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Article ; Online: Feasibility of a Text Messaging–Integrated and Chatbot-Interfaced Self-Management Program for Symptom Control in Patients With Gastrointestinal Cancer Undergoing Chemotherapy

Sameh Gomaa / James Posey / Babar Bashir / Atrayee Basu Mallick / Eleanor Vanderklok / Max Schnoll / Tingting Zhan / Kuang-Yi Wen

JMIR Formative Research, Vol 7, p e

Pilot Mixed Methods Study

2023 Volume 46128

Abstract: BackgroundOutpatient chemotherapy often leaves patients to grapple with a range of complex side effects at home. Leveraging tailored evidence-based content to monitor and manage these symptoms remains an untapped potential among patients with ... ...

Abstract	BackgroundOutpatient chemotherapy often leaves patients to grapple with a range of complex side effects at home. Leveraging tailored evidence-based content to monitor and manage these symptoms remains an untapped potential among patients with gastrointestinal (GI) cancer. ObjectiveThis study aims to bridge the gap in outpatient chemotherapy care by integrating a cutting-edge text messaging system with a chatbot interface. This approach seeks to enable real-time monitoring and proactive management of side effects in patients with GI cancer undergoing intravenous chemotherapy. MethodsReal-Time Chemotherapy-Associated Side Effects Monitoring Supportive System (RT-CAMSS) was developed iteratively, incorporating patient-centered inputs and evidence-based information. It synthesizes chemotherapy knowledge, self-care symptom management skills, emotional support, and healthy lifestyle recommendations. In a single-arm 2-month pilot study, patients with GI cancer undergoing chemotherapy received tailored intervention messages thrice a week and a weekly Patient-Reported Outcomes Version of the Common Terminology Criteria for Adverse Events–based symptom assessment via a chatbot interface. Baseline and postintervention patient surveys and interviews were conducted. ResultsOut of 45 eligible patients, 34 were enrolled (76% consent rate). The mean age was 61 (SD 12) years, with 19 (56%) being females and 21 (62%) non-Hispanic White. The most common cancer type was pancreatic (n=18, 53%), followed by colon (n=12, 35%) and stomach (n=4, 12%). In total, 27 (79% retention rate) participants completed the postintervention follow-up. In total, 20 patients texted back at least once to seek additional information, with the keyword “chemo” or “support” texted the most. Among those who used the chatbot system checker, fatigue emerged as the most frequently reported symptom (n=15), followed by neuropathy (n=7). Adjusted for multiple comparisons, patients engaging with the platform exhibited significantly improved Patient Activation ...
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	JMIR Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Repurposing the FDA-approved anthelmintic pyrvinium pamoate for pancreatic cancer treatment

Benjamin E Leiby / Charles Yeo / James Posey / Avinoam Nevler / Harish Lavu / T Yeo / Francesca M Ponzini / Christopher W Schultz / Shawnna Cannaday / Wilbur B Bowne / Jonathan R Brody

BMJ Open, Vol 13, Iss

study protocol for a phase I clinical trial in early-stage pancreatic ductal adenocarcinoma

2023 Volume 10

Abstract: Background Recent reports of the utilisation of pyrvinium pamoate (PP), an FDA-approved anti-helminth, have shown that it inhibits pancreatic ductal adenocarcinoma (PDAC) cell growth and proliferation in-vitro and in-vivo in preclinical models. Here, we ... ...

Abstract	Background Recent reports of the utilisation of pyrvinium pamoate (PP), an FDA-approved anti-helminth, have shown that it inhibits pancreatic ductal adenocarcinoma (PDAC) cell growth and proliferation in-vitro and in-vivo in preclinical models. Here, we report about an ongoing phase I open-label, single-arm, dose escalation clinical trial to determine the safety and tolerability of PP in PDAC surgical candidates.Methods and analysis In a 3+3 dose design, PP is initiated 3 days prior to surgery. The first three patients will be treated with the initial dose of PP at 5 mg/kg orally for 3 days prior to surgery. Dose doubling will be continued to a reach a maximum of 20 mg/kg orally for 3 days, if the previous two dosages (5 mg/kg and 10 mg/kg) were tolerated. Dose-limiting toxicity grade≥3 is used as the primary endpoint. The pharmacokinetic and pharmacodynamic (PK/PD) profile of PP and bioavailability in humans will be used as the secondary objective. Each participant will be monitored weekly for a total of 30 days from the final dose of PP for any side effects. The purpose of this clinical trial is to examine whether PP is safe and tolerable in patients with pancreatic cancer, as well as assess the drug’s PK/PD profile in plasma and fatty tissue. Potential implications include the utilisation of PP in a synergistic manner with chemotherapeutics for the treatment of pancreatic cancer.Ethics and dissemination This study was approved by the Thomas Jefferson Institutional Review Board. The protocol number for this study is 20F.041 (Version 3.1 as of 27 October 2021). The data collected and analysed from this study will be used to present at local and national conferences, as well as, written into peer-reviewed manuscript publications.Trial registration number ClinicalTrials.gov: NCT05055323.
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission

