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Chang M, Venkatasubramanian S, Barrett H, Urdahl KB, Weigel KM, Cangelosi GA, Shah JA, Saha A, Feng L, Adams KN, Sherman DR, Smith N, Seshadri C, Kublin JG, Murphy SC. Molecular detection of pre-ribosomal RNAs of Mycobacterium bovis bacille Calmette-Guérin and Mycobacterium tuberculosis to enhance pre-clinical tuberculosis drug and vaccine development. Diagn Microbiol Infect Dis 2024; 108:116106. [PMID: 37931386 PMCID: PMC10729053 DOI: 10.1016/j.diagmicrobio.2023.116106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Efforts are underway globally to develop effective vaccines and drugs against M. tuberculosis (Mtb) to reduce the morbidity and mortality of tuberculosis. Improving detection of slow-growing mycobacteria could simplify and accelerate efficacy studies of vaccines and drugs in animal models and human clinical trials. Here, a real-time reverse transcription PCR (RT-PCR) assay was developed to detect pre-ribosomal RNA (pre-rRNA) of Mycobacterium bovis bacille Calmette-Guérin (BCG) and Mtb. This pre-rRNA biomarker is indicative of bacterial viability. In two different mouse models, the presence of pre-rRNA from BCG and Mtb in ex vivo tissues showed excellent agreement with slower culture-based colony-forming unit assays. The addition of a brief nutritional stimulation prior to molecular viability testing further differentiated viable but dormant mycobacteria from dead mycobacteria. This research has set the stage to evaluate pre-rRNA as a BCG and/or Mtb infection biomarker in future drug and vaccine clinical studies.
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Affiliation(s)
- Ming Chang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Holly Barrett
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Kevin B Urdahl
- Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA
| | - Kris M Weigel
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Gerard A Cangelosi
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Javeed A Shah
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA; Veterans' Affairs Puget Sound Healthcare System, Seattle, WA, USA
| | - Aparajita Saha
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Libing Feng
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Kristin N Adams
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Nahum Smith
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - James G Kublin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA; Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Microbiology, University of Washington, Seattle, WA, USA.
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2
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Dayer R, De Marco G, Vazquez O, Tabard-Fougère A, Cochard B, Gavira N, Di Laura Frattura G, Guanziroli Pralong N, Steiger C, Ceroni D. Laboratory diagnostics for primary spinal infections in pediatric and adult populations: a narrative review. NORTH AMERICAN SPINE SOCIETY JOURNAL 2023; 16:100270. [PMID: 37767011 PMCID: PMC10520565 DOI: 10.1016/j.xnsj.2023.100270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/02/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
Primary spinal infection (PSI) is a generic term covering a heterogeneous group of infections that can affect the vertebral body, intervertebral disks, the content of the medullary cavity, and adjacent paraspinal tissues. Patients' characteristics can vary significantly, notably according to their age, and some of these characteristics undoubtedly play a primordial role in the occurrence of a PSI and in the type of offending pathogen. Before approaching the subject of laboratory diagnostics, it is essential to define the characteristics of the patient and their infection, which can then guide the physician toward specific diagnostic approaches. This review critically examined the roles and usefulness of traditional and modern laboratory diagnostics in supporting clinicians' decision-making in cases of pediatric and adult primary spinal infection (PSI). It appears impossible to compare PSIs in children and adults, whether from an epidemiological, clinical, bacteriological, or biological perspective. The recipients are really too different, and the responsible germs are closely correlated to their age. Secondly, the interpretation of traditional laboratory blood tests appears to contribute little guidance for clinicians attempting to diagnose a PSI. Biopsy or needle aspiration for bacterial identification remains a controversial subject, as the success rates of these procedures for identifying causative organisms are relatively uncertain in pediatric populations.Using nucleic acid amplification assays (NAAAs) on biopsy samples has been demonstrated to be more sensitive than conventional cultures for diagnosing PSI. Recent advances in next-generation sequencing (NGS) are particularly interesting for establishing a microbiological diagnosis of a PSI when standard cultures and NAAAs have failed to detect the culprit. We can even imagine that plasma metagenomic NGS using plasma (known as "liquid biopsy") is a diagnostic approach that can detect not only pathogens circulating in the bloodstream but also those causing focal infections, and thus eliminate the need for source sample collection using costly invasive surgical procedures.
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Affiliation(s)
- Romain Dayer
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Giacomo De Marco
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Oscar Vazquez
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Anne Tabard-Fougère
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Blaise Cochard
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Nathaly Gavira
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Giorgio Di Laura Frattura
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Nastassia Guanziroli Pralong
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Christina Steiger
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
| | - Dimitri Ceroni
- Pediatric Orthopedics Unit, Pediatric Surgery Service, Geneva University Hospitals and University of Geneva Rue Willy-Donzé 6, Geneva 1205, Switzerland
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Zhang T, Zeng Q, Ji F, Wu H, Ledesma-Amaro R, Wei Q, Yang H, Xia X, Ren Y, Mu K, He Q, Kang Z, Deng R. Precise in-field molecular diagnostics of crop diseases by smartphone-based mutation-resolved pathogenic RNA analysis. Nat Commun 2023; 14:4327. [PMID: 37468480 DOI: 10.1038/s41467-023-39952-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Molecular diagnostics for crop diseases can guide the precise application of pesticides, thereby reducing pesticide usage while improving crop yield, but tools are lacking. Here, we report an in-field molecular diagnostic tool that uses a cheap colorimetric paper and a smartphone, allowing multiplexed, low-cost, rapid detection of crop pathogens. Rapid nucleic acid amplification-free detection of pathogenic RNA is achieved by combining toehold-mediated strand displacement with a metal ion-mediated urease catalysis reaction. We demonstrate multiplexed detection of six wheat pathogenic fungi and an early detection of wheat stripe rust. When coupled with a microneedle for rapid nucleic acid extraction and a smartphone app for results analysis, the sample-to-result test can be completed in ~10 min in the field. Importantly, by detecting fungal RNA and mutations, the approach allows to distinguish viable and dead pathogens and to sensitively identify mutation-carrying fungicide-resistant isolates, providing fundamental information for precision crop disease management.
