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PALOMINO-KOBAYASHI LA, PONS MJ, RUIZ J. Estimation of inherent bacterial DNA contamination in a qPCR master mix: concerns about background DNA of reagents. MINERVA BIOTECHNOLOGY AND BIOMOLECULAR RESEARCH 2022. [DOI: 10.23736/s2724-542x.22.02925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sebastian S, Malhotra R, Sreenivas V, Kapil A, Chaudhry R, Dhawan B. Utility of 16S rRNA PCR in the Synovial Fluid for the Diagnosis of Prosthetic Joint Infection. Ann Lab Med 2019; 38:610-612. [PMID: 30027708 PMCID: PMC6056385 DOI: 10.3343/alm.2018.38.6.610] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/10/2018] [Accepted: 06/14/2018] [Indexed: 12/03/2022] Open
Affiliation(s)
- Sujeesh Sebastian
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Malhotra
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | | | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
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Sebastian S, Malhotra R, Sreenivas V, Kapil A, Chaudhry R, Dhawan B. A Clinico-Microbiological Study of Prosthetic Joint Infections in an Indian Tertiary Care Hospital: Role of Universal 16S rRNA Gene Polymerase Chain Reaction and Sequencing in Diagnosis. Indian J Orthop 2019; 53:646-654. [PMID: 31488935 PMCID: PMC6699216 DOI: 10.4103/ortho.ijortho_551_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND We determined the magnitude and clinico-microbiological profile of prosthetic joint infection (PJI) at a tertiary hospital. The diagnostic potential of 16S rRNA gene polymerase chain reaction (PCR) and sequencing on periprosthetic tissue samples was evaluated for the diagnosis of PJI. MATERIALS AND METHODS This ambispective cohort study consisted of patients who underwent primary or revision hip or knee arthroplasty from June 2013 to June 2017. The patients were classified as either infected or noninfected according to criteria set out by the musculoskeletal infection society (MSIS). Three to five periprosthetic tissue samples were collected from each patient for culture and 16S rRNA gene PCR sequencing. RESULTS Hundred and six patients were diagnosed to have PJI as per the MSIS Criteria. The cumulative incidence of PJI at our Institute at the end of 36 months was 1.1% (95% confidence interval [CI]: 0.59-2.91). Microorganisms were isolated by periprosthetic tissue culture (PTC) in 84 patients (sensitivity: 79% and specificity: 100%). Gram-negative aerobes were most frequently isolated (61%). Polymicrobial infections were present in 8.3% of cases. The most common infecting microorganism was Staphylococcus aureus (19.5%). Multidrug resistance and methicillin resistance were noted in 54% and 34% of bacterial isolates, respectively. The sensitivity and specificity of 16S rRNA PCR of periprosthetic tissue was 86% (95% CI: 74.9-89.9) and 100% (95% CI: 94.7-100), respectively. Periprosthetic tissue 16S rRNA PCR was more sensitive than PTC (P = 0.008), although both were 100% specific (P = 0.99). CONCLUSIONS The incidence of PJI at our Institute compares well with other published reports. Contrary to previous reports, a predominance of Gram-negative PJI's was found. The preponderance of multidrug-resistant organisms in PJI's is worrisome. The high sensitivity and specificity of the 16S PCR assay used in our study support its use in culture-negative PJI suspected cases.
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Affiliation(s)
- Sujeesh Sebastian
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rajesh Malhotra
- Department of Orthopaedics, All India Institute of Medical Sciences, New Delhi, India
| | | | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India,Address for correspondence: Dr. Benu Dhawan, Department of Microbiology, All India Institute of Medical Sciences, New Delhi - 110 029, India. E-mail:
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Bruno DDCF, Bartelli TF, Rodrigues CR, Briones MR. Prolonged growth of Candida albicans reveals co-isolated bacteria from single yeast colonies. INFECTION GENETICS AND EVOLUTION 2018; 65:117-126. [DOI: 10.1016/j.meegid.2018.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/09/2018] [Accepted: 07/18/2018] [Indexed: 01/14/2023]
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Nelson EA, Wright-Hughes A, Brown S, Lipsky BA, Backhouse M, Bhogal M, Ndosi M, Reynolds C, Sykes G, Dowson C, Edmonds M, Vowden P, Jude EB, Dickie T, Nixon J. Concordance in diabetic foot ulceration: a cross-sectional study of agreement between wound swabbing and tissue sampling in infected ulcers. Health Technol Assess 2018; 20:1-176. [PMID: 27827300 DOI: 10.3310/hta20820] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND There is inadequate evidence to advise clinicians on the relative merits of swabbing versus tissue sampling of infected diabetic foot ulcers (DFUs). OBJECTIVES To determine (1) concordance between culture results from wound swabs and tissue samples from the same ulcer; (2) whether or not differences in bacterial profiles from swabs and tissue samples are clinically relevant; (3) concordance between results from conventional culture versus polymerase chain reaction (PCR); and (4) prognosis for patients with an infected DFU at 12 months' follow-up. METHODS This was a cross-sectional, multicentre study involving patients with diabetes and a foot ulcer that was deemed to be infected by their clinician. Microbiology specimens for culture were taken contemporaneously by swab and by tissue sampling from the same wound. In a substudy, specimens were also processed by PCR. A virtual 'blinded' clinical review compared the appropriateness of patients' initial antibiotic regimens based on the results of swab and tissue specimens. Patients' case notes were reviewed at 12 months to assess prognosis. RESULTS The main study recruited 400 patients, with 247 patients in the clinical review. There were 12 patients in the PCR study and 299 patients in the prognosis study. Patients' median age was 63 years (range 26-99 years), their diabetes duration was 15 years (range 2 weeks-57 years), and their index ulcer duration was 1.8 months (range 3 days-12 years). Half of the ulcers were neuropathic and the remainder were ischaemic/neuroischaemic. Tissue results reported more than one pathogen in significantly more specimens than swabs {86.1% vs. 70.1% of patients, 15.9% difference [95% confidence interval (CI) 11.8% to 20.1%], McNemar's p-value < 0.0001}. The two sampling techniques reported a difference in the identity of pathogens for 58% of patients. The number of pathogens differed in 50.4% of patients. In the clinical review study, clinicians agreed on the need for a change in therapy for 73.3% of patients (considering swab and tissue results separately), but significantly more tissue than swab samples required a change in therapy. Compared with traditional culture, the PCR technique reported additional pathogens for both swab and tissue samples in six (50%) patients and reported the same pathogens in four (33.3%) patients and different pathogens in two (16.7%) patients. The estimated healing rate was 44.5% (95% CI 38.9% to 50.1%). At 12 months post sampling, 45 (15.1%) patients had died, 52 (17.4%) patients had a lower-extremity ipsilateral amputation and 18 (6.0%) patients had revascularisation surgery. LIMITATIONS We did not investigate the potential impact of microbiological information on care. We cannot determine if the improved information yield from tissue sampling is attributable to sample collection, sample handling, processing or reporting. CONCLUSIONS Tissue sampling reported both more pathogens and more organisms overall than swabbing. Both techniques missed some organisms, with tissue sampling missing fewer than swabbing. Results from tissue sampling more frequently led to a (virtual) recommended change in therapy. Long-term prognosis for patients with an infected foot ulcer was poor. FUTURE WORK Research is needed to determine the effect of sampling/processing techniques on clinical outcomes and antibiotic stewardship. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
