Metagenomic Diagnosis of Bacterial Infections

Nakamura, Shota; Maeda, Norihiro; Miron, Ionut Mihai; Yoh, Myonsun; Izutsu, Kaori; Kataoka, Chidoh; Honda, Takeshi; Yasunaga, Teruo; Nakaya, Takaaki; Kawai, Jun; Hayashizaki, Yoshihide; Horii, Toshihiro; Iida, Tetsuya

doi:10.3201/eid1411.080589

Cited by 106 publications

(73 citation statements)

References 15 publications

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“…Anecdotal data have shown that spiral or curved bacteria are sometimes observed on stool smears while Campylobacter growth does not occur. In a recent study, DNA sequences of the Campylobacter genome were detected by a metagenomic analysis, while the standard culture methods were negative (5). In a pilot study using real-time PCR as a diagnostic tool, we also detected more campylobacters than with culture, but without being able to confirm that true positives were detected, since, at that time, we did not use multiple detection methods to establish positivity when culture was negative.…”

mentioning

confidence: 89%

New Methods for Detection of Campylobacters in Stool Samples in Comparison to Culture

Bessède

Delcamp²,

Sifré³

et al. 2011

J Clin Microbiol

120

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Campylobacter species, especially Campylobacter jejuni and Campylobacter coli, are a major cause of human bacterial enteritis. Current detection in stools is done essentially by culture on selective and nonselective media with filtration. These methods were compared to 2 molecular biology methods, an in-house real-time PCR and a multiplex PCR named Seeplex Diarrhea ACE Detection, and 3 immunoenzymatic methods, Premier Campy, RidaScreen Campylobacter, and ImmunoCard Stat!Campy. Out of 242 stool specimens tested, 23 (9.5%) fulfilled the positivity criteria, i.e., they were positive by one or both culture methods or, in case of a negative culture, by a positive molecular method and a positive immunoenzymatic method. The striking feature of this study is the low sensitivity of culture, in the range of 60%, in contrast to immunoenzymatic and molecular tests.The incidence of Campylobacter-associated food poisoning has gradually increased, and the organism is now considered to be the leading cause of bacterial gastroenteritis worldwide (4). These infections can also lead to extraintestinal diseases and severe long-term complications (9). Campylobacter jejuni and Campylobacter coli are the most frequently isolated species in this context and in our experience account for 80% and 16%, respectively, of all the isolates received in our laboratory every year (2a). Campylobacter species are bacteria with a special culture requirement, i.e., a microaerobic environment. During stool processing, the bacteria may have long contact with a normal atmosphere, and in addition, the progressive decrease in oxygen tension when gas-generating kits are used may not favor adequate growth. Furthermore, selective media are commonly used, and the antibiotics incorporated may inhibit certain Campylobacter strains. Anecdotal data have shown that spiral or curved bacteria are sometimes observed on stool smears while Campylobacter growth does not occur. In a recent study, DNA sequences of the Campylobacter genome were detected by a metagenomic analysis, while the standard culture methods were negative (5). In a pilot study using real-time PCR as a diagnostic tool, we also detected more campylobacters than with culture, but without being able to confirm that true positives were detected, since, at that time, we did not use multiple detection methods to establish positivity when culture was negative. Some immunoenzymatic tests have already been commercialized for several years, such as the ProSpecT Campylobacter Microplate Assay (Remel) (8) and the RidaScreen Campylobacter (R-Biopharm, Darmstadt, Germany) evaluated in our study. In this study, we took advantage of the availability of several kits to compare Campylobacter detection by molecular methods (2 PCRs) and by 3 immunoenzymatic methods to the standard culture methods. MATERIALS AND METHODS Materials.From 15 June to 30 October 2009, every stool specimen obtained from a symptomatic patient, i.e., a patient with a gastrointestinal illness, who was hospitalized for less than 48 h at Pellegrin H...

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mentioning

confidence: 89%

New Methods for Detection of Campylobacters in Stool Samples in Comparison to Culture

Bessède

Delcamp²,

Sifré³

et al. 2011

J Clin Microbiol

120

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“…More detailed investigations of the whole pathogen communities infecting these bank voles are now possible from the development of new generation sequencing technologies and metagenomic analyses. These approaches have yet allowed to describe microbial communities and to explore their interactions in different hosts' organs or environments (Nakamura et al 2008;Carpi et al, 2011;Cheval et al, 2011). In the future, the integration of such information in the analysis of PUUV epidemiology will provide a better understanding of the impacts of co-infection on the evolution of tolerance to PUUV in bank voles.…”

Section: Perspectivesmentioning

confidence: 99%

Landscape features and helminth co-infection shape bank vole immunoheterogeneity, with consequences for Puumala virus epidemiology

et al. 2013

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Heterogeneity in environmental conditions helps to maintain genetic and phenotypic diversity in ecosystems. As such, it may explain why the capacity of animals to mount immune responses is highly variable. The quality of habitat patches, in terms of resources, parasitism, predation and habitat fragmentation may, for example, trigger trade-offs ultimately affecting the investment of individuals in various immunological pathways. We described spatial immunoheterogeneity in bank vole populations with respect to landscape features and co-infection. We focused on the consequences of this heterogeneity for the risk of Puumala hantavirus (PUUV) infection. We assessed the expression of the Tnf-a and Mx2 genes and demonstrated a negative correlation between PUUV load and the expression of these immune genes in bank voles. Habitat heterogeneity was partly associated with differences in the expression of these genes. Levels of Mx2 were lower in large forests than in fragmented forests, possibly due to differences in parasite communities. We previously highlighted the positive association between infection with Heligmosomum mixtum and infection with PUUV. We found that Tnf-a was more strongly expressed in voles infected with PUUV than in uninfected voles or in voles co-infected with the nematode H. mixtum and PUUV. H. mixtum may limit the capacity of the vole to develop proinflammatory responses. This effect may increase the risk of PUUV infection and replication in host cells. Overall, our results suggest that close interactions between landscape features, co-infection and immune gene expression may shape PUUV epidemiology.

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“…Furthermore, selective media are commonly used, and the antibiotics incorporated may inhibit certain Campylobacter strains (Bessede et al, 2011). In a recent study, DNA sequences of the Campylobacter genome were detected by a metagenomic analysis, while the standard culture methods were negative (Bessede et al, 2011;Nakamura et al, 2008;Wang et al, 2002;Casademont et al, 2000).…”

mentioning

confidence: 99%

Comparison of immunochromatography, PCR and culture methods for the detection of Campylobacter bacteria

Dey

Nishimura

Okitsu

et al. 2012

Journal of Microbiological Methods

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Metagenomic Diagnosis of Bacterial Infections

Cited by 106 publications

References 15 publications

New Methods for Detection of Campylobacters in Stool Samples in Comparison to Culture

New Methods for Detection of Campylobacters in Stool Samples in Comparison to Culture

Landscape features and helminth co-infection shape bank vole immunoheterogeneity, with consequences for Puumala virus epidemiology

Comparison of immunochromatography, PCR and culture methods for the detection of Campylobacter bacteria

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