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Affiliation(s)
- Ting Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Fan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Honghong Wu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh, NC, 27696, USA
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Keqing Mu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, 610065, China.
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Wang J, Wei B, Chen Z, Chen Y, Liu S, Zhang B, Zhu B, Ye D. A rapid and reliable method for the determination of Lactiplantibacillus plantarum during wine fermentation based on PMA-CELL-qPCR. Front Microbiol 2023; 14:1154768. [PMID: 37529324 PMCID: PMC10389660 DOI: 10.3389/fmicb.2023.1154768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Real-time monitoring of microbial dynamics during fermentation is essential for wine quality control. This study developed a method that combines the fluorescent dye propidium monoazide (PMA) with CELL-qPCR, which can distinguish between dead and live microbes for Lactiplantibacillus plantarum. This method could detect the quantity of microbes efficiently and rapidly without DNA extraction during wine fermentation. The results showed that (1) the PMA-CELL-qPCR enumeration method developed for L. plantarum was optimized for PMA treatment concentration, PMA detection sensitivity and multiple conditions of sample pretreatment in wine environment, and the optimized method can accurately quantify 104-108 CFU/mL of the target strain (L. plantarum) in multiple matrices; (2) when the concentration of dead bacteria in the system is 104 times higher than the concentration of live bacteria, there is an error of 0.5-1 lg CFU/mL in the detection results. The optimized sample pretreatment method in wine can effectively reduce the inhibitory components in the qPCR reaction system; (3) the optimized PMA-CELL-qPCR method was used to monitor the dynamic changes of L. plantarum during the fermentation of Cabernet Sauvignon wine, and the results were consistent with the plate counting method. In conclusion, the live bacteria quantification method developed in this study for PMA-CELL-qPCR in L. plantarum wines is accurate in quantification and simple in operation, and can be used as a means to accurately monitor microbial dynamics in wine and other fruit wines.
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Affiliation(s)
- Jie Wang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bo Wei
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Zhuojun Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Yixin Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Songyu Liu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bolin Zhang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Baoqing Zhu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Dongqing Ye
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
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5
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Ali Q, Zheng H, Rao MJ, Ali M, Hussain A, Saleem MH, Nehela Y, Sohail MA, Ahmed AM, Kubar KA, Ali S, Usman K, Manghwar H, Zhou L. Advances, limitations, and prospects of biosensing technology for detecting phytopathogenic bacteria. CHEMOSPHERE 2022; 296:133773. [PMID: 35114264 DOI: 10.1016/j.chemosphere.2022.133773] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 05/22/2023]
Abstract
Phytopathogenic bacteria cause severe economic losses in agricultural production worldwide. The spread rates, severity, and emerging plant bacterial diseases have become serious threat to the sustainability of food sources and the fruit industry. Detection and diagnosis of plant diseases are imperative in order to manage plant diseases in field conditions, greenhouses, and food storage conditions as well as to maximize agricultural productivity and sustainability. To date, various techniques including, serological, observation-based, and molecular methods have been employed for plant disease detection. These methods are sensitive and specific for genetic identification of bacteria. However, these methods are specific for genetic identification of bacteria. Currently, the innovative biosensor-based disease detection technique is an attractive and promising alternative. A biosensor system involves biological recognition and transducer active receptors based on sensors used in plant-bacteria diagnosis. This system has been broadly used for the rapid diagnosis of plant bacterial pathogens. In the present review, we have discussed the conventional methods of bacterial-disease detection, however, the present review mainly focuses on the applications of different biosensor-based techniques along with point-of-care (POC), robotics, and cell phone-based systems. In addition, we have also discussed the challenges and limitations of these techniques.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China; Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, 210095, China.
| | - Hongxia Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Muhammad Junaid Rao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, 100 Daxue Rd., 8, Nanning, Guangxi, 530004, PR China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yasser Nehela
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Rd, Lake Alfred, FL, 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta, Egypt
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Agha Mushtaque Ahmed
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University Tando Jam, Sindh, Pakistan
| | - Kashif Ali Kubar
- Faculty of Agriculture, Lasbela University of Agriculture, Water and Marine Sciences, Uthal, 90150, Balochistan, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Allama Iqbal Road, 38000, Faisalabad, Pakistan
| | - Kamal Usman
- Agricultural Research Station, Office of VP for Research & Graduate Studies, Qatar University, 2713, Doha, Qatar
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China.
