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Open AccessArticle
Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves
by
Rok Tomazin
Rok Tomazin 1
,
Tjaša Cerar Kišek
Tjaša Cerar Kišek 2
,
Tea Janko
Tea Janko 2,
Tina Triglav
Tina Triglav 1,
Katja Strašek Smrdel
Katja Strašek Smrdel 1
,
Vesna Cvitković Špik
Vesna Cvitković Špik 1,
Andreja Kukec
Andreja Kukec 3,
Janez Mulec
Janez Mulec 4,5 and
Tadeja Matos
Tadeja Matos 1,*
1
Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
2
National Laboratory for Health, Environment and Food, Department for Public Health Microbiology, Grablovičeva Ulica 44, SI-1000 Ljubljana, Slovenia
3
Department of Public Health, Faculty of Medicine, University of Ljubljana, Zaloška Cesta 4, SI-1000 Ljubljana, Slovenia
4
Karst Research Institute, Research Centre of the Slovenian Academy of Sciences and Arts, Titov Trg 2, SI-6230 Postojna, Slovenia
5
UNESCO Chair on Karst Education, University of Nova Gorica, SI-5271 Vipava, Slovenia
*
Author to whom correspondence should be addressed.
Microorganisms 2024, 12(7), 1427; https://doi.org/10.3390/microorganisms12071427 (registering DOI)
Submission received: 28 June 2024
/
Revised: 10 July 2024
/
Accepted: 12 July 2024
/
Published: 14 July 2024
Abstract
The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS’s superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System’s 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection.
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MDPI and ACS Style
Tomazin, R.; Cerar Kišek, T.; Janko, T.; Triglav, T.; Strašek Smrdel, K.; Cvitković Špik, V.; Kukec, A.; Mulec, J.; Matos, T.
Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves. Microorganisms 2024, 12, 1427.
https://doi.org/10.3390/microorganisms12071427
AMA Style
Tomazin R, Cerar Kišek T, Janko T, Triglav T, Strašek Smrdel K, Cvitković Špik V, Kukec A, Mulec J, Matos T.
Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves. Microorganisms. 2024; 12(7):1427.
https://doi.org/10.3390/microorganisms12071427
Chicago/Turabian Style
Tomazin, Rok, Tjaša Cerar Kišek, Tea Janko, Tina Triglav, Katja Strašek Smrdel, Vesna Cvitković Špik, Andreja Kukec, Janez Mulec, and Tadeja Matos.
2024. "Comparison of Culture-Dependent and Culture-Independent Methods for Routine Identification of Airborne Microorganisms in Speleotherapeutic Caves" Microorganisms 12, no. 7: 1427.
https://doi.org/10.3390/microorganisms12071427
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