Hackney and Islington pharmacies have had to turn away customers looking for Strep A medication due to supply-chain issues.
Recent weeks have seen a sharp rise in the number of cases of the bacterial infection.
While it usually only results in mild symptoms like a sore throat, in rare "invasive" cases it can enter the bloodstream and cause serious harm.
At least 60 people have died this year in England from Strep A, among them at least 13 children.
Doctors normally prescribe penicillin or amoxicillin to treat the illness.
Rafique Adam, who owns Finstead Pharmacy in Hoxton, told the Gazette: “We are not able to get any of the antibiotics for the children…We have to tell people to try other pharmacies.
“Every time we ask suppliers if they have any they say they don’t have anything to supply. And they don’t tell us when they’re going to get some more supplies in.”
Some pharmacies in Hackney and Islington have been able to source small amounts of amoxicillin.
Rafique said: “Sometimes we get three bottles, and then it just goes out and we can’t get any anymore.
“It’s touch and go right now every time you order.”
Another Hackney pharmacist said: “You can’t get any antibiotics, it’s very distressing… Especially when people come in with crying babies, it’s just horrible.
“It’s awful, not just for the patients but us pharmacists as well because obviously [the patients] are distressed and it transfers to us. On top of our day-to-day job, it’s really distressing.”
A spokesman for the Department of Health and Social Care said: “There is no supplier shortage of antibiotics available to treat Strep A. We sometimes have surges for products and increased demand means some pharmacies are having difficulties obtaining certain antibiotics.”
The Hackney pharmacist said: “I know the government has said that everything’s fine, but it’s quite funny for them to say that, because no one there is working in a pharmacy situation to know what’s going on.”
Strep A can cause scarlet fever, and the UK Health Security Agency (UKHSA) has noted that the infection's season started early this winter.
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