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1.
Open Forum Infect Dis ; 10(8): ofad354, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37577112

RESUMO

Background: Convenient administration of coronavirus disease 2019 (COVID-19) treatment in community settings is desirable. Sotrovimab is a pan-sarbecovirus dual-action monoclonal antibody formulated for intravenous (IV) or intramuscular (IM) administration for early treatment of mild/moderate COVID-19. Method: This multicenter phase 3 study based on a randomized open-label design tested the noninferiority of IM to IV administration according to an absolute noninferiority margin of 3.5%. From June to August 2021, patients aged ≥12 years with COVID-19, who were neither hospitalized nor receiving supplemental oxygen but were at high risk for progression, were randomized 1:1:1 to receive sotrovimab as a single 500-mg IV infusion or a 500- or 250-mg IM injection. The primary composite endpoint was progression to (1) all-cause hospitalization for >24 hours for acute management of illness or (2) all-cause death through day 29. Results: Sotrovimab 500 mg IM was noninferior to 500 mg IV: 10 (2.7%) of 376 participants vs 5 (1.3%) of 378 met the primary endpoint, respectively (absolute adjusted risk difference, 1.06%; 95% CI, -1.15% to 3.26%). The 95% CI upper limit was lower than the prespecified noninferiority margin of 3.5%. The 250-mg IM group was discontinued early because of the greater proportion of hospitalizations vs the 500-mg groups. Serious adverse events occurred in <1% to 2% of participants across groups. Four participants experienced serious disease-related events and died (500 mg IM, 2/393, <1%; 250 mg IM, 2/195, 1%). Conclusions: Sotrovimab 500-mg IM injection was well tolerated and noninferior to IV administration. IM administration could expand outpatient treatment access for COVID-19. Clinical Trials Registration: ClinicalTrials.gov: NCT04913675.

2.
BMC Health Serv Res ; 22(1): 1209, 2022 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-36171601

RESUMO

BACKGROUND: Seasonal influenza poses a substantial clinical and economic burden in the United States and vulnerable populations, including the elderly and those with comorbidities, are at elevated risk for influenza-related medical complications. METHODS: We conducted a retrospective cohort study using the IQVIA PharMetrics® Plus claims database in two stages. In Stage 1, we identified patients with evidence of medically-attended influenza during influenza seasons from October 1, 2014 to May 31, 2018 (latest available data for Stage 1) and used a multivariable logistic regression model to identify patient characteristics that predicted 30-day influenza-related hospitalization. The findings from Stage 1 informed high-risk subgroups of interest for Stage 2, where we selected cohorts of influenza patients during influenza seasons from October 1, 2014 to March 1, 2019 and used 1:1 propensity score matching to patients without influenza with similar high-risk characteristics to compare influenza-attributable rates of all-cause hospital and emergency department (ED) visits during follow-up (30-day and in the index influenza season). RESULTS: In Stage 1, more than 1.6 million influenza cases were identified, of which 18,509 (1.2%) had a hospitalization. Elderly age was associated with 9 times the odds of hospitalization (≥65 years vs. 5-17 years; OR = 9.4, 95% CI 8.8-10.1) and select comorbidities were associated with 2-3 times the odds of hospitalization. In Stage 2, elderly influenza patients with comorbidities had 3 to 7 times higher 30-day hospitalization rates compared to matched patients without influenza, including patients with congestive heart failure (41.0% vs.7.9%), chronic obstructive pulmonary disease (34.6% vs. 6.1%), coronary artery disease (22.8% vs. 3.8%), and late-stage chronic kidney disease (44.1% vs. 13.1%; all p < 0.05). CONCLUSIONS: The risk of influenza-related complications is elevated in the elderly, especially those with certain underlying comorbidities, leading to excess healthcare resource utilization. Continued efforts, beyond currently available vaccines, are needed to reduce influenza burden in high-risk populations.