| | | | - Sarah Brown
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | | | - Michael Backhouse
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | - Moninder Bhogal
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Mwidimi Ndosi
- School of Healthcare, University of Leeds, Leeds, UK
| | - Catherine Reynolds
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
| | - Gill Sykes
- Podiatry Department, Huddersfield Royal Hospital, Huddersfield, UK
| | | | - Michael Edmonds
- Diabetic Foot Clinic, King's Diabetes Centre, King's College Hospital, London, UK
| | - Peter Vowden
- Department of Vascular Surgery, Bradford Royal Infirmary, Bradford, UK
| | - Edward B Jude
- Department of Diabetes and Endocrinology, Tameside Hospital NHS Foundation Trust, Ashton-under-Lyne, UK
| | - Tom Dickie
- Foot Health Department, St James's University Hospital, Leeds, UK
| | - Jane Nixon
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, UK
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Boujelben I, Gdoura R, Hammami A. A broad-range PCR technique for the diagnosis of infective endocarditis. Braz J Microbiol 2018; 49:534-543. [PMID: 29429763 PMCID: PMC6111453 DOI: 10.1016/j.bjm.2017.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 02/18/2017] [Accepted: 03/23/2017] [Indexed: 11/21/2022] Open
Abstract
Infective endocarditis (IE) remains a severe and potentially fatal disease demanding sophisticated diagnostic strategies for detection of the causative microorganisms. The aim of the present study was to develop a broad-range 16S ribosomal RNA gene polymerase chain reaction in the routine diagnostic of IE for the early diagnosis of fatal disease. A broad-range PCR technique was selected and evaluated in terms of its efficiency in the diagnosis of endocarditis using 19 heart valves from patients undergoing cardiovascular surgeries at the Habib Bourguiba Hospital of Sfax, Tunisia, on the grounds of suspected IE. The results demonstrated the efficiency of this technique particularly in cases involving a limited number of bacteria since it helped to increase detection sensitivity. The technique proved to be efficient, particularly, in the bacteriological diagnosis of IE in contexts involving negative results from conventional culture methods and other contexts involving bacterial species that were not amenable to identification by phenotypic investigations. Indeed, the sequencing of the partial 16S ribosomal RNA gene revealed the presence of Bartonella henselae, Enterobacter sp., and Streptococcus pyogenes in three heart valves with the negative culture. It should be noted that the results obtained from the polymerase chain reaction-sequencing identification applied to the heart valve and the strain isolated from the same tissue were not consistent with the ones found by the conventional microbiological methods in the case of IE caused by Gemella morbillorum. In fact, the results from the molecular identification revealed the presence of Lactobacillus jensenii. Overall, the results have revealed that the proposed method is sensitive, reliable and might open promising opportunities for the early diagnosis of IE.
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Affiliation(s)
- Ines Boujelben
- Hospital Sfax, Department of Microbiology and Research Laboratory "Microorganismes et Pathologie Humaine" Habib Bourguiba, Sfax, Tunisia
| | - Radhouane Gdoura
- Université de Sfax, Faculté des Sciences de Sfax, Laboratoire de recherche Toxicologie Microbiologie Environnementale et Santé LR11ES06, Sfax, Tunisia.
| | - Adnane Hammami
- Hospital Sfax, Department of Microbiology and Research Laboratory "Microorganismes et Pathologie Humaine" Habib Bourguiba, Sfax, Tunisia
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Dubourg G, Raoult D. Emerging methodologies for pathogen identification in positive blood culture testing. Expert Rev Mol Diagn 2015; 16:97-111. [PMID: 26559655 DOI: 10.1586/14737159.2016.1112274] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Bloodstream infections (BSIs) represent a major cause of death in developed countries and are associated with long-term loss of functions. Blood culture remains the gold standard for BSI diagnosis, as it is easy to perform and displays a good analytical sensitivity. However, its major drawback remains the long turnaround time, which can result in inappropriate therapy, fall of survival rate, emergence of antibiotic resistance and increase of medical costs. Over the last 10 years, molecular tools have been the alternative to blood cultures, allowing early identification of pathogens involved in sepsis, as well detection of critical antibiotic resistance genes. Besides, the advent of MALDI-TOF revolutionized practice in routine microbiology significantly reduced the time to result. Reviewed here are recent improvements in early BSI diagnosis and these authors' view for the future is presented, including innovative high-throughput technologies.
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Affiliation(s)
- Grégory Dubourg
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
| | - Didier Raoult
- a Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique - Hôpitaux de Marseille , Marseille , France.,b Université Aix-Marseille, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM 63 CNRS 7278 IRD 198 INSERM U1095, Facultés de Médecine et de Pharmacie , Marseille , France
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Humphrey B, McLeod N, Turner C, Sutton JM, Dark PM, Warhurst G. Removal of Contaminant DNA by Combined UV-EMA Treatment Allows Low Copy Number Detection of Clinically Relevant Bacteria Using Pan-Bacterial Real-Time PCR. PLoS One 2015; 10:e0132954. [PMID: 26172943 PMCID: PMC4501569 DOI: 10.1371/journal.pone.0132954] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 06/21/2015] [Indexed: 01/12/2023] Open
Abstract
Background More than two decades after its discovery, contaminant microbial DNA in PCR reagents continues to impact the sensitivity and integrity of broad-range PCR diagnostic techniques. This is particularly relevant to their use in the setting of human sepsis, where a successful diagnostic on blood samples needs to combine universal bacterial detection with sensitivity to 1-2 genome copies, because low levels of a broad range of bacteria are implicated. Results We investigated the efficacy of ethidium monoazide (EMA) and propidium monoazide (PMA) treatment as emerging methods for the decontamination of PCR reagents. Both treatments were able to inactivate contaminating microbial DNA but only at concentrations that considerably affected assay sensitivity. Increasing amplicon length improved EMA/PMA decontamination efficiency but at the cost of assay sensitivity. The same was true for UV exposure as an alternative decontamination strategy, likely due to damage sustained by oligonucleotide primers which were a significant source of contamination. However, a simple combination strategy with UV-treated PCR reagents paired with EMA-treated primers produced an assay capable of two genome copy detection and a <5% contamination rate. This decontamination strategy could have important utility in developing improved pan-bacterial assays for rapid diagnosis of low pathogen burden conditions such as in the blood of patients with suspected blood stream infection.