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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6
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Weigel KM, Olson AM, Cangelosi GA. Steady-State Pre-rRNA Analysis to Investigate the Functional Microbiome. Curr Protoc 2021; 1:e209. [PMID: 34314573 DOI: 10.1002/cpz1.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The gut microbiome is recognized as a critical regulator of human diseases. Constituents of the microbiota and their individual activities can affect a broad range of disease states related to autoimmunity, cancer, infection, metabolism, mental health, and toxicant exposure. A substantial number of microbiome species are not culturable, limiting their study in vitro. Sequencing methods have allowed quantification of the composition of the microbiome, but methods to characterize the physiological status of bacterial species remain limited. Ribosomal RNA precursors (pre-rRNAs) are species-specific intermediates in bacterial ribosomal synthesis, and their levels are highly responsive to environmental changes. Immediately before and during active growth, pre-rRNA levels are high, whereas in non-dividing cells, copy numbers are orders of magnitude lower. These dynamics are conserved in all bacterial species and occur exclusively in viable cells, allowing the specific characterization of living and functional bacteria in their native states. Pre-rRNA analysis has been shown to yield valuable real-time information on the physiology of individual bacterial species within complex samples, beyond what traditional qPCR and sequencing methods can offer. Herein, we describe a PCR-based protocol to interrogate and quantify the in situ growth status of bacterial species of interest within a complex microbiome. We also describe an in vitro protocol to characterize the pre-rRNA/growth relationship for a given bacterial species to provide greater context for values obtained from natural samples. Improved understanding of microbial physiological responses to exposures could reveal novel toxicological mechanisms, biomarkers, and potential treatments. © 2021 Wiley Periodicals LLC. Basic Protocol: Targeted steady-state pre-rRNA analysis Support Protocol: Characterization of pre-rRNA/growth relationship © 2021 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kris M Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Alaina M Olson
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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7
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Walter ND, Born SEM, Robertson GT, Reichlen M, Dide-Agossou C, Ektnitphong VA, Rossmassler K, Ramey ME, Bauman AA, Ozols V, Bearrows SC, Schoolnik G, Dolganov G, Garcia B, Musisi E, Worodria W, Huang L, Davis JL, Nguyen NV, Nguyen HV, Nguyen ATV, Phan H, Wilusz C, Podell BK, Sanoussi ND, de Jong BC, Merle CS, Affolabi D, McIlleron H, Garcia-Cremades M, Maidji E, Eshun-Wilson F, Aguilar-Rodriguez B, Karthikeyan D, Mdluli K, Bansbach C, Lenaerts AJ, Savic RM, Nahid P, Vásquez JJ, Voskuil MI. Mycobacterium tuberculosis precursor rRNA as a measure of treatment-shortening activity of drugs and regimens. Nat Commun 2021; 12:2899. [PMID: 34006838 PMCID: PMC8131613 DOI: 10.1038/s41467-021-22833-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
There is urgent need for new drug regimens that more rapidly cure tuberculosis (TB). Existing TB drugs and regimens vary in treatment-shortening activity, but the molecular basis of these differences is unclear, and no existing assay directly quantifies the ability of a drug or regimen to shorten treatment. Here, we show that drugs historically classified as sterilizing and non-sterilizing have distinct impacts on a fundamental aspect of Mycobacterium tuberculosis physiology: ribosomal RNA (rRNA) synthesis. In culture, in mice, and in human studies, measurement of precursor rRNA reveals that sterilizing drugs and highly effective drug regimens profoundly suppress M. tuberculosis rRNA synthesis, whereas non-sterilizing drugs and weaker regimens do not. The rRNA synthesis ratio provides a readout of drug effect that is orthogonal to traditional measures of bacterial burden. We propose that this metric of drug activity may accelerate the development of shorter TB regimens.
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Affiliation(s)
- Nicholas D Walter
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Consortium for Applied Microbial Metrics, Aurora, CO, USA.
| | - Sarah E M Born
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gregory T Robertson
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Matthew Reichlen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Victoria A Ektnitphong
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Karen Rossmassler
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Michelle E Ramey
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Allison A Bauman
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Victor Ozols
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shelby C Bearrows
- Rocky Mountain Regional VA Medical Center, Aurora, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Gary Schoolnik
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Gregory Dolganov
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, CA, USA
| | - Benjamin Garcia
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Emmanuel Musisi
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Biochemistry, Makerere University, Kampala, Uganda
| | | | - Laurence Huang
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
| | - J Lucian Davis
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Pulmonary, Critical Care, and Sleep Medicine Section, Yale School of Medicine, New Haven, CT, USA
| | - Nhung V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Hung V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Anh T V Nguyen
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Ha Phan
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
| | - Carol Wilusz
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Brendan K Podell
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Corinne S Merle
- London School of Hygiene and Tropical Medicine, London, UK
- UNICEF/UNDP/World Bank/WHO Special Programme on Research and Training in Tropical Disease, Geneva CH, Switzerland
| | | | - Helen McIlleron
- Division of Clinical Pharmacology, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Maria Garcia-Cremades
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Ekaterina Maidji
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Franceen Eshun-Wilson
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Dhuvarakesh Karthikeyan
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Khisimuzi Mdluli
- Bill & Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | | | - Anne J Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Radojka M Savic
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Payam Nahid
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
- Vietnam National TB Programme/UCSF Research Collaboration Unit, Hanoi, Vietnam
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Joshua J Vásquez
- Consortium for Applied Microbial Metrics, Aurora, CO, USA
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
- Zuckerberg San Francisco General Hospital, San Francisco, CA, USA
- Division of Experimental Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Center for Tuberculosis, University of California, San Francisco, CA, USA
| | - Martin I Voskuil
- Consortium for Applied Microbial Metrics, Aurora, CO, USA.
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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8
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Pareyn M, Hendrickx R, Girma N, Hendrickx S, Van Bockstal L, Van Houtte N, Shibru S, Maes L, Leirs H, Caljon G. Evaluation of a pan-Leishmania SL RNA qPCR assay for parasite detection in laboratory-reared and field-collected sand flies and reservoir hosts. Parasit Vectors 2020; 13:276. [PMID: 32487217 PMCID: PMC7268266 DOI: 10.1186/s13071-020-04141-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/21/2020] [Indexed: 11/15/2022] Open
Abstract
Background In eco-epidemiological studies, Leishmania detection in vectors and reservoirs is frequently accomplished by high-throughput and sensitive molecular methods that target minicircle kinetoplast DNA (kDNA). A pan-Leishmania SYBR green quantitative PCR (qPCR) assay which detects the conserved spliced-leader RNA (SL RNA) sequence was developed recently. This study assessed the SL RNA assay performance combined with a crude extraction method for the detection of Leishmania in field-collected and laboratory-reared sand flies and in tissue samples from hyraxes as reservoir hosts. Methods Field-collected and laboratory-infected sand fly and hyrax extracts were subjected to three different qPCR approaches to assess the suitability of the SL RNA target for Leishmania detection. Nucleic acids of experimentally infected sand flies were isolated with a crude extraction buffer with ethanol precipitation and a commercial kit and tested for downstream DNA and RNA detection. Promastigotes were isolated from culture and sand fly midguts to assess whether there was difference in SL RNA and kDNA copy numbers. Naive sand flies were spiked with a serial dilution of promastigotes to make a standard curve. Results The qPCR targeting SL RNA performed well on infected sand fly samples, despite preservation and extraction under presumed unfavorable conditions for downstream RNA detection. Nucleic acid extraction by a crude extraction buffer combined with a precipitation step was highly compatible with downstream SL RNA and kDNA detection. Copy numbers of kDNA were found to be identical in culture-derived parasites and promastigotes isolated from sand fly midguts. SL RNA levels were slightly lower in sand fly promastigotes (ΔCq 1.7). The theoretical limit of detection and quantification of the SL RNA qPCR respectively reached down to 10−3 and 10 parasite equivalents. SL RNA detection in stored hyrax samples was less efficient with some false-negative assay results, most likely due to the long-term tissue storage in absence of RNA stabilizing reagents. Conclusions This study shows that a crude extraction method in combination with the SL RNA qPCR assay is suitable for the detection and quantification of Leishmania in sand flies. The assay is inexpensive, sensitive and pan-Leishmania specific, and accordingly an excellent assay for high-throughput screening in entomological research.![]()
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Affiliation(s)
- Myrthe Pareyn
- Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium.
