N Esther Babady

Memorial Sloan-Kettering Cancer Center, New York, New York, United States

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Publications (41)149.93 Total impact

  • Tracy McMillen · Mini Kamboj · N Esther Babady
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    ABSTRACT: Clostridium difficile 027/NAP1/B1 is the most common C. difficile strain in the United States. Xpert C. difficile/Epi assay allows rapid, presumptive identification of C. difficile NAP1. We compared Xpert C.difficile/Epi to multilocus sequence typing for identification of C. difficile NAP1 and found "very good" agreement at 97.9% (k=0.86; 95% CI 0.80-0.91).
    No preview · Article · Dec 2015 · Journal of clinical microbiology
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    ABSTRACT: Respiratory viruses (RV) are a leading cause of infection-related morbidity and mortality for patients undergoing treatment for cancer. This analysis compared duration of RV shedding as detected by culture and PCR among patients in a high risk oncologic setting (adult patients with hematologic malignancy and/ or stem cell transplant and all pediatric oncology) and determined risk factors for extended shedding. RV infections due to influenza, PIV, HMPV and RSV from two study periods— January 2009-September 2011 (culture-based testing) and September 2011-April 2013 (PCR-based testing) —were reviewed retrospectively. Data was collected from patients in whom retesting for viral clearance was done within 5-30 days after most recent test. During the study period 456 patients were diagnosed with RV infection, 265 by PCR and 191 by culture. The median range for duration of shedding (days) by culture and PCR respectively are as follows, influenza: 13 (5-38 days) vs 14 days (5-58 days) [p=0.5] ; RSV: 11 (5-35 days) vs 16 days (5-50 days) [p=0.001] ; PIV: 9 (5-41 days) vs 17 (5-45 days) [p=<0.0001]; HMPV 10.5 (5-29 days) vs 14 days (5-42 days) [p=0.2]. In multivariate analysis, age and underlying disease or transplant were not independently associated with extended shedding regardless of testing method. In high risk oncologic settings for respiratory illness due to RSV and PIV, the virus is detectable by PCR for a longer period of time than culture and extended shedding is observed.
    No preview · Article · Dec 2015 · Clinical Microbiology and Infection
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    ABSTRACT: Bordetella holmesii is a globally distributed pathogen that is increasingly recognized as a cause of both pertussis-like respiratory infections and invasive disease. In this study, we describe a case of an immunocompetent man who developed B holmesii infection of his femoral prosthesis—the fifth B holmesii orthopedic infection reported in literature to date. This article highlights the potentially underrecognized role of B holmesii in orthopedic infections by reviewing these previously reported cases in the context of the current literature.
    Preview · Article · Nov 2015 · Open Forum Infectious Diseases
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    ABSTRACT: Background: Immunocompromised patients, especially those receiving treatment with corticosteroids and cytotoxic chemotherapy are at increased risk for developing Legionella pneumonia. Objective: The aim of this study was to determine clinical and radiographic characteristics of pulmonary infection due to Legionella in persons undergoing treatment for cancer and stem cell transplant (SCT) recipients. Methods: Retrospective review of Legionella cases at MSKCC over a fifteen-year study period from January 1999 and December 2013. Cases were identified by review of microbiology records. Results: During the study period, 40 cases of Legionella infection were identified; nine among these were due to non-pneumophila species. Most cases occurred during the summer. The majority [8/9, (89%)] of patients with non-pneumophila infection had underlying hematologic malignancy, compared to 18/31 (58 %) with