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Affiliation(s)
- Bruce Humphrey
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
- * E-mail:
| | - Neil McLeod
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Carrie Turner
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - J. Mark Sutton
- Public Health England, Microbiology Services Division, Porton Down, Salisbury, United Kingdom
| | - Paul M. Dark
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
| | - Geoffrey Warhurst
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom
- Infection, Injury & inflammation Research Group, Salford Royal NHS Foundation Trust, Salford, United Kingdom
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Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12:87. [PMID: 25387460 PMCID: PMC4228153 DOI: 10.1186/s12915-014-0087-z] [Citation(s) in RCA: 2034] [Impact Index Per Article: 203.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/13/2014] [Indexed: 12/11/2022] Open
Abstract
Background The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. Results In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other laboratory reagents, varies greatly in composition between different kits and kit batches, and that this contamination critically impacts results obtained from samples containing a low microbial biomass. Contamination impacts both PCR-based 16S rRNA gene surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Conclusions These results suggest that caution should be advised when applying sequence-based techniques to the study of microbiota present in low biomass environments. Concurrent sequencing of negative control samples is strongly advised. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0087-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susannah J Salter
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Hinxton, UK.
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Expression of CD64 on neutrophils can be used to predict the severity of bloodstream infection before broad range 16S rRNA PCR. Folia Microbiol (Praha) 2014; 60:111-8. [PMID: 25253263 DOI: 10.1007/s12223-014-0346-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 09/05/2014] [Indexed: 10/24/2022]
Abstract
The aging population and increased incidence of severe bacterial infection can lead to sepsis. Interest to early identification of endangered patients and identification of pathogen do not always confirm the infection. To use biomarkers can help in early identification of infection and opportunity to start therapy timeously. All biomarkers were defined in 33 out of 96 patients. Thirty-two (97 %) patients had bacterial infection and 1 (3 %) patient had systemic inflammatory response syndrome (SIRS) without infection. PCR confirmed the infection in 27 cases and blood cultures in 8. Area under curve (AUC) for CD64 was 1.00, meanwhile other biomarkers showed 2-fold smaller AUC for positive infection. CD64 index was associated with bacterial infection (p<0.001) and could be used to confirm assessment of SIRS severity (p=0.037). As regards to our results, limited to only 33 patients, CD64 index served as a good parameter to predict bacterial infection and determine severity. The use of broad range 16S ribosomal RNA (rRNA) PCR proved to be an excellent tool to confirm bloodstream infection. The CD64 index had the highest AUC, which exceeded all the others, and could be used to predict the outcome of broad range 16S rRNA PCR from whole blood. However, C-reactive protein (CRP), procalcitonin (PCT) and sCD14 are much easier and faster to measure, but the values could be elevated in other clinical assessments.
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Hsu CC, Tokarz R, Briese T, Tsai HC, Quan PL, Lipkin WI. Use of staged molecular analysis to determine causes of unexplained central nervous system infections. Emerg Infect Dis 2014; 19:1470-7. [PMID: 23965845 PMCID: PMC3810931 DOI: 10.3201/eid1909.130474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
No agent is implicated in most central nervous system (CNS) infections. To investigate cerebrospinal fluid samples from patients with CNS infections of unknown cause in 1 hospital in Taiwan, we used a staged molecular approach, incorporating techniques including multiplex MassTag PCR, 16S rRNA PCR, DNA microarray, and high-throughput pyrosequencing. We determined the infectious agent for 31 (24%) of 131 previously negative samples. Candidate pathogens were identified for 25 (27%) of 94 unexplained meningitis cases and 6 (16%) of 37 unexplained encephalitis cases. Epstein-Barr virus (18 infections) accounted for most of the identified agents in unexplained meningitis cases, followed by Escherichia coli (5), enterovirus (2), human herpesvirus 2 (1), and Mycobacterium tuberculosis. Herpesviruses were identified in samples from patients with unexplained encephalitis cases, including varicella-zoster virus (3 infections), human herpesvirus 1 (2), and cytomegalovirus (1). Our study confirms the power of multiplex MassTag PCR as a rapid diagnostic tool for identifying pathogens causing unexplained CNS infections.
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Soleimani E, Honarmand H, Nikokar I, Falakian Z. Comparing the Accuracy Rate of Two Different Universal Primers in Enteric Pathogen Diagnosis in Blood. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2014. [DOI: 10.17795/ijep15595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Skvarc M, Stubljar D, Rogina P, Kaasch AJ. Non-culture-based methods to diagnose bloodstream infection: Does it work? Eur J Microbiol Immunol (Bp) 2013; 3:97-104. [PMID: 24265925 DOI: 10.1556/eujmi.3.2013.2.2] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 04/18/2013] [Indexed: 12/11/2022] Open
Abstract
Bloodstream infections are a major cause of morbidity and mortality worldwide. Molecular methods for the detection of pathogens in blood have been developed. The clinical utility of these methods and their integration into the clinical workflow is discussed.
