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Wood JB, Russell K, Davis TE, Park SY, Smollin MJ, Schneider JG. Plasma Microbial Cell-Free DNA Sequencing for Pathogen Detection and Quantification in Children With Musculoskeletal Infections. J Pediatric Infect Dis Soc 2024; 13:211-219. [PMID: 38330338 DOI: 10.1093/jpids/piae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
BACKGROUND Nearly half of all pediatric musculoskeletal infections (MSKIs) are culture negative. Plasma microbial cell-free DNA (mcfDNA) sequencing is noninvasive and not prone to the barriers of culture. We evaluated the performance of plasma mcfDNA sequencing in identifying a pathogen, and examined the duration of pathogen detection in children with MSKIs. METHODS We conducted a prospective study of children, aged 6 months to 18 years, hospitalized from July 2019 to May 2022 with MSKIs, in whom we obtained serial plasma mcfDNA sequencing samples and compared the results with cultures. RESULTS A pathogen was recovered by culture in 23 of 34 (68%) participants, and by initial mcfDNA sequencing in 25 of 31 (81%) participants. Multiple pathogens were detected in the majority (56%) of positive initial samples. Complete concordance with culture (all organisms accounted for by both methods) was 32%, partial concordance (at least one of the same organism(s) identified by both methods) was 36%, and discordance was 32%. mcfDNA sequencing was more likely to show concordance (complete or partial) if obtained prior to a surgical procedure (82%), compared with after (20%), (RR 4.12 [95% CI 1.25, 22.93], p = .02). There was no difference in concordance based on timing of antibiotics (presample antibiotics 60% vs no antibiotics 75%, RR 0.8 [95% CI 0.40, 1.46], p = .65]). mcfDNA sequencing was positive in 67% of culture-negative infections and detected a pathogen for a longer interval than blood culture (median 2 days [IQR 1, 6 days] vs 1 day [1, 1 day], p < .01). CONCLUSIONS Plasma mcfDNA sequencing may be useful in culture-negative pediatric MSKIs if the sample is obtained prior to surgery. However, results must be interpreted in the appropriate clinical context as multiple pathogens are frequently detected supporting the need for diagnostic stewardship.
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Affiliation(s)
- James B Wood
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Center for Pediatric and Adolescent Comparative Effectiveness Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kelsey Russell
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tom E Davis
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | - Jack G Schneider
- Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Xu CH, Chen X, Zhu GQ, Yi HM, Chen SL, Liu T, Yu YT, Zhang QH, Jiang EL, Feng SZ. Diagnostic performance and clinical impacts of metagenomic sequencing after allogeneic hematopoietic stem cell transplantation. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:11-19. [PMID: 38065767 DOI: 10.1016/j.jmii.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/10/2023] [Accepted: 11/17/2023] [Indexed: 02/12/2024]
Abstract
BACKGROUND Metagenomic Next-Generation Sequencing (mNGS) is a rapid, non-culture-based, high-throughput technique for pathogen diagnosis. Despite its numerous advantages, only a few studies have investigated its use in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS We conducted a retrospective analysis of 404 mNGS tests performed on 264 patients after allo-HSCT. The tests were divided into three groups (Phase A, B, C) based on the time spent hospitalized post-transplantation, and we evaluated the analytical performance of mNGS in comparison with conventional microbiological tests (CMT), while also analyzing its clinical utility for clinical impacts. RESULTS Metagenomic sequencing demonstrated a significantly higher rate of positive microbiological findings as compared to CMT (334/404 (82.7 %) vs. 159/404 (39.4 %), respectively, P < 0.001). The detection rates by both mNGS and CMT varied across the three-phase (mNGS: A-60/89 (67.4 %), B-147/158 (93.0 %), C-125/157 (79.6 %), respectively, P < 0.001; CMT: A-21/89 (23.6 %), B-79/158 (50.0 %), C-59/157 (37.6 %), respectively, P < 0.001). The infection sites and types of pathogens were also different across the three phases. Compared to non-GVHD cases, mNGS detected more Aspergillus spp. and Mucorales in GVHD patients (Aspergillus: 12/102 (11.8 %) vs. 8/158 (5.1 %), respectively, P = 0.048; Mucorales: 6/102 (5.9 %) vs. 2/158 (1.3 %), respectively, P = 0.035). Forty-five (181/404) percent of mNGS tests yielded a positive impact on the clinical diagnosis, while 24.3 % (98/404) of tests benefited the patients in antimicrobial treatment. CONCLUSION mNGS is an indispensable diagnostic tool in identifying pathogens and optimizing antibiotic therapy for hematological patients receiving allo-HSCT.
