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Kim M, Parrish RC, Shah VS, Ross M, Cormier J, Baig A, Huang CY, Brenner L, Neuringer I, Whiteson K, Harris JK, Willis AD, Lai PS. Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies. RESEARCH SQUARE 2024:rs.3.rs-3638876. [PMID: 38343829 PMCID: PMC10854296 DOI: 10.21203/rs.3.rs-3638876/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Most respiratory microbiome studies have focused on amplicon rather than metagenomics sequencing due to high host DNA content. We evaluated efficacy of five host DNA depletion methods on previously frozen human bronchoalveolar lavage (BAL), nasal swabs, and sputum prior to metagenomic sequencing. Results Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum and BAL samples had 94.1%, 99.2%, and 99.7% host-reads. The effect of host depletion differed by sample type. Most treatment methods increased microbial reads, species richness and predicted functional richness; the increase in species and predicted functional richness was mediated by higher effective sequencing depth. For BAL and nasal samples, most methods did not change Morisita-Horn dissimilarity suggesting limited bias introduced by host depletion. Conclusions Metagenomics sequencing without host depletion will underestimate microbial diversity of most respiratory samples due to shallow effective sequencing depth and is not recommended. Optimal host depletion methods vary by sample type.
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Affiliation(s)
- Minsik Kim
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
| | - Raymond C Parrish
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Viral S Shah
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Matthew Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine
| | - Juwan Cormier
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine
| | - Aribah Baig
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; College of Science, Northeastern University
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Laura Brenner
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
| | - Isabel Neuringer
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Katrine Whiteson
- Department of Molecular Biology & Biochemistry, University of California
| | - J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus
| | - Amy D Willis
- Department of Biostatistics, University of Washington School of Public Health
| | - Peggy S Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital; Department of Medicine, Harvard Medical School
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Moore CM, Dhillon J, Flynn R, Gizynski K, Adams C, Morgan G, McGurk D, Boada E, Shabestary S, Peat J, O'Halloran J, Stoker NG, Butcher PD, Murton H. A Novel Microfluidic Dielectrophoresis Technology to Enable Rapid Diagnosis of Mycobacteria tuberculosis in Clinical Samples. J Mol Diagn 2023; 25:513-523. [PMID: 37355278 DOI: 10.1016/j.jmoldx.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/28/2023] [Accepted: 04/03/2023] [Indexed: 06/26/2023] Open
Abstract
To achieve the global efforts to end tuberculosis, affordable diagnostics suitable for true point-of-care implementation are required to reach the missing millions. In addition, diagnostics with increased sensitivity and expanded drug susceptibility testing are needed to address drug resistance and to diagnose low-bacterial burden cases. The laboratory-on-a-chip technology described herein used dielectrophoresis to selectively isolate Mycobacterium tuberculosis from sputum samples, purifying the bacterial population ahead of molecular confirmation by multiplex real-time quantitative PCR. After optimization using a panel of 50 characterized sputum samples, the performance of the prototype was assessed against the current gold standards, screening 100 blinded sputum samples using characterized and biobanked sputum provided by Foundation for Innovative New Diagnostics. Concordance with culture diagnosis was 100% for smear-negative samples and 87% for smear-positive samples. Of the smear-positive samples, the high burden sample concordance was 100%. Samples were diagnosed on the basis of visual assessment of the dielectrophoresis array and by multiplex real-time quantitative PCR assay. The results described herein demonstrate the potential of the CAPTURE-XT technology to provide a powerful sample preparation tool that could function as a front-end platform for molecular detection. This versatile tool could equally be applied as a visual detection diagnostic, potentially associated with bacterial identification for low-cost screening or coupled with an expanded PCR assay for genotypic drug susceptibility testing.
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Affiliation(s)
- Catherine M Moore
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Jasvir Dhillon
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Rebecca Flynn
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | | | - Candice Adams
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom
| | - George Morgan
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom
| | - David McGurk
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom
| | - Eduardo Boada
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom
| | | | - Jonathan Peat
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom
| | | | - Neil G Stoker
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom
| | - Philip D Butcher
- Institute for Infection and Immunity, St. George's University of London, London, United Kingdom.
| | - Heather Murton
- QuantuMDx Group Ltd., Newcastle upon Tyne, United Kingdom.
