banner USF Home College of Arts & Sciences OASIS myUSF USF A-Z Index

USF Home > College of Arts and Sciences > Department of Cell Biology, Microbiology and Molecular Biology

Lindsey  Shaw

Lindsey Shaw

Lindsey Shaw
Professor, CMMB Director of Graduate Studies


Office: ISA 6204
Phone: 813/974-2087
Lab: ISA 6014



B.S. (hons) Microbiology, University of East Anglia (England)
Ph.D. Molecular Microbiology, University of Sheffield (England)
Postdoctoral Fellow, University of Georgia
Research Assistant Professor, University of Missouri-Columbia


  • Molecular mechanisms of disease causation in Methicillin Resistant Staphylococcus aureus (MRSA)
  • Antibacterial Drug Discovery Targeting the ESKAPE Pathogens

Current Research

Molecular mechanisms of disease causation in Methicillin Resistant Staphylococcus aureus (MRSA): Staphylococcus aureus is a highly virulent and widely successful human pathogen, which is speculated to be the most common cause of infectious disease and death in the United States. S. aureus is almost entirely unique amongst bacterial pathogens, as it can cause infection in almost every ecological niche of the human host. These range from the relatively benign, such as skin and soft tissue infections, boils, cellulitis and abscesses; to the systemic and life-threatening, such as endocarditis, septic arthritis, osteomyelitis, pneumonia and septicemia. Historically, S. aureus infections were confined to healthcare settings, afflicting the immunocompromised. Recently, however, there has been a meteoric increase of severe invasive disease in healthy subjects lacking any predisposing factors. This trendshift is the result of, hypervirulent strains of MRSA that have evolved in the community (CA-MRSA). Of concern, these CA-MRSA strains appear to be displacing existing hospital-associated MRSA isolates in clinical settings. Molecular MechanismsThe significance of this is further compounded by wide-spread antibiotic resistance in S. aureus, and the emergence of isolates resistant to last resort antibiotics. Thus the search for novel antimicrobial targets is crucial in our fight against a return to the pre-antibiotic era, where invasive S. aureus infections carried mortality rates of up to 90%.

In the Shaw lab, we use molecular tools to investigate the mechanisms of diseases causation by this highly successful bacterium. These broadly proceed along two distinct lines: The first is an analysis of regulatory elements, and how they coordinate and modulate the progression of infection. This includes the study of sigma factors, two-component systems and DNA-binding proteins, and their influence on physiological and pathogenic processes. We use next-generation sequencing tools, biochemical analyses and ex vivo/in vivo models of infection to understand gene targets of these regulatory elements, and their downstream effects of bacterial behavior and infectious capacity. Our second focus is centered on proteases, and their involvement in the virulence process. Typically ~2% of all genomes are dedicated to encoding proteases. In S. aureus, that number is closer to 5%, suggesting an overrepresentation in this organism. From work in our laboratory we have shown that a large number of proteolytic enzymes, be they secreted, or located in the membrane and/or cytoplasm, are key players in the virulence process. As such, we work to understand exactly how these enzymes define the infectious behavior of S. aureus, and to identify their specific protein substrates.

Antibacterial Drug Discovery Targeting the ESKAPE Pathogens: Despite the success of antimicrobial therapeutics in the past 70 years, infectious diseases remain the second-leading cause of mortality worldwide, causing 17 million deaths annually. Of this, the overwhelming majority are the result of bacterial pathogens. In the United States, there are almost 2 million hospital acquired infections each year, resulting in approximately 100,000 deaths. Perhaps the most significant public health concern in the context of bacterial infectious disease is the continued and rapid emergence of drug resistant strains during antibiotic treatment. Many bacteria are now unresponsive to conventional therapeutics, whilst still causing community and hospital acquired infections worldwide, leading to life-threatening and lethal diseases. Recently, the World Health Organization identified antimicrobial resistance as one of the three greatest threats facing mankind in the 21st century. As such, there is an undeniable and desperate need to develop new antibacterial therapeutics to fight the infections caused by these virtually untreatable pathogens. Unfortunately, the pace of drug resistance has outstripped the discovery of new antimicrobial agents, creating an urgent need for new antibiotics with novel mechanisms of action. Drug DiscoveryThe question is how we approach this, given that only 4 new classes of antibiotics have been marketed since 1970, and only 6 new antibiotics were approved by the FDA between 2003 and 2010. Indeed, there was a 75% decline in FDA approval for antibacterial agents from 1983-2007, largely the result of declining drug discovery efforts in industry. The is made even more concerning by the fact that only 4-5 companies are now seriously working on antimicrobial therapeutic development in the marketplace.

As such, in the Shaw lab, we work with a number of chemists and other research groups on the USF campus to identify new antimicrobial agents. These efforts are primarily focused on the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumonia, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter cloacae). These are bacterial species that the CDC estimates cause more than two-thirds of all hospital-associated infections in the United States. They were identified by the Infectious Disease Society of America as causing the majority of infections in US hospitals, and having effectively managed to escape the activity of existing antimicrobial agents. Our work runs the entire spectrum of drug discovery, from hit identification, to lead development, in vivo efficacy testing, assessing anti-biofilm activity and mechanism of action studies.

