A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay
Abstract
:1. Introduction
2. Results
2.1. A DHA Model for Postulated COSM and Pre-Test Analysis
2.2. Clinical Subjects
2.3. Blood Culutre with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MOLDI-TOF MS) for Determination of Ocular Surface Microbiota
2.4. DHA Model for Evaluation of Core Ocular Surface Microbiota
2.5. Integrative Analysis for COSM from DHA and Blood Culture with MALDI-TOF MS
3. Discussion
4. Materials and Methods
4.1. Subjects
4.2. Sample Collection
4.3. Identification of Cultured Microbiota by the MOLDI-TOF Mass Spectrometry
4.3.1. Sample Preparation for MALDI-TOF MS Analysis
4.3.2. Identification of Ocular Surface Microobiota by MALDI Biotyper
4.4. DNA Extraction and PCR Amplification
4.5. The Dot Hybridization Assay for Assessing COSM
4.5.1. Immobilization of Oligonucleotide Probes on a Nylon Membrane
4.5.2. Detection of Microbial DNA with the COSM DHA
4.5.3. Quantification of the Signals for Each Dot in the DHA
4.6. Data Analysis
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
a.u. | Arbitrary Unit |
CGMH | Chang Gung Memorial Hospital |
CoNS | Coagulase Negative Staphylococci |
COSM | Core Ocular Surface Microbiota |
DHA | Dot Hybridization Assay |
MOLDI-TOF | Matrix-Assisted Laser Desorption Ionization-Time Of Flight |
MS | Mass Spectrometry |
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Dot | Assessment Target | Probe Sequence(s) (5′–3′) | Conc. (μM) | Ref. |
---|---|---|---|---|
BPx | All bacteria | GGGGCTAAGTCGTAACAAGGTAGCCGTAtttttttttt b | 20 | [19,20] |
Psu a | Pseudomonas aeruginosa | GTTCTTTAAAAATTTGGGTATGTGATAGAA CAGTGACCAGATTGCTTGGGGTTATATtttttttt b | 10 10 | [19,20] |
Aci | Acinetobacterbaumannii | CGGTAATTAGTGTGATCTGACGAtttttttttt b | 10 | [23] |
Klb | Klebsiella pneumoniae | CTTAAAGAACCTGCCTTTGTAGTGCTC | 20 | [19,20] |
Sem a | Serratiamarcescens | AAGGTACTGCGCGTGACTGTATGGtttttttttt b,c; CATATAGTCCGGTATTTAATACTTCAGAGTtttttttttt b,c | 20 20 | - |
Sta | Staphylococcus aureus | CGTTATTCCGCATCTTCTGAAGAAGAttttt | 20 | [22] |
Ste | Staphylococcus epidermidis | TTGAATAACAATTCAAAATATGGTGGAttttttttttt b | 20 | [22] |
Pro a | Propionibacterium acnes | TTGCTGTATGTGTTCGTGCGACtttttttttt b; GAGCATCTTATTTTTTGTGTGGCTTGTGttttttttttttttt b | 20 20 | [24] |
mecA | Potentially resistant strain | TGATGGTATGCAACAAGTCG | 10 | [22] |
M | Marker | 5′-digoxigenin-TCCTCCGCTTATTGATATGC | 10 | [19,20] |
Isolated Microorganisms | Number of Isolates | Number of Oxacillin Resistant Strains |
---|---|---|
Gram Positive Microorganisms | ||
Staphylococcus aureus | 5 | 1 |
Staphylococcus epidermidis | 16 | 7 |
Staphylococcus haemolyticus | 7 | 6 |
Staphylococcus warneri | 2 | 0 |
Staphylococcus sciuri | 1 | 1 |
Unspecified CoNS | 3 | 0 |
Streptococcus mitis | 1 | 0 |
Streptococcus oralis | 2 | 0 |
Streptococcus salivarius | 1 | 0 |
Enterococcus faecalis | 3 | 0 |
Bacillus cereus | 1 | 0 |
Bacillus spp. | 8 | 0 |
Paenibacillus spp. | 1 | 0 |
Unspecified Gram-positive bacilli | 2 | 0 |
Gram Negative Microorganisms | ||
Microbacterium aurum | 1 | 0 |
Gordonia spp. | 1 | 0 |
Morganella spp. | 1 | 0 |
Serratia marcescens | 1 | 0 |
Citrobacter spp. | 1 | 0 |
Brevundimonas spp. | 1 | 0 |
Research | Sampling Sites | Culture System | No. (%) of CoNS | No. (%) of S. epidermidis | Ref. |
---|---|---|---|---|---|
Mshangila et al. (Uganda, n = 131) | Lower eyelid margin and inferior conjunctival sac | Brain–heart infusion broth | 91/138 (65.9%) | 70/138 (50.7%) | [31] |
Ratnumnoi et al. (Thailand, n = 120) | Eyelid margin and conjunctiva | Blood agar and chocolate agar | 106/115 (92.2%) | N.A. | [32] |
Suto et al. (Japan, n = 579) | Inferior conjunctiva sac | Blood agar and chocolate agar | 164/284 (57.7%) | 164/284 (57.7%) | [33] |
In this study (Taiwan, n = 43) | Upper and lower lid margin | Pediatric blood bottle | 29/59 (49.2%) | 16/59 (27.1%) |
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Kuo, M.-T.; Chao, T.-L.; Kuo, S.-F.; Chien, C.-C.; Chen, A.; Lai, Y.-H.; Huang, Y.-T. A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay. Int. J. Mol. Sci. 2020, 21, 8299. https://doi.org/10.3390/ijms21218299
Kuo M-T, Chao T-L, Kuo S-F, Chien C-C, Chen A, Lai Y-H, Huang Y-T. A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay. International Journal of Molecular Sciences. 2020; 21(21):8299. https://doi.org/10.3390/ijms21218299
Chicago/Turabian StyleKuo, Ming-Tse, Tsai-Ling Chao, Shu-Fang Kuo, Chun-Chih Chien, Alexander Chen, Yu-Hsuan Lai, and Yu-Ting Huang. 2020. "A Genomic Approach to Investigating Ocular Surface Microorganisms: Monitoring Core Microbiota on Eyelid Margin with a Dot hybridization Assay" International Journal of Molecular Sciences 21, no. 21: 8299. https://doi.org/10.3390/ijms21218299