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Kotova EO, Domonova EA, Kobalava ZD, Moiseeva AY, Pisaryuk AS, Silveystrova OY, Karaulova JL, Akimkin VG. [Clinical and diagnostic value of including PCR blood test in the traditional algorithm for identifying causative agents of infective endocarditis: a cohort study of 124 patients]. TERAPEVT ARKH 2023; 95:23-31. [PMID: 37167112 DOI: 10.26442/00403660.2023.01.202042] [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: 09/14/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND If infective endocarditis (IE) is suspected, the determination of the etiology is of fundamental importance for the verification of the disease and the appointment of effective therapy. Microbiological diagnostic features are important, but they often need to be supplemented by culture-independent studies of pathological agents. AIM To investigate of the diagnostic advantage and value of quantitative analysis of molecular biological methods (polymerase chain reaction - PCR, sequencing) in addition to microbiological examination of whole venous blood in IE. MATERIALS AND METHODS We examined 124 patients with suspected or significant IE (DUKE 2015) hospitalized in the Vinogradov City Clinical Hospital (2015-2021). All patients underwent parallel microbiological (cultural) and molecular biological (PCR or PCR followed by sequencing) examination of venous whole blood samples. RESULTS The introduction of an early parallel PCR study into the algorithm for the etiological diagnosis of IE made it possible to obtain an additional advantage in 43/124 (34.7%) patients, which made it possible to exclude unreliable results in the determination of CoNS skin commensals and pathogens atypical for IE or contamination and identify the true pathogens, and also for the first time to isolate the etiopathogenetic pathogen with a negative microbiological study. It was shown that in IE associated with CoNS, the association with the disease was confirmed by PCR in 21.4% (3/14) and refuted in 71.4% (10/14). The coincidence of the results of microbiological and PCR studies of blood samples was obtained only in 35/95 (36.8%). Positive results of PCR analysis of blood of biological material with negative results of culture were obtained in 22/51 (43.1%), of which 2/22 (9.0%) were able to confirm the presence of Bartonella spp DNA. The presented complex algorithm made it possible to significantly increase the possibility of intravital identification of the pathogen in the blood from 58.9 to 76.6%. IE with unknown etiology was present in 29/124 (23.4%) patients. A parallel PCR study allowed timely correction of antibiotic therapy in 43/124 (34.7%) patients. CONCLUSION Expansion of indications for the use of PCR studies, primarily whole venous blood samples, is justified, not only in IE with negative results of microbiological examination, but also as a control method for the reliability of the results of traditional (cultural) diagnostic methods.
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Affiliation(s)
- E O Kotova
- People's Friendship University of Russia (RUDN University)
- Vinogradov City Clinical Hospital
| | | | - Z D Kobalava
- People's Friendship University of Russia (RUDN University)
- Vinogradov City Clinical Hospital
| | - A Y Moiseeva
- People's Friendship University of Russia (RUDN University)
| | - A S Pisaryuk
- People's Friendship University of Russia (RUDN University)
- Vinogradov City Clinical Hospital
| | | | - J L Karaulova
- People's Friendship University of Russia (RUDN University)
- Vinogradov City Clinical Hospital
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Trabelsi I, Soltane R, Nejma MB, Albogami BM, Nour M. Genetic variability of the helix 54 of the 23S rDNA and its use as a molecular target for identification of species within the viridans group streptococci (VGS). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105321. [PMID: 35753621 DOI: 10.1016/j.meegid.2022.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The aim of the present study is to establish a method, based on sequence analysis of the helix 54 of 23S rRNA gene, to identify clinical relevant strains belonging to viridans group streptococci (VGS). A set of 25 randomly selected clinical isolates of alpha-hemolytic streptococci from upper respiratory tract were characterized by the routine phenotypic methods (API 20 Strep test). Molecular characterization was assessed by genotypic analysis of the nucleotide sequence of the helix 54 of 23S rRNA and Intergenic spacer region 16S23S. Partial sequencing of the gdh gene was used on 10 strains of mitis group. Sequence variations of the helix 54 allowed the identification of strains to group level and even to species level for certain strains within sanguinis and anginosus groups. Infact, species identification was ambiguous for some strains belonged to the salivarius group (of VGS16 to VGS20) and the mitis group (of VGS1 to VGS14). These results are almost similar to those obtained by sequencing the 16S23S intergenic region. Thus, we use the gdh gene sequencing for the identification of strains, not recognized, within the mitis group. The results generated herein indicate that no single methodology can be used to provide an accurate identification to the species level of all VGS, although nucleotide sequence analysis of the helix 54 of 23S rRNA gene proved to be a reliable method for the identification of VGS to the group level and even to the species level within sanguinis and anginosus groups.
