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"I feel like I've been very fortunate in that I've stuck like a burr to the dog-leg of the next generation of nerdism. I've been carried into the XXIth century on Bill Gates' pants-cuff."
- William Gibson

Biological Warfare  
  The use of microorganisms to defeat an enemy; this is the first reference in science fiction that I can find to this concept.  

As far as I know, this is the first direct reference in science fiction to the idea of fighting an enemy or defeating an enemy using biological agents. (Note: I've been informed that T. Mullett Ellis wrote on this topic earlier in ZALMA in 1895; aerial anarchists plot to attack capital cities with anthrax dropped from balloons).

In another moment I had scrambled up the earthen rampart and stood upon its crest, and the interior of the redoubt was below me. A mighty space it was, with gigantic machines here and there within it, huge mounds of material and strange shelter places. And scattered about it, some in their overturned war-machines, some in the now rigid handling-machines, and a dozen of them stark and silent and laid in a row, were the Martians--dead!--slain by the putrefactive and disease bacteria against which their systems were unprepared; slain as the red weed was being slain; slain, after all man's devices had failed, by the humblest things that God, in his wisdom, has put upon this earth.

For so it had come about, as indeed I and many men might have foreseen had not terror and disaster blinded our minds. These germs of disease have taken toll of humanity since the beginning of things--taken toll of our prehuman ancestors since life began here. But by virtue of this natural selection of our kind we have developed resisting power; to no germs do we succumb without a struggle, and to many--those that cause putrefaction in dead matter, for instance--our living frames are altogether immune. But there are no bacteria in Mars, and directly these invaders arrived, directly they drank and fed, our microscopic allies began to work their overthrow. Already when I watched them they were irrevocably doomed, dying and rotting even as they went to and fro. It was inevitable. By the toll of a billion deaths man has bought his birthright of the earth, and it is his against all comers; it would still be his were the Martians ten times as mighty as they are. For neither do men live nor die in vain.

From The War of the Worlds, by H.G. Wells.
Published by Unknown in 1898
Additional resources -

Biological warfare has been around for at least 2500 years. In the sixth century B.C., the Assyrians used rye ergot to poison enemy wells. In the fifth century B.C., Scythian archers dipped their arrows into animal dung to cause wounds to fester.

The Romans were known to use dead animals to foul the water supplies of their enemies. The Tartars of Russia reputedly had the idea of catapulting bodies infected with bubonic plague over the walls of the city of Kaffa; this may have aided the spread of the Black Death in Europe.

During the Indian wars in North America, the British distributed blankets that were taken from known smallpox sufferers. It is true that the Native American population was devastated by diseases introduced by the new settlers; whether or not the British strategy actually spread the disease is not known.

(Thanks to Simon for this one!)

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