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1.
J Perinatol ; 44(5): 724-730, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38351274

RESUMO

OBJECTIVE: To assess the impact of active surveillance and decolonization strategies on methicillin-resistant Staphylococcus aureus (MRSA) infection rates in a NICU. STUDY DESIGN: MRSA infection rates were compared before (2014-2016) and during (2017-2022) an active surveillance program. Eligible infants were decolonized with chlorohexidine gluconate (CHG) bathing and/or topical mupirocin. Successful decolonization and rates of recolonization were assessed. RESULTS: Fifty-two (0.57%) of 9 100 hospitalized infants had invasive MRSA infections from 2014 to 2022; infection rates declined non-significantly. During the 6-year surveillance program, the risk of infection was 16.9-times [CI95 8.4, 34.1] higher in colonized infants than uncolonized infants. Those colonized with mupirocin-susceptible MRSA were more likely successfully decolonized (aOR 9.7 [CI95 4.2, 22.5]). Of 57 infants successfully decolonized who remained hospitalized, 34 (60%) became recolonized. CONCLUSIONS: MRSA infection rates did not significantly decline in association with an active surveillance and decolonization program. Alternatives to mupirocin and CHG are needed to facilitate decolonization.


Assuntos
Antibacterianos , Clorexidina , Infecção Hospitalar , Unidades de Terapia Intensiva Neonatal , Staphylococcus aureus Resistente à Meticilina , Mupirocina , Infecções Estafilocócicas , Humanos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Infecções Estafilocócicas/prevenção & controle , Infecções Estafilocócicas/tratamento farmacológico , Recém-Nascido , Mupirocina/administração & dosagem , Mupirocina/uso terapêutico , Clorexidina/análogos & derivados , Clorexidina/administração & dosagem , Clorexidina/uso terapêutico , Feminino , Masculino , Antibacterianos/uso terapêutico , Antibacterianos/administração & dosagem , Infecção Hospitalar/prevenção & controle , Infecção Hospitalar/epidemiologia , Infecção Hospitalar/microbiologia , Anti-Infecciosos Locais/administração & dosagem , Anti-Infecciosos Locais/uso terapêutico , Banhos
2.
Gut Pathog ; 16(1): 10, 2024 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-38383457

RESUMO

BACKGROUND: Microbiome restitution therapies are being developed to prevent gut pathogen colonization among patients in the intensive care unit (ICU) and in other select populations. If preventive therapies are to be effective, they must be administered prior to pathogen acquisition. The timing and risk factors for early acquisition of gut pathogen colonization (within 72 h) are currently unknown and could be helpful to guide ICU trial design. METHODS: This was a prospective cohort study. Patients in the ICU had deep rectal swabs performed within 4 h of ICU admission and exactly 72 h later. Early gut pathogen colonization was classified as the new presence (based on culture of rectal swabs) of one or more of the following organisms of interest: methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant (VRE), and Gram-negative bacteria that showed multidrug resistance (MDR) or third generation Cephalosporin resistance (Ceph-R). Clinical risk factors for early acquisition of gut pathogen colonization were captured using the Acute Physiology and Chronic Health Evaluation IV (APACHE IV) scoring system. FINDINGS: Among 131 patients who were swabbed at ICU admission and 72 h later, the rates of gut pathogen colonization at ICU admission were 11.4%, 10.6%, 38.6%, and 8.3% for MRSA, VRE, MDR and Ceph-R Gram-negatives respectively. Among the patients who were negative for a given pathogen at ICU admission, the rates of early acquisition of gut pathogen colonization were 7.8% for MRSA (95% CI 3.6 to 14.2%), 7.7% for VRE (95% CI 3.6 to 14.1%), 11.3% for MDR Gram-negatives (95% CI 4.4 to 18.8%), and 4.2% for Ceph-R Gram-negatives (95% CI 1.4 to 9.5%). There were no clinical risk factors which independently predicted early acquisition of gut pathogen colonization. INTERPRETATION: Early gut pathogen colonization was common in the ICU, but our single-center study could not identify any clinical risk factors which were significantly associated with acquisition of gut pathogens.