| | - Rik Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Nigatu Girma
- Biology Department, Arba Minch University, Arba Minch, Ethiopia
| | - Sarah Hendrickx
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Lieselotte Van Bockstal
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | | | - Simon Shibru
- Biology Department, Arba Minch University, Arba Minch, Ethiopia
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, Wilrijk, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium.
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9
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Desbrousses C, Archer F, Colin A, Bobet-Erny A, Champavère A, Gros E, Beurdeley P, Cruveiller S, Tardy F, Eloit M. High-Throughput Sequencing (HTS) of newly synthetized RNAs enables one shot detection and identification of live mycoplasmas and differentiation from inert nucleic acids. Biologicals 2020; 65:18-24. [PMID: 32222272 DOI: 10.1016/j.biologicals.2020.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/19/2020] [Accepted: 03/11/2020] [Indexed: 11/26/2022] Open
Abstract
Mycoplasma contamination threatens both the safety of biologics produced in cell substrates as well as the quality of scientific results based on cell-culture observations. Methods currently used to detect contamination of cells include culture, enzymatic activity, immunofluorescence and PCR but suffer from some limitations. High throughput sequencing (HTS) can be used to identify microbes like mycoplasmas in biologics since it enables an unbiased approach to detection without the need to design specific primers to pre-amplify target sequences but it does not enable the confirmation of microbial infection since this could reflect carryover of inert sequences. In order to unambiguously differentiate the presence of live or dead mycoplasmas in biological products, the present method was developed based on metabolic RNA labelling of newly synthetized mycoplasmal RNAs. HTS of labelled RNA detected A549 cell infection with Acholeplasma laidlawii in a manner similar to both PCR and culture and demonstrated that this technique can unambiguously identify bacterial species and differentiates infected cells from cells exposed to a high inoculum of heat-inactivated mycoplasmas. This method therefore combines the advantage of culture (that detects only live microorganisms) with those of molecular tests (rapidity) together with a very broad range of bacterial detection and identification.
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Affiliation(s)
| | - Fabienne Archer
- University of Lyon, Université Claude Bernard Lyon1, INRAE, EPHE, IVPC, Viral Infections and Comparative Pathology, UMR754, F69007, Lyon, France
| | - Adélie Colin
- Université de Lyon, Anses Laboratoire de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, F69364, Lyon, France
| | - Alexandra Bobet-Erny
- University of Lyon, Université Claude Bernard Lyon1, INRAE, EPHE, IVPC, Viral Infections and Comparative Pathology, UMR754, F69007, Lyon, France
| | - Angélique Champavère
- University of Lyon, Université Claude Bernard Lyon1, INRAE, EPHE, IVPC, Viral Infections and Comparative Pathology, UMR754, F69007, Lyon, France
| | | | | | | | - Florence Tardy
- Université de Lyon, Anses Laboratoire de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, F69364, Lyon, France
| | - Marc Eloit
- PathoQuest, Paris, France; Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, 94704 Cedex, France; Pathogen Discovery Laboratory, Institut Pasteur, Paris, France.
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10
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Baymiev AK, Baymiev AK, Kuluev BR, Shvets KY, Yamidanov RS, Matniyazov RT, Chemeris DA, Zubov VV, Alekseev YI, Mavzyutov AR, Ivanenkov YA, Chemeris AV. Modern Approaches to Differentiation of Live and Dead Bacteria Using Selective Amplification of Nucleic Acids. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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11
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RNA-based qPCR as a tool to quantify and to characterize dual-species biofilms. Sci Rep 2019; 9:13639. [PMID: 31541147 PMCID: PMC6754382 DOI: 10.1038/s41598-019-50094-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/06/2019] [Indexed: 12/22/2022] Open
Abstract
While considerable research has focused on studying individual-species, we now face the challenge of determining how interspecies interactions alter bacterial behaviours and pathogenesis. Pseudomonas aeruginosa and Staphylococcus aureus are often found to co-infect cystic-fibrosis patients. Curiously, their interaction is reported as competitive under laboratory conditions. Selecting appropriate methodologies is therefore critical to analyse multi-species communities. Herein, we demonstrated the major biases associated with qPCR quantification of bacterial populations and optimized a RNA-based qPCR able not only to quantify but also to characterize microbial interactions within dual-species biofilms composed by P. aeruginosa and S. aureus, as assessed by gene expression quantification. qPCR quantification was compared with flow-cytometry and culture-based quantification. Discrepancies between culture independent and culture dependent methods could be the result of the presence of viable but not-cultivable bacteria within the biofilm. Fluorescence microscopy confirmed this. A higher sensitivity to detect viable cells further highlights the potentialities of qPCR approach to quantify biofilm communities. By using bacterial RNA and an exogenous mRNA control, it was also possible to characterize bacterial transcriptomic profile, being this a major advantage of this method.
