Antibiotics are on a comeback. And Cubist Pharmaceuticals (NASDAQ:CBST) is in the middle of it.

Gone are the days when it seemed the Food and Drug Administration had a bone to pick with every antibiotic drugmaker. On Friday, the agency approved its second antibiotic in as many months: Durata Therapeutics' (NASDAQ:DRTX) Dalvance last month and Cubist's Sivextro last week.

And last week the agency also gave another of Cubist's antibiotics, ceftolozane/tazobactam, a priority review, which shaves four months off the review of the drug for complicated urinary tract infections and complicated intra-abdominal infections. With a decision expected on or before December 21, Cubist could have two approvals in one year.

Both Durata's Dalvance and Cubist's Sivextro are approved for treating acute bacterial skin and skin structure infections, or ABSSSI, including the nasty methicillin-resistant Staphylococcus aureus, or MRSA, variety that can't be treated with older antibiotics.

Sivextro is available in both intravenous and oral formulations, so patients can transition to the daily oral formulation when they're discharged from the hospital. Dalvance only has to be administered twice, but both doses, administered a week apart, are given intravenously.

It would seem Cubist has the advantage on dosing with the oral formulation, but given the life-threatening nature of MRSA, doctors are more likely to pick a treatment based on efficacy than convenience.

Unfortunately, that's easier said than done at this point. The drugs haven't been compared head to head, and in the clinical trials used to support their approvals, Durata compared Dalvance to Shire's Vancomycin but Cubist compared Sivextro to Pfizer's (NYSE:PFE) Zyvox. Complicating things more, patients in the control group for the Dalvance trials were allowed, but not required, to transition from Shire's Vancomycin to Pfizer's Zyvox after three days.

Both drugs were approved based on clinical trials that showed the drugs are noninferior to their comparators, which is the standard way for an antibiotic to get approved but doesn't tell you much about how good they really are. For Shire the competition isn't a big deal since Vancomycin is already available as a generic, but Pfizer would certainly like to keep the market share Zyvox has. While the efficacy between Sivextro and Zyvox looks similar, Cubist might have Pfizer beat on side effects and certainly has it beat on the convenience front since Sivextro is taken once daily for six days versus twice daily for 10 days for Zyvox.

The fact that we're even talking about competition is a good sign for investors and patients because it means the FDA has woken up and become open to approving new antibiotics. You could argue that the companies have figured out what the FDA wants, and to some degree that's true too, but there's no doubt the Generating Antibiotic Incentives Now part of the Food and Drug Administration Safety and Innovation Act signed into law a few years ago has changed the dynamics of antibiotic drug development.

We're seeing the fruition now. With a pipeline of five drugs including expanded indications for currently approved drugs, Cubist is a company investors should be watching.

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Brian Orelli has no position in any stocks mentioned. The Motley Fool recommends Cubist Pharmaceuticals. The Motley Fool owns shares of Cubist Pharmaceuticals. Try any of our Foolish newsletter services free for 30 days. We Fools may not all hold the same opinions, but we all believe that considering a diverse range of insights makes us better investors. The Motley Fool has a disclosure policy.

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