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3
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Huang W, Lee MKT, Sin ATK, Nazari RS, Chua SY, Sng LH. Evaluation of Xpert MTB/RIF ultra assay for detection of Mycobacterium tuberculosis and rifampicin resistance. Pathology 2023:S0031-3025(23)00116-2. [PMID: 37268484 DOI: 10.1016/j.pathol.2023.03.002] [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: 09/13/2022] [Revised: 01/05/2023] [Accepted: 03/14/2023] [Indexed: 06/04/2023]
Abstract
Tuberculosis (TB) is a public health challenge globally, and molecular testing is recommended to expedite diagnosis. Concerns that Xpert MTB/RIF assay (Xpert) may be less sensitive when testing paucibacillary samples led to the development of the Xpert MTB/RIF Ultra assay (Ultra). We evaluated the performance of Ultra against Xpert on clinical samples sent to the national reference laboratory in Singapore. In total, 149 samples collected between January 2019 and November 2020 were analysed. Mycobacterium tuberculosis complex (MTBC) was isolated from 55 cultures. Using culture as the reference standard, Ultra demonstrated higher sensitivity (96.4% vs 85.5%) and marginally lower specificity (88.3% vs 89.4%) compared to Xpert in the full cohort. When considering only paucibacillary specimens such as extrapulmonary and smear-negative samples, similar results were obtained. Reclassifying Ultra trace results (low levels of MTB are detected but no rifampicin resistant result is detected) as negative in the full cohort led to a decrease in sensitivity by 10.9% and a marginal increase in specificity by 1.1%. In instances of low bacillary load, Ultra also identified rifampicin resistance more accurately than Xpert, when corroborated against other methods such as broth microdilution, line probe assay and whole genome sequencing (WGS). One isolate tested rifampicin-resistant using Xpert and Ultra, but was phenotypically susceptible and WGS demonstrated the presence of the silent mutation Thr444Thr. Ultra is more sensitive than Xpert in the detection of MTBC and rifampicin resistance in our local setting. Nevertheless, the results of molecular testing should still be correlated with phenotypic studies.
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Affiliation(s)
- Wenjie Huang
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore.
| | - Melody Kee Tai Lee
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Amanda Teo Kai Sin
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | | | - Syn Yu Chua
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
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Ishii S, Ishida A, Sugiura Y, Takasaki J, Izumi S, Hojo M. Examination of the utility of cryobiopsy for tuberculous pleurisy in thoracoscopy: A report of seven cases. Respir Med Case Rep 2023; 43:101840. [PMID: 37064571 PMCID: PMC10091113 DOI: 10.1016/j.rmcr.2023.101840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/12/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
Thoracoscopy under local anaesthesia is effective for the diagnosis of tuberculous pleurisy (TP), mesothelioma and pleural metastases of lung cancer, etc. It has recently been reported that cryobiopsy is useful for obtaining sufficient tissue, achieving a greater depth, and avoiding crush artefact than biopsy forceps. However, the utility of the tissue obtained by cryobiopsy for culture for diagnosing TP is unknown. We compared positivity rates of tissue culture obtained by biopsy forceps and cryobiopsy in seven TP patients. The median tissue size was 2 mm by biopsy forceps and 6 mm by cryobiopsy. The pathological diagnostic rate of pleural tissue was 85.7% with biopsy forceps and 100% with cryobiopsy. However, the positivity rate of tissue culture was 57.1% with biopsy forceps and 28.5% with cryobiopsy. Since rapid freezing with a cryoprobe makes it difficult for bacteria to grow, it is possible that cryobiopsy might not be useful for obtaining a tissue culture in TP cases. However, since the sample size of this study was small, analysis of more cases is required to confirm our results.
