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Osborn LJ, Fissel J, Gomez S, Mestas J, Flores-Vazquez J, Lee J, Hakimjavadi H, Costales C, Dien Bard J. Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens. J Clin Microbiol 2024; 62:e0174923. [PMID: 38624235 PMCID: PMC11077995 DOI: 10.1128/jcm.01749-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively. IMPORTANCE To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.
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Affiliation(s)
- Lucas J. Osborn
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - John Fissel
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Samantha Gomez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Javier Mestas
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jessica Flores-Vazquez
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Jaehyeon Lee
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, Jeollabukdo, South Korea
| | - Hesamedin Hakimjavadi
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
| | - Cristina Costales
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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2
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Dumm RE, Glaser LJ, Rodino KG. Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center. Am J Clin Pathol 2023; 160:477-482. [PMID: 37458096 DOI: 10.1093/ajcp/aqad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/25/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data. METHODS Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management. RESULTS Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy. CONCLUSIONS This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.
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Affiliation(s)
- Rebekah E Dumm
- Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, Washington University, St Louis, MO, US
| | - Laurel J Glaser
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
| | - Kyle G Rodino
- Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, US
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Shaw TD, Curran T, Cooke S, McMullan R, Hunter M. The utility of 16S rRNA gene sequencing on intraoperative specimens from intracranial infections: an 8-year study in a regional UK neurosurgical unit. Br J Neurosurg 2021:1-6. [PMID: 34927521 DOI: 10.1080/02688697.2021.2016620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/01/2021] [Accepted: 12/05/2021] [Indexed: 10/19/2022]
Abstract
Background: Optimal management of intracranial infections relies on microbiological diagnosis and antimicrobial choice, but conventional culture-based testing is limited by pathogen viability and pre-sampling antimicrobial exposure. Broad-range 16S rRNA gene sequencing has been reported in the management of culture-negative infections but its utility in intracranial infection is not well-described. We studied the efficacy of 16S rRNA gene sequencing to inform microbiological diagnosis and antimicrobial choice in intracranial infections.Methods: This was a retrospective study of all intraoperative neurosurgical specimens sent for 16S rRNA gene sequencing over an 8-year period at a regional neurosurgical centre in the UK. Specimen selection was performed using multidisciplinary approach, combining neurosurgical and infection specialist discussion.Results: Twenty-five intraoperative specimens taken during neurosurgery from 24 patients were included in the study period. The most common reason for referral was pre-sampling antimicrobial exposure (68%). Bacterial rDNA was detected in 60% of specimens. 16S rRNA gene sequencing contributed to microbiological diagnosis in 15 patients and informed antimicrobial management in 10 of 24 patients with intracranial infection. These included targeted antibiotics after detection of a clinically-significant pathogen that had not been identified through other microbiological testing (3 cases), detection of commensal organisms in neurosurgical infection which justified continued broad cover (2 cases) and negative results from intracranial lesions with low clinical suspicion of bacterial infection which justified avoidance or cessation of antibiotics (5 cases).Conclusion: Overall, 16S rRNA gene sequencing represented an incremental improvement in diagnostic testing and was most appropriately used to complement, rather than replace, conventional culture-based testing for intracranial infection.
