Bugging city communities with impunity: this is the Staph of legend


Whether we know it or not, the human skin is a veritable garden of micro-organisms. The outermost layer (‘epidermis’) of the skin, the shafts of hair follicles, as well as the soft surface inside the nose (‘nasal mucosa’), making up for approximately 1.8 square meter of surfaces, is home to about 1000 species of bacteria among other things. Most of these don’t ordinarily cause disease; some are there for the ride, and some even offer benefits by warding off other nasty bugs from latching on.

Some of these resident microbes, however, may invade the skin to cause disease. Staphylococcus (‘Staph’) aureus is one such bacterium. About 1 in 5 humans carries Staph on the skin and in the nasal passageway without a problem. However, if the skin is breached (as in seriously ill in-patients with in-dwelling medical devices and/or surgical wounds) or the immunity is low (as in HIV infection, organ transplants, or cancer), Staph can cause a range of diseases – from minor skin ailments to majorly life-threatening conditions involving the skin, soft tissue, lungs, bloodstream and the heart.

Staph aureus under microscope; Gram Stained SA (L) courtesy Richard Facklam CDC; SEMs (M & R) courtesy JH Carr CDC

LEFT: spherical (cocci) Gram-positive Staphylococcus aureus bacteria; photo courtesy: Dr. Richard Facklam, CDC, 1980; MIDDLE: scanning electron micrograph (SEM) of Staph clumps; RIGHT: SEM of Staph, showing the sticky-looking substance the bug makes, which helps it colonize surfaces and prevents action of antibiotics; photo (middle and right) courtesy: Janice Haney Carr, CDC, 2005. Images obtained from PHIL, CDC. Composite made by me.

But the greatest threat comes from the emergence of Staph strains resistant to the ‘β-lactam’ class of antibiotics – known as methicillin-resistant Staph aureus (‘MRSA’). Originally considered an agent of nosocomial or ‘healthcare-associated’ bacterial infections, MRSA is now known also to colonize the skin of otherwise healthy individuals, even in the absence of established healthcare risk factors; this is referred to as ‘community-associated’ (CA)-MRSA.

Similar to other Staph, CA-MRSA is transmitted via direct skin-to-skin contact with a colonized or infected individual; the likelihood of this occurring increases in crowded or closely-quartered areas (as in the military barracks, day-care centers, schools, dormitories, prisons, and so forth), and areas with poor hygiene. An oft-overlooked reservoir for community transmission of CA-MRSA is the household; colonization and infection of one household member spreads the infection to others via means that are difficult to control, resulting in high rates of recurrent infections. Associated risk factors include environmental contamination and CA-MRSA infection of fomites (i.e. any object/substance capable of carrying infection, such as shared razors, towels, whirlpools, door knobs, et cetera).

Epidemiologically, skin and nasal carriage of Staph have long been associated with subsequent infection. But two features that distinguish CA-MRSA are: first, its enhanced ability to cause disease in previously healthy people, and with increased severity; in about 1 in every 10-20 cases, CA-MRSA infections are seriously life-threatening, manifesting as pneumonia, severe sepsis, necrotizing fasciitis (a.k.a. “flesh-eating disease”) and other critical diseases. Secondly, its ability to spread rapidly – which has resulted in a global epidemic that includes the US.

And it all started with one. The emergence of CA-MRSA infections in the US has been attributed to a single clone – the genetic ancestor from which arose all the epidemic-associated strains – designated USA300 (by a technique called PFGE) or ST8 (by another technique called MLST). In relation to outbreaks in at least 38 US states, as well as sporadic infections, USA300 has been held responsible, and currently accounts for more than half of all Staph infections. It has also managed to successfully spread to Canada and several European countries.

