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Moppert I, Kim E, Yang SM, Park SH. Development of multiplex PCR for detection of foodborne pathogens in fresh produce. Lett Appl Microbiol 2025; 78:ovaf038. [PMID: 40097293 DOI: 10.1093/lambio/ovaf038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 03/09/2025] [Accepted: 03/13/2025] [Indexed: 03/19/2025]
Abstract
Foodborne pathogens present a significant public health concern where fresh produce is a key agricultural product. Rapid and sensitive detection methods are essential to ensure the safety of such produce. This study aimed to develop and optimize a modified multiplex polymerase chain reaction (mPCR) assay, which incorporates enhancements to conventional PCR, for the simultaneous detection of Escherichia coli, Salmonella, and Listeria monocytogenes in fresh produce. The specificity of each primer pair was validated using 15 strains, confirming 100% accurate detection of pathogenic strains without cross-reactivity. Since no false positives were observed, the assay demonstrated 100% precision, highlighting its reliability in distinguishing target pathogens. The sensitivity of the mPCR assay was demonstrated through serial dilutions, detecting Salmonella down to 10 fg µl-1, L. monocytogenes to 100 fg µl-1, and E. coli to 1 pg µl-1. The mPCR assay was then successfully applied to romaine lettuce and kale, demonstrating its effectiveness in detecting pathogens in mixed samples inoculated at varying concentrations (109-101 CFU ml-1). Kale exhibited greater sensitivity, detecting pathogens at lower levels, while romaine lettuce also provided consistent detection. This study highlights the potential of mPCR for enhancing food safety by providing rapid and sensitive pathogen detection in fresh produce.
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Affiliation(s)
- Ian Moppert
- Department of Food Science and Technology, Oregon State University, Corvallis, OR 97331, United States
| | - Eiseul Kim
- Department of Food Science and Technology, Oregon State University, Corvallis, OR 97331, United States
| | - Seung-Min Yang
- Department of Food Science and Technology, Oregon State University, Corvallis, OR 97331, United States
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, Corvallis, OR 97331, United States
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2
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Butler I, Turner O, Mohammed K, Akhtar M, Evans D, Lambourne J, Harris K, O'Sullivan DM, Sergaki C. Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections. Front Cell Infect Microbiol 2025; 15:1517208. [PMID: 40115075 PMCID: PMC11922894 DOI: 10.3389/fcimb.2025.1517208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 01/28/2025] [Indexed: 03/23/2025] Open
Abstract
The integration of long-read sequencing technology, such as nanopore sequencing technology [Oxford Nanopore Technologies (ONT)], into routine diagnostic laboratories has the potential to transform bacterial infection diagnostics and improve patient management. Analysis of amplicons from long-read sequencing of the 16S rRNA gene generates a comprehensive view of the microbial community within clinical samples, significantly enhancing sensitivity and capacity to analyse mixed bacterial populations compared to short read sequencing approaches. This study evaluates various ONT sequencing approaches and library preparation kits to establish a reliable testing and quality framework for clinical implementation. This study highlights the critical importance of using well-characterized reference materials in validating and revalidating long-read sequencing methods, leveraging a combination of standardized reference materials and clinical samples to navigate the evolving landscape of microbial diagnostics. It presents a robust validation framework for laboratory accreditation and outlines a methodology for comparing the performance of newer ONT chemistries with earlier versions. Additionally, the study details the methods and quality control measures necessary for achieving more accurate and efficient diagnoses of bacterial infections, ultimately reducing time to treatment and enhancing patient outcomes.
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Affiliation(s)
- Ian Butler
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Olivia Turner
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Kulsoom Mohammed
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Mazeda Akhtar
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Daniel Evans
- Molecular and Cell Biology, National Measurement Laboratory (NML), Laboratory of the Government Chemist (LGC), London, United Kingdom
| | - Jonathan Lambourne
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Kathryn Harris
- Department of Microbiology, National Health Services (NHS) East and South East London Pathology Partnership, Bart's Health NHS Trust, London, United Kingdom
| | - Denise M. O'Sullivan
- Molecular and Cell Biology, National Measurement Laboratory (NML), Laboratory of the Government Chemist (LGC), London, United Kingdom
- School of Biosciences & Medicine, University of Surrey, Guildford, United Kingdom
| | - Chrysi Sergaki
- Medicines and Healthcare Products Regulatory Agency (MHRA), London, United Kingdom
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Dillie D, Bamps L, Argudín MA, Rodriguez-Villalobos H, Kirchgesner T, Fomekong E, Yombi JC. A Rare Case of Streptococcus cristatus Spondylodiscitis Identified by Bacterial 16S rRNA Polymerase Chain Reaction Sequencing: A Case Report and a Review of the Literature. Cureus 2024; 16:e59127. [PMID: 38803776 PMCID: PMC11129285 DOI: 10.7759/cureus.59127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2024] [Indexed: 05/29/2024] Open
Abstract
We report here a rare case of spondylodiscitis due to Streptococcus cristatus in a healthy 66-year-old male. Due to an abscess causing neurological deficit, which required immediate surgical intervention, a PCR targeting 16S rRNA was performed on the surgical samples as all blood and tissue cultures remained negative. This molecular assay allowed for the identification of this rare Streptococcus, a member of the mitis group and commensal of the oral cavity, whose pathogenicity remains uncertain although it has been seldom reported in cases of human infections, mostly bacteremia and endocarditis. Notably, our case is distinguished by the absence of comorbidities, although the patient's history was compatible with a dental portal of entry. This case illustrates once more that 16S rRNA PCR can be of great help for documenting the causative pathogen in osteoarticular infections when cultures remain inconclusive. We reviewed in this article the data regarding osteoarticular infections due to S. cristatus and discussed the role of molecular technique in the diagnosis of spondylodiscitis.
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Affiliation(s)
- Damien Dillie
- Internal Medicine and Infectious Diseases, Cliniques Universitaires Saint Luc, Brussels, BEL
| | - Laurence Bamps
- Internal Medicine and Infectious Diseases, Cliniques Universitaires Saint Luc, Brussels, BEL
| | | | | | | | - Edward Fomekong
- Neurosurgery, Cliniques Universitaires Saint Luc, Brussels, BEL
| | - Jean Cyr Yombi
- Internal Medicine and Infectious Diseases, Cliniques Universitaires Saint Luc, Brussels, BEL
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Dupieux C, Descours G, Verhoeven P, Grattard F, Benito Y, Vandenesch F, Cazorla C, Ferry T, Lustig S, Boyer B, Boisset S, Carricajo A, Laurent F, PIRLA investigator group /. Optimized decision algorithm for the microbiological diagnosis of osteoarticular infections in adults using synovial fluid samples: a prospective study in two French hospitals including 423 samples of synovial fluid. J Bone Jt Infect 2024; 9:37-48. [PMID: 38600997 PMCID: PMC11004666 DOI: 10.5194/jbji-9-37-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/30/2023] [Indexed: 04/12/2024] Open
Abstract
No consensus exists about the techniques to use for microbiological diagnosis of bone and joint infections (BJIs). The objective herein was to define an algorithm to optimize BJI diagnosis in adults using various bacteriological methods on synovial fluid samples. This prospective multi-center study included 423 synovial fluids collected from adult patients with suspected BJIs. Culture (using five solid media, an enrichment broth, and blood culture bottles), universal 16S rRNA PCR followed by Sanger sequencing, and seven specific bacterial PCRs were systematically performed. Combinations of methods were compared to arrive at the optimized algorithm. Among 423 synovial fluids, 242 infections were diagnosed (57.2 %): 213 mono- and 29 poly-microbial for a total of 284 bacteria (staphylococci at 54.6 %, streptococci-enterococci at 16.5 %, Gram-negative bacilli at 15.5 %, anaerobic species at 8.8 %). Comparing culture techniques, blood culture bottles had the highest sensitivity (67.6 % for pediatric and 63.9 % for anaerobic bottles) but are not sufficient alone and require being combined with solid media. The 16S rDNA PCR detected only 52.3 % of the bacteria, whereas specific PCRs had a higher sensitivity (Staphylococcus spp. at 66.2 %, S. aureus at 85.2 %, Streptococcus spp. at 91.2 %). Based on these results, an algorithm was proposed associating three solid media; inoculation into blood culture bottles; and 16S, Staphylococcus spp., and Streptococcus spp. PCRs, which would have detected 90.5 % of bacteria in the present cohort versus 79.2 % using all culture techniques on synovial fluid. This prospective study shows that a combination of culture and molecular methods on synovial fluids allows the optimization of bacterial detection.
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Affiliation(s)
- Céline Dupieux
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Ghislaine Descours
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Paul Verhoeven
- Laboratoire de Bactériologie, CHU de Saint-Étienne, Saint-Étienne, 42055, France
| | - Florence Grattard
- Laboratoire de Bactériologie, CHU de Saint-Étienne, Saint-Étienne, 42055, France
| | - Yvonne Benito
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - François Vandenesch
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Céline Cazorla
- Service de Maladies Infectieuses, CHU de Saint-Étienne, Saint-Étienne, 42055, France
| | - Tristan Ferry
- Service de Maladies Infectieuses, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Sébastien Lustig
- Service de Chirurgie Orthopédique, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Bertrand Boyer
- Service de Chirurgie Orthopédique, CHU de Saint-Étienne, Saint-Étienne, 42055, France
| | - Sandrine Boisset
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
| | - Anne Carricajo
- Laboratoire de Bactériologie, CHU de Saint-Étienne, Saint-Étienne, 42055, France
| | - Frédéric Laurent
- Laboratoire de Bactériologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, 69004, France
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Solaghani TH, Nazari R, Mosavari N, Tadayon K, Zolfaghari MR. Isolation and identification of nontuberculous mycobacteria from raw milk and traditional cheese based on the 16S rRNA and hsp65 genes, Tehran, Iran. Folia Microbiol (Praha) 2024; 69:81-89. [PMID: 37507582 DOI: 10.1007/s12223-023-01073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
As an important source of human food, milk can be a carrier of human pathogenic bacteria, including tuberculous and nontuberculous mycobacteria (NTM), in its raw and unpasteurized state. In this research, 175 raw milk samples and 175 traditional cheese samples were collected from traditional dairy stores in 22 regions of Tehran in a 9- month period from August 2019 to May 2020. Samples were prepared and transferred to a specialized laboratory, where they were inoculated in Lowenstein-Jensen (LJ) medium containing glycerol or sodium pyruvate, as well as Herrold's egg-yolk with and without Mycobactin J. to determine the sample's identity of samples. The recommended 16S rRNA (1436 bp) and hsp65 (644 bp) gene fragments from the positive isolates identified in Ziehl-Neelsen (Z-N) staining were amplified and sequenced using PCR and compared with the sequences of the gene fragments of reference strains available in the global GenBank database. No mycobacterial species were isolated from traditional cheese samples in microbial culture. In case of raw milk samples, a total of four bacteria were collected, all of which were found in the genetic differential testing to be NTM, including n = 1 Mycobacterium heraklionense, n = 2 Mycolicibacterium fortuitum, and n = 1 Mycobacterium thermoresistibile. The analysis of the results obtained by isolate sequencing using the 16S rRNA gene showed higher discriminatory power and percentage similarities in the identification of the isolates than the hsp65 gene.
