After structural comparison with different species of Penicillium, Fleming initially believed that his specimen was Penicillium chrysogenum, a species described by an American microbiologist Charles Thom in 1910. He was fortunate that Charles John Patrick La Touche, an Irish botanist, had just recently joined St Marys as a mycologist to investigate fungi as the cause of asthma. La Touche identified the specimen as Penicillium rubrum,' the identification used by Fleming in his publication.
In 1931, Thom re-examined different Penicillium including that of Flemings specimen. He came to a confusing conclusion, stating, "Ad. 35 [Flemings specimen] is P. notatum WESTLING. This is a member of the P. chrysogenum series with smaller conidia than P. chrysogenum itself." From then on, Flemings mould was synonymously referred to as P. notatum and P. chrysogenum. But Thom adopted and popularised the use of P. chrysogenum. In addition to P. notatum, newly discovered species such as P. meleagrinum and P. cyaneofulvum were recognised as members of P. chrysogenum in 1977. To resolve the confusion, the Seventeenth International Botanical Congress held in Vienna, Austria, in 2005 formally adopted the name P. chrysogenum as the conserved name (nomen conservandum). Whole genome sequence and phylogenetic analysis in 2011 revealed that Flemings mould belongs to P. rubens, a species described by Belgian microbiologist Philibert Biourge in 1923.
The source of the fungal contamination in Flemings experiment remained a speculation for several decades. Fleming suggested in 1945 that the fungal spores came through the window facing Praed Street. This story was regarded as a fact and was popularised in literature, starting with George Lackens 1945 book The Story of Penicillin. But it was later disputed by his co-workers including Pryce, who testified much later that Flemings laboratory window was kept shut all the time. Ronald Hare also agreed in 1970 that the window was most often locked because it was difficult to reach due to a large table with apparatuses placed in front of it. In 1966, La Touche told Hare that he had given Fleming thirteen specimens of fungi (ten from his lab) and only one from his lab was showing penicillin-like antibacterial activity. After this, a consensus developed that Flemings mould had come from La Touches lab, a floor below Flemings, as spores which had drifted in through the open doors.
Craddock developed severe infection of the nasal antrum (sinusitis) and had undergone surgery. Fleming made use of the surgical opening of the nasal passage and started injecting penicillin on 9 January 1929 but without any effect, probably because the infection was with H. influenzae, a bacterium unsusceptible to penicillin. Fleming gave some of his original penicillin samples to his colleague, surgeon Arthur Dickson Wright for clinical testing in 1928. Although Wright reportedly said that it "seemed to work satisfactorily," there are no records of its use. In 1930 and 1931, Cecil George Paine, a pathologist at the Royal Infirmary in Sheffield, was the first to successfully use penicillin for medical treatment. He attempted to treat sycosis (eruptions in beard follicles) with penicillin but was unsuccessful, probably because the drug did not penetrate deep enough into the skin. He cured three babies with ophthalmia neonatorum, an eye infection, and a local coal miner whose eye had become infected after an accident, but he did not publish his work.