Graduate Students

Jessie Adams, Kirsten Antonen, Leila Casella, Renee Fleeman, Brittney Moore, Rahmy Tawfik, Andy Weiss

Current Courses

RefCourseSecCourse TitleCRDayTimeLocation
87886MCB 4905003Microbio Undergrad Research

TBA 100
89004MCB 4905004Microbio Undergrad Research

TBA 100
92242BSC 6910029Directed Research

TBA 100
83022PCB 6920001Advs in Cell and Molecular Bio
flyer Note: This course will meet in ISA 6027.
TBA 100
86146BSC 6932020Bac Pathogenesis & Resistance
S/U Grade Consent of Instructor

TBA 100
81767MCB 6971001Thesis: Master's

86017BSC 7910041Directed Research

TBA 100
84080BSC 7980029Dissertation: Doctoral

TBA 100

Recent Publications


  • Carroll RK, Weiss A, Mogen AB, Rice KC, Shaw LN. Genome wide annotation, identification and global transcriptomic analysis of regulatory or small RNA gene expression in Staphylococcus aureus. mBio. Accepted.
  • Weiss A, Broach WH, Lee MC, Shaw LN. Towards the Complete Small RNome of Acinetobacter baumannii. Microbial Genomics (mGen). Accepted.
  • Carroll RK, Weiss A & Shaw LN. (2016). RNA-sequencing of Staphylococcus aureus messenger RNA. Methods in Molecular Biology. 1373: 131-141.
  • Weiss A and Shaw LN. (2015). Small Things Considered: The Small Accessory Subunits of RNA Polymerase in Gram-positive Bacteria. FEMS Microbiology Reviews. 39(4): 541-554.
  • Krute CK, Bell-Temin H, Miller HK, Rivera FE, Weiss A, Stevens SM, Shaw LN. (2015). The Membrane Protein PrsS Mimics sS in Protecting Staphylococcus aureus Against Cell Wall-Targeting Antibiotics and DNA Damaging Agents. Microbiology. 161(5): 1136 – 1148.
  • Krute CK, Carroll RK, Rivera FE, Weiss A, Young RM, Shilling A, Botlani M, Varma S, Baker BJ, Shaw LN. (2015). The Disruption of Prenylation Leads to Pleiotropic Rearrangements in Cellular Behaviour in Staphylococcus aureus. Molecular Microbiology. 95(5): 819-832.
  • Burda WN, Miller HK, Krute CK, Leighton SL, Carroll RK, Shaw LN. (2014). Investigating the Genetic Regulation of the ECF-Sigma Factor sS in Staphylococcus aureus. BMC Microbiology. 14(1): 280.
  • Weiss A, Ibarra JA, Paoletti J, Carroll RK, Shaw LN. (2014). The d Subunit of RNA Polymerase Guides Promoter Selectivity and Virulence in Staphylococcus aureus. Infection and Immunity. 82(4): 1424-1435.
  • Carroll RK, Veillard F, Gagne D, Lindenmuth J, Poreba M, Drag M, Potempa J, Shaw LN. (2013). The Staphylococcus aureus leucine aminopeptidase is localized to the bacterial cytosol and demonstrates a broad substrate range that extends beyond leucine. Biol Chem. 394(6): 791-803.
  • Ibarra JA, Perez-Rueda E, Carroll RK, Shaw LN. (2013). Global Analysis of Transcriptional Regulators in Staphylococcus aureus. BMC Genomics. 14(1):126.
  • Kolar SL, Ibarra AJ, Rivera FE, Mootz JM, Davenport JE, Stevens SM, Horswill AR, Shaw LN. (2013). Extracellular Proteases are Key Mediators of S. aureus Virulence via the Global Modulation of Virulence Determinant Stability. Microbiology Open. 2(1): 18-34.
  • Carroll RK, Robison TM, Rivera FE, Davenport JE, Jonsson IM, Florczyk D, Tarkowski A, Potempa J, Koziel J, Shaw LN. (2012). Identification of an intracellular M17 family leucine aminopeptidase that is required for virulence in Staphylococcus aureus. Microbes & Infection. 14(11): 989-999.
  • Miller HK, Carroll RK, Burda WN, Krute CN, Davenport JE, Shaw LN. (2012). The ECF Sigma Factor, sS, Protects Against Both Cytoplasmic and Intracellular Stresses in Staphylococcus aureus. J Bacteriology. 194(16): 4342-4354.
  • Rivera F, Miller HK, Kolar SL, Stevens SM, Shaw LN. (2012). The Impact of CodY on Virulence Determinant Production in Community-Associated Methicillin Resistant Staphylococcus aureus. Proteomics. 12(2): 263-268.
  • Kolar SL, Nagarajan, V, Oszmiana A, Rivera FE, Miller HK, Davenport JE, Riordan JT, Potempa J, Barber DS, Koziel J, Elasri MO, Shaw LN. (2011). NsaRS is a Cell-Envelope-Stress Sensing Two-Component System of Staphylococcus aureus. Microbiology. 157(8): 2206-2219.
  • Shaw LN, Lindholm C, Prajsnar TK, Miller, HK, Brown, MC, Golonka E, Stewart GC, Tarkowski A, Potempa J. (2008). Identification and Characterization of sS, a novel component of the Staphylococcus aureus stress and virulence responses. PLoS ONE. 3(12):e3844.
  • Shaw LN, Jonsson IM, Singh VK, Tarkowski A, Stewart GC. (2007). Inactivation of traP has no effect on the agr quorum-sensing system of virulence of Staphylococcus aureus. Infection and Immunity. 75(9): 4519-4527.
  • Shaw LN, Aish J, Davenport JE, Brown, MC, Lithgow JK, Simmonite K, Crossley H, Travis J, Potempa J, Foster SJ. (2006). Investigations into sB–modulated regulatory pathways governing extracellular virulence determinant production in Staphylococcus aureus. Journal of Bacteriology. 188(17): 6070-6080.
  • Shaw LN, Golonka E, Szmyd G, Foster SJ, Travis J, Potempa J. (2005). Cytoplasmic control of premature activation of a secreted protease zymogen: deletion of staphostatin B (SspC) in Staphylococcus aureus 8325-4 yields a profound pleiotropic phenotype. Journal of Bacteriology. 187(5): 1751-1762.
  • Shaw L, Golonka E, Potempa J, Foster SJ. (2004). The role and regulation of the extracellular proteases of Staphylococcus aureus. Microbiology. 150(1): 217-28.