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Affiliation(s)
- Chun-Hui Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China; Microbiology Laboratory, Tianjin Union Precision Medical Diagnostic Co., Ltd, Tianjin 301617, China
| | - Xin Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Guo-Qing Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Hui-Ming Yi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shu-Lian Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Teng Liu
- Microbiology Laboratory, Tianjin Union Precision Medical Diagnostic Co., Ltd, Tianjin 301617, China
| | - Yue-Tian Yu
- Department of Critical Care Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiu-Hui Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Er-Lie Jiang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
| | - Si-Zhou Feng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China; Tianjin Institutes of Health Science, Tianjin 301600, China.
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Kitamura M, Dasgupta A, Henricks J, Parikh SV, Nadasdy T, Clark E, Bazan JA, Satoskar AA. Clinicopathological differences between Bartonella and other bacterial endocarditis-related glomerulonephritis - our experience and a pooled analysis. FRONTIERS IN NEPHROLOGY 2024; 3:1322741. [PMID: 38288381 PMCID: PMC10823370 DOI: 10.3389/fneph.2023.1322741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
Background Although Staphylococcus aureus is the leading cause of acute infective endocarditis (IE) in adults, Bartonella spp. has concomitantly emerged as the leading cause of "blood culture-negative IE" (BCNE). Pre-disposing factors, clinical presentation and kidney biopsy findings in Bartonella IE-associated glomerulonephritis (GN) show subtle differences and some unique features relative to other bacterial infection-related GNs. We highlight these features along with key diagnostic clues and management approach in Bartonella IE-associated GN. Methods We conducted a pooled analysis of 89 cases of Bartonella IE-associated GN (54 published case reports and case series; 18 published conference abstracts identified using an English literature search of several commonly used literature search modalities); and four unpublished cases from our institution. Results Bartonella henselae and Bartonella quintana are the most commonly implicated species causing IE in humans. Subacute presentation, affecting damaged native and/or prosthetic heart valves, high titer anti-neutrophil cytoplasmic antibodies (ANCA), mainly proteinase-3 (PR-3) specificity, fastidious nature and lack of positive blood cultures of these Gram-negative bacilli, a higher frequency of focal glomerular crescents compared to other bacterial infection-related GNs are some of the salient features of Bartonella IE-associated GN. C3-dominant, but frequent C1q and IgM immunofluorescence staining is seen on biopsy. A "full-house" immunofluorescence staining pattern is also described but can be seen in IE -associated GN due to other bacteria as well. Non-specific generalized symptoms, cytopenia, heart failure and other organ damage due to embolic phenomena are the highlights on clinical presentation needing a multi-disciplinary approach for management. Awareness of the updated modified Duke criteria for IE, a high index of suspicion for underlying infection despite negative microbiologic cultures, history of exposure to animals, particularly infected cats, and use of send-out serologic tests for Bartonella spp. early in the course of management can help in early diagnosis and initiation of appropriate treatment. Conclusion Diagnosis of IE-associated GN can be challenging particularly with BCNE. The number of Bartonella IE-associated GN cases in a single institution tends to be less than IE due to gram positive cocci, however Bartonella is currently the leading cause of BCNE. We provide a much-needed discussion on this topic.
