Genomics and metagenomics in medical microbiology

SCI-VCF: a cross-platform GUI solution to summarize, compare, inspect and visualize the variant call format

As genomics advances swiftly and its applications extend to diverse fields, bioinformatics tools must enable researchers and clinicians to work with genomic data irrespective of their programming expertise. We developed SCI-VCF, a Shiny-based comprehensive analysis utility to summarize, compare, inspect, analyse and design interactive visualizations of the genetic variants from the variant call format. With an intuitive graphical user interface, SCI-VCF aims to bridge the approachability gap in genomics that arises from the existing predominantly command-line utilities. SCI-VCF is written in R and is freely available at https://doi.org/10.5281/zenodo.11453080. For installation-free access, users can avail themselves of an online version at https://ibse.shinyapps.io/sci-vcf-online.

Skin Microbial Composition and Genetic Mutation Analysis in Precision Medicine for Epidermolysis Bullosa

Epidermolysis bullosa (EB) is an inherited skin disease representing a spectrum of rare genetic disorders. These conditions share the common trait that causes fragile skin, resulting in the development of blisters and erosions. The inheritance follows an autosomal pattern, and the array of clinical presentations leads to significant physical suffering, considerable morbidity, and mortality. Despite EB having no cure, effectively managing EB remains an exceptional challenge due to its rarity and complexity, occasionally casting a profound impact on the lives of affected individuals. Considering that EB management requires a multidisciplinary approach, this sometimes worsens the condition of patients with EB due to inappropriate handling. Thus, more appropriate and precise treatment management of EB is essentially needed. Advanced technology in medicine and health comes into the bioinformatics era. Including treatment for skin diseases, omics-based approaches aim to evaluate and handle better disease management and treatment. In this work, we review several approaches regarding the implementation of omics-based technology, including genetics, pathogenic mutation, skin microbiomics, and metagenomics analysis for EB. In addition, we highlight recent updates on the potential of metagenomics analysis in precision medicine for EB.

Exploring Eimeria Genomes to Understand Population Biology: Recent Progress and Future Opportunities

Eimeria, protozoan parasites from the phylum Apicomplexa, can cause the enteric disease coccidiosis in all farmed animals. Coccidiosis is commonly considered to be most significant in poultry; due in part to the vast number of chickens produced in the World each year, their short generation time, and the narrow profit margins associated with their production. Control of Eimeria has long been dominated by routine chemoprophylaxis, but has been supplemented or replaced by live parasite vaccination in a minority of production sectors. However, public and legislative demands for reduced drug use in food production is now driving dramatic change, replacing reliance on relatively indiscriminate anticoccidial drugs with vaccines that are Eimeria species-, and in some examples, strain-specific. Unfortunately, the consequences of deleterious selection on Eimeria population structure and genome evolution incurred by exposure to anticoccidial drugs or vaccines are unclear. Genome sequence assemblies were published in 2014 for all seven Eimeria species that infect chickens, stimulating the first population genetics studies for these economically important parasites. Here, we review current knowledge of eimerian genomes and highlight challenges posed by the discovery of new, genetically cryptic Eimeria operational taxonomic units (OTUs) circulating in chicken populations. As sequencing technologies evolve understanding of eimerian genomes will improve, with notable utility for studies of Eimeria biology, diversity and opportunities for control.

Shotgun-Metagenomics on Positive Blood Culture Bottles Inoculated With Prosthetic Joint Tissue: A Proof of Concept Study

Clinical metagenomics is actively moving from research to clinical laboratories. It has the potential to change the microbial diagnosis of infectious diseases, especially when detection and identification of pathogens can be challenging, such as in prosthetic joint infection (PJI). The application of metagenomic sequencing to periprosthetic joint tissue (PJT) specimens is often challenged by low bacterial load in addition to high level of inhibitor and contaminant host DNA, limiting pathogen recovery. Shotgun-metagenomics (SMg) performed directly on positive blood culture bottles (BCBs) inoculated with PJT may be a convenient approach to overcome these obstacles. The aim was to test if it is possible to perform SMg on PJT inoculated into BCBs for pathogen identification in PJI diagnosis. Our study was conducted as a laboratory method development. For this purpose, spiked samples (positive controls), negative control and clinical tissue samples (positive BCBs) were included to get a comprehensive overview. We developed a method for preparation of bacterial DNA directly from PJT inoculated in BCBs. Samples were processed using MolYsis5 kit for removal of human DNA and DNA extracted with BiOstic kit. High DNA quantity/quality was obtained, and no inhibition was observed during the library preparation, allowing further sequencing process. DNA sequencing reads obtained from the BCBs, presented a low proportion of human reads (<1%) improving the sensitivity of bacterial detection. We detected a 19-fold increase in the number of reads mapping to human in a sample untreated with MolYsis5. Taxonomic classification of clinical samples identified a median of 96.08% (IQR, 93.85-97.07%; range 85.7-98.6%) bacterial reads. Shotgun-metagenomics results were consistent with the results from a conventional BCB culture method, validating our approach. Overall, we demonstrated a proof of concept that it is possible to perform SMg directly on BCBs inoculated with PJT, with potential of pathogen identification in PJI diagnosis. We consider this a first step in research efforts needed to face the challenges presented in PJI diagnoses.