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Affiliation(s)
- Ines Trabelsi
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia.
| | - Raya Soltane
- Departement of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Departement of Biology, Faculty of sciences, Tunis El Manar University, Tunis 1068, Tunisia.
| | - Mouna Ben Nejma
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
| | - Bander M Albogami
- Taif University, College of Science, Laboratory of Applied and Molecular Microbiology, Saudi Arabia
| | - Mohamed Nour
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
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3
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Andersen C, Bergholt B, Ridderberg W, Nørskov-Lauritsen N. Culture on Selective Media and Amplicon-Based Sequencing of 16S rRNA from Spontaneous Brain Abscess-the View from the Diagnostic Laboratory. Microbiol Spectr 2022; 10:e0240721. [PMID: 35404098 PMCID: PMC9045185 DOI: 10.1128/spectrum.02407-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Forty-one stored samples from cases of spontaneous brain abscess were investigated to gain insight into the natural history, causative agents, and relevant laboratory diagnostics of a rare infection. Samples from a larger collection were selected based on retrospective analysis of patient records. All samples were subjected to amplicon sequencing of 16S rRNA gene fragments. Supplementary culture on selected media was performed as suggested by bioinformatics analysis. For three cases, no microorganism was disclosed, while Toxoplasma gondii, Aspergillus fumigatus, and various bacteria were the cause of 1, 2, and 35 cases, respectively. Bacterial infections were monomicrobial in 20 cases and polymicrobial in 15; the microorganisms of the latter cases were restricted to residents of cavum oris. Amplicon sequencing did not further enhance the importance of the Streptococcus anginosus group, which was involved in 17 cases, and the single primer set used may be suboptimal for amplification of Actinomyces and Nocardia. But, amplicon-based sequencing unquestionably expanded the number of polybacterial infections, with focus on the Fusobacterium nucleatum group, Parvimonas, and Porphyromonas. Culture on selective media confirmed the presence of F. nucleatum group bacteria, which attained a prominence in spontaneous brain abscess similar to the S. anginosus group. Metagenomics is a powerful tool to disclose the spectrum of agents in polymicrobial infections, but a reliable cutoff value for substantial detection is complex. Commercial media for isolation of F. nucleatum group bacteria from mixed infections are available, and these pathogens should be carefully characterized. Isolation of Parvimonas and Porphyromonas in polymicrobial infections has not been resolved. IMPORTANCE Polymicrobial brain abscess is a challenge to the clinical microbiology laboratory due to the aggregative nature of the dental and oral microbiota. Because polymicrobial infections may escape detection by conventional culture methods, directed therapy toward a single detected bacterium is problematic. Amplicon-based sequencing provides important clues to these infections, but only cultured microorganisms can be fully characterized, subjected to antimicrobial susceptibility testing, and formally named. By use of specific selective culture plates, we successfully isolated bacteria of the Fusobacterium nucleatum group, and these bacteria rose to the same prominence as the widely recognized pathogen, the Streptococcus anginosus group. Named and unnamed members of the Fusobacterium nucleatum group must be further investigated to gain insight into a rare but grave disease.
