Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.

Whole genome sequencing (WGS) of Mycobacterium tuberculosis has rapidly progressed from a research tool to a clinical application for the diagnosis and management of tuberculosis and in public health surveillance. This development has been facilitated by drastic drops in cost, advances in technology and concerted efforts to translate sequencing data into actionable information. There is, however, a risk that, in the absence of a consensus and international standards, the widespread use of WGS technology may result in data and processes that lack harmonization, comparability and validation. In this Review, we outline the current landscape of WGS pipelines and applications, and set out best practices for M. tuberculosis WGS, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.

Genotyping of Mycobacterium tuberculosis using whole genome sequencing.

Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB spread in the human population. Due to the accelerating advances in molecular biology, especially in DNA sequencing, in the past decade, the application of these methods has become crucial for TB evolution studies, differentiation of Mycobacterium tuberculosis genotypes, and their distribution. Currently, several molecular genetic methods are available. The oldest typing methods (e.g., IS6110-RFLP, spoligotyping, and MIRU-VNTR) can discover the chain of transmission to the patient. Currently, whole genome sequencing facilitates is furthermore able to identify the source of infection, the transmission trays among individuals sharing the same isolate, as well as determination of the TB evolution and its resistance to antituberculotic agents. It is obvious that this technique will become a new gold standard in genotyping methods in tuberculosis molecular epidemiological studies. In this article, molecular genetic typing methods with a special focus on whole genome sequencing and data management are reviewed.

Validation of Whole-Genome Sequencing for Identification and Characterization of Shiga Toxin-Producing Escherichia coli To Produce Standardized Data To Enable Data Sharing.

Whole-genome sequencing (WGS) is rapidly becoming the method of choice for outbreak investigations and public health surveillance of microbial pathogens. The combination of improved cluster resolution and prediction of resistance and virulence phenotypes provided by a single tool is extremely advantageous. However, the data produced are complex, and standard bioinformatics pipelines are required to translate the output into easily interpreted epidemiologically relevant information for public health action. The main aim of this study was to validate the implementation of WGS at the Scottish Escherichia coli O157/STEC Reference Laboratory (SERL) using the Public Health England (PHE) bioinformatics pipeline to produce standardized data to enable interlaboratory comparison of results generated at two national reference laboratories. In addition, we evaluated the BioNumerics whole-genome multilocus sequence typing (wgMLST) and E. coli genotyping plug-in tools using the same data set. A panel of 150 well-characterized isolates of Shiga toxin-producing E. coli (STEC) that had been sequenced and analyzed at PHE using the PHE pipeline and database (SnapperDB) was assembled to provide identification and typing data, including serotype (O:H type), sequence type (ST), virulence genes (eae and Shiga toxin [stx] subtype), and a single-nucleotide polymorphism (SNP) address. To validate the implementation of sequencing at the SERL, DNA was reextracted from the isolates and sequenced and analyzed using the PHE pipeline, which had been installed at the SERL; the output was then compared with the PHE data. The results showed a very high correlation between the data, ranging from 93% to 100%, suggesting that the standardization of WGS between our reference laboratories is possible. We also found excellent correlation between the results obtained using the PHE pipeline and BioNumerics, except for the detection of stx2a and stx2c when these subtypes are both carried by strains.

Rapid monitoring of vancomycin-resistant Enterococcus faecium in hospital departments by repetitive element palindromic polymerase chain reaction.