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Characterization of Drug-Resistant Lipid-Dependent Differentially Detectable Mycobacterium tuberculosis. J Clin Med 2021; 10:jcm10153249. [PMID: 34362035 PMCID: PMC8348819 DOI: 10.3390/jcm10153249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 01/12/2023] Open
Abstract
An estimated 15–20% of patients who are treated for pulmonary tuberculosis (TB) are culture-negative at the time of diagnosis. Recent work has focused on the existence of differentially detectable Mycobacterium tuberculosis (Mtb) bacilli that do not grow under routine solid culture conditions without the addition of supplementary stimuli. We identified a cohort of TB patients in Lima, Peru, in whom acid-fast bacilli could be detected by sputum smear microscopy, but from whom Mtb could not be grown in standard solid culture media. When we attempted to re-grow Mtb from the frozen sputum samples of these patients, we found that 10 out of 15 could be grown in a glycerol-poor/lipid-rich medium. These fell into the following two groups: a subset that could be regrown in glycerol after “lipid-resuscitation”, and a group that displayed a heritable glycerol-sensitive phenotype that were unable to grow in the presence of this carbon source. Notably, all of the glycerol-sensitive strains were found to be multidrug resistant. Although whole-genome sequencing of the lipid-resuscitated strains identified 20 unique mutations compared to closely related strains, no single genetic lesion could be associated with this phenotype. In summary, we found that lipid-based media effectively fostered the growth of Mtb from a series of sputum smear-positive samples that were not culturable in glycerol-based Lowenstein–Jensen or 7H9 media, which is consistent with Mtb’s known preference for non-glycolytic sources during infection. Analysis of the recovered strains demonstrated that both genetic and non-genetic mechanisms contribute to the observed differential capturability, and suggested that this phenotype may be associated with drug resistance.
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Natali D, Cloatre G, Brosset C, Verdalle P, Fauvy A, Massart JP, Vo Van Q, Gerard N, Dobler CC, Hovette P. What pulmonologists need to know about extrapulmonary tuberculosis. Breathe (Sheff) 2021; 16:200216. [PMID: 33664835 PMCID: PMC7910020 DOI: 10.1183/20734735.0216-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Extrapulmonary tuberculosis (EPT) can affect all organs. Its diagnosis is often challenging, especially when the lung is not involved. Some EPT locations, such as when the central nervous system is involved, are a medical emergency, and some have implications for treatment options and length. This review describes clinical features of EPT, diagnostic tests and treatment regimens. Extrapulmonary tuberculosis can affect any organ, can be potentially life threatening or disabling, poses diagnostic difficulties and may change the type and length of treatment. Looking for concomitant pulmonary tuberculosis is essential.https://bit.ly/2YEaRVb
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Affiliation(s)
| | | | | | - Pierre Verdalle
- Ear-Nose-Throat Diseases, Hanoi French Hospital, Hanoi, Vietnam
| | - Alain Fauvy
- Orthopedic Surgery, Hanoi French Hospital, Hanoi, Vietnam
| | | | - Quy Vo Van
- Urology, Hanoi French Hospital, Hanoi, Vietnam
| | - Nelly Gerard
- Dermatology, Hanoi French Hospital, Hanoi, Vietnam
| | - Claudia C Dobler
- Dept of Respiratory Medicine, Liverpool Hospital, Sydney, Australia.,The George Institute for Global Health, University of New South Wales, Sydney, Australia
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Xpert MTB/RIF ultra for the diagnosis of tuberculous meningitis: A diagnostic accuracy study from India. Tuberculosis (Edinb) 2020; 125:101990. [PMID: 32920283 DOI: 10.1016/j.tube.2020.101990] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/24/2020] [Accepted: 08/31/2020] [Indexed: 11/22/2022]