Kristin N. Nelson / Sarah Talarico / Shameer Poonja / Clinton J. McDaniel / Martin Cilnis / Alicia H. Chang / Kala Raz / Wendy S. Noboa / Lauren Cowan / Tambi Shaw / James Posey / Benjamin J. Silk

Frontiers in Public Health, Vol

2022 Volume 9

Abstract: Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters. Existence of few genomic differences between Mtb isolates might indicate TB cases are the result of ...

Abstract	Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters. Existence of few genomic differences between Mtb isolates might indicate TB cases are the result of recent transmission. However, the variable and sometimes long duration of latent infection, combined with uncertainty in the Mtb mutation rate during latency, can complicate interpretation of WGS results. To estimate the association between infection duration and single nucleotide polymorphism (SNP) accumulation in the Mtb genome, we first analyzed pairwise SNP differences among TB cases from Los Angeles County, California, with strong epidemiologic links. We found that SNP distance alone was insufficient for concluding that cases are linked through recent transmission. Second, we describe a well-characterized cluster of TB cases in California to illustrate the role of genomic data in conclusions regarding recent transmission. Longer presumed latent periods were inconsistently associated with larger SNP differences. Our analyses suggest that WGS alone cannot be used to definitively determine that a case is attributable to recent transmission. Methods for integrating clinical, epidemiologic, and genomic data can guide conclusions regarding the likelihood of recent transmission, providing local public health practitioners with better tools for monitoring and investigating TB transmission.
Keywords	tuberculosis—epidemiology ; prevention and control ; genomic sequencing ; tuberculosis transmission ; public health practice ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Logically Inferred Tuberculosis Transmission (LITT)

Kathryn Winglee / Clinton J. McDaniel / Lauren Linde / Steve Kammerer / Martin Cilnis / Kala M. Raz / Wendy Noboa / Jillian Knorr / Lauren Cowan / Sue Reynolds / James Posey / Jeanne Sullivan Meissner / Shameer Poonja / Tambi Shaw / Sarah Talarico / Benjamin J. Silk

Frontiers in Public Health, Vol

A Data Integration Algorithm to Rank Potential Source Cases

2021 Volume 9

Abstract: Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis ... ...

Abstract	Understanding tuberculosis (TB) transmission chains can help public health staff target their resources to prevent further transmission, but currently there are few tools to automate this process. We have developed the Logically Inferred Tuberculosis Transmission (LITT) algorithm to systematize the integration and analysis of whole-genome sequencing, clinical, and epidemiological data. Based on the work typically performed by hand during a cluster investigation, LITT identifies and ranks potential source cases for each case in a TB cluster. We evaluated LITT using a diverse dataset of 534 cases in 56 clusters (size range: 2–69 cases), which were investigated locally in three different U.S. jurisdictions. Investigators and LITT agreed on the most likely source case for 145 (80%) of 181 cases. By reviewing discrepancies, we found that many of the remaining differences resulted from errors in the dataset used for the LITT algorithm. In addition, we developed a graphical user interface, user's manual, and training resources to improve LITT accessibility for frontline staff. While LITT cannot replace thorough field investigation, the algorithm can help investigators systematically analyze and interpret complex data over the course of a TB cluster investigation.Code available at:https://github.com/CDCgov/TB_molecular_epidemiology/tree/1.0; https://zenodo.org/badge/latestdoi/166261171.
Keywords	tuberculosis ; whole-genome sequencing ; transmission ; genomic epidemiology ; cluster investigation ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic

Marisa Klopper / Tim Hermanus Heupink / Grant Hill-Cawthorne / Elizabeth Maria Streicher / Anzaan Dippenaar / Margaretha de Vos / Abdallah Musa Abdallah / Jason Limberis / Matthias Merker / Scott Burns / Stefan Niemann / Keertan Dheda / James Posey / Arnab Pain / Robin Mark Warren

BMC Medicine, Vol 18, Iss 1, Pp 1-

2020 Volume 14

Abstract: Abstract Background Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and ... ...

