Clinical microbiology laboratories include various processes ranging from identifying a patient’s infection to detecting global disease outbreaks. These processes are becoming increasingly more complex based on the advancements in technology and the need for improved healthcare. Clinical microbiology laboratories and techniques have undergone changes with the introduction of molecular biology principles and bioinformatics.
Several outbreaks over the years such as the H1N1 infections, Zika infection and the most recent COVID-19 pandemic have spurred the need to develop better and more efficient microbiological techniques and treatment strategies. The clinical microbiology laboratory is now being challenged to do more work, identify more microorganisms, report complex and changing drug-related information, automate procedures, integrate traditional lab data with molecular findings, and participate in public health reporting and outbreak detection.
Clinical microbiological techniques are also evolving based on healthcare infrastructure and expenditure. The first and second waves of the COVID-19 pandemic have put a lot of stress on the overall healthcare infrastructure which led to the exhaustion of resources such as ventilators and oxygen cylinders. This drove the need to develop vaccines in a short span of time and constantly improve on them to counteract the emerging variants. Vaccines are a preventative measure and can thus reduce the strain on healthcare infrastructure as well as reduce costs.
Automated systems and bioinformatic principles help to detect and identify (phenotypic and genotypic) microorganisms and resistant organisms. Antibiotic-sensitivity testing and computerized interpretation systems have also helped to track down which pathogens are evading immune response and developing resistance. These advanced techniques enable more samples to be processed by fewer personnel hence improve efficiency and time management.
Some of the groundbreaking developments in clinical microbiology include genetic detection and identification of microbial pathogens through nucleic-acid amplification techniques such as the polymerase chain reaction (PCR). PCR is a technique that uses universal primers and amplifies a nucleic acid sequence from a small sample size. RT-PCR is one of the revolutionary techniques that allows for the rapid detection of the SARS-CoV-2 virus. The amplified nucleic acid samples are then sequenced to accurately identify the causative agent.
Fluorescent probes (such as the TaqMan probe that is produced by Roche Molecular Systems, Inc.) has made real-time monitoring of PCR amplification very easy and possible.
Genetic testing is also used to identify DNA sequences that are associated with antimicrobial resistance. Viral loads are also determined by PCR in order to evaluate antiviral therapies. In the case of the COVID-19 pandemic, using the PCR and sequencing methods helped to identify the variants and develop possible treatments such as Paxlovid. Molecular methods allow typing of microorganisms, which can help to analyse the epidemiology of outbreaks and identify their sources. These methods can also determine the possibility of relapse and re-infection in the case of persisting microorganisms.
Microarray analysis used to detect, identify and analyse the gene expression of various microorganisms. Microarrays consist of probes that are located on a solid substrate, such as glass. The probes can be PCR products or oligonucleotides and the ‘targets’ can be PCR products, genomic DNA, total RNA, amplified RNA, complementary DNA, plasmid DNA, bacterial suspensions or clinical specimens. The probes are attached with a fluorescent agent and can thus help to detect specific antibodies against several infectious agents.
Emerging infections and increased social demand are increasing the volume and altering the nature of the activities required from clinical microbiology laboratories and it can be made easy with informatics. Informatics provides the tools and processes to satisfy most of these demands and also advance the clinical microbiology laboratory techniques, allowing the lab to do more with less. Studies have demonstrated that implementation of informatics tools can improve the efficiency, accuracy, precision, and rapidity of microbiology testing and reporting. Bioinformatics has helped clinical microbiology especially with total laboratory automation (TLA), tele microbiology, and microbial whole-genome sequencing (WGS).
A current problem is that scientific responses to emerging threats are far more rapid than administrative responses, often leading to delays in the approval of new diagnostic tests and therapies. The ongoing technological revolution has rapidly transformed research, diagnostic and therapeutic tools. The clinical microbiologists should adopt and practice evolving technologies, and supply the information to the scientific community and the general public in order to keep up with the ever expanding nature of the global microbiota population