The proof of concept that culturomics can be superior to metagenomics to study atypical stool samples

Dubourg, Grégory; Lagier, Jean-Christophe; Armougom, Fabrice; Robert, Caroline; Hamad, Ibrahim; Brouqui, Philippe; Raoult, Didier

doi:10.1007/s10096-013-1843-7

Cited by 21 publications

(13 citation statements)

References 7 publications

(10 reference statements)

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“…Furthermore, a reduction in microbiome diversity has been associated with inflammatory skin disorders (41). Although many studies evaluating microbial communities have applied a genomic approach, culturomics is emerging as a robust technique for detailed microbial identification to the species level (19)(20)(21)(22)(23)(24)(25)(26). As demonstrated herein, this level of detail is especially important for the skin and nasal flora, where closely related Gram-positive species predominate.…”

Section: Discussionmentioning

confidence: 95%

“…While microbial culture has traditionally been regarded as insensitive for detecting a majority of the microbiota, molecular methods have informed augmented culture approaches, yielding enhanced recovery of these microorganisms (19)(20)(21)(22)(23)(24)(25)(26). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid and costeffective technique that utilizes proteomic profiling for organism identification (27).…”

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confidence: 99%

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Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Burnham

Hogan

Wallace

et al. 2016

Antimicrob Agents Chemother

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Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n ‫؍‬ 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n ‫؍‬ 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the communitydwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P ‫؍‬ 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P ‫؍‬ 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota. N osocomial infections pose significant clinical and financial burdens to patients and health care systems (1, 2). Colonization with potential pathogens serves as an endogenous source of infection (e.g., central line-associated bloodstream infection with Staphylococcus aureus) (3). For hospitalized patients, particularly those in intensive care units (ICUs), decolonization with topical antimicrobials, including chlorhexidine and/or mupirocin, has been demonstrated to reduce the acquisition of antibiotic-resistant microorganisms and the incidence of hospital-acquired infections (4-6). While decolonization has traditionally been employed in health care settings, the emergence of methicillinresistant S. aureus (MRSA) in the community and the resultant epidemic of skin and soft tissue infections (SSTIs) have led to the extrapolation of decolonization to outpatients to prevent recurrent SSTIs (7-10). As these broad-spectrum therapies are not pathogen specific (e.g., for MRSA or Enterobacteriaceae), these agents may suppress or eliminate other organisms on the skin and nasal mucosa, thereby potentially disrupting the balance of the microbiota, an important component of host defense against pathogenic organisms (11, 12). Indeed, this dysbiosis has been demonstrated for the intestinal microbiota following administration of oral antibiotics (13,14).Culture-independent molecular meth...

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Section: Discussionmentioning

confidence: 95%

mentioning

confidence: 99%

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Burnham

Hogan

Wallace

et al. 2016

Antimicrob Agents Chemother

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“…A recent example by McLean et al [17] coupled fluorescenceactivated cell sorting (FACS) and MDA for single-cell genomic analyses of microbial communities in the biofilm from a hospital sink. The incorporation of MDA also avoids the introduction of mutations in the single cell approach, which may result from culturing the individually sorted bacterial cells [62][63][64].…”

Section: Sample and Library Preparationmentioning

confidence: 99%

Metagenomics for pathogen detection in public health

et al. 2013

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Traditional pathogen detection methods in public health infectious disease surveillance rely upon the identification of agents that are already known to be associated with a particular clinical syndrome. The emerging field of metagenomics has the potential to revolutionize pathogen detection in public health laboratories by allowing the simultaneous detection of all microorganisms in a clinical sample, without a priori knowledge of their identities, through the use of next-generation DNA sequencing. A single metagenomics analysis has the potential to detect rare and novel pathogens, and to uncover the role of dysbiotic microbiomes in infectious and chronic human disease. Making use of advances in sequencing platforms and bioinformatics tools, recent studies have shown that metagenomics can even determine the whole-genome sequences of pathogens, allowing inferences about antibiotic resistance, virulence, evolution and transmission to be made. We are entering an era in which more novel infectious diseases will be identified through metagenomics-based methods than through traditional laboratory methods. The impetus is now on public health laboratories to integrate metagenomics techniques into their diagnostic arsenals.

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“…Moreover, the identification of bacteria associated with ticks may provide new tool for the control of ticks and tick-borne diseases. Molecular methods of screening of ticks, extensive use of modern culturomics approach [48], newly developed artificial media [41,49] and different cell line cultures may significantly improve our knowledge about the ticks as the agents of human and animal pathology. …”

Section: Perspectivesmentioning

confidence: 99%