Abstract
SETTING Studies evaluating Xpert MTB/RIF Ultra assay (Xpert Ultra) for diagnosing tuberculous meningitis (TBM) are scarce and have reported contrasting results in comparison to Xpert MTB/RIF assay (Xpert). OBJECTIVE To evaluate the performance of Xpert Ultra in diagnosing TBM and compare it with Xpert and multiplex polymerase chain reaction (MPCR). DESIGN Xpert Ultra was performed on 244 cerebrospinal fluid (CSF) samples: 56 definite TBM, 148 probable TBM and 40 non-TBM controls. 105/244 CSF samples were also subjected to Xpert and MPCR (IS6110, MPB64, protein B). RESULTS The overall sensitivity of Xpert Ultra in diagnosing TBM from 244 CSF samples was 72.05% (96.42% - definite TBM, 62.83% - probable TBM) with a specificity of 100%. 18 (12.24%) cases [8 definite TBM, 10 probable TBM] were reported rifampicin resistant (RifR) by Xpert Ultra and confirmed by rpoB sequencing. 60 (40.81%) cases [9 definite TBM, 51 probable TBM] were reported rifampicin indeterminate (RifI) by Xpert Ultra (all trace category), out of which 45 [8 definite, 37 probable) were rifampicin susceptible (RifS) and 5 probable cases were RifR on rpoB sequencing. Out of 105 CSF samples subjected to all three techniques, TBM was diagnosed in 70.66%, 28% and 88% by Xpert Ultra, Xpert and MPCR, respectively. CONCLUSION Xpert Ultra detected TBM with higher sensitivity than Xpert. Among trace category, constituting 40% of TBM cases, rpoB gene sequencing confirmed 5 RifR cases.
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Tousheed SZ, Ranganatha R, Kumar H, Sagar C, Manjunath PH, Philip D, Punita M, Hibare KR, Reddy M, Muralimohan BV. Yield of pleural biopsy in different types of tubercular effusions. Indian J Tuberc 2020; 67:523-527. [PMID: 33077054 DOI: 10.1016/j.ijtb.2020.07.023] [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: 07/07/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022]
Abstract
INTRODUCTION The yield of mycobacteria is shown to be very low in pleural effusions as it is a pauci-bacillary disease. The present study looked at the yield of mycobacterium tuberculosis (MTB) in terms of GeneXpert for acid fast bacilli (AFB) and culture using a medical thoracoscopy guided biopsy and analysed whether the yield increases in more complicated effusions. MATERIALS AND METHODS This is a retrospective analysis of patients who underwent medical thoracoscopy for tubercular pleural effusions at our institute over the last 5-years. Patients who had no or minimal thin septations were considered as simple effusions and were subjected to semi-rigid thoracoscopy (n = 61). While patients who had multiple loculations and thick septations were considered as complicated effusions and were subjected to rigid thoracoscopy (n = 64). We considered granuloma on a biopsy as the standard for diagnosis of Tuberculosis (TB). Xpert MTB/RIF and The BACTEC MGIT was used for culture. RESULTS Out 125 patients with granulomatous inflammation on biopsy, 56 (44.8%) were positive for either GeneXpert or culture for MTB. Only GeneXpert was positive in 43 and only culture was positive in 13. Amongst 61 patients with simple effusion, 14 had either GeneXpert for AFB or AFB culture being positive and 9 out of these patients had GeneXpert for MTB detected on biopsy sample. Only culture was positive in 5 patients. In complicated pleural effusion group either GeneXpert or culture for mycobacterium was positive in 42 (65.6%) out of 64 patients. Only GeneXpert was positive in 34 and culture alone was positive in 8 patients. CONCLUSION The yield of MTB increases as the pleural effusion becomes more complicated. GeneXpert in a biopsy sample is a useful marker for MTB yield especially in a complicated effusion.
