Diagnostic Pathology Next-Generation Diagnosis of Infectious Diseases Wendy Szymczak, PhD Assistant Professor, Department of Pathology 718.920.4585 wszymcza@montefiore.org View Profile The Clinical Microbiology Laboratory at Montefiore, under the leadership of Wendy Szymczak, PhD, interim director, is working with the research laboratory of Dr. William Jacobs and several Montefiore gastroenterologists to implement next-generation, whole-genome sequencing for pathogen detection, identification, and antimicrobial susceptibility prediction. Sequencing of DNA extracted from clinical specimens has particular utility for the detection of pathogens not recoverable by culture or slow-growing organisms since diagnosis and determination of optimal antimicrobial therapy may not otherwise be possible or significantly delayed. Whole-genome sequencing offers advantages over targeted, PCR-based assays because a broader range of pathogens can be detected and a comprehensive analysis of genotypic resistance and virulence characteristics simultaneously performed. The investigators are exploring the utility of sequencing for predicting the antimicrobial susceptibility of Helicobacter pylori, a gastric pathogen that can cause chronic gastritis, ulceration, or cancer. This is important because therapy is needed for symptom relief and because eradication of H. pylori has been shown to be effective in the prevention of primary gastric cancer. Susceptibility testing of this organism is necessary because H. pylori antimicrobial resistance is increasing, and eradication is improved by susceptibility-guided therapy. H. pylori is a fastidious pathogen that is difficult to isolate and sustain in culture, and the lack of phenotypic susceptibility testing guidelines and interpretation standards for most antibiotics used to treat H. pylori highlight a need for the development of new methods that accurately determine susceptibility. Future projects will also assess the feasibility of H. pylori detection and antimicrobial susceptibility determination directly from gastric-tissue specimens.