Assuntos
Vacinas contra Influenza , Influenza Humana , Idoso , Serviço Hospitalar de Emergência , Hospitalização , Humanos , Influenza Humana/prevenção & controle , Estudos Retrospectivos , Estados Unidos/epidemiologia
3.
Clin Infect Dis ; 74(9): 1659-1668, 2022 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-33870413

RESUMO

BACKGROUND: Standard testing fails to identify a pathogen in most patients with febrile neutropenia (FN). We evaluated the ability of the Karius microbial cell-free DNA sequencing test (KT) to identify infectious etiologies of FN and its impact on antimicrobial management. METHODS: This prospective study (ClinicalTrials.gov; NCT02912117) enrolled and analyzed 55 patients with FN. Up to 5 blood samples were collected per subject within 24 hours of fever onset (T1) and every 2 to 3 days. KT results were compared with blood culture (BC) and standard microbiological testing (SMT) results. RESULTS: Positive agreement was defined as KT identification of ≥1 isolate also detected by BC. At T1, positive and negative agreement were 90% (9/10) and 31% (14/45), respectively; 61% of KT detections were polymicrobial. Clinical adjudication by 3 independent infectious diseases specialists categorized Karius results as: unlikely to cause FN (N = 0); definite (N = 12): KT identified ≥1 organism also found by SMT within 7 days; probable (N = 19): KT result was compatible with a clinical diagnosis; possible (N = 10): KT result was consistent with infection but not considered a common cause of FN. Definite, probable, and possible cases were deemed true positives. Following adjudication, KT sensitivity and specificity were 85% (41/48) and 100% (14/14), respectively. Calculated time to diagnosis was generally shorter with KT (87%). Adjudicators determined real-time KT results could have allowed early optimization of antimicrobials in 47% of patients, by addition of antibacterials (20%) (mostly against anaerobes [12.7%]), antivirals (14.5%), and/or antifungals (3.6%); and antimicrobial narrowing in 27.3% of cases. CLINICAL TRIALS REGISTRATION: NCT02912117. CONCLUSION: KT shows promise in the diagnosis and treatment optimization of FN.


Assuntos
Ácidos Nucleicos Livres , Neutropenia Febril , Antibacterianos/uso terapêutico , Neutropenia Febril/diagnóstico , Neutropenia Febril/tratamento farmacológico , Neutropenia Febril/etiologia , Febre/etiologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Estudos Prospectivos
4.
J Bone Joint Surg Am ; 103(18): 1705-1712, 2021 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-34293751

RESUMO

BACKGROUND: Over 1 million Americans undergo joint replacement each year, and approximately 1 in 75 will incur a periprosthetic joint infection. Effective treatment necessitates pathogen identification, yet standard-of-care cultures fail to detect organisms in 10% to 20% of cases and require invasive sampling. We hypothesized that cell-free DNA (cfDNA) fragments from microorganisms in a periprosthetic joint infection can be found in the bloodstream and utilized to accurately identify pathogens via next-generation sequencing. METHODS: In this prospective observational study performed at a musculoskeletal specialty hospital in the U.S., we enrolled 53 adults with validated hip or knee periprosthetic joint infections. Participants had peripheral blood drawn immediately prior to surgical treatment. Microbial cfDNA from plasma was sequenced and aligned to a genome database with >1,000 microbial species. Intraoperative tissue and synovial fluid cultures were performed per the standard of care. The primary outcome was accuracy in organism identification with use of blood cfDNA sequencing, as measured by agreement with tissue-culture results. RESULTS: Intraoperative and preoperative joint cultures identified an organism in 46 (87%) of 53 patients. Microbial cfDNA sequencing identified the joint pathogen in 35 cases, including 4 of 7 culture-negative cases (57%). Thus, as an adjunct to cultures, cfDNA sequencing increased pathogen detection from 87% to 94%. The median time to species identification for cases with genus-only culture results was 3 days less than standard-of-care methods. Circulating cfDNA sequencing in 14 cases detected additional microorganisms not grown in cultures. At postoperative encounters, cfDNA sequencing demonstrated no detection or reduced levels of the infectious pathogen. CONCLUSIONS: Microbial cfDNA from pathogens causing local periprosthetic joint infections can be detected in peripheral blood. These circulating biomarkers can be sequenced from noninvasive venipuncture, providing a novel source for joint pathogen identification. Further development as an adjunct to tissue cultures holds promise to increase the number of cases with accurate pathogen identification and improve time-to-speciation. This test may also offer a novel method to monitor infection clearance during the treatment period. LEVEL OF EVIDENCE: Diagnostic Level II. See Instructions for Authors for a complete description of levels of evidence.


