1
|
Madico G, Vinhas S, Orr B, White L, Gaeddert M, Miller NS, Mpeirwe M, Orikiriza P, Mwanga-Amumpaire J, Boum Y, Palaci M, Dietze R, Jones-López EC. Further evidence of Mycobacterium tuberculosis in the sputum of culture-negative pulmonary tuberculosis suspects using an ultrasensitive molecular assay. Tuberculosis (Edinb) 2019; 116:1-7. [PMID: 30983569 DOI: 10.1016/j.tube.2019.03.007] [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: 02/13/2019] [Revised: 03/16/2019] [Accepted: 03/18/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Rapid diagnosis of pulmonary tuberculosis (TB) is critical to TB control. However, many patients with paucibacillary TB disease remain undiagnosed. Current TB elimination goals require new tools to diagnose early disease. We evaluated performance of the Totally Optimized PCR (TOP) TB assay, a novel ultrasensitive molecular test. METHODS We assessed analytical specificity against nontuberculous mycobacteria (NTM), and estimated the diagnostic accuracy of TOP in a pilot study in Brazil (n = 46) and a cross-sectional study in Boston (n = 60). We compared TOP results to culture and a composite reference standard (CRS). RESULTS TOP exhibited no cross-reactivity against NTM. We tested 132 respiratory specimens from 106 patients with suspected pulmonary TB. The pilot demonstrated feasibility and 100% (95% CI 85-100) sensitivity in predominantly smear-positive specimens; TOP's specificity against solid media culture was low (58%, 37-77) but improved against a CRS (93%, 68-100). Similarly, when using the CRS in the Boston study, TOP (88%, 1-99) had greater sensitivity than solid or liquid media culture (25%, 3-65) and similar specificity (both 100%, 93-100). CONCLUSIONS The TOP assay enables detection of M. tuberculosis in culture-negative paucibacillary disease. While the use of TOP for the diagnosis of paucibacillary disease will require further clinical validation, its high sensitivity indicate a more immediate utility as a rule out TB test.
Collapse
Affiliation(s)
- Guillermo Madico
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA.
| | - Solange Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil.
| | - Beverley Orr
- Clinical Microbiology Laboratory, Boston Medical Center, Boston, MA, USA.
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA.
| | - Mary Gaeddert
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA.
| | - Nancy S Miller
- Clinical Microbiology Laboratory, Boston Medical Center, Boston, MA, USA; Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Moses Mpeirwe
- Mbarara University of Science and Technology, Mbarara, Uganda.
| | - Patrick Orikiriza
- Mbarara University of Science and Technology, Mbarara, Uganda; Epicentre, Médecins sans Frontières, Mbarara, Uganda.
| | | | - Yap Boum
- Mbarara University of Science and Technology, Mbarara, Uganda; Epicentre, Médecins sans Frontières, Mbarara, Uganda.
| | - Moises Palaci
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil.
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil.
| | - Edward C Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, MA, USA.
| |
Collapse
|
2
|
Genotype-Specific Concordance of Chlamydia trachomatis Genital Infection Within Heterosexual Partnerships. Sex Transm Dis 2018; 43:741-749. [PMID: 27835626 DOI: 10.1097/olq.0000000000000525] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Sexual transmission rates of Chlamydia trachomatis (Ct) cannot be measured directly; however, the study of concordance of Ct infection in sexual partnerships (dyads) can help to illuminate factors influencing Ct transmission. METHODS Heterosexual men and women with Ct infection and their sex partners were enrolled and partner-specific coital and behavioral data collected for the prior 30 days. Microbiological data included Ct culture, and nucleic acid amplification testing (NAAT), quantitative Ct polymerase chain reaction, and ompA genotyping. We measured Ct concordance in dyads and factors (correlates) associated with concordance. RESULTS One hundred twenty-one women and 125 men formed 128 dyads. Overall, 72.9% of male partners of NAAT-positive women and 68.6% of female partners of NAAT-positive men were Ct-infected. Concordance was more common in dyads with culture-positive members (78.6% of male partners, 77% of female partners). Partners of women and men who were NAAT-positive only had lower concordance (33.3%, 46.4%, respectively). Women in concordant dyads had significantly higher median endocervical quantitative Ct polymerase chain reaction values (3,032) compared with CT-infected women in discordant dyads (1013 inclusion forming units DNA equivalents per mL; P < 0.01). Among 54 Ct-concordant dyads with ompA genotype data for both members, 96.2% had identical genotypes. CONCLUSIONS Higher organism load appears associated with concordance among women. Same-genotype chlamydial concordance was high in sexual partnerships. No behavioral factors were sufficiently discriminating to guide partner services activities. Findings may help model coitus-specific transmission probabilities.