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Affiliation(s)
- Camilla Andersen
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Bo Bergholt
- Department of Neurosurgery, Aarhus University Hospital, Aarhus, Denmark
| | - Winnie Ridderberg
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
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Marbjerg LH, Holzknecht BJ, Dargis R, Dessau RB, Nielsen XC, Christensen JJ. Commercial bacterial and fungal broad-range PCR (Micro-Dx™) used on culture-negative specimens from normally sterile sites: diagnostic value and implications for antimicrobial treatment. Diagn Microbiol Infect Dis 2020; 97:115028. [PMID: 32278620 DOI: 10.1016/j.diagmicrobio.2020.115028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/09/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
Abstract
The aim of this study was to evaluate the clinical value of partial 16S/18S rRNA gene sequencing with the commercial kit Micro-Dx™ used with the SelectNA™plus instrument on culture-negative samples. A retrospective study of microbiological and clinical data from a 2.5-year period was performed. Assessment of the clinical relevance of the 16S/18S rRNA gene sequencing results was based on evaluation of the results in the clinical context and changes in antimicrobial therapy. Included were 529 samples from 223 patients, representing 251 episodes. In 191 samples (36.1%), bacterial/fungal DNA was detected. Positive results were judged clinically relevant in 79 (31.5%) episodes. Antimicrobial treatment was adjusted according to the 16S/18S rRNA gene sequence analysis result in 42 (16.7%) episodes. The results from 16S/18S rRNA gene sequence analysis were highly clinically relevant. These findings support the use of this analysis in a routine setting.
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Affiliation(s)
- L H Marbjerg
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark; Department of Clinical microbiology, Odense University Hospital, Odense, Denmark; Department of Clinical microbiology, Vejle Hospital, Vejle, Denmark.
| | - B J Holzknecht
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark; Department of Clinical Microbiology, Herlev and Gentofte Hospital, Herlev, Denmark
| | - R Dargis
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark
| | - R B Dessau
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark; Department of Regional Health Research, University of Southern Denmark
| | - X C Nielsen
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark
| | - J J Christensen
- Department of Clinical Microbiology, Slagelse Hospital, Region Zealand, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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5
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Solomon IH, Lin C, Horback KL, Kanjilal S, Rojas-Rudilla V, Brigl M, Laga AC, Lindeman NI, Padera RF. Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis. Am J Clin Pathol 2019; 152:431-437. [PMID: 31172185 DOI: 10.1093/ajcp/aqz055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES 16S ribosomal RNA (rRNA) sequencing is a powerful but expensive tool for the identification of bacteria in culture-negative endocarditis. Histologic criteria to screen formalin-fixed, paraffin-embedded (FFPE) specimens for testing are evaluated. METHODS Sixty-eight cases of infective endocarditis and controls were histologically reviewed and analyzed by 16S rRNA gene sequencing. RESULTS Sequencing identified a specific pathogenic organism in 33 (49%) of 68 cases with acute inflammation and in 0 of 10 controls (P = .004). Visualization of organisms by Gram or Grocott methenamine silver stains had the strongest association with positive sequencing, while antibiotic treatment effect and acid decalcification decreased sensitivity. Molecular identifications were concordant with blood culture results in 90% of the cases, and a positive sequencing result was obtained in approximately half of the cases with negative valve cultures. CONCLUSIONS Histologic screening criteria are extremely helpful for identifying cases likely to be positive by molecular testing and can provide significant cost savings in filtering out low-yield specimens.