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Affiliation(s)
- Mineaki Kitamura
- Department of Pathology, Division of Renal and Transplant Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Nephrology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Alana Dasgupta
- Department of Pathology, Division of Renal and Transplant Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Jonathan Henricks
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Samir V. Parikh
- Department of Internal Medicine, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Tibor Nadasdy
- Department of Pathology, Division of Renal and Transplant Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Edward Clark
- Department of Internal Medicine, St. Vincent Hospital, Erie, PA, United States
| | - Jose A. Bazan
- Department of Internal Medicine, Division of Infectious Disease, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Anjali A. Satoskar
- Department of Pathology, Division of Renal and Transplant Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Hong H, Li T, Ying Y, An Q, Liu H, Liang K. Cat-scratch disease manifesting as uveitis and binocular fundus nodular lesions: a case report. BMC Ophthalmol 2023; 23:345. [PMID: 37544996 PMCID: PMC10405493 DOI: 10.1186/s12886-023-03063-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND Cat-scratch disease typically presents with various ocular manifestations such as uveitis, vitritis, retinitis, retinochoroiditis, and optic neuritis. However, fundus nodular lesions was rarely reported. In our study, we reported a case of Cat-Scratch disease with binocular fundus nodular lesions. CASE PRESENTATION An 11-year old male presented with uveitis in the right eye and bilateral fundus nodular lesions after indirect contact with unvaccinated cats. Comprehensive ancillary examinations including wide-angle fundus photography, ultrasonography, fluorescein fundus angiography, optical coherence tomography, and orbital magnetic resonance imaging were performed to elucidate the multidimensional features of the binocular lesions. Metagenomics next-generation sequencing was utilized to confirm the diagnosis of Cat-scratch disease. The patient's condition showed improvement after a 6-month combination treatment regimen involving systemic administration of doxycycline hyclate and methylprednisolone tablets, as well as local application of mydriatic and corticosteroid eye drops. CONCLUSIONS We firstly reported a case of Cat-scratch disease presenting simultaneously with uveitis and fundus nodular lesions caused by Bartonella henselae infection in a child. Timely diagnosis and treatment with antibiotics and corticosteroids showed promising outcomes for the prognosis of these ocular disorders.
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Affiliation(s)
- Hao Hong
- Department of Ophthalmology, Nanjing hospital, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Tianxi Li
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Ye Ying
- Department of Ophthalmology, Nanjing hospital, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Qi An
- Department of Ophthalmology, Nanjing hospital, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Hu Liu
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Kang Liang
- Department of Ophthalmology, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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McCormick DW, Rassoulian-Barrett SL, Hoogestraat DR, Salipante SJ, SenGupta D, Dietrich EA, Cookson BT, Marx GE, Lieberman JA. Bartonella spp. Infections Identified by Molecular Methods, United States. Emerg Infect Dis 2023; 29:467-476. [PMID: 36823096 PMCID: PMC9973681 DOI: 10.3201/eid2903.221223] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Molecular methods can enable rapid identification of Bartonella spp. infections, which are difficult to diagnose by using culture or serology. We analyzed clinical test results of PCR that targeted bacterial 16S rRNA hypervariable V1-V2 regions only or in parallel with PCR of Bartonella-specific ribC gene. We identified 430 clinical specimens infected with Bartonella spp. from 420 patients in the United States. Median patient age was 37 (range 1-79) years; 62% were male. We identified B. henselae in 77%, B. quintana in 13%, B. clarridgeiae in 1%, B. vinsonii in 1%, and B. washoensis in 1% of specimens. B. quintana was detected in 83% of cardiac specimens; B. henselae was detected in 34% of lymph node specimens. We detected novel or uncommon Bartonella spp. in 9 patients. Molecular diagnostic testing can identify Bartonella spp. infections, including uncommon and undescribed species, and might be particularly useful for patients who have culture-negative endocarditis or lymphadenitis.