L. pneumophila infections. Radiographic findings were varied-nodular infiltrates mimicking invasive fungal infection were seen only among patients with hematologic malignancy and hematopoietic stem cell transplant (SCT) recipients and were frequently associated with non-pneumophila infections (50% vs 16%; p= 0.0594). All cases of nodular Legionella pneumonia were found incidentally or had an indolent clinical course. Conclusions: Legionella should be considered in the differential diagnosis of nodular lung lesions in immunocompromised patients, especially those with hematologic malignancy and SCT recipients. Most cases of nodular disease due to Legionella are associated with non-pneumophila infections.
    No preview · Article · Oct 2015 · The Journal of infection
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    ABSTRACT: Patients undergoing treatment for cancer with chemotherapy and hematopoietic stem cell recipients are at risk for severe morbidity caused by norovirus (NV). We describe a NV outbreak on the Memorial Sloan Kettering Cancer Center's pediatric oncology unit. Stool testing for diagnosis of NV was performed by real-time polymerase chain reaction (PCR). Twelve NV cases occurred; 7 were hospital acquired. Twenty-five health care workers reported NV compatible illness. Patient-to-patient transmission occurred once. The practices of the Centers for Disease Control and Prevention were supplemented with electronic surveillance, surrogate screening for NV, and heightened cleaning. Two additional cases occurred after implementation of interventions. Long-term shedding was detected in 2 patients. We describe interventions for controlling NV on a pediatric oncology unit. High-risk chronic shedders pose ongoing transmission risks. PCR is a valuable diagnostic tool but may be overly sensitive. Surrogate markers to assess NV burden in stool and studies on NV screening are needed to develop guidelines for high-risk chronic shedders. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.
    No preview · Article · Jul 2015 · American journal of infection control
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    ABSTRACT: We implemented hospital information system (HIS) alerts to deter unnecessary test orders for ova and parasite (O&P) exams and Clostridium difficile polymerase chain reaction (PCR). The HIS alerts decreased non-compliant O&P orders (orders after > 72 h of hospitalization) from 49.8% to 30.9, an overall decrease of 19% and reduced non-compliant C. difficile PCR orders (orders < 7 days after a previous positive result) from 30.6% to 19.2%, an overall decrease of 31.9%. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    No preview · Article · Jun 2015 · Journal of clinical microbiology
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    Preview · Article · May 2015
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    Esther Arguello · Caitlin C Otto · Peter Mead · N Esther Babady
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    ABSTRACT: Arcobacter butzleri is an emerging pathogen that has been implicated as the causative agent of persistent watery diarrhea. We describe a case involving a patient with Chronic Lymphocytic Leukemia who developed invasive A. butzleri bacteremia. This case illustrates the unique diagnostic challenges for emerging gastrointestinal pathogens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Preview · Article · Feb 2015 · Journal of Clinical Microbiology