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12
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Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
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13
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Mauerhofer LM, Pappenreiter P, Paulik C, Seifert AH, Bernacchi S, Rittmann SKMR. Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology. Folia Microbiol (Praha) 2019; 64:321-360. [PMID: 30446943 PMCID: PMC6529396 DOI: 10.1007/s12223-018-0658-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/12/2018] [Indexed: 12/17/2022]
Abstract
Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.
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Affiliation(s)
- Lisa-Maria Mauerhofer
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria
| | - Patricia Pappenreiter
- Institute for Chemical Technology of Organic Materials, Johannes Kepler University Linz, Linz, Austria
| | - Christian Paulik
- Institute for Chemical Technology of Organic Materials, Johannes Kepler University Linz, Linz, Austria
| | | | | | - Simon K-M R Rittmann
- Archaea Physiology & Biotechnology Group, Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, Universität Wien, Althanstraße 14, 1090, Wien, Austria.
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14
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Lee S, Bae S. Molecular viability testing of viable but non-culturable bacteria induced by antibiotic exposure. Microb Biotechnol 2018; 11:1008-1016. [PMID: 29243404 PMCID: PMC6196391 DOI: 10.1111/1751-7915.13039] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid amplification-based methods are limited by their inability to discriminate between viable and dead cells. To overcome this drawback, propidium monoazide (PMA) combined with qPCR has been used to differentiate viable from nonviable cells in environmental samples. However, assessing bacterial physiology using PMA-qPCR remains a challenge due to its incapability of detecting metabolic activities, leading to overestimation of the viable bacteria population under an inactivation condition (e.g. antibiotic treatments). A recent advanced technique to amplify ribosomal RNA precursors (pre-rRNA) has been shown to detect viable cells because pre-rRNAs are intermediates in rRNA synthesis. This study investigated the effect of different types of antibiotics on the bacterial viability or viable but non-culturable (VBNC) state using both PMA-qPCR and pre-rRNA analyses with Pseudomonas aeruginosa. This study demonstrated that P. aeruginosa was more sensitive to colistin than it was to carbenicillin, gentamicin and levofloxacin. We could discriminate VBNCP. aeruginosa cells using PMA-qPCR when antibiotic pressure induced the VBNC state. Also, pre-rRNA was able to distinguish viable cells from colistin-inactivated bacteria cells, and it could detect the presence of VBNC and persister cells. Our results showed that these two molecular methods could successfully eliminate false-positive signals derived from antibiotics-inactivated cells.
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Affiliation(s)
- Seunguk Lee
- Department of Civil and Environmental EngineeringNational University of Singapore1 Engineering Drive 2Singapore117576Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental EngineeringNational University of Singapore1 Engineering Drive 2Singapore117576Singapore
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15
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Shahi S, Zununi Vahed S, Fathi N, Sharifi S. Polymerase chain reaction (PCR)-based methods: Promising molecular tools in dentistry. Int J Biol Macromol 2018; 117:983-992. [DOI: 10.1016/j.ijbiomac.2018.05.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/13/2018] [Accepted: 05/14/2018] [Indexed: 02/06/2023]
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16
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Boss R, Baumgartner A, Kroos S, Blattner M, Fretz R, Moor D. Rapid detection of viableLegionella pneumophilain tap water by a qPCR and RT-PCR-based method. J Appl Microbiol 2018; 125:1216-1225. [DOI: 10.1111/jam.13932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 12/22/2022]
Affiliation(s)
- R. Boss
- Federal Food Safety and Veterinary Office; Berne Switzerland
| | - A. Baumgartner
- Federal Food Safety and Veterinary Office; Berne Switzerland
| | - S. Kroos
- Food Safety and Veterinary Office; Canton of Basel-Landschaft; Liestal Switzerland
| | - M. Blattner
- Food Safety and Veterinary Office; Canton of Basel-Landschaft; Liestal Switzerland
| | - R. Fretz
- Food Safety and Veterinary Office; Canton of Basel-Landschaft; Liestal Switzerland
| | - D. Moor
- Federal Food Safety and Veterinary Office; Berne Switzerland
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17
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Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities. Appl Environ Microbiol 2017; 83:AEM.01363-17. [PMID: 28821552 DOI: 10.1128/aem.01363-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023] Open
Abstract
This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and ProteobacteriaEctothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3-, and PO43- concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity.IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard.
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18
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Vanegas DC, Gomes CL, Cavallaro ND, Giraldo‐Escobar D, McLamore ES. Emerging Biorecognition and Transduction Schemes for Rapid Detection of Pathogenic Bacteria in Food. Compr Rev Food Sci Food Saf 2017; 16:1188-1205. [DOI: 10.1111/1541-4337.12294] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Diana C. Vanegas
- Food Engineering Univ. del Valle 338 Ciudad Universitaria Meléndez Cali Colombia
| | - Carmen L. Gomes
- Biological & Agricultural Engineering Texas A&M Univ. 2117 TAMU, Scoates Hall 201 College Station TX 77843 U.S.A
| | - Nicholas D. Cavallaro
- Agricultural & Biological Engineering Univ. of Florida 1741 Museum Rd Gainesville FL 32606 U.S.A
| | | | - Eric S. McLamore
- Agricultural & Biological Engineering Univ. of Florida 1741 Museum Rd Gainesville FL 32606 U.S.A
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19
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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Molecular Viability Testing of UV-Inactivated Bacteria. Appl Environ Microbiol 2017; 83:AEM.00331-17. [PMID: 28283525 DOI: 10.1128/aem.00331-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/08/2017] [Indexed: 01/01/2023] Open
Abstract
PCR is effective in detecting bacterial DNA in samples, but it is unable to differentiate viable bacteria from inactivated cells or free DNA fragments. New PCR-based analytical strategies have been developed to address this limitation. Molecular viability testing (MVT) correlates bacterial viability with the ability to rapidly synthesize species-specific rRNA precursors (pre-rRNA) in response to brief nutritional stimulation. Previous studies demonstrated that MVT can assess bacterial inactivation by chlorine, serum, and low-temperature pasteurization. Here, we demonstrate that MVT can detect inactivation of Escherichia coli, Aeromonas hydrophila, and Enterococcus faecalis cells by UV irradiation. Some UV-inactivated E. coli cells transiently retained the ability to synthesize pre-rRNA postirradiation (generating false-positive MVT results), but this activity ceased within 1 h following UV exposure. Viable but transiently undetectable (by culture) E. coli cells were consistently detected by MVT. An alternative viability testing method, viability PCR (vPCR), correlates viability with cell envelope integrity. This method did not distinguish viable bacteria from UV-inactivated bacteria under some conditions, indicating that the inactivated cells retained intact cell envelopes. MVT holds promise as a means to rapidly assess microbial inactivation by UV treatment.IMPORTANCE UV irradiation is increasingly being used to disinfect water, food, and other materials for human use. Confirming the effectiveness of UV disinfection remains a challenging task. In particular, microbiological methods that rely on rapid detection of microbial DNA can yield misleading results, due to the detection of remnant DNA associated with dead microbial cells. This report describes a novel method that rapidly distinguishes living microbial cells from dead microbial cells after UV disinfection.