Assuntos
Ácidos Nucleicos Livres/genética , Infecções Relacionadas à Prótese/microbiologia , Idoso , Artroplastia de Quadril , Artroplastia do Joelho , Ácidos Nucleicos Livres/sangue , Feminino , Humanos , Masculino , Estudos Prospectivos
5.
Clin Infect Dis ; 73(7): e2355-e2361, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-32584965

RESUMO

BACKGROUND: Laboratory confirmation of early Lyme borreliosis (LB) is challenging. Serology is insensitive during the first days to weeks of infection, and blood polymerase chain reaction (PCR) offers similarly poor performance. Here, we demonstrate that detection of Borrelia burgdorferi (B.b.) cell-free DNA (cfDNA) in plasma can improve diagnosis of early LB. METHODS: B.b. detection in plasma samples using unbiased metagenomic cfDNA sequencing performed by a commercial laboratory (Karius Inc) was compared with serology and blood PCR in 40 patients with physician-diagnosed erythema migrans (EM), 28 of whom were confirmed to have LB by skin biopsy culture (n = 18), seroconversion (n = 2), or both (n = 8). B.b. sequence analysis was performed using investigational detection thresholds, different from Karius' clinical test. RESULTS: B.b. cfDNA was detected in 18 of 28 patients (64%) with laboratory-confirmed EM. In comparison, sensitivity of acute-phase serology using modified 2-tiered testing (MTTT) was 50% (P = .45); sensitivity of blood PCR was 7% (P = .0002). Combining B.b. cfDNA detection and MTTT increased diagnostic sensitivity to 86%, significantly higher than either approach alone (P ≤ .04). B.b. cfDNA sequences matched precisely with strain-specific sequence generated from the same individual's cultured B.b. isolate. B.b. cfDNA was not observed at any level in plasma from 684 asymptomatic ambulatory individuals. Among 3000 hospitalized patients tested as part of clinical care, B.b. cfDNA was detected in only 2 individuals, both of whom had clinical presentations consistent with LB. CONCLUSIONS: This is the first report of B.b. cfDNA detection in early LB and a demonstration of potential diagnostic utility. The combination of B.b. cfDNA detection and acute-phase MTTT improves clinical sensitivity for diagnosis of early LB.


Assuntos
Ácidos Nucleicos Livres , Eritema Migrans Crônico , Doença de Lyme , Borrelia burgdorferi/isolamento & purificação , Ácidos Nucleicos Livres/isolamento & purificação , DNA Bacteriano/isolamento & purificação , Eritema Migrans Crônico/diagnóstico , Eritema Migrans Crônico/microbiologia , Humanos , Doença de Lyme/diagnóstico
6.
Clin Infect Dis ; 73(11): e3876-e3883, 2021 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-33119063

RESUMO

BACKGROUND: Noninvasive diagnostic options are limited for invasive mold infections (IMIs). We evaluated the performance of a plasma microbial cell-free DNA sequencing (mcfDNA-Seq) test for diagnosing pulmonary IMI after hematopoietic cell transplant (HCT). METHODS: We retrospectively assessed the diagnostic performance of plasma mcfDNA-Seq next-generation sequencing in 114 HCT recipients with pneumonia after HCT who had stored plasma obtained within 14 days of diagnosis of proven/probable Aspergillus IMI (n = 51), proven/probable non-Aspergillus IMI (n = 24), possible IMI (n = 20), and non-IMI controls (n = 19). Sequences were aligned to a database including >400 fungi. Organisms above a fixed significance threshold were reported. RESULTS: Among 75 patients with proven/probable pulmonary IMI, mcfDNA-Seq detected ≥1 pathogenic mold in 38 patients (sensitivity, 51% [95% confidence interval {CI}, 39%-62%]). When restricted to samples obtained within 3 days of diagnosis, sensitivity increased to 61%. McfDNA-Seq had higher sensitivity for proven/probable non-Aspergillus IMI (sensitivity, 79% [95% CI, 56%-93%]) compared with Aspergillus IMI (sensitivity, 31% [95% CI, 19%-46%]). McfDNA-Seq also identified non-Aspergillus molds in an additional 7 patients in the Aspergillus subgroup and Aspergillus in 1 patient with possible IMI. Among 19 non-IMI pneumonia controls, mcfDNA-Seq was negative in all samples, suggesting a high specificity (95% CI, 82%-100%) and up to 100% positive predictive value (PPV) with estimated negative predictive values (NPVs) of 81%-99%. The mcfDNA-Seq assay was complementary to serum galactomannan index testing; in combination, they were positive in 84% of individuals with proven/probable pulmonary IMI. CONCLUSIONS: Noninvasive mcfDNA-Seq had moderate sensitivity and high specificity, NPV, and PPV for pulmonary IMI after HCT, particularly for non-Aspergillus species.


