Lab Matters Fall 2020 - Page 44

APHL 2020 POSTER ABSTRACTS
Infectious Disease resistance to β-lactams , fluoroquinolones , and aminoglycosides per CLSI guidelines ; and found MICs ≤0.25 μg / mL for colistin , polymyxin B , and tigecycline ( no available CLSI breakpoints ). Bioinformatics analysis identified two IncF family plasmids ( IncFIB ( pKPHS1 ), IncFIB ( pQil )) and an IncR plasmid in all the isolates . IncF family plasmids have been associated with extended-spectrum β-lactamases and genes encoding resistance to quinolones and aminoglycoside .
Detailed epidemiological and WGS data point to clonal spread of NDM-producing K . pneumoniae in this outbreak . However , since NDM is typically found on a plasmid , there is potential for horizontal gene transfer of antibiotic resistance between different bacterial genera . We did find two different genera of NDM-1-producing organisms ( K . pneumoniae and E . coli ) with a potential common plasmid . Additional analysis including long-read sequencing is required to demonstrate the presence of plasmids and potential relatedness . Genomic characterization of outbreak isolates is useful in understanding the mechanisms of transmission and the scope of spread . This can inform outbreak response and assessment of infection control interventions .
Presenter : Sarah Namugenyi , Minnesota Department of Health , St . Paul , MN , sarah . namugenyi @ state . mn . us
A Point-of-care Device for Isothermal Amplification Detection of Candida auris
S . Bradrick , N . Butlin Axxin , P . Davis , D . Yarmosh , J . Boone , K . Yeh , MRIGlobal , Gaithersburg , MD
Candida auris is an emerging , multidrug-resistant pathogen that has caused outbreaks in healthcare settings among patients with complex healthcare needs . This pathogenic fungus is difficult to identify by standard laboratory methods and misidentification may lead to inappropriate clinical management . Moreover , delayed identification of C . auris in healthcare facilities can lead to more expansive and damaging outbreaks that are difficult to bring under control . Thus , there is a significant need for a low complexity , pointof-care device that can reliably and inexpensively detect C . auris in skin swab samples . The T1-isothermal ( T1-ISO ) platform uses an integrated consumable designed for swab samples . Our goal is to adapt the T1-ISO for rapid point-of-care detection of C . auris using custom-designed , isothermal amplification assays . To address this , we leveraged a novel bioinformatics approach , previously developed by MRIGlobal , known as TMArC , to reveal motif DNA sequences that differentiate C . auris from related fungi for assay development . TMArC can be used to identify genetic markers that effectively differentiate C . auris from related species . This information is then directed through an automated bioinformatic pipeline which predicts oligonucleotide sequences for high efficiency LAMP assays compatible with the T1-ISO platform . Our long-term goal is to evaluate LAMP assays on the T1-ISO with clinical skin swab samples and compare performance of the T1-ISO to the established qPCR assay . We envision that our overall approach will be amenable to development of point-of-care tests for other infectious diseases .
Presenter : Shelton Bradrick , MRIGlobal , Gaithersburg , MD , sbradrick @ mriglobal . org
A High-Quality , Hybrid Whole Genome Sequencing and Analysis Pipeline for Characterization of Resistance Profiles in Mycobacterium tuberculosis
R . Howard 1 , D . Yarmosh 1 , D . Armstrong 2 , N . Parrish 2 , J . Bagnoli 1 , G . Olinger 1 , A . Terray 1 , E . Tacheny 1 ; 1 MRIGlobal , Gaithersburg , MD ,
2
Johns Hopkins University Hospital , Baltimore , MD
The WHO estimates that in 2017 , 3.6 % of new cases of tuberculosis cases and 17 % of previously treated cases were multi-drug resistant . Of those , an estimated 8.5 % of cases were extensivelydrug resistant . The prioritization of research that allows for characterization of resistance profiles to inform drug treatment of these cases remains crucial . Here , MRIGlobal presents a whole genome sequencing and analysis pipeline for the National Institutes of Health ( NIH-DAIDS ) Mycobacterium tuberculosis ( Mtb ) Quality Assessment Program ( TBQA ), in partnership with Johns Hopkins University ( JHU ) to produce high-quality MTb genomic assemblies . These data seek to connect genomic markers to drug susceptibility . To date , 51 clinical isolates have been received from JHU for analysis . We present an initial set of 11 priority isolates , selected based on drug susceptibility profiles , collection regions , and other phenotypic findings . Using carefully extracted gDNA , the pipeline utilizes both the Oxford Nanopore MinION and the Illumina MiSeq platforms to create a hybrid genome assembly of long reads and short reads . Results are analyzed for predicted markers of antibiotic resistance and cross referenced with existing AST data provided by JHU . This data will contribute to the body of research concerning identification of genetic elements potentially associated with resistance to specific classes of antimicrobial agents . These repository results will supplement ongoing NIH-DAIDS clinical trials by adding to the completeness and quality of the characterization data available for each isolate .
Presenter : Ryan Howard , MRIGlobal , Gaithersburg , MD , rhoward @ mriglobal . org
Development and Validation of a Multiplexed , Custom AmpliSeq Panel for Antimicrobial Resistance Characterization of Isolates for the NIH Mycobacterium tuberculosis Quality Assurance Program
R . Howard 1 , D . Yarmosh 1 , J . Bagnoli 1 , D . Armstrong 2 , N . Parrish 2 , A . Terray 1 , G . Olinger 1 , E . Tacheny 1 ; 1 MRIGlobal , Gaithersburg , MD ,
2
Johns Hopkins University Hospital , Baltimore , MD
The World Health Organization ( WHO ) estimates that in 2016 , 490,000 people developed multidrug-resistant tuberculosis ( MDR- TB ). However , only an estimated 1 in 5 MDR-TB patients receive the correct antibiotic regimen and better , more cost efficient diagnostic tools are essential for detecting and treating MDR-TB patients . Here , MRIGlobal , in collaboration with Johns Hopkins University ( JHU ) and Illumina , Inc , presents a multiplexed amplicon-based sequencing panel to determine antimicrobial resistance ( AMR ) for clinical Mycobacterium tuberculosis ( Mtb ) isolates for the National Institutes of Health ( NIH-DAIDS ) Mycobacterium tuberculosis Quality Assessment Program ( TBQA ). The panel leverages Illumina ’ s AmpliSeq technology and iSeq 100 and MiSeq platforms in conjunction with established single nucleotide polymorphisms ( SNPs ), insertions , and deletions in the Mtb genome that have previously been shown to correlate with phenotypic AMR detection using standardized culture-based detection systems . We present this panel in an effort to provide guidance and better information
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LAB MATTERS Fall 2020