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Affiliation(s)
- David W. McCormick
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Sara L. Rassoulian-Barrett
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Daniel R. Hoogestraat
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Stephen J. Salipante
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Dhruba SenGupta
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Elizabeth A. Dietrich
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
| | - Brad T. Cookson
- Centers for Disease Control and Prevention, Fort Collins, Colorado, USA (D.W. McCormick, E.A. Dietrich, G.E. Marx)
- University of Washington, Seattle, Washington, USA (S.L. Rassoulian-Barrett, D.R. Hoogestraat, S.J. Salipante, D. SenGupta, B.T. Cookson, J.A. Lieberman)
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The effect of a plasma next-generation sequencing test on antimicrobial management in immunocompetent and immunocompromised patients-A single-center retrospective study. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e31. [PMID: 36865703 PMCID: PMC9972541 DOI: 10.1017/ash.2022.356] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 02/19/2023]
Abstract
Objective To describe the use of next-generation sequencing (NGS) and to determine whether NGS leads to changes in antimicrobial management. Design and setting This retrospective cohort study included patients aged ≥18 years admitted to a single tertiary-care center in Houston, Texas, with an NGS test performed between January 1, 2017, and December 31, 2018. Patients In total, 167 NGS tests were performed. Most patients were of non-Hispanic ethnicity (n = 129), white (n = 106), and male (n = 116), with a mean age of 52 years (SD, 16). Moreover, 61 patients were immunocompromised: solid-organ transplant (n = 30), patients with human immunodeficiency virus (n = 14), and rheumatology patients on immunosuppressive therapy (n = 12). Results Of the 167 NGS tests performed, 118 (71%) were positive. Test results associated with a change in antimicrobial management were found in 120 (72%) of 167 cases, with an average of 0.32 (SD, 1.57) fewer antimicrobials after the test. The largest change in antimicrobial management was in glycopeptide use (36 discontinuations) followed by antimycobacterial drug use (27 additions among 8 patients). Also, 49 patients had negative NGS results, but only 36 patients had their antibiotics discontinued. Conclusions Plasma NGS testing is associated with a change in antimicrobial management in most cases. We observed a decrease in glycopeptide use after NGS results, which highlights physicians' comfort in withdrawing methicillin-resistant Staphylococcus aureus (MRSA) coverage. In addition, antimycobacterial coverage increased, corresponding with early mycobacterial detection by NGS. Further studies are needed to determine effective ways to use NGS testing as an antimicrobial stewardship tool.
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Eichenberger EM, Degner N, Scott ER, Ruffin F, Franzone J, Sharma-Kuinkel B, Shah P, Hong D, Dalai SC, Blair L, Hollemon D, Chang E, Ho C, Wanda L, de Vries CR, Fowler VG, Ahmed AA. Microbial Cell-Free DNA Identifies the Causative Pathogen in Infective Endocarditis and Remains Detectable Longer Than Conventional Blood Culture in Patients with Prior Antibiotic Therapy. Clin Infect Dis 2023; 76:e1492-e1500. [PMID: 35684984 PMCID: PMC10169441 DOI: 10.1093/cid/ciac426] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The diagnosis of infective endocarditis (IE) can be difficult, particularly if blood cultures fail to yield a pathogen. This study evaluates the potential utility of microbial cell-free DNA (mcfDNA) as a tool to identify the microbial etiology of IE. METHODS Blood samples from patients with suspected IE were serially collected. mcfDNA was extracted from plasma and underwent next-generation sequencing. Reads were aligned against a library containing DNA sequences belonging to >1400 different pathogens. mcfDNA from organisms present above a statistical threshold were reported and quantified in molecules per milliliter (MPM). Additional mcfDNA was collected on each subject every 2-3 days for a total of 7 collections or until discharge. RESULTS Of 30 enrolled patients with suspected IE, 23 had definite IE, 2 had possible IE, and IE was rejected in 5 patients by modified Duke Criteria. Only the 23 patients with definite IE were included for analysis. Both mcfDNA and blood cultures achieved a sensitivity of 87%. The median duration of positivity from antibiotic treatment initiation was estimated to be approximately 38.1 days for mcfDNA versus 3.7 days for blood culture (proportional odds, 2.952; P = .02771), using a semiparametric survival analysis. mcfDNA (log10) levels significantly declined (-0.3 MPM log10 units, 95% credible interval -0.45 to -0.14) after surgical source control was performed (pre- vs postprocedure, posterior probability >0.99). CONCLUSION mcfDNA accurately identifies the microbial etiology of IE. Sequential mcfDNA levels may ultimately help to individualize therapy by estimating a patient's burden of infection and response to treatment.
