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Matys J, Kensy J, Gedrange T, Zawiślak I, Grzech-Leśniak K, Dobrzyński M. A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review. Int J Mol Sci 2024; 25:4154. [PMID: 38673740 PMCID: PMC11050369 DOI: 10.3390/ijms25084154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.
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Affiliation(s)
- Jacek Matys
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Julia Kensy
- Faculty of Dentistry, Medical University of Wroclaw, 50-425 Wroclaw, Poland;
| | - Tomasz Gedrange
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
| | - Ireneusz Zawiślak
- Faculty of Biotechnology and Food Sciences, Wrocław University of Environmental and Life Sciences, 37 Chełmońskiego Str., 51-630 Wrocław, Poland;
| | - Kinga Grzech-Leśniak
- Oral Surgery Department, Medical University of Wroclaw, 50-425 Wroclaw, Poland; (T.G.); (K.G.-L.)
- Department of Periodontics, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Maciej Dobrzyński
- Department of Pediatric Dentistry and Preclinical Dentistry, Wroclaw Medical University, Krakowska 26, 50-425 Wrocław, Poland;
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Fan G, Zhang R, He X, Tian F, Nie M, Shen X, Ma X. RAP: A Novel Approach to the Rapid and Highly Sensitive Detection of Respiratory Viruses. Front Bioeng Biotechnol 2021; 9:766411. [PMID: 34805120 PMCID: PMC8602363 DOI: 10.3389/fbioe.2021.766411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Recombinase aided amplification (RAA) is an emerging isothermal amplification method used for detecting various pathogens. However, RAA requires a complex and long probe to ensure high sensitivity during fluorescence assay. TaqMan probe used for quantitative PCR (qPCR) is simple and universal. Herein, we developed a new approach for detecting nucleic acids of pathogens, known as RAP (Recombinase aided PCR). The method combines RAA and qPCR to ensure a rapid and highly sensitive detection using a conventional qPCR device. RAP is a two-stage amplification process performed in a single tube within 1 hour. The method involves an RAA reaction for 10 min at 39°C (first stage) followed by 15 cycles of qPCR (second stage). Using human adenovirus 3 (HADV3) and human adenovirus 7 (HADV7) plasmids, the sensitivities of RAP assays for detecting HADV3 and HADV7 were 6 and 17 copies per reaction, respectively. The limit of RAP detection was at least 16-fold lower than the corresponding qPCR, and no-cross reaction with other respiratory viruses was observed. The results of RAP analysis revealed 100% consistency with qPCR assay. This study shows that RAP assay is a rapid, specific, and highly sensitive detection method with a potential for clinical and laboratory application.
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Affiliation(s)
- Guohao Fan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruiqing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaozhou He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fengyu Tian
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mingzhu Nie
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinxin Shen
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuejun Ma
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
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Zhao N, Jia L, He X, Zhang B. Proteomics of mucosal exosomes of Cynoglossus semilaevis altered when infected by Vibrio harveyi. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 119:104045. [PMID: 33582105 DOI: 10.1016/j.dci.2021.104045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The cargo of exosomes contains proteins with various functions, which might be promising biomarkers for disease diagnosis and prognosis. To explore the impact of the Vibrio harveyi pathogen on Cynoglossus semilaevis from a different perspective and develop promising biomarkers for infection, the exosomes from epidermal mucus of healthy controls(EC)and sick fish(ES)were extracted and identified, coupled with proteomic screening through iTRAQ followed with LC-MS/MS. 1531 credible proteins were obtained relating to structural, metabolic and immunological functions. 359 different expressed proteins (DEPs) (FC > 2 or FC < 0.5) were found, with 161 up-regulated and 198 down-regulated in ES. Based on the database of C. semilaevis on Uniprot, 71 proteins were characterized as concrete names, including 19 up-regulated proteins and 52 down-regulated proteins, and were selected as subjects for further studies. Ferritin, Toll-like receptor 5S protein and Calcium-transporting ATPase were upregulated, while Histone H2B and Eukaryotic translation initiation factor 5A were downregulated, consistent with the expression levels of related mRNAs in skin tissue verified by qRT-PCR. The integrated analysis between miRomics and proteomics also provided possible regulatory relationships mediated by mucous exosomes during infection. The signature proteins in mucosal exosomes could make sense in the explanation of the infection defending mechanism and the development of biomarkers which can differentiate diseased and healthy C. semilaevis individuals.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin, China.
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Zhao N, Zhang B, Xu Z, Jia L, Li M, He X, Bao B. Detecting Cynoglossus semilaevis infected with Vibrio harveyi using micro RNAs from mucous exosomes. Mol Immunol 2020; 128:268-276. [PMID: 33190007 DOI: 10.1016/j.molimm.2020.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/29/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022]
Abstract
Exosomes are important mediators of vesicle transportation and contain microRNAs (miRNAs) that mediate transcriptional gene knockout and silencing in biological processes. Moreover, exosomic miRNAs are promising biomarkers for disease diagnosis and physiological status indication in many species, including fish. The impact of the Vibrio harveyi pathogen on Cynoglossus semilaevis aquaculture is becoming more and more serious as the industry expands. To overcome this challenge, miRNAs in mucous exosomes were screened by small RNA sequencing and verified by quantitative real-time PCR to develop biomarkers. This is the first capture of exosomes from flatfish mucus coupled with miRNA profiling. The results revealed significant differences in expression levels of some miRNAs between infected and healthy fish. Three unique miRNAs were identified for V. harveyi infection diagnosis; expression levels of dre-miR-205-5p and dre-miR-205-5p in infected fish were significantly lower than controls, while dre-miR-100-5p expression was higher. These miRNAs in mucous exosomes could be used to differentiate diseased and healthy fish in an early screening method with practical value for breeding disease-resistant C. semilaevis.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Haolingsaiao Biotechnology Co, Ltd, Tianjin, China
| | - Bo Zhang
- Tianjin Fisheries Research Institute, Tianjin, China.
| | - Zihui Xu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Lei Jia
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Ming Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, China
| | - Xiaoxu He
- Tianjin Fisheries Research Institute, Tianjin, China
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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Tümmler B. Molecular epidemiology in current times. Environ Microbiol 2020; 22:4909-4918. [PMID: 32945108 DOI: 10.1111/1462-2920.15238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023]
Abstract
Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.
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Affiliation(s)
- Burkhard Tümmler
- Clinical Research Group, Clinic for Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
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