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Affiliation(s)
- Isaac H Solomon
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Chieyu Lin
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Katharine L Horback
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Sanjat Kanjilal
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Vanesa Rojas-Rudilla
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Manfred Brigl
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Alvaro C Laga
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Robert F Padera
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
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Nielsen S, Nørskov-Lauritsen N. Multispacer sequence typing of Coxiella burnetii DNA from removed prosthetic heart valve material discloses first human case of infective endocarditis caused by MST_18. Int J Infect Dis 2019; 79:139-141. [DOI: 10.1016/j.ijid.2018.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
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Halavaara M, Martelius T, Järvinen A, Antikainen J, Kuusela P, Salminen US, Anttila VJ. Impact of pre-operative antimicrobial treatment on microbiological findings from endocardial specimens in infective endocarditis. Eur J Clin Microbiol Infect Dis 2019; 38:497-503. [PMID: 30680557 PMCID: PMC6394703 DOI: 10.1007/s10096-018-03451-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/05/2018] [Indexed: 01/13/2023]
Abstract
Treatment of infective endocarditis (IE) should be initiated promptly. This might hamper the chances to identify the causative organism in blood cultures. Microbiological sampling of infected valve in patients undergoing surgery might identify the causative organism. The impact of pre-operative antimicrobial treatment on the yield of valve samples is not known. This study evaluated the impact of the duration of the pre-operative antibiotic treatment on valve culture and 16S rRNA PCR findings from resected endocardial samples. Patients meeting the modified Duke criteria of definite or possible IE and undergoing valve surgery due to IE during 2011–2016 were included from Southern Finland. Eighty-seven patients were included. In patients with shorter than 2 weeks of pre-operative antimicrobial treatment, PCR was positive in 91% (n = 42/46) and valve culture in 41% (n = 19/46) of cases. However, in patients who had 2 weeks or longer therapy before operation, PCR was positive in 53% (n = 18/34) and all valve cultures were negative. In 14% of patients, PCR had a diagnostic impact. In blood-culture negative cases (n = 13), PCR could detect the causative organism in ten patients (77%). These included five cases of Bartonella quintana, one Tropheryma whipplei, and one Coxiella burnetii. Long pre-operative antimicrobial treatment was shown to have a negative impact on microbiological tests done on resected endocardial material. After 2 weeks of therapy, all valve cultures were negative, but PCR was positive in half of the cases. PCR aided in diagnostic work-up, especially in blood culture negative cases.
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Affiliation(s)
- Mika Halavaara
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland.
| | - Timi Martelius
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
| | - Asko Järvinen
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
| | - Jenni Antikainen
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Pentti Kuusela
- Division of Clinical Microbiology, HUSLAB, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Ulla-Stina Salminen
- Department of Cardiac Surgery, Heart and Lung Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Veli-Jukka Anttila
- Department of Infectious Diseases, Inflammation Center, Helsinki University Hospital (HUH) and University of Helsinki, Meilahti Triangle Hospital, open-plan office, 1st floor, P.O. BOX 372, 00029, Helsinki, Finland
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8
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Laboratory Approach to the Diagnosis of Culture-Negative Infective Endocarditis. Heart Lung Circ 2017; 26:763-771. [PMID: 28372886 DOI: 10.1016/j.hlc.2017.02.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 02/01/2017] [Indexed: 12/31/2022]
Abstract
Blood-culture negative endocarditis (BCNE) accounts for up to 35% of all cases of infective endocarditis (IE) and is a serious life-threatening condition with considerable morbidity and mortality. Rapid detection and identification of the causative pathogen is essential for timely, directed therapy. Blood-culture negative endocarditis presents a diagnostic and therapeutic challenge. Causes of BCNE are varied including: treatment with antibiotic agents prior to blood culture collection; sub-optimal specimen collection; and/or infection due to fastidious (eg. nutritionally variant streptococci), intracellular (eg. Coxiella burnetii, Bartonella species) or non-culturable or difficult to culture organisms (eg. Mycobacteria, Tropheryma whipplei and fungi); as well as non-infective aetiologies. Here, we review aetiological and diagnostic approaches to BCNE including newer molecular based techniques, with a brief summary of imaging investigation and treatment principles.