3.
Front Cell Infect Microbiol ; 13: 1208235, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37389220

RESUMO

Introduction: In the Northeast US, respiratory viruses such as influenza and respiratory syncytial virus (RSV), which were largely suppressed by COVID-19-related social distancing, made an unprecedented resurgence during 2022, leading to a substantial rise in viral co-infections. However, the relative rates of co-infection with seasonal respiratory viruses over this period have not been assessed. Methods: Here we reviewed multiplex respiratory viral PCR data (BioFire FilmArray™ Respiratory Panel v2.1 [RPP]) from patients with respiratory symptoms presenting to our medical center in New York City to assess co-infection rates of respiratory viruses, which were baselined to total rates of infection for each virus. We examined trends in monthly RPP data from adults and children during November 2021 through December 2022 to capture the full seasonal dynamics of respiratory viruses across periods of low and high prevalence. Results: Of 50,022 RPPs performed for 34,610 patients, 44% were positive for at least one target, and 67% of these were from children. The overwhelming majority of co-infections (93%) were seen among children, for whom 21% of positive RPPs had two or more viruses detected, as compared to just 4% in adults. Relative to children for whom RPPs were ordered, children with co-infections were younger (3.0 vs 4.5 years) and more likely to be seen in the ED or outpatient settings than inpatient and ICU settings. In children, most viral co-infections were found at significantly reduced rates relative to that expected from the incidence of each virus, especially those involving SARS-CoV-2 and influenza. SARS-CoV-2 positive children had an 85%, 65% and 58% reduced rate of co-infection with influenza, RSV, and Rhino/enteroviruses, respectively, after compensating for the incidence of infection with each virus (p< 0.001). Discussion: Our results demonstrate that most respiratory viruses peaked in different months and present in co-infections less than would be expected based on overall rates of infection, suggesting a viral exclusionary effect between most seasonal respiratory viruses, including SARS-CoV-2, influenza and RSV. We also demonstrate the significant burden of respiratory viral co-infections among children. Further work is necessary to understand what predisposes certain patients for viral co-infection despite this exclusionary effect.


Assuntos
COVID-19 , Coinfecção , Influenza Humana , Vírus Sincicial Respiratório Humano , Adulto , Criança , Humanos , Coinfecção/epidemiologia , COVID-19/epidemiologia , Incidência , Influenza Humana/epidemiologia , Vírus Sincicial Respiratório Humano/genética , SARS-CoV-2 , Pré-Escolar
4.
BMC Infect Dis ; 23(1): 26, 2023 Jan 13.
Artigo em Inglês | MEDLINE | ID: mdl-36639740

RESUMO

INTRODUCTION: Mycolicibacter kumamotonensis is a slowly growing, non-chromogenic non-tuberculous mycobacteria (NTM) that was initially distinguished from the M. terrae complex in 2006. Since then it has been rarely reported as the cause of pulmonary and soft-tissue infections in both immunocompromised and immunocompetent patients. CASE PRESENTATION: We present a case of severe pulmonary disease due to Mycolicibacter kumamotonensis in a 57-year-old male who was immunocompetent at time of diagnosis, with a history of interstitial lung disease and a prior diagnosis of tuberculosis (TB). After initial treatment for TB in 2017, his condition stabilized until a recurrence in September 2021, leading to an evaluation for lung transplant in the setting of pulmonary fibrosis and emphysema which led to the identification of Mycolicibacter kumamotonensis. A lung transplant was completed, and the patient was successfully treated with a combination of Ethambutol, Azithromycin, and Rifabutin. CONCLUSIONS: This represents the first case reported of M. kumamotonensis in a patient undergoing lung transplant, and the first case with rapid culture growth during identification of the organism (4 days). This report highlights the need for consideration of M. kumamotonensis as a pathogen in humans, with the potential for rapid growth in liquid media, and the importance of early identification to inform empiric therapy.


Assuntos
Pneumopatias , Infecções por Mycobacterium não Tuberculosas , Tuberculose , Masculino , Humanos , Pessoa de Meia-Idade , Cidade de Nova Iorque , Micobactérias não Tuberculosas , Infecções por Mycobacterium não Tuberculosas/diagnóstico , Infecções por Mycobacterium não Tuberculosas/tratamento farmacológico , Infecções por Mycobacterium não Tuberculosas/microbiologia
5.
Diagn Cytopathol ; 51(1): 98-100, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36369992
6.
Infect Control Hosp Epidemiol ; 44(2): 186-190, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-35702900