Collapse
|
3
|
Madico G, Mpeirwe M, White L, Vinhas S, Orr B, Orikiriza P, Miller NS, Gaeddert M, Mwanga-Amumpaire J, Palaci M, Kreiswirth B, Straight J, Dietze R, Boum Y, Jones-López EC. Detection and Quantification of Mycobacterium tuberculosis in the Sputum of Culture-Negative HIV-infected Pulmonary Tuberculosis Suspects: A Proof-of-Concept Study. PLoS One 2016; 11:e0158371. [PMID: 27391604 PMCID: PMC4938528 DOI: 10.1371/journal.pone.0158371] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/14/2016] [Indexed: 12/11/2022] Open
Abstract
RATIONALE Rapid diagnosis of pulmonary tuberculosis (TB) is critical for timely initiation of treatment and interruption of transmission. Yet, despite recent advances, many patients remain undiagnosed. Culture, usually considered the most sensitive diagnostic method, is sub-optimal for paucibacillary disease. METHODS We evaluated the Totally Optimized PCR (TOP) TB assay, a new molecular test that we hypothesize is more sensitive than culture. After pre-clinical studies, we estimated TOP's per-patient sensitivity and specificity in a convenience sample of 261 HIV-infected pulmonary TB suspects enrolled into a TB diagnostic study in Mbarara, Uganda against MGIT culture, Xpert MTB/RIF and a composite reference standard. We validated results with a confirmatory PCR used for sequencing M. tuberculosis. MEASUREMENTS AND RESULTS Using culture as reference, TOP had 100% sensitivity but 35% specificity. Against a composite reference standard, the sensitivity of culture (27%) and Xpert MTB/RIF (27%) was lower than TOP (99%), with similar specificity (100%, 98% and 87%, respectively). In unadjusted analyses, culture-negative/TOP-positive patients were more likely to be older (P<0·001), female (P<0·001), have salivary sputum (P = 0·05), sputum smear-negative (P<0.001) and less advanced disease on chest radiograph (P = 0.05). M. tuberculosis genotypes identified in sputum by DNA sequencing exhibit differential growth in culture. CONCLUSIONS These findings suggest that the TOP TB assay is accurately detecting M. tuberculosis DNA in the sputum of culture-negative tuberculosis suspects. Our results require prospective validation with clinical outcomes. If the operating characteristics of the TOP assay are confirmed in future studies, it will be justified as a "TB rule out" test.
