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Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens

Published on Feb 1, 2016in Journal of Clinical Microbiology4.96
· DOI :10.1128/JCM.01965-15
Yanhua Zhou32
Estimated H-index: 32
(WashU: Washington University in St. Louis),
Kristine M. Wylie23
Estimated H-index: 23
(WashU: Washington University in St. Louis)
+ 5 AuthorsGeorge M. Weinstock98
Estimated H-index: 98
(UMMC: University of Mississippi Medical Center)
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Abstract
ABSTRACT The potential to rapidly capture the entire microbial community structure and/or gene content makes metagenomic sequencing an attractive tool for pathogen identification and the detection of resistance/virulence genes in clinical settings. Here, we assessed the consistency between PCR from a diagnostic laboratory, quantitative PCR (qPCR) from a research laboratory, 16S rRNA gene sequencing, and metagenomic shotgun sequencing (MSS) for Clostridium difficile identification in diarrhea stool samples. Twenty-two C. difficile-positive diarrhea samples identified by PCR and qPCR and five C. difficile-negative diarrhea controls were studied. C. difficile was detected in 90.9% of C. difficile-positive samples using 16S rRNA gene sequencing, and C. difficile was detected in 86.3% of C. difficile-positive samples using MSS. CFU inferred from qPCR analysis were positively correlated with the relative abundance of C. difficile from 16S rRNA gene sequencing ( r 2 = −0.60) and MSS ( r 2 = −0.55). C. difficile was codetected with Clostridium perfringens, norovirus, sapovirus, parechovirus, and anellovirus in 3.7% to 27.3% of the samples. A high load of Candida spp. was found in a symptomatic control sample in which no causative agents for diarrhea were identified in routine clinical testing. Beta-lactamase and tetracycline resistance genes were the most prevalent (25.9%) antibiotic resistance genes in these samples. In summary, the proof-of-concept study demonstrated that next-generation sequencing (NGS) in pathogen detection is moderately correlated with laboratory testing and is advantageous in detecting pathogens without a priori knowledge.
  • References (37)
  • Citations (23)
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References37
Newest
Published on Dec 1, 2014in BMC Biology6.72
Kristine M. Wylie23
Estimated H-index: 23
(WashU: Washington University in St. Louis),
Kathie A. Mihindukulasuriya14
Estimated H-index: 14
(WashU: Washington University in St. Louis)
+ 3 AuthorsGeorge M. Weinstock98
Estimated H-index: 98
(WashU: Washington University in St. Louis)
Background: The Human Microbiome Project (HMP) was undertaken with the goal of defining microbial communities in and on the bodies of healthy individuals using high-throughput metagenomic sequencing analysis. The viruses present in these microbial communities, the ‘human virome,’ are an important aspect of the human microbiome that is particularly understudied in the absence of overt disease. We analyzed eukaryotic double-stranded DNA (dsDNA) viruses, together with dsDNA replicative intermediate...
Published on Oct 1, 2014in Journal of Microbiological Methods1.80
Paul Ruegger9
Estimated H-index: 9
(UCR: University of California, Riverside),
Robin T. Clark5
Estimated H-index: 5
(UCR: University of California, Riverside)
+ 2 AuthorsJames Borneman30
Estimated H-index: 30
(UCR: University of California, Riverside)
Current high throughput sequencing (HTS) methods are limited in their ability to resolve bacteria at or below the genus level. While the impact of this limitation may be relatively minor in whole-community analyses, it constrains the use of HTS as a tool for identifying and examining individual bacteria of interest. The limited resolution is a consequence of both short read lengths and insufficient sequence variation within the commonly targeted variable regions of the small-subunit rRNA (SSU) g...
Published on Jun 19, 2014in The New England Journal of Medicine70.67
Michael R. Wilson19
Estimated H-index: 19
(UCSF: University of California, San Francisco),
Samia N. Naccache21
Estimated H-index: 21
+ 19 AuthorsSteve Miller18
Estimated H-index: 18
A 14-year-old boy with severe combined immunodeficiency presented three times to a medical facility over a period of 4 months with fever and headache that progressed to hydrocephalus and status epilepticus necessitating a medically induced coma. Diagnostic workup including brain biopsy was unrevealing. Unbiased next-generation sequencing of the cerebrospinal fluid identified 475 of 3,063,784 sequence reads (0.016%) corresponding to leptospira infection. Clinical assays for leptospirosis were neg...