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Arabestani MR, Fazzeli H, Bahram NE, Alikhani MY. Development and Assessment of a Single Tube Internally Controlled Multiplex PCR Assay to Detect Different Pathogenic Bacteria Involved in Blood Stream Infections. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2013. [DOI: 10.17795/ijep10601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Garson JA, Patel P, McDonald C, Ball J, Rosenberg G, Tettmar KI, Brailsford SR, Pitt T, Tedder RS. Evaluation of an ethidium monoazide-enhanced 16S rDNA real-time polymerase chain reaction assay for bacterial screening of platelet concentrates and comparison with automated culture. Transfusion 2013; 54:870-8. [PMID: 23701338 PMCID: PMC4282358 DOI: 10.1111/trf.12256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 12/01/2022]
Abstract
BACKGROUND Culture-based systems are currently the preferred means for bacterial screening of platelet (PLT) concentrates. Alternative bacterial detection techniques based on nucleic acid amplification have also been developed but these have yet to be fully evaluated. In this study we evaluate a novel 16S rDNA polymerase chain reaction (PCR) assay and compare its performance with automated culture. STUDY DESIGN AND METHODS A total of 2050 time-expired, 176 fresh, and 400 initial-reactive PLT packs were tested by real-time PCR using broadly reactive 16S primers and a "universal" probe (TaqMan, Invitrogen). PLTs were also tested using a microbial detection system (BacT/ALERT, bioMérieux) under aerobic and anaerobic conditions. RESULTS Seven of 2050 (0.34%) time-expired PLTs were found repeat reactive by PCR on the initial nucleic acid extract but none of these was confirmed positive on testing frozen second aliquots. BacT/ALERT testing also failed to confirm any time-expired PLTs positive on repeat testing, although 0.24% were reactive on the first test. Three of the 400 "initial-reactive" PLT packs were found by both PCR and BacT/ALERT to be contaminated (Escherichia coli, Listeria monocytogenes, and Streptococcus vestibularis identified) and 14 additional packs were confirmed positive by BacT/ALERT only. In 13 of these cases the contaminating organisms were identified as anaerobic skin or oral commensals and the remaining pack was contaminated with Streptococcus pneumoniae. CONCLUSION These results demonstrate that the 16S PCR assay is less sensitive than BacT/ALERT and inappropriate for early testing of concentrates. However, rapid PCR assays such as this may be suitable for a strategy of late or prerelease testing.
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Affiliation(s)
- Jeremy A Garson
- National Transfusion Microbiology Laboratories, NHSBT/HPA Epidemiology Unit, NHS Blood and Transplant, Colindale, London; Research Department of Infection, Division of Infection and Immunity, University College London, London; Blood Borne Virus Unit, Viral Reference Department, Centre for Infections, Health Protection Agency, Colindale, London, UK
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Burke DG, Dong L, Bhat S, Forbes-Smith M, Fu S, Pinheiro L, Jing W, Emslie KR. Digital Polymerase Chain Reaction Measured pUC19 Marker as Calibrant for HPLC Measurement of DNA Quantity. Anal Chem 2013; 85:1657-64. [DOI: 10.1021/ac302925f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Lianhua Dong
- National Institute of Metrology, Beijing, China, 100013
| | - Somanath Bhat
- National Measurement Institute, Lindfield, Australia 2070
| | | | - Shuang Fu
- National Measurement Institute, Lindfield, Australia 2070
| | | | - Wang Jing
- National Institute of Metrology, Beijing, China, 100013
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Ohlin A, Bäckman A, Ewald U, Schollin J, Björkqvist M. Diagnosis of neonatal sepsis by broad-range 16S real-time polymerase chain reaction. Neonatology 2012; 101:241-6. [PMID: 22205207 DOI: 10.1159/000334655] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 10/22/2011] [Indexed: 11/19/2022]
Abstract
BACKGROUND The standard diagnostic test (blood culture) for suspected neonatal sepsis has limitations in sensitivity and specificity, and 16S polymerase chain reaction (PCR) has been suggested as a new diagnostic tool for neonatal sepsis. OBJECTIVES To develop and evaluate a new real-time PCR method for detection of bacterial DNA in blood samples collected from infants with suspected neonatal sepsis. METHODS Immediately after blood culture, a study sample of 0.5-1.0 ml whole blood was collected and used for a novel 16S real-time PCR assay. All positive samples were sequenced. Detailed case studies were performed in all cases with conflicting results, to verify if PCR could detect pathogens in culture negative sepsis. RESULTS 368 samples from 317 infants were included. When compared with blood culture, the assay yielded a sensitivity of 79%, a specificity of 90%, a positive predictive value of 59%, and a negative predictive value of 96%. Seven of the 31 samples with a positive PCR result and a negative blood culture had definite or suspected bacterial sepsis. In five samples, PCR (but not blood culture) could detect a pathogen that was present in a blood culture collected more than 24 h prior to the PCR sample. CONCLUSIONS This study presents an evaluation of a new real-time PCR technique that can detect culture-positive sepsis, and suggests that PCR has the potential to detect bacteria in culture-negative samples even after the initiation of intravenous antibiotics.
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Affiliation(s)
- Andreas Ohlin
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden.
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18
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Patel P, Garson JA, Tettmar KI, Ancliff S, McDonald C, Pitt T, Coelho J, Tedder RS. Development of an ethidium monoazide-enhanced internally controlled universal 16S rDNA real-time polymerase chain reaction assay for detection of bacterial contamination in platelet concentrates. Transfusion 2011; 52:1423-32. [PMID: 22188457 DOI: 10.1111/j.1537-2995.2011.03484.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Bacterial contamination of platelet (PLT) concentrates remains a problem for blood transfusion services. Culture-based bacterial screening techniques are available but offer inadequate speed and sensitivity. Alternative techniques based on polymerase chain reaction (PCR) amplification have been described but their performance is often compromised by traces of bacterial DNA in reagents. STUDY DESIGN AND METHODS Universal 16S rDNA primers were used to develop a real-time PCR assay (TaqMan, Applied Biosystems) and various reagent decontamination strategies were explored. Detection sensitivity was assessed by spiking PLT concentrates with known concentrations of 13 different organisms. RESULTS Restriction enzyme digestion, master mix ultrafiltration, and use of alternative Taq polymerases all reduced the level of reagent DNA contamination to some extent but all proved unreliable. In contrast, ethidium monoazide (EMA) treatment of the PCR master mix followed by photoactivation was reliable and effective, permitting a full 40 amplification cycles, and totally eliminated contamination without compromising assay sensitivity. All 13 organisms were efficiently detected and the limit of detection for Escherichia coli-spiked PLTs was approximately 1 colony-forming unit/mL. Coamplification of human mitochondrial DNA served to confirm efficient nucleic acid extraction and the absence of PCR inhibition in each sample. One of five automated extraction platforms evaluated was found to be contamination free and capable of high-throughput processing. CONCLUSION Cross-linking of EMA to DNA via photoactivation solved the previously intractable problem of reagent contamination and permitted the development of a high-sensitivity universal bacterial detection system. Trials are ongoing to assess the suitability of the system for high-throughput screening of PLT concentrates.
