BPGA- an ultra-fast pan-genome analysis pipeline

Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG & COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Quantifying the burden of emotional ill-health amongst patients referred to a specialist rheumatology service.

OBJECTIVES: (1) To determine the prevalence of emotional disorders (DSM IV depression, anxiety and panic disorders) amongst patients referred to a rheumatology out-patient service and the proportion of these detected by the rheumatologist. (2) To test the hypotheses that emotional disorders are associated with (i) broad categories of rheumatological diagnosis (systemic, inflammatory vs non-systemic, non-inflammatory), (ii) female gender, (iii) greater symptom burden and disability and (iv) markers of socio-economic deprivation. METHODS: A cross-sectional study was made of consecutive newly referred attenders at a hospital-based, regional rheumatology service. Emotional disorders, pain, health status and socio-economic factors were assessed by questionnaire. The letter to the referrer was scrutinized for the rheumatological diagnosis and mention of emotional disorder. RESULTS: A total of 256 patients were eligible and 203 (79%) participated. The sample was 69% female, had a mean age of 50 yr and 68 patients (33.5%) had one or more emotional disorders. Only a minority were detected. There was no association with type of rheumatological diagnosis. Patients with an emotional disorder were more likely to be female (81 vs 62%; P<0.007), to report more pain (mean Visual Analogue Score 70 vs 50 mm, P<0.001), a greater number of somatic symptoms (median 3 vs 1, P<0.001) and greater disability (median Health Assessment Questionnaire 1.1 vs 0.5, P<0.001). Emotional disorders were also associated with some, but not all, measures of lower social and economic status and life dissatisfaction. CONCLUSIONS: Emotional disorder is present in one-third of new rheumatology referrals. The course, causation and management of this important component of rheumatological illness merit further attention

Medically unexplained symptoms in patients referred to a specialist rheumatology service: prevalence and associations.

OBJECTIVES: To determine the prevalence of medically unexplained rheumatic symptoms amongst patients newly referred to a rheumatology out-patient service and to examine their relationship with pain, disability, socioeconomic factors and the presence of emotional disorders (anxiety, depression and panic). METHODS: A sample of newly referred consecutive patients to a hospital-based, regional rheumatology service was administered a questionnaire for assessment of emotional disorders, pain, health status and socioeconomic factors. Rheumatologists rated the degree to which patients' symptoms were explained by organic disease (organicity rating). RESULTS: Two hundred and fifty-six patients were eligible and 203 (79%) participated. The sample included 69% females and mean age was 50 yr. Ninety-three (46%) had symptoms that were completely explained, 52 (26%) largely explained, 41 (20%) somewhat explained and 17 (8%) not at all explained by organic disease. Patients whose symptoms were of "low organicity" (somewhat or not at all explained) were more likely to be female [relative risk (RR) 1.8, 95% confidence interval (CI) 1.0-3.1], younger (mean age 44 vs 52 yr, P<0.001) and to report more somatic symptoms (median 2 vs 1, P=0.021). On univariate analysis they were more likely to be experiencing financial hardship (RR 1.7, 95% CI 1.1-2.6) and work dissatisfaction (RR 1.6, 95% CI 1.0-2.4) and to live in rented housing (RR 1.8, 95% CI 1.2-2.8) or with dependent relatives (RR 1.6, 95% CI 1.0-2.5). Logistic regression showed that female gender and living in rented housing were the significant independent predictors of low organicity. Organicity ratings were not associated with pain severity, disability, physical and mental health status or the presence of emotional disorders. CONCLUSIONS: Twenty-nine per cent of patients newly referred to rheumatology clinics had symptoms that were poorly explained by identifiable rheumatic disease. Having unexplained symptoms was associated with socioeconomic factors but not levels of pain, disability or emotional disorders

Multilocus Sequence Typing (MLST) of Chlamydiales

Developed two decades ago as a molecular method to provide definite characterization of a bacterial isolate, Multilocus Sequence Typing (MLST) is today globally adopted as a universal fine-detailed molecular typing tool and has been applied to numerous pathogenic and nonpathogenic bacterial as well eukaryotic organisms. MLST utilizes DNA sequence of several conserved housekeeping (HK) genes which are assigned an allelic number, which then collectively constitute an allelic profile or sequence type (ST), a “molecular barcode” of the interrogated bacterial strain or a eukaryotic organism. Here, we describe the principles and molecular approaches for generating MLST data for an analysis of a bacteria in the order Chlamydiales, using a Chlamydia pecorum-specific MLST scheme as an example