Learning How Bacteria Causes Infections


Research Description

Dr. Robert Shanks Learns how Bacteria Cause Infections

Imagine you are an alien and want to know how automobile headlights work. You have no concept of which of the thousands of parts of the car are necessary for the lights to work.

"Scanning electron micrograph of Serratia marcescens bacteria isolated from a contact lens forming a sticky biofilm."  Image taken by the Center for Biological Imaging, University of Pittsburgh

One thing you could do is line up a million cars and zap them at random with your ray gun. Most of the cars that you shoot will have working headlights (assuming you did not set your laser gun to it maximum setting), but when you get into a few of those zapped cars, and turn the switch, the lights won’t go on. You can then determine what parts of the car you damaged with your laser and start to understand what parts of the car are necessary for those lights to work: wires, the battery and the light bulb.

We use this approach to learn about bacteria, except that we make mutations in DNA rather than zap cars with a laser, although, that sounds fun too. This is called a genetic approach.

My laboratory used a genetic approach to learn how bacteria cause infections and stick to surfaces in slimy clusters called biofilms. Biofilms are important because they protect the bacteria from antibiotics and the immune system. “It can take over 1000 times the amount of antibiotic to kill a bacteria in a biofilm than it takes to kill the same bacteria not in a biofilm*.”

The bacteria that we focus on cause eye diseases and hospital acquired infections.

These bacteria are:

1. Serratia marcescens

This bacteria causes 1.4% of total hospital acquired infections that can be deadly, and about 11% of the corneal ulcer infections at the UPMC Eye Center. It is one of the most common contaminating bacterial species of contact lenses and contact lens cases. It can be highly resistant to cleaning agents, such that it is a major contaminant of medical devices and fluids.

This bacterium is famous for its red pigment. We are studying this red pigment because it shows the ability to kill tumor cells, and may be used in future approaches to cure cancer. We have developed strains that increase pigment production a hundred-fold compared to the normal strain.

Pigment Production by Serratia marcescens

2. Pseudomonas aeruginosa

According to the TODAR’s textbook of bacteriology Pseudomonas aeruginosa infection is a serious problem for cancer, cystic fibrosis, and burn unit hospital patients. Half of these patients will die from Pseudomonas aeruginosa infections.

Additionally, it is one of the most common causes of contact lens related infections (~15% of corneal ulcer infections seen at the UPMC eye Center). Infection with this bacterium can rapidly cause vision loss. (Source: Campbell laboratory Web page).

Staphylococcus aureus biofilm

3. Staphylococcus aureus

This bacterium looks like a bunch of grapes under the microscope, and can be found in the noses of many people. Unfortunately it infects over 500,000 American patients each year in hospitals. It causes a wide range of infections from pimples to necrotizing fasciitis (flesh eating bacteria), as well as a range of eye infections including keratitis (~27% of corneal ulcer infections seen at the UPMC eye Center). Sources: Wikipedia, Campbell laboratory Web page

Staphylococcus aureus

4. Acinetobacter baumannii

This bacterium is most notable in war wound infections, as it was a common infectious agent among wounded soldiers during the Vietnam War, and is today in the conflicts in the middle east. Because of this, many call it the “Iraqibacter”. It is notable because it can be highly resistant to known antibiotics, and has shown up in hospitals in Europe and North America.

Source: Associated Content

Our major research questions are:

  • What genes do bacteria need to cause keratitis?
  • What genes do bacteria need to form biofilms?

By understanding the basis of these processes, we can direct future therapeutics to help prevent vision loss and death.

Main Publications

  • Wu, E., Romanowski, E.G., Kowalski, R.P., Mah, F.S., Gordon, Y.J., Shanks, R.M.Q. (2010) AzaSite® inhibits Staphylococcus aureus and coagulase negative Staphylococcus biofilm formation in vitro. J Ocul Pharmacol Ther. 26:557-62.
  • Kalivoda, E.J., Horzempa, J., Stella, N.A., Sadaf, A., Kowalski, R.P., Nau, G.J., Shanks, R.M. (2011) New vector tools with a hygromycin resistance marker for use with opportunistic pathogens.  Mol Biotechnol.  48:7-14.
  • Miller, K.V. Eisley, K.M., Shanks, R.M.Q., Lahr, R.M., Lathrop, K.L., Kowalski, R.P., Noecker, R.J. (2011) Recurrent enterococcal endophthalmitis seeded by an intraocular lens biofilm. J Cataract Refract Surg  37:1355-9.
  • Wingard, J.B., Romanowski, E.G., Kowalski, R.P., Mah, F.S., Ling, Y, Bilonick, R.A., Shanks, R.M.Q. (2011) A novel cell-associated protection assay (CAPA) demonstrates the ability of certain antibiotics to protect ocular surface cell lines from subsequent clinical Staphylococcus aureus challenge. Antimicrob. Agents. Chemother. 55:3788-94.
  • Costerton, J. W., P. S. Stewart, and E. P. Greenberg. 1999. Bacterial biofilms: a common cause of persistent infections. Science 284:1318-22.
  • Richards, M. J., J. R. Edwards, D. H. Culver, and R. P. Gaynes. 2000. Nosocomial infections in combined medical-surgical intensive care units in the United States. Infect Control Hosp Epidemiol 21:510-5.
  • Shanks, R. M., N. A. Stella, E. J. Kalivoda, M. R. Doe, O. D. D. M., K. L. Lathrop, F. L. Guo, and G. J. Nau. 2007. A Serratia marcescens OxyR homolog mediates surface attachment and biofilm formation. J Bacteriol 189:7262-72.
  • Zegans, M. E., R. M. Shanks, and A. O'Toole G. 2005. Bacterial biofilms and ocular infections. Ocul Surf 3:73-80.


  • R01 grant from the NIH, NIAID  Novel regulators of bacterial exoenzyme production
  • Career Development Award from Research to Prevent Blindness