Author Correction: System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster.

Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the "success" of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 394 cluster strains were used to describe the main genetic features of the population. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrated that expression of the whiB6 which contains cluster-specific polymorphism (a151c) increased almost 40 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 was increased by more than 7 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes. In summary, our analysis allowed us to summarize the available results and also to obtain fundamentally new data.

Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains.

Nowadays proteomics is one of the major instruments for editing and correcting annotation of genomic information. The correct genome annotation is necessary for omics studies of clinically relevant pathogens like Mycobacterium tuberculosis as well as for the progress in drug design and in silico biology. Here, we focused on the proteogenomic analysis of W-148 strain belonging to the Beijing B0/W148 cluster. This cluster, also known as a "successful" clone possesses unique pathogenic properties and has a unique genome organization. Taking into account high similarity of cluster strains at the genomic level we analyzed MS/MS dataset obtained for 63 clinical isolates of Beijing B0/W148. Based on H37Rv and W-148 annotations we identified 2546 proteins representing more than 60% of total proteome. A set of peptides (n = 404) specific for W-148 was found when compared with H37Rv. Start sites for 32 genes were corrected based on the combination of LC-MS/MS proteomic data with genomic six-frame translation. Additionally, we have shown the presence of peptides related to 10 genes earlier known as "pseudogenes". SIGNIFICANCE: Mycobacterium tuberculosis is one of the most dangerous pathogens. Phylogenetically, it may be divided into major lineages and among them, lineage 2 (predominantly Beijing genotype) one of the most successful lineages with an increasing prevalence in the global population. At the same time, strains of the Beijing B0/W148 cluster, a "successful" clone of Mycobacterium tuberculosis possess even more interesting features. Only one complete genome of this cluster, W-148, present in the NCBI database (CP012090.1) and it demonstrates a number of significant differences from the well-known reference genome H37Rv. For the W-148 strain many genes are annotated as "pseudo" and no attempts were made to correct this. Thereby, in this study, we have conducted a proteomic analysis of the cluster strains and corrected current genome annotation. We hope that the data obtained will help to increase the quality of identifications in proteomic and transcriptomic analysis of M. tuberculosis Beijing B0/W148 cluster strain in subsequent studies.

Prevalence and characteristics of fibromyalgia among HIV-positive patients in southern Israel.

OBJECTIVES: Fibromyalgia and chronic pain have previously associated with HIV infection for over two decades. We aimed to evaluate the prevalence of FMS symptoms in an ethnically heterogeneous population of HIV-infected individuals in southern Israel, applying the proposed new diagnostic criteria for diagnosis of fibromyalgia symdrome (FMS). METHODS: 156 HIV-positive patients followed at the AIDS clinic of the Soroka University Medical Center (SUMC) who gave written informed consent were recruited in the trial. FMS was diagnosed based on the widespread pain index (WPI) and the Symptom Severity Score (SSS) comprising the modified 2011 diagnostic criteria for FMS. CD4 levels ad viral load were obtained. RESULTS: One hundred and thirty-nine patients (89.1%) were receiving HAART (Highly Active Antiretroviral Therapy). A total of 22 patients (14.1%) were found to fulfill current criteria for diagnosis of FMS. FMS-criteria positive individuals were slightly younger than criteria-negative individuals (40.3±9.2 vs. 42.6±11.9, p=0.39), but this difference did not reach statistical significance. There was no significant difference between the groups regarding gender, family status, religion, occupation or education. No correlation was found between CD4 and viral load levels and symptoms of FMS. CONCLUSIONS: Despite the dramatic improvement in management of HIV, FMS symptoms remain highly prevalent among these patients and are not directly correlated with indices of active disease. FMS is an important clinical issue to address among patients suffering from HIV infection.

Disagreement in the interpretation of chest radiographs among specialists and clinical outcomes of patients hospitalized with suspected pneumonia.

BACKGROUND: Pneumonia is diagnosed by a combination of clinical symptoms and findings on chest X-ray (CXR). However, there is often disagreement, even among experts, upon the interpretation of the CXR. The purpose of this study was to compare the agreement rates in CXR interpretation of suspected community-acquired pneumonia (CAP) between a radiologist, a pulmonologist, an infectious disease specialist, and an internal medicine staff and to establish the correlation of such an agreement with the length of hospitalization and 30-day mortality rate. METHODS: We prospectively enrolled in our study all patients admitted to the Department of Medicine with suspected CAP, as defined by the admitting physician, within the first 24 h of hospitalization. A radiologist, pulmonologist, and infectious disease specialist who were aware of the suspected diagnosis independently interpreted the CXR. The final diagnosis was obtained from the discharge notes. RESULTS: A total of 262 patients participated in the study, 214 of whom (81.7%) were eventually discharged with a diagnosis of CAP. The agreement rates between the readers of the CXR ranged from a kappa of 0.09 to 0.44. There were no differences in terms of background illness, PORT (Pneumonia Patients Outcomes Research Team) score, length of hospitalization, or mortality rates between patients discharged with or without a diagnosis of CAP. In multivariate analysis, only the PORT score was a significant predictor of length of hospitalization and mortality rate. CONCLUSION: We found a low to moderate agreement rate of the diagnosis of CAP between CXR readers. Identification of an infiltrate on CXR, either by specialists or by the attending physician, did not impact the clinical outcomes.