Studies of USA300’s disease-causing abilities (‘virulence’) have documented how it shifts virulence-associated genes to overdrive and acquires unique genetic characters. Molecular evidence points to CA-MRSA undergoing an evolutionary process, making identical copies (‘clones’) of itself and diversifying into the USA300 sub-population with varying degrees of virulence. What we didn’t understand quite well until now is how USA300 invaded within community households, evolved, and spread from one to another. A recent paper – published in Proceedings of the National Academy of Sciences (PNAS), USA, by Anne-Catrin Uhlemann of Columbia University, and co-authors – has successfully used a technique called whole genome sequencing (WGS) to reconstruct USA300’s evolutionary history from clinical isolates obtained from 161 CA-MRSA infected residents of a large urban community – encompassing Northern Manhattan and the Bronx in New York city.

Whole genome sequencing is an impressive technique that takes a snapshot of an organism’s complete genetic complement, or ‘genome’, at a given time, and determines the DNA sequence of all genetic material – present in chromosomes in the cell, as well as in organelles such as mitochondria or chloroplasts. This powerful technique has applications in studying evolutionary biology and epidemiology of microbial diseases, and Uhlemann and her fellow scientists have used it successfully to integrate genomic and epidemiological data to gain insights into USA300’s spread during a period covering 2009-2011. Additionally, they compared their dataset with data obtained across the country during an earlier period, 2004-2009.

Small, unit changes (called  ‘SNP’ or ‘snips’) – in the genomic DNA sequence may serve as signatures for an organism, and establish their lineage from an ancestor. In the sequenced whole genome of close to four hundred USA300 isolates, the authors looked at over 12000 such snips to reconstruct its lineage and figured out the rate at which these changes occur. This, in turn, helped them determine the approximate time when USA300 first arose (around 1993) and where (the Washington Heights area), and that the copies it made of itself were mostly identical to begin with. Interspersing these molecular signatures with geographic localization allowed them to surmise that USA300 came to northern Manhattan many times.

Given CA-MRSA’s propensity for hiding in plain sight – by colonizing surfaces without causing overt disease (‘asymptomatic colonization’) – identifying how USA300 snuck into communities and households was a challenging task. Knowing that the rate at which changes occurred in the genome was low, the authors took a clever approach: they retrieved the bug from various skin areas, such as throat, armpit and groin, of 21 asymptomatic individuals many times over and analyzed the genomic signatures and relationships between the isolates. This allowed them to determine that USA300 isolates obtained within a household were rather similar, indicating transmission and reinfection within the members, whereas those from different households were generally different enough to rule out a community outbreak.

A larger examination of all 170 households revealed 47 which yielded a subgroup of isolates with shared SNP signatures and some epidemiological connections; of these, a smaller, geographically dispersed, non-household subgroup shared a common ancestor that arose around 2002, and had peculiar signatures which may represent further evolution of USA300.

Deeper study of the genomic DNA sequence of USA300 revealed the varying presence of genetic elements it has acquired over time from various phages (viruses that infect bacteria) – including the genes responsible for resistance to various antibiotics including the β-lactams. This provided a window into genetic adjustments necessary for USA300 to survive and thrive. The authors also discovered a smaller subgroup of USA300 resistant to another antibiotic-class, fluoroquinolones, which appeared to emerge around the time when outpatient fluoroquinolone prescription rates had soared in the US (mirroring a similar observation made in the UK with nosocomial MRSA).

To conclude, the reconstruction of CA-MRSA USA300’s onslaught on some households and communities in New York City, using comparative genome analysis, offers valuable insights into this bug’s evolution, transmission and infection patterns, and establishes households as environmental reservoirs of the bug. The occurrence of multi-antibiotic resistant subgroups highlights the ill effects of indiscriminately wide use antibiotics at a population level. Finally, the observation of patterns of transmission of CA-MRSA within households and inside communities can help produce a “search-and-destroy” disinfection strategy to break the pattern, thereby reducing the possibilities of large-scale outbreaks.

Uhlemann, A., Dordel, J., Knox, J., Raven, K., Parkhill, J., Holden, M., Peacock, S., & Lowy, F. (2014). Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1401006111

[An abridged and edited version of this post has been published at The Conversation UK.]