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11th Annual Sequencing, Finishing, and Analysis in the Future Meeting DRUG RESISTANCE DIAGNOSIS IN TUBERCULOSIS PATIENTS USING TARGETED NGS Wednesday, 1st June 10:00 La Fonda Ballroom Talk (OS‐1.01) Rebecca Colman 1 , Julia Anderson 2 , Darrin Lemmer 3 , Valeriu Crudu 4 , David Dolinger 5 , Claudia Denkinger 5 , David Engelthaler 2 , Timothy Rodwell 1 1 University of California, San Diego, 2 Translational Genomics Research Institute, 3 TGen North, 4 Phthisiopneumology Institute (PPI), 5 Foundation for Innovative New Diagnostics The spread of drug resistant TB (DRTB) is a major threat to global TB control, and the reason why universal drug susceptibility testing (DST) is a key component of the WHO “End TB” strategy. The able to rapidly detect complete drug resistance profiles in TB patients represents the most urgent need in TB treatment, but no scalable solution currently exists. All of the efforts to expand phenotypic methods for DST for case management and surveillance are hindered by cost, and by the need for complex laboratory infrastructure including TB culture facilities. We have developed a rapid and sensitive amplicon next generation sequencing (NGS) solution for producing comprehensive genotypic resistant profiles for Mycobacterium tuberculosis (Mtb) populations direct from patient samples. In addition to improvements in patient care, an amplicon approach also has the potential to accelerate broadly implementable “culture‐free” surveillance systems to quantify the worldwide distribution of TB drug resistance. In order for NGS to be successfully integrated into patient care and surveillance at a global scale we envision the need for a standardized and validated sequencing pipeline including an automated DNA extraction front‐end, and a standardized, validated analysis, interpretation and archiving system on the back‐end. The Relational Sequencing TB Data Platform (ReSeqTB) is a repository that is currently being developed for cataloging phenotypic, genotypic, and metadata associated with clinical DRTB isolates. Integrating our targeted sequencing approach into this repository, utilizing the vetted and standardized analysis pipeline, storage, and sharing platform of ReSeqTB, will help to develop and validate a simple, standardized NGS platform for the detection and interpretation of drug resistance in Mtb from sequences obtained directly from patient sputum. 9
11th Annual Sequencing, Finishing, and Analysis in the Future Meeting GENOMIC SEQUENCING AND ANALYSIS OF NEISSERIA GONORRHOEAE CLINICAL ISOLATES TO CHARACTERIZE ANTIMICROBIAL RESISTANCE IN RIO DE JANEIRO, BRAZIL Wednesday, 1st June 10:20 La Fonda Ballroom Talk (OS‐1.02) A. Jeanine Abrams 1 , Ana Paula Ramalho 2 , David Trees 1 1 Centers for Disease Control and Prevention, 2 Universidade Federal do Rio de Janeiro Neisseria gonorrhoeae, the etiological agent responsible for the sexually transmitted infection gonorrhea, is the second most common notifiable infection in the United States, and approximately 106 million new gonorrhea cases were globally estimated in 2008. Antimicrobial resistance to former first‐line antibiotics (e.g., penicillins, tetracyclines, fluoroquinolones, and cephalosporins) in N. gonorrhoeae have been facilitated by both plasmid‐ and chromosome‐mediated mechanis This acquired resistance has led to the current CDC treatment recommendation for uncomplicated gonorrhea, which outlines the dual‐use of ceftriaxone with either azithromycin or doxycycline. This study utilized genomic sequencing and analysis to characterize the rates and phylogenetic patterns associated with resistance to penicillin, tetracycline, ciprofloxacin, azithromycin, cefixime, and ceftriaxone in isolates from Rio de Janeiro, Brazil. We examined the genomes of 117 gonococcal isolates that were collected from public and private healthcare clinics between 2006 and 2015 in Rio de Janeiro. In addition to genomic data, we examined phenotypic data (antimicrobial susceptibility profiles) to further clarify the detected resistance patterns. The results indicated relatively low levels of reduced susceptibility to cefixime and azithromycin compared to the levels observed for the other antibiotics, and multi‐drug resistance was detected in several samples. Moreover, two samples exhibited reduced susceptibility to all of the tested antibiotics, with the exception of ceftriaxone. These results will not only further our understanding of the evolution of decreased susceptibility to a variety of antibiotics in Rio de Janeiro, but will also potentially inform the development of local and global treatment guidelines. 10
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Reliable solutions for focused NGS
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