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Affiliation(s)
- Poorvi Patel
- National Transfusion Microbiology Laboratories, NHS Blood and Transplant, Colindale, London, UK
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19
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Esparcia O, Montemayor M, Ginovart G, Pomar V, Soriano G, Pericas R, Gurgui M, Sulleiro E, Prats G, Navarro F, Coll P. Diagnostic accuracy of a 16S ribosomal DNA gene-based molecular technique (RT-PCR, microarray, and sequencing) for bacterial meningitis, early-onset neonatal sepsis, and spontaneous bacterial peritonitis. Diagn Microbiol Infect Dis 2011; 69:153-60. [PMID: 21251558 DOI: 10.1016/j.diagmicrobio.2010.10.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 10/25/2010] [Accepted: 10/26/2010] [Indexed: 12/27/2022]
Abstract
The diagnostic accuracy of a 16S ribosomal DNA (rDNA) gene-based molecular technique for bacterial meningitis (BM), early-onset neonatal sepsis (EONS), and spontaneous bacterial peritonitis (SBP) is evaluated. The molecular approach gave better results for BM diagnosis: sensitivity (S) was 90.6% compared to 78.1% for the bacterial culture. Percentages of cases correctly diagnosed (CCD) were 91.7% and 80.6%, respectively. For EONS diagnosis, S was 60.0% for the molecular approach and 70.0% for the bacterial culture; and CCD was 95.2% and 96.4%, respectively. For SPB diagnosis, the molecular approach gave notably poorer results than the bacterial cultures. S and CCD were 48.4% and 56.4% for the molecular approach and 80.6% and 89.1% for bacterial cultures. Nevertheless, bacterial DNA was detected in 53.3% of culture-negative samples. Accuracy of the 16S rDNA PCR approach differs depending on the sample, the microorganisms involved, the expected bacterial load, and the presence of bacterial DNA other than that from the pathogen implied in the infectious disease.
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Affiliation(s)
- Oscar Esparcia
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
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20
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21
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Lund M, Bjerrum L, Pedersen K. Quantification of Faecalibacterium prausnitzii- and Subdoligranulum variabile-like bacteria in the cecum of chickens by real-time PCR. Poult Sci 2010; 89:1217-24. [PMID: 20460669 DOI: 10.3382/ps.2010-00653] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intestinal microbial community is playing an important role in health and production performance of chickens. To understand the effect on the intestinal microflora induced by various feeding strategies, feed additives, infections, and intestinal disorders, it is important to have methods for quantifying potentially important bacteria in the intestine. We describe a real-time quantitative assay for detection and quantification of a whole group of Faecalibacterium prausnitzii and Subdoligranulum variabile-like bacteria, which has recently been found to dominate in the cecum of broiler chickens. The F. prausnitzii-S. variabile-like bacteria were quantified using a multiprobe assay in which one primer set was used to amplify DNA from all bacteria, whereas 2 probes detected all bacteria and the group of F. prausnitzii-S. variabile-like bacteria, respectively. The multiprobe assay accurately quantified the percentage of this group in a sample if it constituted more than approximately 5% of the total bacterial community. If the fraction of F. prausnitzii-S. variabile-like bacteria was lower than 5%, a duplex assay was applied in which the total bacteria were amplified in one tube and the F. prausnitzii-S. variabile-like group of bacteria was amplified in another tube using a specific forward primer. The F. prausnitzii-S. variabile-like group of bacteria was quantified in the cecum and ileum of conventional and organic raised chickens, in chickens kept in an isolator from 1 d of age, and in hatcher material. Quantification of this group of F. prausnitzii-S. variabile-like bacteria has not been performed before by real-time PCR, but results confirm previous results obtained by cloning and sequencing showing that the F. prausnitzii-S. variabile-like group of bacteria constitutes a major fraction of the cecal bacterial community in chickens. Furthermore, results indicate that the poultry farm environment plays a role in recruitment and development of these bacteria in the intestinal microflora.
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Affiliation(s)
- M Lund
- National Veterinary Institute, Technical University of Denmark, Hangøvej 2, DK-8200 Aarhus N, Denmark.
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22
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Cherkaoui A, Emonet S, Ceroni D, Candolfi B, Hibbs J, Francois P, Schrenzel J. Development and validation of a modified broad-range 16S rDNA PCR for diagnostic purposes in clinical microbiology. J Microbiol Methods 2009; 79:227-31. [PMID: 19782706 DOI: 10.1016/j.mimet.2009.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 09/15/2009] [Accepted: 09/17/2009] [Indexed: 10/20/2022]
Abstract
Broad-range PCR followed by sequencing identifies bacterial pathogens, even in challenging settings such as patients receiving antibiotics or infected with fastidious or non-cultivable organisms. The major problem with broad-range PCR is the risk of sample contamination. Risk is present at every step of the procedure, starting from sample collection. Contaminating bacterial DNA may be present not only in laboratory reagents but also at the surface of plastic consumables and containers used for specimen drawing and transport to the diagnostic laboratory. Contaminating DNA is amplified efficiently, leading to false-positive results. Thus, high specificity depends on eliminating such spurious targets, an awkward problem given the abundance of such targets and a highly sensitive method that detects very small numbers of molecules. Several investigators have reported strategies for eliminating the amplification of contaminating DNA sequences. So far, none of these methods has been entirely effective and reproducible. Here we describe a method that uses Exonuclease III (ExoIII) to disable contaminating sequences from acting as templates, while maintaining the high sensitivity of PCR for pathogen DNA. We use this assay in 144 clinical specimens from normally sterile sites, identifying pathogens from 24 (17%). Conventional methods identified pathogens in only four of these specimens, all of which were positive for the same pathogen by PCR. Compared with conventional methods, broad-range PCR with ExoIII pre-treatment of reagents substantially improves the diagnostic yield of bacterial pathogen identification from normally sterile sites.
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Affiliation(s)
- Abdessalam Cherkaoui
- Clinical Microbiology Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, Geneva 14, Switzerland
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Spangler R, Goddard NL, Thaler DS. Optimizing Taq polymerase concentration for improved signal-to-noise in the broad range detection of low abundance bacteria. PLoS One 2009; 4:e7010. [PMID: 19753123 PMCID: PMC2737620 DOI: 10.1371/journal.pone.0007010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 08/11/2009] [Indexed: 11/18/2022] Open
Abstract
Background PCR in principle can detect a single target molecule in a reaction mixture. Contaminating bacterial DNA in reagents creates a practical limit on the use of PCR to detect dilute bacterial DNA in environmental or public health samples. The most pernicious source of contamination is microbial DNA in DNA polymerase preparations. Importantly, all commercial Taq polymerase preparations inevitably contain contaminating microbial DNA. Removal of DNA from an enzyme preparation is problematical. Methodology/Principal Findings This report demonstrates that the background of contaminating DNA detected by quantitative PCR with broad host range primers can be decreased greater than 10-fold through the simple expedient of Taq enzyme dilution, without altering detection of target microbes in samples. The general method is: For any thermostable polymerase used for high-sensitivity detection, do a dilution series of the polymerase crossed with a dilution series of DNA or bacteria that work well with the test primers. For further work use the concentration of polymerase that gave the least signal in its negative control (H2O) while also not changing the threshold cycle for dilutions of spiked DNA or bacteria compared to higher concentrations of Taq polymerase. Conclusions/Significance It is clear from the studies shown in this report that a straightforward procedure of optimizing the Taq polymerase concentration achieved “treatment-free” attenuation of interference by contaminating bacterial DNA in Taq polymerase preparations. This procedure should facilitate detection and quantification with broad host range primers of a small number of bona fide bacteria (as few as one) in a sample.