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Akram A, Maley M, Gosbell I, Nguyen T, Chavada R. Utility of 16S rRNA PCR performed on clinical specimens in patient management. Int J Infect Dis 2017; 57:144-149. [PMID: 28216180 DOI: 10.1016/j.ijid.2017.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Broad-range 16S rRNA PCR can be used for the detection and identification of bacteria from clinical specimens in patients for whom there is a high suspicion of infection and cultures are negative. The aims of this study were (1) to compare 16S rRNA PCR results with microbiological culture results, (2) to assess the utility of 16S rRNA PCR with regard to antimicrobial therapy, and (3) to compare the yield of 16S rRNA PCR for different types of clinical specimen and to perform a cost analysis of the test. METHODS A retrospective study was performed on different clinical specimens which had 16S performed over 3 years (2012-2015). Standard microbiological cultures were performed on appropriate media, as per the laboratory protocol. Patient clinical and microbiological data were obtained from the electronic medical records and laboratory information system, respectively. 16S rRNA PCR was performed in a reference laboratory using a validated method for amplification and sequencing. The outcomes assessed were the performance of 16S rRNA PCR, change of antimicrobials (rationalization, cessation, or addition), and duration of therapy. Concordance of 16S rRNA PCR with bacterial cultures was also determined for tissue specimens. RESULTS Thirty-two patients were included in the study, for whom an equal number of specimens (n=32) were sent for 16S rRNA PCR. 16S rRNA PCR could identify an organism in 10 of 32 cases (31.2%), of which seven were culture-positive and three were culture-negative. The sensitivity was 58% (confidence interval (CI) 28.59-83.5%) and specificity was 85% (CI 61.13-96%), with a positive predictive value of 70% (CI 35.3-91.9%) and negative predictive value of 77.2% (CI 54.17-91.3%). Antimicrobial therapy was rationalized after 16S rRNA PCR results in five patients (15.6%) and was ceased in four based on negative results (12.5%). Overall the 16S rRNA PCR result had an impact on antimicrobial therapy in 28% of patients (9/32). The highest concordance of 16S rRNA PCR with bacterial culture was found for heart valve tissue (80%), followed by joint fluid/tissue (50%). CONCLUSIONS Despite the low diagnostic yield, results of 16S rRNA PCR can still have a significant impact on patient management due to rationalization or cessation of the antimicrobial therapy. The yield of 16S rRNA PCR was highest for heart valves.
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Affiliation(s)
- A Akram
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia
| | - I Gosbell
- Department of Microbiology and Infectious Diseases, Sydney South West Pathology Services, Liverpool Hospital, Liverpool, NSW, Australia; Antibiotic Resistance and Mobile Elements Group, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia; Molecular Medicine Research Group, School of Medicine, University of Western Sydney, Campbelltown, NSW, Australia
| | - T Nguyen
- Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia
| | - R Chavada
- Department of Microbiology and Infectious Diseases, Pathology North, Gosford/Wyong Hospitals, Gosford, NSW, Australia.
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Kotova EO, Domonova EA, Karaulova YL, Milto AS, Pisaryuk AS, Silveistrova OY, Shipulina OY, Shipulin GA, Moiseev VS. [Infective endocarditis: Importance of molecular biological techniques in etiological diagnosis]. TERAPEVT ARKH 2016; 88:62-67. [PMID: 28005033 DOI: 10.17116/terarkh2016881162-67] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To investigate the specific features of conventional bacteriological methods and current molecular biological techniques for the etiological diagnosis of infective endocarditis (IE). SUBJECTS AND METHODS Examinations were made in 53 patients treated at City Clinical Hospital Sixty-Four, Moscow Healthcare Department, in 2012-2015 who underwent simultaneous bacteriological and molecular biological (polymerase chain reaction (PCR) or PCR with further sequencing) examinations of blood or resected cardiac valve tissues. RESULTS The investigation included 53 patients (31 men; median age, 62 years) with IE (Duke 2009); its primary form was observed in 32 (60.4%) patients. Blood bacteriological tests and PCR assays were positive in 28 (52.8%) and 34 (64.2%) patients, respectively. There were concordant results in 21 of the 28 positive blood culture cases and discordant results in 7 (25%); at the same time 3 cases showed a compete discordance in the detected causative agents (the growth of Enterococcus spp. was revealed by bacteriological examination and that of Staphylococcus spp., Streptococcus spp., and Escherichia coli by DNA PCR) and a pathogen could not be identified by DNA PCR in 4 patients who had positive blood bacteriological results. The positive PCR results for cocci and fungi were obtained in 10 of the 25 (47.2%) examinees with culture-negative IE. Rare causative agents were not revealed. The tissues obtained from 8 resected damaged heart valves displayed a wider spectrum of pathogens than did blood samples, which was associated with the formation of bacterial films. CONCLUSION The etiological agent of IE was revealed in venous blood by bacteriological examination in 52.8% of the examinees, by PCR in 64.2%, and by either in 71.7%. There were concordant and discordant results in 67.9 and 32.1% of the patients, respectively; among whom 18.9% were found to have pathogen DNA revealed by PCR in culture-negative IE.
