A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches.

The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.

Molecular diagnosis of visceral leishmaniasis: a French study comparing a reference PCR method targeting kinetoplast DNA and a commercial kit targeting ribosomal DNA.

IMPORTANCE: PCR revolutionized the direct diagnosis of infectious diseases, especially protozooses, where the infectious load is usually low. Commercial PCR methods are available and offer many advantages, including convenience and batch tracking as part of a quality system. For most parameters, the performance of commercial methods is at least as good as that of finely optimized methods developed in expert laboratories. This comparison work has not been done for the molecular diagnosis of visceral leishmaniasis. Leishmania sp. has a unique organelle, the kinetoplast, which corresponds to the mitochondrial DNA. It is organized into a large number of minicircles, which has made it a target for the development of diagnostic PCR. The quanty Leishmaniae, Clonit kit targeting ribosomal DNA was compared to a widely used laboratory-developed method based on kinetoplast DNA. This reference method gave significantly better results, probably due to the difference in the number of repeats of the PCR targets.

Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation.

Shigellosis is an acute enteric infection caused mainly by the species Shigella flexneri and Shigella sonnei. Since surveillance of these pathogens indicated an increase in ciprofloxacin-resistant samples collected in Belgium between 2013 and 2018, a subset of 148 samples was analyzed with whole genome sequencing (WGS) to investigate their dispersion and underlying genomic features associated with ciprofloxacin resistance. A comparison between observed phenotypes and WGS-based resistance prediction to ciprofloxacin revealed perfect correspondence for all samples. Core genome multi-locus sequence typing and single nucleotide polymorphism-typing were used for phylogenomic investigation to characterize the spread of these infections within Belgium, supplemented with data from international reference collections to place the Belgian isolates within their global context. For S. flexneri, substantial diversity was observed with ciprofloxacin-resistant isolates assigned to several phylogenetic groups. Besides travel-related imports, several clusters of highly similar Belgian isolates could not be linked directly to international travel suggesting the presence of domestically circulating strains. For S. sonnei, Belgian isolates were all limited to lineage III, and could often be traced back to travel to countries in Asia and Africa, sometimes followed by domestic circulation. For both species, several clusters of isolates obtained exclusively from male patients were observed. Additionally, we illustrated the limitations of conventional serotyping of S. flexneri, which was impacted by serotype switching. This study contributes to a better understanding of the spread of shigellosis within Belgium and internationally, and highlights the added value of WGS for the surveillance of this pathogen.

Management of gestational trophoblastic diseases in a low resource country: establishment of a national center and its results.

To describe the process of establishing a reference center for gestational trophoblastic diseases (GTD) in Senegal and to report its main results so far. We describe the history and establishment of the center, which is based on the experience of the main international centers. The adaptations made to patient follow-up are detailed, while we follow FIGO and WHO diagnostic and management criteria. Finally, we report our main results. Between 2011 and 2017, 878 files were registered at the Center. More than half of the women had no histological confirmation of GTD (60.8 %). The diagnosis was then based on ultrasound images or macroscopic examination of molar vesicles. Spontaneous remission occurred in 64.5 % of the cases, while gestational trophoblastic neoplasia developed in 23.5 %. The FIGO criteria were slightly adapted for hCG monitoring. Methotrexate was the drug of choice in the low-risk group (97.8 %), while the EMACO protocol was financially difficult for nearly half of the high-risk group. The overall remission rate was 83 % and the specific lethality 11.6 %. Our center has demonstrated the efficiency of centralizing the management of GTDs. Difficulty in access to hCG and antimitotic drugs makes management difficult. However, we have introduced alternative solutions that we are working to improve.

Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept.

Despite being a well-established research method, the use of whole-genome sequencing (WGS) for routine molecular typing and pathogen characterization remains a substantial challenge due to the required bioinformatics resources and/or expertise. Moreover, many national reference laboratories and centers, as well as other laboratories working under a quality system, require extensive validation to demonstrate that employed methods are "fit-for-purpose" and provide high-quality results. A harmonized framework with guidelines for the validation of WGS workflows does currently, however, not exist yet, despite several recent case studies highlighting the urgent need thereof. We present a validation strategy focusing specifically on the exhaustive characterization of the bioinformatics analysis of a WGS workflow designed to replace conventionally employed molecular typing methods for microbial isolates in a representative small-scale laboratory, using the pathogen Neisseria meningitidis as a proof-of-concept. We adapted several classically employed performance metrics specifically toward three different bioinformatics assays: resistance gene characterization (based on the ARG-ANNOT, ResFinder, CARD, and NDARO databases), several commonly employed typing schemas (including, among others, core genome multilocus sequence typing), and serogroup determination. We analyzed a core validation dataset of 67 well-characterized samples typed by means of classical genotypic and/or phenotypic methods that were sequenced in-house, allowing to evaluate repeatability, reproducibility, accuracy, precision, sensitivity, and specificity of the different bioinformatics assays. We also analyzed an extended validation dataset composed of publicly available WGS data for 64 samples by comparing results of the different bioinformatics assays against results obtained from commonly used bioinformatics tools. We demonstrate high performance, with values for all performance metrics >87%, >97%, and >90% for the resistance gene characterization, sequence typing, and serogroup determination assays, respectively, for both validation datasets. Our WGS workflow has been made publicly available as a "push-button" pipeline for Illumina data at https://galaxy.sciensano.be to showcase its implementation for non-profit and/or academic usage. Our validation strategy can be adapted to other WGS workflows for other pathogens of interest and demonstrates the added value and feasibility of employing WGS with the aim of being integrated into routine use in an applied public health setting.

Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center.

The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulent S. aureus lineages [clonal complexes (CCs): CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based on de novo assembly (reference-free approach), single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers. We examined the phylogeographic diversity of the French dominant hospital-acquired CC8-MRSA (methicillin-resistant S. aureus) Lyon clone through WGS analysis which did not demonstrate evidence of large-scale geographic clustering. We analyzed sporadic cases along with two outbreaks of a CC1-MSSA (methicillin-susceptible S. aureus) clone containing the Panton-Valentine leukocidin (PVL) and results showed that two sporadic cases were closely related. We investigated an outbreak of PVL-positive CC30-MSSA in a school environment and were able to reconstruct the transmission history between eight families. We explored different outbreaks among newborns due to the CC5-MRSA Geraldine clone and we found evidence of an unsuspected link between two otherwise distinct outbreaks. Here, WGS provides the resolving power to disprove transmission events indicated by conventional methods (same sequence type, spa type, toxin profile, and antibiotic resistance profile) and, most importantly, WGS can reveal unsuspected transmission events. Therefore, WGS allows to better describe and understand outbreaks and (inter-)national dissemination of S. aureus lineages. Our findings underscore the importance of adding WGS for (inter-)national surveillance of infections caused by virulent clones of S. aureus but also substantiate the fact that technological optimization at the bioinformatics level is still urgently needed for routine use. However, the greatest limitation of WGS analysis is the completeness and the correctness of the reference database being used and the conversion of floods of data into actionable results. The WGS bioinformatics pipeline (EpiSeqTM) we used here can easily generate a uniform database and associated metadata for epidemiological applications.

Caracterización de las principales variables clínicas del glaucoma en pacientes con retinosis pigmentaria / Main clinical variables in characterization of patients with retinitis pigmentosa and glaucoma

Se realizó un estudio epidemiológico, descriptivo y transversal de 85 pacientes con alguna de las formas clínicas de glaucoma, dispensarizados en el Centro Nacional de Referencia de Retinosis Pigmentaria durante el primer semestre del 2010. Entre las variables analizadas de acuerdo con la clasificación de la Escuela Cubana de Retinosis Pigmentaria, figuraron: agudeza visual, alteraciones campimétricas, herencia de retinosis y consanguinidad, hipertensión ocular y espesor corneal, según los tipos de dichas afecciones. En la serie, 32,9 % tenía visión entre 0,1 y 0,3; 47,05 %, reducción concéntrica del campo visual (5 y 10 °) y patrón autosómico recesivo; 17,64 %, antecedentes de consanguinidad y 38,8 %, comienzo juvenil. Se halló hipertensión ocular en 82,35 %, con predominio en la retinosis típica de grado IV (40,0 %), así como disminución del espesor corneal en 34,1% de la casuística. La letalidad visual por la asociación de ambas oftalmopatías exige que sea investigada detenidamente. Hasta el momento, la medición adecuada de la presión intraocular (aplanación con ajuste a los valores del espesor corneal) constituye la herramienta más útil para diagnosticar la enfermedad y evaluar su evolución en estos pacientes.

An epidemiological, descriptive and cross-sectional study was carried out in 85 patients with some clinical forms of glaucoma, attended and monitored at the National Reference Center of Retinitis Pigmentosa during the first semester of 2010. Among the analyzed variables according to the classification of the Cuban School of Retinitis Pigmentosa were visual acuity, visual field defects, retinitis inheritance and consanguinity, ocular hypertension and corneal thickness according to the types of these conditions. In the series 32,9 % had vision between 0,1 and 0,3; concentric reduction of vision field (5 and 10 °) and autosomal recessive pattern in 47,05 %; history of consanguinity in 17,4 % and juvenile onset in 38.8%. Ocular hypertension was found in 82,35 % with predominance in grade IV typical retinitis (40,0 %), as well as reduction of corneal thickness in 34,1 % of all cases. The visual letality caused by association of both eye diseases requires to be studied carefully. So far, proper measurement of intraocular pressure (applanation adjusted to the values of corneal thickness) is the most useful tool to diagnose disease and to evaluate its progress in these patients.