Lab Matters Fall 2023 | Page 77

APHL 2023 POSTER ABSTRACTS demonstrates the ability to quickly develop and implement protocols for sequencing novel pathogens with multiple sequencing technologies and produce high quality results for surveillance and scientific query .

Presenter : Nicholas Palmateer , nicholas . palmateer @ doh . nj . gov

The Impacts and Considerations for Usage of Automated Liquid Handling Robots for Sample Preparation for Next Generation Sequencing in Small Public Health Laboratories

A . Grant , T . Southern , C . Carlson ; South Dakota Public Health Laboratory

With the rise in antibiotic resistance amongst human bacterial pathogens and in the wake of the SARS-CoV-2 pandemic , the necessity for rapid and cost-effective sequencing technology to identify bacterial and viral strains is readily apparent to those involved in the fields of patient care and public health . The advent of second and third generation sequencing technology provided a means for public health scientists to investigate the genomes of pathogens at decreased cost and time investment for laboratory personnel compared to earlier sequencing strategies . As sequencing technology has improved and the output of genetic information increased , so has the demand for the frequency and number of pathogens sequenced by laboratory scientists . Despite current advancements and lowering of cost compared to early sequencing methods , the molecular biology inherent in sequencing strategies still requires a major investment of public health laboratory resources both in reagent costs and health laboratory personnel lab hours . Additionally , health laboratory personnel ’ s responsibilities by their very nature are consistently in flux as they respond to the mercurial nature of public health matters , increasing the strain on laboratory personnel . The introduction of robotic liquid handlers was one means to ameliorate the strains on laboratory staff and increase throughput for the number of sequenced specimens . The usage of liquid handling robots allows for laboratory scientist to assign automated repetitive tasks to liquid handling instruments , increasing or maintaining sample throughput but decreasing dedicated personnel hours to those steps . In heavily populated areas under the purview of large public health systems with dedicated sequencing facilities , the usage of these robots has allowed for increased sample throughput and alleviated some of the inherent issues with dedicating lab hours / staff to a task . However , the problems faced by the public health laboratory staff in more rural states with lower population density differ from those referenced above . Are there similar benefits in labor time and throughput garnered from the introduction of such automated liquid handling systems in public health laboratories in more rural or less populous states ? We at the South Dakota Public Health Laboratory ( SDPHL ) sought to compare associated reagent costs , number dedicated laboratory staff hours , plastic waste and increased sample output between liquid handling automation and manual sequencing preparation by lab testing staff . This poster outlines our findings regarding the above mentioned as well as provides some considerations that might assist other public health labs when using liquid handling automation .

Presenter : Austin Grant , austin . grant @ state . sd . us

Time and Motion Study of a Fully Automated Isolate Whole Genome Sequencing ( iWGS ) Platform for Surveillance of Foodborne Pathogens

A Bartling 1 , A . Roden 1 , E . McCutchen 1 , E . Mitchell 2 , S . Hoeffel 2 , M . Balamotis 2 , M . Deiparine 2 , A . Singh 2 , A . Allred 2 , S . Shokralla 2 , J . Ng 2 , K . Rhoden 2 , P . Iwen 1 , R . Khaksar 2 , P . Thwar 2 ; 1 Nebraska Public Health Laboratory , 2 Clear Labs

Background : PulseNet , developed by the US Centers for Disease Control and Prevention , established whole genome sequencing ( WGS ) as the gold standard for the surveillance of foodborne pathogens . The MiSeq-based sequencing platform currently used for WGS has drawbacks that limit use for rapid epidemiological applications of this technology . Clear DxTM Microbial Surveillance WGS ( Clear Labs , San Carlos , CA ) has developed a platform that addresses some of the recognized limitations . This study was done to compare the Clear Labs sequencing process with the current process used by PulseNet . Methods : Time and motion studies to compare the manual MiSeq Illumina workflow currently used in the Nebraska Public Health Lab ( NPHL ), were done with a beta prototype of the Clear DxTM platform . Both workflows were independently performed by two technicians . Comparisons included the number of human touch points encountered , the total hands-on time for sample processing including DNA extraction , total run time , and the number of disparate pieces of lab equipment required for the entire workflow . Results : The MiSeq-based manual workflow used 4 disparate instruments and 3 kits from different vendors , whereas the Clear DxTM workflow used one integrated instrument and one kit from Clear Labs . The total workflow time from set up-to-results for the MiSeq-based method was 44 hours , while for the Clear DxTM was 27 hours . The most significant differences between the two workflows were the number of contiguous human touch points , which were > 20 ( manual ) and 1 ( Clear DxTM ) and the total handson-time , 140 min ( manual ) and 33 min ( Clear DxTM ) respectively . Conclusions : The fully automated Clear DxTM platform would improve laboratory efficiency and provide results faster to optimize epidemiological investigating . Additionally , a lower skill threshold for laboratory staff to perform the Clear Dx system would allow for greater flexibility in lab operations . Additional studies are needed to define hardware tolerance and to meet the PulseNet criteria for reporting .

Presenter : Emily McCutchen , emily . mccutchen @ unmc . edu

Tracing Anthrax-like Capsule Biosynthesis Genes in Non-Bacillus anthracis Species through Whole Genome Sequencing

S . J . Sabin , C . B . Kolton , R . M . Traxler , C . A . Gulvik , G . A . Sprenger , M . E . Bell , J . R . McQuiston , Z . P . Weiner ; US Centers for Disease Control and Prevention

Bacillus anthracis is the causative agent of anthrax , an acute disease in humans and non-human mammals , and is a Tier 1 select agent in the United States . Molecular tests for B . anthracis generally rely on detection of its toxin or protective capsule . PCR methods amplify DNA housed on its two virulence plasmids , pXO1 and pXO2 , encoding the tripartite toxin ( protective antigen , lethal factor and edema factor proteins in combination ), and the antiphagocytic capsule , respectively . It has been reported previously