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Affiliation(s)
- E O Kotova
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
| | - E A Domonova
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - Yu L Karaulova
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia; City Clinical Hospital Sixty-Four, Moscow Healthcare Department, Moscow, Russia
| | - A S Milto
- City Clinical Hospital Sixty-Four, Moscow Healthcare Department, Moscow, Russia
| | - A S Pisaryuk
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
| | - O Yu Silveistrova
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - O Yu Shipulina
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Welfare, Moscow, Russia
| | - V S Moiseev
- Peoples' Friendship University of Russia, Ministry of Education and Science of Russia, Moscow, Russia
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PCR-Based Identification of Oral Streptococcal Species. Int J Dent 2016; 2016:3465163. [PMID: 27703479 PMCID: PMC5039290 DOI: 10.1155/2016/3465163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 11/17/2022] Open
Abstract
The microbial etiology of dental caries is still debated. Among the hypothesized contributors are the "low pH streptococci," a designation given to unusually acid proficient strains among the primary plaque colonizers S. oralis, S. mitis, S. gordonii, and S. anginosus. However, accurate assignment of species is difficult among the oral streptococci. Our objective was to develop a streamlined method for identifying strains of S. oralis and S. mitis from plaque samples so that they could be analyzed in a separate study devoted to low pH streptococci and caries. Two independent PCR amplifications of a locus highly conserved among streptococci were used for presumptive species identification. Multilocus sequence analysis (MLSA) was used to measure accuracy. Sensitivity was 100% for selecting S. oralis and S. mitis among the clones sampled. Specificity was good except for the most closely related species that could not be reliably distinguished even by MLSA. The results with S. oralis and S. mitis were used to identify new primer sets that expanded the utility of the approach to other oral streptococcal species. These novel primer sets offer a convenient means of presumptive identification that will have utility in many studies where large scale, in-depth genomic analyses are not practical.
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12
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Miller RJH, Chow B, Pillai D, Church D. Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis 2016; 16:146. [PMID: 27066823 PMCID: PMC4828839 DOI: 10.1186/s12879-016-1476-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
Background The study aimed to explore the sensitivity and specificity of a novel fast 16S rDNA PCR and sequencing assay for the improved diagnosis of infective endocarditis (IE) in patients with suspected native or prosthetic heart valve (HV) infection over a multi-year period at our cardiovascular center. Methods Sixty-eight patients were prospectively enrolled who underwent HV replacement for suspected or confirmed IE between February 1, 2009 and September 1, 2014. Patient demographics, medical co-morbidities, Duke’s criteria, culture results, and antibiotic therapy were collected by detailed chart reviews. Dual-priming oligonucleotide primers targeted to 500 bps of the V1-V3 region of the 16S rRNA gene were used to perform fast broad-range 16S rDNA PCR and Sanger sequencing on ribosomal DNA extracted from HV tissues. The performance/diagnostic efficiency of the molecular test was evaluated against blood cultures and Gram stain and culture of HV tissue in patients’ with definite IE according to Duke’s criteria. Results Fifty patients (73.5 %) had definite IE and another 8 (11.8 %) had possible IE according to Duke’s criteria. Cardiac surgery was delayed an average of 15.4 days from the time of the patient’s last positive blood culture, and appropriate antibiotic therapy was given in the pre-operative period. While 44/50 (88 %) patients had a positive blood culture, HV tissue culture was only positive in 23 (46 %) of them. Molecular testing of all HV tissues had sensitivity, specificity, NPV and PPV of 92, 77.8, 77.8 and 92 % compared to 44, 100, 39.1 and 100 % respectively for culture for diagnosis of definite IE. For prosthetic HV tissue, 16S rDNA PCR had sensitivity of 93 % and specificity of 83 % compared to 35 and 100 % respectively for culture. A literature review showed that the diagnostic accuracy of our novel fast broad-range 16S rDNA PCR assay was similar or better than that of previously published studies. Conclusions This novel fast broad-range 16S rDNA PCR/sequencing test had superior sensitivity compared to tissue Gram stain and culture for identifying underlying bacterial pathogen in both native and prosthetic valve endocarditis.
