Human skin is a garden of microbes that is home to about 1,000 bacterial species. Most are benign, but some invade the skin and cause illness—of these, antibiotic-resistant bacteria are particularly dangerous.

We normally associate these resistant bugs with hospitals, but new research finds that they could be living and spreading in households and within communities, too. For one notoriously resistant bug, scientists have also been able to pinpoint where and when it first began spreading. The hope is that this knowledge will allow a better way of controlling infection and stopping epidemics.

The Staph of nightmares

About one in five humans carries the disease-causing bacteria Staphylococcus aureus, or Staph, on their skin without any problem. However, breached skin, surgical wounds, or low immunity (often caused by HIV infection or cancer treatments) may allow Staph to cause diseases ranging from minor skin ailments to catastrophic infections.

The spread of methicillin-resistant Staphylococcus aureus (MRSA) is well known. Originally associated with infections in hospitals and nursing homes, MRSA is now known to colonize the skin of otherwise healthy individuals—these infections are called "community-associated" (CA-MRSA).

CA-MRSA spreads by contact with an infected individual. That's why the spread of CA-MRSA can occur in households, where the contact between house members is difficult to control. This also results in high rates of recurrent infection due to contaminated household objects such as shared razors, towels, and door knobs.

Global epidemic

While the presence of Staph on skin has always put people at risk for infection, two features make CA-MRSA riskier. It can cause severe disease in previously healthy people. In about one in every ten cases, CA-MRSA infections lead to deadly pneumonia, severe sepsis, or the dreaded "flesh-eating disease" (aka necrotizing fasciitis). They also have the ability to spread rapidly, which has helped propel them to a global epidemic.

The global epidemic has been attributed to a single CA-MRSA microbe known as USA300. In the US, it is responsible for outbreaks in 38 states, and it has spread to Canada and several European countries. Studies of USA300 have found molecular evidence that suggests it has the ability to readily evolve into more harmful versions.

USA300’s invasion of community households is less well understood. To change that, Anne-Catrin Uhlemann at Columbia University Medical Center and her colleagues have used whole-genome sequencing to reconstruct USA300’s evolutionary history. The results have been published in PNAS.

Whole-genome sequencing takes a snapshot of an organism’s complete genetic makeup. Uhlemann obtained Staph cells from 161 CA-MRSA-infected residents in New York City and combined their genome data with health statistics to gain insights into USA300’s spread during a period covering 2009-2011.

They looked for small changes in the genome, which often give clues about how the cell evolved. After investigating more than 12,000 small changes in the USA300 genome, the authors reconstructed its genetic history. This helped them determine that USA300 first arose around 1993. The molecular signatures allowed them to also home in on the geographic location where this happened, which they determined to be right in Columbia’s neighborhood: northern Manhattan.

Sneaky bug

Detailed study of USA300's genome showed it acquired antibiotic resistant genes from viruses that infect bacteria. The authors also discovered a smaller subgroup of USA300 resistant to another antibiotic class, fluoroquinolones, which appeared to evolve around the time when fluoroquinolone prescription rates had soared in the US.

All this information put together shows that USA300 originally evolved and spread in households and communities in New York City before going global. The occurrence of different antibiotic-resistant bugs highlights the effects of overuse of antibiotics. But working out how CA-MRSA spread within households and inside communities may help researchers devise an infection control strategy that can break this pattern of spread and reduce the possibility of another large-scale outbreak.

PNAS, 2014. DOI: 10.1073/pnas.1401006111 (About DOIs).

Kausik Datta is a post-doctoral fellow at the Johns Hopkins Medicine. First published on The Conversation.