Childhood diarrhoeal diseases in developing countries

Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.

Genome sequence-based criteria for demarcation and definition of species in the genus Rickettsia

Over recent years, genomic information has increasingly been used for prokaryotic species definition and classification. Genome sequence-based alternatives to the gold standard DNA–DNA hybridization (DDH) relatedness have been developed, notably average nucleotide identity (ANI), which is one of the most useful measurements for species delineation in the genomic era. However, the strictly intracellar lifestyle, the few measurable phenotypic properties and the low level of genetic heterogeneity made the current standard genomic criteria for bacterial species definition inapplicable to Rickettsia species. We evaluated a range of whole genome sequence (WGS)-based taxonomic parameters to develop guidelines for the classification of Rickettsia isolates at genus and species levels. By comparing the degree of similarity of 74 WGSs from 31 Rickettsia species and 61 WGSs from members of three closely related genera also belonging to the order Rickettsiales ( Orientia , 11 genomes; Ehrlichia , 22 genomes; and Anaplasma , 28 genomes) using digital DDH (dDDh) and ANI by orthology (OrthoANI) parameters, we demonstrated that WGS-based taxonomic information, which is easy to obtain and use, can serve for reliable classification of isolates within the Rickettsia genus and species. To be classified as a member of the genus Rickettsia , a bacterial isolate should exhibit OrthoANI values with any Rickettsia species with a validly published name of ≥83.63 %. To be classified as a new Rickettsia species, an isolate should not exhibit more than any of the following degrees of genomic relatedness levels with the most closely related species: >92.30 and >99.19 % for the dDDH and OrthoANI values, respectively. When applied to four rickettsial isolates of uncertain status, the above-described thresholds enabled their classification as new species in one case. Thus, we propose WGS-based guidelines to efficiently delineate Rickettsia species, with OrthoANI and dDDH being the most accurate for classification at the genus and species levels, respectively.

Metagenomic Assessment of Different Interventions for Treatment of Chronic Periodontitis: A Systematic Review and Meta-Analysis

Background:

Chronic periodontitis is attributed to oral microbial imbalance and host inflammatory reaction.

Objective:

Our review addresses the question of: Are the available interventions able to regain oral microbial balance in patients having chronic periodontitis?

Data Sources:

We performed a comprehensive systematic search of MEDLine via Pubmed, Cochrane CENTRAL, Clinicalkey, Clarivate Analytics, Springer materials, Wiley, SAGE, Elsevier, Taylor & Francis group, and Wolter Kluwer, together with hand searching and searching the grey literature.

Eligibility Criteria:

We included interventional studies testing the microbiome analysis using metagenomic techniques as an outcome to any intervention for chronic periodontitis.

Study Appraisal and Synthesis Methods:

All studies were imported in Mendeley. The risk of bias was assessed using the specific tool for each study design. The results were analysed using RevMan. All the review steps were performed in duplicates.

Results:

The search yielded 2700 records. After exclusion steps, 10 records were found eligible. We included 5 RCTs, 1 non-RCT, 3 before-and-after studies, and 1 ongoing study. The studies tested non-surgical periodontal treatment with and without antibiotic coverage, probiotics, sodium hypochlorite rinse, and different toothpaste ingredients. One RCT tested the use of enamel matrix derivatives in cases with furcation involvement.

Limitations:

The eligible available studies were small in number. Also, the risk of bias and lack of a standardized protocol impaired the ability to pool all the results.

Conclusions:

The body of the available evidence is not sufficient, and future studies are recommended to better evaluate the effect of periodontal treatments on the periodontal microbiome.

Metataxonomics of Internal Transcribed Spacer amplicons in cerebrospinal fluid for diagnosing and genotyping of cryptococcal meningitis

BACKGROUND

Cryptococcal meningitis is a severe infectious disease associated with high morbidity and mortality. Rapidity and accuracy of diagnosis contribute to better prognosis, but readily available tools, such as microscopy, culture, and antigens do not perform well all the time. Our study attempted to diagnose and genotype cryptococcus in the cerebrospinal fluid (CSF) samples from patients with cryptococcal meningitis using the approach of metataxonomics of Internal Transcribed Spacer (ITS) amplicons.