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Affiliation(s)
- Rudolph Spangler
- Sackler Laboratory of Molecular Genetics and Informatics, The Rockefeller University, New York, New York, USA.
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24
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Diagnosis of bacteremia in whole-blood samples by use of a commercial universal 16S rRNA gene-based PCR and sequence analysis. J Clin Microbiol 2009; 47:2759-65. [PMID: 19571030 DOI: 10.1128/jcm.00567-09] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
In a prospective, multicenter study of 342 blood samples from 187 patients with systemic inflammatory response syndrome, sepsis, or neutropenic fever, a new commercial PCR test (SepsiTest; Molzym) was evaluated for rapid diagnosis of bacteremia. The test comprises a universal PCR from the 16S rRNA gene, with subsequent identification of bacteria from positive samples by sequence analysis of amplicons. Compared to blood culture (BC), the diagnostic sensitivity and specificity of the PCR were 87.0 and 85.8%, respectively. Considering the 34 BC-positive patients, 28 were also PCR positive in at least one of the samples, resulting in a patient-related sensitivity of 82.4%. The concordance of PCR and BC for both positive and negative samples was (47 + 247)/342, i.e., 86.0%. In total, 31 patients were PCR/sequencing positive and BC negative, in whom the PCR result was judged as possible or probable to true bacteremia in 25. In conclusion, the PCR approach facilitates the detection of bacteremia in blood samples within a few hours. Despite the indispensability of BC diagnostics, the rapid detection of bacteria by SepsiTest appears to be a valuable tool, allowing earlier pathogen-adapted antimicrobial therapy in critically ill patients.
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Döring G, Unertl K, Heininger A. Validation criteria for nucleic acid amplification techniques for bacterial infections. Clin Chem Lab Med 2008; 46:909-18. [PMID: 18605949 DOI: 10.1515/cclm.2008.152] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nucleic acid techniques (NATs), such as species-specific and universal polymerase chain reactions (PCRs), are finding ever wider use in the diagnosis of bacterial infection. However, although universal PCR assays, in particular, approach a type of modern Petri dish, they have a number of limitations which restrict their applicability. The sensitivity of universal PCR is lower than that of many species-specific PCRs, and the contamination of samples and PCR reagents with irrelevant DNA from various sources remains a problem. Thus, NATs in general and universal PCR assays in particular require careful validation to be of value for the diagnosis of infection. Validation includes sampling, DNA extraction/isolation, template amplification and visualisation of the results. Furthermore, it implies the establishment of measures of asepsis, the inclusion of positive and negative controls, techniques to optimise the release of DNA from bacterial cells, adequate repetition of the amplification reaction, and routine testing of reagent negative and inhibition controls. Finally, it entails the comparison of results obtained by NATs with those obtained by conventional microbiological methods and matching with clinical evidence of infection. Validation of NATs in clinical diagnosis remains an ongoing challenge. Because of these limitations, NATs can only serve as adjunct tools for the diagnosis of infection in selected cases; they cannot replace conventional culturing techniques.
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Affiliation(s)
- Gerd Döring
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Eberhard-Karls-Universität Tübingen, Tübingen, Germany.
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26
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Activity and DNA contamination of commercial polymerase chain reaction reagents for the universal 16S rDNA real-time polymerase chain reaction detection of bacterial pathogens in blood. Diagn Microbiol Infect Dis 2008; 66:41-9. [PMID: 18722072 DOI: 10.1016/j.diagmicrobio.2008.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 11/24/2022]
Abstract
Universal 16S rRNA gene polymerase chain reaction (PCR) is a promising means of detecting bacteremia. Among other factors, the PCR reagents play a prominent role for obtaining a high sensitivity of detection. The reagents are ideally optimized with respect to the amplifying activity and absence of contaminating DNA. In this study, it was shown in a universal 16S rDNA real-time PCR assay that commercial PCR reagents can vary greatly among each other in these characters. Only 1 of the 5 reagents tested met the criteria of sensitive detection of pathogen DNA with a minimum of false-positive results. The reagent was validated by the detection of pathogens at low titers using bacterial DNA extracted from blood that was spiked with various Gram-positive and Gram-negative bacteria.
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27
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Gram stain-specific-probe-based real-time PCR for diagnosis and discrimination of bacterial neonatal sepsis. J Clin Microbiol 2008; 46:2613-9. [PMID: 18550744 DOI: 10.1128/jcm.02237-07] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Sepsis is a serious disease with high mortality in newborns. It is very important to have a convenient and accurate method for pathogenic diagnosis of neonatal sepsis. We developed a method of simultaneous detection and Gram classification of clinically relevant bacterial pathogens causing sepsis directly from blood samples with Gram stain-specific-probe-based real-time PCR (GSPBRT-PCR). With GSPBRT-PCR, 53 clinically important strains representing 25 gram-positive and 28 gram-negative bacterial species were identified correctly with the corresponding Gram probe. The limits of the GSPBRT-PCR assay in serial dilutions of the bacteria revealed that Staphylococcus aureus could be detected at concentrations of 3 CFU per PCR and Escherichia coli at concentrations as low as 1 CFU per PCR. The GSPBRT-PCR assay was further evaluated on 600 blood specimens from patients with suspicion of neonatal sepsis and compared to the results obtained from blood cultures. The positive rate of the GSPBRT-PCR array was 50/600 (8.33%), significantly higher than that of blood culture (34/600; 5.67%) (P = 0.00003). When blood culture was used as a control, the sensitivity of GSPBRT-PCR was 100%, the specificity was 97.17%, and the index of accurate diagnosis was 0.972. This study suggests that GSPBRT-PCR is very useful for the rapid and accurate diagnosis of bacterial infection and that it can have an important impact on the current inappropriate and unnecessary use of antibiotics in the treatment of newborns.