RESUMO

OBJECTIVE: To reduce both inappropriate testing for and diagnosis of healthcare-onset (HO) Clostridioides difficile infections (CDIs). DESIGN: We performed a retrospective analysis of C. difficile testing from hospitalized children before (October 2017-October 2018) and after (November 2018-October 2020) implementing restrictive computerized provider order entry (CPOE). SETTING: Study sites included hospital A (a ∼250-bed freestanding children's hospital) and hospital B (a ∼100-bed children's hospital within a larger hospital) that are part of the same multicampus institution. METHODS: In October 2018, we implemented CPOE. No testing was allowed for infants aged ≤12 months, approval of the infectious disease team was required to test children aged 13-23 months, and pathology residents' approval was required to test all patients aged ≥24 months with recent laxative, stool softener, or enema use. Interrupted time series analysis and Mann-Whitney U test were used for analysis. RESULTS: An interrupted time series analysis revealed that from October 2017 to October 2020, the numbers of tests ordered and samples sent significantly decreased in all age groups (P < .05). The monthly median number of HO-CDI cases significantly decreased after implementation of the restrictive CPOE in children aged 13-23 months (P < .001) and all ages combined (P = .003). CONCLUSION: Restrictive CPOE for CDI in pediatrics was successfully implemented and sustained. Diagnostic stewardship for CDI is likely cost-saving and could decrease misdiagnosis, unnecessary antibiotic therapy, and overestimation of HO-CDI rates.


Assuntos
Clostridioides difficile , Infecções por Clostridium , Infecção Hospitalar , Lactente , Humanos , Criança , Clostridioides , Estudos Retrospectivos , Infecções por Clostridium/diagnóstico , Hospitais Pediátricos
7.
mSphere ; 7(6): e0040922, 2022 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-36218345

RESUMO

Methicillin-susceptible Staphylococcus aureus (MSSA) is a more prevalent neonatal intensive care unit (NICU) pathogen than methicillin-resistant S. aureus (MRSA). However, the introduction and spread of MSSA, the role of systematic decolonization, and optimal infection prevention and control strategies remain incompletely understood. We previously screened infants hospitalized in a university-affiliated level III to IV NICU twice monthly over 18 months for S. aureus colonization and identified several prevalent staphylococcal protein A (spa) types. Here, we performed whole-genome sequencing (WGS) and phylogenetic comparisons of 140 isolates from predominant spa types t279, t1451, and t571 to examine possible transmission routes and identify genomic and epidemiologic features associated with the spread of dominant clones. We identified two major MSSA clones: sequence type 398 (ST398), common in the local community, and ST1898, not previously encountered in the region. ST398 NICU isolates formed distinct clusters with closely related community isolates from previously published data sets, suggesting multiple sources of acquisition, such as family members or staff, including residents of the local community. In contrast, ST1898 isolates were nearly identical, pointing to clonal expansion within the NICU. Almost all ST1898 isolates harbored plasmids encoding mupirocin resistance (mupA), suggesting an association between the proliferation of this clone and decolonization efforts with mupirocin. Comparative genomics indicated genotype-specific pathways of introduction and spread of MSSA via community-associated (ST398) or health care-associated (ST1898) sources and the potential role of mupirocin resistance in dissemination of ST1898. Future surveillance efforts could benefit from routine genotyping to inform clone-specific infection prevention strategies. IMPORTANCE Methicillin-susceptible Staphylococcus aureus (MSSA) is a significant pathogen in neonates. However, surveillance efforts in neonatal intensive care units (NICUs) have focused primarily on methicillin-resistant S. aureus (MRSA), limiting our understanding of colonizing and infectious MSSA clones which are prevalent in the NICU. Here, we identify two dominant colonizing MSSA clones during an 18-month surveillance effort in a level III to IV NICU, ST398 and ST1898. Using genomic surveillance and phylogenetic analysis, coupled with epidemiological investigation, we found that these two sequence types had distinct modes of spread, namely the suggested exchange with community reservoirs for ST398 and the contribution of antibiotic resistance to dissemination of ST1898 in the health care setting. This study highlights the additional benefits of whole-genome surveillance for colonizing pathogens, beyond routine species identification and genotyping, to inform targeted infection prevention strategies.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Humanos , Recém-Nascido , Lactente , Staphylococcus aureus/genética , Unidades de Terapia Intensiva Neonatal , Staphylococcus aureus Resistente à Meticilina/genética , Mupirocina , Meticilina , Infecções Estafilocócicas/prevenção & controle , Filogenia , Genômica
8.
Open Forum Infect Dis ; 9(8): ofac356, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35937646

