Lab Matters Fall 2024 | Page 71

APHL 2024 POSTER ABSTRACTS separate brands of Mueller Hinton Agar ( MHA ), Becton Dickinson BBL ( BBL ) and Hardy Diagnostics ( Hardy ), were evaluated with the MTS . MTS MICs were rounded up to the next concentration of the standard doubling dilution scale when necessary . The accuracy of MTS was determined by the level of essential agreement ( EA ). Bias , the proportion of MICs at least one doubling dilution higher ( positive ) or lower ( negative ) than the reference BMD , was also assessed . Categorical agreement was not evaluated , as interpretive criteria for ATM-AVI have not been established . Escherichia coli ATCC 25922 , Pseudomonas aeruginosa ATCC 27853 , E . coli ATCC 35218 and Klebsiella pneumoniae ATCC 700603 were used as quality controls for both MTS and BMD .

Results : Of the 94 isolates , 76 ( 81 %) yielded on-scale BMD results for both MTS Hardy and MTS BBL . Using on-scale values only , the use of Hardy MHA resulted in a slightly higher EA ( 96 %) compared to BBL ( 92 %). Considering off-scale low and high results to be in EA , MTS Hardy EA remained the same at 96 % while MTS BBL EA increased to 93 %. A + 21 % bias was noted for MTS BBL MHA whereas an + 8 % bias was observed for MTS Hardy MHA compared to BMD . Among all MIC values generated by MTS Hardy and MTS BBL , 63 % and 55 %, respectively , were identical to reference BMD .

Conclusion : Using MHA from two different manufacturers , the MTS method yielded > 90 % EA to reference BMD , even with a more robust assessment using on-scale MICs only . We conclude that the MTS method represents an accurate , practical and cost-effective method that clinical and public health laboratories can use to perform ATM-AVI susceptibility testing where there is a lack of capacity for BMD testing . This testing will allow laboratories to support clinical decision making for the treatment of severe infections caused by highly resistant isolates of Enterobacterales . Isolates with established reference MICs for aztreonam-avibactam are available and can be requested through the CDC & FDA AR Isolate Bank .

Presenter : Rocio Balbuena , nyq0 @ cdc . gov

Expanding Bactopia as a Framework for Bacterial , Viral and Metagenomic Analysis

T . Fearing , C . Rowley , R . Petit , J . Mildenberger , R . Christensen , Wyoming Public Health Laboratory

Bactopia is a Nextflow pipeline for the complete analysis of bacterial genomes . Bactopia allows users on all types of systems such as laptops , HPC and cloud platforms to quickly analyze bacterial genomes using more than 150 bioinformatic tools . Users can seamlessly switch between Conda , Docker and Singularity . Bactopia has extensive version control , data auditing and includes extensive testing to ensure reliability . Bactopia offers users the ability to rapidly scale from a single sample to tens of thousands of samples , making it ideal for large-scale on-going genome surveillance projects .

After more than five years , Bactopia is one of the few analysis pipelines that has stood the test of time when it comes to consistent updates and user feedback . Here at the Wyoming Public Health Laboratory , we have regularly tested the adaptability of Bactopia to meet our needs . While Bactopia is an extensive pipeline for the endto-end analysis of bacterial genomes , at its core it is just a bunch of modules , or “ building blocks ,” for genomic analysis . In version three of Bactopia , we made a number of improvements to allow us to better use Bactopia as a framework , instead of just an analysis pipeline .

To demonstrate this , we have developed a few new workflows with Bactopia and applied them to viral and metagenomic sequences . Utilizing existing modules for cleaning sequencing reads , we developed the “ Clean-Yer-Reads ” workflow , which will allow us to rapidly clean our Illumina and ONT reads , no matter their origin . Similarly , we used existing host-removal modules in Bactopia to develop “ Teton ,” which we can apply to all our sequencing to ensure all human reads are removed prior to any analysis or public repository submission . These workflows required no additional training for those already familiar with Bactopia , as they share the same parameters and output structures .

While we still use Bactopia for our bacterial surveillance and WPHL , we have been able to also use it as a framework for genomic analysis . We have demonstrated how we could reshuffle existing modules within Bactopia and apply it to sequences Bactopia was not originally intended for . This allows us , as well as many from academia and public health agencies around the globe , to continue to use Bactopia for other sequencings such as metagenomic sequencing , without having to learn a completely new pipeline .

Presenter : Robert Petit , robert . petit @ wyo . gov

Expanding PAH Extraction Methods for Exposure Knowledge in Human Blood Serum

A . Kramer , E . Percival , California Department of Toxic Substance and Control

Polycyclic aromatic hydrocarbons ( PAHs ) are persistent organic pollutants that are naturally produced during the combustion of organic material , such as coal . Some PAHs are also used in industrial processes . Studies have shown that PAHs react in the environment , becoming hydroxylated derivates that have been measured in all environmental matrices . Currently , there are PAHs on the US Environmental Protection Agency ’ s Priority Pollutant List due to their toxic , mutagenic and carcinogenic properties . The most common method of exposure to PAHs is inhalation , making inhalation toxicity a high value research area . It has been widely accepted that upon exposure , PAHs can be metabolized into hydroxy substituted PAHs ( OHPAHs ) and excreted through feces or urine . Due to OHPAHs being considered a metabolite from PAH exposure , urinalysis for OHPAHs has been the standard exposure analysis for primary PAH testing in human populations . However , recent studies have revealed the highest concentration of primary PAHs measured in blood samples differ from the highest concentration of OHPAHs commonly measured in urine . There are many possible explanations for the measured differences and one explanation could stem from the higher volatility of primary PAHs , indicating a higher initial exposure and appearing as more metabolites in urine . The difference may also indicate that the hydrophobicity of the larger PAHs found within blood may have played a role in preventing the larger compounds from being metabolized by the liver or kidneys as readily as their smaller counterparts . This would be of concern as they could theoretically remain within the body while remaining virtually undetected . According to the CDC ’ s Toxic Substance and Control , PAHs affect reproductive , hepatic and developmental systems . Aside from their toxicity , PAHs also bioaccumulate over