Assuntos
Ácidos Nucleicos Livres , Transplante de Células-Tronco Hematopoéticas , Pneumonia , Fungos , Transplante de Células-Tronco Hematopoéticas/efeitos adversos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Biópsia Líquida , Estudos Retrospectivos , Transplantados
7.
Appl Health Econ Health Policy ; 19(2): 231-241, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-32944831

RESUMO

BACKGROUND: Invasive fungal infection is a major source of morbidity and mortality. The usage of microbial cell-free DNA for the detection and identification of invasive fungal infection has been considered as a potential alternative to invasive procedures allowing for rapid results. OBJECTIVE: This analysis aimed to assess the budget implications of using the Karius® Test in patients suspected of invasive fungal infection in an average state in the USA from a healthcare payer perspective. METHODS: The analysis used a decision tree to capture key stages of the patient pathway, from suspected invasive fungal infection to either receiving treatment for invasive fungal infection or being confirmed as having no invasive fungal infection. The analysis used published costs and resource use from a targeted review of the literature. Because of the paucity of published evidence on the reduction of diagnostic tests displaced by the Karius Test, the analysis used a 50% reduction in the use of bronchoscopy and/or bronchoalveolar lavage. The impact of this reduction was tested in a scenario analysis. RESULTS: The results of the analysis show that the introduction of the Karius Test is associated with a cost saving of US$2277 per patient; when multiplied by the estimated number of cases per year, the cost saving is US$17,039,666. The scenario analysis showed that the Karius Test only had an incremental cost of US$87 per patient when there was no reduction in bronchoscopy and bronchoalveolar lavage. CONCLUSIONS: The Karius Test may offer a valuable and timely option for the diagnosis of invasive fungal infection through its non-invasive approach and subsequent cost savings.


Assuntos
Ácidos Nucleicos Livres , Infecções Fúngicas Invasivas , Ácidos Nucleicos Livres/isolamento & purificação , Humanos , Hospedeiro Imunocomprometido , Infecções Fúngicas Invasivas/diagnóstico , Infecções Fúngicas Invasivas/economia
8.
Open Forum Infect Dis ; 7(7): ofaa189, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32715017

RESUMO

Granulomatous amoebic encephalitis (GAE) caused by Balamuthia mandrillaris is a rare subacute infection with exceptionally high mortality. Diagnosis is typically made by brain biopsy or at autopsy. Detection of Balamuthia mandrillaris cell-free DNA by next-generation sequencing of plasma enabled rapid, noninvasive diagnosis in a case of amoebic encephalitis.

9.
Med Mycol Case Rep ; 27: 77-80, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32149044

RESUMO

Diagnosis of invasive fungal disease remains an ongoing challenge for clinicians, while continuously evolving treatment regimens increase patient risk for invasive infection. This case highlights how molecular testing led to the diagnosis of co-infection with two fungal pathogens producing invasive disease in a hematopoietic stem cell transplant recipient with graft-versus-host disease (GVHD).

