scholarly journals Evaluation of the Xpert MTB/RIF Performance on Tissues: Potential Impact on Airborne Infection Isolation at a Tertiary Cancer Care Center

2018 ◽  
Vol 39 (4) ◽  
pp. 462-466 ◽  
Author(s):  
Tracy McMillen ◽  
Shauna C. Usiak ◽  
Liang Hua Chen ◽  
Luz Gomez ◽  
Peter Ntiamoah ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Limit Of Detection ◽  
Tertiary Care ◽  
Ffpe Tissue ◽  
Cancer Center ◽  
Oncology Patients ◽  
Tissue Samples ◽  
Airborne Infection ◽  
Potential Impact ◽  
Tissue Specimens

OBJECTIVESIn this study, we sought to evaluate the performance of the Xpert MTB/RIF (Cepheid) assay for the detection of Mycobacterium tuberculosis (MTB) complex DNA on fresh and formalin-fixed, paraffin-embedded (FFPE) tissue specimens from oncology patients in an area with a low prevalence of tuberculosis. We also aimed to retrospectively assess the potential impact of Xpert MTB/RIF on the duration of airborne infection isolation (AII).SETTINGA 473-bed, tertiary-care cancer center in New York City.DESIGNA total of 203 tissue samples (101 FFPE and 102 fresh) were tested using Xpert MTB/RIF, including 133 pulmonary tissue samples (65.5%) and 70 extrapulmonary tissue samples (34.5%). Acid-fast bacilli (AFB) culture was used as the diagnostic gold standard. The limit of detection (LOD) and reproducibility were also evaluated for both samples types using contrived specimens. The potential impact of the Xpert MTB PCR assay on tissue samples from AII patients on AII duration was retrospectively assessed.RESULTSUsing the Xpert MTB/RIF for fresh tissue specimens, the sensitivity was 50% (95% CI, 1.3%–98.7%) and the specificity was 99% (95% CI, 94.5%–99.9%). For FFPE tissue specimens, the sensitivity was 100% (95% CI, 63.1%–100%) and the specificity was 98.3% (95% CI, 95.5%–100%. The LOD was 103 colony-forming units (CFU)/mL for both fresh and FFPE tissue specimens, and the Xpert MTB/RIF was 100% reproducible at concentrations 10 times that of the LOD. With an expected turnaround time of 24 hours, the Xpert MTB PCR could decrease the duration of AII from a median of 8 days to a median of 1 day.CONCLUSIONSThe Xpert MTB/RIF assay offers a valid option for ruling out Mycobacterium tuberculosis complex (MTBC) on tissue samples from oncology patients and for minimizing AII resource utilization.Infect Control Hosp Epidemiol 2018;39:462–466

scholarly journals High sensitivity sanger sequencing detection of BRAF mutations in metastatic melanoma FFPE tissue specimens

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lauren Y. Cheng ◽  
Lauren E. Haydu ◽  
Ping Song ◽  
Jianyi Nie ◽  
Michael T. Tetzlaff ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Limit Of Detection ◽  
False Negative ◽  
High Sensitivity ◽  
Ffpe Tissue ◽  
Braf Mutations ◽  
Tissue Samples ◽  
Ffpe Samples ◽  
Droplet Pcr ◽  
Tissue Specimens

AbstractMutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the single variant (V600E). These can result in false negatives for samples with low VAFs due to low tumor content or subclonal heterogeneity, or harbor non-V600 mutations. Here, we show that Sanger sequencing using the NuProbe VarTrace BRAF assay, based on the Blocker Displacement Amplification (BDA) technology, is capable of detecting BRAF V600 mutations down to 0.20% VAF from FFPE lymph node tissue samples. Comparison experiments on adjacent tissue sections using BDA Sanger, immunohistochemistry (IHC), digital droplet PCR (ddPCR), and NGS showed 100% concordance among all 4 methods for samples with BRAF mutations at ≥ 1% VAF, though ddPCR did not distinguish the V600K mutation from the V600E mutation. BDA Sanger, ddPCR, and NGS (with orthogonal confirmation) were also pairwise concordant for lower VAF mutations down to 0.26% VAF, but IHC produced a false negative. Thus, we have shown that Sanger sequencing can be effective for rapid detection and quantitation of multiple low VAF BRAF mutations from FFPE samples. BDA Sanger method also enabled detection and quantitation of less frequent, potentially actionable non-V600 mutations as demonstrated by synthetic samples.