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Affiliation(s)
| | - Razieh Nazari
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran.
| | - Nader Mosavari
- Bovine Tuberculosis Reference Laboratory, Agricultural Research, Education and Extension Organization (AREEO), Razi Vaccine and Serum Research Institute, Karaj, Iran.
| | - Keyvan Tadayon
- Agricultural Research Education and Extension Organization (AREEO), Tuberculin and Mallein Research & Production Department, Razi Vaccine and Serum Research Institute, Bovine Tuberculosis Laboratory, Karaj, Iran
| | - Mohammad Reza Zolfaghari
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran
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6
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Moorlag SJCFM, Coolen JPM, van den Bosch B, Jin EHM, Buil JB, Wertheim HFL, Melchers WJG. Targeting the 16S rRNA Gene by Reverse Complement PCR Next-Generation Sequencing: Specific and Sensitive Detection and Identification of Microbes Directly in Clinical Samples. Microbiol Spectr 2023; 11:e0448322. [PMID: 37227289 PMCID: PMC10269728 DOI: 10.1128/spectrum.04483-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
The detection and accurate identification of bacterial species in clinical samples are crucial for diagnosis and appropriate antibiotic treatment. To date, sequencing of the 16S rRNA gene has been widely used as a complementary molecular approach when identification by culture fails. The accuracy and sensitivity of this method are highly affected by the selection of the 16S rRNA gene region targeted. In this study, we assessed the clinical utility of 16S rRNA reverse complement PCR (16S RC-PCR), a novel method based on next-generation sequencing (NGS), for the identification of bacterial species. We investigated the performance of 16S RC-PCR on 11 bacterial isolates, 2 polymicrobial community samples, and 59 clinical samples from patients suspected of having a bacterial infection. The results were compared to culture results, if available, and to the results of Sanger sequencing of the 16S rRNA gene (16S Sanger sequencing). By 16S RC-PCR, all bacterial isolates were accurately identified to the species level. Furthermore, in culture-negative clinical samples, the rate of identification increased from 17.1% (7/41) to 46.3% (19/41) when comparing 16S Sanger sequencing to 16S RC-PCR. We conclude that the use of 16S RC-PCR in the clinical setting leads to an increased sensitivity of detection of bacterial pathogens, resulting in a higher number of diagnosed bacterial infections, and thereby can improve patient care. IMPORTANCE The identification of the causative infectious pathogen in patients suspected of having a bacterial infection is essential for diagnosis and the start of appropriate treatment. Over the past 2 decades, molecular diagnostics have improved the ability to detect and identify bacteria. However, novel techniques that can accurately detect and identify bacteria in clinical samples and that can be implemented in clinical diagnostics are needed. Here, we demonstrate the clinical utility of bacterial identification in clinical samples by a novel method called 16S RC-PCR. Using 16S RC-PCR, we reveal a significant increase in the number of clinical samples in which a potentially clinically relevant pathogen is identified compared to the commonly used 16S Sanger method. Moreover, RC-PCR allows automation and is well suited for implementation in a diagnostic laboratory. In conclusion, the implementation of this method as a diagnostic tool is expected to result in an increased number of diagnosed bacterial infections, and in combination with adequate treatment, this could improve clinical outcomes for patients.
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Affiliation(s)
- Simone J. C. F. M. Moorlag
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Bart van den Bosch
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Elisabeth Hui-Mei Jin
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jochem B. Buil
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
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Ngamprasertchai T, Rattanaumpawan P, Kaewkungwal J, Phisalprapa P, Chongtrakool P, Kerdsin A, Luvira V, Thaipadungpanit J, Kajeekul R, Srisompong J, Yincharoen P, Chokephaibulkit K, Lawpoolsri S. Pneumococcal carriage among high-risk adults in a country with nonmandatory pneumococcal vaccination during the coronavirus disease 2019 pandemic. J Infect Public Health 2023; 16:1102-1108. [PMID: 37220711 DOI: 10.1016/j.jiph.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/19/2023] [Accepted: 05/07/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Streptococcus pneumoniae carriage is a prerequisite for clinical infections and is used to make public health decisions on vaccine licensure. Pneumococcal carriage data among high-risk Thai adults are needed before national vaccine program introduction. The association between coronavirus disease 2019 (COVID-19) and pneumococcal carriage were also investigated. METHODS During the COVID-19 pandemic, a multi-center cross-sectional study was conducted among high-risk Thai adults from September 2021 to November 2022. Pneumococcal carriage and serotypes were investigated using both conventional and molecular methods. Demographics and co-morbidities were determined for carriage while accounting for case clustering from various study sites. RESULTS A total of 370 individuals were enrolled. The prevalence of pneumococcal carriage, as determined by the molecular method, was 30.8 % (95 % confidence interval (CI): 26.1-35.8), while after excluding non-typeable pneumococci from the oropharyngeal sample, the carriage prevalence was 20.8 % (95 % CI: 16.79-25.31). The serotype coverage rates by pneumococcal vaccine were 12.3 %, 13.1 %, and 16.4 % for PCV13, PCV15 or PCV20, and PPSV23, respectively, while the non-vaccine type was the majority (45.1 %). The most common serotype was 19B/C (35.5 %), followed by 6 A/B/C/D (10.7 %). The age group under 65 years was associated with a higher pneumococcal carriage rate than the age group 85 and older (odds ratio (OR): 5.01, 95 % CI: 1.75-14.36). There was no significant difference between SARS-CoV-2 and carriage status. CONCLUSIONS The prevalence of pneumococcal carriage in Thais was high. The majority of serotypes were not covered by the vaccine. Further studies on the link between carriage serotypes and disease are required. The magnitude and serotype distribution of carriage were comparable in the SARS-CoV-2 positive and negative groups.
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Affiliation(s)
- Thundon Ngamprasertchai
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Pinyo Rattanaumpawan
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Jaranit Kaewkungwal
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pochamana Phisalprapa
- Division of Ambulatory Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Piriyaporn Chongtrakool
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon 47000, Thailand.
| | - Viravarn Luvira
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand.
| | - Rattagan Kajeekul
- Department of Medicine, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand.
| | - Jintana Srisompong
- Department of Medicine, Suratthani Hospital, Suratthani 84000, Thailand.
| | - Picha Yincharoen
- Bhumirajanagarindra Kidney Institute Hospital, Bangkok 10400, Thailand.
| | - Kulkanya Chokephaibulkit
- Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Siriraj Institute of Clinical Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | - Saranath Lawpoolsri
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Eamsakulrat P, Santanirand P, Phuphuakrat A. Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens. Microbiol Spectr 2022; 10:e0209422. [PMID: 36374024 PMCID: PMC9769669 DOI: 10.1128/spectrum.02094-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.
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Affiliation(s)
- Pruke Eamsakulrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pitak Santanirand
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angsana Phuphuakrat
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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9
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Harris KA, Brown JR. Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms. J Med Microbiol 2022; 71. [PMID: 36748452 DOI: 10.1099/jmm.0.001633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.
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Affiliation(s)
- Kathryn A Harris
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK.,Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Julianne R Brown
- Microbiology, Virology and Infection Prevention & Control, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, WC1N 3JH, UK
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10
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Hoffman JJ, Dart JKG, De SK, Carnt N, Cleary G, Hau S. Comparison of culture, confocal microscopy and PCR in routine hospital use for microbial keratitis diagnosis. Eye (Lond) 2022; 36:2172-2178. [PMID: 34741122 PMCID: PMC9581916 DOI: 10.1038/s41433-021-01812-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 09/23/2021] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
AIMS To evaluate the sensitivity and specificity of polymerase chain reaction (PCR), in vivo confocal microscopy (IVCM) and culture for microbial keratitis (MK) diagnosis. METHODS Retrospective review of PCR, IVCM and culture results for MK diagnosis at Moorfields Eye Hospital between August 2013 and December 2014. RESULTS PCR results were available for 259 MK patients with concurrent culture for 203/259 and IVCM for 149/259. Sensitivities and specificities with 95% confidence intervals [95% CI] were calculated for Acanthamoeba keratitis (AK) and fungal keratitis (FK), by comparison with culture, for both IVCM and PCR. For AK, FK and bacterial keratitis (BK) sensitivities were calculated, for each diagnostic method, by comparison with a composite reference standard (a positive result for one or more of culture, PCR or IVCM having a specificity of 100% by definition). For the latter, sensitivities with [95% CI] were: for AK, IVCM 77.1% [62.7-88.0%], PCR 63.3% [48.3-76.6%], culture 35.6 [21.9-51.2]; for FK, IVCM 81.8% [48.2-97.7%], PCR 30.8% [9.09-61.4%], culture 41.7% [15.2-72.3%]; for BK, PCR 25.0% [14.7-37.9%], culture 95.6% [87.6-99.1%]. CONCLUSION IVCM was the most sensitive technique for AK and FK diagnosis but culture remains our gold standard for BK. These findings reflect results to be expected from service providers to UK ophthalmology units and demonstrates the need at our centre for ongoing diagnostic result audit leading to the potential to improve PCR diagnosis. Both FK and AK are now common in the UK; ophthalmology units need to have all these techniques available to optimise their MK management.
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Affiliation(s)
- Jeremy J Hoffman
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.
- International Centre for Eye Health, London School of Hygiene and Tropical Medicine, London, UK.
- National Institute of Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.
| | - John K G Dart
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- National Institute of Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Surjo K De
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Department of Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Nicole Carnt
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Georgia Cleary
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Scott Hau
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
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11
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Kim MGJ, Payne S, Post J. A subacute presentation of Mycoplasma hominis prosthetic valve endocarditis. BMJ Case Rep 2022; 15:e252972. [PMID: 36319037 PMCID: PMC9628652 DOI: 10.1136/bcr-2022-252972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 11/07/2022] Open
Abstract
Mycoplasma hominis is a rare but important cause of prosthetic valve endocarditis. It is usually associated with acute progression of symptoms and can be difficult to diagnose as it does not grow in standard culture media. We report a case of an immunocompetent man in his 70s who presented with 14-month subacute decline with shortness of breath and evidence of a splenic infarct. Following a redo aortic valve replacement and diagnosis of M. hominis through 16S ribosomal ribonucleic acid PCR, he improved clinically with oral doxycycline therapy. He remained well at follow-up 2 years post-cessation of antibiotics. We present a literature review highlighting the role of PCR testing in the microbiological identification of M. hominis.
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Affiliation(s)
- Myong Gyu Joshua Kim
- Faculty of Medicine, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
- Infectious Diseases, Prince of Wales Hospital and Community Health Services, Randwick, New South Wales, Australia
| | - Susannah Payne
- Infectious Diseases, Prince of Wales Hospital and Community Health Services, Randwick, New South Wales, Australia
| | - Jeffrey Post
- Faculty of Medicine, Prince of Wales Clinical School, University of New South Wales, Randwick, New South Wales, Australia
- Infectious Diseases, Prince of Wales Hospital and Community Health Services, Randwick, New South Wales, Australia
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12
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Multiple Polymerase Chain Reaction for Direct Detection of Bloodstream Infection After Cardiac Surgery in a PICU. Crit Care Explor 2022; 4:e0707. [PMID: 35651736 PMCID: PMC9150881 DOI: 10.1097/cce.0000000000000707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nosocomial infections are a prevalent cause of death and complications in critically ill children. Conventional cultures are able to detect only up to 25% of bacteremia. Several studies have suggested that molecular tests could be a faster and effective tool for detection of bacterial infections. The objective of this study is to compare molecular tests for bacterial detection in whole blood samples, with routine blood culture for the diagnosis of nosocomial bloodstream infections (BSIs).
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13
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Oliveira AR, de Castro MF, Pimentel SP, de Carvalho TP, Santana CH, Santos DDO, Tinoco HP, Coelho CM, Pessanha AT, da Paixão TA, Santos RL. Streptococcus pasteurianus-induced valvular endocarditis and sepsis in a puerperal emperor tamarin (Saguinus imperator). J Med Primatol 2022; 51:388-391. [PMID: 35451506 DOI: 10.1111/jmp.12587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 11/29/2022]
Abstract
Streptococcus pasteurianus is associated with endocarditis and sepsis in humans. A puerperal emperor tamarin died, and necropsy showed a bacterial endocarditis with sepsis. DNA sequencing from the paraffinized heart tissue was compatible with S. pasteurianus. S. pasteurianus could be an important agent associated with sepsis in tamarins.
