By Julie Donnelly

I just received a research note from an investment analyst titled “Genzyme: Always making life interesting.” A big understatement, especially for journalists.

Wednesday, the company revealed that it expected to pay $175 million in fines to the FDA to settle an enforcement action over its troubled Allston plant, swinging the company’s first quarter performance into the loss column.

If this were not bad enough, the company disclosed yet another hold up to its manufacturing operations. The company was having some problems with its water system, and then the plant was hit with an electric-power outage.

The result was that “the level of bioburden was above historical levels,” according to Genzyme officials during an earnings call Wednesday.

This means the water had too many contaminating microbes. The company had to stop production for several days last month. In addition, it’s not clear whether unfinished batches of two drugs, in production at the time of the power failure, will be usable. These are the same two drugs that are part of the ongoing shortage that began last summer after the plant was closed temporarily due to viral contamination. The result is that the shortage of Cerezyme, which treats the rare Gaucher disease, will be pushed out an additional two to three months. It will also rub salt in the company’s Fabrazyme-shortage wound as well.

Company officials said that the equipment was sanitized, gaskets were replaced and chemical decontamination was employed to solve the water problem. The water system is fine today, they say. The investigation will be complete this week, and the company can start shipping those medicines again next week.

But every delay exposes the company to more risk that patients will turn to competitors, since there are now two alternatives to Cerezyme on the market.

It also raises the question of the future of the Allston plant. The FDA enforcement action, called a consent decree, requires the company to relocate all of its fill/finish operations — the last part of the manufacturing process — to other locations. Currently half of that work, company wide, is done in Allston. There will also be continued scrutiny of other manufacturing functions at Allston Landing, which will be under a multi-year remediation plan that the FDA will set up soon.

Genzyme is a company with many good people, and it has an admirable mission to treat devastating diseases.

It’s unfortunate that the steady downpour of bad news there has made last month’s monsoons feel more like a passing sprinkle.