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Stephen B. Beres, PhD

Research Professor of Pathology and Genomic Medicine, Academic Institute
Full Research Member, Research Institute
Houston Methodist


After earning his PhD in Molecular Biology in 1995 from Northwestern University, Dr. Beres completed post-doctoral fellowships at Baylor College of Medicine and the National Institute of Allergy and Infectious Diseases. Dr. Beres joined the Houston Methodist Research Institute HMRI at its inception in 2006, where he is currently a Full Research Member, Research Institute, Professor, Academic Institute, and Director of Microbial Informatics for the Center for Molecular and Translational Human Infectious Disease Research. Dr. Beres’s research focuses on employing bacterial whole-genome sequencing to understand human infectious diseases caused by microbial pathogens, including Streptococcus pyogenes, Staphylococcus aureus, and Klebsiella pneumoniae.

Description of Research

The primary focus of Dr. Beres’s research is identifying the genetic/genomic basis for intrinsic differences and adaptive changes in the pathogenic behavior of human bacterial infections. Over the last 17 years, Dr. Beres has used bacterial pathogen whole-genome sequencing and related genome-scale strategies on populations of hundreds to thousands of human clinical isolates to obtain initial genomic assessments. Dr. Beres has then used DNA sequencing to further analyze strain-to-strain variation in gene content and RNA/cDNA sequencing for genome-wide gene transcriptome assessment. Dr. Beres is one of few specialists who has focused particularly on the human bacterial pathogen S. pyogenes, colloquially referred to as the “flesh-eating” bacteria. Dr. Beres’s research has contributed 40 of 166 (24%) of the complete genome sequences for S. pyogenes that are currently in the National Center Biotechnology Information GenBank database.

One prominent theme of Dr. Beres’s research has been the use of population pathogenomics to determine the molecular genetic underpinnings responsible for the epidemic shifts of different S. pyogenes genotypes that are responsible for severe invasive infections with high human morbidity and mortality. One important discovery of his research is that recurrent epidemic waves of type emm3 S. pyogenes stemmed from the emergence of newly evolved strains with enhanced fitness, and not from recycling of the same clone responsible for the preceding wave. Similarly, his analysis of 3,615 samples of type emm1 S. pyogenes obtained from global sources found that only four molecular genetic events were responsible for the pandemic of severe invasive infections worldwide. He also discovered that an emm89 S. pyogenes epidemic clone evolved through a complex series of multiple horizontal-transfer genetic recombination events, one of which was virtually identical to the recombination event responsible for triggering the pandemic of invasive infections caused by the emm1 strain. These three studies are some of the largest population pathogenomic infectious disease investigations that have been conducted.


Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis
Kachroo, P, Eraso, JM, Beres, SB, Olsen, RJ, Zhu, L, Nasser, W, Bernard, PE, Cantu, CC, Saavedra, MO, Arredondo, MJ, Strope, B, Do, H, Kumaraswami, M, Vuopio, J, Gröndahl-Yli-Hannuksela, K, Kristinsson, KG, Gottfredsson, M, Pesonen, M, Pensar, J, Davenport, ER, Clark, AG, Corander, J, Caugant, DA, Gaini, S, Magnussen, MD, Kubiak, SL, Nguyen, HAT, Long, SW, Porter, AR, DeLeo, FR & Musser, JM 2019, Nature Genetics, vol. 51, no. 3, pp. 548-559.

Gene fitness landscape of group A streptococcus during necrotizing myositis
Zhu, L, Olsen, RJ, Beres, SB, Eraso, JM, Saavedra, MO, Kubiak, SL, Cantu, CC, Jenkins, L, Charbonneau, ARL, Waller, AS & Musser, JM 2019, The Journal of clinical investigation, vol. 129, no. 2, pp. 887-901.

RocA Has Serotype-Specific Gene Regulatory and Pathogenesis Activities in Serotype M28 Group A Streptococcus
Bernard, PE, Kachroo, P, Zhu, L, Beres, SB, Eraso, JM, Kajani, Z, Long, SW, Musser, JM & Olsen, RJ 2018, Infection and immunity, vol. 86, no. 11, e00467-18.

Postpartum Group A Streptococcus Case Series: Reach Out to Infection Prevention!
Alexander, AJ, Myers, C, Beres, SB, Olsen, RJ, Musser, JM & Mangino, JE 2018, Open Forum Infectious Diseases, vol. 5, no. 7, pp. ofy159.

Genome sequence analysis of emm89 Streptococcus pyogenes strains causing infections in Scotland, 2010–2016
Beres, SB, Olsen, RJ, Saavedra, MO, Ure, R, Reynolds, A, Lindsay, DSJ, Smith, AJ & Musser, JM 2017, Journal of Medical Microbiology, vol. 66, no. 12, 000622, pp. 1765-1773.

Novel genes required for the fitness of Streptococcus pyogenes in human saliva
Zhu, L, Charbonneau, ARL, Waller, AS, Olsen, RJ, Beres, SB & Musser, JM 2017, mSphere, vol. 2, no. 6, e00460-17.

Rapid emergence of a new clone impacts the population at risk and increases the incidence of type emm89 group A Streptococcus invasive disease
Teatero, S, Coleman, BL, Beres, SB, Olsen, RJ, Kandel, C, Reynolds, O, Athey, TBT, Musser, JM, McGeer, A & Fittipaldi, N 2017, Open Forum Infectious Diseases, vol. 4, no. 2, ofx042.

