The flooding of many parts of Pakistan has led to an outbreak of many forms of water-borne diseases, with diarrhoea and related diseases being quite common. Outbreaks of diarrhoeal diseases have come from the districts of Balochistan - Charsadda, Mardan, Nowshera District and Naseerabad. However, you should observe the general rules for water quality in all areas as you would in any non-third world country. Be careful of water that has not been boiled or purified, and stick to bottled water where possible.
Pakistan has a fairly high incident of Malaria, excepting for those areas above 2000m above sea level. Coastal and low lying areas quite obviously have a higher incident of Malaria, and any areas affected by flooding where there are large bodies of still water can be considered to carry a higher risk of Malaria. Strong strains of Malaria that are resistant to Chloroquine and sulfadoxine-pyrimethamine exist in Pakistan, and these strains are harder to treat. The added danger is that Pakistan has few high level hospitals outside of the major urban cities, so treatment outside of those areas may be problematic.
Pakistan does have a general problem with insect borne diseases, and in addition to Malaria, dengue fever, Crimean-Congo haemorrhagic fever and Japanese encephalitis, are present with outbreaks occurring periodically. Now, none of those diseases sound like a lot of fun to have, and there's a reason for that. There all fairly nasty, debilitating and generally unpleasant, so do everything you can to avoid getting any of them.
Dengue fever is problematic in that there does not yet exist a vaccination of specific treatment for dengue fever. Consult your doctor about possibly vaccinations for other insect borne diseases present in Pakistan before you leave.
Strict preventative measures against insect borne diseases should be put into place and used wherever appropriate, as the best defence is not getting bitten in the first place. Ensure that your accommodation is insect proof, especially at night, use an insect repellent at all times and where long loose fitting, light coloured clothing.
As for unique local colour, as well as avoiding the street vendor food stalls which look like they might be dodgy, also avoid the temporary henna tattoos, as they more often than not contain a dye which can cause serious skin reactions.
Restaurant hygiene in Pakistan can be outright dangerous and unlike many other countries, judging by price won't work. While in many countries the more expensive the restaurant the safer it is, this is not the case in Pakistan. If a restaurant is expensive yet either empty or not that busy, there's a high chance that the food has just been sitting around in the open and breeding bacteria like it's going out of style. Choosing an eating venue via turnover is often a safer bet, as a high turnover means that the food remains fresh and hot rather than lukewarm and festering.
If you have a sensitive stomach or are generally prone to stomach upsets and you do encounter intestinal problems, ask the chemists for "Medicine Stop Motion", they will be aware of exactly what you're after. Better still, take anti-diarrhoea medication with you when you leave.
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