Research

Research Statement

The Centers for Disease Control and Prevention has labelled bacterial antimicrobial resistance (AMR) a global threat [1] due to the consistent increase in yearly AMR-associated human cases [2,3]. AMR is most concerning in six “ESKAPE” bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) due to their role in hospital-acquired infections [4]. However, AMR in non-pathogenic bacteria is also concerning as these bacteria have been shown to be a reservoir for AMR genes, which can be horizontally transferred into human pathogens [5,6]. While being extremely useful traditional antimicrobial compounds are typically non-specific and target a wide range of microbes, including beneficial bacteria, depending on their mechanism of action [7]. The emergence of high throughput sequencing techniques and utilization of CRISPR-Cas systems has allowed for a more specific targeting of bacteria carrying specific genes or sequences [8].

During my graduate career I worked with the foodborne human pathogen Listeria monocytogenes, which is notorious for its ability to persist in food processing facilities due to its antimicrobial resistance, resistance to cold temperatures and ability to form biofilms [9]. It can also cause serious illness in humans due to its ability to cross the blood-brain and placental-neonatal barriers [10]. I studied antimicrobial reistance in L. monocytogenes and the use of bacteriophage as an alternative antimicrobial agent against hypervirulent L. monocytogenes strains. I investigated bacteriophage resistance prevalence and the genetic determinants responsible for bacteriophage resistance in L. monocytogenes. Through the use of high-throughput screening and whole-genome sequence analysis I was able to determine common bacteriophage resistance mechanisms and how they were distributed across the L. monocytogenes species, which harbors an large amount of genetic diversity. This information is crucial to understand when developing and deploying bacteriophage as an antimicrobial, either as a therapeutic or to decontaminated surfaces in hospitals or food processing facilities.

Since joining the NCSU Biotechnology Program, and working predominantly with undergraduate students, I have shifted my focus to the opportunistic human pathogen Serratia marcescens, which you may recognize as the pink residue found in bathrooms. I have also moved from the use of native bacteriophage as an antimicrobial to bacteriophage equipped with CRISPR-Cas systems in order to increase the efficiency of cell killing while also circumventing the typical phage lytic cycle, which controls the spread of these phage into the environment.

Figure 1. Maximum likelihood phylogenetic analysis based on the core gene alignment of 35 Listeria reference strains and the 12 isolates of this study. Distance estimation was obtained by the GTR+F+I+G4 model, based on an alignment of 80,539 positions. Branch lengths represent the number of nucleotide substitutions per site, and bootstrap percentages of 1,000 replicates are shown. GenBank accession numbers are provided in brackets. Listeria tempestatis sp. nov. and Listeria rocourtiae subsp. hofi subsp. nov. are highlighted in bold.

Recent Publication in the International Journal of Systematic and Evoluationary Microbiology

Listeria tempestatis sp. nov. and Listeria rocourtiae subsp. hofi subsp. nov.

Abstract: In September 2018, Hurricane Florence resulted in major flooding in North Carolina, USA. Efforts to isolate Listeria monocytogenes and other Listeria spp. from Hurricane Florence floodwaters repeatedly yielded non-haemolytic Listeria-like isolates that could not be readily assigned to known Listeria taxa. Whole-genome sequence analyses against the 28 currently known Listeria species confirmed that the isolates constitute two new taxa within the genus Listeria. Taxon I, with one isolate, showed the highest similarity to Listeria goaensis, with an average nucleotide identity blast of 85.3±4.4% and an in silico DNA–DNA hybridization (isDDH) of 32.4% (range: 30–35%), differing from the latter by its ability to reduce nitrate, ferment d-ribose and sucrose, and by its inability to produce catalase or ferment d-trehalose and d-lactose. Taxon II, represented by 11 isolates, showed the highest similarity to Listeria rocourtiae, with an average nucleotide identity blast of 92.64±3.8% and an isDDH of 49.9% (range: 47.3–52.5%), differing from the latter by its ability to ferment l-arabinose and its inability to ferment l-rhamnose, d-galactose, d-lactose and d-melibiose. The names Listeria tempestatis sp. nov. and Listeria rocourtiae subsp. hofi subsp. nov. are proposed for taxon I and II, respectively, with type strains CLIP 2022/01175T (F6L-1A=CIP 112444T = DSM 117029T) and CLIP 2022/01000T (F66L-1A=CIP 112443T= DSM 117030T), respectively. Both taxa lack known Listeria pathogenic islands, suggesting a lack of pathogenicity for humans.