scholarly journals High Sensitivity Sanger Sequencing Detection of BRAF Mutations in Metastatic Melanoma FFPE Tissue Specimens

2020 ◽  
Author(s):  
Lauren Cheng ◽  
Lauren Haydu ◽  
Ping Song ◽  
Jianyi Nie ◽  
Michael Tetzlaff ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Limit Of Detection ◽  
False Negative ◽  
High Sensitivity ◽  
Ffpe Tissue ◽  
Braf Mutations ◽  
Tissue Samples ◽  
Ffpe Samples ◽  
Droplet Pcr ◽  
Tissue Specimens

Abstract Mutations in the BRAF gene at or near the p. V600 locus are informative for therapy selection, but current methods for analyzing FFPE tissue DNA generally have a limit of detection of 5% variant allele frequency (VAF), or are limited to the single variant (V600E). These can result in false negatives for samples with low VAFs due to low tumor content or subclonal heterogeneity, or harbor non-V600 mutations. Here, we show that Sanger sequencing using the NuProbe VarTraceTM BRAF assay, based on the Blocker Displacement Amplification (BDA) technology, is capable of detecting BRAF V600 mutations down to 0.26% VAF from FFPE lymph node tissue samples. Comparison experiments on adjacent tissue sections using BDA Sanger, immunohistochemistry (IHC), digital droplet PCR (ddPCR), and NGS showed 100% concordance among all 4 methods for samples with BRAF mutations at ≥1% VAF, though ddPCR did not distinguish the V600K mutation from the V600E mutation. BDA Sanger, ddPCR, and NGS (with orthogonal confirmation) were also pairwise concordant for lower VAF mutations down to 0.26% VAF, but IHC produced a false negative. Thus, we have shown that Sanger sequencing can be effective for rapid detection and quantitation of multiple low VAF BRAF mutations from FFPE samples. BDA Sanger method also enabled detection and quantitation of less frequent, potentially actionable non-V600 mutations as demonstrated by synthetic samples.

Mycobacterium tuberculosis infection in cancer patients at a tertiary care cancer center in Japan

2014 ◽  
Vol 20 (3) ◽  
pp. 213-216 ◽  
Author(s):  
Takahiro Fujita ◽  
Masahiro Endo ◽  
Yoshiaki Gu ◽  
Tomoaki Sato ◽  
Norio Ohmagari
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Cancer Patients ◽  
Tertiary Care ◽  
Tuberculosis Infection ◽  
Cancer Center ◽  
Mycobacterium Tuberculosis Infection

Effect of patient education on palliative care knowledge and acceptability of outpatient palliative care service among gynecologic oncology patients.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 11583-11583 ◽  
Author(s):  
Ashley Graul ◽  
Ashley Ford Haggerty ◽  
Carolyn Stickley ◽  
Pallavi Kumar ◽  
Knashawn Morales ◽  
...  
Keyword(s):  
Palliative Care ◽  
Care Service ◽  
Gynecologic Oncology ◽  
Tertiary Care ◽  
Palliative Care Service ◽  
Cancer Center ◽  
Educational Video ◽  
Oncology Patients ◽  
Care Services ◽  
Palliative Care Services

