Microbiological detection: NGS and mass spectrometry bring opportunities for Industry Transformation

DETAILS

Microbial detection is mainly used for auxiliary diagnosis, and has great potential in the market space of tens of billions of market.

As you may know, the abuse of antibiotics is common in China. To change this situation, we must rely on microbiological detection. In 2011, the Ministry of Health promulgated the most stringent "Antimicrobial Drug Clinical Management Measures" to raise the status of microbial testing to an unprecedented height.

Microbial detection belongs to a subdivision of IVD, is the pathogen of infectious diseases or metabolites for detection and analysis, in clinical commonly used for auxiliary diagnosis, to determine the type of infection, guide the use of drugs, identification of the more accurate link, the more appropriate diagnosis results and treatment options. Without microbial testing, doctors tend to overuse drugs, or repeat trials, which can lead to microbial resistance or delays in disease.

There are 7 types and 152 items of routine clinical microbial testing in medical institutions in China, which mainly include eight categories: fungi, actinomycetes, spirochetes, bacteria, Rickettsia, chlamydia, viruses and mycoplasma. Among them, 81 bacteria were detected, accounting for 52.5%.

There are many shortcomings in the traditional microbial detection methods, such as detection time, detectable microbial quantity, sensitivity and so on.

At present, most of the testing products used in microbiological laboratories are based on traditional methods. The traditional detection methods are divided into three types: dyeing, culture and non culture. At present, the commonly used method is biochemical principle testing, first to determine whether the Gram-negative or positive, and then according to morphology, enzyme reaction, color and other different methods, the specific types of microorganisms identified.

Staining and culture methods are based on traditional smear microscopy and observe changes under microscope. Culture technology is microbial culture, identification and drug sensitivity testing, but also the most important and mature part of microbial detection technology. The non-culture method is based on enzymatic biochemical reactions, using specific enzymes produced in the process of microbial reproduction to react with a chromogenic substrate to achieve detection, mainly suitable for detection of bacterial vaginosis.

For the vast majority of microorganism detection, there is a link which is unable to open, that is, specimen processing and cultivation. Samples need to be pretreated first, and suitable culture media should be selected according to the results of smear staining. Then according to the characteristics of colonies, select appropriate biochemical reaction or automatic instrument identification. Drug sensitivity test was carried out by paper method or directly automated instrument analysis.

Only through the culture of all kinds of pathogenic bacteria, that is, positive specimens, will further identification and drug sensitivity testing. The positive rate of bacterial culture in Europe and America is about 35%; according to the data published in the Blue Book on the Development of China's in vitro Diagnostic Industry 2015, the positive rate in China is relatively low, only 20% - 30%.

Summarized, the traditional microbial detection methods have three aspects. One is that sample culture leads to long detection time, traditional biological detection time as short as a few hours, long as a few days are possible. Two, the types of identification are limited and the accuracy is general. The bacterial culture positive rate described above is very low, and the number of culturable bacteria accounts for only a small proportion of pathogenic microorganisms. Third, the process is more complex, can not be separated from manual intervention, especially in the sample processing and culture stage is difficult to replace with automated instruments.

Microbiological detection technology based on NGS and mass spectrometry brings opportunities for industrial transformation

The analysis method of microbial detection data based on NGS and mass spectrometry has the characteristics of no need for pre-cultured samples, high sensitivity, and can detect unknown microorganisms. It provides a new solution for disease prevention and control and bio-food safety.

The two have several obvious advantages: 1. Fast speed, such as mass spectrometry detection time in minutes, can achieve high-throughput detection. 2, the sample culture link is omitted, and the microorganism which can not be cultured can also be detected. Up to now, up to 2000 kinds of pathogenic microorganisms can be detected at most, far higher than the traditional 152 species. 3, reagent consumption is relatively less than traditional use, and the cost is mainly input from sequencer and mass spectrometer.

Whether it is NGS or clinical mass spectrometry, the exploration and development of clinical application is only about ten years. Illumina, the leader of NGS, established its leading position in the industry by launching Hiseq2000 in 2010. In the same year, NIPT began preliminary clinical application, and NIPT is still the most mature commercial application of NGS. In the field of clinical mass spectrometry, the relatively mature application of microbial identification in the world has not been developed for more than ten years.

The clinical applications of NGS and mass spectrometry have not been fully developed, and there is still a strong platform extension in the future. Gene detection can be used in many fields, such as maternal and child, tumor, genetic disease and so on. Mass spectrometry can directly detect various substances and their metabolites in vivo, and monitor the diagnosis, treatment and prognosis of the disease. It has been used in maternal and child, infection, genetic diseases and other fields. Gene sequencing requires large data analysis to obtain the correlation between the results and the disease, while mass spectrometry requires continuous improvement of the database to improve the accuracy of the test results.

At present, only Merrier and BD, two foreign companies, and Beijing Yixin Bochuang Microbial Mass Spectrometry were approved by CFDA. Although foreign companies have a relatively short marketing time (about 2-3 years) and no more than 400 machines are installed in the market, according to the 2016 Laboratory Medicine Network data, in 2015, Meriere's mass spectrometer has reached 2% of the market share in bacterial identification and drug susceptibility testing, a rapid growth. Overall, occupy the main