METHODS

The CSF samples were collected from 11 clinically suspected cryptococcal meningitis patients and four non-infectious controls. Samples were recruited from the First Affiliated Hospital of Fujian Medical University Hospital, Fuzhou Fourth Hospital and the 476th Hospital of Chinese People's Liberation Army from December 2017 to December 2018. ITS1 ribosomal deoxyribonucleic acid (rDNA) genes of 15 whole samples were amplified by universal forward primer ITS1 (CTTGGTCATTTAGAGGAAGTAA) and reverse primer ITS2 (GCTGCGTTCTTCATCGATGC), sequenced by Illumina MiSeq Benchtop Sequencer. The results were confirmed by sanger sequencing of ITS1 region and partial CAP59 gene of microbial isolates from 11 meningitic samples. Pair-wise comparison between infectious group and control group was conducted through permutational multivariate analysis (PERMANOVA) in R software.

RESULTS

The 30,000 to 340,000 high-quality clean reads were obtained from each of the positively stained or cultured CSF samples and 8 to 60 reads from each control. The samples from 11 infected patients yielded detectable cryptococcal-specific ITS1 DNA with top abundance (from 95.90% to 99.97%), followed by many other fungal groups (each <1.41%). ITS genotype was defined in 11 CSF samples, corresponding to ITS type 1, and confirmed by Sanger sequencing. A statistically significant difference (r = 0.65869, P = 0.0014) between infectious group and control group was observed.

CONCLUSIONS

The metataxonomics of ITS amplicons facilitates the diagnosis and genotype of cryptococcus in CSF samples, which may provide a better diagnostic approach of cryptococcal infection.

Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling

The aim of this work was to analyze and compare the bacterial communities of 663 samples from a Brazilian hospital by using high-throughput sequencing of the 16S rRNA gene. To increase taxonomic profiling and specificity of 16S-based identification, a strict sequence quality filtering process was applied for the accurate identification of clinically relevant bacterial taxa. Our results indicate that the hospital environment is predominantly inhabited by closely related species. A massive dominance of a few taxa in all taxonomic levels down to the genera was observed, where the ten most abundant genera in each facility represented 64.4% of all observed taxa, with a major predominance of Acinetobacter and Pseudomonas. The presence of several nosocomial pathogens was revealed. Co-occurrence analysis indicated that the present hospital microbial network had low connectedness, forming a clustered topology, but not structured among groups of nodes (i.e., modules). Furthermore, we were able to detect ecologically relevant relationships between specific microbial taxa, in particular, potential competition between pathogens and non-pathogens. Overall, these results provide new insight into different aspects of a hospital microbiome and indicate that 16S rRNA sequencing may serve as a robust one-step tool for microbiological identification and characterization of a wide range of clinically relevant bacterial taxa in hospital settings with a high resolution.

Molecular Methods for Detection of Antimicrobial Resistance

The increase in bacteria harboring antimicrobial resistance (AMR) is a global problem because there is a paucity of antibiotics available to treat multidrug-resistant bacterial infections in humans and animals. Detection of AMR present in bacteria that may pose a threat to veterinary and public health is routinely performed using standardized phenotypic methods. Molecular methods are often used in addition to phenotypic methods but are set to replace them in many laboratories due to the greater speed and accuracy they provide in detecting the underlying genetic mechanism(s) for AMR. In this article we describe some of the common molecular methods currently used for detection of AMR genes. These include PCR, DNA microarray, whole-genome sequencing and metagenomics, and matrix-assisted laser desorption ionization-time of flight mass spectrometry. The strengths and weaknesses of these methods are discussed, especially in the context of implementing them for routine surveillance activities on a global scale for mitigating the risk posed by AMR worldwide. Based on current popularity and ease of use, PCR and single-isolate whole-genome sequencing seem irreplaceable.

Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora

Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille‐P2481 (= CSUR P2481 =  DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram‐positive, strictly aerobic, spore‐forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille‐P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0–8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12‐methyl‐tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille‐P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103^T, the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille‐P2481^T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.