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Hassard F, Gwyther CL, Farkas K, Andrews A, Jones V, Cox B, Brett H, Jones DL, McDonald JE, Malham SK. Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review. Front Microbiol 2016; 7:1692. [PMID: 27847499 PMCID: PMC5088438 DOI: 10.3389/fmicb.2016.01692] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.
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Affiliation(s)
| | - Ceri L. Gwyther
- Department of Engineering and Innovation, Open UniversityMilton Keynes, UK
| | - Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
| | | | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
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Spooner R, Weigel KM, Harrison PL, Lee K, Cangelosi GA, Yilmaz Ö. In Situ Anabolic Activity of Periodontal Pathogens Porphyromonas gingivalis and Filifactor alocis in Chronic Periodontitis. Sci Rep 2016; 6:33638. [PMID: 27642101 PMCID: PMC5027532 DOI: 10.1038/srep33638] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/31/2016] [Indexed: 12/17/2022] Open
Abstract
Porphyromonas gingivalis and Filifactor alocis are fastidious anaerobic bacteria strongly associated with chronic forms of periodontitis. Our understanding of the growth activities of these microorganisms in situ is very limited. Previous studies have shown that copy numbers of ribosomal-RNA precursor (pre-rRNA) of specific pathogen species relative to genomic-DNA (gDNA) of the same species (P:G ratios) are greater in actively growing bacterial cells than in resting cells. The method, so-called steady-state pre-rRNA-analysis, represents a novel culture-independent approach to study bacteria. This study employed this technique to examine the in situ growth activities of oral bacteria in periodontitis before and after non-surgical periodontal therapy. Sub-gingival paper-point samples were taken at initial and re-evaluation appointments. Pre-rRNA and gDNA levels of P. gingivalis and F. alocis were quantified and compared using reverse-transcriptase qPCR. The results indicate significantly reduced growth activity of P. gingivalis, but not F. alocis, after therapy. The P:G ratios of P. gingivalis and F. alocis were compared and a low-strength, but statistically significant inter-species correlation was detected. Our study demonstrates that steady-state pre-rRNA-analysis can be a valuable culture-independent approach to studying opportunistic bacteria in periodontitis.
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Affiliation(s)
- Ralee Spooner
- Divison of Periodontics, Department of Stomatology, Medical University of South Carolina, Charleston, SC 29425, USA.,Lieutenant, Dental Corps, Navy Professional Medicine Development Center, Bethesda, MD 20889, USA
| | - Kris M Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Peter L Harrison
- Department of Periodontology, University of Florida, Gainesville, FL 32610, USA
| | - KyuLim Lee
- Department of Periodontology, University of Florida, Gainesville, FL 32610, USA
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Özlem Yilmaz
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA.,Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
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23
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Abstract
Nucleic acid-based analytical methods, ranging from species-targeted PCRs to metagenomics, have greatly expanded our understanding of microbiological diversity in natural samples. However, these methods provide only limited information on the activities and physiological states of microorganisms in samples. Even the most fundamental physiological state, viability, cannot be assessed cross-sectionally by standard DNA-targeted methods such as PCR. New PCR-based strategies, collectively called molecular viability analyses, have been developed that differentiate nucleic acids associated with viable cells from those associated with inactivated cells. In order to maximize the utility of these methods and to correctly interpret results, it is necessary to consider the physiological diversity of life and death in the microbial world. This article reviews molecular viability analysis in that context and discusses future opportunities for these strategies in genetic, metagenomic, and single-cell microbiology.
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24
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González-Andrade P, Camara M, Ilboudo H, Bucheton B, Jamonneau V, Deborggraeve S. Diagnosis of trypanosomatid infections: targeting the spliced leader RNA. J Mol Diagn 2014; 16:400-4. [PMID: 24814957 DOI: 10.1016/j.jmoldx.2014.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/12/2014] [Accepted: 02/26/2014] [Indexed: 10/25/2022] Open
Abstract
Trypanosomatids transcribe their genes in large polycistronic clusters that are further processed into mature mRNA molecules by trans-splicing. During this maturation process, a conserved spliced leader RNA (SL-RNA) sequence of 39 bp is physically linked to the 5' end of the pre-mRNA molecules. Trypanosomatid infections cause a series of devastating diseases in man (sleeping sickness, leishmaniasis, Chagas disease) and animals (nagana, surra, dourine). Here, we investigated the SL-RNA molecule for its diagnostic potential using reverse transcription followed by real-time PCR. As a model, we used Trypanosoma brucei gambiense, which causes sleeping sickness in west and central Africa. We showed that the copy number of the SL-RNA molecule in one single parasitic cell is at least 8600. We observed a lower detection limit of the SL-RNA assay in spiked blood samples of 100 trypanosomes per milliliter of blood. We also proved that we can detect the trypanosome's SL-RNA in the blood of sleeping sickness patients with a sensitivity of 92% (95% CI, 78%-97%) and a specificity of 96% (95% CI, 86%-99%). The SL-RNA is thus an attractive new molecular target for next-generation diagnostics in diseases caused by trypanosomatids.
