Lab Matters Fall 2023 | Page 100

APHL 2023 POSTER ABSTRACTS

variants had logistic growth rates 0.13 . Only one sublineage had a log growth rate warranting a “ high risk ” designation ( BA . 1 ), 7 sublineages met medium risk criteria ( BA . 4 , BA . 5 , BA . 4.6 , BA . 2.75 , BF . 7 , BQ . 1 , BQ . 1.1 ). These metrics were considered alongside other epidemiological indicators to inform public health responses , like proof of vaccination requirements . The public-academic partnership at the heart of RIPHL has enabled innovative techniques to be quickly incorporated into public health responses , and continued innovation will be required to continue to respond to SARS-CoV-2 and other infectious threats .

Presenter : Hannah Barbian , hannah . j . barbian @ rush . edu

Evolution of Echinocandin Resistance in Massive Southern Nevada Outbreak

L . Massic , D . Siao , A . Gorzalski , D . Hess , M . Pandori ; Nevada State Public Health Laboratory

As of 2019 , Candida auris , an inherently drug resistant fungus , is one of five pathogens under the US Center for Disease Control ( CDC ) antimicrobial resistance ( AMR ) urgent threat category . Since the identification of C . auris in 2009 , the pathogen has caused ongoing outbreaks in healthcare settings in over thirty countries with a mortality rate ranging from 33-60 % among the immunocompromised population . Echinocandins are the drug class of choice for treating C . auris candidemia . Resistance to echinocandins has been shown primarily to occur due to mutations in a “ hotspot ” region of the FKS1 gene . Other genomic sites have been implicated . Southern Nevada is currently experiencing the fastest-growing outbreak of C . auris to reach 100 cases . Eighteen months later , this outbreak has surpassed 1,000 cases , affecting over 30 health care facilities . The Nevada State Public Health Laboratory has aggressively sequenced the genomes of isolates associated with the outbreak , with over 800 isolates assessed by WGS . Analysis has shown this to be two genomically distinct simultaneous outbreaks , consisting of both Clade I and Clade III organism . This aggressive genomic surveillance has allowed a visualization of genomic changes over time , including a detailed assessment of mutations associated with minimum inhibitory concentrations ( MIC ) to echinocandins . Herein , we show data assessing potential correlations of specific mutations in the FKS1 gene with susceptibility ( MIC ) to echinocandins . In at least two instances , we visualize genomically and phenotypically , the evolution of resistance within individual patients , during treatment . These data demonstrate that genomic data applied to outbreak surveillance can provide not only phylogenetic intelligence , but also highly informative data with regard to antibiotic stewardship and susceptibility .

Presenter : Lauryn Massic , lmassic @ unr . edu

Genomic Epidemiological Characterization of SARS-CoV-2 Reinfection Cases , Colorado August 2020 – February 2022

M . Hetherington-Rauth , A . Bell , A . Rossheim , L . Bankers and S . Matzinger ; Colorado Department of Public Health and Environment

Background : Despite global SARS-CoV-2 whole genome sequencing ( WGS ) efforts , few studies investigating SARS-CoV-2 reinfection cases have used WGS to characterize both primary and subsequent infections . The paucity of studies is likely due to two challenges : 1 ) the viral load associated with reinfection cases is often lower relative to primary infections , which results in poor sequence quality or a complete inability to sequence the reinfection specimen ; and 2 ) only one specimen from either the primary infection or reinfection is available for sequencing but not both ( i . e ., paired viral specimens are not available ), making a paired whole genome sequence comparison not possible . Methods : We investigated 27,985 SARS-CoV-2 reinfection cases occurring in Colorado from August 2020 to February 2022 that were reported to the Colorado Department of Public Health and Environment ( CDPHE ). We defined a reinfection case as a positive antigen or RT-PCR diagnostic test occurring at least 90 days after the primary infection . We collected descriptive data on age , gender , vaccination status at time of reinfection and whether the patient showed symptoms , was hospitalized , resided in a congregate living setting or whose case could be traced to an outbreak . We also performed whole genome sequencing on all specimens available at the State Laboratory ( n = 11,141 specimens ), resulting in high quality (> 90 % of the genome represented ) paired consensus sequences for 344 cases . We performed lineage characterization on all sequences and calculated the pairwise single nucleotide variant ( SNV ) difference between each pair of sequences . Results : Among the 344 cases with paired sequencing data , the average number of days between infections was 368 ( range : 93 – 635 days ). The majority of reinfection cases were caused by the Omicron variant ( n = 304 cases , 88.4 %), while the majority of primary infections were caused by non-variants of concern ( non-VOCs ) ( n = 303 cases , 88.1 %). The average number of pairwise SNV between primary and reinfection sequences was 59.9 ( range : 0 – 84 ). The highest number of average pairwise SNVs occurred in the S gene ( 23.2 ), followed by the ORF1ab region ( 19.9 ) and the N gene ( 5.68 ). Significance : With 344 paired primary and reinfection sequences , this study represents the largest genomic dataset of SARS-CoV-2 reinfections to date . Genomic epi characterization of SARS-CoV-2 reinfection cases can add real world data to the understanding of SARS-CoV-2 viral evolution and immune evasion . Additional studies utilizing this dataset to look at specific mutations and their prevalence compared to vaccine breakthrough-only cases may help to better understand both waning immunity and vaccine breakthrough as a result of SARS-CoV-2 infection or currently available vaccines .

Presenter : Molly Hetherington-Rauth , molly . hetheringtonrauth @ state . co . us

Genomic Epidemiological Investigation of a Multi-year Carbapenem-resistant Pseudomonas aeruginosa ( CRPA ) Outbreak at a Colorado Healthcare Facility

L . Bankers , D . Mallal , B . Maldonado , J . Driscoll , J . Nichols , C . Czaja , S . Matzinger ; Colorado Department of Public Health and Environment

Background : Carbapenem-resistant Pseudomonas aeruginosa ( CRPA ) is a serious antibiotic resistance threat to public health . We used epidemiological and genomic methods to investigate CRPA patient samples from a bone marrow transplant ( BMT ) unit spanning the years of 2019 to 2022 to investigate whether these infections constitute one or multiple outbreak clusters . Methods : Our investigation focused on facility-wide and unit-specific case counts to initially identify 24 cases from 2019 to 2021 . Medical record reviews combined with two on-site infection control assessments were conducted to determine epidemiological links . For our genomics investigation , we identified all CRPA samples that