APHL 2021 Poster Abstracts
INFECTIOUS DISEASE
Genetic Relatedness of NDM-1 Producing Klebsiella pneumoniae by Whole Genome Sequencing in Southeast Michigan
S . Dietrich , H . Blankenship , E . Burgess , S . McNamara , B . Brennan , B . Mabvakure , C . Vue and A . Rogers , Michigan Bureau of Laboratories , Lansing , MI
Introduction : New Delhi metallo-β-lactamase ( NDM ) is an emerging cause of carbapenem resistance in Gram-negative bacteria . The NDM gene is a plasmid-encoded carbapenemase enzyme which can hydrolyze all β-lactam antibiotics except aztreonam . NDM strains also often carry other resistance mechanisms , making infections very difficult to treat . Due to increase in the epidemiologically linked NDM-1 producing K . pneumoniae in Southeast Michigan , the main objective of this study is to characterize the genetic relatedness and potential transmission patterns by WGS .
Methods : Carbapenem resistant Enterobacterales species were submitted to the Michigan Department of Health and Human Services Bureau of Laboratories ( MDHHS-BOL ) for further phenotypic and genotypic characterization . A total of 67 K . pneumoniae isolates from 2014 – 2021 harboring the NDM-1 gene were subsequently characterized by WGS . WGS libraries were prepared with Illumina Flex and Nextera XT kits and sequenced on Illumina MiSeq sequencers . Bioinformatic analyses were performed to examine the relatedness of isolates with pan genome and single nucleotide polymorphism ( SNP ) analysis . Additional resistance genes were identified with Abricate and the ResFinder database .
Results : Based on WGS analysis , 39 isolates from 2019 – 2021 associated with a patient sharing network of acute care and longterm care facilities were closely related ( Cluster 1 , SNP 0 - 41 ), suggesting potential transmission . All isolates of Cluster 1 were multi-locus sequence type 219 and harbored blaNDM-1 , blaSHV-145 , and blaCTX-M-15 genes . The remaining NDM isolates that were not included in Cluster 1 demonstrated greater strain diversity .
Discussion : As part of the Antimicrobial Resistance Laboratory Network , antimicrobial surveillance and outbreak investigations are being performed in Michigan to detect the emergence and spread of organisms harboring plasmid and chromosomal genes conferring carbapenem resistance mechanisms . The addition of WGS to the existing laboratory capacity can provide further characterization and discrimination of strain relatedness . This provides valuable epidemiologic-informed genomic subtyping which can enhance the detection of potential transmission of NDM , thereby allowing for the implementation of targeted infection prevention interventions in healthcare settings to slow the spread of resistance .
Presenter : Nandukumar Balakrishnan , Michigan Bureau of Laboratories , baladrishnann @ michigan . gov
Analysis of a Short Tandem Repeat Genotyping Assay for Candida auris
R . Boone , R . Morris , D . Baynham , V . Stone , P . Gibbs , K . Levinson , R . Steece , Tennessee Department of Health , Nashville , TN
Candida auris is an emerging pathogenic fungus that causes severe infections leading to high mortality rates . C . auris is considered an urgent threat and is reportable in the state of Tennessee due to its multi-drug resistance and ability to easily spread although it has not been detected in the state . C . auris consists of five main clades : South American , African , South Asian , East Asian , and Iranian that appeared simultaneously across the globe . Each clade has been identified in the United States , likely due to international travel . To control the spread it is pertinent to track the organism , which starts with accurate identification . C . auris clade information can be crucial to contact tracing , especially in healthcare facilities , because they are specific to certain regions giving context on spread . While whole genome sequencing is accurate it is expensive , time-consuming , and many facilities lack the capability . As an alternative , de Groot et al . developed a simple short tandem repeat ( STR ) typing assay that demonstrated correlation to the C . auris clade ID determined through whole-genome sequencing . The objective of this study was to assess the use and reliability of this genotyping method within a public health laboratory . C . auris isolates from the CDC & FDA Antibiotic Resistance ( AR ) Isolate Bank representing four of five clades were extracted using the KingFisher Flex System . Regions flanking di- , tri- , or nonanucleotide repeat sequences were amplified using the published sequences . The generated STR fragments were analyzed using Applied Biosystems ’ 3500xL Genetic Analyzer and size was determined using the Microsatellite Analysis application ( ThermoFisher ). Based on the size , the number of repeats were calculated and the genotype corresponding to the distinct clades was determined from the STR repeat profile determined by de Groot et al . Overall , the C . auris STR genotyping method was fast , cost-effective and reproducible with small variation . These findings indicate that this genotyping method may be valuable for identifying C . auris clades at the Tennessee Department of Health .
Presenter : RaNashia Boone , Tennessee Department of Health , ranashia . boone @ tn . gov
HDPCR Data Analytics Offers Unique Opportunities for Tracking Diversity and Coexistence of Tick-Borne Pathogens
J . Burke , S . Dowell , N . Clark , H . Carolan , L . Brumbach , P . Flook and M . Wang , ChromaCode , Carlsbad , CA
Background : In 2018 , state and local health departments reported 47,743 cases of tickborne disease to CDC .¹ Detection of these pathogens and tracking of tick-related epidemiological trends can be very challenging due to the expanding geographic range of tick-borne cases . ChromaCode has developed the HDPCR™ Tick-Borne Pathogen Panel ( TBP ) Research Use Only ( RUO ) for the simultaneous detection and identification of nine of the most common tick-borne pathogens . Data analysis is performed using the ChromaCode Cloud analysis software featuring a data analytics module that provides actionable data insights and the ability to track wider epidemiological trends .
Materials / Methods : The HDPCR technology combines TaqMan chemistry with robust encoding and unique analysis software to analyze and manage data generated by HDPCR assays . Data is
Infectious Disease
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Summer 2021 LAB MATTERS 57 |