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Affiliation(s)
- Emily M Eichenberger
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Felicia Ruffin
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - John Franzone
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Batu Sharma-Kuinkel
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Pratik Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - David Hong
- Karius, Inc., Redwood City, California, USA
| | | | - Lily Blair
- Karius, Inc., Redwood City, California, USA
| | | | | | - Carine Ho
- Karius, Inc., Redwood City, California, USA
| | - Lisa Wanda
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Vance G Fowler
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
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Cuperus T, de Vries A, Jaarsma RI, Sprong H, Maas M. Occurrence of Rickettsia spp., Hantaviridae, Bartonella spp. and Leptospira spp. in European Moles ( Talpa europaea) from the Netherlands. Microorganisms 2022; 11:microorganisms11010041. [PMID: 36677332 PMCID: PMC9861085 DOI: 10.3390/microorganisms11010041] [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] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
The European mole (Talpa europaea) has a widespread distribution throughout Europe. However, little is known about the presence of zoonotic pathogens in European moles. We therefore tested 180 moles from the middle and the south of the Netherlands by (q)PCR for the presence of multiple (tick-borne) zoonotic pathogens. Spotted fever Rickettsia was found in one (0.6%), Leptospira spp. in three (1.7%), Bartonella spp. in 69 (38.3%) and Hantaviridae in 89 (49.4%) of the 180 moles. Infections with Anaplasma phagocytophilum, Babesia spp., Neoehrlichia mikurensis, Borrelia spp., Spiroplasma spp. and Francisella tularensis were not found. In addition, in a subset of 35 moles no antibodies against Tick-borne encephalitis virus were found. The obtained sequences of Bartonella spp. were closely related to Bartonella spp. sequences from moles in Spain and Hungary. The Hantaviridae were identified as the mole-borne Nova virus, with high sequence similarity to sequences from other European countries, and Bruges virus. Though the zoonotic risk from moles appears limited, our results indicate that these animals do play a role in multiple host-pathogen cycles.
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Shi Y, Yang J, Qi Y, Xu J, Shi Y, Shi T, Liu C, Ma X. Detection of Bartonella vinsonii subsp. berkhoffii in a HIV patient using metagenomic Next Generation Sequencing. Emerg Microbes Infect 2022; 11:1764-1767. [PMID: 35736664 PMCID: PMC9295814 DOI: 10.1080/22221751.2022.2094287] [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: 11/28/2022]
Abstract
Bartonella species are fastidious, aerobic bacteria that are transmitted by blood-sucking arthropods. Bartonella spp. are responsible for cat scratch disease, Carrion’s disease, bacillary angiomatosis and trench fever. On the other hand, Bartonella vinsonii is rarely reported in the literature and there exist a few reports of systemic infection caused by Bartonella vinsonii in patients with acquired immunodeficiency syndrome. A 31-year-old male (diagnosed with AIDS six years ago) had persistent fever and ulceration in the right knee. The elevated levels of inflammatory markers suggested an infectious aetiology. Despite the negative findings of blood culture, metagenomic Next-Generation Sequencing of plasma detected Bartonella vinsonii. The polymerase chain reaction of whole blood and Sanger sequencing confirmed the mNGS findings. Immunohistochemical staining had later suggested bacillary angiomatosis, which was consistent with Bartonella infection. Following antibiotic treatment, the ulcers subsided significantly, but a high fever persisted. The patient died due to sudden respiratory failure.