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Affiliation(s)
| | | | | | | | | | | | | | - Carlyle Mendes Coelho
- Fundação de Parques Municipais e Zoobotânica de Belo Horizonte, Belo Horizonte, Brazil
| | | | - Tatiane Alves da Paixão
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Renato Lima Santos
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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14
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Labetoulle R, Rigaill J, Lleres-Vadeboin M, Grattard F, Pozzetto B, Cazorla C, Botelho-Nevers E, Boyer B, Dupieux-Chabert C, Laurent F, Verhoeven PO, Carricajo A. Evaluation of the MRSA/SA ELITe MGB Assay for the Detection of Staphylococcus aureus in Bone and Joint Infections. J Clin Microbiol 2022; 60:e0083521. [PMID: 34788112 PMCID: PMC8769721 DOI: 10.1128/jcm.00835-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Bone and joint infections represent a potentially devastating complication of prosthetic orthopedic joint replacement, thus requiring both rapid and appropriate antibiotic treatment. Staphylococcus aureus is one of the most common pathogens involved in this pathology. Being able to assert its presence is the first step of efficient patient management. This monocenter study evaluated the MRSA/SA ELITe MGB assay for the molecular detection of S. aureus and methicillin-resistant S. aureus (MRSA) in bone and joint biopsy specimens and synovial fluids. This test, together with conventional techniques, including standard cultures and the 16S rRNA amplification assay, was performed on 208 successive perioperative samples collected prospectively for 1 year obtained from 129 patients. Using conventional techniques, we detected a microbial pathogen in 76 samples from 58 patients, 40 of which were identified as S. aureus. The limit of detection (LOD) of the MRSA/SA ELITe MGB assay was experimentally determined for bone and joint biopsy specimens and synovial fluids using negative samples spiked with S. aureus ATCC 43300. The sensitivities of S. aureus detection with the MRSA/SA ELITe MGB assay were 82.5% (33/40 samples) and 97.5% (39/40 samples) using the manufacturer's LOD and an experimentally determined LOD, respectively. Interestingly, using the osteoarticular specific LOD, 15 additional samples were determined to be positive for S. aureus DNA with the MRSA/SA ELITe MGB assay; in all cases, these samples were obtained from patients considered to be infected with S. aureus according to their clinical and microbiological records. The results were available within 24 h, which could help to expedite therapeutic decisions.
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Affiliation(s)
- R. Labetoulle
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
| | - J. Rigaill
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
| | - M. Lleres-Vadeboin
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon, Associated Center), University Hospital of St-Etienne, St-Etienne, France
| | - F. Grattard
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
| | - B. Pozzetto
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
| | - C. Cazorla
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon, Associated Center), University Hospital of St-Etienne, St-Etienne, France
- Department of Infectious Diseases, University Hospital of St-Etienne, St-Etienne, France
| | - E. Botelho-Nevers
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
- Department of Infectious Diseases, University Hospital of St-Etienne, St-Etienne, France
| | - B. Boyer
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon, Associated Center), University Hospital of St-Etienne, St-Etienne, France
- Department of Orthopaedic Surgery, University Hospital of St-Etienne, St-Etienne, France
| | - C. Dupieux-Chabert
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal Pathogenesis Team, University of Lyon, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL, Lyon, France
- Department of Bacteriology, Institute for Infectious Agents, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- French National Reference Center for Staphylococci, Lyon, France
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon), Hospices Civils de Lyon, Lyon, France
| | - F. Laurent
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal Pathogenesis Team, University of Lyon, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL, Lyon, France
- Department of Bacteriology, Institute for Infectious Agents, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France
- French National Reference Center for Staphylococci, Lyon, France
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon), Hospices Civils de Lyon, Lyon, France
| | - P. O. Verhoeven
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon, Associated Center), University Hospital of St-Etienne, St-Etienne, France
| | - A. Carricajo
- Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
- CIRI, Centre International de Recherche en Infectiologie, GIMAP team, University of Lyon, University of St-Etienne, INSERM, U1111, CNRS UMR5308, ENS de Lyon, UCBL, St-Etienne, France
- Interregional Reference Centre for Complex Bone and Joint Infection (CRIOAc Lyon, Associated Center), University Hospital of St-Etienne, St-Etienne, France
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Wu Y, Zhang D, Duan A, Ao Y, Li S. The application of riboswitch sequencing for human gut bacterial classification and identification. Mol Phylogenet Evol 2022; 169:107409. [PMID: 35063674 DOI: 10.1016/j.ympev.2022.107409] [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: 07/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/15/2022]
Abstract
Bacteria, especially gut bacteria play important roles in human health and diseases. The classification of many bacterial genera by the 16S ribosomal RNA (rRNA) has failed due to its low inter-species resolution. Given the wide distribution of riboswitches in bacteria, they may help 16S rRNA differentiate closely related species. We found that among 28 groups of species that could not be distinguished by 16S rRNA, eight of them could be separated by the TPP riboswitch and other riboswitches. Moreover, the species in the 16S rRNA database and these riboswitch databases overlap, therefore, using riboswitch databases can help 16S rRNA better identify species. In addition, we used Klenow DNA polymerase and a pair of short primers to facilitate the library construction of TPP riboswitches for sequencing. The sequencing results showed that the TPP riboswitch could detect the major phyla similar to those detected by 16S rRNA. Therefore, the TPP riboswitch and other riboswitch classes could potentially be applied to gut bacteria classification.
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Affiliation(s)
- Yaoyao Wu
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Deying Zhang
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510627, P. R. China(2)
| | - Anqi Duan
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Yaqi Ao
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China
| | - Sanshu Li
- Medical School, Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, P. R. China.
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16
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Wei Q, Li J, Yang S, Wang W, Min F, Guo M, Zhang S, Dong X, Hu L, Li Z, Wang X. Streptomyces rhizophilus Causes Potato Common Scab Disease. PLANT DISEASE 2022; 106:266-274. [PMID: 34615364 DOI: 10.1094/pdis-09-20-1902-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Common scab (CS) caused by Streptomyces spp. is a significant soilborne potato disease that results in tremendous economic losses globally. Identification of CS-associated species of the genus Streptomyces can enhance understanding of the genetic variation of these bacterial species and is necessary for the control of this epidemic disease. The present study isolated Streptomyces strain 6-2-1(1) from scabby potatoes in Keshan County, Heilongjiang Province, China. PCR analysis confirmed that the strain harbored the characteristic Streptomyces pathogenicity island (PAI) genes (txtA, txtAB, nec1, and tomA). Pathogenicity assays proved that the strain caused typical scab lesions on potato tuber surfaces and necrosis on radish seedlings and potato slices. Subsequently, the strain was systemically characterized at morphological, physiological, biochemical, and phylogenetic levels. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6-2-1(1) shared 99.86% sequence similarity with Streptomyces rhizophilus JR-41T, isolated initially from bamboo in rhizospheric soil in Korea. PCR amplification followed by Sanger sequencing of the 16S rRNA gene of 164 scabby potato samples collected in Heilongjiang Province from 2019 to 2020 demonstrated that approximately 2% of the tested samples were infected with S. rhizophilus. Taken together, these results demonstrate that S. rhizophilus is capable of causing potato CS disease and may pose a potential challenge to potato production in Heilongjiang Province of China.
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Affiliation(s)
- Qi Wei
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Jie Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shuai Yang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Wenzhong Wang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Fanxiang Min
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Mei Guo
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Shu Zhang
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Xuezhi Dong
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Linshuang Hu
- Potato Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Zhugang Li
- Institute of Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin 150016, China
| | - Xiaodan Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
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17
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Sri A, Droscher E, De Palma R. Capnocytophaga canimorsus and infective endocarditis-making a dog's dinner of the aortic valve: a case report. Eur Heart J Case Rep 2021; 5:ytab278. [PMID: 34423243 PMCID: PMC8374984 DOI: 10.1093/ehjcr/ytab278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/17/2020] [Accepted: 06/30/2021] [Indexed: 11/20/2022]
Abstract
Background Capnocytophaga canimorsus, a bacterium found in the oral cavities of healthy cats and dogs, is rarely reported as a cause of infective endocarditis. In this report we describe such a case in a young, male dog owner who presented acutely unwell in heart failure. Case summary A 47-year-old male presented with a subacute onset of fever, night sweats, weight loss, dyspnoea, and peripheral oedema. On clinical examination typical features of infective endocarditis, heart failure, and aortic regurgitation were found. The patient had no conventional risk factors for infective endocarditis but was a dog owner. Transthoracic echocardiography revealed vegetations on the right coronary and non-coronary cusps of the aortic valve causing severe eccentric aortic regurgitation and left ventricular dilatation. Initial blood cultures taken prior to the initiation of antimicrobial therapy showed no growth. The patient underwent aortic valve and root replacement and a 16S ribosomal RNA polymerase chain reaction (16S rRNA PCR) of the resected aortic valve tissue, using the additional primer set 785F/1175R targeting the V5–7 region of 16S rRNA, identified C. canimorsus. The patient was treated post-operatively with a 6-week course of meropenem and made a good recovery. Discussion Suspicion of C. canimorsus causing infective endocarditis should be considered in culture-negative infective endocarditis in individuals who have close contact with dogs or cats. Those who are immunocompetent can be susceptible to this infection and so this diagnosis should not be disregarded in healthy individuals. A 16S rRNA PCR can help identify this bacterium and should be used early in cases of culture-negative infective endocarditis.
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Affiliation(s)
- Anita Sri
- Department of Cardiology, Buckinghamshire NHS Foundation Trust, Queen Alexandra Road, Wycombe, Buckinghamshire HP11 2TT, UK
| | - Edward Droscher
- Department of Cardiology, Buckinghamshire NHS Foundation Trust, Queen Alexandra Road, Wycombe, Buckinghamshire HP11 2TT, UK
| | - Rodney De Palma
- Department of Cardiology, Buckinghamshire NHS Foundation Trust, Queen Alexandra Road, Wycombe, Buckinghamshire HP11 2TT, UK
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18
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Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit. J Infect 2021; 83:167-174. [PMID: 34146598 DOI: 10.1016/j.jinf.2021.06.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/16/2023]
Abstract
OBJECTIVES Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU). METHODS Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing. RESULTS Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%). CONCLUSIONS This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.
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19
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Lenart M, Simoniti M, Strašek-Smrdel K, Špik VC, Selič-Kurinčič T, Avšič-Županc T. Case report: first symptomatic Candidatus Neoehrlichia mikurensis infection in Slovenia. BMC Infect Dis 2021; 21:579. [PMID: 34130635 PMCID: PMC8207769 DOI: 10.1186/s12879-021-06297-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/09/2021] [Indexed: 11/29/2022] Open
Abstract
Background Candidatus Neoehrlichia mikurensis (CNM) is an emerging tick-born pathogen and usually causes symptomatic infection only in immunocompromised patients. Apart from one described case found in the literature where cultivation was successful, all cases so far were diagnosed by using broad-range 16S rDNA PCR. Case presentation Our patient presented with a prolonged febrile state of unknown origin. Clinical presentation, extensive medical workup and classic microbiologic testing were non-conclusive. Several infectious agents and other causes for the febrile state were excluded. In the end, a broad-range 16S rDNA PCR was to be performed to confirm the diagnosis of CNM infection. Treatment was successful with doxycycline. Conclusions Due to the obscurity of the pathogen, diagnostic workup in CNM is prolonged and challenging. More awareness is need about this emerging infectious disease in countries with high prevalence of tick-borne diseases as standard microbiological methods are not successful in confirming the diagnosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06297-z.
