotype, a normal karyotype, were free from Sendai viral vectors and reprogramming factors, presented a normal morphology, expressed endogenous pluripotency markers, and could be differentiated into ectodermal, mesodermal and endodermal cells, confirming its pluripotency.