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The Paperless Microbiology Laboratory
by Nicola Wilson, PhD, and John Boother
Westward Laboratories is a microbiology laboratory based in the U.K. that conducts daily routine microbiological testing on finished products, regular pathogen tests for evidence of Salmonella, Listeria, E. coli, and other food poisoning organisms, as well as environmental monitoring. Each month the lab handles over 44,000 tests, almost all are microbiological analyses, such as total viable count, yeast and mold, coliforms, Enterobacteriaceae, etc. Around 200,000 samples are processed each year, with almost half a million tests performed. The lab complies with the current United Kingdom Accreditation Service (UKAS) requirements and helps to ensure food manufacturers are implementing Hazard Analysis and Critical Control Points (HACCP). By adopting a Laboratory Information Management System (LIMS) as its backbone and using automated microbiology equipment, Westward Laboratories has developed almost production line techniques to handle the sample throughput. With the LIMS managing the results and report formats for different customers, and the utilization of a specially developed web reporting system, reports and invoices can be accessed online or sent electronically to customers to minimize the use of paper.
Westward Laboratories was established in 1992 following the Food Safety Act of 1990 which required food manufacturers to monitor their processes, practices, and finished products. Although part of the Samworth Brothers group, Westward Labs is an independent food testing facility and has to compete for business from other group members and from external companies. Westward Labs holds the ISO17025 standard and is accredited by UKAS and leading supermarket outlets such as Marks & Spencer and Tesco. Over the years, increasing sample throughput has led to the need for innovation and the use of automation and mechanization technology to keep up with demand.
All received samples are registered, tests are assigned, labels are produced for each test suite, and then the samples are placed in a large fridge prior to entering the lab. Samples are then collected by lab staff and prepared prior to being plated. Samples are weighed out and then placed in a holding fridge prior to dilution and plating. Workflow in the lab is very conventional with samples moving through from registration to being put in the incubator as quickly as possible. After incubation, samples are counted, the results recorded, reports prepared and issued, and invoices prepared. Most of the samples received are processed during the same day.
Automating the Process
One of the key factors in the laboratory workflow process is the need to track and trace the samples and associated results to fully comply with the regulatory requirements. To help, Westward Laboratories uses the Matrix LIMS from Autoscribe Ltd., which can be readily tailored to the needs of individual laboratories and provide comprehensive audit trails, version control, and sample tracking functionality. The “OneTime configuration tools” within Matrix allow the system to be configured without the use of custom programming or esoteric basic scripting tools. A configuration wizard allows free choice of screens, workflows and menu designs, customer specific tables/modules, multiple screens for the same function (e.g. registration screens optimized for each sample category), and multiple sample numbering systems. These tools also allow the system to be further configured or reconfigured to keep it in step with any changes to the laboratory workflow or business practices. All samples are booked into the Matrix LIMS on arrival at the laboratory, and once registered, barcode labels are generated, one for each test group that they will undergo. The labels are configurable and could include a barcode, a unique human readable sample code, sample weight, sample description, and a list of the tests required. Registration screens have been created for individual sample types. For example, the registration screen for swabs differs from the general sample registration screen.
Further automation is provided by systems from Kiestra Lab Automation, which control weighing and dilution operations, automated plate preparation, and are used to prepare the media used in the plates. These systems are linked to the LIMS to determine which tests are required. Dilution is performed by Kiestra’s gravimetric dilutor, the SynergA, which is connected to a PC via TraceA software that provides full traceability of all dilution operations. In fully automatic mode, the sample barcode includes information about the type of dilution required (sample information including the weight of sample and dilution factor is also recorded giving improved traceability). When the sample barcode is scanned, the system automatically checks to see if the starting weight is within the predefined limits, selects the bottle of media to be used (if several are connected at the same time), makes the dilution, and checks if the accuracy is correct. The TraceA software package ensures all relevant data is stored automatically (date, time, analyst ID, sample ID, weight of sample, media batch number, weight added, and media).