Application of Metagenomic Analyses in Dentistry as a Novel Strategy Enabling Complex Insight into Microbial Diversity of the Oral Cavity

The composition of the oral microbiome in healthy individuals is complex and dynamic, and depends on many factors, such as anatomical location in the oral cavity, diet, oral hygiene habits or host immune responses. It is estimated at present that worldwide about 2 billion people suffer from diseases of the oral cavity, mainly periodontal disease and dental caries. Importantly, the oral microflora involved in local infections may spread and cause systemic, even life-threatening infections. In search for etiological agents of infections in dentistry, traditional approaches are not sufficient, as about 50% of oral bacteria are not cultivable. Instead, metagenomic analyses are particularly useful for studies of the complex oral microbiome - both in healthy individuals, and in patients with oral and dental diseases. In this paper we review the current and future applications of metagenomic studies in evaluation of both the composition of the oral microbiome as well as its potential pathogenic role in infections in dentistry.

Studying the human oral microbiome: challenges and the evolution of solutions

Since the pioneering work of van Leeuwenhoek in 1684, subsequently built upon by other renowned microbiologists Robert Koch, Willoughby Miller and GV Black, oral microbiology has developed innovative techniques to study the oral microflora (now termed the 'oral microbiome'). The advent of molecular techniques such as DNA-DNA hybridization, polymerase chain reaction and DNA sequencing has created an array of opportunities to construct a comprehensive picture of the diversity and composition of the oral microbiome. Approximately 700 oral bacterial species have been identified, of which 50% have yet to be cultivated, and some of these are known only by their signature DNA sequences. The synergism of ever-evolving culture-based and state-of-the-art culture-independent molecular techniques has facilitated in-depth understanding of the dynamics, acquisition and transfer of oral bacteria, along with their role in oral and general health and disease. Further research is needed to not only analyse but also to make sense of the ever-increasing volumes of data which these molecular techniques (especially high-throughput DNA sequencing) are generating, as well as why particular bacteria are present and what they are 'actually doing' there. This review presents a comprehensive literature search of oral microbiology-related methods currently used to study the oral microbiome.

[Description and role of bacteriological techniques in the management of lung infections]

Les pneumopathies aiguës recouvrent des contextes cliniques variés et les étiologies bactériennes impliquées le sont tout autant. Aucun outil microbiologique n’est 100 % sensible ni 100 % spécifique et malgré les investigations, plus de 30 % des pneumopathies restent sans étiologie identifiée. Si aucun prélèvement n’est indiqué pour les patients traités en ambulatoire, les prélèvements respiratoires non invasifs sont à privilégier pour les pneumopathies aiguës hospitalisées (communautaires ou associées aux soins), tandis que les prélèvements invasifs sont indiqués en seconde ligne pour les pneumopathies aiguës communautaires en réanimation, et en première ligne pour les pneumopathies aiguës de l’immunodéprimé. La culture microbiologique garde une place importante, à condition que le malade soit prélevé avant instauration de l’antibiothérapie. Certains contextes peuvent justifier le recours aux hémocultures, à la recherche d’antigènes urinaires ou aux sérologies. Les PCR rendent déjà service au quotidien mais l’avenir à court terme appartient probablement aux panels moléculaires multiplex capables de détecter de nombreux micro-organismes en quelques heures, surtout dans les pneumopathies communautaires sévères de réanimation et les pneumopathies aiguës de l’immunodéprimé. Le séquençage nucléotidique haut débit révolutionnera bientôt le diagnostic microbiologique, en pneumologie comme dans les autres domaines de l’infectiologie.

Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue

Background

Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences.

Results

Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences.

Conclusions

The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-1035-2) contains supplementary material, which is available to authorized users.

The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing

The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative “infection” at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most “informative” area to be examined. Tissue genotyping indicated male gender, thereby confirming the notary’s report. 16S ribosomal RNA sequencing showed that Proteobacteria and Actinobacteria were more abundant than Firmicutes and Bacteroidetes, and that Pseudomonas was the most abundant bacterial genus in the Pseudomonadaceae family. These data suggest that the patient most likely died from Pseudomonas osteomyelitis. This case is an example of how new technological approaches, like laser microdissection and next-generation sequencing, can resolve ancient cases of uncertain etiopathology. Lastly, medical samples may contain a wealth of information that may not be accessible until more sophisticated technology becomes available. Therefore, one may envisage the possibility of systematically storing medical samples for evaluation by future generations.

Molecular Testing in Emerging Infectious Diseases

It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.

Clinical metagenomic analysis of bacterial communities in breast abscesses of granulomatous mastitis

BACKGROUND

Granulomatous mastitis (GM) is a chronic inflammatory breast lesion. Its etiology remains incompletely defined. Although mounting evidence suggests the involvement of Corynebacterium in GM, there has been no systematic study of GM bacteriology using -omics technology.

