Kyle G. Rodino, Ph.D., D(ABMM)
Assistant Professor of Clinical Pathology and Laboratory Medicine
Assistant Director, Clinical Microbiology
Hospital of the University of Pennsylvania and Perelman School of Medicine, University of Pennsylvania

Next-Generation Sequencing in Clinical Microbiology: Current Applications and What’s Next

Advanced molecular diagnostics, including next-generation sequencing (NGS)-based technologies, are increasingly integrating into the clinical microbiology laboratory. These new technologies have the ability to provide information not previously attainable, with current applications including organism identification, outbreak investigation and mutation surveillance, and detection of resistance determinants. Of particular interest to the diagnosis of infectious diseases is the use of metagenomic NGS (mNGS), targeted or unbiased, for pathogen detection direct from patient specimens. Case reports have shown the undeniable power of mNGS to provide diagnostic evidence where other methods have failed. However, a number of hurdles to routine use remain, including technical performance characteristics and clinical utility. Addressing these issues will be important to broad adoption of mNGS methods for infectious disease testing in the clinical microbiology laboratory, particularly as we look toward future applications, including rapid sequencing assays, antimicrobial susceptibility modeling, and disease-predictive host biomarkers.

Fabio Bagnoli, Ph.D.
Project Leader
GSK Vaccines

“Staphylococcus aureus – the immune evader”

Virtual Meeting
5 – 6pm

Zoom meeting details to be emailed to branch members. Non-branch members can watch the live stream on our YouTube Video Channel

upcoming Branch events
May 24 – Student chapter sponsored event, keynote speaker Shantanu Bhatt, Ph.D., St. Joseph’s University
June 14 – Norman Willett Memorial Lecture, keynote speaker Amy Vollmer, Swarthmore College

John Mekalanos, Ph.D.
Adele Lehman Professor of Microbiology & Molecular Genetics
Department of Microbiology
Harvard Medical School

Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs based on genomic similarities to bat and civet viruses. Here we report the analysis of conserved interactions between amino acid residues in all proteins encoded by SARS-CoV-related viruses. We identified pairs and networks of residue variants that exhibited statistically high frequencies of covariance with each other. While these interactions are likely key to both protein structure and other protein-protein interactions, we have also found that they can be used for understanding viral evolution and adaptation. Our data provide evidence that the evolutionary processes that converted a bat virus into human pathogen occurred through recombination with other viruses in combination with new adaptive mutations important for entry into human cells.

Lecture: 5 – 6pm

Also available on our branch YouTube channel

Friday December 4th, 2020

Virtual and Live Streamed on YouTube – click here

Morning Session
8:35 A.M. Introduction and Welcome- EPA-ASM student chapter
8:40 A.M. ASM Membership Benefits – Dieter Schifferli, DVM, PhD, President EPA-ASM Chapter
8:45 A.M. Paula Watnick, MD, PhD,
Associate Professor of Pediatrics, Harvard Medical School
“How microbial metabolites control innate immunity and metabolism in a model host intestine”

Graduate Student and Postdoctroal Fellow Presentations
9:45 A.M. Jean-Bernard Lubin, PhD, Postdoctoral Fellow, Children’s Hospital of Philadelphia “A gnotobiotic mouse model of pediatric host-commensal interactions”
10:05 A.M. Break
10:15 A.M. Rina Matsuda, Graduate Student, University of Pennsylvania “Inflammatory monocytes enhance control of Yersinia pseudotuberculosis by intestinal pyogranulomas”
10:35 A.M. Elisha Segrist, Graduate Student, University of Pennsylvania “Microbiota-derived cyclic dinucleotides drive dSTING-dependent enteric antiviral immunity in enterocytes”
10:55 A.M. Ruchika Dehinwal, PhD, Postdoctoral Fellow University of Pennsylvania “Salmonella outer membrane vesicles serve as traps for antibacterial host molecules “

11:15 A.M Poster Sessions and Lunch Break
11:15 A.M. to 12:15 P.M. Odd number poster presentations
12:15 P.M. to 1:15 P.M. Even number poster presentations

Afternoon Session
1:30 P.M. Tajie Harris, PhD
Associate Professor of Neuroscience, University of Virginia School of Medicine
“Alarmin’ the Immune System in the Brain”

Graduate Student and Postdoctoral Fellow Talks
2:30 P.M. Ronald Lucarelli, Graduate Student, Lewis Katz School of Medicine at Temple University “Eicosanoid-activated PPARα inhibits NFκB-dependent Bacterial Clearance during post-Influenza Superinfection”
2:50 P.M. Hager Mohamed, Graduate Student, Drexel University College of Medicine “Exposure to non-thermal plasma increases markers of immunogenicity in a model of latent HIV-1 infection”
3:10 P.M. Break
3:20 P.M. Carolina Rezende Melo-Silva, PhD,  Postdoctoral Fellow, Thomas Jefferson University “Type I interferon receptor signaling coordinates innate immune cells to control an acute viral disease”

3:40 P.M. 2020 Pestka Lecturer
Stanley Plotkin, MD, Emeritus Professor, University of Pennsylvania, Perelman School of Medicine
“The Past, Present, and Future of Vaccines”

4:40 P.M. Presenter Recognition and Poster Presentation Awards* *sponsored by the American Society for Microbiology and PBL Assay Science
5:00 P.M. Meeting Close

Abstract submissions:
see abstract submission guidelines

Please submit all abstracts to

Important Dates:
Oral Presentation Abstract Deadline: November 20th, 2020
Poster Presentation Abstract Deadline: November 25th, 2020
On time Meeting Registration Deadline: December 2nd, 2020

Click to register: PIIF2020registration

Organized by the Eastern Pennsylvania Branch & Student Chapter of the American Society for Microbiology