RESUMO

Background: Herpes simplex virus-1 is the most common cause of sporadic encephalitis worldwide and requires prompt antiviral treatment. Traditionally, herpes simplex virus-1 (HSV-1) cerebrospinal fluid (CSF) testing is conducted using standalone polymerase chain reaction (PCR). The BioFire CSF FilmArray Meningitis/Encephalitis Panel (BioFire ME Panel) was introduced in 2015 at our institution, providing an alternative method of HSV-1 CSF testing. This study assesses the impact of the BioFire ME Panel on duration of intravenous acyclovir treatment. Methods: A retrospective review of electronic medical records between 2010 and 2019 was performed. Information on intravenous acyclovir treatment and HSV-1 CSF testing was collected and analyzed. Our descriptive analysis included Mann-Whitney tests, 2 proportion Z-tests, and logistic regression. Results: Our CSF HSV-1-negative cohort included 524 BioFire patients (125 pediatric, 399 adult) and 287 standalone PCR patients (115 pediatric, 172 adult). Across both pediatric and adult groups, patients who were tested for HSV-1 with the BioFire ME Panel had shorter average (SD) durations of intravenous acyclovir treatment (pediatric: 2.00 [5.71] days; adult: 3.26 [6.59] days) compared with patients tested with standalone PCR (pediatric: 4.83 [8.62] days; adult: 4.93 [8.46] days; P < .001). Time from lumbar puncture collection to HSV-1 results was additionally faster on average for the BioFire ME Panel than the standalone PCR (P < .001). Conclusions: The implementation of the BioFire ME Panel shortened CSF HSV-1 PCR result time and intravenous acyclovir duration. The shortened treatment and testing times from the BioFire ME Panel implementation may reduce hospital treatment costs and unnecessary use of antiviral treatments.

9.
J Clin Microbiol ; 60(7): e0017422, 2022 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-35642519

RESUMO

COVID-19 is associated with prolonged hospitalization and a high risk of intubation, which raises concern for bacterial coinfection and antimicrobial resistance. Previous research has shown a wide range of bacterial pneumonia rates for COVID-19 patients in a variety of clinical and demographic settings, but none have compared hospitalized COVID-19 patients to patients testing negative for severe acute respiratory syndrome coronavirus (SARS-CoV-2) in similar care settings. We performed a retrospective cohort study on hospitalized patients with COVID-19 testing from March 10th, 2020 to December 31st, 2020. A total of 19,219 patients were included, of which 3,796 tested positive for SARS-CoV-2. We found a 2.6-fold increase (P < 0.001) in respiratory culture ordering in COVID-19 patients. On a per-patient basis, COVID-19 patients were 1.5-fold more likely than non-COVID patients to have positive respiratory cultures (46.8% versus 30.9%, P < 0.001), which was primarily driven by patients requiring intubation. Among patients with pneumonia, a significantly higher proportion of COVID-19 patients had ventilator-associated pneumonia (VAP) relative to non-COVID patients (86.3% versus 70.8%, P < 0.001), but a lower proportion had community-acquired (11.2% vs 25.5%, P < 0.01) pneumonia. There was also a significantly higher proportion of respiratory cultures positive for methicillin-resistant Staphylococcus aureus, Klebsiella pneumoniae, and antibiotic-resistant organisms in COVID-19 patients. Increased rates of respiratory culture ordering for COVID-19 patients therefore appear to be clinically justified for patients requiring intubation, but further research is needed to understand how SARS-CoV-2 increases the risk of VAP.


Assuntos
COVID-19 , Coinfecção , Staphylococcus aureus Resistente à Meticilina , Pneumonia Bacteriana , Teste para COVID-19 , Coinfecção/epidemiologia , Hospitais Urbanos , Humanos , Cidade de Nova Iorque/epidemiologia , Pneumonia Bacteriana/epidemiologia , Estudos Retrospectivos , SARS-CoV-2
10.
medRxiv ; 2022 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-35547854

RESUMO

Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

11.
J Clin Microbiol ; 60(6): e0060022, 2022 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-35582905

RESUMO

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.