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Affiliation(s)
- Mitja Lenart
- Department of Infectious diseases, General Hospital Celje, Oblakova ulica 5, 3000, Celje, Slovenia.
| | - Miha Simoniti
- Department of Infectious diseases, General Hospital Celje, Oblakova ulica 5, 3000, Celje, Slovenia
| | - Katja Strašek-Smrdel
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Vesna Cvitković Špik
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
| | - Tanja Selič-Kurinčič
- Department of Infectious diseases, General Hospital Celje, Oblakova ulica 5, 3000, Celje, Slovenia
| | - Tatjana Avšič-Županc
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Zaloška cesta 4, Ljubljana, 1000, Slovenia
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20
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Malczynski M, Zhu A, Zembower T, Qi C. Diagnostic performance of Ion 16S metagenomics kit and Ion reporter metagenomics workflow for bacterial pathogen detection in culture-negative clinical specimens from sterile sources. Diagn Microbiol Infect Dis 2021; 101:115451. [PMID: 34237647 DOI: 10.1016/j.diagmicrobio.2021.115451] [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: 02/09/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 12/17/2022]
Abstract
PCR-based deep sequencing of 16S rRNA gene allows for detection of a wide array of bacterial pathogens in culture-negative specimens. Ion 16S metagenomics kit and Ion Reporter metagenomics workflow (Ion 16S mNGS) provides an end-to-end solution with integrated workflow. Ninety-eight clinical samples with the diagnosis generated with 16S rRNA gene PCR/chain termination (Sanger) sequencing (16S CS) was used to assess the performance of Ion 16S mNGS. Compared to species level detection of 16S CS, the Ion 16S mNGS had 88% sensitivity and 76% specificity. When accounting for genus level of detection, the Ion 16S mNGS had 100% sensitivity. Notably, Ion 16S mNGS generated diagnosis in 13% of 16S CS and culture-negative samples. In addition, Ion 16S mNGS had the advantage of detecting more than 1 pathogen in 16S CS positive samples. We showed that the workflow had high reproducibility.
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Affiliation(s)
- Michael Malczynski
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA
| | - Alex Zhu
- Northwestern University, Evanston, IL, USA
| | - Teresa Zembower
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Clinical Microbiology Laboratory, Department of Pathology, Northwestern Memorial Hospital, Chicago, IL, USA; Northwestern University, Evanston, IL, USA; Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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Abstract
Pleural infections cause major morbidity and mortality, particularly amongst paediatric and elderly populations. The aetiology is broad, but pleural culture fails to yield a causative pathogen in approximately 40 % of cases. Alternative pathogen identification methods are therefore required. The aim of the study was to investigate the yield from and impact on patient care when performing 16S rRNA PCR on culture-negative pleural fluid specimens and to determine whether any individual laboratory parameters were associated with a positive 16S rRNA PCR result. We conducted a study on 90 patients with suspected pleural infection, who had a culture-negative pleural fluid specimen, which underwent 16S rRNA PCR analysis between August 2017 and June 2019. This study was undertaken at a large NHS Trust in London, UK. Thirty-one per cent of culture-negative pleural fluid specimens tested by 16S rRNA PCR yielded a positive PCR result. Our data demonstrated that 16S rRNA PCR detected a significantly higher proportion of Streptococcus pneumoniae (P<0.0001) and fastidious, slow-growing and anaerobic pathogens (P=0.0025) compared with culture-based methods. Of the 25 16S rRNA PCR results that were positive for a causative pathogen, 76 % had a direct impact on clinical management. No single laboratory variable was found to be associated with a positive 16S rRNA PCR result. The findings from our real-world evaluation highlight the importance of 16S rRNA PCR in confirming pleural infection when the aetiology is unknown, and its direct, positive impact on clinical management.
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Affiliation(s)
- Temi Lampejo
- Division of Infection, Barts Health NHS Trust, London, UK
| | - Holly Ciesielczuk
- Queen Mary's College, University of London, London, UK
- Division of Infection, Barts Health NHS Trust, London, UK
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22
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Ahmed W, Dewar S, Williams R, Stansby G, Harris K, Weiand D. Lawsonella clevelandensis is a rare cause of infected chronic contained rupture of abdominal aortic aneurysm. Access Microbiol 2021; 3:acmi000183. [PMID: 33997614 PMCID: PMC8115980 DOI: 10.1099/acmi.0.000183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/09/2020] [Indexed: 11/18/2022] Open
Abstract
Lawsonella clevelandensis is an anaerobic, partially acid-fast, Gram-positive bacillus associated with abscess formation. We present the case of a 70-year-old male with chronic contained rupture of abdominal aortic aneurysm (CCR-AAA) complicated by intra-abdominal abscess formation. An abdominal computed tomography scan revealed a rim-enhancing retroperitoneal collection tracking into the subcutaneous layer of the left flank and buttock, suggestive of CCR-AAA with infected haematoma. He underwent ultrasound-guided needle aspiration of the intra-abdominal collection. Conventional culture techniques failed to isolate L. clevelandensis, and the diagnosis was only confirmed by means of 16S rRNA PCR. The patient underwent branched endovascular repair of his aneurysm, and was commenced on treatment with co-amoxiclav, resulting in significant reduction in the size of the infected collection. This is only the second reported case of infection with L. clevelandensis in the UK, and the first reported case of this organism causing infected CCR-AAA.
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Affiliation(s)
- Wissam Ahmed
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Simon Dewar
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Robin Williams
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Gerard Stansby
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
| | - Kathryn Harris
- Great Ormond Street Hospital, Great Ormond St., Holborn, London WC1N 3JH, UK
| | - Daniel Weiand
- Freeman Hospital, Freeman Rd, High Heaton, Newcastle upon Tyne NE7 7DN, UK
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23
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Nadrah K, Biškup UG, Špik VC, Premru MM, Šoba B. Ignatzschineria larvae Bacteremia Following Lucilia sp. Myiasis in an Irregular Migrant: A Case Report. THE KOREAN JOURNAL OF PARASITOLOGY 2021; 59:159-165. [PMID: 33951772 PMCID: PMC8106986 DOI: 10.3347/kjp.2021.59.2.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/23/2021] [Indexed: 11/23/2022]
Abstract
Bacteremia induced by wound myiasis is uncommon and therefore rarely suspected by clinicians when treating patients with neglected wounds. We present a case of Ignatzschineria larvae bacteremia as a complication of Lucilia sp. maggot wound myiasis in a young male migrant. This is the first reported human case of Ignatzschineria bacteremia in Slovenia and one of the 2 described in the literature where the fly larvae infesting the wounds of the patient with Ignatzschineria bacteremia were not only suspected to be Lucilia sp. but also entomologically identified.
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Affiliation(s)
- Kristina Nadrah
- Department of Infectious Diseases, University Medical Centre Ljubljana, Japljeva 2, 1000 Ljubljana, Slovenia
| | - Urška Glinšek Biškup
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Vesna Cvitković Špik
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Manica Müller Premru
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Barbara Šoba
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
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24
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Zhang J, Hu DK, Gao CY, Shen WW, Luo XH, Yu J, Li XY, Jiang XY, Zhu WS, Chen WQ. Homology analysis of 51 penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China. J Int Med Res 2021; 48:300060520919061. [PMID: 32529912 PMCID: PMC7294386 DOI: 10.1177/0300060520919061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objective To investigate drug resistance features and homology among penicillin-intermediate Streptococcus pneumoniae isolates from Wenzhou City, China. Methods Fifty-one penicillin-intermediate S. pneumoniae isolates were obtained from respiratory samples of infants and children hospitalized with lung infections. An antimicrobial susceptibility test was used to assess drug resistance. Polymerase chain reaction and agarose gel electrophoresis were used to identify S. pneumoniae isolates and pulsed-field gel electrophoresis (PFGE) was used to analyze molecular subtypes. Hierarchical cluster analysis of PFGE fingerprints was used to compare genetic diversity and relatedness of S. pneumoniae isolates. The Quellung test was used for serotyping. Results Fifty-one penicillin-intermediate S. pneumoniae isolates showed evidence of multi-drug resistance and polyclonal origins. The isolates were classified into 25 subtypes through hierarchical cluster analysis of PFGE fingerprints. Three of these subtypes formed a supertype (15/51, 16/51 and 8/51 isolates), while the remaining subtypes occurred sporadically (12/51 isolates). Conclusions Transmission of penicillin-intermediate S. pneumoniae is mostly vertical and to a lesser extent horizontal. Effective prevention strategies, including respiratory tract management and contact isolation, are essential to control nosocomial S. pneumoniae infection. Once susceptibility is confirmed, vancomycin, high-dose penicillin or third-generation cephalosporins (cefotaxime and ceftriaxone) may be used to treat penicillin-intermediate S. pneumoniae.
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Affiliation(s)
- Jin Zhang
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Da-Kang Hu
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Chun-Yan Gao
- Department of Laboratory Medicine, Tangshan Maternal and Child Health Hospital, Tangshan, Hebei Province, China
| | - Wei-Wei Shen
- Department of Microbiology, Taizhou Center for Disease Control and Prevention, Taizhou, Zhejiang Province, China
| | - Xin-Hua Luo
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiang-Yang Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xin-Yu Jiang
- Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wu-Shuang Zhu
- Department of Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, Zhejiang Province, China
| | - Wei-Qing Chen
- Department of Laboratory Medicine, Taizhou Women and Children's Hospital, Taizhou, Zhejiang Province, China
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25
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Tranberg A, Samuelsson C, Klarin B. Disturbance in the oropharyngeal microbiota in relation to antibiotic and proton pump inhibitor medication and length of hospital stay. APMIS 2021; 129:14-22. [PMID: 32981186 PMCID: PMC7756849 DOI: 10.1111/apm.13087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/21/2020] [Indexed: 12/30/2022]
Abstract
The aim of this study was to investigate the appearance of a disturbed oropharyngeal microbiota during hospitalization and explore the patient characteristics that maybe associated with such a disturbance. Oropharyngeal swabs were collected from 134 patients at hospital admission and every 3-4 days thereafter. The samples were cultivated to determine the presence of a disturbed microbiota, which, in turn, was subcategorized into respiratory tract pathogens, gut microbiota and yeast species. Demographics, medical history data and hospitalization events were compared. The percentage of disturbed oropharyngeal microbiota increased significantly with length of stay (LOS). Receiving antibiotic treatment during the hospitalization tended to be associated with a disturbed microbiota (OR 2.75 [0.99-7.60]). Proton pump inhibitor (PPI) medication and receiving antibiotics before hospitalization were associated with the development of a disturbed oropharyngeal microbiota with colonization of gut pathogens (OR 3.49 [1.19-10.2] and OR 4.52 [1.13-18.1], respectively), while acute hospital admission was associated with a lower risk of colonization of gut pathogens (OR: 0.23 [0.074-0.72]). The risk of developing a disturbed oropharyngeal microbiota increased with LOS in hospitalized patients. PPI medication and receiving antibiotics before hospitalization were independent risk factors for developing oropharyngeal colonization of gut pathogens.
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Affiliation(s)
- Anna Tranberg
- Division of Intensive and Perioperative CareSkane University HospitalLundSweden
| | - Carolina Samuelsson
- Division of Intensive and Perioperative CareSkane University HospitalLundSweden
| | - Bengt Klarin
- Division of Intensive and Perioperative CareSkane University HospitalLundSweden
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26
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Abstract
Anatomic pathology is an important resource for detection and exclusion of infectious diseases in tissue specimens. Detection of a microorganism (i.e. bacteria, fungi, parasite) in tissue sections is frequently the beginning of a work-up and occasionally sufficient for definitive microbiologic identification. Close correlation with cultures and ancillary testing in the microbiology laboratory is of paramount importance in arriving at a diagnosis and identify with certitude causative pathogen(s). This review will discuss the adequacy and limitations of histopathology in the diagnosis of infectious diseases, describe potential pitfalls, and discuss the appropriate use of molecular diagnostics in formalin-fixed, paraffin embedded tissues.