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis
Skwark, MJ, Croucher, NJ, Puranen, S, Chewapreecha, C, Pesonen, M, Xu, YY, Turner, P, Harris, SR, Beres, SB, Musser, JM, Parkhill, J, Bentley, SD, Aurell, E & Corander, J 2017, PLoS Genetics, vol. 13, no. 2, pp. e1006508.

Population genomic analysis of 1,777 extended-spectrum beta-lactamase-producing Klebsiella pneumoniae isolates, Houston, Texas: Unexpected abundance of clonal group 307
Long, SW, Olsen, RJ, Eagar, TN, Beres, SB, Zhao, P, Davis, JJ, Brettin, T, Xia, F & Musser, JM 2017, mBio, vol. 8, no. 3, e00489-17.

Case Series Description and Genomic Characterization of Invasive Group A Streptococcal Infections in Pediatric Patients
Bard, JD, Mongkolrattanothai, K, Kachroo, P, Beres, S & Olsen, RJ 2016, Pediatric Infectious Disease Journal.

Genomic Characteristics Behind the Spread of Bacteremic Group A Streptococcus Type emm89 in Finland, 2004-2014
Latronico, F, Nasser, W, Puhakainen, K, Ollgren, J, Hyyryläinen, H-L, Beres, SB, Lyytikäinen, O, Jalava, J, Musser, JM & Vuopio, J 2016, Journal of Infectious Diseases, vol. 214, no. 12, pp. 1987-1995.

Genomic Landscape of Intrahost Variation in Group A Streptococcus: Repeated and Abundant Mutational Inactivation of the fabT Gene Encoding a Regulator of Fatty Acid Synthesis
Eraso, JM, Olsen, RJ, Beres, SB, Kachroo, P, Porter, AR, Nasser, W, Bernard, PE, DeLeo, FR & Musser, JM 2016, Infection and Immunity, vol. 84, no. 12, pp. 3268-3281.

Transcriptome remodeling contributes to epidemic disease caused by the human pathogen Streptococcus pyogenes
Beres, SB, Kachroo, P, Nasser, W, Olsen, RJ, Zhu, L, Flores, AR, de la Riva, I, Paez-Mayorga, J, Jimenez, FE, Cantu, C, Vuopio, J, Jalava, J, Kristinsson, KG, Gottfredsson, M, Corander, J, Fittipaldi, N, Di Luca, MC, Petrelli, D, Vitali, LA, Raiford, A, Jenkins, L & Musser, JM 2016, mBio, vol. 7, no. 3, e00403-16.

A molecular trigger for intercontinental epidemics of group A Streptococcus
Zhu, L, Olsen, RJ, Nasser, W, Beres, SB, Vuopio, J, Kristinsson, KG, Gottfredsson, M, Porter, AR, DeLeo, FR & Musser, JM 2015, The Journal of clinical investigation, vol. 125, no. 9, pp. 3545-3559.

Comparative whole genome sequencing of community-associated methicillin-resistant Staphylococcus aureus sequence type 8 from primary care clinics in a Texas community
Lee, GC, Long, SW, Musser, JM, Beres, SB, Olsen, RJ, Dallas, SD, Nunez, YO & Frei, CR 2015, Pharmacotherapy, vol. 35, no. 2, pp. 220-228.

The majority of 9,729 group A streptococcus strains causing disease secrete SpeB cysteine protease: Pathogenesis implications
Olsen, RJ, Raghuram, A, Cantu, C, Hartman, MH, Jimenez, FE, Lee, S, Ngo, A, Rice, KA, Saddington, D, Spillman, H, Valson, C, Flores, AR, Beres, SB, Long, SW, Nasser, W & Musser, JM 2015, Infection and Immunity, vol. 83, no. 12, pp. 4750-4758.

Absence of Patient-to-Patient intrahospital transmission of staphylococcus aureus as determined by Whole-Genome sequencing
Long, SW, Beres, SB, Olsen, RJ & Musser, JM 2014, mBio, vol. 5, no. 5, e01692-1.

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences
Nasser, W, Beres, SB, Olsen, RJ, Dean, MA, Rice, KA, Long, SW, Kristinsson, KG, Gottfredsson, M, Vuopio, J, Raisanen, K, Caugant, DA, Steinbakk, M, Low, DE, McGeer, A, Darenberg, J, Henriques-Normark, B, Van Beneden, CA, Hoffmann, S & Musser, JM 2014, Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 17.

Clinical laboratory response to a mock outbreak of invasive bacterial infections: A preparedness study
Olsen, RJ, Fittipaldi, N, Kachroo, P, Sanson, MA, Long, SW, Como-Sabetti, KJ, Valson, C, Cantu, C, Lynfield, R, Van Beneden, C, Beres, SB & Musser, JM 2014, Journal of Clinical Microbiology, vol. 52, no. 12, pp. 4210-4216.

Asymptomatic carriage of group A streptococcus is associated with elimination of capsule production
Flores, AR, Jewell, BE, Olsen, RJ, Shelburne, SA, Fittipaldi, N, Beres, SB & Musser, JM 2014, Infection and Immunity, vol. 82, no. 9, pp. 3958-3967.

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