Collapse
Affiliation(s)
- Guillermo Madico
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
- Thisis Diagnostics Inc., Boston, Massachusetts, United States of America
| | - Moses Mpeirwe
- Epicentre, Médecins sans Frontières, Mbarara, Uganda
- Mbarara University of Science and Technology, Mbarara, Uganda
| | - Laura White
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Solange Vinhas
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Beverley Orr
- Clinical Microbiology Laboratory, Boston Medical Center, Boston, Massachusetts, United States of America
| | | | - Nancy S. Miller
- Clinical Microbiology Laboratory, Boston Medical Center, Boston, Massachusetts, United States of America
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Mary Gaeddert
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | | | - Moises Palaci
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Barry Kreiswirth
- Public Health Research Institute (PHRI) – Rutgers University, Newark, New Jersey, United States of America
| | - Joe Straight
- Thisis Diagnostics Inc., Boston, Massachusetts, United States of America
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Yap Boum
- Epicentre, Médecins sans Frontières, Mbarara, Uganda
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
- Thisis Diagnostics Inc., Boston, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
4
|
Ma W, Lager KM, Richt JA, Stoffregen WC, Zhou F, Yoon KJ. Development of real-time polymerase chain reaction assays for rapid detection and differentiation of wild-type pseudorabies and gene-deleted vaccine viruses. J Vet Diagn Invest 2008; 20:440-7. [PMID: 18599848 DOI: 10.1177/104063870802000405] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The successful eradication of pseudorabies in U.S. domestic swine was accomplished through the use of glycoprotein E (gE) deleted modified live virus vaccines and an accompanying gE differential enzyme-linked immunosorbent assay (ELISA). Yet, pseudorabies virus (PRV) was established in feral swine in the United States, becoming a potential reservoir of PRV for infection of domestic swine and other native wildlife. A critical need for the current PRV surveillance program in the United States is the rapid detection of PRV infection. For this reason, a set of 2 real-time polymerase chain reaction (PCR) assays by using TaqMan chemistry was developed and evaluated for their capability in the detection and differentiation of field and vaccine strains of PRV. PCR primers and probes were designed for gB and gE genes of PRV, respectively. The newly developed PRV-specific real-time PCR assays could detect all wild-type PRV isolates from diagnostic submissions and differentiate them from vaccine strains. The analytical sensitivity of the assays was approximately 0.1 plaque-forming units per reaction. The assays were highly specific for PRV, because no positive results were obtained from testing other common swine viral pathogens and other animal herpesviruses. The results of testing samples from domestic and feral swine and from bovine showed that the real-time PCR assays are more sensitive than gel-based PCR. These results demonstrated the potential application of the developed real-time PCR assays as a differential test for rapid and specific detection of PRV in domestic and feral swine, as well as nonporcine species that can be infected with PRV and serve as carriers.
Collapse
Affiliation(s)
- Wenjun Ma
- Department of Veterinary Diagonostic and Production Animal Services, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | | | | | | | | | | |
Collapse
|
5
|
Yoon HA, Eo SK, Aleyas AG, Cha SY, Lee JH, Chae JS, Jang HK, Cho EG, Song HJ. Investigation of pseudorabies virus latency in nervous tissues of seropositive pigs exposed to field strain. J Vet Med Sci 2006; 68:143-8. [PMID: 16520536 DOI: 10.1292/jvms.68.143] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The prevalence and quantity of latent pseudorabies virus (PrV) in nervous tissues of pigs exposed to field strain in Korea was investigated by nested and real-time PCR. Nervous tissues including trigeminal ganglion (TG), olfactory bulb (OB), and brain stem (BS) were collected from 94 seropositive pigs. PrV latent infection in nervous tissues was initially investigated by nested PCR targeting three glycoprotein genes (gB, gE, and gG). Based on the obtained result, latent infection was detected in 95.7% of screened animals. Furthermore, it was revealed that the examined tissues harbored different copy numbers of latent PrV genome ranging from <10(2.0) to 10(7.1) copies per microgram of genomic DNA in real-time PCR analysis. These results show that under normal conditions, levels of latent PrV in the nervous tissues of pigs can vary across a wide range. Therefore, the data presented here provides information regarding control of the endemic state of PrV in Korea.