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Affiliation(s)
- Alvaro C Laga
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Amory-3, Boston, MA 02115, USA.
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27
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 158] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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28
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Molecular Detection and Identification of Bacteria in Urine Samples of Asymptomatic and Symptomatic Pregnant Women by 16S rRNA Gene Sequencing. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.101136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives: The purpose of this study was to identify bacteria in urine samples of pregnant women of asymptomatic and symptomatic women by 16S rRNA gene sequencing. This study aims to identify different strains of microbes causing urinary tract infection (UTI). Methods: In the semi-quantitative culture technique, bacterial isolates such as Escherichia coli, Klebsiella, Pseudomonas, Staphylococcus, Coagulase-negative Staphylococcus, and Proteus were subjected to 16S rRNA gene sequencing followed by BLAST analysis and phylogenetic tree formation. The 16S rRNA gene sequencing was carried out to identify the specific strains of bacteria causing UTI. Results: According to the BLAST analysis, sample 1 revealed a 100% similarity to E. coli strain U5/41. Likewise, samples 2, 3, 4, 5 and 6 exhibited a 100% similarity to Klebsiella aerogenes strain F26, Pseudomonas entomophila strain 2014, Staphylococcus aureus strain NCTC13616, Staphylococcus saprophyticus strain FDAARGOS_355, Proteus mirabilis strain NCTC 11938, respectively. Conclusions: Six bacterial isolates were analyzed by 16S RNA gene sequencing followed by the construction of a phylogenetic tree construction up to the species level. This method was a valuable tool for cost-effective and accurate diagnosis of an array of uropathogens in both asymptomatic and symptomatic pregnant women.
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29
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Aggarwal D, Kanitkar T, Narouz M, Azadian BS, Moore LSP, Mughal N. Clinical utility and cost-effectiveness of bacterial 16S rRNA and targeted PCR based diagnostic testing in a UK microbiology laboratory network. Sci Rep 2020; 10:7965. [PMID: 32409679 PMCID: PMC7224368 DOI: 10.1038/s41598-020-64739-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/26/2020] [Indexed: 11/09/2022] Open
Abstract
16S ribosomal-ribonucleic acid polymerase chain reaction (PCR) and targeted PCR aid microbiological diagnosis in culture-negative clinical samples. Despite routine clinical use, there remains a paucity of data on their effectiveness across a variety of clinical sample types, and cost-effectiveness. In this 4 year multicentre retrospective observational study, all clinical samples referred for 16S PCR and/or targeted PCR from a laboratory network serving seven London hospitals were identified. Laboratory, clinical, prescribing, and economic variables were analysed. 78/607 samples were 16S PCR positive; pus samples were most frequently positive (29/84; p < 0.0001), and CSF least (8/149; p = 0.003). 210/607 samples had targeted PCR (361 targets requested across 23 organisms) with 43/361 positive; respiratory samples (13/37; p = 0.01) had the highest detection rate. Molecular diagnostics provided a supportive microbiological diagnosis for 21 patients and a new diagnosis for 58. 14/91 patients with prescribing information available and a positive PCR result had antimicrobial de-escalation. For culture-negative samples, mean cost-per-positive 16S PCR result was £568.37 and £292.84 for targeted PCR, equating to £4041.76 and £1506.03 respectively for one prescription change. 16S PCR is more expensive than targeted PCR, with both assisting in microbiological diagnosis but uncommonly enabling antimicrobial change. Rigorous referral pathways for molecular tests may result in significant fiscal savings.
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Affiliation(s)
- Dinesh Aggarwal
- Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.,North West London Pathology, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Tanmay Kanitkar
- Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK
| | - Michael Narouz
- Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Berge S Azadian
- Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.,Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Luke S P Moore
- Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK. .,North West London Pathology, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK. .,Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
| | - Nabeela Mughal
- Chelsea and Westminster NHS Foundation Trust, 369 Fulham Road, London, SW10 9NH, UK.,North West London Pathology, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK.,Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
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30
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Yoshimura K, Morotomi N, Fukuda K, Kubo T, Taniguchi H. Changes of intravaginal microbiota and inflammation after self-replacement ring pessary therapy compared to continuous ring pessary usage for pelvic organ prolapse. J Obstet Gynaecol Res 2020; 46:931-938. [PMID: 32189434 DOI: 10.1111/jog.14242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/04/2020] [Indexed: 11/29/2022]
Abstract
AIM Continuous usage of a ring pessary for pelvic organ prolapse may cause a disturbance of intravaginal microbiota and intravaginal mucosal damage. To avoid the side effects of continuous ring pessary therapy, daily self-replacement of the ring pessary is recommended. The purpose of this study is to evaluate the outcomes of self-replacement versus continuous ring usage, by analysing clinical findings and intravaginal microbiota. METHODS Thirty seven patients who managed self-replacement ring pessary therapy and 13 patients with continuous ring pessary therapy participated in this study. The clinical symptoms were checked at 1 month after the initial ring pessary insertion. The changes in the intravaginal microbiota were evaluated by conventional methods, i.e. pH in the vagina, Lactobacillary grade, Nugent score, inflammatory cell counts, and culture-based bacterial detection methods. In addition, our clone library method using 16S rRNA sequencing of vaginal fluid was performed. RESULTS Patients were divided into four groups: self-replacement pre/post-menopause and continuous and pre/post-menopause. Five patients of the self-replacement group (n = 37) and all patients of the continuous use group (n = 13) complained of increased discharge. However, both the conventional methods and the clone library method revealed that the number of the self-replacement group patients who had abnormal intravaginal microbiota were not significantly different from that of the continuous use group. CONCLUSION Daily self-replacement ring pessary therapy prevented adverse clinical symptoms. However, abnormal intravaginal microbiota was frequently observed during self-replacement of ring pessary therapy as with continuous usage. Regardless, pelvic examinations should be performed routinely.
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Affiliation(s)
- Kazuaki Yoshimura
- Department of Obstetrics and Gynecology, Wakamatsu Hospital of University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Nobuo Morotomi
- Department of Microbiology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Tatsuhiko Kubo
- Department of Public Health, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Hatsumi Taniguchi
- Department of Microbiology, University of Occupational and Environmental Health, Kitakyushu, Japan
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31
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Saje A, Velnar T, Smrke B, Spazzapan P, Keše D, Kobal B, Beović B. Ureaplasma parvum ventriculitis related to surgery and ventricular peritoneal drainage. J Infect Chemother 2020; 26:513-515. [PMID: 32007385 DOI: 10.1016/j.jiac.2019.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/17/2019] [Accepted: 12/20/2019] [Indexed: 11/29/2022]
Abstract
Ureaplasma spp. usually causes genitourinary infections; few reports in the literature describe extragenital infections, usually in immunocompromised patients. We present a case of Ureaplasma parvum ventriculitis in an immunocompetent patient related to ventriculoperitoneal drainage and surgery. Ureaplasma parvum was detected with broad range 16S rRNA PCR and cultured on A8 agar.
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Affiliation(s)
- Andreja Saje
- Department of Infectious Diseases, University Medical Centre Ljubljana, Slovenia.
| | - Tomaž Velnar
- Department of Neurosurgery, University Medical Centre Ljubljana, Slovenia
| | - Barbara Smrke
- Department of Neurosurgery, University Medical Centre Ljubljana, Slovenia
| | - Peter Spazzapan
- Department of Neurosurgery, University Medical Centre Ljubljana, Slovenia
| | - Darja Keše
- Institute of Microbiology and Immunology Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Borut Kobal
- Department of Gynaecology, University Medical Centre Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Slovenia
| | - Bojana Beović
- Department of Infectious Diseases, University Medical Centre Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Slovenia
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32
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Nagrodzki J, Sharrocks KE, Wong VK, Carmichael AJ. A mycotic aneurysm related to Salmonella Rissen infection: a case report. BMC Infect Dis 2020; 20:97. [PMID: 32005105 PMCID: PMC6995202 DOI: 10.1186/s12879-020-4819-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/23/2020] [Indexed: 11/10/2022] Open
Abstract
Background Salmonella species commonly causes infection in humans and on occasion leads to serious complications, such as mycotic aneurysms. Here, we present the first case reported of a patient with a mycotic aneurysm likely secondary to Salmonella Rissen infection. Case presentation The patient presented with 4 weeks of lower back pain, chills and a single episode of diarrhoea 2 months prior during a 14-day trip to Hong Kong and Taiwan. Magnetic resonance imaging revealed an aneurysmal left internal iliac artery with adjacent left iliacus rim-enhancing collection. A stool culture was positive for Salmonella Rissen ST 469 EBG 66 on whole genome sequencing. The patient underwent an emergency bifurcated graft of his internal iliac aneurysm and was successfully treated with appropriate antibiotics. Conclusions This case highlights the importance of considering the diagnosis of a mycotic aneurysm in an unusual presentation of back pain with features of infection.
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Affiliation(s)
- Jakub Nagrodzki
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK. .,Trinty College, University of Cambridge, Cambridge, CB2 1TQ, UK.
| | | | - Vanessa K Wong
- Infectious Diseases Department, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.,Microbiology Department, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Andrew J Carmichael
- Infectious Diseases Department, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
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33
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Oeser C, Pond M, Butcher P, Bedford Russell A, Henneke P, Laing K, Planche T, Heath PT, Harris K. PCR for the detection of pathogens in neonatal early onset sepsis. PLoS One 2020; 15:e0226817. [PMID: 31978082 PMCID: PMC6980546 DOI: 10.1371/journal.pone.0226817] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/05/2019] [Indexed: 11/21/2022] Open
Abstract
Background A large proportion of neonates are treated for presumed bacterial sepsis with broad spectrum antibiotics even though their blood cultures subsequently show no growth. This study aimed to investigate PCR-based methods to identify pathogens not detected by conventional culture. Methods Whole blood samples of 208 neonates with suspected early onset sepsis were tested using a panel of multiplexed bacterial PCRs targeting Streptococcus pneumoniae, Streptococcus agalactiae (GBS), Staphylococcus aureus, Streptococcus pyogenes (GAS), Enterobacteriaceae, Enterococcus faecalis, Enterococcus faecium, Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis and Mycoplasma genitalium, a 16S rRNA gene broad-range PCR and a multiplexed PCR for Candida spp. Results Two-hundred and eight samples were processed. In five of those samples, organisms were detected by conventional culture; all of those were also identified by PCR. PCR detected bacteria in 91 (45%) of the 203 samples that did not show bacterial growth in culture. S. aureus, Enterobacteriaceae and S. pneumoniae were the most frequently detected pathogens. A higher bacterial load detected by PCR was correlated positively with the number of clinical signs at presentation. Conclusion Real-time PCR has the potential to be a valuable additional tool for the diagnosis of neonatal sepsis.
