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1. Detection of SARS-CoV-2 using qRT-PCR in saliva obtained from asymptomatic or mild COVID-19 patients, comparative analysis with matched nasopharyngeal samples

Author

Kenji Ota, Katsunori Yanagihara, Daisuke Sasaki, Norihito Kaku, Naoki Uno, Kei Sakamoto, Kosuke Kosai, Taiga Miyazaki, Hiroo Hasegawa, Ayumi Fujita, Masato Tashiro, Takeshi Tanaka, Koichi Izumikawa, Koya Ariyoshi, Hiroshi Mukae, Jiro Yasuda, Kouichi Morita, and Shigeru Kohno

Subjects
Medicine, Science
Abstract

Objectives The accurate detection of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is essential for the diagnosis of coronavirus disease 2019 (COVID-19). We compared the quantitative RT-PCR results between nasopharyngeal swabs and saliva specimens. Methods A COVID-19 outbreak occurred on a cruise ship at Nagasaki port, Japan. We obtained 123 nasopharyngeal swabs and saliva each from asymptomatic or mild patients in the late phase of infection. Results The intervals from the diagnosis to the sampling were 25.5 days for nasopharyngeal swabs and 28.9 days for saliva. The positive rate was 19.5% (24/123) for nasopharyngeal swabs and 38.2% (47/123) for saliva (P = 0.48). The quantified viral copies (mean ± SEM copies/5 μl) were 9.3±2.6 in nasopharyngeal swabs and 920±850 in saliva (P = 0.0006). Conclusions The advantages of saliva specimens include positive rate improvement and accurate viral load detection. Saliva may be used as a reliable sample for SARS-CoV-2 detection.

Published
2021

2. Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model.

Author

Yoshitomo Morinaga, Yuki Take, Daisuke Sasaki, Kenji Ota, Norihito Kaku, Naoki Uno, Kei Sakamoto, Kosuke Kosai, Taiga Miyazaki, Hiroo Hasegawa, Koichi Izumikawa, Hiroshi Mukae, and Katsunori Yanagihara

Subjects
Medicine, Science
Abstract

The alteration of the microbial community in the upper respiratory tract (URT) can contribute to the colonization and invasion of respiratory pathogens. However, there are no studies regarding whether the characteristics of the URT microbiota can be affected by infections in lower respiratory tract (LRT). To elucidate the microbial profiles of the URT during pneumonia, the oral, nasal, and lung microbiota was evaluated at the early phase in a murine pneumonia model by direct intratracheal inoculation of Klebsiella pneumoniae. The meta 16S rRNA sequencing of bronchoalveolar lavage fluid after K. pneumoniae inoculation presented alterations in the beta diversity of the microbes, but not in the alpha diversity. At this point, a significant increase in microbial alpha diversity was observed in the oral cavity, but not in the nasal cavity. The significant increase was observed in the family Carnobacteriaceae and family Enterococcaceae. These results suggest that characterizing the microbial community of the respiratory tract may not just involve a simple downstream relationship from the URT to the LRT. The health status of the LRT may influence the oral microbiota. Thus, evaluation of the oral microbiota may contribute towards monitoring lung health; the oral microbiota may act as a diagnostic marker of pneumonia.

Published
2019
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3. Detection of SARS-CoV-2 using qRT-PCR in saliva obtained from asymptomatic or mild COVID-19 patients, comparative analysis with matched nasopharyngeal samples

Author

Katsunori Yanagihara, Kei Sakamoto, Kouichi Morita, Norihito Kaku, Daisuke Sasaki, Ayumi Fujita, Hiroo Hasegawa, Koya Ariyoshi, Naoki Uno, Hiroshi Mukae, Taiga Miyazaki, Shigeru Kohno, Masato Tashiro, Koichi Izumikawa, Jiro Yasuda, Kenji Ota, Takeshi Tanaka, and Kosuke Kosai

Subjects
RNA viruses, Saliva, Viral Diseases, Pulmonology, Physiology, Coronaviruses, Artificial Gene Amplification and Extension, 030204 cardiovascular system & hematology, Gastroenterology, Polymerase Chain Reaction, law.invention, 0302 clinical medicine, Medical Conditions, law, Nasopharynx, Medicine and Health Sciences, Medicine, 030212 general & internal medicine, Medical Personnel, Respiratory system, Polymerase chain reaction, Pathology and laboratory medicine, Virus Testing, Multidisciplinary, Medical microbiology, Viral Load, Body Fluids, Professions, Real-time polymerase chain reaction, Infectious Diseases, COVID-19 Nucleic Acid Testing, Viruses, medicine.symptom, Anatomy, SARS CoV 2, Pathogens, Viral load, Research Article, medicine.medical_specialty, SARS coronavirus, Science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Research and Analysis Methods, Asymptomatic, Microbiology, Specimen Handling, 03 medical and health sciences, Respiratory Disorders, stomatognathic system, Diagnostic Medicine, Internal medicine, Virology, Humans, Molecular Biology Techniques, Molecular Biology, business.industry, SARS-CoV-2, Organisms, Viral pathogens, Outbreak, Biology and Life Sciences, COVID-19, Covid 19, Microbial pathogens, People and Places, Respiratory Infections, Population Groupings, business, Viral Transmission and Infection
Abstract