10.
JAMA Oncol ; 6(4): 552-556, 2020 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-31855231

RESUMO

Importance: Bloodstream infection (BSI) is a common, life-threatening complication of treatment for cancer. Predicting BSI before onset of clinical symptoms would enable preemptive therapy, but there is no reliable screening test. Objective: To estimate sensitivity and specificity of plasma microbial cell-free DNA sequencing (mcfDNA-seq) for predicting BSI in patients at high risk of life-threatening infection. Design, Setting, and Participants: A prospective pilot cohort study of mcfDNA-seq for predicting BSI in pediatric patients (<25 years of age) with relapsed or refractory cancers at St Jude Children's Research Hospital, a specialist quaternary pediatric hematology-oncology referral center. Remnant clinical blood samples were collected during chemotherapy and hematopoietic cell transplantation. Samples collected during the 7 days before and at onset of BSI episodes, along with negative control samples from study participants, underwent blinded testing using a mcfDNA-seq test in a Clinical Laboratory Improvement Amendments/College of American Pathologists-approved laboratory. Main Outcomes and Measures: The primary outcomes were sensitivity of mcfDNA-seq for detecting a BSI pathogen during the 3 days before BSI onset and specificity of mcfDNA-seq in the absence of fever or infection in the preceding or subsequent 7 days. Results: Between August 9, 2017, and June 4, 2018, 47 participants (27 [57%] male; median age [IQR], 10 [5-14] years) were enrolled; 19 BSI episodes occurred in 12 participants, and predictive samples were available for 16 episodes, including 15 bacterial BSI episodes. In the 3 days before the onset of infection, predictive sensitivity of mcfDNA-seq was 75% for all BSIs (12 of 16; 95% CI, 51%-90%) and 80% (12 of 15; 95% CI, 55%-93%) for bacterial BSIs. The specificity of mcfDNA-seq, evaluated on 33 negative control samples from enrolled participants, was 82% (27 of 33; 95% CI, 66%-91%) for any bacterial or fungal organism and 91% (30 of 33; 95% CI, 76%-97%) for any common BSI pathogen, and the concentration of pathogen DNA was lower in control than predictive samples. Conclusions and Relevance: A clinically relevant pathogen can be identified by mcfDNA-seq days before the onset of BSI in a majority of episodes, potentially enabling preemptive treatment. Clinical application appears feasible pending further study. Trial Registration: ClinicalTrials.gov identifier: NCT03226158.


Assuntos
Infecções Relacionadas a Cateter/sangue , Ácidos Nucleicos Livres/sangue , Neoplasias/sangue , Sepse/sangue , Adolescente , Infecções Relacionadas a Cateter/complicações , Infecções Relacionadas a Cateter/microbiologia , Infecções Relacionadas a Cateter/patologia , Criança , Pré-Escolar , Feminino , Humanos , Masculino , Neoplasias/complicações , Neoplasias/microbiologia , Neoplasias/patologia , Sepse/complicações , Sepse/microbiologia , Sepse/patologia , Análise de Sequência de DNA
11.
BMC Infect Dis ; 19(1): 371, 2019 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-31046692

RESUMO

BACKGROUND: There is an ongoing outbreak of Mycobacterium chimaera infections among patients exposed to contaminated heater-cooler devices used during cardiac surgery. Recognition of M. chimaera infection is hampered by its long latency and non-specific symptoms. Standard diagnostic methods using acid-fast bacilli (AFB) culture often require invasive sampling, have low sensitivity, and can take weeks to result. We describe the performance of a plasma-based next-generation sequencing test (plasma NGS) for the diagnosis of M. chimaera infection. METHODS: We conducted a retrospective study of 10 patients with a history of cardiac surgery who developed invasive M. chimaera infection and underwent testing by plasma NGS between February 2017 and April 2018. RESULTS: Plasma NGS detected M. chimaera in 9 of 10 patients (90%) with invasive disease in a median of 4 days from specimen collection, including all 8 patients with disseminated infection. In 7 of these 9 cases (78%), plasma NGS was the first test to provide microbiologic confirmation of M. chimaera infection. In contrast, AFB cultures required a median of 20 days to turn positive, and the median time for confirmation of M. chimaera was 41 days. Of 24 AFB blood cultures obtained in this cohort, only 4 (17%) were positive. Invasive procedures were performed in 90% of cases, and in 5 patients (50%), mycobacterial growth was achieved only by culture of these deep sites. CONCLUSIONS: Plasma NGS can accurately detect M. chimaera noninvasively and significantly faster than AFB culture, making it a promising new diagnostic tool.