Check out the article here

Publications

Brown P, Parsons C, Niedermeyer J, Kathariou S. 2025. Characterization of a novel putative lantibiotic biosynthesis island in emerging clones of Listeria monocytogenes serotype 4b. FEMS Microbiol Lett. fnaf112. doi: 10.1093/femsle/fnaf112
Brown P, Moura A, Valès G, Tessaud-Rita N, Niedermeyer J, Parsons C, Leclercq A, Harris A, Emanuel RE, Kathariou S, Lecuit M. 2025. Listeria tempestatis sp. nov. and Listeria rocourtiae subsp. hofi subsp. nov. Int J Syst Evol Microbiol. 75(5). doi: 10.1099/ijsem.0.006774
Brown P, Chen SH. 2025. A 3D-printed Sanger sequencing activity addresses student misconceptions. J Microbiol Biol Educ. e20924. doi: 10.1128/jmbe.00209-24
Ivanova M, Kragh ML, Szarvas J, Tosun ES, Holmud NF, Gmeiner A, Amar C, Guldimann C, Huyanh TA, Karpíšková R, García CR, Gomez D, Aboagye E, Etter A, Centorame P, Torresi M, De Angelis ME, Pomilio F, Okholm AH, Xiao Y, Kleta S, Lueth S, Pietzka A, Kovacevic J, Pagotto F, Rychli K, Zdovč I, Papič B, Heir E, Langsrud S, Møretrø T, Stephan R, Brown P, Kathariou S, Tasara T, Dalgaard P, Njage PMK, Fagerlund A, Aarestrup F, Hansen LT, Leekitcharoenphon P. 2025. Large-scale phenotypic and genomic analysis of Listeria monocytogenes reveals diversity in the sensitivity to quaternary ammonium compounds but not to peracetic acid. Appl Environ Microbiol. e182924. doi: 10.1128/aem.01829-24
Brown P, Hernandez K, Parsons C, Chen Y, Gould N, DePerno CS, Niedermeyer J, Kathariou S. 2023. Tetracycline resistance in Listeria monocytogenes and L. innocua from black bears (Ursus americanus) in the United States is mediated by novel transposable elements. Appl Environ Microbiol. 89(11):e120523. doi: 10.1128/aem.01205-23
Brown P, Lee S, Elhanafi D, Tham W, Danielsson-Tham ML, Lopez-Valladares G, Chen Y, Ivanova M, Leekitcharoenphon P, Kathariou S. 2023. Investigation of a Listeria monocytogenes chromosomal immigration control region reveals diverse restriction modification systems with complete sequence type conservation. Microorganisms. 11(3):699. doi: 10.3390/microorganisms11030699
Brown P, Kucerova Z, Gorski L, Chen Y, Ivanova M, Leekitcharoenphon P, Parsons C, Niedermeyer J, Jackson J, Kathariou S. 2023. Horizontal gene transfer and loss of serotype-specific genes in Listeria monocytogenes can lead to incorrect serotype designations using a commonly-employed molecular serotyping scheme. Microbiol Spectr. 11(1):e0274522. doi: 10.1128/spectrum.02745-22
Brown P, Chen Y, Siletzky R, Parsons C, Jaykus LA, Eifert JD, Ryser E, Logue C, Stamm C, Brown E, Kathariou S. 2021. Harnessing whole genome sequence data for facility-specific signatures for Listeria monocytogenes: a case study with turkey processing plants in the United States. Front Sustain Food Syst. 363. doi: 10.3389/fsufs.2021.742353
Parsons C, Brown P, Kathariou S. 2021. Use of bacteriophage amended with CRISPR-Cas systems to combat antimicrobialresistance in the bacterial foodborne pathogen Listeria monocytogenes. Antibiotics. 10(3):308. doi: 10.3390/antibiotics10030308
Brown P, Chen Y, Parsons C, Brown E, Loessner MJ, Shen Y, Kathariou S. 2021. Whole genome sequence analysis of phage-resistant Listeria monocytogenes serotype 1/2a strains from turkey processing plants. Pathogens. 10(2):199. doi:10.3390/pathogens10020199
Parsons C, Niedermeyer J, Gould N, Brown P, Strules J, Parsons AW, Bernardo Mesa-Cruz J, Kelly MJ, Hooker MJ, Chamberlain MJ, Olfenbuttel C, DePerno C, Kathariou S. 2020. Listeria monocytogenes at the human-wildlife interface: black bears (Ursus americanus) as potential vehicles for Listeria. Microb Biotechnol. 13(3):706–721. doi: 10.1111/1751-7915.13509
Parsons C, Costolo B, Brown P, Kathariou S. 2017. Penicillin-binding protein encoded by pbp4 is involved in mediating copper stress in Listeria monocytogenes. FEMS Microbiol Lett. 364(20). doi: 10.1093/femsle/fnx207

