Lab Matters Fall 2020 - Page 46

Infectious Disease collection of intra-patient PCR-positive isolates are sent for short ( Illumina ® NextSeq ® ) and potentially long ( Oxford Nanopore MinION ) read sequencing and analyzed through bioinformatic pipelines to establish genetic variation among isolates . Initial work with 18 positive rectal swabs from 3 health care facilities has identified blaKPC-Escherichia coli , blaKPC-Klebsiella pneumoniae , blaKPC- Pseudomonas aeruginosa , blaKPC-Citrobacter freundii , blaNDM-K . pneumoniae , and blaVIM-P . aeruginosa . We aim to characterize the intra-patient genetic variability of CP-CROs . This data , along with additional genomic and epidemiologic data , will allow for robust characterization of the spread of carbapenem resistance and will inform the reporting of relatedness of CP-CROs in future investigations .
Presenter : June Chan , Wadsworth Center , New York State Department of Health , Albany , NY , june . chan @ health . ny . gov
Veterinary Laboratory High Consequence Pathogen Triage Protocol and the Laboratory Response Network
R . Nickla 1 , M . Ackerman 2 , M . Philpott 3 , K . O ’ Reilly 2 , R . Leman 4 , E . DeBess 4 , J . Jacob 2 ; 1 Oregon State Public Health Laboratory , Hillsboro , OR , 2 Oregon Veterinary Diagnostic Laboratory , Corvallis , OR 3 Oregon State University , 4 Oregon Health Authority
In 2018 , there was a unique case involving a human infection with Francisella tularensis following exposure to a squirrel . F . tularensis is a Tier 1 Select Agent and poses high morbidity risk . The Oregon Veterinary Diagnostic Lab ( OVDL ) at Oregon State University received a deceased squirrel from an OR resident who had cared for it in her home , resulting in her exposure . The OVDL quickly identified lesions of concern within tissue samples and provided them to the ODVL Bacteriology Section for culture . Utilizing the American Society for Microbiology Sentinel Clinical Laboratory Guidelines , the OVDL promptly suspected the presence of F . tularensis and notified the Oregon State Public Health Lab ( OSPHL ). Arrangements were made for shipment to OSPHL that day for confirmation via the OSPHL courier service . OSPHL expedited Laboratory Response Network reference level testing and confirmed F . tularensis . The results were communicated back to the exposed person , who subsequently sought further medical attention and proper antibiotic treatment . Existing relationships between OVDL and the Oregon Health Authority facilitated timely , effective communication throughout the case . The case led to collaborative discussions and strengthened working relationships between public health and veterinary lab systems in several ways and resulted in a joint risk assessment and further expansion of the High-Consequence Pathogen Triage Protocol at the OVDL . Since the OVDL accepts samples from numerous animal species across the US , triage of animals with potential for Tier 1 Select Agent infection is complex . Upon review , the group broadened and enhanced the existing protocol to potentially speed recognition and processing of such animals , and to reinforce use of appropriate precautions when handling these samples . The OVDL sample intake form was also modified to facilitate prompt collection of pertinent risk-based information , which helps prioritize certain sample types , provide precautionary info to minimize potential exposures to high risk samples , and is expected to lead to earlier recognition and notification to public health and to OVDL staff when such agents are present . These collaborative efforts have further strengthened existing relationships and contributed to the safety of all those who may come in contact with samples at high risk for containing transmissible select agents .
These efforts put all agencies involved in a better position to protect the health of the general public . The triage protocol may be a useful template for other veterinary diagnostic laboratories and the collaborative process that produced it may be useful for addressing other types of disease conditions seen in animals that can affect the health of animal owners or forensic investigations .
Presenter : Robert Nickla , Oregon State Public Health Laboratory , Hillsboro , OR , robert . e . nickla @ dhsoha . state . or . us
Potential Transfer of a Klebsiella pneumoniae Carbapenemase-Carrying Plasmid Between Klebsiella pneumoniae ST307 and Escherichia coli in a Single Patient
W . Hottel , V . Reeb , M . Nelson , A . Kampoowale , W . Aldous , M . Pentella and R . Jepson , State Hygienic Laboratory at the University of Iowa , Iowa City , IA
Klebsiella pneumoniae carbapenemase ( KPC ) is an Ambler class A carbapenemase of critical public health importance . KPC ’ s are typically found on plasmids of Klebsiella pneumoniae , but can be acquired by other Enterobacteriaceae via horizontal gene transfer . In 2018 , as part of routine carbapenem resistant Enterobacteriaceae surveillance , the State Hygienic Laboratory at the University of Iowa ( UI ) identified an Escherichia coli isolate harboring a KPC . Nearly one year later , a Klebsiella pneumoniae isolate from the same patient was also confirmed as KPC positive . Whole-genome sequencing utilizing the Illumina MiSeq platform was performed for both isolates . Multi locus sequence typing demonstrated that the K . pneumoniae was ST307 , a worldwide emerging clone harboring plasmid-mediated antimicrobial resistance genes . Bioinformatics analysis conducted using an in-house pipeline run on the UI Argon High Performance Computing cluster indicated that both Klebsiella and E . coli isolates were KPC-3 variants and shared identical repA plasmid replicon sequences . Further BLAST and sequence mapping analysis demonstrated high sequence similarity between the two isolates for an approximately 45,000bp region containing both the KPC-3 gene and the repA replicon . In order to demonstrate the potential transfer of plasmids between the two organisms , we intend to reconstruct and compare the entire plasmid sequences using both short- ( Illumina MiSeq ) and long- ( Oxford Nanopore MinIon ) sequences reads . Transfer of plasmids harboring genes conferring resistance to carbapenems pose a serious threat to public health . This may pose an additional challenge to effective treatment and infection control if these transfer events can occur between two common human pathogens within the same patient potentially over the course of a prolonged time period .
Presenter : Wesley Hottel , State Hygienic Laboratory at the University of Iowa , Iowa City , IA , wesley-hottel @ uiowa . edu
Bioinformatic Characterization of Mobile Genetic Elements Conferring Pathogen Antimicrobial Resistance
R . St . Jacques , L . Turner and K . Libuit , Virginia Division of Consolidated Laboratory Services , Richmond , VA
Each year , approximately 700,000 premature deaths worldwide are related to antimicrobial resistant ( AMR ) pathogens . It is estimated that by the year 2050 , this number could rise as high as 10 million . Genes conferring antimicrobial resistance disseminate through both vertical and horizontal gene transfer via mobile genetic