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Niger has seen more than 1,300 cases of cholera since the beginning of the year, with 51 people dying of the disease, the United Nations has said.

In September alone there were 38 reported deaths from cholera, said the UN's Office for the Coordination of Humanitarian Affairs (OCHA) in the capital Niamey on its website on Monday.

The spike in the number of cholera deaths was due in part of heavy flooding which has inundated Niger since June.

Steps are being taken "to contain the illness" and "prevent it from appearing in new places," said OCHA, noting that cholera has broken out in four of Niger's eight regions.

Of special concern is the southeast region of Diffa where since 2013 some 105,000 people have taken refuge fleeing from the deadly attacks in Nigeria by the armed group Boko Haram and the crackdown by the Nigerian army.

Many refugees have settled on the islands of Lake Chad "where access to drinking water is limited and the conditions of hygiene and sanitation are precarious," the UN office said.

Cholera is transmitted by ingesting food or drink contaminated with human waste. It causes diarrhoea, dehydration and death if left untreated.