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Affiliation(s)
- Syed Zulkharnain Tousheed
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India.
| | - Ramanjenaya Ranganatha
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - Hemanth Kumar
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - Chandrasekar Sagar
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - P H Manjunath
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - Danne Philip
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - M Punita
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - Kedar R Hibare
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
| | - Mallika Reddy
- Department of Microbiology, Narayana Health City, Bangalore, India
| | - B V Muralimohan
- Department of Pulmonology and Internal Medicine, Mazumdar Shaw Medical Center, Narayana Health City, Bangalore, India
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Tan YZ, Chong YQ, Khong E, Liew YK, Chieng N. Effect of disaccharide-polyol systems on the thermal stability of freeze-dried Mycobacterium bovis. Int J Pharm 2019; 566:400-409. [DOI: 10.1016/j.ijpharm.2019.05.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/04/2019] [Accepted: 05/23/2019] [Indexed: 11/25/2022]
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Lee HB, Inoue S, Kim JH, Jeong M, Chung JH. Electrokinetic Behavior of Heat-Treated Mycobacterium Bacillus Calmette-Guérin Cells. J Med Device 2018. [DOI: 10.1115/1.4040677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Dielectrophoresis (DEP) can be an effective tool to show the physiological change of bacterial cells. The behavior of bacterial cells under an electric field is complicated due to the combined effects of electrokinetic phenomena. This paper presents the study of the electrokinetic behavior of heat-treated Mycobacterium bovis Bacillus Calmette-Guérin (BCG) cells for a cell counting method. Through numerical and experimental study, heat-treated BCG cells are compared with control BCG cells. At various frequencies with the medium conductivity of 0.07 S/m, the equilibrium positions of both control- and heat-treated cells are analyzed in the combined fields of DEP and AC electroosmosis (ACEO). As DEP changes from negative to positive in electroosmotic flow, the equilibrium position of cells is bifurcated from the upper center between two electrodes onto the edges of both electrodes. It was found that the cells floating on electrodes should not be counted as attracted cells because the floating was resulted from the combined effect of the negative DEP and ACEO. According to the analysis, an optimum frequency is proposed to differentiate control cells from heat-treated cells using a cell counting method. The presented study will offer physical insight for the cell counting to differentiate live and dead Mycobacterium bovis BCG cells treated with heat and drugs.
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Affiliation(s)
- Hyun-Boo Lee
- Department of Mechanical Engineering, University of Washington, P.O. Box 352600, Seattle, WA 98195 e-mail:
| | - Shinnosuke Inoue
- Department of Mechanical Engineering, University of Washington, P.O. Box 352600, Seattle, WA 98195 e-mail:
| | - Jong-Hoon Kim
- School of Engineering and Computer Science, Washington State University, Vancouver, WA 98686 e-mail:
| | - Minjoong Jeong
- National Supercomputing Center, Korea Institute of Science and Technology Information, Daejeon 34141, South Korea e-mail:
| | - Jae-Hyun Chung
- Department of Mechanical Engineering, University of Washington, P.O. Box 352600, Seattle, WA 98195 e-mail:
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Evaluation of the Xpert MTB/RIF Ultra Assay for Direct Detection of Mycobacterium tuberculosis Complex in Smear-Negative Extrapulmonary Samples. J Clin Microbiol 2018; 56:JCM.00659-18. [PMID: 29950333 DOI: 10.1128/jcm.00659-18] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
The rapid detection of Mycobacterium tuberculosis complex (MTUBC) in clinical samples is essential for successful treatment. New techniques such as real-time PCR have been developed in order to facilitate rapid diagnosis, but their sensitivity is low in extrapulmonary specimens, due to the low bacillary load in such samples. A next-generation assay has recently been developed to try to overcome this limitation. The aim of this study was to analyze the effectiveness of the Xpert MTB/RIF Ultra (GX-Ultra) for the detection of MTUBC DNA in 108 smear-negative extrapulmonary specimens that were MTUBC culture positive. In addition, 40 extrapulmonary culture-negative samples and 20 samples with nontuberculous mycobacteria were tested to evaluate the specificity of the assay. All samples were collected between May 1999 and May 2017. The GX-Ultra detected DNA of MTUBC in 82 extrapulmonary specimens that were MTUBC culture positive (75.9% sensitivity; 95% confidence interval [CI], 66.6 to 83.4%). The assay was negative for all clinical specimens that were MTUBC culture negative and the samples with nontuberculous mycobacteria (100% specificity). Furthermore, two (1.8%) samples presented mutations related to rifampin resistance. The highest sensitivity was obtained in samples of lymph nodes (94.1%) and nonsterile fluids (93.7%), followed by tissue specimens (86.6%), stool material (80%), abscess aspirates (64.7%), and sterile fluids (60.5%). Pleural fluids, one of the least optimal samples for detecting DNA of MTUBC, were GX-Ultra positive in 10/21 (47.6%) of cases. In summary, GX-Ultra showed excellent specificity and high sensitivity in paubacillary specimens, making it a useful tool for rapid diagnosis of extrapulmonary tuberculosis.