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Affiliation(s)
| | - Mamady Camara
- National Sleeping Sickness Control Program, Ministry of Health and Public Hygiene, Conakry, Guinea
| | - Hamidou Ilboudo
- International Center for Development Research on Aging in Sub-Humid Areas (CIRDES), Bobo-Dioulasso, Burkina Faso
| | - Bruno Bucheton
- Institute of Research for Development, Mixed Research Unit IRD-CIRAD 177, Montpellier, France
| | - Vincent Jamonneau
- International Center for Development Research on Aging in Sub-Humid Areas (CIRDES), Bobo-Dioulasso, Burkina Faso; Institute of Research for Development, Mixed Research Unit IRD-CIRAD 177, Montpellier, France
| | - Stijn Deborggraeve
- Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium.
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25
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Do JS, Weigel KM, Meschke JS, Cangelosi GA. Biosynthetic enhancement of the detection of bacteria by the polymerase chain reaction. PLoS One 2014; 9:e86433. [PMID: 24466092 PMCID: PMC3895033 DOI: 10.1371/journal.pone.0086433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/11/2013] [Indexed: 11/18/2022] Open
Abstract
Molecular viability testing (MVT) was previously reported to specifically detect viable bacterial cells in complex samples. In MVT, brief nutritional stimulation induces viable cells, but not non-viable cells, to produce abundant amounts of species-specific ribosomal RNA precursors (pre-rRNA). Quantitative polymerase chain reaction (qPCR) is used to quantify specific pre-rRNAs in a stimulated aliquot relative to a non-stimulated control. In addition to excluding background signal from non-viable cells and from free DNA, we report here that MVT increases the analytical sensitivity of qPCR when detecting viable cells. Side-by-side limit-of-detection comparisons showed that MVT is 5-fold to >10-fold more sensitive than standard (static) DNA-targeted qPCR when detecting diverse bacterial pathogens (Aeromonas hydrophila, Acinetobacter baumannii, Listeria monocytogenes, Mycobacterium avium, and Staphylococcus aureus) in serum, milk, and tap water. Sensitivity enhancement may come from the elevated copy number of pre-rRNA relative to genomic DNA, and also from the ratiometric measurement which reduces ambiguity associated with weak or borderline signals. We also report that MVT eliminates false positive signals from bacteria that have been inactivated by moderately elevated temperatures (pasteurization), a condition that can confound widely-used cellular integrity tests that utilize membrane-impermeant compounds such as propidium iodide (PI) or propidium monoazide (PMA) to differentiate viable from inactivated bacteria. MVT enables the sensitive and specific detection of very small numbers of viable bacteria in complex matrices.
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Affiliation(s)
- Julie S. Do
- AttoDx, Inc., Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - John S. Meschke
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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26
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Gürtler V, Grando D. Reprint of New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. METHODS IN MICROBIOLOGY 2013; 95:425-40. [PMID: 24050948 DOI: 10.1016/j.mimet.2013.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 11/24/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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27
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New concepts in diagnostics for infectious diarrhea. Mucosal Immunol 2013; 6:876-85. [PMID: 23881355 DOI: 10.1038/mi.2013.50] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/11/2013] [Indexed: 02/04/2023]
Abstract
Conventional approaches to the diagnosis of infectious diarrhea must include several modalities to detect an array of potential viruses, bacteria, and parasites. We will provide a general overview of the wide range of diagnostic modalities available for enteropathogens, briefly discuss some of the limitations of conventional methods, and then focus on new molecular methods, including real-time PCR and next-generation sequencing. In particular, we will discuss quantitation of pathogen load with these techniques. We will then describe examples whereby novel diagnostics may help illuminate the etiology of infectious diarrhea, where they may not, and how they may benefit studies of immunity to enteric infections.
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28
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Gürtler V, Grando D. New opportunities for improved ribotyping of C. difficile clinical isolates by exploring their genomes. J Microbiol Methods 2013; 93:257-72. [PMID: 23545446 DOI: 10.1016/j.mimet.2013.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/26/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
Clostridium difficile causes outbreaks of infectious diarrhoea, most commonly occurring in healthcare institutions. Recently, concern has been raised with reports of C. difficile disease in those traditionally thought to be at low risk i.e. community acquired rather than healthcare acquired. This has increased awareness for the need to track outbreaks and PCR-ribotyping has found widespread use to elucidate epidemiologically linked isolates. PCR-ribotyping uses conserved regions of the 16S rRNA gene and 23S rRNA gene as primer binding sites to produce varying PCR products due to the intergenic spacer (ITS1) regions of the multiple operons. With the explosion of whole genome sequence data it became possible to analyse the start of the 23S rRNA gene for a more accurate selection of regions closer to the end of the ITS1. However the following questions must still be asked: (i) Does the chromosomal organisation of the rrn operon vary between C. difficile strains? and (ii) just how conserved are the primer binding regions? Eight published C. difficile genomes have been aligned to produce a detailed database of indels of the ITS1's from the rrn operon sets. An iPad Filemaker Go App has been constructed and named RiboTyping (RT). It contains detail such as sequences, ribotypes, strain numbers, GenBank numbers and genome position numbers. Access to various levels of the database is provided so that details can be printed. There are three main regions of the rrn operon that have been analysed by the database and related to each other by strain, ribotype and operon: (1) 16S gene (2) ITS1 indels (3) 23S gene. This has enabled direct intra- and inter-genomic comparisons at the strain, ribotype and operon (allele) levels in each of the three genomic regions. This is the first time that such an analysis has been done. By using the RT App with search criteria it will be possible to select probe combinations for specific strains/ribotypes/rrn operons for experiments to do with diagnostics, typing and recombination of operons. Many more incomplete C. difficile whole genome sequencing projects are recorded in GenBank as underway and the rrn operon information from these can also be added to the RT App when available. The RT App will help simplify probe selection because of the complexity of the ITS1 in C. difficile even in a single genome and because other allele-specific regions (16S and 23S genes) of variability can be relationally compared to design extra probes to increase sensitivity.