11583 Background: This was a randomized control trial to estimate the effect of an interventional video on improving palliative care knowledge and acceptability of outpatient services in gynecologic oncology patients. Methods: Women receiving active treatment for gynecologic malignancy (persistent or progressive disease despite primary treatment) were recruited at an academic tertiary care center from 2/2018 to 1/2019 and randomized to: palliative care educational video or non-directive cancer center informational video (control). The primary outcome was desire for referral to palliative care. Function and knowledge were assessed using the Functional Assessment of Cancer Therapy (FACT-G) and the Palliative Care Knowledge Scales. Data analyses were performed using t-tests, Wilcoxon rank sum or Fisher’s exact tests with significance level of α=0.05. Results: 111 women were enrolled. Demographic characteristics were equally distributed between groups (mean age 63.4 vs 65.4 years; 78% vs 82% Caucasian, 58% vs 68% stage III, 71% vs 64% ovarian cancer, 65% vs 72% platinum-sensitive). There was no statistical difference in knowledge scores or in desire for referral to palliative care (29% vs 27%; p=0.79). Secondary analysis showed a statistically significant increase in utilization of palliative care services compared to historic institutional data (8.8% to 29.7%; p=<0.001). Further, those that desired referral had significantly worse FACT-G scores at time of referral choice (table). Conclusions: Use of a palliative care educational video did not increase knowledge or acceptability of palliative care services within this RCT. However, the rate of patients seeking palliative care referral tripled compared to historic rates. Further studies should investigate whether discussion regarding palliative care services alone may increase desire for referral, and if use of Fact-G scores may identify patients in greatest need of services. [Table: see text]

scholarly journals Use of Disinfection Cap to Reduce Central-Line–Associated Bloodstream Infection and Blood Culture Contamination Among Hematology–Oncology Patients

2015 ◽  
Vol 36 (12) ◽  
pp. 1401-1408 ◽  
Author(s):  
Mini Kamboj ◽  
Rachel Blair ◽  
Natalie Bell ◽  
Crystal Son ◽  
Yao-Ting Huang ◽  
...  
Keyword(s):  
High Risk ◽  
Blood Culture ◽  
Bloodstream Infection ◽  
Tertiary Care ◽  
Central Line ◽  
Cancer Center ◽  
Cell Transplant ◽  
Oncology Patients ◽  
Hematopoietic Stem ◽  
The Impact

OBJECTIVEIn this study, we examined the impact of routine use of a passive disinfection cap for catheter hub decontamination in hematology–oncology patients.SETTINGA tertiary care cancer center in New York CityMETHODSIn this multiphase prospective study, we used 2 preintervention phases (P1 and P2) to establish surveillance and baseline rates followed by sequential introduction of disinfection caps on high-risk units (HRUs: hematologic malignancy wards, hematopoietic stem cell transplant units and intensive care units) (P3) and general oncology units (P4). Unit-specific and hospital-wide hospital-acquired central-line–associated bloodstream infection (HA-CLABSI) rates and blood culture contamination (BCC) with coagulase negative staphylococci (CONS) were measured.RESULTSImplementation of a passive disinfection cap resulted in a 34% decrease in hospital-wide HA-CLABSI rates (combined P1 and P2 baseline rate of 2.66–1.75 per 1,000 catheter days at the end of the study period). This reduction occurred only among high-risk patients and not among general oncology patients. In addition, the use of the passive disinfection cap resulted in decreases of 63% (HRUs) and 51% (general oncology units) in blood culture contamination, with an estimated reduction of 242 BCCs with CONS. The reductions in HA-CLABSI and BCC correspond to an estimated annual savings of $3.2 million in direct medical costs.CONCLUSIONRoutine use of disinfection caps is associated with decreased HA-CLABSI rates among high-risk hematology oncology patients and a reduction in blood culture contamination among all oncology patients.Infect. Control Hosp. Epidemiol. 2015;36(12):1401–1408

scholarly journals Direct PCR on tissue samples to detect Mycobacterium tuberculosis complex: an alternative to the bacteriological culture

2020 ◽  
Author(s):  
V Lorente-Leal ◽  
E Liandris ◽  
M Pacciarini ◽  
A Botelho ◽  
K Kenny ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Limit Of Detection ◽  
Cross Reactivity ◽  
Whole Genome Sequence ◽  
The European Union ◽  
Direct Pcr ◽  
Tissue Samples ◽  
Complex Species ◽  
Diagnostic Sensitivity And Specificity ◽  
Pcr Targeting

