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Extra-pulmonary TB (EPTB) is difficult to diagnose due to paucibacillary nature of disease. Current study evaluated accuracy of Truenat MTB and MTB-Rif Dx (TN), for detection of  Mycobacterium tuberculosis  and resistance to rifampicin. Samples were collected from 2103 treatment naive adults with presumptive EPTB, and tested by smear microscopy, liquid culture (LC) (MGIT-960) and GeneXpert MTB/RIF (GX) (Microbiological Reference Standards, MRS). TN results were compared to MRS and Composite Reference Standards (CRS, Microbiology, histopathology, radiology, clinical features prompting decision to treat, response to treatment). CRS grouped patients into 551 confirmed, 1096 unconfirmed, and 409 as unlikely TB. TN sensitivity and specificity was 73.7% and 90.4% against GX. Against LC, Overall sensitivity of GX was 67.6%, while that of TN was 62.3%. Highest sensitivity by TN was observed in pus samples (89%) and highest specificity (92%) in CSF samples, similar to GX. TN sensitivity was better in fluid and biopsy samples and slightly inferior for lymph node aspirates compared to GX. TN sensitivity for RIF resistance detection was slightly superior to GX. TN and GX results were further compared to Clinical Reference Standards. TN detected 170 TB patients initiated on treatment missed by GX, while GX detected 113 such patients missed by TN. Of 124 samples with RIF resistance discordance between GX and TN, GX reported 103/124 as sensitive, 3/124 as indeterminate and 18 as resistant (13/18 samples had low/very low DNA load) while TN reported RIF resistance indeterminate in 103/111 low/very low DNA load samples. Due to paucibacillary nature of EPTB samples, culture yield was poor and phenotypic drug susceptibility testing failed to resolve the discordance. The study establishes TN at par with GX and can be utilized for quick and accurate diagnosis of EPTB.

The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of microbiome analyses. In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.

Metagenomic and microbial sequence data are made easier to interpret with the addition of 1,003 genomes to the Genomic Encyclopedia of Bacteria and Archaea. We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies. The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources. The human genome The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature , the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Background Biofilms are formed by a complex bacterial community encapsulated by a polymeric matrix, with strong adherent properties and persistent phenotype. Biofilms are considered one of the most challenging areas of modern medicine. Existing antibiotics have been developed against free-floating bacterial cells, and thus, many treatments of biofilm-related infection fail. In this study, we compared the effects of different media on biofilm growth of clinical reference strains of Staphylococci and Enterococci , including multi-drug resistant representatives. Further, we optimized the resazurin-based assay for determining the minimal biofilm inhibitory concentration (MBIC) of standard antibiotics, and evaluated its use for the determination of minimal biofilm eradication concentration (MBEC). Results We showed that tryptic soy broth supplemented with 1% glucose was an optimal media for maximum biofilm growth of all strains tested, with an extended incubation time for Enterococci. A range of parameters were tested for the resazurin assay, including concentration, temperature and time of incubation. Using quality parameters to analyze the assay’s performance, the conditions for the resazurin assay were set as follows: 4 μg/mL and 8 μg/mL, with incubation at 25 °C for 20 min and 40 min for Staphylococci and Enterococci , respectively. Conclusions In summary, we defined conditions for optimal biofilm growth and for standardized resazurin assay for MBIC determination against six Gram-positive clinical reference strains. We also observed that MBEC determination by the resazurin-based assay is limited due to the poor detection limit of the assay. Complementary cell counting data is needed for precise determination of MBEC.

Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research. This tutorial explains how to evaluate and benchmark metagenome assembly, binning and profiling methods using standards and software provided by the CAMI initiative.

Selection of a reliable internal control gene is critical for quantitative real-time PCR, which is a rapid, highly sensitive, and easy method for evaluating gene expression levels in different samples or tissues. Colletotrichum scovillei , which belongs to the C. acutatum species complex, is a common and aggressive species that can cause anthracnose in chili peppers. However, stable reference genes have not yet been identified for C. scovillei . In our study, reference genes were selected and validated in C. scovillei during different growth stages, including conidia, conidial germination, and mycelium growth, during host interactions, and after treatment with the common solvent 0.5% dimethyl sulfoxide (DMSO) and plant extracts with antifungal activity against C. scovillei . Eight candidate reference genes ( CsUCE , CsCK , CsTBP , CsTIF , CsPP2A , CsTUB , CsCAL , and CsNADH ) were selected from C. scovillei based on transcriptomic and genomic data. Several statistical methods, including the comparative quantification cycle threshold (Ct) method, geNorm, NormFinder, and Bestkeeper, were used to assess the stabilities of reference gene transcripts. The results indicated that CsPP2A had better stability during the C. scovillei growth stage, CsTUB had the best stability during host interactions, and CsUCE was more stable after treatment with the general solvent 0.5% DMSO and Cestrum glanduliferum kerber ex Francey extracts. Our study provides the most suitable reference gene for future studies to quantify target gene expression levels in C. scovillei under different conditions.

BACKGROUNDThe microscopical diagnosis of male urethritis was recently questioned by Rietmeijer and Mettenbrink, lowering the diagnostic criteria of the diagnosis to ≥2 polymorphonuclear leucocytes (PMNL) per high power field (HPF), and adopted by Centers for Disease Control and Prevention in their 2015 STD Treatment Guidelines. The European Non-Gonococcal Urethritis Guideline advocates a limit of ≥5 PMNL/HPF. OBJECTIVETo determine if syndromic treatment of urethritis should be considered with a cutoff value of ≥2 PMNL/HPF in urethral smear. METHODSThe design was a cross-sectional study investigating the presence and degree of urethritis relative to specific infections in men attending an STI clinic as drop-in patients. RESULTSThe material included 2 cohortsa retrospective study of 13,295 men and a prospective controlled study including 356 men. We observed a mean chlamydia prevalence of 2.3% in the 0–9 stratum, and a 12-fold higher prevalence (27.3%) in the strata above 9. Of the chlamydia cases, 89.8% were diagnosed in strata above 9. For Mycoplasma genitalium, the prevalence was 1.4% in the 0–9 stratum and 11.2% in the stratum ≥10, and 83.6% were diagnosed in strata above 9. For gonorrhea, a significant increase in the prevalence occurred between the 0–30 strata and >30 strata from 0.2% to 20.7%. The results of the prospective study were similar. CONCLUSIONSOur data do not support lowering the cutoff to ≥2 PMNL/HPF. However, a standardization of urethral smear microscopy seems to be impossible. The cutoff value should discriminate between low and high prevalence of chlamydia, mycoplasma, and gonorrhea to include as many as possible with a specific infection in syndromic treatment, without overtreating those with few PMNL/HPF and high possibility of having nonspecific or no urethritis.

The human body is mostly made up of water. The largest proportion of the human body is water, hence the growing interest of specialists in defining the importance of water in the body and the risks of dehydration. This study determined the physico-chemical and microbiological parameters of the drinking water distributed in the public network in the area of operation of Water Distribution Operator in Mureș County and samples of bottled water existing on the market in Mureş County (mineral, spring or table). The water supplied to the network can be safely consumed. This is demonstrated both by the results of the analyses of the physico-chemical and microbiological parameters related to the legislative standards and by the values of the similar parameters analyzed for the bottled water.