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Affiliation(s)
- Timothy D Shaw
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Medical Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Tanya Curran
- Department of Medical Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Stephen Cooke
- Regional Neurosciences Unit, Belfast Health and Social Care Trust, Belfast, UK
| | - Ronan McMullan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
- Department of Medical Microbiology, Belfast Health and Social Care Trust, Belfast, UK
| | - Michael Hunter
- Infectious Diseases Unit, Belfast Health and Social Care Trust, Belfast, UK
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5
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Teoh T, McNamara R, Powell J, O’Connell NH, Dunne CP. A retrospective observational study of the impact of 16s and 18s ribosomal RNA PCR on antimicrobial treatment over seven years: A tertiary hospital experience. PLoS One 2021; 16:e0258552. [PMID: 34637486 PMCID: PMC8509882 DOI: 10.1371/journal.pone.0258552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/29/2021] [Indexed: 01/15/2023] Open
Abstract
Background Although culture-based methods remain a staple element of microbiology analysis, advanced molecular methods increasingly supplement the testing repertoire. Since the advent of 16s and 18s ribosomal RNA PCR in the 2000s, there has been interest in its utility for pathogen detection. Nonetheless, studies assessing the impact on antimicrobial prescribing are limited. We report a single-centre experience of the influence of 16s and 18s PCR testing on antimicrobial treatment, including a cost-analysis. Methods Data were collected retrospectively for all samples sent for 16s and 18s PCR testing between January 2014 and December 2020. Results were compared to any culture-based result. Assessment focused on any change of antimicrobial treatment based on PCR result, or use of the result as supportive evidence for microbiological diagnosis. Results 310 samples relevant to 268 patients were referred for 16s/18s rRNA PCR testing during the period. Culture was performed for 234 samples. Enrichment culture was performed for 83 samples. 82 of 300 samples sent for 16s PCR had positive results (20.8%). When culture was performed, enrichment reduced the outcome of 16s PCR only positive results (4/36 [11.1%] versus 14/35 [40.0%], p = 0.030 where a pathogen found). 18s PCR yielded 9 positive results from 67 samples. The 16s PCR result influenced antimicrobial change for 6 patients (2.2%). We estimated the cost for 16s PCR testing to result in one significant change in antimicrobial therapy to be €3,340. 18s PCR did not alter antimicrobial treatment. Conclusion There was limited impact of 16s PCR results on antimicrobial treatments. Relevance to practice was affected by relatively long turn-around-time for results. Utility may be increased in specialised surgical centres, or by reducing turn-around-time. Enrichment culture should be considered on samples where 16s PCR is requested. There remains limited evidence for use of 18s PCR in clinical management, and further studies in this area are likely warranted.
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Affiliation(s)
- TeeKeat Teoh
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Rachel McNamara
- Department of Medicine and Infectious Diseases, University Hospital Limerick, Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
| | - Nuala H. O’Connell
- Department of Clinical Microbiology, University Limerick Hospital Group, Limerick, Ireland
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
| | - Colum P. Dunne
- Centre for Interventions in Infection, Inflammation & Immunity (4i) and School of Medicine, University of Limerick, Limerick, Ireland
- * E-mail:
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6
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Fida M, Khalil S, Abu Saleh O, Challener DW, Sohail MR, Yang JN, Pritt BS, Schuetz AN, Patel R. Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice. Clin Infect Dis 2021; 73:961-968. [PMID: 34407178 DOI: 10.1093/cid/ciab167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear. METHODS We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019. RESULTS A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P < .001). 16S rRNA PCR/sequencing identified a probable pathogen in 10% culture-negative specimens. CONCLUSION 16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.
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Affiliation(s)
- Madiha Fida
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarwat Khalil
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Omar Abu Saleh
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas W Challener
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Muhammad Rizwan Sohail
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Disease, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Joshua N Yang
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Bobbi S Pritt
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Audrey N Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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7
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Uejima Y, Niimi H, Kato R, Furuichi M, Sato S, Kitajima I, Kawano Y, Oh-Ishi T, Kawashima H, Suganuma E. Infected simple renal cyst due to Streptococcus pneumoniae rapidly diagnosed by the melting temperature mapping method: a case report. BMC Pediatr 2021; 21:265. [PMID: 34090356 PMCID: PMC8178924 DOI: 10.1186/s12887-021-02736-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/26/2021] [Indexed: 11/10/2022] Open
Abstract
Background Spontaneous infection of preexisting solitary renal cysts has been documented in adults but is extremely rare in children. To date, no cases of simple renal cysts infected with Streptococcus pneumoniae have been described. Recently, reports have described the diagnosis of bacterial infection using the 16 S rRNA gene as well as the accompanying antimicrobial stewardship for microorganisms that are difficult to culture and for culture-negative cases after preceding antibacterial administration. Case presentation A four-year-old Japanese girl who had a pleuroperitoneal shunt inserted to drain a right pleural effusion due to occlusion of the hepatic portion of the inferior vena cava at three years old visited our hospital due to fever and respiratory discomfort. She was incidentally found to have a right simple renal cyst 10 months before admission. The patient was suspected to have pneumonitis or catheter-related blood stream infection on chest X-ray, which showed right-side pleural effusion. She was diagnosed with invasive pneumococcal infection, as Streptococcus pneumoniae was detected from blood culture on admission. Transient improvements in her symptoms and decreases in the white blood cell count and C-reactive protein level were observed after effective antibiotic administration, but her respiratory condition deteriorated. Enhanced CT showed right renal cyst enlargement and enhancement and thickening of the surrounding wall. Using the melting temperature (Tm) mapping method, S. pneumoniae was rapidly detected directly from pus 4.5 hours after drainage. The specimen culture was negative, but the extracted 16 S rDNA sequence revealed 100 % identity for S. pneumoniae from the same specimen the subsequent day. We successfully performed optimal treatment and reduced medical cost based on the positive Tm mapping method result. Conclusions We report the first case of a S. pneumoniae-infected simple renal cyst. The drainage culture was negative, but the Tm mapping method rapidly detected S. pneumoniae directly from the drainage. The Tm mapping method may have great impacts on rapid diagnosis and effective antimicrobial stewardship.