Assuntos
COVID-19 , SARS-CoV-2 , Sequência de Bases , Humanos , Mutação , SARS-CoV-2/genética
12.
Arch Pathol Lab Med ; 146(2): 194-200, 2022 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-34086848

RESUMO

CONTEXT.­: The FilmArray Meningitis/Encephalitis (ME) panel is the first US Food and Drug Administration-cleared multiplex polymerase chain reaction panel for the detection of central nervous system infections. While the assay's performance characteristics have been described, the real-world significance of positive results has not been fully characterized. OBJECTIVE.­: To evaluate the clinical significance of positive ME panel results in a tertiary care medical center in New York, New York. DESIGN.­: Four physicians independently performed retrospective clinical assessments of all positive ME panel results at Columbia University Irving Medical Center, including the Children's Hospital of New York, during an 18-month period. Each reviewer determined the likelihood of central nervous system infection for all cases and whether cases fit Brighton diagnostic criteria for meningitis, encephalitis, or meningoencephalitis. RESULTS.­: Among 119 cases, there was 75% positive agreement (95% CI, 54%-89%) between ME panel results and clinical consensus, which varied among panel targets. CONCLUSIONS.­: The ME panel showed good agreement with expert clinical consensus for patients presenting with acute meningitis/encephalitis. Factors contributing to clinically insignificant ME positive results included low pretest probability, traumatic lumbar puncture, specimen contamination, and detection of incidental viral targets such as human herpesvirus 6. Notably, the ME panel detected more than twice the number of cases of bacterial meningitis detected by culture alone, particularly among patients receiving empiric antimicrobial therapy before lumbar puncture. Appropriate test use and contextual interpretation of results are critical to leveraging the advantages of the platform while avoiding potential pitfalls.


Assuntos
Encefalite , Meningite , Criança , Encefalite/líquido cefalorraquidiano , Encefalite/diagnóstico , Humanos , Meningite/líquido cefalorraquidiano , Meningite/diagnóstico , Reação em Cadeia da Polimerase Multiplex/métodos , Estudos Retrospectivos , Centros de Atenção Terciária , Estados Unidos
13.
Open Forum Infect Dis ; 8(8): ofab411, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34430675

RESUMO

Multiplex polymerase chain reaction testing for gastrointestinal pathogens was performed on a longitudinal cohort of 110 men who have sex with men taking human immunodeficiency virus preexposure prophylaxis. At least 1 pathogen was detected among 50 (45%) participants, with some participants testing positive for the same pathogen on multiple consecutive visits over a period of months.

14.
J Pediatric Infect Dis Soc ; 10(7): 766-773, 2021 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-34129043

RESUMO

BACKGROUND: Staphylococcus aureus protein A (spa) typing can be used to expand characterization of the epidemiology of methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA) in neonatal intensive care units (NICU). METHODS: From January 2017 to June 2018, twice-monthly surveillance for S. aureus was performed in an academically affiliated NICU. Decolonization of infants colonized with S. aureus included chlorhexidine gluconate bathing and/or mupirocin for those with mupirocin-susceptible strains. Spa typing and mupirocin-resistance testing were performed. Demographic and clinical characteristics were compared between infants colonized with MSSA vs MRSA and infants with and without the most common MSSA spa type, MSSA-t279. RESULTS: Overall, 14% and 2% of 1556 hospitalized infants had positive surveillance cultures for MSSA and MRSA, respectively. Thirty-six infants harbored unique MSSA spa types, 5 infants harbored unique MRSA spa types, and 30 MSSA and 6 MRSA spa types were identified in ≥2 infants. No outbreaks were identified during the study period. MSSA-t279 was isolated from 3% of infants and largely detected from infants hospitalized in one section of the NICU; 96% of t279 isolates were mupirocin resistant. Infection rates, length of hospitalization, and mortality were similar among infants initially colonized with t279 vs other MSSA spa types. CONCLUSIONS: The MSSA colonization burden was 5-fold larger than that of MRSA. Numerous unique spa types were identified. The most common spa type, MSSA-t279, was not associated with increased morbidity or mortality but was mupirocin resistant and associated with clustered NICU beds. This suggests potential transmission from the environment, shared staff, and/or workflow issues requiring further study. Other decolonization strategies for S. aureus in the NICU are needed.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Antibacterianos/farmacologia , Antibacterianos/uso terapêutico , Humanos , Lactente , Recém-Nascido , Unidades de Terapia Intensiva Neonatal , Staphylococcus aureus Resistente à Meticilina/genética , Mupirocina , Infecções Estafilocócicas/diagnóstico , Infecções Estafilocócicas/tratamento farmacológico , Infecções Estafilocócicas/epidemiologia , Staphylococcus aureus/genética
17.
Open Forum Infect Dis ; 8(2): ofab003, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33604401