Assuntos
Infecções por Mycobacterium/diagnóstico , Mycobacterium/genética , Idoso , DNA Bacteriano/sangue , DNA Bacteriano/metabolismo , Surtos de Doenças , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Mycobacterium/isolamento & purificação , Infecções por Mycobacterium/microbiologia , Estudos Retrospectivos , Análise de Sequência de DNA
12.
Pediatr Blood Cancer ; 66(7): e27734, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30941906

RESUMO

BACKGROUND: We sought to determine if next-generation sequencing (NGS) of microbial cell-free DNA (cfDNA) in plasma would detect pathogens in pediatric patients at risk for invasive fungal disease (IFD). PROCEDURES: Pediatric hematology, oncology, and stem cell transplant patients deemed at risk for new IFD had blood samples drawn at three time-points separated by 1-month intervals. The primary outcome measure was detection of fungal pathogens compared to standard clinical testing. Secondary outcomes included identification of other infectious pathogens, relationship to European Organization for Research and Treatment of Cancer's Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases' Mycoses Study Group (EORTC/MSG) guidelines, and assessment of antifungal therapy. RESULTS: NGS identified fungal pathogens in seven of 40 at-risk patients for IFD and results were identical in four of six proven cases, including Aspergillus fumigatus by lung biopsy, Candida albicans by blood or pancreatic pseudocyst cultures, and Rhizopus delemar by skin biopsy. Rhizopus oryzae identified on skin biopsy and A. fumigatus isolated on day 27 of 28 of culture from lung biopsy were not detected by cfDNA NGS, possibly due to lack of bloodstream penetration and questionable pathogenicity, respectively. Numerous DNA viruses were detected in patients with prolonged febrile neutropenia or abnormal imaging. Extended antifungal therapy was used in 73% of patients. Follow-up cfDNA sequencing in patients who were positive at enrollment was negative at 1 and 2 months. CONCLUSIONS: cfDNA NGS detected fungal pathogens from blood confirming its potential to guide treatment decisions in pediatric patients at risk for IFD and limit excessive empiric antifungal use. Future studies are needed to better understand the sensitivity and specificity of this approach.


Assuntos
Ácidos Nucleicos Livres , DNA Fúngico , Transplante de Células-Tronco Hematopoéticas , Sequenciamento de Nucleotídeos em Larga Escala , Infecções Fúngicas Invasivas , Neoplasias , Adolescente , Adulto , Ácidos Nucleicos Livres/sangue , Ácidos Nucleicos Livres/genética , Criança , Pré-Escolar , DNA Fúngico/sangue , DNA Fúngico/genética , Feminino , Humanos , Lactente , Infecções Fúngicas Invasivas/sangue , Infecções Fúngicas Invasivas/genética , Masculino , Neoplasias/sangue , Neoplasias/genética , Neoplasias/microbiologia , Neoplasias/terapia , Projetos Piloto
13.
Diagn Microbiol Infect Dis ; 94(2): 188-191, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30819624

RESUMO

Community-acquired pneumonia (CAP) is a common cause of pediatric hospital admission. Empiric antibiotic therapy for hospitalized children with serious CAP now targets the most likely pathogen(s), including those that may demonstrate significant antibiotic resistance. Cell-free plasma next-generation sequencing (CFPNGS) was first made available for Pediatric Infectious Diseases physicians in June 1, 2017, to supplement standard-of-care diagnostic techniques. A retrospective chart review was performed for children hospitalized with CAP between June 1, 2017, and January 22, 2018, to evaluate the impact of CFPNGS. We identified 15 hospitalized children with CAP without other underlying medical conditions for whom CFPNGS was performed. CFPNGS identified a pathogen in 13 of 15 (86%) children compared with 47% for those using standard culture and PCR-based methods alone. Changes in antibiotic management were made in 7 of 15 (47%) of children as a result of CFPNGS.