Abstract	Abstract Background Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. Methods We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. Results Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. Conclusion The presence of the ethA mutation in otherwise susceptible isolates from ...
Keywords	Tuberculosis ; Drug-resistant ; Beyond-XDR-TB ; Missed resistance ; Weakened regimen ; Whole genome sequencing ; Medicine ; R
Subject code	630
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Author Correction

Matthew Ezewudo / Amanda Borens / Álvaro Chiner-Oms / Paolo Miotto / Leonid Chindelevitch / Angela M. Starks / Debra Hanna / Richard Liwski / Matteo Zignol / Christopher Gilpin / Stefan Niemann / Thomas Andreas Kohl / Robin M. Warren / Derrick Crook / Sebastien Gagneux / Sven Hoffner / Camilla Rodrigues / Iñaki Comas / David M. Engelthaler /

David Alland / Leen Rigouts / Christoph Lange / Keertan Dheda / Rumina Hasan / Ruth McNerney / Daniela M. Cirillo / Marco Schito / Timothy C. Rodwell / James Posey

Scientific Reports, Vol 10, Iss 1, Pp 1-

Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

2020 Volume 1

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-02-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance

Timothy M Walker, DPhil / Paolo Miotto, PhD / Claudio U Köser, PhD / Philip W Fowler, PhD / Jeff Knaggs, BSc / Zamin Iqbal, DPhil / Martin Hunt, PhD / Leonid Chindelevitch, PhD / Maha R Farhat, MD / Daniela Maria Cirillo, PhD / Iñaki Comas, PhD / James Posey, PhD / Shaheed V Omar, PhD / Timothy EA Peto, ProfFRCP / Anita Suresh, MSc / Swapna Uplekar, PhD / Sacha Laurent, PhD / Rebecca E Colman, PhD / Carl-Michael Nathanson, PhD /

Matteo Zignol, MD / Ann Sarah Walker, ProfPhD / Derrick W Crook, ProfFRCPath / Nazir Ismail, FRCPath SA / Timothy C Rodwell, ProfMD / A Sarah Walker / Adrie J C Steyn / Ajit Lalvani / Alain Baulard / Alan Christoffels / Alberto Mendoza-Ticona / Alberto Trovato / Alena Skrahina / Alexander S Lachapelle / Alice Brankin / Amy Piatek / Ana Gibertoni Cruz / Anastasia Koch / Andrea Maurizio Cabibbe / Andrea Spitaleri / Angela P Brandao / Angkana Chaiprasert / Anita Suresh / Anna Barbova / Annelies Van Rie / Arash Ghodousi / Arnold Bainomugisa / Ayan Mandal / Aysha Roohi / Babak Javid / Baoli Zhu

The Lancet Microbe, Vol 3, Iss 4, Pp e265-e

a genotypic analysis

2022 Volume 273

Abstract: Summary: Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to ...

Abstract	Summary: Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 ...
Keywords	Medicine (General) ; R5-920 ; Microbiology ; QR1-502
Subject code	572
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Integrating standardized whole genome sequence analysis with a global Mycobacterium tuberculosis antibiotic resistance knowledgebase

David Alland / Leen Rigouts / Christoph Lange / Keertan Dheda / Rumina Hasan / Ruth McNerney / Daniela M. Cirillo / Marco Schito / Timothy C. Rodwell / James Posey

Scientific Reports, Vol 8, Iss 1, Pp 1-

2018 Volume 10

Abstract: Abstract Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole ... ...

Abstract	Abstract Drug-resistant tuberculosis poses a persistent public health threat. The ReSeqTB platform is a collaborative, curated knowledgebase, designed to standardize and aggregate global Mycobacterium tuberculosis complex (MTBC) variant data from whole genome sequencing (WGS) with phenotypic drug susceptibility testing (DST) and clinical data. We developed a unified analysis variant pipeline (UVP) (https://github.com/CPTR-ReSeqTB/UVP ) to identify variants and assign lineage from MTBC sequence data. Stringent thresholds and quality control measures were incorporated in this open source tool. The pipeline was validated using a well-characterized dataset of 90 diverse MTBC isolates with conventional DST and DNA Sanger sequencing data. The UVP exhibited 98.9% agreement with the variants identified using Sanger sequencing and was 100% concordant with conventional methods of assigning lineage. We analyzed 4636 publicly available MTBC isolates in the ReSeqTB platform representing all seven major MTBC lineages. The variants detected have an above 94% accuracy of predicting drug based on the accompanying DST results in the platform. The aggregation of variants over time in the platform will establish confidence-graded mutations statistically associated with phenotypic drug resistance. These tools serve as critical reference standards for future molecular diagnostic assay developers, researchers, public health agencies and clinicians working towards the control of drug-resistant tuberculosis.
Keywords	Medicine ; R ; Science ; Q
Subject code	572 ; 020
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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