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Norris LJ, Watral V, Kent ML. Survival of Bacterial and Parasitic Pathogens from Zebrafish (Danio rerio) After Cryopreservation and Thawing. Zebrafish 2018; 15:188-201. [PMID: 29369747 PMCID: PMC5878546 DOI: 10.1089/zeb.2017.1528] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Cryopreservation is a common method used to preserve the sperm of various animal species, and it is widely used with zebrafish (Danio rerio). As with other animals, there is a possibility of paternal pathogen transmission through sperm. We evaluated the ability of five common and important pathogens of zebrafish to survive cryopreservation as used with zebrafish sperm and freezing without cryopreservant. We evaluated Mycobacterium chelonae, Mycobacterium marinum, and Edwardsiella ictaluri, each originally isolated from zebrafish, eggs of Pseuodocapillaria tomentosa, and spores of Pseudoloma neurophilia. Each mycobacterial isolate showed relatively minimal reduction in survival after freezing and thawing, particularly when subjected to cryopreservation. E. ictaluri also showed survival after cryopreservation, but exhibited a several log reduction after freezing at -80°C without cryopreservant. With P. neurophilia, two separate experiments conducted 3 years apart yielded very similar results, showing some, but reduced, survival of spores by using three different viability assays: SYTOX stain, Fungi-Fluor stain, and presence of a spore vacuole. Eggs of P. tomentosa showed no survival based on larvation of eggs when subjected to either freezing method. Given that four of the five pathogens exhibited survival after cryopreservation, we recommend that sperm samples or donor male zebrafish fish be tested for pathogens when sperm are to be stored by using cryopreservation.
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Affiliation(s)
- Lauren J Norris
- 1 Department of Microbiology, Oregon State University , Corvallis, Oregon
| | - Virginia Watral
- 1 Department of Microbiology, Oregon State University , Corvallis, Oregon
| | - Michael L Kent
- 1 Department of Microbiology, Oregon State University , Corvallis, Oregon
- 2 Department of Biomedical Science, Oregon State University , Corvallis, Oregon
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A Rapid Method for Quantifying Viable Mycobacterium avium subsp. paratuberculosis in Cellular Infection Assays. Appl Environ Microbiol 2016; 82:5553-62. [PMID: 27371585 DOI: 10.1128/aem.01668-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Determining the viability of bacteria is a key outcome of in vitro cellular infection assays. Currently, this is done by culture, which is problematic for fastidious slow-growing bacteria such as Mycobacterium avium subsp. paratuberculosis, where it can take up to 4 months to confirm growth. This study aimed to identify an assay that can rapidly quantify the number of viable M. avium subsp. paratuberculosis cells in a cellular sample. Three commercially available bacterial viability assays along with a modified liquid culture method coupled with high-throughput quantitative PCR growth detection were assessed. Criteria for assessment included the ability of each assay to differentiate live and dead M. avium subsp. paratuberculosis organisms and their accuracy at low bacterial concentrations. Using the culture-based method, M. avium subsp. paratuberculosis growth was reliably detected and quantified within 2 weeks. There was a strong linear association between the 2-week growth rate and the initial inoculum concentration. The number of viable M. avium subsp. paratuberculosis cells in an unknown sample was quantified based on the growth rate, by using growth standards. In contrast, none of the commercially available viability assays were suitable for use with samples from in vitro cellular infection assays. IMPORTANCE Rapid quantification of the viability of Mycobacterium avium subsp. paratuberculosis in samples from in vitro cellular infection assays is important, as it allows these assays to be carried out on a large scale. In vitro cellular infection assays can function as a preliminary screening tool, for vaccine development or antimicrobial screening, and also to extend findings derived from experimental animal trials. Currently, by using culture, it takes up to 4 months to obtain quantifiable results regarding M. avium subsp. paratuberculosis viability after an in vitro infection assay; however, with the quantitative PCR and liquid culture method developed, reliable results can be obtained at 2 weeks. This method will be important for vaccine and antimicrobial screening work, as it will allow a greater number of candidates to be screened in the same amount of time, which will increase the likelihood that a favorable candidate will be found to be subjected to further testing.