Assuntos
Bactérias/isolamento & purificação , Infecções Comunitárias Adquiridas/diagnóstico , DNA Bacteriano/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Técnicas de Diagnóstico Molecular/métodos , Plasma/química , Pneumonia Bacteriana/diagnóstico , Antibacterianos/administração & dosagem , Bactérias/efeitos dos fármacos , Bactérias/genética , Criança , Pré-Escolar , Infecções Comunitárias Adquiridas/tratamento farmacológico , DNA Bacteriano/genética , Gerenciamento Clínico , Feminino , Humanos , Lactente , Masculino , Pneumonia Bacteriana/tratamento farmacológico , Estudos Retrospectivos
14.
Nat Microbiol ; 4(4): 663-674, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30742071

RESUMO

Thousands of pathogens are known to infect humans, but only a fraction are readily identifiable using current diagnostic methods. Microbial cell-free DNA sequencing offers the potential to non-invasively identify a wide range of infections throughout the body, but the challenges of clinical-grade metagenomic testing must be addressed. Here we describe the analytical and clinical validation of a next-generation sequencing test that identifies and quantifies microbial cell-free DNA in plasma from 1,250 clinically relevant bacteria, DNA viruses, fungi and eukaryotic parasites. Test accuracy, precision, bias and robustness to a number of metagenomics-specific challenges were determined using a panel of 13 microorganisms that model key determinants of performance in 358 contrived plasma samples, as well as 2,625 infections simulated in silico and 580 clinical study samples. The test showed 93.7% agreement with blood culture in a cohort of 350 patients with a sepsis alert and identified an independently adjudicated cause of the sepsis alert more often than all of the microbiological testing combined (169 aetiological determinations versus 132). Among the 166 samples adjudicated to have no sepsis aetiology identified by any of the tested methods, sequencing identified microbial cell-free DNA in 62, likely derived from commensal organisms and incidental findings unrelated to the sepsis alert. Analysis of the first 2,000 patient samples tested in the CLIA laboratory showed that more than 85% of results were delivered the day after sample receipt, with 53.7% of reports identifying one or more microorganisms.


Assuntos
Ácidos Nucleicos Livres/genética , Doenças Transmissíveis/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Estudos de Coortes , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/parasitologia , Doenças Transmissíveis/virologia , DNA Bacteriano/genética , DNA Fúngico/genética , DNA Viral/genética , Humanos , Sepse/diagnóstico , Sepse/microbiologia
15.
Open Forum Infect Dis ; 5(12): ofy301, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30581881

RESUMO

Allogeneic hematopoietic stem cell transplant patients are at risk for common and atypical infections. Superior diagnostics can decrease infection-related morbidity and mortality. A novel plasma cell-free DNA next-generation sequencing test detected an uncommon presentation of Chlamydia trachomatis and recurrent and metastatic complications of Staphylococcus aureus bacteremia before standard microbiology.

16.
Diagn Microbiol Infect Dis ; 92(3): 210-213, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-30017314

RESUMO

Diagnosis of life-threatening deep-seated infections currently requires invasive sampling of the infected tissue to provide a microbiologic diagnosis. These procedures can lead to high morbidity in patients and add to healthcare costs. Here we describe a novel next-generation sequencing assay that was used to detect pathogen-derived cell-free DNA in peripheral blood of patients with biopsy-proven invasive fungal infections. The noninvasive nature of this approach could provide rapid, actionable treatment information for invasive fungal infections when a biopsy is not possible.


Assuntos
Doenças Transmissíveis/diagnóstico , Biópsia Líquida , Adulto , Idoso , Ácidos Nucleicos Livres , Doenças Transmissíveis/sangue , Doenças Transmissíveis/microbiologia , DNA Fúngico/sangue , DNA Fúngico/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Infecções Fúngicas Invasivas/sangue , Infecções Fúngicas Invasivas/diagnóstico , Infecções Fúngicas Invasivas/microbiologia , Biópsia Líquida/métodos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular , Adulto Jovem
17.
Open Forum Infect Dis ; 3(3): ofw144, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27704003

RESUMO

We report the case of a 60-year-old man with septic shock due to Capnocytophaga canimorsus that was diagnosed in 24 hours by a novel whole-genome next-generation sequencing assay. This technology shows great promise in identifying fastidious pathogens, and, if validated, it has profound implications for infectious disease diagnosis.