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Affiliation(s)
- Clarissa Oeser
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
- * E-mail:
| | - Marcus Pond
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Philip Butcher
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | | | - Philipp Henneke
- Pediatric Infectious Disease and Rheumatology, University Medical Center Freiburg, Freiburg, Germany
| | - Ken Laing
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Timothy Planche
- Molecular Microbiology, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Paul T. Heath
- Paediatric Infectious Diseases, Institute of Infection and Immunity, St George’s, University of London, London, United Kingdom
| | - Kathryn Harris
- Microbiology, Virology and Infection Control, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
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34
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Sune D, Rydberg H, Augustinsson ÅN, Serrander L, Jungeström MB. Optimization of 16S rRNA gene analysis for use in the diagnostic clinical microbiology service. J Microbiol Methods 2020; 170:105854. [PMID: 31982454 DOI: 10.1016/j.mimet.2020.105854] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/01/2022]
Abstract
Broad-range amplification and sequencing of the 16S rRNA gene, directly from clinical samples, is a method that potentially allows detection of any cultivable or non-cultivable bacteria. However, the method is prone to false positive results due to PCR contamination. Another concern is the human DNA abundance compared to bacterial DNA in samples from sterile sites. Those factors may decrease the sensitivity and specificity of the assay and can complicate the analysis and interpretation of the results. The objective of this prospective study was to try to avoid the most common pitfalls, mentioned above, and develop a molecular 16S assay with a high clinical sensitivity and specificity. Fifty-six consecutive tissue samples from patients with suspected deep infections were extracted by 3 different DNA-extraction methods; two based on a principle of bacterial DNA enrichment, and one conventional DNA extraction method. We compared three primer pairs, including both conventional and DPO principle, targeting different variable regions of the 16S rRNA gene. Results from routine tissue culture were used as reference. Clinical data was recorded from patient charts and analyzed in parallel. Of a total of 56 samples, collected from 39 patients, 70% (39 samples) were assessed as true infections by analysis of clinical data. Bacterial enrichment extraction increased sensitivity from 54% to 72%. The 2 sets of primer pairs defining region V1-V3 and V3-V4, showed similar sensitivity, but DPO-primers resulted in better specificity, i.e. less contaminations. The primer pairs covering V1-V8 show significantly lower sensitivity (p < .001) than V1-V3 and V3-V4. Optimizing extraction protocols and choice of primers can increase the sensitivity and specificity of a molecular 16S-analysis, rendering a valuable complement to tissue culture.
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Affiliation(s)
- Dan Sune
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Sweden.
| | - Helene Rydberg
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - Åsa Nilsdotter Augustinsson
- Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Sweden.
| | - Lena Serrander
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
| | - Malin Bergman Jungeström
- Division of Clinical Microbiology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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Salem A, Azeez S, Stirrup J, Lawrence D, Ruparelia N. Streptococcus intermedius masquerading as fungal infective endocarditis. Br J Hosp Med (Lond) 2019; 80:674-675. [PMID: 31707889 DOI: 10.12968/hmed.2019.80.11.674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Infective endocarditis remains an important clinical entity with an incidence of 1.7–10/100 000 person years (Marks et al, 2015). Despite improvements in health care, it still results in significant morbidity and in-hospital mortality approaches 16% (Marks et al, 2015). There are likely multiple causes including late diagnosis, poor response to therapy and the challenges in identifying the causative pathogen and instigating the correct treatment. This is particularly the case for causative organisms that are difficult to culture or identify using routine laboratory methods.
An example of this is Streptococcus intermedius, which belongs to the S. milleri group along with other two species (S. anginosus group and S. constellatus). It is a commensal organism that can turn into an opportunistic pathogen (Whiley et al, 1992). It is a rare cause of infective endocarditis and may initially present with abscesses in the liver, spleen or brain which may mimic fungal infection (Woo et al, 2004; Rashid et al, 2007; Tran et al, 2008). Difficulty in identifying this organism has led to the development of molecular testing to aid diagnosis. To the authors' knowledge, there are very few cases in the literature of infective endocarditis caused by S. intermedius that have been confirmed using 16S polymerase chain reaction (Woo et al, 2004). This article describes a patient presenting with S. intermedius infective endocarditis which was diagnosed using this method.
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Affiliation(s)
- A Salem
- Specialist Registrar in Cardiology, Department of Cardiology, Milton Keynes University Hospital, Milton Keynes MK9 1LA
| | - S Azeez
- Specialist Registrar in Cardiology, Department of Cardiology, Royal Berkshire Hospital, Reading
| | - J Stirrup
- Consultant Cardiologist, Department of Cardiology, Royal Berkshire Hospital, Reading
| | - D Lawrence
- Consultant Cardiothoracic Surgeon, Department of Cardiothoracic Surgery, St Bartholomew's Hospital, London
| | - N Ruparelia
- Consultant Cardiologist, Department of Cardiology, Royal Berkshire Hospital, Reading
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Bishay M, Simchowitz V, Harris K, Macdonald S, De Coppi P, Klein N, Eaton S, Pierro A. The Effect of Glutamine Supplementation on Microbial Invasion in Surgical Infants Requiring Parenteral Nutrition: Results of a Randomized Controlled Trial. JPEN J Parenter Enteral Nutr 2019; 44:80-91. [PMID: 31502272 DOI: 10.1002/jpen.1700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/04/2019] [Accepted: 08/17/2019] [Indexed: 11/11/2022]
Abstract
BACKGROUND To determine whether parenteral plus enteral glutamine supplementation influences microbial invasion in surgical infants who require parenteral nutrition (PN). METHODS An prospective double-blind randomized controlled trial studying surgical infants receiving PN for at least 5 days for congenital or acquired intestinal anomalies (2009-2012) was used. Infants were randomized to receive either glutamine supplementation (parenteral plus enteral; total 400 mg/kg/d) or isonitrogenous control. The primary end point was microbial invasion evaluated after 5 days of supplementation and defined as: (i) positive conventional blood culture, (ii) evidence of microbial DNA in blood (polymerase chain reaction), (iii) plasma endotoxin level ≥50 pg/mL, or (iv) plasma level of lipopolysaccharide binding protein ≥50 ng/mL. Data are given as median (range) and compared by logistic regression. RESULTS Sixty infants were randomized and reached the primary end point. Twenty-five patients had intestinal obstruction, 19 had abdominal wall defects, and 13 had necrotizing enterocolitis. Thirty-six infants showed evidence of microbial invasion during the study, and 17 of these were not detected by conventional blood culture. There was no significant difference between the 2 groups in the primary outcome; evidence of microbial invasion after 5 days was found in 9/31 (control group) and 8/29 (glutamine group) (odds ratio 0.83 [0.24-2.86; P = 0.77]). CONCLUSION More than half of surgical infants requiring PN showed evidence of microbial invasion. Approximately half of this was not detectable by conventional blood cultures. Parenteral plus enteral glutamine supplementation had no effect on incidence of microbial invasion.
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Affiliation(s)
- Mark Bishay
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Venetia Simchowitz
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Kathryn Harris
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Sarah Macdonald
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Paolo De Coppi
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nigel Klein
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Simon Eaton
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | - Agostino Pierro
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom.,Great Ormond Street Hospital for Children, London, United Kingdom
| | -
- University College of London Great Ormond Street Institute of Child Health, London, United Kingdom
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Identification of Potential Cerebrospinal Fluid Biomarkers To Discriminate between Infection and Sterile Inflammation in a Rat Model of Staphylococcus epidermidis Catheter Infection. Infect Immun 2019; 87:IAI.00311-19. [PMID: 31262978 PMCID: PMC6704599 DOI: 10.1128/iai.00311-19] [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: 04/19/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus epidermidis cerebrospinal fluid (CSF) shunt infection is a common complication of hydrocephalus treatment, creating grave neurological consequences for patients, especially when diagnosis is delayed. The current method of diagnosis relies on microbiological culture; however, awaiting culture results may cause treatment delays, or culture may fail to identify infection altogether, so newer methods are needed. Staphylococcus epidermidis cerebrospinal fluid (CSF) shunt infection is a common complication of hydrocephalus treatment, creating grave neurological consequences for patients, especially when diagnosis is delayed. The current method of diagnosis relies on microbiological culture; however, awaiting culture results may cause treatment delays, or culture may fail to identify infection altogether, so newer methods are needed. To investigate potential CSF biomarkers of S. epidermidis shunt infection, we developed a rat model allowing for serial CSF sampling. We found elevated levels of interleukin-10 (IL-10), IL-1β, chemokine ligand 2 (CCL2), and CCL3 in the CSF of animals implanted with S. epidermidis-infected catheters compared to sterile controls at day 1 postinfection. Along with increased chemokine and cytokine expression early in infection, neutrophil influx was significantly increased in the CSF of animals with infected catheters, suggesting that coupling leukocyte counts with inflammatory mediators may differentiate infection from sterile inflammation. Mass spectrometry analysis revealed that the CSF proteome in sterile animals was similar to that in infected animals at day 1; however, by day 5 postinfection, there was an increase in the number of differently expressed proteins in the CSF of infected compared to sterile groups. The expansion of the proteome at day 5 postinfection was interesting, as bacterial burdens began to decline by this point, yet the CSF proteome data indicated that the host response remained active, especially with regard to the complement cascade. Collectively, these results provide potential biomarkers to distinguish S. epidermidis infection from sterile postoperative inflammation.
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Broad-range PCR Application in a Large Academic Pediatric Center: Clinical Value and Challenges in Diagnosis of Infectious Diseases. Pediatr Infect Dis J 2019; 38:786-790. [PMID: 30920482 DOI: 10.1097/inf.0000000000002308] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Broad-range polymerase chain reaction (BR-PCR) detects infectious pathogens from clinical specimens using targets for bacteria (16S rRNA), fungi (28S rDNA), and mycobacteria (fluorescence resonance energy transfer and heat shock protein 65 gene) with reported diagnostic sensitivity and specificity ranging from 43% to 100% and 100%, respectively. We describe our experience when applying BR-PCR to clinical samples submitted for conventional infectious disease testing [conventional testing (CT)] from pediatric patients with concern for infection. METHODS Retrospective analysis of clinical samples obtained from Nationwide Children's Hospital microbiology laboratory from January 2011 to December 2014 and sent for BR-PCR. Medical record review collected data on patient characteristics, clinical manifestations, laboratory results and antimicrobials prescribed, and a determination of clinical value of BR-PCR was assigned. RESULTS There were 247 clinical samples from 163 patients identified; 71 (44%) patients were immunocompromised and 192 (78%) samples reflected pretreatment with antimicrobials. A clinically significant putative organism was identified for 59 samples (24%) between all diagnostic modalities. Conventional testing identified organisms in 41 (17%) samples, 17 of which were corroborated by BR-PCR. Broad-range polymerase chain reaction identified an organism in an additional 18 samples with negative CT results and was considered to provide additional important clinical information. Broad-range polymerase chain reaction detected a bacterial or fungal organism more frequently from tissue samples than from bronchoalveolar lavage or other fluid samples (P = 0.0096, χ). CONCLUSIONS In our cohort, BR-PCR was an important adjunctive diagnostic in identifying bacteria and fungi in complex clinical situations. Additional data are needed to define the optimal clinical circumstances and specimen type in which BR-PCR can provide the highest diagnostic yield.
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Genetic Diversity of Canine Babesia Species Prevalent in Pet Dogs of Punjab, Pakistan. Animals (Basel) 2019; 9:ani9070439. [PMID: 31337004 PMCID: PMC6680441 DOI: 10.3390/ani9070439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Babesiosis is caused by the intra-erythrocytic Babesia species in dogs. Different species are reported worldwide. The present study was conducted on pet dogs of two districts of Punjab, Pakistan, including Lahore and Narowal. Conventional microscopic and molecular tests, including conventional and nested PCR, were used for identification of diseased dogs and prevalent species. About 42% of dogs were tested positive for babesiosis and only two species including Babesia canis and gibsoni were prevalent. Abstract Canine babesiosis is a serious threat to dogs’ health worldwide, caused by the intra-erythrocytic Babesia species. The present study was carried out in pet dogs presented at three clinics of Lahore and one of Narowal in Punjab, Pakistan. Two hundred blood samples (50 from each clinic) were collected and screened by microscopy for Babesia spp. Out of 200 samples, 84 (42%) were found to be positive for babesiosis. The highest number of positive cases (50%) was recorded in dogs at Narowal clinic. Non-significant variation (p > 0.05) was observed in the prevalence of babesiosis in dogs in relation to sex and age. Positive samples were further confirmed by a polymerase chain reaction using 18S-rRNA genus-specific and species-specific primers. Amplicons were further analyzed by nucleotide sequencing for genetic diversity. Babesia canis and gibsoni were confirmed by genome sequencing in all diseased dogs. These isolates closely resembled each other, but differed from previous reported strains. In conclusion, pet dogs suffering from babesiosis were infected with B. canis and gibsoni, while in other countries, other Babesia species are also prevalent.