Objectives: The accurate detection of severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) is essential for the diagnosis of coronavirus disease 2019 (COVID-19). We compared the quantitative RT-PCR results between nasopharyngeal swabs and saliva specimens. Methods: A COVID-19 outbreak occurred on a cruise ship at Nagasaki port, Japan. We obtained 123 nasopharyngeal swabs and saliva each from asymptomatic or mild patients in the late phase of infection. Results: The intervals from the diagnosis to the sampling were 25.5 days for nasopharyngeal swabs and 28.9 days for saliva. The positive rate was 19.5% (24/123) for nasopharyngeal swabs and 38.2% (47/123) for saliva (P = 0.48). The quantified viral copies (mean ± SEM copies/5 μl) were 9.3±2.6 in nasopharyngeal swabs and 920±850 in saliva (P = 0.0006). Conclusions: The advantages of saliva specimens include positive rate improvement and accurate viral load detection. Saliva may be used as a reliable sample for SARS-CoV-2 detection., PLoS ONE, 16(6), art. no. e0252964; 2021

Published
2021

4. Exploring the microbiota of upper respiratory tract during the development of pneumonia in a mouse model

Author

Daisuke Sasaki, Kei Sakamoto, Yoshitomo Morinaga, Kosuke Kosai, Hiroshi Mukae, Naoki Uno, Taiga Miyazaki, Kenji Ota, Koichi Izumikawa, Yuki Take, Hiroo Hasegawa, Norihito Kaku, and Katsunori Yanagihara

Subjects
0301 basic medicine, Nasal cavity, Bacterial Diseases, Pulmonology, Klebsiella pneumoniae, Physiology, Pathology and Laboratory Medicine, Klebsiella Pneumoniae, Mice, Klebsiella, RNA, Ribosomal, 16S, Medicine and Health Sciences, Lung, Multidisciplinary, medicine.diagnostic_test, biology, Microbiota, Genomics, Animal Models, respiratory system, Bacterial Pathogens, medicine.anatomical_structure, Infectious Diseases, Experimental Organism Systems, Medical Microbiology, Medicine, Female, Pathogens, Bronchoalveolar Lavage Fluid, Research Article, Science, 030106 microbiology, Mouse Models, Respiratory physiology, Microbial Genomics, Nose, Research and Analysis Methods, Microbiology, 03 medical and health sciences, Model Organisms, Streptococcal Infections, medicine, Genetics, Pneumonia, Bacterial, Animals, Microbiome, Respiratory Physiology, Microbial Pathogens, Mouth, Bacteria, business.industry, Organisms, Biology and Life Sciences, Pneumonia, medicine.disease, biology.organism_classification, Klebsiella Infections, Mice, Inbred C57BL, stomatognathic diseases, Disease Models, Animal, 030104 developmental biology, Bronchoalveolar lavage, Immunology, Respiratory Infections, Animal Studies, business, Respiratory tract
Abstract

The alteration of the microbial community in the upper respiratory tract (URT) can contribute to the colonization and invasion of respiratory pathogens. However, there are no studies regarding whether the characteristics of the URT microbiota can be affected by infections in lower respiratory tract (LRT). To elucidate the microbial profiles of the URT during pneumonia, the oral, nasal, and lung microbiota was evaluated at the early phase in a murine pneumonia model by direct intratracheal inoculation of Klebsiella pneumoniae. The meta 16S rRNA sequencing of bronchoalveolar lavage fluid after K. pneumoniae inoculation presented alterations in the beta diversity of the microbes, but not in the alpha diversity. At this point, a significant increase in microbial alpha diversity was observed in the oral cavity, but not in the nasal cavity. The significant increase was observed in the family Carnobacteriaceae and family Enterococcaceae. These results suggest that characterizing the microbial community of the respiratory tract may not just involve a simple downstream relationship from the URT to the LRT. The health status of the LRT may influence the oral microbiota. Thus, evaluation of the oral microbiota may contribute towards monitoring lung health; the oral microbiota may act as a diagnostic marker of pneumonia., PLoS ONE, 14(9), art.no.e0222589; 2019

Published
2019

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