METHODS

The bacterial diversity and relative abundances in breast abscesses from 19 women with GM were investigated using 16S rDNA metagenomic sequencing and Sanger sequencing. A quantitative PCR (qPCR) assay was also developed to identify Corynebacterium kroppenstedtii.

RESULTS

A bioinformatic analysis revealed that Corynebacterium was present in the 19 GM patients, with abundances ranging from 1.1% to 58.9%. Of note, Corynebacterium was the most abundant taxon in seven patients (more than a third of the subjects). The predominance of Corynebacterium kroppenstedtii infection (11 of 19 patients, 57.9%) was confirmed with Sanger sequencing and the qPCR assay.

CONCLUSIONS

This study profiled the microbiota of patients with GM and indicated an important role for Corynebacterium, and in particular C. kroppenstedtii, in the pathogenesis of this disease.

Comparative Microbial Genomics and Forensics

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

Detection of Listeria monocytogenes in CSF from Three Patients with Meningoencephalitis by Next-Generation Sequencing

Background and Purpose

Encephalitis caused by Listeria monocytogenes (L. monocytogenes) is rare but sometimes fatal. Early diagnosis is difficult using routine cerebrospinal fluid (CSF) tests, while next-generation sequencing (NGS) is increasingly being used for the detection and characterization of pathogens.

Methods

This study set up and applied unbiased NGS to detect L. monocytogenes in CSF collected from three cases of clinically suspected listeria meningoencephalitis.

Results

Three cases of patients with acute/subacute meningoencephalitis are reported. Magnetic resonance imaging and blood cultures led to a suspected diagnosis of L. monocytogenes, while the CSF cultures were negative. Unbiased NGS of CSF identified and sequenced reads corresponding to L. monocytogenes in all three cases.

Conclusions

This is the first report highlighting the feasibility of applying NGS of CSF as a diagnostic method for central nervous system (CNS) L. monocytogenes infection. Routine application of this technology in clinical microbiology will significantly improve diagnostic methods for CNS infectious diseases.

Targeting cell membrane adaptation as a novel antimicrobial strategy

Emergence of antibiotic resistance is an example of the incredible plasticity of bacteria to survive in all environments. The search for new antibiotics active against traditional targets is more challenging due not only to the lack of novel natural products to fulfill the current clinical needs against multidrug-resistant (MDR) bacteria, but also for the possible 'collateral' effects on the human microbiota. Thus, non-traditional approaches to combat MDR bacteria have been proposed. Here, we discuss the possibility of targeting the membrane response to the antibiotic attack (cell membrane adaptation) as a viable strategy to increase the activity of current antimicrobials, enhance the activity of the innate immune system and prevent development of resistance during therapy using the three-component regulatory system LiaFSR of enterococci as a model.

Optimization of alignment-based methods for taxonomic binning of metagenomics reads

MOTIVATION

Alignment-based taxonomic binning for metagenome characterization proceeds in two steps: reads mapping against a reference database (RDB) and taxonomic assignment according to the best hits. Beyond the sequencing technology and the completeness of the RDB, selecting the optimal configuration of the workflow, in particular the mapper parameters and the best hit selection threshold, to get the highest binning performance remains quite empirical.

RESULTS

We developed a statistical framework to perform such optimization at a minimal computational cost. Using an optimization experimental design and simulated datasets for three sequencing technologies, we built accurate prediction models for five performance indicators and then derived the parameter configuration providing the optimal performance. Whatever the mapper and the dataset, we observed that the optimal configuration yielded better performance than the default configuration and that the best hit selection threshold had a large impact on performance. Finally, on a reference dataset from the Human Microbiome Project, we confirmed that the optimized configuration increased the performance compared with the default configuration.

AVAILABILITY AND IMPLEMENTATION

Not applicable.

CONTACT

magali.dancette@biomerieux.com

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Depletion of Human DNA in Spiked Clinical Specimens for Improvement of Sensitivity of Pathogen Detection by Next-Generation Sequencing

Next-generation sequencing (NGS) technology has shown promise for the detection of human pathogens from clinical samples. However, one of the major obstacles to the use of NGS in diagnostic microbiology is the low ratio of pathogen DNA to human DNA in most clinical specimens. In this study, we aimed to develop a specimen-processing protocol to remove human DNA and enrich specimens for bacterial and viral DNA for shotgun metagenomic sequencing. Cerebrospinal fluid (CSF) and nasopharyngeal aspirate (NPA) specimens, spiked with control bacterial and viral pathogens, were processed using either a commercially available kit (MolYsis) or various detergents followed by DNase prior to the extraction of DNA. Relative quantities of human DNA and pathogen DNA were determined by real-time PCR. The MolYsis kit did not improve the pathogen-to-human DNA ratio, but significant reductions (>95%;P< 0.001) in human DNA with minimal effect on pathogen DNA were achieved in samples that were treated with 0.025% saponin, a nonionic surfactant. Specimen preprocessing significantly decreased NGS reads mapped to the human genome (P< 0.05) and improved the sensitivity of pathogen detection (P< 0.01), with a 20- to 650-fold increase in the ratio of microbial reads to human reads. Preprocessing also permitted the detection of pathogens that were undetectable in the unprocessed samples. Our results demonstrate a simple method for the reduction of background human DNA for metagenomic detection for a broad range of pathogens in clinical samples.