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Affiliation(s)
- Yuru Shi
- Infection hospital area of the First Affiliated Hospital of University of science and technology of China, Hefei, China
| | - Jing Yang
- Infection hospital area of the First Affiliated Hospital of University of science and technology of China, Hefei, China
| | - Yingjie Qi
- Infection hospital area of the First Affiliated Hospital of University of science and technology of China, Hefei, China
| | - Junlan Xu
- Infection hospital area of the First Affiliated Hospital of University of science and technology of China, Hefei, China
| | - Yingqi Shi
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Tiantian Shi
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Chao Liu
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, China
| | - Xiaoling Ma
- Infection hospital area of the First Affiliated Hospital of University of science and technology of China, Hefei, China
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Shishido AA, Noe M, Saharia K, Luethy P. Clinical impact of a metagenomic microbial plasma cell-free DNA next-generation sequencing assay on treatment decisions: a single-center retrospective study. BMC Infect Dis 2022; 22:372. [PMID: 35418022 PMCID: PMC9006594 DOI: 10.1186/s12879-022-07357-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Metagenomic next-generation sequencing of microbial cell-free DNA (mcfDNA) allows for non-invasive pathogen detection from plasma. However, there is little data describing the optimal role for this assay in real-world clinical decision making.
Methods We performed a single-center retrospective cohort study of adult patients for whom a mcfDNA (Karius©) test was sent between May 2019 and February 2021. Clinical impact was arbitrated after review and discussion of each case. Results A total of 80 patients were included. The most common reason for sending the assay was unknown microbiologic diagnosis (78%), followed by avoiding invasive procedures (14%). The test had a positive impact in 34 (43%), a negative impact in 2 (3%), and uncertain or no impact in 44 (55%). A positive impact was observed in solid organ transplant recipients (SOTR, 71.4%, p = 0.003), sepsis (71.4%, p = 0.003), and those receiving antimicrobial agents for less than 7 days prior to mcfDNA testing (i.e., 61.8%, p = 0.004). Positive impact was driven primarily by de-escalation of antimicrobial therapy. Conclusion Clinical impact of mcfDNA testing was highest in SOTR, patients with sepsis and patients who had been on antimicrobial therapy for less than 7 days. Positive impact was driven by de-escalation of antimicrobial therapy which may highlight a potential role for mcfDNA in the realm of stewardship. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07357-8. This is a retrospective study evaluating the clinical impact of mcfDNA testing at a single center. mcfDNA positively impacted clinical care in 43% of cases. Patients admitted with sepsis, patients receiving antibiotics for less than 7 days, and solid organ transplant recipients derived the most benefit from mcfDNA testing.
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Affiliation(s)
- Akira A Shishido
- Division of Infectious Diseases, University of Maryland Medical Center, Baltimore, MD, USA.
| | | | - Kapil Saharia
- Division of Infectious Diseases, University of Maryland Medical Center, Baltimore, MD, USA.,Institute of Human Virology, University of Maryland School of Medicine, 22 E Greene St, Baltimore, MD, USA
| | - Paul Luethy
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
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11
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Zeng X, Wu J, Li X, Xiong W, Tang L, Li X, Zhuang J, Yu R, Chen J, Jian X, Lei L. Application of Metagenomic Next-Generation Sequencing in the Etiological Diagnosis of Infective Endocarditis During the Perioperative Period of Cardiac Surgery: A Prospective Cohort Study. Front Cardiovasc Med 2022; 9:811492. [PMID: 35369282 PMCID: PMC8965566 DOI: 10.3389/fcvm.2022.811492] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Objective The present study aimed to prospectively evaluate the role of metagenomic next-generation sequencing (mNGS) in the etiological diagnosis of patients with perioperative infective endocarditis (IE). Methods From May 1st, 2019 to December 31st, 2020, a total of 99 patients with IE were enrolled in the present study according to the modified Duke criteria, etiological, and pathological results. 11 non-IE patients undergoing heart valve surgery in the same period were selected as the control group. A blood culture test was performed immediately after admission, and the valves harvested operatively were examined by blood culture and mNGS. Results In the IE group, there were 29 cases (29.3%) with positive blood culture, 16 cases (16.2%) with positive valve culture, and 85 cases (85.9%) with positive valve mNGS. Compared to culture-based detection, mNGS achieved better performance with a sensitivity, specificity, area under the curve (AUC) of 0.859, 0.727, and 0.793, respectively. The combined approach using culture and mNGS further improved the diagnostic accuracy (sensitivity 89.9%, specificity 72.7%, AUC 0.813). Preoperative white blood cell (P = 0.029) and neutrophils (P = 0.046) were identified as independent factors affecting the detection rate of mNGS. In the mNGS-positive group, 95 strains of pathogens were found and 10 cases were identified with mixed infection. There were 72 gram-positive bacteria and 14 gram-negative bacteria. mNGS positive group displayed higher species richness than mNGS negative group with enrichment of Streptococcus sanguis, Streptococcus buccalis, and Streptococcus griseus. Proteobacteria and Actinomycetes were enriched in mNGS negative group. Notably, six patients showed disconcordant results between culture and mNGS. Rothia aeria was identified in the blood culture, valve culture, and valve mNGS in one patient. Bartonella Quintana and Coxiella burnetii, which were fastidious intracellular bacteria, were found in two blood and valve culture-negative cases. Conclusions mNGS outperformed the conventional culture method and displayed high accuracy in detecting pathogens in IE patients. This study provided support for the use of mNGS in the etiological diagnosis of IE.
