Tempting though it may be to blame the spies, the buggers cause unrest (and 15% at least for each faction - not sure for each spy), not corruption. Which would mean you would have to lower the tax rate of Antioch, which would mean Antioch wouldn't 'pull its weight' which means negative income in that city.
Contribution of each city to income is weighed according to total income. If cities are performing below par, they show up on the map as having negative income.
Now if you look at those cities that have a distance to capital of 80%, they are usually the ones with Low Taxes and therefore negative income. To counter the situation, move your capital to the center of your empire (check with your finances tab to get the lowest amount of loss due to corruption). So try out a few cities and see which works best.
Ports, roads, traders do the rest. Make sure you dont use big garrisons for big cities, use Games, Races, & lower the growth rate (dont build farms). If its too late for that: Exterminate.
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