BACKGROUND: The current increase in nosocomial infections caused by vancomycin-resistant enterococci (VRE) warrants improvement of detection methods and hygiene measures. Knowledge of the local epidemiology is important for monitoring compliance of medical personnel with hygiene measures. AIM: To evaluate semi-automated repetitive element palindromic polymerase chain reaction (rep-PCR) for rapid molecular typing of VRE. METHODS: Primary VRE isolates were collected during an observation period of one year and retrospectively typed by rep-PCR. Molecular typing was performed on isolates from two departments with elevated VRE rates and patients with increased risk for systemic VRE infections. Typing results were correlated with temporal and spatial information on patient moves, VRE laboratory results and multi-locus sequence typing (MLST). FINDINGS: Approximately 70% of VRE isolates within a department could be assigned to similarity clusters. Spread of VRE was limited to the individual departments. There was no evidence for spread of endemic VRE strains within the geographical catchment area of the hospital. Our results demonstrate the utility of rep-PCR typing on a department level. However, a Diversilab® threshold of ≥98% had to be applied to claim similarity, and suspected transmissions needed to be confirmed by vanA/B genotyping and compiled information on spatial and temporal patient contact. MLST verified the findings. CONCLUSION: Spread of predominantly detected vancomycin-resistant Enterococcus faecium was limited to the department level with no evidence for wider dissemination within the hospital. Well-standardized and validated (semi-)automated rep-PCR systems are useful for rapid detection of possible VRE transmission. However, suspected transmissions need to be confirmed by clinical and microbiological parameters.

Development and validation of a protocol for optimizing the use of paraffin blocks in molecular epidemiological studies: The example from the HPV-AHEAD study.

Worldwide use of formalin-fixed paraffin-embedded blocks (FFPE) is extensive in diagnosis and research. Yet, there is a lack of optimized/standardized protocols to process the blocks and verify the quality and presence of the targeted tissue. In the context of an international study on head and neck cancer (HNC)-HPV-AHEAD, a standardized protocol for optimizing the use of FFPEs in molecular epidemiology was developed and validated. First, a protocol for sectioning the FFPE was developed to prevent cross-contamination and distributed between participating centers. Before processing blocks, all sectioning centers underwent a quality control to guarantee a satisfactory training process. The first and last sections of the FFPEs were used for histopathological assessment. A consensus histopathology evaluation form was developed by an international panel of pathologists and evaluated for four indicators in a pilot analysis in order to validate it: 1) presence/type of tumor tissue, 2) identification of other tissue components that could affect the molecular diagnosis and 3) quality of the tissue. No HPV DNA was found in sections from empty FFPE generated in any histology laboratories of HPV-AHEAD consortium and all centers passed quality assurance for processing after quality control. The pilot analysis to validate the histopathology form included 355 HNC cases. The form was filled by six pathologists and each case was randomly assigned to two of them. Most samples (86%) were considered satisfactory. Presence of >50% of invasive carcinoma was observed in all sections of 66% of cases. Substantial necrosis (>50%) was present in <2% of samples. The concordance for the indicators targeted to validate the histopathology form was very high (kappa > 0.85) between first and last sections and fair to high between pathologists (kappa/pabak 0.21-0.72). The protocol allowed to correctly process without signs of contamination all FFPE of the study. The histopathology evaluation of the cases assured the presence of the targeted tissue, identified the presence of other tissues that could disturb the molecular diagnosis and allowed the assessment of tissue quality.

Molecular surveillance of measles and rubella in the WHO European Region: new challenges in the elimination phase.

BACKGROUND: The WHO European Region (EUR) has adopted the goal of eliminating measles and rubella but individual countries perform differently in achieving this goal. Measles virus spread across the EUR by mobile groups has recently led to large outbreaks in the insufficiently vaccinated resident population. As an instrument for monitoring the elimination process and verifying the interruption of endemic virus transmission, molecular surveillance has to provide valid and representative data. Irrespective of the country's specific situation, it is required to ensure the functionality of the laboratory surveillance that is supported by the WHO Global Measles and Rubella Laboratory Network. AIMS: To investigate whether the molecular surveillance in the EUR is adequate for the challenges in the elimination phase, we addressed the quality assurance of molecular data, the continuity and intensity of molecular monitoring, and the analysis of transmission chains. SOURCES: Published articles, the molecular External Quality Assessment Programme of the WHO, the Centralized Information System for Infectious Diseases of the WHO EUR and the WHO Measles and Rubella Nucleotide Surveillance databases served as information sources. CONTENT: Molecular proficiency testing conducted by the WHO in 2016 has shown that the expertise for measles and rubella virus genotyping exists in all parts of the EUR. The analysis of surveillance data reported nationally to the WHO in 2013-2016 has revealed some countries with outbreaks but not sufficiently representative molecular data. Long-lasting supranational MV transmission chains were identified. IMPLICATIONS: A more systematic molecular monitoring and recording of the transmission pattern for the whole EUR could help to create a meaningful picture of the elimination process.

