1887

Journal of Medical Microbiology logo

Volume 70, Issue 10

Evaluation of Culture Top transport systems for assessing the bacterial diversity of microbiota by culturomics as compared to a routine transport system No Access

Abstract

In recent years, metagenomics and then culturomics, which consists of the multiplication of media and culture conditions and the rapid identification of all bacterial colonies, have generated renewed interest in the human microbiota, and diseases associated with modifications in its composition in particular. The sample transport media included in diverse swab transport systems and the storage conditions are among the factors that influence the results of the culturomics. In this study, we compared the results of culturomics from paired skin, oral and rectal swabs from intensive care unit (ICU) patients using Culture Top sample transport medium as compared to our routine one. From 152 clinical samples, we were able to isolate and identify 45 600 colonies, belonging to 338 different bacterial species. The transport system Culture Top identified 282 different bacterial species, while 244 were identified by our routine system. Of these, 188 different bacterial species were commonly identified using both transport systems, while 94 (27.8 %) and 56 (16.5 %) were only identified using Culture Top and our routine system, respectively (<0.001), but there was no significant difference in bacterial diversity at the genus or phylum level, or in terms of their type of respiration and cell wall. In conclusion, the Culture Top transport system appears to be complementary to our routine system, although it seems slightly superior in terms of isolated bacterial species.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Culture Top , culturomics , micro-organisms , samples , transport media , viability and Σ-Swab
Funding
This study was supported by the:
  • European Regional Developmental Fund (Award PRIMI)
    • Principle Award Recipient: BernardLa Scola
  • Agence Nationale de la Recherche (Award 10-1AHU-03)
    • Principle Award Recipient: BernardLa Scola
© 2021 The Authors
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.001411
2021-10-19
2024-04-19
Loading full text...

Full text loading...

References

  1. Lagier J-C, Khelaifia S, Alou MT, Ndongo S, Dione N et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 2016; 1:16203 [View Article] [PubMed]
     [Google Scholar]
  2. Cassir N, Simeoni U, La Scola B. Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates. Future Microbiol 2016; 11:273–292 [View Article] [PubMed]
     [Google Scholar]
  3. Jneid J, Cassir N, Schuldiner S, Jourdan N, Sotto A. Exploring the microbiota of diabetic foot infections with culturomics. Front Cell Infect Microbiol 2018; 8:282 [View Article] [PubMed]
     [Google Scholar]
  4. Cassir N, Benamar S, Bou Khalil J, Croce O, Saint-Faust M. Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates. Clin Infect Dis 2015; 61:1107–1115 [View Article] [PubMed]
     [Google Scholar]
  5. DeMarco AL, Rabe LK, Austin MN, Stoner KA, Avolia HA. Survival of vaginal microorganisms in three commercially available transport systems. Anaerobe 2017; 45:44–49 [View Article] [PubMed]
     [Google Scholar]
  6. Hindiyeh M, Acevedo V, Carroll KC. Comparison of three transport systems (Starplex StarSwab II, the new Copan Vi-Pak Amies Agar Gel collection and transport swabs, and BBL Port-A-Cul) for maintenance of anaerobic and fastidious aerobic organisms. J Clin Microbiol 2001; 39:377–380 [View Article] [PubMed]
     [Google Scholar]
  7. Wilson ML. General principles of specimen collection and transport. Clin Infect Dis 1996; 22:766–777 [View Article] [PubMed]
     [Google Scholar]
  8. Gizzie N, Adukwu E. Evaluation of liquid-based swab transport systems against the new approved CLSI M40-A2 standard. J Clin Microbiol 2016; 54:1152–1156 [View Article] [PubMed]
     [Google Scholar]
  9. Khelaifia S, Lagier J-C, Nkamga VD, Guilhot E, Drancourt M et al. Aerobic culture of methanogenic archaea without an external source of hydrogen. Eur J Clin Microbiol Infect Dis 2016; 35:985–991 [View Article] [PubMed]
     [Google Scholar]
  10. Citron DM, Warren YA, Hudspeth MK, Goldstein EJ. Survival of aerobic and anaerobic bacteria in purulent clinical specimens maintained in the Copan Venturi Transystem and Becton Dickinson Port-a-Cul transport systems. J Clin Microbiol 2000; 38:892–894 [View Article] [PubMed]
     [Google Scholar]
  11. Van Horn KG, Audette CD, Tucker KA, Sebeck D. Comparison of 3 swab transport systems for direct release and recovery of aerobic and anaerobic bacteria. Diagn Microbiol Infect Dis 2008; 62:471–473 [View Article] [PubMed]
     [Google Scholar]
  12. Stoner KA, Rabe LK, Austin MN, Meyn LA, Hillier SL. Quantitative survival of aerobic and anaerobic microorganisms in Port-A-Cul and Copan transport systems. J Clin Microbiol 2008; 46:2739–2744 [View Article] [PubMed]
     [Google Scholar]
  13. Lagier J-C, Armougom F, Million M, Hugon P, Pagnier I et al. Microbial culturomics: Paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18:1185–1193 [View Article] [PubMed]
     [Google Scholar]
  14. Seng P, Drancourt M, Gouriet F, La Scola B, Fournier P-E et al. Ongoing revolution in bacteriology: Routine identification of bacteria by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Clin Infect Dis 2009; 49:543–551 [View Article] [PubMed]
     [Google Scholar]
  15. Ramasamy D, Kokcha S, Lagier J-C, Nguyen T-T, Raoult D et al. Genome sequence and description of Aeromicrobium massiliense sp. nov. Stand Genomic Sci 2012; 7:246–257 [View Article] [PubMed]
     [Google Scholar]
  16. Belkacemi S, Cassir N, Delerce J, Cadoret F, La Scola B. Bacteroides cutis,’ a new bacterial species isolated from human skin. New Microbes New Infect 2018; 22:17–18 [View Article] [PubMed]
     [Google Scholar]
  17. Belkacemi S, Cassir N, Delerce J, Cadoret F, La Scola B. Selenomonas massiliensis,’ a new anaerobic bacterial species isolated from human oral microbiota. New Microbes New Infect 2018; 24:1–3 [View Article] [PubMed]
     [Google Scholar]
  18. Belkacemi S, Lo CI, Khelaifia S, Raoult D, Fournier P-E et al. Description of Prevotella rectalis sp. nov., a new bacterium isolated from human rectum. New Microbes New Infect 2020; 36:100703 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jmm/10.1099/jmm.0.001411
Loading
Evaluation of Culture Top transport systems for assessing the bacterial diversity of microbiota by culturomics as compared to a routine transport system
J. Med. Microbiol. 70, 001411 (2021); https://doi.org/10.1099/jmm.0.001411
/content/journal/jmm/10.1099/jmm.0.001411
/content/journal/jmm/10.1099/jmm.0.001411
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error