The recent emergence of multiplexed molecular technologies has enabled clinical microbiology laboratories to test for broad panels of pathogens with high sensitivity and specificity in a matter of few hours instead of a few days. These comprehensive molecular panels have been associated with improved patient outcomes and reduced hospital costs. This paradigm shift toward rapid, multiple-pathogen detection technologies is driving the need for more advanced biological controls to meet the requirements for validating, verifying, and monitoring these complex systems. While individual live culture controls are necessary for growth-based testing and testing of individual targets, modern molecular technologies do not rely on culturing microorganisms prior to testing. Inactivated microorganisms, genomic extracts, and synthetic materials are a few examples of the innovative controls entering the market for quality control testing of molecular instruments. Pooled controls take this a step further and are necessary for effective and efficient quality check of multiplex panels. Specialized biomaterial producers have the expertise to develop highly stable tittered controls containing multiple analytes to support users of multiplex assays.

Digital microbiology has revolutionized the clinical laboratories. Automated specimen processors plant and streak samples onto culture plates, prepare Gram slides and subculture broths, and apply Kirby-Bauer and ID discs. The specimen processors are connected to conveyor belts that take the processed culture plates to smart incubators. In the smart incubators, high-quality images of the plates are captured, using different lighting, at different time intervals. The images are used for digital image analysis. By reading the cultures on a computer, instead of traditional benches, laboratories are saving time by discarding all negative cultures without having to touch the plates. Laboratory professionals can now focus on handling only the positive cultures, streamlining their workflow for faster turnaround times. Digital PCR is a breakthrough technology that provides ultrasensitive and absolute nucleic acid quantification. This technique is particularly useful for low abundance targets, targets in complex backgrounds, allelic variants, and for monitoring of subtle changes in target levels.

Indian Market Dynamics

Indian Microbiology Instruments and Reagents Market 2014The microbiology instruments and reagents market for the clinical sector in 2014 is estimated at Rs.250 crore. Contributing a major Rs.200 crore, reagents are the mainstay. The balance Rs.50 crore is accounted for by instrumentation into clinical microbiology.

bioMèrieux, is the leading player in this segment. BD India has aggressive presence. Other players are Beckman Coulter (Siemens products) and Thermo Fisher Scientific. Beckman Coulter entered into a definitive agreement to purchase the clinical microbiology business of Siemens Healthcare Diagnostics in July 2014. The Siemens clinical microbiology business is an active player in microbial identification and antibiotic sensitivity testing (ID/AST).

The instruments-based reagents market in 2014 is estimated at Rs.110 crore. The major vendors are bioMérieux, BD India, Beckman Coulter (Siemens products), and Thermo Fisher Scientific.

The non-instruments-based reagents market, broadly comprising dehydrated culture media, antibiotic sensitivity discs, blood culture bottles, and identification kits, is estimated at Rs.90 crore. Led by HiMedia, this segment has players as Microxpress (Tulip Diagnostics), Bio-rad, BD India, bioMérieux, Beckman Coulter (Siemens products), Thermo Fisher Scientific, Merck Millipore, and Titan Biotech.

There are numerous technologies under development or with only limited objective supporting literature which are sure to play a role in the future of clinical microbiology. Likewise, investigators continue to push the limits of current technologies, including digital PCR, next-generation sequencing, and MALDI-TOF MS, to broaden their utility in areas including antimicrobial susceptibility testing and identification of oncogenes. The combined efforts of progressive investigators and availability of increasingly sensitive technologies are sure to improve the quality and add value to the services provided by clinical laboratorians.

Global Market

The global clinical microbiology market is expected to reach USD 12,411.36 million in 2014-19 at a CAGR of 13.03 percent. Increasing disease burden of infectious diseases and increased funding for healthcare expenditure are the important growth drivers for this market during the forecast period. Clinical microbiology consists of a wide array of techniques for the detection of infectious diseases. The respiratory diseases segment accounted for the largest application segment of the clinical microbiology market in 2014. There were several new cases of multidrug-resistant tuberculosis (MDR-TB), and extensively drug-resistant tuberculosis (XDR-TB) which further added to the demand in market. Furthermore, the outbreak of new diseases such as Ebola is expected to increase the disease burden and the demand for clinical microbiology products.

The instruments and reagents market of clinical microbiology segment is expected to grow at the highest CAGR during the same period. The clinical microbiology instruments market is sub-segmented into automated microbiology instruments, laboratory instruments, and microbiology analyzers. The laboratory instruments accounted for the largest share of the clinical microbiology instruments market in 2014, whereas the automated microbiology instruments segment is expected to grow at the highest CAGR between 2014 and 2019. 