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    ABSTRACT: Cytomegalovirus (CMV) viral loads in hematopoietic stem cell transplant (HSCT) recipients are typically monitored using quantitative molecular assays. The Roche COBAS Ampliprep/COBAS TaqMan CMV test (COBAS CMV) has recently become FDA-cleared for monitoring of CMV viral loads in plasma samples of transplant patients. In this study, we compare and correlate viral loads obtained by a laboratory-developed test (LC CMV) (Roche ASR on the LightCycler 2.0) on whole blood specimens with those obtained on corresponding plasma and whole blood specimens by the COBAS CMV assay. Testing was performed on 773 archived patient specimens. The strength of the agreement was good for the two assays performed on whole blood (κ=0.6, 95% CI 0.51-0.7) and moderate when the tests were performed on different sample types ((κ=0.54, 95% CI 0.47-0.62 for LC CMV WB vs COBAS PL; κ=0.57, 95% CI 0.5-0.65 for LC CMV WB vs COBAS PL) although the difference was not statistically significant. Using a combination gold standard, the sensitivity and specificity of the assays were respectively 78.8% and 99.3% for LC CMV; 85.2% and 98.1% for the COBAS CMV WB and 100% and 90.5% for COBAS CMV PL. Comparison of CMV viral loads trends in both plasma and whole blood of a few patients with multiple positive successive samples showed similar slopes with differences in slope ranging from 0.01-0.22. However, the absolute value for individual viral load differed markedly with whole blood viral loads on average 0.5-1.22 log higher than in plasma. The COBAS CMV assay provides a valid option for monitoring of viral loads in transplant patients. Due to its increased sensitivity, detection of patients with low viral loads (i.e. below LOQ) is increased with the COBAS CMV assay in plasma specimens. Longitudinal prospective studies will be needed to examine the clinical significance of these low level viral loads. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Preview · Article · Feb 2015 · Journal of Clinical Microbiology
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    ABSTRACT: Cancer patients treated with targeted therapies (e.g., epidermal growth factor receptor inhibitors) are susceptible to dermatologic adverse events (AEs) including secondary skin infections. Whereas infections such as paronychia and cellulitis have been reported, nasal vestibulitis (NV) has not been described with the use of these agents. The aim of our study was to characterize NV in cancer patients treated with targeted therapies. We utilized a retrospective chart review of cancer patients who had been referred to dermatology and were diagnosed with NV. We recorded data including demographics, referral reason, underlying malignancy, targeted anticancer regimen, NV treatment, and nasal bacterial culture results. One Hundred Fifteen patients were included in the analysis, of which 13 % experienced multiple NV episodes. Skin rash was the most common reason (90 %) for a dermatology referral. The most common underlying malignancies were lung (43 %), breast (19 %), and colorectal (10 %) cancer. Sixty-eight percent of patients had been treated with an EGFRI-based regimen. Nasal cultures were obtained in 60 % of episodes, of which 94 % were positive for one or more organisms. Staphylococcus aureus was the most commonly isolated organism [methicillin-sensitive S. aureus 43 %; methicillin-resistant S. aureus 3 %]. We report the incidence and characteristics of an unreported, yet frequent dermatologic condition in cancer patients treated with targeted therapies. These findings provide the basis for additional studies to describe the incidence, treatment, and consequences of this event. A better understanding of NV would mitigate its impact on patients' quality of life and risk for additional dermatologic AEs.
    Preview · Article · Jan 2015 · Supportive Care Cancer
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    ABSTRACT: We describe the case of an immunocompromised patient, positive for influenza A virus (H3N2), in whom the neuraminidase R292K mutation was transiently detected during oseltamivir treatment. The R292K mutation was identified by direct testing in three of eleven respiratory specimens collected throughout the patient's illness, but in none of the cultures from those specimens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Preview · Article · Jan 2015 · Journal of Clinical Microbiology
  • T. McMillen · J. Chen · J. Sun · S. Nie · F. Fan · N. Babady · Y. Tang

