The microbiology lab today is continuously faced with changes in antimicrobial resistance, formularies, therapies, in the healthcare landscape. Automation had revolutionized clinical chemistry and hematology laboratories many years ago, but the degree of sophistication required to automate the microbiology lab has proven to be a much greater challenge.

The microbiology lab is very complex a with significant variations in sample types, culturing requirements, and the final identification of an organism from among hundreds of potential microbes. Automating the microbiology lab has been a primary area of focus for the companies in recent times, with significant strides being made in the right direction.

Technology Trends

Rapid diagnostic technologies. Early detection and diagnosis of infections is critical to ensuring patients receive effective therapy as early as possible which will help prevent the emergence and spread of multi-drug resistant microorganisms (MDROs). Rapid diagnostic technologies such as peptide nucleic acid-based fluorescence in situ hybridization (PNA FISH), polymerase chain reaction (PCR), and mass spectrometry (MS) allow for the early identification of causative pathogens. These methods can identify microbial pathogens and resistance markers within a couple of hours, compared to conventional culture-based methods which can take up to one to two days for organism identification and two to four days for antibiotic susceptibility results.

The PNA FISH assays require a fluorescence microscope and can identify a limited number of organisms in 20 minutes following a Gram stain. Various PCR-based methods can identify Gram-positive bacteria, Gram-negative bacteria, and yeasts. These systems can also detect selected resistance markers such as mecA for MRSA detection, vanA/vanB for VRE detection, and various beta-lactam and carbapenem-resistance genes including CTX-M, IMP, KPC, NDM, OXA, and VIM found in Gram-negative bacteria in one to two hours or less from positive blood cultures and respiratory and wound samples.

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS instruments can identify organisms in minutes from isolated colonies. Full laboratory automation and digital microbiology are trending topics high on the list. The increase in interest in this technology is mostly driven by budget cuts, shrinking workforce, and legislation-mandated testing, as well as increasing pressure to maintain quality.

Smart incubators. The key component of full laboratory automation in microbiology is the use of smart incubators which place each individual plate on its own shelf. The initial rationale for individual shelves inside the smart incubators is mainly for random and faster retrieval when the laboratory professional wishes to access a particular plate.

Discriminative image analysis software. Image acquisition stations 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 laboratorians to zoom in on the culture plates and to detect even small colonies that could be obscured or potentially be hard to see. Discriminative image analysis software that uses the plate image taken at a time, and compares it with the images taken after incubation enables discrimination of artifacts present on the plate at time zero, focus on growth, and recognizes even small colonies. According to the estimated number of colonies, the system sorts the plates from most estimated colonies to least estimated colonies for interpretation and analysis.

Decentralization of testing. Another trend that has gained traction is the decentralization of testing. As hospitals merge into larger systems, these systems have turned to core microbiology labs to manage the ever-growing demand for microbiology testing services. Automation plays a key role in this, but automated technology is only half the process. High performance is achieved through a combination of many processes working in collaboration.

While microbial culture has been the mainstay of clinical microbiology for the past century and will likely remain so for decades to come, with current pressure and its manual nature, clinical microbiology is experiencing unprecedented changes and evolving at a rapid pace.

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