Technology Trends

Indian Microbiology Instruments and Reagents Market 2014

Point of care for tangible clinical benefits. With the advent of new technologies, clinically robust point-of-care testing (POCT) for infectious disease now seems like an achievable goal. Next-generation lateral flow immunoassays incorporating digital output of results have entered the market, with reports of enhanced sensitivity and specificity for influenza and group A Streptococcus. Isothermal technologies for detection of DNA and RNA targets have also been introduced recently. The value of immediate and actionable results at the point-of-care (POC) at acceptable price points is often balanced against the relative sensitivity and specificity of the tests, and the concerns over sensitivity and specificity has often been the barrier to POCT in microbiology. Another new technology that shows great promise is rapid-cycling polymerase chain reaction (PCR), which provides a true cycling PCR reaction within the context of a POCT environment which results in 15-20 minutes, depending on the assay. The clinical response of a clinician to any test result is directly impacted by one's confidence in the test result, and PCR gold standard testing represents a potential leap forward in the era of POCT.

Digital PCR for next generation sequencing. Digital PCR is a new approach to nucleic acid detection and quantification that offers an alternate method to conventional real-time quantitative PCR for absolute quantification and rare allele detection. Digital PCR works by partitioning a sample of DNA or cDNA into many individual, parallel PCR reactions; some of these reactions contain the target molecule (positive) while others do not (negative). A single molecule can be amplified a million-fold or more. During amplification, dye-labeled probes are used to detect sequence-specific targets. When no target sequence is present, no signal accumulates. Following PCR analysis, the fraction of negative reactions is used to generate an absolute count of the number of target molecules in the sample, without the need for standards or endogenous controls.

The use of a nanofluidic chip provides a convenient and straightforward mechanism to run thousands of PCR reactions in parallel. Each well is loaded with a mixture of sample, master mix, and reagents, and individually analyzed to detect the presence (positive) or absence (negative) of an endpoint signal. Digital PCR builds on traditional PCR amplification and fluorescent-probe-based detection methods to provide highly sensitive absolute quantification of nucleic acids without the need for standard curves. Digital PCR clear has the clear potential to offer more sensitive and considerably more reproducible clinical methods that could lend themselves to diagnostic, prognostic, and predictive tests.

Automation and digitalization. A downstream indirect benefit of full laboratory automation in microbiology is the standardization and rationalization of sample containers. The adoption of automated specimen processing technology, however, is driving laboratories to standardize and rationalize the containers they receive to optimize the use of the automated processors.  Automated specimen processors are able to handle non-liquid samples. In order to maximize the use of the processors, microbiology laboratories are optimizing workflow by standardizing containers, such as vacuum tubes for urines, elution swabs, and sputum liquefying containers, among others. Standardization of sample collection devices benefits clinicians by simplifying and reducing the number of specimen containers needed at specimen collection sites. Automated specimen preparation technology continues to improve, increasing efficiency in workflow in the clinical microbiology laboratory. This efficiency derives from freeing skilled staff to perform more technical tasks, and by absorbing expanded operations without the need for additional staff.

Digital plate reading is increasingly being adopted as a means to facilitate the analysis and improve the quality and efficiency within the clinical microbiology laboratory. The image acquisition stations built into the full laboratory automation systems use highly sophisticated cameras and versatile lighting systems to obtain sharp, unparalleled high-resolution images. The high quality of the images acquired by the system enables clinicians to zoom in on the culture plates and to detect even small colonies that could be obscured or potentially be hard to see. This new technology helps speed up the workup of positive cultures, by presenting them to the operator first, and leaving the no-growth cultures for last. In case of no-growth cultures, the laboratory professional, after reviewing the plates, can result them in groups, without having to manually discard the plates. It is important to emphasize that the new systems do not make the decisions for the laboratory personnel; the software simplifies and groups culture plates for faster interpretation and increased operational efficiencies. 

Second Opinion
Need for Accurate Results

Microbiology as a discipline has been traditionally linked closely with human health and disease. Thus, many of the seminal discoveries of beneficial/harmful microbes dates back many decades. Most of the initial discoveries were at the level of molecular marker or metabolites but the understanding of the genetic basis of their uniqueness or cause for its severity in evolving strains was very limited. One of the major challenges faced by microbiologists was the inability of many microbes to survive outside the host and thus limiting subsequent studies.