Published on Jan 1, 2014in Genome Biology14.03
Yanhua Zhou32
Estimated H-index: 32
(UW: University of Washington),
Kathie A. Mihindukulasuriya14
Estimated H-index: 14
(UW: University of Washington)
+ 8 AuthorsErica Sodergren11
Estimated H-index: 11
(University of Connecticut Health Center)
Background Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project.
Published on Dec 1, 2013in Journal of Pediatric Gastroenterology and Nutrition3.02
Rana E. El Feghaly5
Estimated H-index: 5
,
Jennifer Stauber6
Estimated H-index: 6
+ 1 AuthorsDavid B. Haslam22
Estimated H-index: 22
Clostridium difficile infections in children are increasing. In this cohort study, we enrolled 62 children with diarrhea and C. difficile. We performed polymerase chain reaction (PCR) assays to detect viral agents of gastroenteritis and quantify C. difficile burden. Fifteen (24%) children diagnosed with C. difficile infection had a concomitant viral co-infection. These patients tended to be younger and had a higher C. difficile bacterial burden than children with no viral co-infections (median d...
Published on Dec 1, 2013in The Journal of Pediatrics3.74
Rana E. El Feghaly5
Estimated H-index: 5
(WashU: Washington University in St. Louis),
Jennifer Stauber6
Estimated H-index: 6
(WashU: Washington University in St. Louis)
+ 1 AuthorsDavid B. Haslam22
Estimated H-index: 22
(WashU: Washington University in St. Louis)
Objectives To identify specific fecal biomarkers for symptomatic Clostridium difficile infection and predictors of poor outcomes. Study design We enrolled 65 children with positive C difficile testing (cases) and 37 symptomatic controls. We also analyzed stool samples from colonized and non-colonized asymptomatic children. We performed enzyme immunoassays to determine fecal interleukin (IL)-8, lactoferrin, and phosphorylated-p38 protein concentrations, and quantitative polymerase chain reaction ...
Published on Nov 13, 2013in PLOS ONE2.78
Aimee Moore5
Estimated H-index: 5
(WashU: Washington University in St. Louis),
Sanket Patel7
Estimated H-index: 7
(WashU: Washington University in St. Louis)
+ 6 AuthorsGautam Dantas30
Estimated H-index: 30
(WashU: Washington University in St. Louis)
Emerging antibiotic resistance threatens human health. Gut microbes are an epidemiologically important reservoir of resistance genes (resistome), yet prior studies indicate that the true diversity of gut-associated resistomes has been underestimated. To deeply characterize the pediatric gut-associated resistome, we created metagenomic recombinant libraries in an Escherichia coli host using fecal DNA from 22 healthy infants and children (most without recent antibiotic exposure), and performed fun...
Published on Oct 1, 2013in Nature Communications11.88
Yongfei Hu21
Estimated H-index: 21
,
Xi Yang15
Estimated H-index: 15
+ 21 AuthorsXin Wang10
Estimated H-index: 10
The appearance of antibiotic resistance has been attributed to the misuse of antibiotics. By analysing the diversity of antibiotic resistance genes present in 162 human gut microbiota samples, the authors find that Chinese individuals harbour a larger pool of resistance genes than Spanish or Danish counterparts.
Published on Sep 1, 2013in Journal of Clinical Microbiology4.96
Vijay C. Antharam6
Estimated H-index: 6
(UF: University of Florida),
Eric Li7
Estimated H-index: 7
(UF: University of Florida)
+ 4 AuthorsGary P. Wang19
Estimated H-index: 19
(UF: University of Florida)
Clostridium difficile infection (CDI) causes nearly half a million cases of diarrhea and colitis in the United States each year. Although the importance of the gut microbiota in C. difficile pathogenesis is well recognized, components of the human gut flora critical for colonization resistance are not known. Culture-independent high-density Roche 454 pyrosequencing was used to survey the distal gut microbiota for 39 individuals with CDI, 36 subjects with C. difficile-negative nosocomial diarrhea...
Published on Aug 1, 2013in Nature Reviews Microbiology34.65
Pierre-Edouard Fournier66
Estimated H-index: 66
,
Michel Drancourt65
Estimated H-index: 65
+ 3 AuthorsDidier Raoult138
Estimated H-index: 138
In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these...
