Center for Pathogen Genomics and Microbial Evolution

Providing specialized expertise in pathogen-specific sequence analysis and bioinformatics for emerging and ongoing infectious disease threats.

The development of next generation DNA sequencing approaches has revolutionized genomics. As these technologies have become more affordable, easier to use and widely available, there has been an explosion of genomic sequence generated with hundreds of thousands of bacterial, viral and fungal genome sequences currently available through public databases. The wealth of microbial sequence data available, however, has far outpaced expertise and tools for analysis of these data. Owing in part to the considerable biological diversity among microbes - including bacteria, fungi and viruses - microbial genome sequence analysis has been difficult to standardize. Often, analysis approaches are not “one-size-fits-all” and a technique that is successful for studying one organism may not be directly applicable to another. To fully leverage the power of these tools, diverse expertise is required across several fields including microbiology, infectious disease clinical care, epidemiology and computational bioinformatics.

When properly harnessed through an integrated pipeline from sample acquisition to sequencing and bioinformatic analysis, pathogen genomics and molecular epidemiology can define the determinants of pathogen transmission, pathogenesis and evolution and so inform best practices in clinical care and public health. Indeed, the essentiality of rapid and effective microbial sequence analysis has been underscored by the global COVID-19 pandemic. Novel and creative approaches to SARS-CoV-2 viral sequencing and analysis have been central to important discoveries throughout the pandemic that have dictated diagnostic paradigms, facilitated drug discovery, charted routes of transmission and helped define best public health practices.

Northwestern has unmatched abilities in this field that is critical to the national and global efforts to track and study infectious disease threats. Implementing and expanding microbial genomic sequencing and innovative analysis capabilities pays dividends in infections prevented and lives saved.”

–Egon A. Ozer, MD, PhD, Director, Center for Pathogen Genomics and Microbial Evolution

Our Mission and Vision

Mission

We seek to facilitate the investigation of microbial transmission, pathogenesis, evolution and antimicrobial resistance to support discoveries and interventions in medicine, science and public health to address current and prepare for future infectious disease threats.

Vision

Our vision is to advance understanding, utilization and innovation in pathogen genomics at Northwestern by expanding available genome sequencing and analysis services, building expertise through education, facilitating academic development by writing and supporting funding awards, and attracting new talent to Northwestern by contributing to a dynamic research community.

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Why It's Important

Microbial genomics: the study of the complete genetic code of pathogenic organisms

Quickly and effectively defining, studying, and tracking genomic sequences of pathogens that cause infectious diseases is critical. As shown by the COVID-19 pandemic, microbial genomics can be instrumental in rapidly identifying a disease-causing virus or other pathogen, thus allowing for diagnosis and tracking of the infection as well as kickstarting development of effective vaccines and other therapeutics. Techniques applied to and lessons learned from microbial genomics are crucial to recognition, treatment, and prevention of future emerging and re-emerging infectious disease threats. Similarly, new and existing approaches in genomics are needed to address the continuing global pandemic of antibiotic resistance in bacteria.

Pathogen Genomics Symposium April 24, 2024

3rd Annual Pathogen Genomics Symposium

The 3rd Annual Pathogen Genomics Symposium, hosted by the Robert J. Havey, MD Institute for Global Health’s Center for Pathogen Genomics and Microbial Evolution, will include two days of scholarly events, including a pathogen genomics workshop, research talks, flash talks, keynote address, poster session, and reception. A full agenda can be found below.

The Pathogen Genomics Symposium was held on Wednesday, April 24th, 2024 in the Simpson Querrey Biomedical Research Center.

Featuring a Keynote Address by James Mullins, PhD
“A Deep Look at HIV Evolutionary Dynamics Early in Infection”

Agenda

Symposium participant presenting their poster to an attendee

Headshots of Pathogen Genomics Symposium speakers, including keynote speaker James Mullins, PhD

Event Agenda:

When: Wednesday, April 24th, 2024Time: 8:30 a.m. - 5:00 p.m.
Location: Simpson Querrey Biomedical Research Center,
303 E. Superior St, Chicago

Coffee / Pastries
8:30 - 9:00 a.m.
Outside of SQ Auditorium

9:00 - 9:30 a.m.: James Davis (Argonne National Laboratory)
“Machine Learning Based Prediction of AMR Phenotypes and Genotypes”
Simpson Querrey Auditorium, SQBRC 1-230