    No preview · Conference Paper · Nov 2014

  • No preview · Conference Paper · Nov 2014
  • Lauren Richardson · Anna Sheahan · N. Esther Babady · Janet Eagan · Mini Kamboj
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    ABSTRACT: Background: Community respiratory viruses (CRV) are a leading cause of infection related morbidity and mortality for patients undergoing cancer treatment. Molecular based testing (PCR) is a faster, more sensitive diagnostic method than culture. PCR does not differentiate between active viral replication and resolved infection, thus making test of cure and isolation policies for CRV-positive patients unclear. Aim: The goal of this analysis was to compare duration of CRV shedding as detected by culture and PCR for patients with hematologic malignancy. Methods: Results of respiratory virus tests from two study periods, Jan. 2009-Sept. 2011 (culture) and Sept. 2011-Apr. 2013 (PCR) were reviewed for patients with hematologic malignancy [hematopoietic stem cell transplant, leukemia, lymphoma, and pediatric oncology]. Patients were included if tested positive for influenza A, influenza B, parainfluenza (PIV), human metapneumovirus (HMPV), and/or respiratory syncytial virus (RSV), and if first re-tested within 5-30 days after initial diagnosis. The patients' symptoms at time of each re-test were also reviewed. Results: This study included 651 CRV infection episodes; 203 detected by culture and 448 by PCR. Fig 1 shows the median and range of shedding for each virus. The median length of shedding by culture and PCR respectively is as follows, influenza A: 13 vs 15; influenza B: 14 vs 16; RSV:13 vs 18; PIV: 9 vs 17; HMPV 10 vs 16.5. Of the 72 (16%) PCR-positive patients who shed virus for >30 days, most (74%) were non-influenza viruses. There was no correlation between symptoms at time of test and result of test. Patients with ALC< 200 at time of retesting were more likely to still shed the virus (Table 1). Conclusion: For our cohort of immunosuppressed patients, longer shedding was seen with PCR than culture. Shedding of influenza viruses was similar across both methods, seldom lasting > 1 month. Overall, shedding >1 month was rare, and seen most with RSV and PIV. Symptom based assessment of viral shedding is unreliable. Our findings should help guide infection control practices for CRV in high risk patients. Fig 1. Viral shedding Table 1. Symptoms at repeat test Result Count %fever %cough %rhinorrhea %sinus congestion %LRI %ALC<=200 + 186 6.5% 56.5% 41.9% 12.4% 14.0% 11.80% - 262 4.6% 33.6% 20.6% 7.3% 3.4% 3.10%
    No preview · Conference Paper · Oct 2014
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    ABSTRACT: We evaluated the Lyra Direct HSV 1+2/VZV multiplex real-time PCR assay for the detection and differentiation of herpes simplex virus 1 (HSV-1), HSV-2, and varicella-zoster virus (VZV) on 695 consecutive cutaneous and mucocutaneous lesion specimens. The intra-assay and interassay coefficient of variation values for the Lyra assay were 0.29 to 1.30% and 2.33 to 2.61%, respectively. The sensitivities, specificities, and positive and negative predictive values were 93.4 to 95.0%, 96.1 to 96.8%, 78.0 to 80.3%, and 99.0 to 99.1%, respectively, in comparison to those of viral culture. The values were further improved when a resolution analysis was performed with a laboratory-developed PCR assay.
    Preview · Article · Jul 2014 · Journal of Clinical Microbiology
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    ABSTRACT: Rapid and accurate diagnosis of influenza (Flu) is important for infection control as well as for patient management. Alere i Influenza A&B is an isothermal nucleic acid amplification-based integrated system for detection and differentiation of FluA and FluB. The performance of the Alere i Influenza A&B was screened using frozen nasopharyngeal swab specimens collected in viral transport media (VTM) that were originally tested fresh with the FilmArray Respiratory Panel (RP) assay during the 2012/2013 influenza outbreak. In total, 360 VTM specimens were selected for Alere i Influenza A&B testing, including 40 FluA H1N1-2009 (FluA-1), 40 FluA H3N2 (FluA-3), 37 FluA "equivocal" or "no subtype detected" (FluA-u), 41 FluB and 202 Flu-negatives as initially determined by the FilmArray RP assay. The Alere assay showed sensitivities of 87.2%, 92.5%, 25.0% and 97.4% for FluA-1, FluA-3, FluA-u, and FluB, respectively, after discordant resolution by Prodesse ProFLU+ PCR. The specificities were 100% for both FluA and FluB. In general, the Alere i Influenza A&B provided good sensitivity although the assay did show poorer sensitivity with samples determined to be of low FluA titer by Prodesse ProFlu+ PCR (mean real-time PCR threshold cycle (CT) value of 31.9 ± 2.0), which included the majority of the samples called FluA "equivocal" or "no subtype detected" by a single BioFire FilmArray RP test. The integrated, rapid and simple characteristics of the Alere i Influenza A&B make it potential for point-of-care testing with a test turnaround time less than 15 minutes.
    Preview · Article · Jul 2014 · Journal of Clinical Microbiology