  • Bionda N, Fleeman RM, Fuente-Nunez C, Rodriguez MC, Reffuveille F, Shaw LN, Pastar I, Davis SC, Hancock REW, Cudic P. (2016). Identification of novel cyclic lipopeptides from a positional scanning combinatorial library with enhanced antibacterial and antibiofilm activities. European Journal of Medicinal Chemistry.108: 354-363.
  • Fleeman RM, LaVoi T, Santos RG, Morales A, Nefzi A, Welmaker GS, Medina-Franco J, Houghten RA, Giulianotti MA, Shaw LN. (2015). Combinatorial libraries as a tool for the discovery of novel antibacterial agents targeting the ESKAPE pathogens. Journal of Medicinal Chemistry. 58(8): 3340-3355.
  • Van Horn K, Burda WN, Shaw LN, Manetsch R. (2014). Antibacterial Activity of a Series of N2,N4-Disubstituted Quinazoline-2,4-Diamines. Journal of Medicinal Chemistry. 57: 3075-3093.
  • Bionda N, Fleeman RM, Shaw LN, Cudic P. (2013). Effect of Ester to Amide or N-methyl Amide Substitution on Membrane Depolarization and Antibacterial Activity of Novel Cyclic Lipopeptides. ChemMedChem. 8(8): 1394-1402.
  • Cormier R, Burda WN, Harrington L, Edlinger J, Kodigepalli KM, Thomas J, Kapolka R, Roma G, Anderson BE, Turos E, Shaw LN. (2012). Studies on the antimicrobial properties of N-Acylated ciprofloxacins. Bioorganic & Medicinal Chemistry Letters. 22(20): 6513-6520.
  • Niu Y, Padhee S, Wu H, Bai G, Harrington L, Burda WN, Shaw LN, Cao C, Cai J. (2012). Lipo-?-AApeptides as a New Class of Potent and Broad Spectrum Antimicrobial Agents. J Med Chem. 55(8): 4003-4009.
  • Beau J, Mahid N, Burda WN, Harrington L, Shaw LN, Mutka T, Kyle DE, Barisic B, Van Olphen A, Baker BJ. (2012). Epigenetic Tailoring for the Production of Anti-infective Cytosporones from the Mangrove Endophyte Leucostoma persoonii. Marine Drugs. 10(4): 762-774.
  • Burda WN, Fields KB, Gill JB, Burt R, Shepherd M, Zhang XP, Shaw LN. (2012). Neutral Metallated and Meso-Substituted Porphyrins as Antimicrobial Agents Against Gram-Positive Pathogens. European Journal of Clinical Microbiology and Infectious Disease. 31(3): 327-335.
  • Niu Y, Padhee S, Wu H, Bai G, Harrington L, Burda WN, Shaw LN, Cao C, Cai J. (2011). Identification of ?-AApeptides with potent and broad-spectrum antimicrobial activity. Chemical Communications. 47: 12197-12199.
  • Prosen KR, Carroll R, Burda WN, Krute CK, Bhattacharya B, Dao ML, Turos ET, Shaw LN. (2011). The Impact of Fatty Acids on the Antibacterial Properties of N-Thiolated ß-Lactams. Bioorganic and Medicinal Chemistry Letters. 21(18): 5293-5.
  • Padhee S, Hu Y, Niu Y, Bai G, Wu H, Costanza F, West L, Harrington L, Shaw LN, Cao C, Cai J. (2011). Non-Hemolytic a-AApeptides as antimicrobial peptidomimetics. Chemical Communications. 47: 9729-9731.