MICROBIAL TECHNOLOGY drop in CDI test positivity.
In a final assessment using that most scientific of measures (a show of hands!), it was apparent that around half of the audience was currently using some form of molecular technique within their enteric sections, with the other half seeking to in the future. It would be interesting to see how this would compare in future years.
Orthopaedic device infections Next, Dr Kevin Cole, a senior biomedical scientist from North Tyneside General Hospital, Newcastle upon Tyne, gave a review of the advantages and disadvantages of molecular methods over culture in the detection of orthopaedic device infections, and described work he had undertaken at the Royal Sussex Hospital in Brighton for his PhD. Although rates of orthopedic device-
Twenty commercial partners sponsored and supported the event.
genomic data obtained in the laboratory. This in turn enables outbreak surveillance, infection control, and AMR prediction to be carried out. He described a proof-of- principle trial in which 50 Gram-negative isolates were sequenced as they were thought to potentially contain OXA-48 or KPC. The isolates were extracted and then sequenced simultaneously using the Nanopore minION system. Some 41% of the final data were available within 24 hours and a very high coverage of the whole genome was achieved. He showed that one staff member could sequence up to 96 bacterial isolates in a working day, and the turnaround for complete typing results was between 24 and 72 hours and the cost per sample was approximately £45 per isolate. Importantly there was no requirement for highly trained staff or bioinformaticians and a huge amount of data was provided for IPC use and outbreak analysis. Clearly, this could be a way forward and should reduce or avoid altogether the need to send samples to external reference laboratories.
Enteric issues in Wales Michael Perry, Clinical Scientist from the Anaerobe Reference Unit in Cardiff, presented his experience and the impact of introducing molecular techniques as a replacement for enteric culture. The arguments for nucleic acid amplification tests (NAATs) in this area have been well made previously. The resource demands and slow turnaround times of traditional methods contrast with the more streamlined and increased sensitivity offered by PCR or other molecular methodologies. Michael Perry presented a
20
comprehensive study conducted within the Welsh network encompassing over 960,000 data points. This highlighted a significant increase in the diagnosis of key infections specifically Campylobacter and Giardia. Given that Giardia frequently requires intervention and treatment, this represents a significant diagnostic improvement. Another advantage to molecular methods is the ability to target specific gene targets linked to pathogenicity and the molecular approach showed a significant increase in the detection of non-O157:H7 shiga toxin-producing E. coli. When implemented across the network some initial reluctance was recognised with biomedical scientists concerned about the loss of traditional skills. However, as the advantages became clear, both to laboratory workflow and patient care, support was easily built. Culture is retained (for now) through the need to isolate pathogens for further investigation and typing but skilled biomedical scientist time can now be focused on those specimens with the greatest likelihood of positivity. This has removed the need for resource- heavy manipulations of large numbers of ultimately negative stools. Clostridioides difficile testing has also often been an area of keen debate within diagnostic microbiology. Significant variation is seen in EIA-based assays and again comprehensive data gathered from the experience in Wales suggests that fears of a surge in positivity with PCR appear to be unfounded. In fact, by using NAAT as the primary test there was a better ability to identify mild and moderate disease C. difficile excretors, and there was an overall
related infection (ODRI) may be fairly low at between 1% and 2%, they can be a disaster for the individual patient, and the increased number of procedures is leading to a large increase in the overall burden of infection. The device provides a nidus for bacterial growth allowing the formation of biofilms. The lack of a vascular system means that an effective immune response cannot be mounted, and antibiotics may not be able to penetrate the site. He took us through the familiar methods of culture and antibiogram determination using methods that are common, standardised, easy to perform and give results that are normally easy to interpret, and of course are relatively cheap. Plus, the causative organism is obtained, and further work can be done on it, such as determining relatedness of different isolates. Disadvantages include the slow
turnaround times, the problems of negative culture and the fact that different strains can have identical or similar antibiograms. In addition, resistance genes may not always be expressed or indeed carried on all isolates of a particular strain if they are on mobile genetic elements (MGE).
Dr Cole then gave an overview of the various molecular methods that are available. Apart from the obvious in-house PCR methods for the detection of specific organisms and resistance genes, there are two readily available commercial systems: BioFire Film Array Joint Infection Panel and Unyvero Implant and Tissue Infection (ITI). These are expensive and have a limited number of targets, but are rapid and easy to perform and have obvious advantages over an in-house PCR method. Going beyond this Dr Cole described the advantages of metagenomic NGS (mNGS) which is ‘agnostic’ as it can
JUNE 2023
WWW.PATHOLOGYINPRACTICE.COM
Page 1 |
Page 2 |
Page 3 |
Page 4 |
Page 5 |
Page 6 |
Page 7 |
Page 8 |
Page 9 |
Page 10 |
Page 11 |
Page 12 |
Page 13 |
Page 14 |
Page 15 |
Page 16 |
Page 17 |
Page 18 |
Page 19 |
Page 20 |
Page 21 |
Page 22 |
Page 23 |
Page 24 |
Page 25 |
Page 26 |
Page 27 |
Page 28 |
Page 29 |
Page 30 |
Page 31 |
Page 32 |
Page 33 |
Page 34 |
Page 35 |
Page 36 |
Page 37 |
Page 38 |
Page 39 |
Page 40 |
Page 41 |
Page 42 |
Page 43 |
Page 44 |
Page 45 |
Page 46 |
Page 47 |
Page 48 |
Page 49 |
Page 50 |
Page 51 |
Page 52 |
Page 53 |
Page 54 |
Page 55 |
Page 56