[Research progress in molecular classification of gastric cancer].

Gastric cancer(GC) is a highly heterogeneous malignancy. The present widely used histopathological classifications have gradually failed to meet the needs of individualized diagnosis and treatment. Development of technologies such as microarray and next-generation sequencing (NGS) has allowed GC to be studied at the molecular level. Mechanisms about tumorigenesis and progression of GC can be elucidated in the aspects of gene mutations, chromosomal alterations, transcriptional and epigenetic changes, on the basis of which GC can be divided into several subtypes. The classifications of Tan's, Lei's, TCGA and ACRG are relatively comprehensive. Especially the TCGA and ACRG classifications have large sample size and abundant molecular profiling data, thus, the genomic characteristics of GC can be depicted more accurately. However, significant differences between both classifications still exist so that they cannot be substituted for each other. So far there is no widely accepted molecular classification of GC. Compared with TCGA classification, ACRG system may have more clinical significance in Chinese GC patients since the samples are mostly from Asian population and show better association with prognosis. The molecular classification of GC may provide the theoretical and experimental basis for early diagnosis, therapeutic efficacy prediction and treatment stratification while their clinical application is still limited. Future work should involve the application of molecular classifications in the clinical settings for improving the medical management of GC.

Detailed chronological analysis of microevolution events in herds infected persistently by Mycobacterium bovis.

Various studies have analyzed microevolution events leading to the emergence of clonal variants in human infections by Mycobacterium tuberculosis. However, microevolution events in animal tuberculosis remain unknown. We performed a systematic analysis of microevolution events in eight herds that were chronically infected by Mycobacterium bovis for more than 12 months. We analyzed 88 animals using a systematic screening procedure based on discriminatory MIRU-VNTR genotyping at sequential time points during the infection. Microevolution was detected in half of the herds studied. Emergence of clonal variants did not require long infection periods or a high number of infected animals in the herd. Microevolution was not restricted to strains from specific spoligotypes, and the subtle variations detected involved different MIRU loci. The genetic locations of the subtle genotypic variations recorded in the clonal variants indicated potential functional significance. This finding was consistent with the dynamics of some clonal variants, which outcompeted the original strains, suggesting an advantageous phenotype. Our data constitute a first step in defining the thresholds of variability to be tolerated in molecular epidemiology studies of M. bovis. We could therefore ensure that related clonal variants emerging as a result of microevolution events are not going to be misinterpreted as unrelated isolates.

Multiple-clone infections of Plasmodium vivax: definition of a panel of markers for molecular epidemiology.

BACKGROUND: Plasmodium vivax infections commonly contain multiple genetically distinct parasite clones. The detection of multiple-clone infections depends on several factors, such as the accuracy of the genotyping method, and the type and number of the molecular markers analysed. Characterizing the multiplicity of infection has broad implications that range from population genetic studies of the parasite to malaria treatment and control. This study compared and evaluated the efficiency of neutral and non-neutral markers that are widely used in studies of molecular epidemiology to detect the multiplicity of P. vivax infection. METHODS: The performance of six markers was evaluated using 11 mixtures of DNA with well-defined proportions of two different parasite genotypes for each marker. These mixtures were generated by mixing cloned PCR products or patient-derived genomic DNA. In addition, 51 samples of natural infections from the Brazil were genotyped for all markers. The PCR-capillary electrophoresis-based method was used to permit direct comparisons among the markers. The criteria for differentiating minor peaks from artifacts were also evaluated. RESULTS: The analysis of DNA mixtures showed that the tandem repeat MN21 and the polymorphic blocks 2 (msp1B2) and 10 (msp1B10) of merozoite surface protein-1 allowed for the estimation of the expected ratio of both alleles in the majority of preparations. Nevertheless, msp1B2 was not able to detect the majority of multiple-clone infections in field samples; it identified only 6 % of these infections. The merozoite surface protein-3 alpha and microsatellites (PvMS6 and PvMS7) did not accurately estimate the relative clonal proportions in artificial mixtures, but the microsatellites performed well in detecting natural multiple-clone infections. Notably, the use of a less stringent criterion to score rare alleles significantly increased the sensitivity of the detection of multi-clonal infections. CONCLUSIONS: Depending on the type of marker used, a considerable amplification bias was observed, which may have serious implications for the characterization of the complexity of a P. vivax infection. Based on the performance of markers in artificial mixtures of DNA and natural infections, a minimum panel of four genetic markers (PvMS6, PvMS7, MN21, and msp1B10) was defined, and these markers are highly informative regarding the genetic variability of P. vivax populations.

