Streamlining Microbiology Workflow with Automation

Thanks to the ongoing sophistication in the instruments, the time taken to identify an outbreak of infectious disease has been sharply reduced from what could take days, down to minutes.

Over the years, there have been many efforts to bring automation to the clinical microbiology lab in order to streamline the workflow. Prior to introduction of automation, the sector entirely depended on highly skilled manpower to receive, process, and interpret the outcomes from a wide variety of clinical specimens with limited aid from automation, which was subject to the risk of human error. The various advantages associated with these technologies over conventional manual systems have led to their rapid adoption in the laboratories. Additionally, improvement in software has played a key role in pushing the technology forward.

The technological advancements have boosted the market by making microbiology tests faster, cheaper, and more accurate, and have increased the use of microbiology tests for the diagnosis of various diseases. Globally, the clinical microbiology market was valued at USD 9.01 billion in 2016 and is projected to grow at a CAGR of 7.3 percent from 2017 to 2024, predicts Grand View Research. In addition, industry is gaining high momentum with launch of innovative products such as MALDI Biotyper, GeneXpert, and Myla IT performance management solutions. Moreover, with the US FDA approving the Xpert Carba-R, commercialization of clinical microbiology instruments is expected to increase significantly over the next few years.

Indian Market Dynamics
The Indian market for microbiology instruments and reagents in 2016 is estimated at Rs. 310 crore, maintaining an annual 5–6 percent growth. Reagents dominate with an 83 percent share. The instruments-based reagents are more popular, and commanded a share of 67 percent in 2016, while the non-instrument based reagents contributed the balance of 33 percent, having declined from 44 percent in 2015.

bioMrieux and BD India continue to lead the segment. Hi-Media has aggressive presence in the noninstruments based reagents segment. Beckman Coulter is gaining strength having acquired the microbiology business of Siemens Healthcare in January 2015.

2016–2017 saw microbiology automation as an important emerging trend in the industry with enrichment and transport media at the heart of it. It is being appreciated that flocked swabs facilitate greater specimen collection and complete elution, particularly for swine flu. The elution of a specimen from such swabs into liquid has demonstrated a significant increase in the release of viable organisms from the swab, which translates into increased sensitivity for detection of microorganisms in the specimen. Consequently, more and more labs are using flocked swabs in combination with a transport media to aid the recovery and detection of pathogens after collection.

Technology Trends
When a state experiences an outbreak of an infectious disease, the time it takes to identify the disease can have a significant impact on the treatment and outbreak response. Now, that time period has been sharply reduced from what could take days, down to minutes thanks to the sophisticated type of mass spectrometry (MALDI-TOF). After organisms are cultured, the time for a bacterial identification is in minutes when compared to the traditional methods, which can take days. From walk-away multiplex PCR assays to total laboratory automation, microbiologists are able to produce faster results of higher quality than ever before.

WGS. In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionize clinical microbiology. It has shown advantages over conventional genotyping approaches for investigating epidemics. Since genomic sequencing information can be obtained in a few days, pathogen identification can be achieved in early states of a disease outbreak. Recent advances show that it can distinguish between different pathogen strains, detect co-infections, and even uncover new pathogens. This benefit also includes the discovery of emerging disease-causing viruses.

In addition to detecting emerging drug-resistant microorganisms, the application of WGS helped to uncover mutations and other genetic factors associated with the spread of drug-resistant pathogens.

MALDI-TOF mass spectrometry. Perhaps the most revolutionary advancement has been the application of MALDI-TOF mass spectrometry for organism identification. Not only is organism identification more accurate than growth-based systems, but identifications are produced more rapidly and at significantly lower cost. Taken together, these factors have led to widespread adoption and universal acceptance of the technology for routine clinical use globally. MALDI-TOF has reduced the identification time, thus, leading to reductions in turnaround time and potentially beneficial patient impacts.

PCR. The discovery of PCR has revolutionized how clinicians diagnose infectious diseases and genetic disorders. Today, new advances in PCR technology, including more sensitive assays and high-throughput instruments, may further revolutionize healthcare. dPCR has become an important new tool for use in the clinical microbiology laboratory. Its advantages over quantitative PCR (qPCR), including absolute quantification without a standard curve, improved precision, improved accuracy in the presence of inhibitors, and more accurate quantitation when amplification efficiency is low, make dPCR the assay of choice for several specimen testing applications.

FISH. Fluorescence in situ hybridization (FISH) is one of the rapid methods for easy identification of microbial pathogens, and diagnosis of pathogens in human infections in the laboratory diagnostic routine. As a microscopic technique, FISH has the potential to provide information about spatial resolution, morphology, and identification of key pathogens in mixed species samples. Ongoing automation and commercialization of the FISH procedure have led to significant shortening of the time-to-result and increased test reliability.

The Road Ahead
The winds of change are blowing through clinical microbiology. Molecular techniques will revolutionize the routine practice of the identification and characterization of pathogens, opening many new opportunities and challenges in all areas of clinical microbiology from routine diagnosis to basic research. Technological advancements and launch of new products will allow more exhaustive and rapid analysis of microbes and will lead the field of clinical microbiology toward a healthy growth path.