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    ABSTRACT: The use of molecular methods to diagnose Clostridium difficile infection (CDI) has improved diagnostic yield compared to conventional methods. However, PCR testing can detect colonization and has introduced several practical challenges pertaining to need for treatment and isolation of cases. For all new cases detected by real-time PCR, concurrent cytotoxin assay was performed and genetic characterization with MLVA (multi-locus variable number tandem repeat analysis) was done to determine relatedness. We used PCR cycle threshold (Ct) of detection as surrogate marker for bacterial burden in stool. Overall, 54 cases of CDI were detected during the study period. 42 were concurrently tested by CYT and characterized by MLVA .MLVA analysis revealed marked genetic diversity with no ongoing outbreaks; four cases were due to NAP1 strain. CYT -/PCR + cases had a higher median Ct value of detection compared to CYT+/PCR + cases (28.2 vs 22.5; p = 0.01). Among 25 strains that were genetically related, 9/11 isolates in this dominant cluster were positive by CYT compared to 4/14 in non-dominant clusters (p = 0.02). CYT-/PCR+ cases contribute to hospital based transmission. However, the risk of transmission of C. difficile from CYT +/PCR+ cases may be higher than those that are CYT-/PCR+.
    Preview · Article · Feb 2014 · PLoS ONE
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    ABSTRACT: We describe here the use of an immunomagnetic separation enrichment process coupled with a modified real-time cellular analysis (RTCA) system (RTCA version 2) for the detection of C. difficile toxin (CDT) in stool. The limit of CDT detection by RTCA version 2 was 0.12 ng/ml. Among the consecutively collected 401 diarrheal stool specimens, 53 (13.2%) were toxin-producing C. difficile strains by quantitative toxigenic culture (qTC); bacterial loads ranged from 3.00 × 101 to 3.69 × 106 CFU/ml. The RTCA version 2 method detected CDT in 51 samples, resulting in a sensitivity of 96.2%, a specificity of 99.7%, and positive and negative predictive values of 98.1% and 99.4%, respectively. The positive step time ranged from 1.43 to 35.85 h, with <24 h for 80% of the samples. The CDT concentrations in stool samples determined by RTCA version 2 correlated with toxigenic C. difficile bacterial load (R2 = 0.554, P = 0.00002) by qTC as well as the threshold cycle (R2 = 0.343, P = 0.014) by real-time PCR. A statistically significant correlation between the CDT concentrations and the clinical severity of CDI was observed (P = 0.015). The sensitivity of the RTCA version 2 assay for the detection of functional toxins in stool specimens was significantly improved when the immunomagnetic separation enrichment process was incorporated. More than 80% positive results can be obtained within 24 h. The stool specimen CDT concentration derived using the RTCA version 2 assay correlates with clinical severity and may be used as a marker for monitoring the status of CDI.
    Preview · Article · Jan 2014 · Journal of clinical microbiology
  • N Esther Babady
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    ABSTRACT: The FilmArray Respiratory Panel (RP) (BioFire(™) Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray RP targets 20 pathogens including 17 viruses and subtypes and three bacteria, and is performed with minimal sample manipulation. The FilmArray RP has a fully automated sample-to-answer workflow with a turn-around-time of approximately 1 h. The reported sensitivity and specificity of the assay ranges from 80 to 100 and 100%, respectively, with the sensitivity for the adenovirus as low as 46%. A new version of the FilmArray RP assay (version 1.7) with improved sensitivity for the adenovirus was released in 2013. The performance characteristics and simplified workflow have allowed its implementation in a wide range of laboratories. The FilmArray RP has changed the diagnostic landscape and will have a significant impact on the care of patients with respiratory tract infection.
    No preview · Article · Nov 2013 · Expert Review of Molecular Diagnostics
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    ABSTRACT: We report disseminated adenovirus (ADV) infection in four adult cancer patients presenting with focal pulmonary consolidation. In all cases, ADV was recovered from respiratory specimens and ADV viremia (>1 × 105 copies/ml) was determined by a quantitative PCR assay. Despite antiviral therapy, 3 (75%) patients died. ADV should be considered as a possible cause of severe pneumonia in immunosuppressed patients.
    Preview · Article · Oct 2013 · Journal of clinical microbiology

Publication Stats

419 Citations
149.93 Total Impact Points

Institutions

  • 2010-2015
    • Memorial Sloan-Kettering Cancer Center
      • Infectious Diseases Service
      New York, New York, United States
    • University of Texas Health Science Center at Tyler
      Tyler, Texas, United States
  • 2013
    • Cornell University
      Итак, New York, United States
  • 2011
    • Mayo Clinic - Rochester
      • Department of Laboratory Medicine & Pathology
      Рочестер, Minnesota, United States