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Emara K, Aiyer A, Rogero R. What Is the Role of Molecular Techniques for Detection of Pathogen Deoxyribonucleic Acid (DNA) (Polymerase Chain Reaction [PCR] or Next-Generation Sequencing) in Patients With Infected Total Ankle Arthroplasty (TAA)? Foot Ankle Int 2019; 40:29S-31S. [PMID: 31322966 DOI: 10.1177/1071100719859578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RECOMMENDATION Molecular techniques, particularly next-generation sequencing and the Ibis T5000 technology, have the potential to be used as an important adjunct in the diagnosis of bacterial infection following total ankle arthroplasty (TAA), although sufficient clinical evidence is lacking. LEVEL OF EVIDENCE Limited. DELEGATE VOTE Agree: 100%, Disagree: 0%, Abstain: 0% (Unanimous, Strongest Consensus).
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Affiliation(s)
| | - Amiethab Aiyer
- 2 University of Miami/Miller School of Medicine, Miami, FL, USA
| | - Ryan Rogero
- 3 Rothman Orthopaedic Institute, Philadelphia, PA, USA
- 4 Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
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41
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Comparison of MALDI-TOF MS Biotyper and 16S rDNA sequencing for the identification of Pseudomonas species isolated from fish. Microb Pathog 2019; 132:313-318. [PMID: 30999019 DOI: 10.1016/j.micpath.2019.04.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/20/2022]
Abstract
Effective and reliable methods of identification of Pseudomonas species are important for the characterization of microorganisms. Freshwater ecosystems are an important source of Pseudomonas species, including those pathogenic to fish and humans. The aim of the present study was to compare the identification conducted with MALDI-TOF MS Biotyper and 16S rDNA sequencing of fish-borne Pseudomonas spp. Altogether, 13 different Pseudomonas spp. were isolated from freshwater fish. Phylogenetic analysis showed a clear taxonomic placement only for 13 out of 15 Pseudomonas isolates. Accordance of identification method was found only in 6 out of 15 isolates. The human pathogenic Pseudomonas spp. were not found in our study, indicating that the fish could be considered as safe for consumption. The present study revealed a high discriminatory power of the mass spectra investigation and 16S rDNA gene sequencing technology for the identification of Pseudomonas spp. associated with freshwater fish.
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42
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Glaser LJ, Montone KT. A Practical Guide to the Role of Ancillary Techniques in the Diagnosis of Infectious Agents in Fine Needle Aspiration Samples. Acta Cytol 2019; 64:81-91. [PMID: 30889574 DOI: 10.1159/000497076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/19/2019] [Indexed: 12/17/2022]
Abstract
Fine needle aspiration samples and small biopsies provide a minimally invasive diagnostic modality for mass lesions. When an infectious process is suspected based on initial evaluation, ancillary techniques can assist in making a specific diagnosis. Here we review the cytopathology that should prompt additional testing and review the availability and interpretation of special stains, immunohistochemistry, and in situ hybridization. In addition, this review addresses when special cultures may be necessary and the use of newer molecular techniques for pathogen identification.
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Affiliation(s)
- Laurel J Glaser
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen T Montone
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,
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Coiffier G, David C, Gauthier P, Le Bars H, Guggenbuhl P, Jolivet-Gougeon A, Albert JD. Broad-range 16 s rDNA PCR in synovial fluid does not improve the diagnostic performance of septic arthritis in native joints in adults: cross-sectional single-center study in 95 patients. Clin Rheumatol 2019; 38:1985-1992. [PMID: 30850963 DOI: 10.1007/s10067-019-04492-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/12/2019] [Accepted: 02/24/2019] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To evaluate the diagnostic performance of bacterial identification by broad-range polymerase chain reaction (PCR) of ribosomal DNA (rDNA) 16 s (16S rDNA PCR) for the diagnosis of septic arthritis on native joints. METHODS Patients with acute mono or oligoarthritis who underwent synovial fluid puncture and prospective follow-up allowing definitive diagnosis (septic arthritis, crystal related disease, chronic inflammatory arthritis, undifferentiated arthritis) were recruited in this single-center study. Systematic analysis of synovial fluid included leukocytes count, search for urate and pyrophosphate crystals with polarized light microscopy, direct bacteriological examination (gram staining), bacteriological culture, and 16S rDNA PCR. RESULTS Ninety-five patients were included, 34 of which (35.8%) had septic arthritis. Nineteen (20.0%) patients had received probabilistic antibiotic therapy prior to joint puncture. Gram + cocci infection accounted for 79.4% of septic arthritis, of which nearly half (47.1%) was caused by Staphylococcus aureus. Eight (23.5%) septic arthritis patients had a 16S rDNA PCR positive in the synovial fluid with an AUC of 0.618 (95% CI, 0.493-0.742), a sensitivity of 0.24 (95% CI, 0.12-0.40), and a specificity of 1.00 (95% CI 0.94-1.00). The diagnostic performance of 16S rDNA PCR was lower than that of direct examination (AUC at 0.691, CI 95%, 0.570-0.812), blood cultures (AUC at 0.727, CI 95%, 0.610-0.844), and culture (0.925, CI 95%, 0.856-0.994) for the diagnosis of septic arthritis. There was no difference in the positivity of 16S rDNA PCR according to previous exposure to antibiotics. CONCLUSIONS 16 s rDNA PCR in the synovial fluid does not improve the diagnostic performance of septic arthritis on native adult joints, particularly for Gram-positive cocci infections.
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Affiliation(s)
- G Coiffier
- Service de Rhumatologie, CHU Hôpital Sud, 16 boulevard de Bulgarie, 35203, Rennes, France.,Institut NUMECAN, INSERM U 1241, INRA U 1341, 35000, Rennes, France
| | - C David
- Service de Rhumatologie, CHU Hôpital Sud, 16 boulevard de Bulgarie, 35203, Rennes, France
| | - P Gauthier
- EA 1254 Microbiologie Université de Rennes 1, Laboratoire Bactériologie CHU Pontchaillou, 35000, Rennes, France
| | - H Le Bars
- EA 1254 Microbiologie Université de Rennes 1, Laboratoire Bactériologie CHU Pontchaillou, 35000, Rennes, France
| | - P Guggenbuhl
- Service de Rhumatologie, CHU Hôpital Sud, 16 boulevard de Bulgarie, 35203, Rennes, France.,Institut NUMECAN, INSERM U 1241, INRA U 1341, 35000, Rennes, France
| | - A Jolivet-Gougeon
- Institut NUMECAN, INSERM U 1241, INRA U 1341, 35000, Rennes, France.,EA 1254 Microbiologie Université de Rennes 1, Laboratoire Bactériologie CHU Pontchaillou, 35000, Rennes, France
| | - J D Albert
- Service de Rhumatologie, CHU Hôpital Sud, 16 boulevard de Bulgarie, 35203, Rennes, France. .,Institut NUMECAN, INSERM U 1241, INRA U 1341, 35000, Rennes, France.
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Amin M, Yousef pour S, Navidifar T. Detection of the major bacterial pathogens among children suffering from empyema in Ahvaz city, Iran. J Clin Lab Anal 2019; 33:e22855. [PMID: 30739335 PMCID: PMC6528561 DOI: 10.1002/jcla.22855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/12/2018] [Accepted: 12/19/2018] [Indexed: 11/07/2022] Open
Abstract
Introduction Empyema is one of the important causes of pediatric hospital admissions. Aim In this study, we had investigated the frequency rates of S aureus, S pneumoniae, H influenzae, and P aeruginosa using PCR and bacterial culture among children suffering from empyema in Ahvaz city, Iran. Methods This was a descriptive study conducted on the patients hospitalized in ICUs of two teaching Hospitals of Ahvaz, Iran, between March and September 2018 on 105 pleural fluid (PF) samples of the children less than 16 years of age with the diagnosis of empyema thoracis. These specimens were inoculated on the bacterial culture media and identified using biochemical characteristics. Then, the existence of the four pathogens mentioned above was evaluated using PCR method. Result In this study, these bacteria agents were identified in 81 (77.14%) and 30 (28.57%) cases using the PCR assay and bacterial culture, respectively. Moreover, the PCR assay identified the infectious agents in 51 (68%) of PFs where the culture method failed. S pneumoniae (63 cases) was recognized as the most common pathogen, followed by P aeruginosa(19 cases), S aureus(15 cases), and H influenzae (9 cases) using the bacterial culture and PCR. Co‐infections were detected in 21 samples (20%) using PCR and one sample using the bacterial culture (P aeruginosa and S pneumoniae). Conclusion In this study, we found the higher frequencies of these microorganisms using PCR than culture. In addition, we showed that PCR was a sensitive and accurate method that unaffected by antibiotic therapy and could detect well co‐infections.
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Affiliation(s)
- Mansour Amin
- Infectious and Tropical Diseases Research CenterHealth Research Institute, Ahvaz Jundishapur University of Medical SciencesAhvazIran
- Department of microbiology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Samaneh Yousef pour
- Department of microbiology, school of scienceIslamic Azad UniversityYasoujIran
| | - Tahereh Navidifar
- Department of microbiology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
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O'Rourke S, Meehan M, Bennett D, O'Sullivan N, Cunney R, Gavin P, McNamara R, Cassidy N, Ryan S, Harris K, Drew R. The role of real-time PCR testing in the investigation of paediatric patients with community-onset osteomyelitis and septic arthritis. Ir J Med Sci 2019; 188:1289-1295. [PMID: 30706296 DOI: 10.1007/s11845-019-01973-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 01/19/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND Culture yield in osteomyelitis and septic arthritis is low, emphasising the role for molecular techniques. AIMS The purpose of this study was to review the laboratory investigation of childhood osteomyelitis and septic arthritis. METHODS A retrospective review was undertaken in an acute tertiary referral paediatric hospital from January 2010 to December 2016. Cases were only included if they had a positive culture or bacterial PCR result from a bone/joint specimen or blood culture, or had radiographic evidence of osteomyelitis. RESULTS Seventy-eight patients met the case definition; 52 (66%) were male. The median age was 4.8 years. Blood cultures were positive in 16 of 56 cases (29%), with 11 deemed clinically significant (Staphylococcus aureus = 8, group A Streptococcus = 3). Thirty-seven of 78 (47%) bone/joint samples were positive by culture with S. aureus (n = 16), coagulase-negative Staphylococcus (n = 9) and group A Streptococcus (n = 4), being the most common organisms. Sixteen culture-negative samples were sent for bacterial PCR, and four were positive (Kingella kingae = 2, Streptococcus pneumoniae = 1, group A Streptococcus = 1). CONCLUSIONS Sequential culture and PCR testing can improve the detection rate of causative organisms in paediatric bone and joint infections, particularly for fastidious microorganisms such as K. kingae. PCR testing can be reserved for cases where culture is negative after 48 h. These results have been used to develop a standardised diagnostic test panel for bone and joint infections at our institution.