As sequencing based application/s started to evolve gene-specific queries were the first of the shelf. As the field progressed, it was realized that gene-specific approach would not capture the whole picture, more so in compact microbial genomes. The gene regulatory features or variations affecting the structure were difficult to query. Thus, there was a need for sequencing technologies, which can help sequence the whole genome (to query single nucleotide variations) or transcriptome (for differential transcript level) vis-a-vis diseased and healthy states.

With the advent of next-generation sequencing (NGS) platforms, the twin advantage of sequencing at reasonable cost and time became a reality. Additionally, earlier constraint of unculturable microbes could now be studied for its genetic makeup. This has resulted in grand-scale global initiatives like human microbiome project (HMP) and metagenomics of the human intestinal tract (MetaHIT). Inferences arising out of these initiatives have helped immensely the understanding of host-microbe functional relationship. With informed usage of combination of read-length and read-depth, many discoveries have happened. Additionally, approaches like metabolomics have also aided better understanding of the host-pathogen interaction. Recent times have also seen a massive boom in the genome announcements of microbes isolated from different sources and locations leading to better clue about genetic adaptation for different habitats/challenges.

Collectively, the gains out of functional usage of the potential of NGS have immensely aided microbial research. Many scientific efforts, e.g., hundreds of Mtb strains have been sequenced to develop better understanding of its biology and design appropriate therapeutic intervention or prevention strategies. With emerging links of diet, lifestyle, and genetic link of the host-microbiome interaction, the field is still to reach its zenith. But for sure, it opens a wide filed of possibilities with interesting times ahead for both microbiologists and genomic scientists.

Rajesh Pandey
Project Scientist,
CSIR Ayurgenomics Unit-TRISUTRA,
New Delhi

Whole genome sequencing. Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology. The growth and availability of bench-top WGS analyzers has facilitated the feasibility of genomics in clinical and public health microbiology. Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories. As WGS represents the pinnacle for strain characterization and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection, and other sequence-based investigations in the near future. Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardized quality control and data interpretation, bioinformatics expertise, and infrastructure.

Translating the power of high-throughput sequencing technologies from the research sphere into the clinical laboratories is a current major focus for many healthcare providers and researchers, and the power of these technologies is being harnessed to address an increasingly diverse range of problems. Excitingly, real benefits for patients are starting to emerge. The scale and efficiency of sequencing that can now be achieved is providing unprecedented progress in areas from infectious disease and cancer, to common and rare genetic disorders and pre-natal testing. High-profile successes in the application of next-generation sequencing in the laboratories include using sequencing to follow the spread of infections, and uncovering the genetic basis of inherited diseases, such as the molecular mechanisms underlying renal developmental disorders and ciliopathies. In addition, sequencing is informing clinical diagnostics and could be used to classify cancer sub-types for appropriate therapies.

Way Forward

The future of microbiology is in the development of broad molecular panels that offer laboratories the ability to respond to clinician ordering patterns based on their unique patient populations and treatment algorithms, and report and ultimately pay only for the subsets of targets that are relevant for each patient. Such tests would enable platform consolidation and provide a flexible solution to meet the laboratory's workflow and cost needs while satisfying the physician's requirement for timely, accurate, cost-effective results. The recent surge in high-throughput sequencing of cancer genomes has supported an expanding molecular classification of cancer. This has identified putative predictive biomarkers signifying aberrant oncogene pathway activation and may provide a rationale for matching patients with molecularly targeted therapies in clinical trials. Technologies will continue to evolve, allowing faster, more sensitive and less expensive methods for pathogen surveillance and discovery. Although multiplex PCR is relatively mature, microarray technology is still in its infancy; near-term modifications already in development include microfluidic sample processing and direct measurement of conductance changes associated with hybridization.

The cost of implementation includes equipment set-up, routine sequencing costs for reagents and consumables, as well as post-processing bioinformatics costs is an obvious, but significant factor. These expenses can be measured in cost per sequencing run, cost per organism genome sequenced, or cost per megabase of output data. To be a financially viable option for clinical microbiology laboratories WGS must be able to replace current technologies or provide additional benefits in patient outcomes and clinical or laboratory efficiency. Faster colony growth, grouping culture plates by estimated number of colonies for streamlined analysis, providing clinicians with digital patient records with images of cultures and Gram stains for clinical actionable results faster, and laboratory standardization are paving the way for full laboratory automation and digital microbiology. As more and more laboratories embrace this new technology, the benefits in terms of faster turnaround times, better patient care, and the relevance of traditional culture will be substantial.

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