The DOH may have anticipated too soon the ending of the rainy season when it issued a press release on September 24 that reported the 80% drop in leptospirosis cases in the last nine months of the year compared to the same period last year.  The day before, however, Olongapo City officials already declared a state of calamity after 12 hours of continuous rains due to the southwest monsoon enhanced by a tropical storm outside the Philippine area of responsibility. This resulted in the highest levels of floods in the history of the city. Exactly two weeks later, on October 7, the James L. Gordon Memorial Hospital was swamped by patients diagnosed with leptospirosis. On October 9, the DOH-Central Luzon declared an outbreak of leptospirosis with six deaths and 210 cases in 48 hours.  The following day, Secretary Ona visited the city and talked to patients and hospital staff. He also held a press conference and said the outbreak was under control and cases were expected to go down. Meanwhile, PhilHealth directed all public hospitals in the city to ensure that expenses of leptospirosis patients are covered.

Ona disclosed that urban rat infestation probably caused by poor garbage disposal and collection was the cause of outbreak. However, in other news reports, Olongapo City Mayor Rolen Paulino contradicted Ona's statement, saying he believed the rats were washed down by the flashfloods from an abandoned mine in Mt. Redondo.

Leptospirosis is a bacterial infection that is commonly associated with rat urine, but infection can also come from animals like cattle, pigs, horses, dogs and wild animals. The bacteria are acquired not only through cuts in the skin but also by swallowing the bacteria directly from water or through food. The disease causes a wide range of symptoms that begins with fever, body aches, rashes, flu-like symptoms and may end up in meningitis, liver damage (causing jaundice), and renal failure. Death may also occur.

The flooding in Olongapo reached 580 cases with 11 deaths as of October 13.  During this time, the DOH was also closely monitoring  the condition of Zamboanga City that was hit by severe flooding immediately after the end of the 21-day stand-off between government forces and Moro National Liberation Front.  Hoping to avert another leptospirosis outbreak, the DOH sent a supply of prophylaxis medicine for distribution to health personnel who would directly observe the taking of the antibiotic by  high risk individuals in the affected areas. Fortunately, no outbreak was reported here.