Every sample tested requires a petri dish (apart from pathogen samples that are tested in a separate laboratory). Dishes are automatically labeled with a barcode at a rate of 1,000 per hour using Kiestra’s BarcodA system, which can also code tubes and bottles. Real-time barcoding dramatically reduces the transcription error rates to only 1 in 36 trillion characters, compared to manual coding/reading/writing where there can be at least 1 error in 300 characters. This barcode contains all of the important sample information such as use-by date. With this barcode, every sample is uniquely recorded, resulting in full sample traceability for the laboratory. Sample barcodes are scanned at the pipetting bench and the LIMS then sends the tests associated with the particular sample so that the petri dishes can be labeled with a second barcode specific for each test. The technician instantly receives the right set of test plates per sample. After pipetting, a Kiestra AgarrA module automatically scans the barcode on each dish and pours the plate with the correct molten media for the test—after which mixing, solidifying, and stacking takes place. The laboratory estimates that there has been a 30 percent saving on media costs since this system was installed due to more accurate dispensing of media. Following incubation the plates are counted—by hand. Westward Laboratories opted not to use automated plate counters due to the possible presence of food particles on the plates leading to false positives. Results are entered into the LIMS and are checked before they are made available for reporting. The LIMS also holds information about test costs, etc. so it is used to produce invoices for the customers. The entire system has been developed around a Matrix LIMS backbone with other tools being used at appropriate stages in the lab workflow to provide added speed and functionality to the system. Figure 1 shows this interaction in the workflow.
Reports and invoices can be accessed online or sent electronically to customers to minimize the use of paper.
Matrix LIMS enables authorized users in the lab to modify existing reports or to create new ones. This is used extensively to ensure customers receive whatever reports/data analysis and interpretation they require such as daily, weekly, and monthly retailer reports. Whilst the LIMS system allows paper in the laboratory itself to be kept to a minimum, Westward Laboratories also recognized the opportunity to develop a paperless reporting system for its customers, so its in-house IT developed LabSTAR (Lab Service for Trend Analysis and Results). It’s a web-based reporting module which replaced an earlier system based on Excel. It queries the LIMS database but is separate from the LIMS itself. This approach was chosen because the customers did not require access to the LIMS itself, only to the reporting module which does the database querying. LabSTAR is used for results, trends, and exception reporting. It features a simple website with user name and password login and allows access to sample registration and results on a read only basis.
In a further move towards paperless reporting, the LIMS holds all the pricing information for tests enabling invoices to be produced for online access or as downloadable PDFs. The LabSTAR/Matrix LIMS combination also provides other paperless functionality for customers. All of the Manuals, Standard Operating Procedures, Specifications, even price lists are held in a database and can be accessed through the LabSTAR interface.
Whilst the system established at Westward labs has significant benefits for customers and the busy analysis team alike, there are also additional benefits to the operation of the lab. Preparation of the media used for incubation is currently managed by the Kiestra system. The SolventA software contains the media recipes and also controls batch numbers and expiry dates for media stock. Another piece of software, RegistrA, records autoclave cycles, etc. The media usage is managed by Matrix LIMs and there is a screen that prominently displays the amount of media used and the stock level. The levels are calculated from the data about the number and types of required tests and the amount of plates already prepared. This acts as an early warning system for media shortages, but also ensures that an excessive amount is not made available.
More recently, a temperature monitoring system (IceSpy from IMC Group) was installed for the fridges, water baths, and incubators in the laboratory. It replaced the manual task of going around with a sheet of paper on a clipboard to record the various temperatures. It also, of course, obviates the need to open a fridge door to read the temperature.
This automated and paperless approach adopted by Westward brings other significant benefits, including cost savings—agar, paper, and reporting; reduced human errors; bespoke trend analysis, period reports, and decision support tools; efficient information dissemination; increased productivity and efficiency; and improved tracking and traceability.
Dr. Wilson, general manager at Westward Laboratories, has been an industrial microbiologist for 16 years and is a technical expert in laboratory management and food safety. She can be reached at +44 1579 386219. Boother is managing director at Autoscribe Ltd. and has had involvement in around 5000 LIMS projects. Reach him at firstname.lastname@example.org.