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Silkie SS, Tolcher MP, Nelson KL. Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. J Microbiol Methods 2007; 72:275-82. [PMID: 18280599 DOI: 10.1016/j.mimet.2007.12.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 12/14/2007] [Accepted: 12/18/2007] [Indexed: 11/30/2022]
Abstract
The application of real-time quantitative PCR (qPCR) for the detection of low concentrations of Escherichia coli as well as universal 16S rDNA has been hindered by false-positives due to endogenous contamination of PCR reagents with E. coli and other bacterial DNA. We optimized a DNase I decontamination method to eliminate false-positives in a qPCR assay targeting the uidA gene in E. coli. In contrast to previous methods reported in the literature, our decontamination method did not cause PCR inhibition. We determined that residual DNase I activity was the cause of the inhibition in the previous methods, and eliminated it by ensuring complete inactivation prior to qPCR. DNase inactivation was accomplished by adding dithiothreitol (DTT) and then heating for 30 min at 80 degrees C. The optimized DNase method was compared to another decontamination method, ultrafiltration, and to untreated controls. We detected contamination in 85% of the untreated commercial PCR master mix samples at a level of about 10 copies per well (12.5 microL of master mix). Both decontamination methods could eliminate up to 100 copies of added contaminant DNA and did not cause PCR inhibition, resulting in a reduction of the detection limit to 10 copies per reaction well.
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Affiliation(s)
- Sarah S Silkie
- Civil and Environmental Engineering Department, University of California, Berkeley, CA 94720-1710, USA
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29
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Kidd L, Hegarty B, Sexton D, Breitschwerdt E. Molecular characterization of Rickettsia rickettsii infecting dogs and people in North Carolina. Ann N Y Acad Sci 2007; 1078:400-9. [PMID: 17114748 DOI: 10.1196/annals.1374.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Rocky Mountain spotted fever (RMST) is an important cause of morbidity and mortality in people and dogs in the United States. Disease manifestations are strikingly similar in both species, and illness in dogs can precede illness in people. R. rickettsii has been identified as a Select Agent by the CDC as a Category C priority pathogen by the National Institute of Allergic and Infectious Diseases because it is amenable to use as a bioterror agent. The clinical and temporal relationship of naturally occurring diseases in dogs and people suggests that dogs could serve as sentinels for natural infection and bioterrorist attacks using this organism. Recognizing genetic modifications in naturally occurring disease agents in order to distinguish them from intentionally released agents are priorities put forth by the NIAID. To determine whether the rickettsiae naturally infecting dogs is the same as those that infect persons in a given geographical region, we characterized rickettsial isolates obtained from three dogs and two persons diagnosed with RMSF in North Carolina. Portions of three genes (ompA, rrs, and gltA) amplified by PCR were cloned and sequenced or directly sequenced. Reactions were run in duplicate in forward and reverse directions. Gene sequences were aligned with known sequences deposited in GenBank and with each other. Sequences of the 5' region of the ompA gene were 100% homologous with a tick strain (Bitterroot) of R. rickettsii for all five isolates. Sequences of the rrs gene were 99.8 99.9% homologous with a tick strain (Sawtooth) of R. rickettsii. rrs gene sequences from one dog and the two persons was identical. Sequences of one dog isolate differed from these by one base pair. Sequences from another dog isolate differed by two base pairs. Sequences of the gltA gene are pending. This confirms on a molecular level that R. rickettsii causing naturally occurring RMSF in dogs in North Carolina is highly homologous to R. rickettsii that causes the disease in people in the same region. Sequence data will be deposited in GenBank, thereby providing genetic information regarding naturally occurring R. rickettsii.
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Affiliation(s)
- Linda Kidd
- TheScripps Research Institute, Department of Immunology, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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30
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Rueckert A, Morgan HW. Removal of contaminating DNA from polymerase chain reaction using ethidium monoazide. J Microbiol Methods 2006; 68:596-600. [PMID: 17187883 DOI: 10.1016/j.mimet.2006.11.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Accepted: 11/10/2006] [Indexed: 11/15/2022]
Abstract
The presence of exogenous DNA in PCR reagents and DNA polymerase is a common occurrence. In particular, the amplification of 16S rRNA genes with universal primers for non-culture-based study is often hampered by the formation of false positives. Here, we describe the use of ethidium monoazide (EMA) to eliminate contaminating DNA in a polymerase chain reaction. The advantage of the proposed methodology is the retention of the highly sensitive nature of PCR with the ability to amplify template DNA at concentrations lower than those of contaminating DNA. The treatment of PCR master mix with EMA concentrations that exceeded those required to remove contaminating DNA can interfere with the amplification of low-template concentrations. The methodology presented is straightforward and can be accomplished within 10 min.
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Affiliation(s)
- Andreas Rueckert
- Thermophile Research Unit, Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, New Zealand.
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31
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Zucol F, Ammann RA, Berger C, Aebi C, Altwegg M, Niggli FK, Nadal D. Real-time quantitative broad-range PCR assay for detection of the 16S rRNA gene followed by sequencing for species identification. J Clin Microbiol 2006; 44:2750-9. [PMID: 16891488 PMCID: PMC1594602 DOI: 10.1128/jcm.00112-06] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we determined the analytical sensitivities of broad-range real-time PCR-based assays employing one of three different genomic DNA extraction protocols in combination with one of three different primer pairs targeting the 16S rRNA gene to detect a panel of 22 bacterial species. DNA extraction protocol III, using lysozyme, lysostaphin, and proteinase K, followed by PCR with the primer pair Bak11W/Bak2, giving amplicons of 796 bp in length, showed the best overall sensitivity, detecting DNA of 82% of the strains investigated at concentrations of < or =10(2) CFU in water per reaction. DNA extraction protocols I and II, using less enzyme treatment, combined with other primer pairs giving shorter amplicons of 466 bp and 342 or 346 bp, respectively, were slightly more sensitive for the detection of gram-negative but less sensitive for the detection of gram-positive bacteria. The obstacle of detecting background DNA in blood samples spiked with bacteria was circumvented by introducing a broad-range hybridization probe, and this preserved the minimal detection limits observed in samples devoid of blood. Finally, sequencing of the amplicons generated using the primer pair Bak11W/Bak2 allowed species identification of the detected bacterial DNA. Thus, broad-spectrum PCR targeting the 16S rRNA gene in the quantitative real-time format can achieve an analytical sensitivity of 1 to 10 CFU per reaction in water, avoid detection of background DNA with the introduction of a broad-range probe, and generate amplicons that allow species identification of the detected bacterial DNA by sequencing. These prerequisites are important for its application to blood-containing patient samples.