Bovine tuberculosis (bTB) is an ongoing issue in several countries within the European Union (EU). Microbiological culture is the official confirmation technique for the presence of Mycobacterium tuberculosis complex (MTBC) members in bovine tissues, but several methodological issues, such as moderate sensitivity and long incubation times, require the development of more sensitive and rapid techniques. This study evaluates the analytical and diagnostic performance, comparatively to culture, of a real-time PCR targeting the MTBC-specific IS6110 transposon using a panel of bovine tissue samples sourced from the Spanish bTB eradication campaign. Robustness and repeatability were evaluated in an inter-laboratory trial between EU National Reference Laboratories. The limit of detection with 95% confidence was established at 65 fg/reaction of purified genomic. Diagnostic sensitivity and specificity was, respectively, 96.45% and 93.66%, and the overall agreement (κ) was 0.88. Cross-reactivity was detected against two mycobacterial isolates identified as M. marinum and “M. avium subsp. hominissuis” species, and Whole Genome Sequence analysis of the latter isolate revealed an IS6110-like sequence with 83% identity. An identical IS-like element was found in other Mycobacterium avium Complex species in the NCBI nucleotide and WGS databases. Despite this finding, this methodology is considered a valuable alternative to culture and the strategy of use should be defined depending on the control or eradication programmes.

scholarly journals Co-infection of COVID-19 and Tuberculosis in a Tertiary Care Hospital

2021 ◽  
Author(s):  
. Anuradha ◽  
Shiwangi Sharma ◽  
Bani Rai ◽  
Arvind Achra ◽  
Stuti Kansra ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Virus Disease ◽  
Tertiary Care ◽  
Data Entry ◽  
Final Analysis ◽  
Care Hospital ◽  
Microsoft Excel ◽  
Polymerase Chain ◽  
Spss Software ◽  
Potential Impact

Introduction: The burden of Tuberculosis (TB) has managed to remain an age old menace to our society, especially India. The potential impact of Corona Virus Disease-19 (COVID-19) on TB patients continues to be worrisome due to the disruption of the national program and its services. Aim: To compare the TB infection in COVID-19 vs non-COVID-19 patients. Materials and Methods: The study was undertaken at Department of Microbiology, ABVIMS, Dr. RML Hospital Delhi, India. The data was collected, retrospectively from 15thSeptember 2020 to 15th January 2021 from admitted 1094 non-COVID-19 and 150 COVID-19 patients, >18 years of age, either sex. Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) was done to diagnose COVID-19 and GeneXpert was used to detect Mycobacterium tuberculosis. The data entry was done in the Microsoft Excel spreadsheet and the final analysis was done with the use of Statistical Package for Social Sciences(SPSS) software version 21.0. Two by two contingency table was used for calculating the Odd’s ratio. Results: During the study period, 1094 samples were received from non-COVID-19 ward and 150 from COVID-19 ward. Out of 150 COVID-19 positive patients, 30 (20%) were also positive for Mycobacterium tuberculosis Complex (MTBC) and 120 (80%) were negative for MTBC. Out of 1094 COVID-19 negative patients, 98 (8.96%) were positive for MTBC and 996 (91.04%) were negative for MTBC. The Odd’s ratio/Risk Ratio (RR) of TB infection in COVID-19 infected patients was 3.08 {Confidence Interval (CI) 95%}. The mortality was 10% in the COVID-19 positive group. Conclusion: It was observed that the chances of contracting TBare thrice in COVID-19 patients and thus TB diagnosis should be equally emphasised and further strengthened in this ongoing pandemic.

