92 years after fungus gave the world its first antibiotic penicillin, scientists have sequenced its genome

Alexander Fleming’s original penicillin-producing mold was regrown from a sample, frozen over 50 years ago, and researchers extracted the DNA for sequencing


                            92 years after fungus gave the world its first antibiotic penicillin, scientists have sequenced its genome
(Getty Images)

Over 90 years ago, Alexander Fleming discovered the world’s first antibiotic, penicillin, while working at St Mary’s Hospital Medical School, which is now part of Imperial College London. The antibiotic was produced by a mold in the genus Penicillium that accidentally started growing in a petri dish. Now, for the first time, scientists have sequenced the genome of Fleming’s original penicillin strain by using samples that were frozen alive more than 50 years ago. Penicillium is a fungus that can be commonly found growing on food products such as bread or cheese.

The researchers also used the new genome to compare Fleming’s mold with two strains of Penicillium from the US that are used to produce the antibiotic on an industrial scale. The results reveal that the US and the UK strains use slightly different methods to produce penicillin, potentially suggesting new routes for industrial production. Molds like Penicillium produce antibiotics to fight off microbes and are in a constant arms race as microbes evolve ways to evade these defenses. The UK and the US strains likely evolved differently to adapt to their local microbes, explain authors. The team includes experts from Imperial College London, Centre for Agriculture and Biosciences International (CABI), and the University of Oxford.

“We originally set out to use Fleming’s fungus for some different experiments, but we realized, to our surprise, that no-one had sequenced the genome of this original Penicillium, despite its historical significance to the field,” writes lead researcher Professor Timothy Barraclough, Department of Life Sciences at Imperial and the Department of Zoology at Oxford, in the study published in Scientific Reports.

Fleming’s sample in a tube. (CABI)

 

The discovery

In 1928, Fleming was studying influenza at St Mary’s Hospital in London and noted that a mold, growing accidentally on a bacterial culture dish, had “created a bacteria-free circle, known as a zone of inhibition, around itself.” He identified the fungus as a member of the genus Penicillium. This led to the discovery of the first antibiotic, penicillin.

Fleming had himself initially struggled to identify the exact strain of the fungus. He had thought it was Penicillium rubrum until American mycologist Charles Thom named it P. griseoroseum. Over the years, several species of Penicillium have been identified as producing penicillin, including P. griseoroseum, P. notatum, and P. chrysogenum. Many of these molds have now been re-examined by molecular methods and Fleming’s strain is now known as Penicillium rubens, according to CABI. 

During the 1930s and 1940s, research groups in the UK and the US evaluated many different Penicillium strains to see if any could be used to mass-produce penicillin. From this work, many of the historic strains have been deposited in CABI’s Genetic Resource Collection. One strain from Fleming’s investigations was transferred to the Imperial Mycological Institute, part of CABI, in 1945. The strain Fleming originally sent to Thom was transferred to CABI in 1950. The first strain to be used to produce pure cultures of penicillin by “submerged culture production” was from Belgium and it was deposited at CABI in 1947. 

While Fleming’s mold is famous as the original source of penicillin, industrial production quickly moved to use fungus from “moldy cantaloupes in the US.” From these natural beginnings, the Penicillium samples were artificially selected for strains that produce higher volumes of penicillin.

The current analysis

Fleming’s original Penicillium was re-grown from a frozen sample that was kept at the culture collection at CABI and the researchers extracted the DNA for sequencing. The resulting genome was compared to the previously published genomes of two industrial strains of Penicillium used later in the US. “Nearly a century since Alexander Fleming discovered the action of penicillin in bacterial cultures contaminated by P. rubens, we report the first draft genome sequence of his original strain,” write authors. 

Fleming had himself initially struggled to identify the exact strain of the fungus, and over the years, several species of Penicillium have been identified as producing penicillin. (CABI)

In particular, the scientists looked at two kinds of genes: those that encode the enzymes that the fungus uses to produce penicillin, and those that regulate the enzymes, for example by controlling how many enzymes are made. In both the UK and US strains, the regulatory genes had the same genetic code, but the US strains had more copies of the regulatory genes, helping those strains produce more penicillin. “However, the genes coding for penicillin-producing enzymes differed between the strains isolated in the UK and US. This shows that wild penicillium in the UK and US evolved naturally to produce slightly different versions of these enzymes,” the findings state.

Microbial evolution is a big problem today as many are becoming resistant to antibiotics. While the authors say that they do not yet know the consequences of the different enzyme sequences in the US and the UK strains for the eventual antibiotic, they say it does raise the prospect of new ways to modify penicillin production.

“Our research could help inspire novel solutions to combatting antibiotic resistance. Industrial production of penicillin concentrated on the amount produced, and the steps used to artificially improve production led to changes in numbers of genes. But it is possible that industrial methods might have missed some solutions for optimizing penicillin design, and we can learn from natural responses to the evolution of antibiotic resistance,” concludes first author Ayush Pathak, Department of Life Sciences at Imperial College London. 

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