Collapse
Affiliation(s)
- Hyun-A Yoon
- Laboratory of Microbiology, College of Veterinary Medicine and Bio-Safety Research Institute, Chonbuk National University, Jeonju 561-756, Republic of Korea
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Lee CY, Panicker G, Bej AK. Detection of pathogenic bacteria in shellfish using multiplex PCR followed by CovaLink NH microwell plate sandwich hybridization. J Microbiol Methods 2003; 53:199-209. [PMID: 12654491 DOI: 10.1016/s0167-7012(03)00032-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Outbreak of diseases associated with consumption of raw shellfish especially oysters is a major concern to the seafood industry and public health agencies. A multiplex PCR amplification of targeted gene segments followed by DNA-DNA sandwich hybridization was optimized to detect the etiologic agents. First, a multiplex PCR amplification of hns, spvB, vvh, ctx and tl was developed enabling simultaneous detection of total Salmonella enterica serotype Typhimurium, Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus from both pure cultures and seeded oysters. Amplicons were then subjected to a colorimetric CovaLink NH microwell plate sandwich hybridization using phosphorylated and biotinlylated oligonucleotide probes, the nucleotide sequences of which were located internal to the amplified DNA. The results from the hybridization with the multiplexed PCR amplified DNA exhibited a high signal/noise ratio ranging between 14.1 and 43.2 measured at 405 nm wavelength. The sensitivity of detection for each pathogen was 10(2) cells/g of oyster tissue homogenate. The results from this study showed that the combination of the multiplex PCR with a colorimetric microwell plate sandwich hybridization assay permits a specific, sensitive, and reproducible system for the detection of the microbial pathogens in shellfish, thereby improving the microbiological safety of shellfish to consumers.
Collapse
Affiliation(s)
- Chi-Ying Lee
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA
| | | | | |
Collapse
|
7
|
Sidhu H, Holmes RP, Allison MJ, Peck AB. Direct quantification of the enteric bacterium Oxalobacter formigenes in human fecal samples by quantitative competitive-template PCR. J Clin Microbiol 1999; 37:1503-9. [PMID: 10203513 PMCID: PMC84815 DOI: 10.1128/jcm.37.5.1503-1509.1999] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Homeostasis of oxalic acid appears to be regulated, in part, by the gut-associated bacterium Oxalobacter formigenes. The loss of this bacterium from the gut flora is associated with an increased susceptibility to hyperoxaluria, a condition which can lead to the formation of calcium oxalate crystalluria and kidney stones. In order to identify and quantify the presence of O. formigenes in clinical specimens, a quantitative-PCR-based assay system utilizing a competitive DNA template as an internal standard was developed. This quantitative competitive-template PCR test allows for the rapid, highly specific, and reproducible quantification of O. formigenes in fecal samples and provides a prototype for development of DNA-based quantitative assays for enteric bacteria.
Collapse
Affiliation(s)
- H Sidhu
- Ixion Biotechnology, Inc., Alachua, Florida.
| | | | | | | |
Collapse
|
8
|
Arnauld C, Legeay O, Laurian Y, Thiery R, Denis M, Blanchard P, Jestin A. Development of a PCR-based method coupled with a microplate colorimetric assay for the detection of Porcine Parvovirus and application to diagnosis in piglet tissues and human plasma. Mol Cell Probes 1998; 12:407-16. [PMID: 9843658 DOI: 10.1006/mcpr.1998.0205] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new method for Porcine Parvovirus (PPV) diagnosis was developed. The method is based on polymerase chain reaction (PCR) amplification followed by hybridization and colorimetric detection of PCR products in microwell plates. A highly specific and sensitive amplification step was ensured by primers carefully selected in the VP2 structural gene and optimized PCR conditions. Uracyl-DNA-Glycosylase (UDG) in combination with dUTP was used to avoid false-positive results, and 100 copies of internal control (IC) were added to each PCR reaction to reveal any false-negative samples. Biotinylated amplified fragments were hybridized on specific capture probes covalently linked to microwell plates. Finally, the detection of hybridized PCR products was performed by means of a colorimetric reaction, which was automated. The method permitted the detection of 10(3) copies (6 fg) of replicative form DNA (RF-DNA) in 20 mg of lung sample, and 500 copies (3 fg) in 100 microl of plasma. It was used to analyse 24 field piglet tissue samples, and 35 human plasma or serum specimens collected from patients treated with porcine Factor VIII concentrates.
Collapse
Affiliation(s)
- C Arnauld
- Centre National d'Etudes Vétérinaires et Alimentaires (CNEVA), Unité de Biologie Moléculaire, BP 53, Ploufragan, 22 440, France
| | | | | | | | | | | | | |
Collapse
|