Nosing around for staphylococci

In my last post about the newly described MRSA strains that carry the mecA_LGA251, I referred again to the “empty cassette variants” (or “mecA dropouts”) that are missed by commercial MRSA PCR tests that target the orfX gene but don’t contain mecA primers. I also mentioned that we’d soon be publishing our first year of experience with this. Well, here is the short report I was talking about, describing our ~8% rate of false positivity due to empty cassette variants, and characterizing the strains in question. We found substantial genetic diversity among the “drop-out” strains, meaning that the problem wasn’t due to the introduction of a single clone. When we tested these MSSA isolates using the newer GeneXpert MRSA/SA Nasal Assay (the “Nasal Complete” assay), they were correctly identified as S. aureus but not MRSA (this new assay has primers for the mecA gene). Even the “Nasal Complete” assay is susceptible to false positives, though, from the simultaneous presence of an MSSA and a methicillin-resistant coagulase-negative staphylococcus (MR-CoNS) in the same nose (the prevalence of MR-CoNS + MSSA co-colonization was 3.4% in one study). Indeed, the package insert describes a PPV of about 75% for the Nasal Complete—for MRSA, the 25% “false positives” divide equally between those for which culture was negative (which might reflect increased sensitivity of PCR) and those for which the culture grew only MSSA (which may reflect MR-CoNS/MSSA co-colonization). Who knew the nares would be such a vexing place for those who design and market PCR tests?

Always playing catch-up

Reports of the emergence of novel MRSA strains bearing mecA_LGA251, discussed in Eli’s excellent post, were published just as I finished a pro-con session at ASM on the use of culture versus PCR for clinical detection of MRSA. I pointed to the ongoing evolution of MRSA as a drawback to existing PCR methods, and included reference to the "empty cassette variants" that I previously discussed.

Because I think the "empty cassette" or "mecA dropout" story is instructive here. When the orfX-based assays were initially released, the published data described a very low incidence of these variants (in the case of the "mecA dropouts", isolates of MSSA that tested positive by the GeneOhm-GeneXpert-BD test...the opposite problem we see with the mecA_LGA251 isolates, which are MRSA that test negative....). So the potential problem was minimized, mainly for lack of good data and an assumption that clinical labs wouldn't run across these strains very often. Of course, some labs (including ours) did run across them quite often (“empty cassette variants” constitute almost 8% of our positive tests, a finding we'll soon publish (manuscript "in press" at JCM)).

Similarly, we are going to hear about how rare these mecA_LGA251 isolates are, how clinical labs are not likely to run across them, the tests still perform well, etc., etc. But how will we know when we start running across them? Of the hundreds of labs doing MRSA nares screening by PCR, how many are doing culture in parallel (not just on positives, but on negatives as well)? Of the labs that do only culture, how many are also doing confirmatory mecA PCR and following up on any phenotypic MRSA that test PCR negative?

More to come on this topic, and what is says about the future of PCR testing for MDRO detection, in future posts...

Super Sneaky MRSA (but only if you use PCR)

Lost in the din of our Rice Crispies or even the E. Coli outbreak in Europe, are a couple papers out of UK/Denmark and Ireland reporting novel mecA containing MRSA in human and bovine populations.  The concern here, of course, is that in many centers these novel MRSA strains would be missed by static PCR tests, which is what actually happened in these reports. 

The report out of Ireland discusses two clinical MRSA isolates that were PBP2a-positive but mecA negative by conventional mecA PCR - ie they were called MSSA by GeneXpert. The first strain was isolated from a 64-year old in a Dublin acute care hospital, while the second was isolated from an 85 year-old in a South-East Ireland regional hospital. Evaluation determined that these strains contained a novel SCCmec element (Similar to SCCmec XI) with divergent mecA, mecI, mecRI, blaZ and ccr genes. 

In the second report, investigators out of England noticed bovine MRSA strains which tested negative after standard PCR tests for mecA. They determined that they contained a novel mecA homologue, mecALGA251. They then searched collections in Scotland, England and Denmark for similar strains and 51 human isolates with the same mecALGA251. 14 of 25 from London, 12 of 16 from Glasgow and 24 of 32 clinical strains from Copenhagen contained the novel mecA. One human strain dated back to 1975, although detection increased substantially between 2007 and 2010. 54% (13/24) of the bovine isolates were also positive. The distribution of cattle and human isolates in England is shown above.

The authors of this paper suggest that new PCR primers will solve the problem. It is true that it will solve this particular problem, but is it a good long term solution?  Do we think MRSA evolution will stop here? Also, they suggest that dairy cows could be a reservoir of infection, but I would think that humans could also be the reservoir.

What this suggests to me is that if you isolate/decolonize patients using a static PCR for mecA, it is not surprising to me that other novel strains could emerge.  Hand hygiene would not be so easily circumvented, nor would simpler culture-based microbiology methods.

Hopefully our resident microbiologist Dan will chime in too...

UK and Denmark report: Garcia-Alvarez et al. Lancet ID June 3, 2011

Ireland report: Shore AC et al. AAC, June 2, 2011

Tara Smith's take can be found here and Scientific American's report by Katherine Harmon here