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Murray KN, Varga ZM, Kent ML. Biosecurity and Health Monitoring at the Zebrafish International Resource Center. Zebrafish 2016; 13 Suppl 1:S30-8. [PMID: 27031282 PMCID: PMC4931758 DOI: 10.1089/zeb.2015.1206] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Zebrafish International Resource Center (ZIRC) is a repository and distribution center for mutant, transgenic, and wild-type zebrafish. In recent years annual imports of new zebrafish lines to ZIRC have increased tremendously. In addition, after 15 years of research, we have identified some of the most virulent pathogens affecting zebrafish that should be avoided in large production facilities, such as ZIRC. Therefore, while importing a high volume of new lines we prioritize safeguarding the health of our in-house fish colony. Here, we describe the biosecurity and health-monitoring program implemented at ZIRC. This strategy was designed to prevent introduction of new zebrafish pathogens, minimize pathogens already present in the facility, and ensure a healthy zebrafish colony for in-house uses and shipment to customers.
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Affiliation(s)
- Katrina N. Murray
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon
| | - Zoltán M. Varga
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon
| | - Michael L. Kent
- Zebrafish International Resource Center, University of Oregon, Eugene, Oregon
- Department of Microbiology, Oregon State University, Corvallis, Oregon
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Phenotypically Adapted Mycobacterium tuberculosis Populations from Sputum Are Tolerant to First-Line Drugs. Antimicrob Agents Chemother 2016; 60:2476-83. [PMID: 26883695 PMCID: PMC4808147 DOI: 10.1128/aac.01380-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 02/06/2016] [Indexed: 12/12/2022] Open
Abstract
Tuberculous sputum contains multiple Mycobacterium tuberculosis populations with different requirements for isolation in vitro. These include cells that form colonies on solid media (plateable M. tuberculosis), cells requiring standard liquid medium for growth (nonplateable M. tuberculosis), and cells requiring supplementation of liquid medium with culture supernatant (SN) for growth (SN-dependent M. tuberculosis). Here, we describe protocols for the cryopreservation and direct assessment of antimicrobial tolerance of these M. tuberculosis populations within sputum. Our results show that first-line drugs achieved only modest bactericidal effects on all three populations over 7 days (1 to 2.5 log10 reductions), and SN-dependent M. tuberculosis was more tolerant to streptomycin and isoniazid than the plateable and nonplateable M. tuberculosis strains. Susceptibility of plateable M. tuberculosis to bactericidal drugs was significantly increased after passage in vitro; thus, tolerance observed in the sputum samples from the population groups was likely associated with mycobacterial adaptation to the host environment at some time prior to expectoration. Our findings support the use of a simple ex vivo system for testing drug efficacies against mycobacteria that have phenotypically adapted during tuberculosis infection.
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Inoue S, Lee HB, Becker AL, Weigel KM, Kim JH, Lee KH, Cangelosi GA, Chung JH. Dielectrophoretic characterization of antibiotic-treated Mycobacterium tuberculosis complex cells. Anal Bioanal Chem 2015; 407:7673-80. [DOI: 10.1007/s00216-015-8928-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/13/2015] [Accepted: 07/17/2015] [Indexed: 12/01/2022]
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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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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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