Respiratory Infections

The majority of respiratory tract infections (RTIs) are community acquired and are the single most common cause of physician office visits and among the most common causes of hospitalizations. The morbidity and mortality associated with RTIs are significant and the financial and social burden high due to lost time at work and school. The scope of clinical symptoms can significantly overlap among the respiratory pathogens, and the severity of disease can vary depending on patient age, underlying disease, and immune status, thereby leading to inaccurate presumptions about disease etiology. The rapid and accurate diagnosis of the causative agent of RTIs improves patient care, reduces morbidity and mortality, promotes effective hospital bed utilization and antibiotic stewardship, and reduces length of stay. This chapter focuses on the clinical utility, advantages, and disadvantages of viral and bacterial tests cleared by the Food and Drug Administration (FDA), and new promising technologies for the detection of bacterial agents of pneumonia currently in development or in US FDA clinical trials are briefly reviewed.

Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of central nervous system of unknown etiology. However, some infectious agents have been suggested to play a significant role in its pathogenesis. Next-generation sequencing (NGS) and metagenomics can be employed to characterize microbiome of MS patients and to identify potential causative pathogens. In this study, 12 patients with idiopathic inflammatory demyelinating disorders (IIDD) of the central nervous system were studied: one patient had clinically isolated syndrome, one patient had recurrent optic neuritis, and ten patients had multiple sclerosis (MS). In addition, there was one patient with other non-inflammatory neurological disease. Cerebrospinal fluid (CSF) was sampled from all patients. RNA was extracted from CSF and subjected to a single-primer isothermal amplification followed by NGS and comprehensive data analysis. Altogether 441,608,474 reads were obtained and mapped using blastn. In a CSF sample from the patient with clinically isolated syndrome, 11 varicella-zoster virus reads were found. Other than that similar bacterial, fungal, parasitic, and protozoan reads were identified in all samples, indicating a common presence of contamination in metagenomics. In conclusion, we identified varicella zoster virus sequences in one out of the 12 patients with IIDD, which suggests that this virus could be occasionally related to the MS pathogenesis. A widespread bacterial contamination seems inherent to NGS and complicates the interpretation of results.

Improvement in detecting bacterial infection in lower respiratory tract infections using the Intensive Care Infection Score (ICIS)

Immediate treatment of lower respiratory tract infections (LRTI) caused by bacteria is important to reduce pneumonia and other complications such as systemic inflammatory response syndrome and sepsis. Nowadays procalcitonin (PCT) is the gold standard to differentiate between bacterial and non-bacterial infections in LRTI. The aim of this study was to evaluate if the new Intensive Care Infection Score (ICIS) which is a combination of various cellular measurements made on hematology analyzers could be a potential method to differentiate between bacterial and non-bacterial infections in LRTI.

The ICIS is composed of five blood-cell derived parameters characterizing the early innate immune response; (1) mean fluorescence intensity of mature (segmented) neutrophils; (2) the difference in hemoglobin concentration between newly formed red blood cells and the mature ones; (3) absolute number of segmented neutrophils; (4) absolute count of antibody secreting lymphocytes and (5) absolute count of number of granulocytes.

The discriminative power of ICIS to differentiate between patients with LRTI of bacterial and non-bacterial origin is as good or even better as the commonly used infection biomarkers PCT, CRP and IL-6.

Beside PCT, CRP and IL-6, ICIS could be used as infection marker in LRTI.

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform

BACKGROUND

The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as uniformly available. Pathosphere (found at Pathosphere.org) is a cloud - based open - sourced community tool that allows for communication, collaboration and sharing of NGS analytical tools and data amongst scientists working in academia, industry and government. The architecture allows for users to upload data and run available bioinformatics pipelines without the need for onsite processing hardware or technical support.

