N Esther Babady

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

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Publications (15)58.48 Total impact

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    ABSTRACT: We evaluated a Lyra HSV 1+2/VZV multiplex real-time PCR assay for detection and differentiation of HSV-1, HSV-2 and VZV on 695 consecutive skin and mucosal lesion specimens. Intra-assay and inter- assay coefficient of variances of the Lyra assay were 0.29-1.30% and 2.33-2.61%. Sensitivities, specificities, positive and negative predictive values were 93.4-95.0%, 96.1-96.8%, 78.0-80.3% and 99.0-99.1%, respectively, in comparison to viral culture. The values were further improved when a resolution analysis was performed with a laboratory developed PCR assay.
    Journal of clinical microbiology. 07/2014;
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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.
    Journal of clinical microbiology. 07/2014;
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    ABSTRACT: We described the use of an immunomagnetic separation enrichment process coupled with modified real-time cellular analysis (RTCA) system (RTCA v.2) for detection of C. difficile toxin (CDT) in stool. The limit of CDT detection by RTCA v.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 3.00×10(1) to 3.69×10(6) colony-forming units/mL. The RTCA v.2 method detected CDT in 51 samples resulting in sensitivity of 96.2%, specificity of 99.7%, positive and negative predictive value of 98.1% and 99.4% respectively. The positive step time ranged from 1.43 to 35.85 hours with less than 24 hours for 80% samples. The CDT concentration in stool samples determined by RTCA v.2 correlated with toxigenic C. difficile bacterial load (R(2)=0.554, P=0.00002) by qTC as well as the threshold cycle (R(2)=0.343, P=0.014) by real-time PCR. A statistically significant correlation between the CDT concentrations and clinical severity of CDI was observed (P=0.015). The sensitivity of the RTCA v.2 assay for 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 hours. CDT concentration in stool specimens derived from the RTCA v.2 assay co-relates with clinical severity and may be used as a marker for monitoring the status of CDI.
    Journal of clinical microbiology 01/2014; · 4.16 Impact Factor
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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+.
    PLoS ONE 01/2014; 9(2):e88262. · 3.53 Impact Factor
  • 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.
    Expert Review of Molecular Diagnostics 11/2013; 13(8):779-88. · 4.09 Impact Factor
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    ABSTRACT: We evaluated the performance characteristics of the FilmArray Respiratory Panel and the eSensor Respiratory Viral Panel on clinical and spiked lower respiratory tract specimens (LRTS) The overall agreement between the two methods was 89.5% (51/57). The lower limit of detection of both assays for all targets in LRTS was comparable to that in nasopharyngeal swab specimens.
    Journal of clinical microbiology 10/2013; · 4.16 Impact Factor
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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 (>1×10(5) copies/ml) was determined by a quantitative PCR assay. Despite antiviral therapy, 3 (75%) patients died. ADV should be considered as cause of severe pneumonia in immunosuppressed patients.
    Journal of clinical microbiology 10/2013; · 4.16 Impact Factor
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    ABSTRACT: We compared the performance characteristics of culture and the Cepheid Xpert vanA assay for routine surveillance of vancomycin-resistant enterococci (VRE) from rectal swabs in patients at high risk for VRE carriage. The Cepheid Xpert vanA assay had a limit of detection of 100 CFU/ml and correctly detected 101 well-characterized clinical VRE isolates with no cross-reactivity in 27 non-VRE and related culture isolates. The clinical sensitivity, specificity, positive predictive value, and negative predictive value of the Xpert vanA PCR assay were 100%, 96.9%, 91.3%, and 100%, respectively, when tested on 300 consecutively collected rectal swabs. This assay provides excellent predictive values for prompt identification of VRE-colonized patients in hospitals with relatively high rates of VRE carriage.
    Journal of clinical microbiology 09/2012; 50(11):3659-63. · 4.16 Impact Factor
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    ABSTRACT: Respiratory viruses are increasingly recognized as serious causes of morbidity and mortality in immunocompromised patients. The rapid and sensitive detection of respiratory viruses is essential for the early diagnosis and administration of appropriate antiviral therapy, as well as for the effective implementation of infection control measures. We compared the performance of two commercial assays, xTAG RVP Fast (Luminex Diagnostics, Toronto, Canada) and FilmArray RVP (FA RVP; Idaho Technology, Salt Lake City, UT), in pediatric patients at Memorial Sloan-Kettering Cancer Center. These assays detect the following viruses: respiratory syncytial virus; influenza A and B viruses; parainfluenza viruses 1, 2, 3, and 4; human metapneumovirus; adenovirus; enterovirus-rhinovirus; coronaviruses NL63, HKU1, 229E, and OC43; and bocavirus. We tested a total of 358 respiratory specimens from 173 pediatric patients previously tested by direct fluorescence assay (DFA) and viral culture. The overall detection rate (number of positive specimens/total specimens) for viruses tested by all methods was 24% for DFA/culture, 45% for xTAG RVP Fast, and 51% for FA RVP. The agreement between the two multiplex assays was 84.5%, and the difference in detection rate was statistically significant (P < 0.0001). Overall, the FA RVP assay was more sensitive than the xTAG RVP Fast assay and had a turnaround time of approximately 1 h. The sensitivity, simplicity, and random-access platform make FA RVP an excellent choice for laboratory on-demand service with low to medium volume.
    Journal of clinical microbiology 04/2012; 50(7):2282-8. · 4.16 Impact Factor