9:30 - 10:00 a.m.: Hannah Barbian (Rush University)
“Pathogen Surveillance and Characterization by Indoor Air Sampling”
Simpson Querrey Auditorium, SQBRC 1-230

Coffee Break
10:00 - 10:15 a.m.
Outside of SQ Auditorium

10:15 - 10:45 a.m.: Ramon Lorenzo Redondo (Northwestern University)
“Evolutionary Analysis of Genetic Diversity, the Main Driver of Viral Population Dynamics"
Simpson Querrey Auditorium, SQBRC 1-230

10:45 - 11:15 a.m.: Matthew Anderson (University of Wisconsin, Madison)
“Parasex Generates Highly Recombinant Candida albicans Progeny”
Simpson Querrey Auditorium, SQBRC 1-230

11:15 - 11:45 a.m.: Rachel Whitaker (University of Illinois, Urbana-Champaign)
“Spatiotemporal Within-Host Evolutionary Dynamics of Pseudomonas aeruginosa”
Simpson Querrey Auditorium, SQBRC 1-230

Lunch
12:00 - 12:45 p.m.
Potocsnak Family Atrium, SQBRC
*Lunch will be provided

Flash Talks & Awards
12:45 - 1:30 p.m.
Potocsnak Family Atrium, SQBRC

Presenters:
Daniel Amusin
Suchen Feng
Alex Grote
Brooks Mitchell
Madeleine Vessely

Keynote Address by James Mullins, PhD
“A Deep Look at HIV Evolutionary Dynamics Early in Infection”
1:30 - 2:30 p.m.
Simpson Querrey Auditorium, SQBRC 1-230

Poster Session and Reception:
2:30p.m. - 5:00 p.m.
Potocsnak Family Atrium, SQBRC
*Drinks and small bites will be served

Thank you for joining us at the 2024 Pathogen Genomics Symposium!

Center Leadership

Judd F Hultquist, PhD

Associate Director

Faculty Profile

Ramon Lorenzo Redondo, PhD

Bioinformatics Director

Faculty Profile

Lacy Simons

Lab Coordinator

Services

Our center offers Northwestern units assistance with sequencing and analytical support. Contact us for information on our services and pricing.

Featured Projects

SARS-CoV-2 Surveillance and Variant Tracking

Northwestern PIs: Egon A Ozer, MD, PhD; Judd F Hultquist, PhD

Early funding through the Dixon Family Foundation and the Northwestern University Clinical and Translational Sciences Institute supported the rapid establishment of SARS-CoV-2 sequencing within weeks of the first cases of COVID-19 diagnosed at Northwestern Memorial Hospital. This has led to ongoing genomic surveillance at Northwestern to perform tracking of emerging viral variants and study clinical impacts.

Surveillance and Transmission of SARS-CoV-2 Among Children in Chicago

Northwestern PIs: Larry K Kociolek, MD, MSCI

This project, led by researchers at Lurie Children’s Hospital and funded by the Walder Foundation, seeks to characterize and map potential SARS-CoV-2 transmissions among students, teachers, and school workers in classrooms where in-person instruction is occurring. It also tracks SARS-CoV-2 dynamics among pediatric infections in Chicago to study viral transmission and dynamics in children and adolescents.

The Global Threat of Antibiotic Resistance

Northwestern PIs: Mehreen Arshad, MBBS; Erica Hartmann PhD.

Infections caused by antibiotic-resistant bacteria are a growing threat around the world. This pilot study funded by the Northwestern Buffett Institute for Global Affairs seeks to develop an infrastructure to share clinical and pathogen genomic data as well as specimens from infections caused by antibiotic-resistant infections between institutions in the US and Pakistan. It also seeks to understand local and global factors influencing decision-making around antibiotic prescribing by healthcare providers.

Successful Clinical Response in Pneumonia Therapy (SCRIPT)

Northwestern PIs: Richard Wunderink, MD; Alan Hauser, MD, PhD

This U19 systems biology center funded by the NIAID investigates host/pathogen interactions that result in unsuccessful responses to therapy in severe pneumonia. The study combines clinical phenomics, host transcriptomics and epigenomics, pathogen genomics and alveolar metagenomics to model disease dynamics during ventilator-associated pneumonia.