Genome Announcements

Lee S, Brown P, Tham W, Danielsson-Tham ML, Lopez-Valladares G, Ward T, Elhanafi D, Chen Y, Kathariou S. 2024. Draft genome sequences of Listeria monocytogenes strains from human listeriosis in Sweden harboring premature stop codons in the virulence determinant inlA. Microbiol Resour Announc. 13(11):e0046424. doi: 10.1128/mra.00464-24
Brown P, Kilcher S, Kim JW, Loessner M, Kathariou S. 2024. Draft Genome Sequences of two wide-host-range phages of Listeria monocytogenes from food processing environments in the United States. Microbiol Resour Announc. 13(7):e0035824. doi: 10.1128/mra.00358-24
Brown P, Murray RGE, Galsworthy S, Ivanova M, Leekitcharoenphon P, Ward T, Kucerova Z, Elhanafi D, Kathariou S. 2023. Draft genome sequences of historical Listeria monocytogenes from humans and other sources, 1926-1964. Microbiol Resour Announc. 12(10):e0062523. doi: 10.1128/mra/00625-23
Lee S, Tham W, Danielsson-Tham ML, Lopez-Valladares G, Chen Y, Brown P, Kathariou S. 2023. Draft genome sequences of heavy metal-resistant Listeria monocytogenes strains of sequence type 14 from human listeriosis in Sweden. Microbiol Resour Announc. 12(8):e0040623. doi: 10.1128/mra/00406-23
Brown P, Chen Y, Ivanova M, Leekitcharoenphon P, Parsons C, Niedermeyer J, Gould N, Strules J, Bernardo Mesa-Cruz J, Kelly MJ, Hooker MJ, Chamberlain MJ, Olfenbuttel C, DePerno C, Elhanafi D, Kathariou S. 2023. Draft genome sequences of 158 Listeria monocytogenes strains isolated from black bears (Ursus americanus) in the United States. Microbiol Resour Announc.12(7):e0024823. doi: 10.1128/mra.00248-23
Brown P, Kanenaka R, Chen Y, Ivanova M, Leekitcharoenphon P, Elhanafi D, Kathariou S. 2023. Draft genome sequences of closely related Listeria monocytogenes lineage III strains from a food processing environment and a case of human listeriosis. Microbiol Resour Announc. 12(6):e0025023. doi: 10.1128/mra.00250-23

Thesis & Dissertation

Brown P. 2022. Investigation of bacteriophage resistance and underlying mechanisms in Listeria monocytogenes. Ph.D. Dissertation, North Carolina State University, Raleigh, NC, United States. https://www.lib.ncsu.edu/resolver/1840.20/40113
Brown P. 2019. Genetic characterization of a serotype 4b-specific inhibition phenotype in Listeria monocytogenes. M.S. Thesis, North Carolina State University, Raleigh, NC, United States. http://www.lib.ncsu.edu/resolver/1840.20/36887