397 Intra-tumor immunotherapy injections utilizing image guidance in interventional radiology: clinical trial experience at a tertiary care cancer center

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A422-A422
Author(s):  
Ravi Murthy ◽  
Rahul Sheth ◽  
Alda Tam ◽  
Sanjay Gupta ◽  
Vivek Subbiah ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Interventional Radiology ◽  
Real Time ◽  
Image Guidance ◽  
Tertiary Care ◽  
Cancer Center ◽  
Imaging Guidance ◽  
Image Guided ◽  
Real Time Image ◽  
Time Image

BackgroundImage guided intra-tumor administration of investigational immunotherapeutic agents represents an expanding field of interest. We present a retrospective review of the safety, feasibility & technical nuances of real-time image guidance for injection & biopsy across a spectrum of extracranial solid malignancies utilizing the discipline of Interventional Radiology.MethodsPatients who were enrolled in image guided intratumoral immunotherapy injection (ITITI) clinical trials over a 6 year period (2013–19) at a single tertiary care cancer center were included in this analysis. Malignancy, location, imaging guidance utilized for ITITI & biopsy for injected (adscopal) & non-injected (abscopal) lesions were determined and categorized. Peri-procedural adverse events were noted.Results262 pts (146 female, 61 yrs median) participating in 29 immunotherapeutic clinical trials (TLR & STING agonists, gene therapy, anti CD-40, viral/bacterial/metabolic oncolytics) met study criteria. Malignancies included melanoma 88, sarcoma 32, colorectal 29, breast 23, lung 17, head & neck 15, ovarian 8, neuroendocrine 7, pancreatic adenocarcinoma 6, 3 each (cholangioCA, endometrial, bladder, GI tract), 2 each (RCC, thymicCA, lymphoma, merkel cell, prostate) & others 1 each (CUP, GIST, dermatofibrosarcoma, DSRT, neuroblastoma, thyroid). All 169 & 93 patients received the intended 1371 ITITI in parietal (abdominal/chest wall, extremity, neck, pelvis) or visceral (liver, lung, peritoneum, adrenal) locations respectively; 83 patients received lymph node injections within either location. Imaging guidance was US in 68% of the cohort (US 161, CT+US 19); CT was used in 30% (81) & MRI in 1 patient. Median diameter of the ITITI lesion was 32 mm (8–230 mm). Median volume of the ITITI therapeutic material/session was 2 ml (1–6.9 ml). Lesions were accessed using a coaxial technique. ITITI delivery needles used at operator preference & tailored to lesion characteristics were either a 21G/22G Chiba, 21G Profusion (Cook Medical), 22G Morrison (AprioMed), 25G hypodermic (BD) & 18G Quadrafuse (Rex Medical). 2840 core biopsies (>18G Tru-cut core, Mission, Bard Medical) were performed in 237 patients during 690 procedures; biopsy sessions were often concurrent & of the ITITI site. 137 patients also underwent biopsy of a non-ITITI site (89 parietal location). Dimensions of the non-ITITI lesion were median 10 mm (7–113 mm); US image guidance was used in 97 patients (72%) to obtain a total of 1257, >18G Tru-core samples. 1.3% of injections resulted in SAE (NCI CTC AE >3) and 0.5% of 4097 biopsies developed major complications (SIR Criteria); both categories were manageable.ConclusionsUtilizing real time image guidance, ITITI to the administration of a myriad of investigational immunotherapeutic agents with concomitant biopsy procedures to date are associated with a high technical success rate & favorable safety profile.AcknowledgementsJoshua Hein, Mara Castaneda, Jyotsna Pera, Yunfang Jiang,Shuang Liu, Holly Liu and Anna LuiTrial RegistrationN/AEthics ApprovalThe study was approved by Institution’s Ethics Board, approval number 2020-0536: A retrospective study to determine the safety, feasibility and technical challenges of real-time image guidance for intra-tumor injection and biopsy across multiple solid tumors.Consent2020-0536 Waiver of Informed ConsentReferenceSheth RA, Murthy R, Hong DS, et al. Assessment of image-guided intratumoral delivery of immunotherapeutics in patients with cancer. JAMA Netw Open 2020;3(7):e207911. doi:10.1001/jamanetworkopen.2020.7911

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