Cited By23
Newest
Stephanie L. Mitchell2
Estimated H-index: 2
(University of Pittsburgh),
Patricia J. Simner7
Estimated H-index: 7
(JHUSOM: Johns Hopkins University School of Medicine)
Published on Oct 23, 2018in Clinical Infectious Diseases9.05
Mohammad Enayet Hossain3
Estimated H-index: 3
(International Centre for Diarrhoeal Disease Research, Bangladesh),
Rajibur Rahman3
Estimated H-index: 3
(International Centre for Diarrhoeal Disease Research, Bangladesh)
+ 7 AuthorsMustafizur Rahman6
Estimated H-index: 6
(International Centre for Diarrhoeal Disease Research, Bangladesh)
Published on Jun 20, 2019in bioRxiv
M. C. Sevillano (NU: Northeastern University), Zihan Dai (Glas.: University of Glasgow)+ 5 AuthorsAmeet J. Pinto10
Estimated H-index: 10
(NU: Northeastern University)
Antimicrobial resistance (AMR) in drinking water has received less attention than counterparts in the urban water cycle. While culture-based techniques or gene-centric PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on AMR in drinking water, to our knowledge there is no systematic comparison of AMR traits between disinfected and disinfectant residual-free drinking water systems. We use metagenomics to assess the associations between disinfectant residuals and ...
Published on May 21, 2019in Inflammatory Bowel Diseases4.00
Rafal Tokarz15
Estimated H-index: 15
(Columbia University),
Jeffrey S. Hyams66
Estimated H-index: 66
+ 18 AuthorsBarbara Sachs40
Estimated H-index: 40
(Women & Children's Hospital of Buffalo)
Published in Clinical Infectious Diseases9.05
Amanda M. Casto1
Estimated H-index: 1
(UW: University of Washington),
Amanda L. Adler (UW: University of Washington)+ -3 AuthorsAlexander L. Greninger23
Estimated H-index: 23
(UW: University of Washington)
Published on Dec 1, 2018in Scientific Reports4.01
Keunje Yoo5
Estimated H-index: 5
(Columbia University),
Hyunji Yoo2
Estimated H-index: 2
(Yonsei University)
+ 2 AuthorsJoonhong Park23
Estimated H-index: 23
(Yonsei University)
Despite progress in monitoring and modeling Asian dust (AD) events, real-time public hazard prediction based on biological evidence during AD events remains a challenge. Herein, both a classification and regression tree (CART) and multiple linear regression (MLR) were applied to assess the applicability of prediction for potential urban airborne bacterial hazards during AD events using metagenomic analysis and real-time qPCR. In the present work, Bacillus cereus was screened as a potential patho...
Published on Dec 1, 2018in BMC Infectious Diseases2.56
Nicholas Petronella5
Estimated H-index: 5
(Health Canada),
Jennifer Ronholm7
Estimated H-index: 7
(McGill University)
+ 5 AuthorsNeda Nasheri3
Estimated H-index: 3
Background Human norovirus is the leading cause of viral gastroenteritis globally, and the GII.4 has been the most predominant genotype for decades. This genotype has numerous variants that have caused repeated epidemics worldwide. However, the molecular evolutionary signatures among the GII.4 variants have not been elucidated throughout the viral genome.
Published on Dec 1, 2018in Mbio6.75
Qiyun Zhu (UCSD: University of California, San Diego), Christopher L. Dupont23
Estimated H-index: 23
(JCVI: J. Craig Venter Institute)
+ 4 AuthorsSarah K. Highlander6
Estimated H-index: 6
(TGen: Translational Genomics Research Institute)
Background Travelers’ diarrhea (TD) is often caused by enterotoxigenic Escherichia coli, enteroaggregative E. coli, other bacterial pathogens, Norovirus, and occasionally parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 40% of TD patients. It is predicted that new pathogens may be causative agents of the disease.
Published on Nov 14, 2018in Journal of Clinical Microbiology4.96
Qun Yan2
Estimated H-index: 2
(CSU: Central South University),
Yu Mi Wi2
Estimated H-index: 2
(SKKU: Sungkyunkwan University)
+ 6 AuthorsRobin Patel6
Estimated H-index: 6
(Mayo Clinic)
ABSTRACT We previously demonstrated that shotgun metagenomic sequencing can detect bacteria in sonicate fluid, providing a diagnosis of prosthetic joint infection (PJI). A limitation of the approach that we used is that data analysis was time-consuming and specialized bioinformatics expertise was required, both of which are barriers to routine clinical use. Fortunately, automated commercial analytic platforms that can interpret shotgun metagenomic data are emerging. In this study, we evaluated t...