Presentations & Accepted Abstracts

Lee S, Tham W, Danielsson-Tham ML, Lopez-Valladares G, Chen Y, Brown P, Kathariou S. (2025, July 27-30). Genome-wide analysis of cadmium resistance genes harbored by cadmium-resistant Listeria monocytogenes strains from Sweden. [Conference poster presentation]. Annual Meeting of the International Association for Food Protection. Cleveland, OH, USA.
Griggs C, Brown P. (2025, July 25). Combating AMR with CRISPR-equipped bacteriophage P1. [Conference poster presentation]. NC State Undergraduate Research & Creativity Summer Symposium. Raleigh, NC, USA.
Srougi MC, Corbett A, Garcia CB, Hayward J, Comstra S, Sabaoun M, Santisteban MS, Sivaraman V, Brown P, Chen SH, Haggerty R, Huggins H, Noel S, Goller CC, Kelly RM. (2025, April 12-15). Enhancing Molecular Biotechnology Laboratory Education for Diverse Institutions. [Conference poster presentation]. American Society for Biochemistry and Molecular Biology Conference Chicago, IL, USA.
Chen S, Goller C, Srougi M, Brown P, Couture P, Willis C, Wrights, Earnest A, Sanchez R. (2025, March 6). Using videos to support student time management in a high structure course. [Conference poster presentation]. NC State Conference on Faculty Excellence. Raleigh, NC, USA.
Samuta M, Brown P. (2024, June 26). CRISPR-Cas12a engineered bacteriophage P1 as a novel antimicrobial against Serratia marcescens. [Conference poster presentation]. NC State Undergraduate Research & Creativity Summer Symposium. Raleigh, NC, USA.
Fogelson R, Brown P. (2024, June 26). Using CRISPR-associated transposons (CASTs) for precise gene editing in Serratia marcescens. [Conference poster presentation]. NC State Undergraduate Research & Creativity Summer Symposium. Raleigh, NC, USA.
Chen S, Goller C, Srougi M, Brown P, Couture P, Willis C, Wrights, Earnest A, Snyder M, Sanchez R. (2024, May 20-22). Setting the stage for high structure courses. [Conference poster presentation]. Lily Conferences – Evidence-Based Teaching & Learning. Austin, TX, USA.
Brown P, Chen S. (2024, March 6). Understanding how the use of communication-focused assessments impacts student learning outcomes and self-efficacy in a course-based research experience. [Conference poster presentation]. NC State Conference on Faculty Excellence. Raleigh, NC, USA.
Fletcher S, Joglekar P, Fagen J, Brown P. (2023, July 27). Serratia marcescens growth inhibition: targeting essential genes with an engineered CRISPR-Cas12a system [Conference poster presentation]. NC State Undergraduate Research & Creativity Summer Symposium. Raleigh, NC, USA.
Brown P. (2022, October 20). Investigation of bacteriophage resistance and underlying mechanisms in Listeria monocytogenes [Oral Presentation]. Public Ph.D. Defense Seminar. North Carolina State University, Raleigh, NC, USA.
Brown P, Parsons C, Kathariou S. (2022, June 22). Combating antimicrobial resistance with bacteriophage: Distribution of native CRISPR Systems in the foodborne pathogen Listeria monocytogenes [Oral presentation]. North Carolina State University BioLunch Summer Seminar Series. Raleigh, NC, USA.
Brown P, Parsons C, Kathariou S. (2022, June 9-13). Distribution of native CRISPR Systems in the foodborne pathogen Listeriamonocytogenes [Conference poster presentation]. ASM Microbe – American Society of Microbiology Annual Meeting. Washington, D.C., USA.
McInnis A, Brown P, Kathariou S. (2022, April 26-27). A hidden defense: prophage as a phage resistance mechanism in Listeria monocytogenes [Conference poster presentation]. NC State Undergraduate Research & Creativity Spring Symposium. Raleigh, NC, USA.
Brown P, Kathariou S. (2022, March 28-29). Bacteriophage resistance heterogeneity by source and serotype in the foodborne pathogen Listeria monocytogenes [Oral presentation]. L.W. Parks Distinguished Lectureship in Microbiology. Virtual.
DePerno C, Parsons C, Niedermeyer J, Brown P, Gould N, Strules J, Parsons A, Mesa-Cruz J, Kelly M, Hooker M, Chamberlain M, Olfenbuttel C, Kathariou S. (2022, February 15-17). Black bears (Ursus americanus) are novel vehicles for Listeria monocytogenes [Oral Presentation]. Annual Meeting of the North Carolina Chapter of The Wildlife Society. Trinity Center, Pine Knoll Shores, NC, USA.
Brown P, Parsons C, Kathariou S. (2022, January 26). Utilization of bacteriophage as a CRISPR-Cas System delivery vector to combat antimicrobial resistant Listeria monocytogenes [Oral Presentation]. National Institute of Antimicrobial Resistance Research & Education Research Symposium. Virtual.
Brown P, Kathariou S. (2021, July 28). Diverse bacteriophage resistance mechanisms in emerging clones of Listeria monocytogenes [Oral Presentation]. North Carolina State University BioLunch Summer Seminar Series. Virtual.
Kathariou S, Brown P, Lee S, Parsons C, Chen Y, Kim JW, Elhanafi D, Suleyman Y, Shen Y, Loessner MJ. (2021, March 31). Listeria phage: Can it reveal secrets, and can it be deployed? [Oral Presentation]. Food Safety and Inspection Service Science and Technology Seminar Series. Virtual.
Brown P, Kathariou S. (2020, September 29). Genetic analysis of phage-resistant food processing plant isolates of Listeria monocytogenes [Conference poster presentation]. L.W. Parks Distinguished Lectureship in Microbiology. Virtual.
Brown P, Parsons C, Yang S, Loessner M, Niedermeyer J, Elhanafi D, Kathariou S. (2020, June 22). Involvement of the serotype 4b-specific putative teichoic acid biosynthesis gene tagC in a novel inhibition phenotype of Listeria monocytogenes [Conference poster presentation]. ASM Microbe – American Society of Microbiology Annual Meeting. Virtual.
Brown P, Parsons C, Elhanafi D, Niedermeyer J, Kathariou S. (2019, September 24-27). Characterization of two novel genomic islands in serotype 4b emerging clones ST558 and CC554 of Listeria monocytogenes [Conference poster presentation]. International Symposium on Problems of Listeria and Listeriosis. Toronto, ON, Canada.
Brown P. (2019, June 28). Genetic characterization of a serotype 4b-specific inhibition phenotype in Listeria monocytogenes [Oral Presentation]. Public Master’s Defense Seminar. North Carolina State University, Raleigh, NC, USA.
Brown P, Parsons C, Kathariou S. (2017, October 21). Phenotypic characterization of a putative lantibiotic biosynthesis genomic island in Listeria monocytogenes [Conference poster presentation]. North Carolina American Society of Microbiology Branch Annual Meeting. Raleigh, NC, USA.
Parsons C, Niedermeyer J, Brown P, Chen Y, Gould N, DePerno C, Strules J, Mesa-Cruz J, Kelly M, Hooker M, Chamberlain M., Olfenbuttel C, Kathariou S. (2017, June 1-5). Prevalence and characteristics of Listeria monocytogenes isolated from black bears, Ursus americanus [Conference poster presentation]. American Society of Microbiology Annual Meeting, New Orleans, LA, USA.
Parsons C, Brown P, Kathariou S. (2016, December 5-8). Functional genomics of heavy metal resistance in the foodborne pathogen Listeria monocytogenes [Conference poster presentation]. National Institute of Environmental Health Sciences Environmental Health Sciences FEST, Durham, NC, USA.
Parsons C, Niedermeyer J, Brown P, Kathariou S, Gould N, Strules J, Mesa-Cruz J, Kelly M, Hooker M, Chamberlain M, Olfenbuttel C, DePerno C. (2016, October 15-19). Black bears as novel vectors/reservoirs for potential human and animal pathogens [Conference poster presentation]. The Wildlife Society Annual Conference, Raleigh, NC, USA.
Parsons C, Brown P, Lee S, Kathariou S. (2016, June 16-20). Novel locus mediating metal homeostasis in Listeria monocytogenes [Conference poster presentation]. ASM Microbe – American Society of Microbiology Annual Meeting, Boston, MA, USA.

