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Company develops system for more rapid identification of bacteria that cause hospital infections

Neoprospecta’s Laboratory: sequencing of microorganisms and identification...

NEOPROSPECTANeoprospecta’s Laboratory: sequencing of microorganisms and identification…NEOPROSPECTA

According to data from the World Health Organization (WHO), 14% of hospitalized patients worldwide suffer from hospital infections. In Brazil alone, according to the National Biosafety Association (ANBio), 100,000 people die each year from infections contracted in hospitals and clinics while seeking treatment there for other diseases. One of the difficulties in controlling these infections is the delay in identifying the microorganisms found in hospitals. This problem led two doctoral students of genetics and molecular biology at the Federal University of Rio Grande do Sul (UFRGS) to develop a technology that can analyze up to 512 samples and identify, in each of them, tens of thousands of species of microorganisms, within three to five days, on average. This is comparable to the amount of time it takes to detect just one bacterium by the traditional method. The two doctoral students, Marcos de Oliveira Carvalho, a pharmacist, and Luiz Felipe Valter de Oliveira, a biologist, started Neoprospecta, a small business located in Sapiens Park in the city of Florianópolis, Santa Catarina State.

The old technique of identifying bacteria, still the one most often employed, uses Petri dishes, in which species are cultivated and identified one by one. The problem is that each bacterium can take up to one week to be cultivated. The Neoprospecta technology associates DNA analysis with an algorithm—mathematical instructions for computer software—which automates the entire process. “It’s a platform that involves several stages, technologies and systems,” says Carvalho, the company’s CEO. The whole process is done in four stages: collection of material at various points throughout the hospital—or other institutions and companies such as clinics, health centers, food factories and water treatment plants—genome sequencing, data analysis and presentation of the results.

The collection is done at potential points of infection, including hands, coats and instruments used by professionals of the institution (doctors, nurses, assistants), invasive devices, rooms, hallways, drinking fountains, doors, doorknobs, beds, and even the patients themselves. “To obtain each sample, we use cotton swabs measuring up to 15 centimeters in size,” says Carvalho. “Each swab has a capsule on the end with a liquid known as lysis solution and a plastic valve, through which this solution comes into contact with the collected material.” This solution is made ​​of a mixture of water, soap and sodium chloride, commonly known as table salt, and is used to break the cell membrane. “And so the swab itself starts to break the cells of the bacteria, which provides more security in transporting the material, and begins the process of DNA purification,” says Carvalho. “Hundreds of swabs are used in the analysis of a hospital. After collection, they are placed in special containers that we designed, which are then taken to our laboratory where the DNA of the microorganisms is purified. At this point, the genetic material of all the species present in the samples is mixed.”

... of the species and amount of bacteria related to the sample site

NEOPROSPECTA … of the species and amount of bacteria related to the sample siteNEOPROSPECTA

The next stage is the sequencing. But before doing that, this “soup” of the purified DNA of hundreds or thousands of species of bacteria must be prepared. “Our company developed and perfected this preparation technique, which allows us to increase the multiplexing of samples without sacrificing quality,” says Carvalho. “With it, we can analyze multiple samples in parallel, resulting in faster turnaround and lower costs.” He notes that the price for cultivating each bacterium is around R$100.00. Each swab costs around R$150.00, but it can identify hundreds or even thousands of species, which reduces to pennies the amount spent to identify each bacterium. In the analysis of the sequencing data—potentially tens of gigabytes of data—the DNA, which is still all mixed up, is separated by species. Thus, it will be possible to identify which species are in the sample and the amount of bacteria. “At this stage, the data are subjected to other algorithms, which classify each species and catalog them,” says Carvalho. “All processing is done on Neoprospecta’s servers, on which data are encoded and processed under a high security regime.”

To identify each species of microorganism, the algorithm compares the DNA of the bacteria sequenced in the sample with the billions that make up the company’s database. Despite the large number of cataloged bacteria, up to 50% of those identified from a hospital setting are not found in the database, and many of them are unknown to science. When this occurs, the new bacteria are labeled and become part of the database. The task of classifying them can be done by other researchers in the area of taxonomy, for example.

Accelerated investment
The last phase is presentation of the results. “To do this the data are loaded into a system we developed for microbial risk analysis and quality control of a hospital environment,” says Carvalho. “This system presents a view of the microbiological load in the collected samples.” Neoprospecta currently has three hospitals as clients, two in São Paulo and one in Porto Alegre, the capital city of Rio Grande do Sul State; he cannot reveal their names.

It may not be much, but it is significant for a small business with just a little more than a year of operation. The story of Neoprospecta began in 2010, when Carvalho and Valter de Oliveira won the Santander Prize for Entrepreneurship with the company’s business model. The following year they won the Ibero-American Prize for Innovation and Entrepreneurship, awarded by the Secretaría General Iberoamericana (SEGIB), based in Madrid. At that time, Neoprospecta was developing slowly because the two partners were working on their doctorates at UFRGS. At the end of 2012, they found some investors. In 2013, an angel investor invested R$500,000 in the company, and it moved from Porto Alegre to Sapiens Park in Florianópolis, where it was able to accelerate the process of developing its proprietary technology. More recently Neoprospecta received a R$4 million injection of funds from the Cventures Primus fund. “The money is being used for infrastructure, marketing and research and development,” says Carvalho. “In addition, funds were also used for the construction of five laboratories and the purchase of equipment.”