Race and ancestry in the age of inclusion: technique and meaning in post-genomic science.

This article examines how race and ancestry are taken up in gene-environment interaction (GEI) research on complex diseases such as heart disease, diabetes, and cancer. Using 54 in-depth interviews of 33 scientists and over 200 hours of observation at scientific conferences, we explore how GEI researchers use and interpret race, ethnicity, and ancestry in their work. We find that the use of self-identified race and ethnicity (SIRE) exists alongside ancestry informative markers (AIMs) to ascertain genetic ancestry. Our participants assess the utility of these two techniques in relative terms, downplaying the accuracy and value of SIRE compared to the precision and necessity of AIMs. In doing so, we argue that post-genomic scientists seeking to understand the interactions of genetic and environmental disease determinants actually undermine their ability to do so by valorizing precise characterizations of individuals' genetic ancestry over measurement of the social processes and relations that differentiate social groups.

Data sharing in large research consortia: experiences and recommendations from ENGAGE.

Data sharing is essential for the conduct of cutting-edge research and is increasingly required by funders concerned with maximising the scientific yield from research data collections. International research consortia are encouraged to share data intra-consortia, inter-consortia and with the wider scientific community. Little is reported regarding the factors that hinder or facilitate data sharing in these different situations. This paper provides results from a survey conducted in the European Network for Genetic and Genomic Epidemiology (ENGAGE) that collected information from its participating institutions about their data-sharing experiences. The questionnaire queried about potential hurdles to data sharing, concerns about data sharing, lessons learned and recommendations for future collaborations. Overall, the survey results reveal that data sharing functioned well in ENGAGE and highlight areas that posed the most frequent hurdles for data sharing. Further challenges arise for international data sharing beyond the consortium. These challenges are described and steps to help address these are outlined.

A simple approach to obtain comparable Shigella sonnei MLVA results across laboratories.

Multilocus variable-number tandem repeat analysis (MLVA) is a promising subtyping tool to complement pulsed-field gel electrophoresis for discriminating closely related strains of some monomorphic organisms, including Shigella sonnei, which is one of the major foodborne pathogens. However, MLVA results are usually difficult to compare directly between laboratories, impeding the application of MLVA as a subtyping tool for disease surveillance and investigation of common outbreaks across regions or countries. It has long been a big challenge in seeking an approach that can be implemented to obtain comparable MLVA results across laboratories. By implementing a panel of calibration strains in each participating laboratory for data normalization, the MLVA results of 20 test strains were comparable even though some analytical conditions were different among the laboratories. This approach is simple, protocol independent, and easy to implement in every laboratory, and a small calibration set is sufficient to generate mathematical equations for accurate copy number conversion.

Challenges for standardization of Clostridium difficile typing methods.

Typing of Clostridium difficile facilitates understanding of the epidemiology of the infection. Some evaluations have shown that certain strain types (for example, ribotype 027) are more virulent than others and are associated with worse clinical outcomes. Although restriction endonuclease analysis (REA) and pulsed-field gel electrophoresis have been widely used in the past, PCR ribotyping is the current method of choice for typing of C. difficile. However, global standardization of ribotyping results is urgently needed. Whole-genome sequencing of C. difficile has the potential to provide even greater epidemiologic information than ribotyping.