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Affiliation(s)
- Robert J H Miller
- Department of Cardiac Sciences, University of Calgary, Calgary, Alberta, T2N 2T9, Canada
| | - Barbara Chow
- Calgary Laboratory Services, Calgary, Alberta, T2L 2K8, Canada
| | - Dylan Pillai
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada
| | - Deirdre Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Calgary Laboratory Services, 9-3535 Research Rd. NW, Calgary, Alberta, T2L 2K8, Canada.
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Ring HC, Riis Mikkelsen P, Miller IM, Jenssen H, Fuursted K, Saunte DM, Jemec GBE. The bacteriology of hidradenitis suppurativa: a systematic review. Exp Dermatol 2015; 24:727-31. [PMID: 26119625 DOI: 10.1111/exd.12793] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2015] [Indexed: 12/14/2022]
Abstract
Hidradenitis suppurativa (HS) is a chronic inflammatory disabling skin disease consisting of recurrent nodules, sinuses, fistulas and scarring involving the intertriginous regions. HS is often a therapeutic challenge and most treatments are off-label. A better understanding of aetiology and pathogenesis of HS may facilitate the development of effective treatment. Although the clinical presentation is strongly reminiscent of bacterial infection, the role of bacteria remains controversial. Studies have isolated an array of different bacteria specimens. Consistent findings of Gram-positive cocci and Gram-positive rods including Staphylococus aureus, coagulase-negative staphylococci (CoNS) and Corynebacterium species in deep tissue samples have been demonstrated in HS and may constitute a central target for the immune system. Efficacy of antibiotics, that is rifampicin, clindamycin or tetracycline, supports a microbial role in disease pathogenesis. However, these antibiotics also work as immunomodulators of especially T cells, and the underlying mechanisms may therefore be more complex. We performed a systematic review of previous studies investigating the bacterial flora in hidradenitis suppurativa. We searched PubMed, EMBASE, Royal Danish Library and Cochrane library (search date 11 December 2014). A total of 66 papers were identified and nine papers published between 1988 and 2014 matched our inclusion criteria, yielding bacteriological data of a total of 324 patients with HS (mean age 36.8 years and female/male ratio 215/109). This overview of the bacteriology may aid researchers and physicians exploring the potential role of bacteria in HS. Furthermore, to stimulate a broader debate, we also present different viewpoints on the possible role of bacteria in HS.
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Affiliation(s)
- Hans Christian Ring
- Department of Dermatology, Roskilde Hospital, University of Copenhagen, Roskilde, Denmark
| | - Peter Riis Mikkelsen
- Department of Dermatology, Roskilde Hospital, University of Copenhagen, Roskilde, Denmark
| | - Iben Marie Miller
- Department of Dermatology, Roskilde Hospital, University of Copenhagen, Roskilde, Denmark
| | - Håvard Jenssen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Kurt Fuursted
- Department of bacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Ditte Marie Saunte
- Department of Dermatology, Roskilde Hospital, University of Copenhagen, Roskilde, Denmark
| | - Gregor B E Jemec
- Department of Dermatology, Roskilde Hospital, University of Copenhagen, Roskilde, Denmark
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