Invited Talks

"Research Opportunities in Microbial Biotechnology", NCSU Biology Club, Raleigh, NC, USA (September 22, 2025)
“Is Graduate School the Right Choice for You?”, NCSU Undergraduate Microbiology Club, Raleigh, NC, USA (March 22, 2023)
“Horizontal gene transfer and loss of serotype-specific genes in Listeria monocytogenes”, United States Food & Drug Administration GenomeTrakr Monthly Lab Call. Virtual. (March 16, 2023)

References

Centers for Disease Control and Prevention. https://www.cdc.gov/DrugResistance/
Antimicrobial Resistance Collaborators. 2022. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet. 400:1102. doi: 10.1016/S0140-6736(21)02724-0
World Health Organization. https://www.who.int/news/item/09-12-2022-report-signals-increasing-resistance-to-antibiotics-in-bacterial-infections-in-humans-and-need-for-better-data
Rice LB. 2008. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis. 197:1079-81. doi: 10.1086/533452
Poirel L, Madec JY, Lupo A, Schink AK, Kieffer N, Nordmann P, Schwarz S. 2018. Antimicrobial resistance in Escherichia coli. Microbiol Spectr. 6. doi: 10.1128/microbiolspec.ARBA-0026-2017
Soucy SM, Huang J, Gogarten JP. 2015. Horizontal gene transfer: building the web of life. Nat Rev Genet. 16:472-82. doi: 10.1038/nrg3962
Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A. 2021. Unravelling the collateral damage of antibiotics on gut bacteria. Nature. 599:120-124. doi: 10.1038/s41586-021-03986-2
Jiang Y, Chen B, Duan C, Sun B, Yang J, Yang S. 2016. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol. 82:3693. doi: 10.1128/AEM.04023-14
Dos Santos JS, Biduski B, Dos Santos LR. 2021. Listeria monocytogenes: health risk and a challenge for food processing establishments. Arch Microbiol. 203:5907-5919. doi: 10.1007/s00203-021-02590-2
Schlech WF. 2019. Epidemiology and clinical manifestations of Listeria monocytogenes Infection. Microbiol Spectr. 7. doi: 10.1128/microbiolspec.GPP3-0014-2018

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