Visit the SCRIPT Website

Group A Streptococcus Molecular Epidemiology

Northwestern PIs: Ami Patel, MD, MPH; Judy Guzman-Cotrill, Robert Tanz, MD, Stan Shulman, MD

Infections with group A streptococci commonly cause can cause strep throat, but also severe invasive infections and post-infectious complications such as rheumatic fever. This CDC-supported project seeks to identify relationships between group A streptococci from across the United States and establish an active clinical and genomic surveillance network.

Role of HIV-1 Recombination in the Tissue Reservoir

Northwestern PIs: Richard T D'Aquila, MD; Ramon Lorenzo Redondo, PhD

This project through the Third Coast Center for AIDS Research (TC-CFAR) aims to develop a multidisciplinary experimental approach to study HIV-1 recombination levels in gastrointestinal tissue explant infection experiments. We plan to optimize this methodology to systematically and directly examine the mechanisms behind diversity preservation in infected tissues.

Phylodynamics and molecular epidemiology of SARS-CoV-2 in Nigeria

Northwestern PIs: Ramon Lorenzo Redondo, PhD

Supported by a Global Health Research Catalyzer Award, this study aims to study SARS-CoV-2 population dynamics in Nigeria in the framework of the current global pandemic to inform public-health responses. Additionally, it examines the population evolution and viral genes under selective pressure as potential therapeutic or immune targets.

Advanced molecular and network data combination to understand the HIV-1 epidemic among youth in Nigeria

Northwestern PIs: Babafemi O Taiwo, MBBS; Ramon Lorenzo Redondo, PhD

This project through the NICHD combines the use of social network and viral phylogenetic data to obtain the most complete picture of the HIV-1 epidemic in the young men who have sex with men (YMSM) population that Intensive Combination Approach to Rollback the Epidemic (iCARE) in Nigerian Adolescents is engaging in Nigeria.

Evolution of SARS-CoV-2 and Other Respiratory Viruses in Hospitalized Adults

Northwestern PIs: Michael G Ison, MD MS

This study aims to define the evolution of respiratory viruses including SARS-CoV-2, influenza, and RSV over time in isolates derived from hospital adults. Information about viral evolution over the course of respiratory infection combined with clinical data can provide insight into global evolutionary trends and host and viral responses and adaptations to infection.

Surveillance of antimicrobial-resistant Gram negative bacteria and fungi in a Pakistan health care system

Surveillance of antimicrobial-resistant Gram negative bacteria and fungi in a Pakistan health care system - CDC

Northwestern Faculty: PI Egon Ozer, MD, PhD

This project is focused on improving surveillance of infections with the antifungal-resistant yeast Candida auris in Pakistan through capacity-building for whole-genome sequencing and bioinformatic analysis.

SARS-CoV-2 surveillance and capacity building in Peru and Bolivia

Northwestern PIs: Egon A. Ozer, MD, PhD

Most countries in South America are underrepresented in global SARS-CoV-2 genomic surveillance efforts. In this project, we are establishing and enriching partnerships in Peru and Bolivia to fill critical gaps in global SARS-CoV-2 genomic surveillance infrastructure and build local capacity for pathogen genomics.

Antiviral resistance of HIV in Nigeria

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

In collaboration with researchers from the University of Ibadan, we are studying the emergence and circulation of drug-resistant HIV variants that could render therapy regimens inefficacious in drug experienced HIV patients from Nigeria. We are performing full genome deep-sequencing to analyze the presence of mutations both at the consensus and at minority levels in these patients to understand the effects of suboptimal HIV-1 therapy.

Pediatric SARS-CoV-2 surveillance in Massachusetts, Tennessee, and Illinois

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

In collaboration with Boston Children's Hospital and Vanderbilt University we are performing molecular surveillance of SARS-COV-2 in pediatric population around the country. The CPGME is performing whole genome sequencing and molecular evolution analysis to understand the viral population dynamics in children infected with SARS-CoV-2

Unraveling the Mechanisms of HIV Persistence and Rebound (P01 project)

Northwestern PIs: Ramon Lorenzo-Redondo, PhD

By leveraging new insights and technologies, we are investigating the dynamics of the HIV reservoir at high resolution, including dissecting the role of little known, tissue resident cell targets of HIV infection of myeloid origins. CPGME is sequencing and analyzing viral reservoir intra-host dynamics using PT/CT-guided deep-sequencing approaches.

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