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Affiliation(s)
- Franziska Zucol
- Division of Infectious Diseases, University Children's Hospital of Zurich, Steinwiesstr. 75, CH-8032 Zurich, Switzerland
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Gookin JL, Copple CN, Papich MG, Poore MF, Stauffer SH, Birkenheuer AJ, Twedt DC, Levy MG. Efficacy of Ronidazole for Treatment of FelineTritrichomonas foetusInfection. J Vet Intern Med 2006. [DOI: 10.1111/j.1939-1676.2006.tb02893.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Sauer P, Gallo J, Kesselová M, Kolár M, Koukalová D. Universal primers for detection of common bacterial pathogens causing prosthetic joint infection. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2005; 149:285-8. [PMID: 16601773 DOI: 10.5507/bp.2005.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The diagnosis of low grade prosthetic joint infection is difficult and time consuming. Nested-PCR for universal bacterial DNA segments detection of "orthopaedic" bacteria was tested in a laboratory setting. This method is based on amplification of the 16S bacterial ribosomal RNA coding sequences. 11 species of the most frequent bacterial pathogens (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Serratia marcescens) involved in prosthetic joint infections were studied. All could be detected rapidly and sensitively by this method.
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Affiliation(s)
- Pavel Sauer
- Institute of Microbiology, Palacký University, Teaching Hospital, Olomouc, Czech Republic
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Rolain JM, Raoult D. Molecular detection of Coxiella burnetii in blood and sera during Q fever. QJM 2005; 98:615-7; author reply 617-20. [PMID: 16027172 DOI: 10.1093/qjmed/hci099] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Davies CE, Hill KE, Wilson MJ, Stephens P, Hill CM, Harding KG, Thomas DW. Use of 16S ribosomal DNA PCR and denaturing gradient gel electrophoresis for analysis of the microfloras of healing and nonhealing chronic venous leg ulcers. J Clin Microbiol 2004; 42:3549-57. [PMID: 15297496 PMCID: PMC497624 DOI: 10.1128/jcm.42.8.3549-3557.2004] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene products. Cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes Staphylococcus and Pseudomonas spp. (89 and 80%, respectively). Sequencing of 16S ribosomal DNAs selected on the basis of DGGE profiling allowed the identification of strains not detected by cultural means. Of considerable interest was the finding that more than 40% of the sequences represented organisms not cultured from the wound from which they were amplified. DGGE profiles also revealed that all of the wounds possessed one apparently common band, identified by sequencing as Pseudomonas sp. The intensity of this PCR signal suggested that the bacterial load of nonhealing wounds was much higher for pseudomonads compared to healing wounds and that it may have been significantly underestimated by cultural analysis. Hence, the present study shows that DGGE could give valuable additional information about chronic wound microflora that is not apparent from cultural analysis alone.
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Affiliation(s)
- Charlotte E Davies
- Wound Biology Group, Department of Oral Surgery, Medicine, and Pathology, University of Wales College of Medicine, Heath Park, Cardiff CF14 4XY, United Kingdom
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Heininger A, Binder M, Ellinger A, Pfisterer J, Botzenhart K, Unertl K, Döering G. Effect of comprehensive validation of the template isolation procedure on the reliability of bacteraemia detection by a 16S rRNA gene PCR. Clin Microbiol Infect 2004; 10:452-8. [PMID: 15113325 DOI: 10.1111/j.1469-0691.2004.00877.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of the DNA extraction method on the sensitivity and specificity of bacteraemia detection by a 16S rRNA gene PCR assay was investigated. The detection limit of the assay was 5 fg with purified DNA from Escherichia coli or Staphylococcus aureus, corresponding to one bacterial cell. However, with spiked blood samples, the detection limits were 10(4) and 10(6) CFU/mL, respectively. The sensitivity of the S. aureus assay was improved to the level of the E. coli test with the addition of proteinase K to the commercial DNA extraction kit protocol. Ten (16.6%) of 60 amplification reactions were positive with templates isolated from sterile blood, while PCR reagent controls were negative, thereby indicating contamination during the DNA extraction process. Blood samples were spiked with serial dilutions of E. coli and S. aureus cells, and six PCR results were obtained from three extractions for each blood sample. A classification threshold system was devised, based on the number of positive reactions for each sample. Samples were deemed positive if at least four positive reactions were recorded, making it possible to avoid false-positive results caused by contamination. These results indicate that a comprehensive validation procedure covering all aspects of the assay, including DNA extraction, can improve considerably the validity of PCR assays for bacteraemia, and is a prerequisite for the meaningful detection of bacteraemia by PCR in the clinical setting.
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Affiliation(s)
- A Heininger
- Klinik für Anästhesiologie und Transfusionsmedizin, Abteilung für Anästhesiologie und Intensivmedizin, Eberhard-Karls-Universität, Tübingen, Germany
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Schuurman T, de Boer RF, Kooistra-Smid AMD, van Zwet AA. Prospective study of use of PCR amplification and sequencing of 16S ribosomal DNA from cerebrospinal fluid for diagnosis of bacterial meningitis in a clinical setting. J Clin Microbiol 2004; 42:734-40. [PMID: 14766845 PMCID: PMC344470 DOI: 10.1128/jcm.42.2.734-740.2004] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have evaluated the use of a broad-range PCR aimed at the 16S rRNA gene in detecting bacterial meningitis in a clinical setting. To achieve a uniform DNA extraction procedure for both gram-positive and gram-negative organisms, a combination of physical disruption (bead beating) and a silica-guanidiniumthiocyanate procedure was used for nucleic acid preparation. To diminish the risk of contamination as much as possible, we chose to amplify almost the entire 16S rRNA gene. The analytical sensitivity of the assay was approximately 1 x 10(2) to 2 x 10(2) CFU/ml of cerebrospinal fluid (CSF) for both gram-negative and gram-positive bacteria. In a prospective study of 227 CSF samples, broad-range PCR proved to be superior to conventional methods in detecting bacterial meningitis when antimicrobial therapy had already started. Overall, our assay showed a sensitivity of 86%, a specificity of 97%, a positive predictive value of 80%, and a negative predictive value of 98% compared to culture. We are currently adapting the standard procedures in our laboratory for detecting bacterial meningitis; broad-range 16S ribosomal DNA PCR detection is indicated when antimicrobial therapy has already started at time of lumbar puncture or when cultures remain negative, although the suspicion of bacterial meningitis remains.
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Affiliation(s)
- Tim Schuurman
- Department of Research and Development, Regional Public Health Laboratory for Groningen and Drenthe, Groningen, The Netherlands.
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