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Affiliation(s)
- Yoji Uejima
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan. .,Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan.
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Reiko Kato
- Department of Pediatric Surgery, Saitama Children's Medical Center, Saitama, Japan
| | - Mihoko Furuichi
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan
| | - Satoshi Sato
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan
| | - Isao Kitajima
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Yutaka Kawano
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan
| | - Tsutomu Oh-Ishi
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan
| | - Hiroshi Kawashima
- Department of Pediatric Surgery, Saitama Children's Medical Center, Saitama, Japan
| | - Eisuke Suganuma
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, 1-2 Shintoshin, Chuou-ku, 330-8777, Saitama, Japan
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Ursenbach A, Schramm F, Séverac F, Hansmann Y, Lefebvre N, Ruch Y, Argemi X. Revised version (INFD-D-20-00242): impact of 16S rDNA sequencing on clinical treatment decisions: a single center retrospective study. BMC Infect Dis 2021; 21:190. [PMID: 33602178 PMCID: PMC7890971 DOI: 10.1186/s12879-021-05892-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/12/2021] [Indexed: 11/23/2022] Open
Abstract
Background PCRs targeting 16S ribosomal DNA (16S PCR) followed by Sanger’s sequencing can identify bacteria from normally sterile sites and complement standard analyzes, but they are expensive. We conducted a retrospective study in the Strasbourg University Hospital to assess the clinical impact of 16S PCR sequencing on patients’ treatments according to different sample types. Methods From 2014 to 2018, 806 16S PCR samples were processed, and 191 of those were positive. Results Overall, the test impacted the treatment of 62 of the 191 patients (32%). The antibiotic treatment was rationalized in 31 patients (50%) and extended in 24 patients (39%), and an invasive procedure was chosen for 7 patients (11%) due to the 16S PCR sequencing results. Positive 16S PCR sequencing results on cerebrospinal fluid (CSF) had a greater impact on patients’ management than positive ones on cardiac valves (p = 0.044). The clinical impact of positive 16S PCR sequencing results were significantly higher when blood cultures were negative (p < 0.001), and this difference appeared larger when both blood and sample cultures were negative (p < 0.001). The diagnostic contribution of 16S PCR was higher in patients with previous antibiotic treatment (p < 0.001). Conclusion In all, 16S PCR analysis has a significant clinical impact on patient management, particularly for suspected CSF infections, for patients with culture-negative samples and for those with previous antibiotic treatments. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05892-4.
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Affiliation(s)
- Axel Ursenbach
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France.
