Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study

Schneeberger, Pierre H. H.; Becker, Sören L.; Pothier, Joël F.; Duffy, Brion; N’Goran, Eliézer K.; Beuret, Christian; Frey, Jürg E.; Utzinger, Jürg

doi:10.1016/j.meegid.2015.08.044

Cited by 37 publications

(28 citation statements)

References 37 publications

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“…These were submitted to next-generation sequencing followed by metagenomic analysis as described elsewhere [14–16]. The PCR products were sequenced using next-generation sequencing.…”

Section: Methodsmentioning

confidence: 99%

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Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth

Itthitaetrakool

Pinlaor

et al. 2016

PLoS ONE

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Adults of Opisthorchis viverrini reside in the biliary system, inducing inflammation of bile ducts and cholangitis, leading to hepatobiliary disease (HBD) including cholangiocarcinoma. O. viverrini infection also has major implications for the bacterial community in bile ducts and liver. To investigate this in chronic O. viverrini infection (≥ 8 months p.i.), bacterial genomic DNA from livers of hamsters and from worms was investigated using culture techniques, PCR for Helicobacter spp. and high-throughput next-generation sequencing targeting the V3-V4 hypervariable regions of prokaryotic 16S rRNA gene. Of a total of 855,046 DNA sequence reads, 417,953 were useable after filtering. Metagenomic analyses assigned these to 93 operational taxonomic units (OTUs) consisting of 80 OTUs of bacteria, including 6 phyla and 42 genera. In the chronic O. viverrini-infected group, bacterial community composition and diversity were significantly increased compared to controls. Sequences of Fusobacterium spp. were the most common (13.81%), followed by Streptococcus luteciae (10.76%), Escherichia coli (10.18%), and Bifidobacterium spp. (0.58%). In addition, Helicobacter pylori (0.17% of sequences) was also identified in the liver of chronic O. viverrini infections, but not in normal liver. The presence of H. pylori was confirmed by PCR and by use of an antibody against bacterial antigen, supporting the metagenomics data. The identities of bacteria cultured for enrichment suggested that chronic O. viverrini infection changes the liver microbiome and promotes Helicobacter spp. growth. There may be synergy between O. viverrini and the liver microbiome in enhancing immune response-mediated hepatobiliary diseases.

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“…These were submitted to next-generation sequencing followed by metagenomic analysis as described elsewhere [14–16]. The PCR products were sequenced using next-generation sequencing.…”

Section: Methodsmentioning

confidence: 99%

“…Several techniques were used including culture for aerobic bacteria, PCR for Helicobacter spp. and metagenomic analysis of portions of the 16S rRNA gene generated using high-throughput next-generation sequencing [14–16]. We found considerable bacterial diversity and identified H .…”

Section: Introductionmentioning

confidence: 99%

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth

Itthitaetrakool

Pinlaor

et al. 2016

PLoS ONE

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“…However, as demonstrated for urinary tract infections [19], the technology can be applied directly to clinical samples, potentially advancing diagnostics and leading to even more rapid diagnostic results. Furthermore, it was recently demonstrated that the detection of Clostridium difficile by NGS is correlated with the already existing laboratory testing [20] and metagenomics sequencing has been employed on a limited number of patient stool samples for the detection of pathogens [21, 22]. In addition to species detection, NGS offers detection of resistance and virulence genes, which can further shorten the time needed for pathogen-directed treatment to be initiated.…”

Section: Introductionmentioning

confidence: 99%

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

Joensen

Engsbro

Lukjancenko

et al. 2017

Eur J Clin Microbiol Infect Dis

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The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included. DNA was extracted from faecal samples and sequenced on the Illumina MiSeq system. Species distribution was determined with MGmapper and NGS-based diagnostic prediction was performed based on the relative abundance of pathogenic bacteria and Giardia and detection of pathogen-specific virulence genes. NGS-based diagnostic results were compared to conventional findings for 55 of the diarrhoeal samples; 38 conventionally positive for bacterial pathogens, two positive for Giardia, four positive for virus and 11 conventionally negative. The NGS-based approach enabled detection of the same bacterial pathogens as the classical approach in 34 of the 38 conventionally positive bacterial samples and predicted the responsible pathogens in five of the 11 conventionally negative samples. Overall, the NGS-based approach enabled pathogen detection comparable to conventional diagnostics and the approach has potential to be extended for the detection of all pathogens. At present, however, this approach is too expensive and time-consuming for routine diagnostics.Electronic supplementary materialThe online version of this article (doi:10.1007/s10096-017-2947-2) contains supplementary material, which is available to authorized users.

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“…This study also revealed an interesting phenomenon: while D. fragilis was detected in 10.9% of undiagnosed outbreak samples, a higher frequency was reported (44%) in pediatric samples. A more recent study applied several diagnostic techniques (metagenomics, microscopy, and multiplex PCR) to four diarrheal samples as a means to detect multiple pathogens simultaneously (Schneeberger et al, 2016). Metagenomics detected 8–11 plausible enteric pathogens in all samples.…”

Section: Next-generation Sequencing As a Diagnostic Assaymentioning

confidence: 99%

Metagenomics: The Next Culture-Independent Game Changer

et al. 2017

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A trend towards the abandonment of obtaining pure culture isolates in frontline laboratories is at a crossroads with the ability of public health agencies to perform their basic mandate of foodborne disease surveillance and response. The implementation of culture-independent diagnostic tests (CIDTs) including nucleic acid and antigen-based assays for acute gastroenteritis is leaving public health agencies without laboratory evidence to link clinical cases to each other and to food or environmental substances. This limits the efficacy of public health epidemiology and surveillance as well as outbreak detection and investigation. Foodborne outbreaks have the potential to remain undetected or have insufficient evidence to support source attribution and may inadvertently increase the incidence of foodborne diseases. Next-generation sequencing of pure culture isolates in clinical microbiology laboratories has the potential to revolutionize the fields of food safety and public health. Metagenomics and other ‘omics’ disciplines could provide the solution to a cultureless future in clinical microbiology, food safety and public health. Data mining of information obtained from metagenomics assays can be particularly useful for the identification of clinical causative agents or foodborne contamination, detection of AMR and/or virulence factors, in addition to providing high-resolution subtyping data. Thus, metagenomics assays may provide a universal test for clinical diagnostics, foodborne pathogen detection, subtyping and investigation. This information has the potential to reform the field of enteric disease diagnostics and surveillance and also infectious diseases as a whole. The aim of this review will be to present the current state of CIDTs in diagnostic and public health laboratories as they relate to foodborne illness and food safety. Moreover, we will also discuss the diagnostic and subtyping utility and concomitant bias limitations of metagenomics and comparable detection techniques in clinical microbiology, food and public health laboratories. Early advances in the discipline of metagenomics, however, have indicated noteworthy challenges. Through forthcoming improvements in sequencing technology and analytical pipelines among others, we anticipate that within the next decade, detection and characterization of pathogens via metagenomics-based workflows will be implemented in routine usage in diagnostic and public health laboratories.

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Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study

Cited by 37 publications

References 37 publications

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth

Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease

Metagenomics: The Next Culture-Independent Game Changer

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