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    ABSTRACT: The aim of this study was to compare the clinical and laboratory characteristics of Clostridium difficile infection (CDI) in patients with discordant test results for the cytotoxin assay (CYT) and PCR assays. A retrospective study from May to August 2008 and March to May 2010 was performed. CDI was diagnosed in 128 patients. PCR increased the yield of C. difficile cases by 2-fold compared to that of the CYT assay. Fifty-six cases (44%) were detected by PCR only (CYT negative). Forty-nine percent of patients with non-NAP1 strains were detected by PCR only, compared to 28% of those infected with NAP1 strains (P < 0.05). No significant differences were found in the clinical severity of illness and outcome among patients that tested positive for CDI by both tests (CYT and PCR) compared to those that tested positive by PCR only.
    Journal of clinical microbiology 01/2012; 50(4):1303-7. · 4.16 Impact Factor
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    ABSTRACT: Capnocytophaga species are known commensals of the oral cavity of humans and animals (mainly dogs and cats) and are a rare cause of respiratory tract infections. We report a case of cavitary lung abscess caused by a Capnocytophaga species in a patient with a metastatic neuroendocrine tumor.
    Journal of clinical microbiology 11/2011; 50(1):204-7. · 4.16 Impact Factor
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    ABSTRACT: Molecular typing was used to examine surveillance definitions for recurrent Clostridium difficile-associated diarrhea. Among 102 patients, 85 had a second episode within 8 weeks, 88% of which were relapses. Of 49 second episodes occurring after > 8 weeks, 65% were relapses. Categorization of a recurrent episode occurring after >8 weeks as a new infection may misrepresent the majority of episodes for surveillance.
    Clinical Infectious Diseases 11/2011; 53(10):1003-6. · 9.37 Impact Factor
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    ABSTRACT: Invasive fungal infections (IFI) remain a serious threat to immunocompromised hosts. Current diagnostic methods, including fungal culture and antigen detection, are slow and often lack specificity. Rapid diagnostic tools with increased sensitivity and specificity could improve the care of patients with IFI. Recently, Luminex Molecular Diagnostics (Toronto, Canada) developed 23 analyte-specific reagents (ASRs) for the detection of the most common clinically relevant fungi. This study's objective was to evaluate the sensitivity and specificity of a subset of these ASRs for fungal isolates and clinical specimens. Previously characterized fungal and bacterial isolates (n = 110), blood culture specimens (n = 34), and respiratory specimens (n = 44) were tested using either a Candida 7-plex panel (Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, Candida lusitaniae, Candida guilliermondii, and Candida krusei) or a mold 11-plex panel (Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Scedosporium prolificans, Scedosporium apiospermum, Fusarium oxysporum/Fusarium solani, Rhizopus arrhizus, Rhizopus microsporus, Mucor indicus, and Cunninghamella bertholletiae). The Candida 7-plex panel correctly identified all Candida isolates as confirmed by fungal culture and biochemical tests, for a sensitivity and specificity of 100%. The mold 11-plex panel correctly identified all mold isolates tested except for A. niger. Fungal isolates of Rhizopus and Mucor species were not detected, either, although they could represent species other than those targeted by the ASRs. Further evaluation will be necessary to confirm the sensitivities of some of the mold ASRs. Implementation of these ASRs will allow same-day detection of fungal DNA in clinical specimens.
    Journal of clinical microbiology 08/2011; 49(11):3777-82. · 4.16 Impact Factor
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    ABSTRACT: Recent surveillance from US hospitals shows that more than 99.5% of vancomycin-resistant enterococci (VRE) isolates remain susceptible to daptomycin. This report describes emergence of daptomycin-resistant VRE at a major cancer center. The percentage of patients with daptomycin-resistant VRE bacteremia increased from 3.4% in 2007 to 15.2% in 2009 ([Formula: see text]). Without susceptibility data, empiric daptomycin therapy for VRE infections should be used with caution.
    Infection Control and Hospital Epidemiology 04/2011; 32(4):391-4. · 4.02 Impact Factor
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    ABSTRACT: Clostridium difficile is the most common cause of health care-associated diarrhea. Accurate and rapid diagnosis is essential to improve patient outcome and prevent disease spread. We compared our two-step diagnostic algorithm, an enzyme immunoassay for glutamate dehydrogenase (GDH) followed by the cytotoxin neutralization test (CYT) with a turnaround time of 24 to 48 h, versus the Cepheid Xpert C. difficile Epi assay, a PCR-based assay with a turnaround time of <1 h. In the first phase of the study, only GDH-positive stool samples were tested by both CYT and Xpert PCR. Discordant results were resolved by toxigenic culture. In the second phase, all stool samples were tested by GDH and Xpert PCR. Only GDH-positive stools were further tested by CYT. Genotypic characterization of 45 Xpert PCR-positive stools was performed by sequencing of the tcdC gene and PCR ribotyping. In phase 1, the agreement between the GDH-CYT and the GDH-Xpert PCR was 72%. The sensitivities and specificities of GDH-CYT and GDH-Xpert PCR were 57% and 97% and 100% and 97%, respectively. In phase 2, the agreement between GDH-CYT and Xpert PCR alone was 95%. As in phase 1, sensitivity of the Xpert PCR was higher than that of the GDH-CYT. The correlation between PCR-ribotyping, sequencing, and Xpert PCR for detection of NAP1 strains was excellent (>90%). The excellent sensitivity and specificity and the rapid turnaround time of the Xpert PCR assay as well as its strain-typing capability make it an attractive option for diagnosis of C. difficile infection.
    Journal of clinical microbiology 10/2010; 48(12):4519-24. · 4.16 Impact Factor