RESUMO

BACKGROUND: The relationship between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and patient symptom duration in both in- and outpatients, and the impact of these factors on patient outcomes, are currently unknown. Understanding these associations is important to clinicians caring for patients with coronavirus disease 2019 (COVID-19). METHODS: We conducted an observational study between March 10 and May 30, 2020 at a large quaternary academic medical center in New York City. Patient characteristics, laboratory values, and clinical outcomes were abstracted from the electronic medical records. Of all patients tested for SARS-CoV-2 during this time (N = 16 384), there were 5467 patients with positive tests, 4254 of which had available cycle threshold (Ct) values and were included in further analysis. Univariable and multivariable logistic regression models were used to test associations between Ct values, duration of symptoms before testing, patient characteristics, and mortality. The primary outcome is defined as death or discharge to hospice. RESULTS: Lower Ct values at diagnosis (ie, higher viral load) were associated with significantly higher mortality among both in- and outpatients. It is interesting to note that patients with a shorter time since the onset of symptoms to testing had a worse prognosis, with those presenting less than 3 days from symptom onset having 2-fold increased odds of death. After adjusting for time since symptom onset and other clinical covariates, Ct values remained a strong predictor of mortality. CONCLUSIONS: Severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction Ct value and duration of symptoms are strongly associated with mortality. These 2 factors add useful information for clinicians to risk stratify patients presenting with COVID-19.

18.
Transplantation ; 105(7): 1445-1448, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-33606483

RESUMO

BACKGROUND: The optimal duration of transmission-based precautions among immunocompromised patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unknown. METHODS: Retrospective review of patients with solid organ transplant with positive SARS-CoV-2 polymerase chain reaction result from nasopharyngeal specimens admitted to the hospital between March 13, 2020 and May 15, 2020. RESULTS: Twenty-one percent of solid organ transplant recipients with positive SARS-CoV-2 polymerase chain reaction detected ≥20 d after symptom onset (or after first positive test among asymptomatic individuals) had a low cycle threshold (ie, high viral load). The majority of these patients were asymptomatic or symptomatically improved. CONCLUSIONS: Solid organ transplant recipients may have prolonged high viral burden of SARS-CoV-2. Further data are needed to understand whether cycle threshold data can help inform strategies for prevention of healthcare-associated transmission of SARS-CoV-2 and for appropriate discontinuation of transmission-based precautions.


Assuntos
Teste para COVID-19 , COVID-19/virologia , Transplante de Órgãos , Complicações Pós-Operatórias/virologia , Carga Viral , Adulto , Idoso , Infecções Assintomáticas , COVID-19/diagnóstico , COVID-19/prevenção & controle , COVID-19/transmissão , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Complicações Pós-Operatórias/diagnóstico , Complicações Pós-Operatórias/prevenção & controle , Estudos Retrospectivos
19.
Clin Infect Dis ; 72(2): 239-245, 2021 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-31942944

RESUMO

BACKGROUND: Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA has emerged as an attractive diagnostic modality allowing broad-range pathogen detection, noninvasive sampling, and earlier diagnosis. However, little is known about its real-world clinical impact as used in routine practice. METHODS: We performed a retrospective cohort study of all patients for whom plasma mNGS (Karius test) was performed for all indications at 5 United States institutions over 1.5 years. Comprehensive records review was performed, and standardized assessment of clinical impact of the mNGS based on the treating team's interpretation of Karius results and patient management was established. RESULTS: A total of 82 Karius tests were evaluated from 39 (47.6%) adults and 43 (52.4%) children and a total of 53 (64.6%) immunocompromised patients. Karius positivity rate was 50 of 82 (61.0%), with 25 (50.0%) showing 2 or more organisms (range, 2-8). The Karius test results led to positive impact in 6 (7.3%), negative impact in 3 (3.7%), and no impact in 71 (86.6%), and was indeterminate in 2 (2.4%). Cases with positive Karius result and clinical impact involved bacteria and/or fungi but not DNA viruses or parasites. In 10 patients who underwent 16 additional repeated tests, only 1 was associated with clinical impact. CONCLUSIONS: The real-world impact of the Karius test as currently used in routine clinical practice is limited. Further studies are needed to identify high-yield patient populations, define the complementary role of mNGS to conventional microbiological methods, and discern how best to integrate mNGS into current testing algorithms.


Assuntos
Ácidos Nucleicos Livres , Doenças Transmissíveis , Adulto , Criança , Doenças Transmissíveis/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Metagenômica , Plasma , Estudos Retrospectivos , Sensibilidade e Especificidade
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