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Affiliation(s)
- Xiaodong Zeng
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jinlin Wu
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Li
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Weiping Xiong
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Lili Tang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xueming Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | | | - Jimei Chen
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Xuhua Jian
- Department of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liming Lei
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
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12
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Solanky D, Ahmed AA, Fierer J, Golts E, Jones M, Mehta SR. Utility of Plasma Microbial Cell-Free DNA Decay Kinetics After Aortic Valve Replacement for Bartonella Endocarditis: Case Report. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.842100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BackgroundDetection and sequencing of circulating microbial cell-free DNA (mcfDNA) in plasma is an increasingly popular tool for diagnosing many infectious diseases, but could also be used to monitor the progress of infection. However, the decay of this microbial cell-free DNA in blood following treatment has not been previously characterized.Case PresentationA 53 year-old male was diagnosed with Bartonella quintana bioprosthetic aortic valve endocarditis by sequencing of the mcfDNA in the blood (Karius, Redwood City, CA). We then monitored the kinetics of decay of mcfDNA after parenteral antibiotics and valve resection in this individual. We measured plasma mcfDNA (Karius) in serial samples obtained in the operating room to calculate mcfDNA half-life after valve resection. After four weeks of parenteral antibiotics, Bartonella mcfDNA signal decreased by 78%. The signal subsequently rose during operative manipulation of the infected valve but dropped 81-fold over four hours following valve resection. The half-life of mcfDNA between the time shortly following resection of the infected valve and 24 to 48 hours post-operatively was between 35 and 115 minutes. The trend in mcfDNA signal was characterized by rapid and then slower phases of decay within 24 hours, and little change between 24 and 48 hours.ConclusionsThis study is one of the first to characterize decay kinetics of mcfDNA and highlights the potential of monitoring mcfDNA in addressing major challenges in infective endocarditis management, including monitoring the response to therapy, and as an early screen for recurrence.
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13
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Maggi R, Breitschwerdt EB, Qurollo B, Miller JC. Development of a Multiplex Droplet Digital PCR Assay for the Detection of Babesia, Bartonella, and Borrelia Species. Pathogens 2021; 10:pathogens10111462. [PMID: 34832618 PMCID: PMC8620149 DOI: 10.3390/pathogens10111462] [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: 10/25/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/16/2022] Open
Abstract
We describe the development, optimization, and validation of a multiplex droplet digital PCR (ddPCR) assay for the simultaneous detection of Babesia, Bartonella, and Borrelia spp. DNA from several sample matrices, including clinical blood samples from animals and humans, vectors, in-vitro infected human and animal cell lines, and tissues obtained from animal models (infected with Bartonella and/or B. burgdorferi). The multiplex ddPCR assay was able to detect 31 Bartonella, 13 Borrelia, and 24 Babesia species, including Theileria equi, T. cervi, and Cytauxzoon felis. No amplification of Treponema or Leptospira spp. was observed. Sensitivity of 0.2-5 genome equivalent DNA copies per microliter was achieved for different members of the Bartonella and Borrelia genus, depending on the species or matrix type (water or spiked blood DNA) tested. The ddPCR assay facilitated the simultaneous detection of co-infections with two and three vector-borne pathogens comprising four different genera (Babesia, Bartonella, Borrelia, and Theileria) from clinical and other sample sources.