| | - Frédéric Schramm
- Laboratoire de bactériologie, Faculté de Médecine, Université de Strasbourg, 3 rue Koeberlé, 67000, Strasbourg, France
| | - François Séverac
- Service de Santé Publique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yves Hansmann
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Nicolas Lefebvre
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvon Ruch
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Xavier Argemi
- Maladies Infectieuses et Tropicales, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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9
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Esquer Garrigos Z, Sohail MR, Greenwood-Quaintance KE, Cunningham SA, Vijayvargiya P, Fida M, Friedman PA, Mandrekar J, DeSimone DC, Baddour LM, Patel R. Molecular Approach to Diagnosis of Cardiovascular Implantable Electronic Device Infection. Clin Infect Dis 2021; 70:898-906. [PMID: 30944928 DOI: 10.1093/cid/ciz266] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/26/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Sonicate fluid (SF), a solution derived from vortexing and sonication of explanted cardiovascular implantable electronic devices (CIEDs), is a higher-yield specimen compared with swabs or tissues for culture-based detection of microorganisms associated with CIED infection. Despite this, SF culture fails to identify a causative organism in ~50% of cases. We aimed to evaluate the diagnostic performance of 16S ribosomal RNA gene (rRNA) polymerase chain reaction (PCR)/sequencing of SF and compare it with that of SF culture. METHODS We identified 322 SF specimens from extracted CIEDs and reviewed clinical data for each patient. Subjects were classified as having or not having CIED infection. Cases were subcategorized as culture negative if no significant growth was reported from SF cultures and as culture positive if an organism was detected above predefined thresholds. 16S rRNA PCR/sequencing was performed, with the organisms identified reported according to Clinical and Laboratory Standards Institute guidelines for sequence data interpretation. RESULTS A total of 278 SF samples corresponded to infected cases, of which 160 were culture positive and 118 culture negative. The remaining 44 were from noninfected cases, of which 2 were culture positive. Compared with SF culture, the sensitivity of 16S rRNA PCR/sequencing was higher (64% vs 57.5%, P = .003). 16S rRNA PCR/sequencing detected a potential pathogen in 28 of 118 culture-negative cases, identifying staphylococci in the majority (18/28). CONCLUSIONS 16S rRNA PCR/sequencing has higher sensitivity to detect bacteria in SF from extracted CIEDs than does SF culture.
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Affiliation(s)
- Zerelda Esquer Garrigos
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - M Rizwan Sohail
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | | | - Scott A Cunningham
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Prakhar Vijayvargiya
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Madiha Fida
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Paul A Friedman
- Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Jayawant Mandrekar
- Department of Health Sciences Research, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Daniel C DeSimone
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Larry M Baddour
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota.,Department of Cardiovascular Diseases, Mayo Clinic College of Medicine and Science, Rochester, Minnesota
| | - Robin Patel
- Division of Infectious Diseases Mayo Clinic College of Medicine and Science, Rochester, Minnesota
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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: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Bador J, Nicolas B, Chapuis A, Varin V, Dullier-Taillefumier N, de Curraize C, Amoureux L, Putot A, Neuwirth C. 16S rRNA PCR on clinical specimens: Impact on diagnosis and therapeutic management. Med Mal Infect 2019; 50:63-73. [PMID: 31611135 DOI: 10.1016/j.medmal.2019.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/16/2018] [Accepted: 09/17/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVE 16S rRNA PCR (16S PCR) performed on clinical samples contributes to bacterial identification in cases of negative culture due to an antibiotic therapy. Sensitivity of the 16S PCR is low (19-42%). Little data is available on its impact on the management of patients. We aimed to evaluate the contribution of 16S PCR to diagnosis and therapeutic management at the university hospital of Dijon, France. PATIENTS AND METHODS 16S PCR was performed on the clinical specimens of 132 patients. Clinical settings, laboratory results, and data on antibiotic therapy were collected, as well as conclusions drawn from the 16S PCR result by physicians. Each case was analyzed to determine if the 16S PCR was helpful. The relevance of the 16S PCR was also assessed. RESULTS The 16S PCR yield was 27.3%, ranging from 14.3% to 64.3% depending on the type of specimen. 16S PCR had a positive impact on diagnosis in 28.8% of cases. Five negative 16S PCR results were considered helpful as they contributed to ruling out bacterial infection. 16S PCR led to treatment changes in six patients (4.5%): three narrower spectrums, two treatment adaptations, and one discontinuation. The 16S PCR was considered "non-relevant" in 35 cases (26.5%). None of these 35 PCRs contributed to the patient's management. CONCLUSION Physicians should be aware of performances of 16S PCR. Dialogue between physicians and bacteriologists is essential for appropriate selection of indications and correct interpretation of results.
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Affiliation(s)
- J Bador
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France.
| | - B Nicolas
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - A Chapuis
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - V Varin
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - N Dullier-Taillefumier
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - C de Curraize
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - L Amoureux
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - A Putot
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
| | - C Neuwirth
- Laboratoire de bactériologie, hôpital universitaire de Dijon, BP 37013, 21070 Dijon cedex, France
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