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Affiliation(s)
- Sadhbh O'Rourke
- Department of Clinical Microbiology, Temple Street Children's University Hospital, Dublin 1, Ireland.
| | - Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Désirée Bennett
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Nicola O'Sullivan
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland.,Health Protection Surveillance Centre, Dublin 1, Ireland
| | - Patrick Gavin
- Department of Infectious Diseases, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Roisin McNamara
- Emergency Department, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Noelle Cassidy
- Department of Orthopaedics, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Stephanie Ryan
- Department of Radiology, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Kathryn Harris
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street NHS Foundation Trust, London, UK
| | - Richard Drew
- Irish Meningitis and Sepsis Reference Laboratory, Temple Street Children's University Hospital, Dublin 1, Ireland.,Department of Clinical Microbiology, Royal College of Surgeons, Dublin 2, Ireland.,Clinical Innovation Unit, Rotunda Hospital, Dublin 1, Ireland
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CSF inflammatory markers differ in gram-positive versus gram-negative shunt infections. J Neuroinflammation 2019; 16:7. [PMID: 30626412 PMCID: PMC6325818 DOI: 10.1186/s12974-019-1395-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/02/2019] [Indexed: 12/28/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) shunt placement is frequently complicated by bacterial infection. Shunt infection diagnosis relies on bacterial culture of CSF which can often produce false-negative results. Negative cultures present a conundrum for physicians as they are left to rely on other CSF indices, which can be unremarkable. New methods are needed to swiftly and accurately diagnose shunt infections. CSF chemokines and cytokines may prove useful as diagnostic biomarkers. The objective of this study was to evaluate the potential of systemic and CSF biomarkers for identification of CSF shunt infection. Methods We conducted a retrospective chart review of children with culture-confirmed CSF shunt infection at Children’s Hospital and Medical Center from July 2013 to December 2015. CSF cytokine analysis was performed for those patients with CSF in frozen storage from the same sample that was used for diagnostic culture. Results A total of 12 infections were included in this study. Patients with shunt infection had a median C-reactive protein (CRP) of 18.25 mg/dL. Median peripheral white blood cell count was 15.53 × 103 cells/mL. Those with shunt infection had a median CSF WBC of 332 cells/mL, median CSF protein level of 406 mg/dL, and median CSF glucose of 35.5 mg/dL. An interesting trend was observed with gram-positive infections having higher levels of the anti-inflammatory cytokine interleukin (IL)-10 as well as IL-17A and vascular endothelial growth factor (VEGF) compared to gram-negative infections, although these differences did not reach statistical significance. Conversely, gram-negative infections displayed higher levels of the pro-inflammatory cytokines IL-1β, fractalkine (CX3CL1), chemokine ligand 2 (CCL2), and chemokine ligand 3 (CCL3), although again these were not significantly different. CSF from gram-positive and gram-negative shunt infections had similar levels of interferon gamma (INF-γ), tumor necrosis factor alpha (TNF-α), IL-6, and IL-8. Conclusions This pilot study is the first to characterize the CSF cytokine profile in patients with CSF shunt infection and supports the distinction of chemokine and cytokine profiles between gram-negative and gram-positive infections. Additionally, it demonstrates the potential of CSF chemokines and cytokines as biomarkers for the diagnosis of shunt infection.
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Fitzgerald FC, Lhomme E, Harris K, Kenny J, Doyle R, Kityo C, Shaw LP, Abongomera G, Musiime V, Cook A, Brown JR, Brooks A, Owen-Powell E, Gibb DM, Prendergast AJ, Sarah Walker A, Thiebaut R, Klein N. Microbial Translocation Does Not Drive Immune Activation in Ugandan Children Infected With HIV. J Infect Dis 2019; 219:89-100. [PMID: 30107546 PMCID: PMC6284549 DOI: 10.1093/infdis/jiy495] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Immune activation is associated with morbidity and mortality during human immunodeficiency virus (HIV) infection, despite receipt of antiretroviral therapy (ART). We investigated whether microbial translocation drives immune activation in HIV-infected Ugandan children. Methods Nineteen markers of immune activation and inflammation were measured over 96 weeks in HIV-infected Ugandan children in the CHAPAS-3 Trial and HIV-uninfected age-matched controls. Microbial translocation was assessed using molecular techniques, including next-generation sequencing. Results Of 249 children included, 142 were infected with HIV; of these, 120 were ART naive, with a median age of 2.8 years (interquartile range [IQR], 1.7-4.0 years) and a median baseline CD4+ T-cell percentage of 20% (IQR, 14%-24%), and 22 were ART experienced, with a median age of 6.5 years (IQR, 5.9-9.2 years) and a median baseline CD4+ T-cell percentage of 35% (IQR, 31%-39%). The control group comprised 107 children without HIV infection. The median increase in the CD4+ T-cell percentage was 17 percentage points (IQR, 12-22 percentage points) at week 96 among ART-naive children, and the viral load was <100 copies/mL in 76% of ART-naive children and 91% of ART-experienced children. Immune activation decreased with ART use. Children could be divided on the basis of immune activation markers into the following 3 clusters: in cluster 1, the majority of children were HIV uninfected; cluster 2 comprised a mix of HIV-uninfected children and HIV-infected ART-naive or ART-experienced children; and in cluster 3, the majority were ART naive. Immune activation was low in cluster 1, decreased in cluster 3, and persisted in cluster 2. Blood microbial DNA levels were negative or very low across groups, with no difference between clusters except for Enterobacteriaceae organisms (the level was higher in cluster 1; P < .0001). Conclusion Immune activation decreased with ART use, with marker clustering indicating different activation patterns according to HIV and ART status. Levels of bacterial DNA in blood were low regardless of HIV status, ART status, and immune activation status. Microbial translocation did not drive immune activation in this setting. Clinical Trials Registration ISRCTN69078957.
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Affiliation(s)
| | - Edouard Lhomme
- INSERM, Bordeaux Population Health Research Centre, UMR 1219, University of Bordeaux, ISPED
- Statistics in System Biology and Translational Medicine (SISTM Team), INRIA Research Centre
- Vaccine Research Institute (VRI), Créteil, France
| | - Kathryn Harris
- Microbiology, Virology, and Infection Prevention and Control, Camelia Botnar Laboratories, GOS National Health Service Foundation Trust
| | - Julia Kenny
- Infection, Immunity, and Inflammation Programme
| | - Ronan Doyle
- Microbiology, Virology, and Infection Prevention and Control, Camelia Botnar Laboratories, GOS National Health Service Foundation Trust
| | | | - Liam P Shaw
- Infection, Immunity, and Inflammation Programme
| | | | | | - Adrian Cook
- Medical Research Council Clinical Trials Unit at UCL
| | - Julianne R Brown
- Microbiology, Virology, and Infection Prevention and Control, Camelia Botnar Laboratories, GOS National Health Service Foundation Trust
| | - Anthony Brooks
- University College London (UCL) Genomics, UCL Great Ormond Street (GOS) Institute of Child Health
| | | | - Diana M Gibb
- Medical Research Council Clinical Trials Unit at UCL
| | - Andrew J Prendergast
- Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | | | - Rodolphe Thiebaut
- INSERM, Bordeaux Population Health Research Centre, UMR 1219, University of Bordeaux, ISPED
- Statistics in System Biology and Translational Medicine (SISTM Team), INRIA Research Centre
- Vaccine Research Institute (VRI), Créteil, France
| | - Nigel Klein
- Infection, Immunity, and Inflammation Programme
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Reuwer AQ, van den Bijllaardt W, Murk JL, Buiting AGM, Verweij JJ. Added diagnostic value of broad-range 16S PCR on periprosthetic tissue and clinical specimens from other normally sterile body sites. J Appl Microbiol 2018; 126:661-666. [PMID: 30431696 DOI: 10.1111/jam.14156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/22/2018] [Accepted: 11/08/2018] [Indexed: 12/01/2022]
Abstract
AIMS Evaluation of 16S PCR in addition to the standard culture to improve the pathogen detection rate in clinical specimens. METHODS AND RESULTS Microbiological culture and direct 16S PCR was performed on specimens from suspected prosthetic joint infection patients (cohort-1) and on tissues and fluids from other normally sterile body sites (cohort-2). Based on clinical and microbiological data, the detection rate for both methods was assessed, assuming no superiority of either 16S PCR or culture. In cohort-1, 469 specimens were obtained. Culture was positive in 170 (36·2%) specimens, 16S PCR detected 70 (41·2%) of those pathogens. Additionally, 16S PCR detected pathogens in 13 of 299 (4·3%) culture-negative specimens. In cohort-2, pathogens were cultured in 52 of 430 (12·1%) specimens and 16S PCR revealed those pathogens in 32 (61·5%) specimens. 16S PCR detected pathogens in 31 of 378 (8·2%) culture-negative specimens. CONCLUSIONS Overall, the yield with 16S PCR was low. For cohort-1 16S PCR detected pathogens in 4·3% of culture-negative specimens, where this was 8·2% for cohort-2. SIGNIFICANCE AND IMPACT OF THE STUDY Although direct 16S PCR cannot replace culture, it may offer a valuable additional diagnostic option for detection of difficult to culture micro-organisms in culture-negative clinical specimens.
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Affiliation(s)
- A Q Reuwer
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - W van den Bijllaardt
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands.,Microvida Laboratory for Microbiology, Amphia Hospital, Breda, The Netherlands
| | - J L Murk
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - A G M Buiting
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | - J J Verweij
- Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
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Establishment of a method for measuring leukocyte phagocytosis based on 16S rDNA. Mol Biol Rep 2018; 46:833-840. [PMID: 30506506 DOI: 10.1007/s11033-018-4538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
The goal of this study was to develop a method for measuring leukocyte phagocytosis based on 16S rDNA, and to investigate its clinical significance. Whole blood was collected and incubated with bacteria. Free bacteria were removed using differential centrifugation. Bacteria phagocytosed by leukocytes were measured using real-time PCR technology based on universal primers of 16S rDNA. The change rate of bacterial DNA (CRD) was considered as a criterion of phagocyte function. In the test, the CRD of whole blood leukocytes from a healthy volunteer was repeatedly measured (five times) by the new method in order to document the repeatability. The CRD from the new method and the rate of phagocytosis measured using traditional microscopy were compared in a young healthy group and an aged group of volunteers to observe the relationship between the new method and traditional microscopy and to assess the clinical value of the new method. There was a significant correlation between real-time PCR technology and traditional microscopy (r = 0.82, P < 0.01). The coefficient of variation (CV) was 2.7% for the new method. The CRD was statistically significantly lower in the aged group than in the healthy young group (P < 0.05). The real-time PCR method established for measuring leukocyte phagocytosis was accurate and reliable, and has potential clinical application.
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Yatera K, Noguchi S, Mukae H. The microbiome in the lower respiratory tract. Respir Investig 2018; 56:432-439. [PMID: 30392534 DOI: 10.1016/j.resinv.2018.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
With the advent of new technologies evaluating the microbiome in the sample such as next-generation sequencer (NGS), current increase of an interest in understanding of the lung microbiome and its roles in lung diseases are marked. Gathering the data of bacterial flora in the lung and their changes during disease courses is unraveling the pathogenesis and the mechanism of disease progression particularly in patients with bronchial asthma, chronic obstructive pulmonary disease and infectious lung diseases. To clarify the relationship between the lung microbiome and pulmonary diseases, new information may help us to create new treatment and prevention strategies of some pulmonary diseases by controlling the lung microbiome. Using bacterial 16S ribosomal RNA gene sequence, NGS can rapidly estimate large amount of bacterial sequences in the phylum and genus levels, and some of them in species levels in a very short period of time. In addition to new information of the microbiome using NGS in the respiratory tract, other techniques using basically Sanger method in combination with the clone library construction can also be useful to identify pathogenic bacterial species with their ratio in the respiratory samples such as bacterial pneumonia, lung abscess and nontuberculous mycobacteriosis. These modalities to identify and semi-quantify bacterial burden in the respiratory tract have revealed new bacterial information in each infectious lung disease. This review describes current understanding of the lung microbiome in several representative lung diseases.
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Affiliation(s)
- Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, Nagasaki, Japan.
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