Resistencia a los antirretrovirales: Informe preliminar del capítulo de Guatemala, del estudio de epidemiología molecular del VIH en la región de mesoamerica / Antiretroviral resistance: initial report of Guatemala chapter, the study of molecular epidemiology of HIV in the region of Mesoamerica

El uso más extendido de los fármacos antirretrovirales ha traído como consecuencia la transmisión de variantes virales con mutaciones de resistencia que se pueden mantener en individuos sin tratamiento antirretroviral. La frecuencia de estas mutaciones de resistencia transmitida es relativamente alta en países desarrollados, muchas veces con tendencias de aumento. En países en vías de desarrollo, en los que la terapia antirretroviral (ARV) se introdujo posteriormente, las frecuencias de resistencia primaria tienden a ser menores, probablemente porque su uso se encuentra basado en una disponibilidad relativamente limitada...

STrengthening the Reporting of OBservational studies in Epidemiology: Molecular Epidemiology STROBE-ME. An extension of the STROBE statement.

Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility, and clinical outcomes are used as proxies for investigating the interactions between external and/or endogenous agents and the body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as STrengthening Reporting of Observational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE Statement implementing 9 existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.

STrengthening the Reporting of OBservational studies in Epidemiology - Molecular Epidemiology (STROBE-ME): an extension of the STROBE statement.

Advances in laboratory techniques have led to a rapidly increasing use of biomarkers in epidemiological studies. Biomarkers of internal dose, early biological change, susceptibility and clinical outcomes are used as proxies for investigating interactions between external and/or endogenous agents and body components or processes. The need for improved reporting of scientific research led to influential statements of recommendations such as the STrengthening Reporting of OBservational studies in Epidemiology (STROBE) statement. The STROBE initiative established in 2004 aimed to provide guidance on how to report observational research. Its guidelines provide a user-friendly checklist of 22 items to be reported in epidemiological studies, with items specific to the three main study designs: cohort studies, case-control studies and cross-sectional studies. The present STrengthening the Reporting of OBservational studies in Epidemiology -Molecular Epidemiology (STROBE-ME) initiative builds on the STROBE statement implementing nine existing items of STROBE and providing 17 additional items to the 22 items of STROBE checklist. The additions relate to the use of biomarkers in epidemiological studies, concerning collection, handling and storage of biological samples; laboratory methods, validity and reliability of biomarkers; specificities of study design; and ethical considerations. The STROBE-ME recommendations are intended to complement the STROBE recommendations.

Quality control issues and the identification of rare functional variants with next-generation sequencing data.

Next-generation sequencing of large numbers of individuals presents challenges in data preparation, quality control, and statistical analysis because of the rarity of the variants. The Genetic Analysis Workshop 17 (GAW17) data provide an opportunity to survey existing methods and compare these methods with novel ones. Specifically, the GAW17 Group 2 contributors investigate existing and newly proposed methods and study design strategies to identify rare variants, predict functional variants, and/or examine quality control. We introduce the eight Group 2 papers, summarize their approaches, and discuss their strengths and weaknesses. For these investigations, some groups used only the genotype data, whereas others also used the simulated phenotype data. Although the eight Group 2 contributions covered a wide variety of topics under the general idea of identifying rare variants, they can be grouped into three broad categories according to their common research interests: functionality of variants and quality control issues, family-based analyses, and association analyses of unrelated individuals. The aims of the first subgroup were quite different. These were population structure analyses that used rare variants to predict functionality and examine the accuracy of genotype calls. The aims of the family-based analyses were to select which families should be sequenced and to identify high-risk pedigrees; the aim of the association analyses was to identify variants or genes with regression-based methods. However, power to detect associations was low in all three association studies. Thus this work shows opportunities for incorporating rare variants into the genetic and statistical analyses of common diseases.

European efforts to harmonize typing of meningococci.

Neisseria meningitidis causes life-threatening disease in infants, toddlers, and adolescents. Besides representative case notification, public health management of the disease requires bacterial typing information. European reference laboratories and state epidemiologists in collaboration with European institutions have driven forward the harmonization of typing by rigorously adopting DNA sequence typing and using common reference databases. External quality assessment has been provided by supranational networks, i.e. EU-IBIS and IBD-Labnet. The recent development of novel protein-based vaccines targeting serogroup B strains highlights the necessity to complement standard typing schemes by specific vaccine antigen typing including antigen expression analysis. Although not yet feasible for routine application on hundreds of strains, novel database structures have been developed to accommodate deep sequencing data.