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Affiliation(s)
- Ricardo Maggi
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
- Correspondence:
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
| | - Barbara Qurollo
- Department of Clinical Sciences, The Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, 1060 William Moore Drive, Raleigh, NC 27607, USA; (E.B.B.); (B.Q.)
| | - Jennifer C. Miller
- Galaxy Diagnostics, Inc., 6 Davis Drive, Suite 201, Research Triangle Park, NC 27709, USA;
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14
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Shishido AA, Vostal A, Mayer R, Ho CY, Baddley JW. Diagnosis of central nervous system invasive aspergillosis in a liver transplant recipient using microbial cell-free next generation DNA sequencing. Transpl Infect Dis 2021; 23:e13592. [PMID: 33655668 DOI: 10.1111/tid.13592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/06/2021] [Accepted: 02/14/2021] [Indexed: 12/20/2022]
Abstract
Invasive aspergillosis (IA) is an important opportunistic infection among patients with liver disease and liver transplants. Diagnosis of IA may be challenging, especially among patients with central nervous system infection. Herein, we demonstrate the utility of next-generation sequencing of microbial cell-free DNA in the diagnosis of fungal brain abscess in a liver transplant recipient.
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Affiliation(s)
- Akira A Shishido
- Division of Infectious Diseases, University of Maryland Medical Center, Baltimore, MD, USA
| | - Alexander Vostal
- Division of Infectious Diseases, University of Maryland Medical Center, Baltimore, MD, USA
| | - Romana Mayer
- Department of Pathology, University of Maryland, Baltimore, MD, USA
| | - Cheng-Ying Ho
- Department of Pathology, University of Maryland, Baltimore, MD, USA
| | - John W Baddley
- Division of Infectious Diseases, University of Maryland Medical Center, Baltimore, MD, USA
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15
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Lieberman JA, Naureckas Li C, Lamb GS, Kane DA, Stewart MK, Mamedov RA, Cookson BT, Salipante SJ. Case Report: Comparison of Plasma Metagenomics to Bacterial PCR in a Case of Prosthetic Valve Endocarditis. Front Pediatr 2020; 8:575674. [PMID: 33489996 PMCID: PMC7819283 DOI: 10.3389/fped.2020.575674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular assays for infectious diseases have emerged as important clinical decision-making tools. Unbiased, metagenomic next-generation sequencing is a novel approach holding promise to detect pathogens missed by conventional modalities and to deconvolute admixed nucleic acid sequences from polymicrobial infections in order to identify constituent pathogens. Recent studies have raised concerns about the clinical impact of metagenomics assays and whether their expense is justified. Here, we report a case of polyclonal Streptococcus cristatus endocarditis in a 14-year-old woman with a history of Tetralogy of Fallot. Three sets of admission blood cultures and a commercial plasma metagenomics assay were negative for pathogens, despite persistent vegetations observed on the valve during a later procedure. Multiple strains of Streptococcus cristatus were identified from the explanted valve by amplicon-based 16S rRNA sequencing, confirming the patient had received appropriate antibiotic therapy. This case highlights limitations in the use and interpretation of clinical metagenomics for infectious disease diagnosis and indicates that the clinical yield of these tools may depend upon infection type and anatomic location.
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Affiliation(s)
- Joshua A Lieberman
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Caitlin Naureckas Li
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - Gabriella S Lamb
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, MA, United States
| | - David A Kane
- Department of Cardiology, Boston Children's Hospital, Boston, MA, United States
| | - Mary K Stewart
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Ruslan A Mamedov
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
| | - Brad T Cookson
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States.,Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Stephen J Salipante
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, United States
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