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Affiliation(s)
- Volker Gürtler
- School of Applied Sciences, Building 223, Level 1, Bundoora Campus RMIT University, PO Box 71, Bundoora 3083, Australia.
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29
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Weigel KM, Jones KL, Do JS, Melton Witt J, Chung JH, Valcke C, Cangelosi GA. Molecular viability testing of bacterial pathogens from a complex human sample matrix. PLoS One 2013; 8:e54886. [PMID: 23365682 PMCID: PMC3554692 DOI: 10.1371/journal.pone.0054886] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022] Open
Abstract
Assays for bacterial ribosomal RNA precursors (pre-rRNA) have been shown to distinguish viable from inactivated bacterial cells in drinking water samples. Because the synthesis of pre-rRNA is rapidly induced by nutritional stimulation, viable bacteria can be distinguished from inactivated cells and free nucleic acids by measuring the production of species-specific pre-rRNA in samples that have been briefly stimulated with nutrients. Here, pre-rRNA analysis was applied to bacteria from serum, a human sample matrix. In contrast to drinking water, serum is rich in nutrients that might be expected to mask the effects of nutritional stimulation. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assays were used to detect pre-rRNA of four bacterial species: Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, and the Mycobacterium tuberculosis complex. These species were chosen for their clinical significance and phylogenetic diversity (Proteobacteria, Firmicutes, and Actinobacteria). To maximize resolving power, pre-rRNA was normalized to genomic DNA of each pathogen. When viable cells were shifted from serum to bacteriological culture medium, rapid replenishment of pre-rRNA was always observed. Cells of P. aeruginosa that were inactivated in the presence of serum exhibited no pre-rRNA response to nutritional stimulation, despite strong genomic DNA signals in these samples. When semi-automated methods were used, pre-rRNA analysis detected viable A. baumannii cells in serum at densities of ≤100 CFU/mL in <5.5 hours. Originally developed for rapid microbiological analysis of drinking water, ratiometric pre-rRNA analysis can also assess the viability of bacterial cells derived from human specimens, without requiring bacteriological culture.
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Affiliation(s)
- Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kelly L. Jones
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Julie S. Do
- AttoDx, Inc., Seattle, Washington, United States of America
| | - Jody Melton Witt
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, United States of America
| | - Christian Valcke
- Novartis Diagnostics, Emeryville, California, United States of America
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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30
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Pinto AJ, Xi C, Raskin L. Bacterial community structure in the drinking water microbiome is governed by filtration processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:8851-9. [PMID: 22793041 DOI: 10.1021/es302042t] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The bacterial community structure of a drinking water microbiome was characterized over three seasons using 16S rRNA gene based pyrosequencing of samples obtained from source water (a mix of a groundwater and a surface water), different points in a drinking water plant operated to treat this source water, and in the associated drinking water distribution system. Even though the source water was shown to seed the drinking water microbiome, treatment process operations limit the source water's influence on the distribution system bacterial community. Rather, in this plant, filtration by dual media rapid sand filters played a primary role in shaping the distribution system bacterial community over seasonal time scales as the filters harbored a stable bacterial community that seeded the water treatment processes past filtration. Bacterial taxa that colonized the filter and sloughed off in the filter effluent were able to persist in the distribution system despite disinfection of finished water by chloramination and filter backwashing with chloraminated backwash water. Thus, filter colonization presents a possible ecological survival strategy for bacterial communities in drinking water systems, which presents an opportunity to control the drinking water microbiome by manipulating the filter microbial community. Grouping bacterial taxa based on their association with the filter helped to elucidate relationships between the abundance of bacterial groups and water quality parameters and showed that pH was the strongest regulator of the bacterial community in the sampled drinking water system.
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Affiliation(s)
- Ameet J Pinto
- Department of Civil and Environmental Engineering, University of Michigan, USA
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31
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Mechanical disruption of lysis-resistant bacterial cells by use of a miniature, low-power, disposable device. J Clin Microbiol 2011; 49:2533-9. [PMID: 21543569 DOI: 10.1128/jcm.02171-10] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular detection of microorganisms requires microbial cell disruption to release nucleic acids. Sensitive detection of thick-walled microorganisms such as Bacillus spores and Mycobacterium cells typically necessitates mechanical disruption through bead beating or sonication, using benchtop instruments that require line power. Miniaturized, low-power, battery-operated devices are needed to facilitate mechanical pathogen disruption for nucleic acid testing at the point of care and in field settings. We assessed the lysis efficiency of a very small disposable bead blender called OmniLyse relative to the industry standard benchtop Biospec Mini-BeadBeater. The OmniLyse weighs approximately 3 g, at a size of approximately 1.1 cm(3) without the battery pack. Both instruments were used to mechanically lyse Bacillus subtilis spores and Mycobacterium bovis BCG cells. The relative lysis efficiency was assessed through real-time PCR. Cycle threshold (C(T)) values obtained at all microbial cell concentrations were similar between the two devices, indicating that the lysis efficiencies of the OmniLyse and the BioSpec Mini-BeadBeater were comparable. As an internal control, genomic DNA from a different organism was spiked at a constant concentration into each sample upstream of lysis. The C(T) values for PCR amplification of lysed samples using primers specific to this internal control were comparable between the two devices, indicating negligible PCR inhibition or other secondary effects. Overall, the OmniLyse device was found to effectively lyse tough-walled organisms in a very small, disposable, battery-operated format, which is expected to facilitate sensitive point-of-care nucleic acid testing.
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