19.
Hosp Pediatr ; 3(4): 355-61, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-24435193

RESUMO

OBJECTIVE: The appropriate duration of hospitalization for infants ≤ 30 days admitted for fever or other concerns for a serious bacterial infection is an understudied area. We sought to determine the risk of a positive, pathogenic bacterial culture of blood or cerebrospinal fluid (CSF) in this population beyond 24 hours after collection. METHODS: This study was a retrospective review of 1145 infants aged ≤30 days who had a blood or CSF culture from 1999 to 2010 at Santa Clara Valley Medical Center, a county health system in San Jose, California. Time to notification and the probability of a positive culture result after 24 hours were calculated. Infants were considered high risk if they had either a white blood cell count <5000 or >15 000 per µL, a band count >1500 per µL, or an abnormal urinalysis. RESULTS: We identified 1876 cultures (1244 blood, 632 CSF) in 1145 infants aged ≤30 days; 901 (79%) of 1145 were hospitalized and 408 (45%) of 901 hospitalizations were for fever without source (FWS). Thirty-one (2.7%) of the 1145 infants had pathogenic cultures; 6 of 1145 infants (0.5% [95% confidence interval: 0.2-1.1]) had a time to notification >24 hours. All 6 patients had FWS (1.5% of hospitalized FWS sample) and met high-risk criteria on presentation. No low-risk patients had a time to notification >24 hours. Low-risk characteristics were found in 57% (232 of 408) of the entire hospitalized FWS population. CONCLUSIONS: Low-risk infants hospitalized for FWS or other concerns for serious bacterial infection may not need hospitalization for a full 48 hours simply to rule out bacteremia and bacterial meningitis.

20.
Vaccine ; 30(2): 254-64, 2012 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-22085545

RESUMO

The development of pre-pandemic influenza A H5N1 vaccines that confer both antigen-sparing and cross-clade protection are a high priority given the limited worldwide capacity for influenza vaccine production, and the antigenic and genetic heterogeneity of circulating H5N1 viruses. The inclusion of potent adjuvants in vaccine formulations may achieve both of these aims. Here we show that the addition of JVRS-100, an adjuvant consisting of cationic liposome-DNA complexes (CLDC) to a clade 1-derived H5N1 split vaccine induced significantly higher virus-specific antibody than unadjuvanted formulations, with a >30-fold dose-sparing effect and induction of increased antigen-specific CD4(+) T-cell responses in mice. All mice that received one dose of adjuvanted vaccine and subsequent H5N1 viral challenges exhibited mild illness, lower lung viral titers, undetectable spleen and brain viral titers, and 100% survival after either homologous clade 1 or heterologous clade 2 H5N1 viral challenges, whereas unadjuvanted vaccine recipients showed significantly increased weight loss, viral titers, and mortality. The protective immunity induced by JVRS-100 adjuvanted H5N1 vaccine was shown to last for over one year without significant waning. Thus, JVRS-100 adjuvanted H5N1 vaccine elicited enhanced humoral and T-cell responses, dose-sparing, and cross-clade protection in mice. CLDC holds promise as an adjuvant for human pre-pandemic inactivated H5N1 vaccines.


Assuntos
Adjuvantes Imunológicos/administração & dosagem , Cátions/administração & dosagem , DNA/administração & dosagem , Portadores de Fármacos/administração & dosagem , Virus da Influenza A Subtipo H5N1/imunologia , Vacinas contra Influenza/imunologia , Lipossomos/administração & dosagem , Animais , Anticorpos Antivirais/sangue , Linfócitos T CD4-Positivos/imunologia , Modelos Animais de Doenças , Feminino , Vacinas contra Influenza/administração & dosagem , Camundongos , Camundongos Endogâmicos BALB C , Infecções por Orthomyxoviridae/mortalidade , Infecções por Orthomyxoviridae/patologia , Infecções por Orthomyxoviridae/virologia , Análise de Sobrevida , Vacinas de Subunidades Antigênicas/administração & dosagem , Vacinas de Subunidades Antigênicas/imunologia
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