Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections

Escherichia coli is the most frequent Gram-negative bacilli involved in intra-abdominal infections. However, despite high mortality rates associated with biliary tract infections due to E. coli, there is no study focusing on this pathogen. In this study, we have characterized a group of 15 E. coli isolates obtained from 12 patients with biliary tract infections. Demographic and clinical data of the patients were recovered. Phylogeny, resistome, and virulome analysis through whole genome sequencing and biofilm formation were investigated. Among the 15 E. coli isolates, no predominant sequence type (ST) was identified, although 3 of them belonged to unknown STs (20%). Resistance to ampicillin, amoxicillin/clavulanic acid, cotrimoxazole, and quinolones was more present in these isolates; whereas, third and fourth generation cephalosporins, carbapenems, amikacin, tigecycline, and colistin were highly active. Moreover, high diversity of virulence factors has been found, with sfa, fimH, and gad the most frequently detected genes. Interestingly, 26.6% of the E. coli isolates were high biofilm-producers. Altogether, our data characterized for the first time E. coli isolates associated with biliary tract infections in terms of genomic relationship, resistome, and virulome.España, Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades (CP15/00132)España, Plan Nacional de I+D+i 2013-2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, Spanish Network for Research in Infectious Diseases (RD16/0016/0009

[Smoking and alcohol use among Chilean teenagers aged 10 to 14 years].

BACKGROUND: Smoking and alcohol use are risky behaviors that can start early in life. AIM: To determine the lifetime prevalence of tobacco and alcohol use in adolescents aged 10 to 14 years and related factors. SUBJECTS AND METHODS: A survey about smoking and alcohol use was answered by 1,392 teenagers aged 10 to 14 years (46% women) from seven schools in a small city near Santiago. Personal, family, and school factors were evaluated through self-report scales. Smoking and alcohol use, as dichotomous dependent variables, were defined as having consumed any of these substances throughout life. Prevalence was calculated as percentages with 95% confidence intervals. Association analyses were conducted using multivariable logistic regression models. RESULTS: Six and eleven percent of participants reported having smoked and used alcohol in their life, respectively. Smoking was associated with age, having behavioral problems, mothers� smoking, perceiving that parents had drug problems, and not living with both parents. Alcohol use was mainly associated with age, having behavioral problems, perceiving that other students consumed drugs, alcohol use by both parents, and perceiving a lack of family support. CONCLUSIONS: Tobacco and alcohol use is highly prevalent in adolescents aged 10-14 years. There were common risk factors for smoking and alcohol use such as age and having behavioral problems, while other factors were more specific such as mothers� smoking, or parental alcohol use

Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences

[Background] The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.[Results] We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (<20%).[Conclusions] Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.This work is supported by grant PT17/0009/0006 from the Spanish Ministry of Economy and Competitiveness, COVID-0012–2020 from Consejería de Salud y Familias, Junta de Andalucía, and postdoctoral contract PAIDI2020- DOC_00350 for C.L., from Junta de Andalucía, co-funded by the European Social Fund (FSE) 2014–2020.Peer reviewe

Full-length study protocol (Spanish). Study protocol for a randomized clinical trial to assess 7 versus 14-days of treatment for Pseudomonas aeruginosa bloodstream infections (SHORTEN-2 trial)

Eficacia y seguridad de 7 versus 14 días de tratamiento antibiótico para la bacteriemia producida por Pseudomonas aeruginosa: un ensayo clínico multicéntrico, aleatorizado (SHORTEN-2) con un análisis DOOR/RADAR.Peer reviewe

Full-length study protocol (English). Study protocol for a randomized clinical trial to assess 7 versus 14-days of treatment for Pseudomonas aeruginosa bloodstream infections (SHORTEN-2 trial)

Efficacy and safety of 7 versus 14 days of antibiotic treatment for Pseudomonas aeruginosa bacteraemia: a multicentre, randomized clinical trial (SHORTEN-2) with a DOOR/RADAR analysis.Peer reviewe

Results of the survey among participating centers regarding diagnostic and clinical routines for the management of BSI-PA

S4 File. Results of the survey among participating centers regarding diagnostic and clinical routines for the management of BSI-PAPeer reviewe

List of participating centers. Study protocol for a randomized clinical trial to assess 7 versus 14-days of treatment for Pseudomonas aeruginosa bloodstream infections (SHORTEN-2 trial)

S1 File. List of participating centers.Peer reviewe

Definitions for main trial variables. Study protocol for a randomized clinical trial to assess 7 versus 14-days of treatment for Pseudomonas aeruginosa bloodstream infections (SHORTEN-2 trial)

S2 File. Definitions for main trial variables.Peer reviewe

Statistical analysis plan. Study protocol for a randomized clinical trial to assess 7 versus 14-days of treatment for Pseudomonas aeruginosa bloodstream infections (SHORTEN-2 trial)

Efficacy and safety of 7 versus 14 days of antibiotic treatment for Pseudomonas aeruginosa bacteraemia: a multicentre, randomized clinical trial (SHORTEN-2) with a DOOR/RADAR analysis.Peer reviewe

Epidemiological and clinical characteristics of Streptococcus tigurinus endocarditis

Background: Streptococcus tigurinus was recently described as a new streptococcal species within the viridans group streptococci (VGS). The objectives of the present work were to analyse the clinical and microbiological characteristics of S. tigurinus isolated from patients with bacteraemias, to determine the prevalence of S. tigurinus among VGS endocarditis in Spain, and to compare the clinical characteristics and outcomes of endocarditis caused by S. tigurinus and other VGS. Methods: Retrospective nationwide study, performed between 2008 and 2016 in 9 Spanish hospitals from 7 different provinces comprising 237 cases of infective endocarditis. Streptococcal isolates were identified by sequencing fragments of their 16S rRNA, sodA and groEL genes. Clinical data of patients with streptococcal endocarditis were prospectively collected according to a pre-established protocol. Results: Patients with endocarditis represented 7/9 (77.8%) and 26/86 (30.2%) of the bacteraemias caused by S. tigurinus and other VGS, respectively (p < 0.001), in two of the hospital participants. Among patients with streptococcal endocarditis, 12 different Streptococcus species were recognized being S. oralis, S. tigurinus and S. mitis the three more common. No relevant statistical differences were observed in the clinical characteristics and outcomes of endocarditis caused by the different VGS species. Conclusions: In this multicenter study performed in Spain, S. tigurinus showed a higher predilection for the endocardial endothelium as compared to other VGS. However, clinical characteristics and outcomes of endocarditis caused by S. tigurinus did not significantly differ from endocarditis caused by other oral streptococci.JMM received a personal 80:20 research grant from the Institut d’InvestigacionsBiomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain during 2017–19. Nofunding entity played any role in the design of the study and data collection,analysis, and interpretation of data and in writing the manuscript