RESULTS

The pathogen detection capabilities hosted on Pathosphere were tested by analyzing pathogen-containing samples sequenced by NGS with both spiked human samples as well as human and zoonotic host backgrounds. Pathosphere analytical pipelines developed by Edgewood Chemical Biological Center (ECBC) identified spiked pathogens within a common sample analyzed by 454, Ion Torrent, and Illumina sequencing platforms. ECBC pipelines also correctly identified pathogens in human samples containing arenavirus in addition to animal samples containing flavivirus and coronavirus. These analytical methods were limited in the detection of sequences with limited homology to previous annotations within NCBI databases, such as parvovirus. Utilizing the pipeline-hosting adaptability of Pathosphere, the analytical suite was supplemented by analytical pipelines designed by the United States Army Medical Research Insititute of Infectious Diseases and Walter Reed Army Institute of Research (USAMRIID-WRAIR). These pipelines were implemented and detected parvovirus sequence in the sample that the ECBC iterative analysis previously failed to identify.

CONCLUSIONS

By accurately detecting pathogens in a variety of samples, this work demonstrates the utility of Pathosphere and provides a platform for utilizing, modifying and creating pipelines for a variety of NGS technologies developed to detect pathogens in complex sample backgrounds. These results serve as an exhibition for the existing pipelines and web-based interface of Pathosphere as well as the plug-in adaptability that allows for integration of newer NGS analytical software as it becomes available.

Detection of virus in CSF from the cases with meningoencephalitis by next-generation sequencing

We screened for viral DNA in cerebrospinal fluid samples using next-generation sequencing (NGS) technology to diagnose CNS viral infections. We collected CSF samples from four cases with clinically suspected viral meningoencephalitis. DNA extracted from the samples was analyzed with NGS, and the results were further validated using PCR. Herpes simplex virus 1 (HSV-1) was detected in the CSF of two patients, HSV-2 and human herpes virus type 3 (HHV-3, VZV) in the CSF of two other patients separately. The number of unique reads of the identified viral genes ranged from 144 to 44205 (93.51 to 99.57%). The coverage of identified viral genes ranged from 12 to 98% with a depth value of 1.1 to 35, respectively. The results were further confirmed using PCR in three cases. The clinical presentation and outcomes of these four cases were consistent with the diagnostic results of NGS. NGS of CSF samples can be used as a diagnostic assay for CNS viral infection. Its further application for "pan-viral" or even "pan-microbial" screening of CSF might influence the diagnosis of CNS infectious diseases.

Rapid detection and identification of infectious pathogens based on high-throughput sequencing

Background:

The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians.

Methods:

In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing.

Results:

Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein–Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive.

Conclusions:

This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.

Characterization of the Bacterial Community Naturally Present on Commercially Grown Basil Leaves: Evaluation of Sample Preparation Prior to Culture-Independent Techniques

Fresh herbs such as basil constitute an important food commodity worldwide. Basil provides considerable culinary and health benefits, but has also been implicated in foodborne illnesses. The naturally occurring bacterial community on basil leaves is currently unknown, so the epiphytic bacterial community was investigated using the culture-independent techniques denaturing gradient gel electrophoresis (DGGE) and next-generation sequencing (NGS). Sample preparation had a major influence on the results from DGGE and NGS: Novosphingobium was the dominant genus for three different basil batches obtained by maceration of basil leaves, while washing of the leaves yielded lower numbers but more variable dominant bacterial genera including Klebsiella, Pantoea, Flavobacterium, Sphingobacterium and Pseudomonas. During storage of basil, bacterial growth and shifts in the bacterial community were observed with DGGE and NGS. Spoilage was not associated with specific bacterial groups and presumably caused by physiological tissue deterioration and visual defects, rather than by bacterial growth.

[Current perspectives on genome-based diagnostic tests in Pediatrics]

Etiological diagnosis is essential in the clinical management of individual patients. Some children with complex medical conditions are subjected to numerous testing, known as "diagnostic odyssey", which often gives no conclusive results. In recent years, a revolution in genomic medicine is underway with the use of technologies that promise to increase the ability to make a diagnosis and reduce the time involved. The main advantages and limitations of genomic diagnosis, as opposed to usual methodologies are reviewed with an emphasis on Pediatrics.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.

Individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology

For bacteria, replication mainly involves growth by binary fission. However, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. They thereby evade detection by conventional culture-based methods. Such dormant cells may also be observed in laboratory cultures and in clinical microbiology. They are usually more tolerant to stresses such as antibiotics, and in clinical microbiology they are typically referred to as 'persisters'. Bacterial cultures necessarily share a great deal of relatedness, and inclusive fitness theory implies that there are conceptual evolutionary advantages in trading a variation in growth rate against its mean, equivalent to hedging one's bets. There is much evidence that bacteria exploit this strategy widely. We here bring together data that show the commonality of these phenomena across environmental, laboratory and clinical microbiology. Considerable evidence, using methods similar to those common in environmental microbiology, now suggests that many supposedly non-communicable, chronic and inflammatory diseases are exacerbated (if not indeed largely caused) by the presence of dormant or persistent bacteria (the ability of whose components to cause inflammation is well known). This dormancy (and resuscitation therefrom) often reflects the extent of the availability of free iron. Together, these phenomena can provide a ready explanation for the continuing inflammation common to such chronic diseases and its correlation with iron dysregulation. This implies that measures designed to assess and to inhibit or remove such organisms (or their access to iron) might be of much therapeutic benefit.

Survival and activity of individual bioaugmentation strains

Successful application of bioaugmentation for enhanced degradation of environmental pollutants is often limited by the lack of methods to monitor the survival and activity of individual bioaugmentation strains. However, recent advancements in sequencing technologies and molecular techniques now allow us to address these limitations. Here a complementing set of general applicable molecular methods are presented that provides detailed information on the performance of individual bioaugmentation strains under in situ conditions. The approach involves genome sequencing to establish highly specific qPCR and RT-qPCR tools for cell enumerations and expression of involved genes, stable isotope probing to follow growth on the target compounds and GFP-tagging to visualize the bioaugmentation strains directly in samples, all in combination with removal studies of the target compounds. The concept of the approach is demonstrated through a case study involving degradation of aromatic hydrocarbons in activated sludge augmented with the bioaugmentation strain Pseudomonas monteilii SB3078.

The world's microbiology laboratories can be a global microbial sensor network

The microbes that infect us spread in global and local epidemics, and the resistance genes that block their treatment spread within and between them. All we can know about where they are to track and contain them comes from the only places that can see them, the world's microbiology laboratories, but most report each patient's microbe only to that patient's caregiver. Sensors, ranging from instruments to birdwatchers, are now being linked in electronic networks to monitor and interpret algorithmically in real-time ocean currents, atmospheric carbon, supply-chain inventory, bird migration, etc. To so link the world's microbiology laboratories as exquisite sensors in a truly lifesaving real-time network their data must be accessed and fully subtyped. Microbiology laboratories put individual reports into inaccessible paper or mutually incompatible electronic reporting systems, but those from more than 2,200 laboratories in more than 108 countries worldwide are now accessed and translated into compatible WHONET files. These increasingly web-based files could initiate a global microbial sensor network. Unused microbiology laboratory byproduct data, now from drug susceptibility and biochemical testing but increasingly from new technologies (genotyping, MALDI-TOF, etc.), can be reused to subtype microbes of each genus/species into sub-groupings that are discriminated and traced with greater sensitivity. Ongoing statistical delineation of subtypes from global sensor network data will improve detection of movement into any patient of a microbe or resistance gene from another patient, medical center or country. Growing data on clinical manifestations and global distributions of subtypes can automate comments for patient's reports, select microbes to genotype and alert responders.

Identification of a novel coronavirus from guinea fowl using metagenomics

While classical virology techniques such as virus culture, electron microscopy, or classical PCR had been unsuccessful in identifying the causative agent responsible for the fulminating disease of guinea fowl, we identified a novel avian gammacoronavirus associated with the disease using metagenomics. Next-generation sequencing is an unbiased approach that allows the sequencing of virtually all the genetic material present in a given sample.

Small-intestinal or colonic microbiota as a potential amino acid source in animals

Factors affecting physiological impacts of the microbiome on protein nutrition are discussed for hind-gut fermenters (humans, pigs, rodents). The microbiome flourishes in all gastrointestinal organs, and is a major source of amino acids to fore-gut fermenting animals. In humans, rats and pigs the net effect of microbiome biomass synthesis on amino acid requirements is much less certain. Dietary proteins, amino acids, peptides, endogenous-secreted protein and recycled urea may all be utilized as nitrogen source by growing bacteria in the small intestine and colon. The inclusions of radiolabelled amino acid precursors will result in labeled bacteria which can be digested and absorbed in the ileum and to some degree in the colon. This does not necessarily indicate a significant nutritional role of the microbiome in humans, pigs and rodents. The physiological attributes required for small-intestinal and colon microbiome utilization are a vigorous proteolytic digestion with pancreatic or intestinal enzymes and the presence of amino acid transporters. Findings to date seem to suggest that these two physiological attributes for effective bacterial protein utilization are present in the small intestine; however, these attributes have a much lower capacity/impact in the colon. The gastrointestinal microbiome is likely a protein source of medium to high nutritional quality, but overall the microbiome is not an important amino acid source in humans and animals fed amino acids at requirement levels.