Lab Matters Fall 2023 | Page 105

APHL 2023 POSTER ABSTRACTS saliva samples for SARS-CoV-2 via a direct RT-LAMP assay one to three days-a-week . In addition to monitoring the presence / absence of SARS-CoV-2 across the employee population , NEB participates in a non-CLIA variant identification program . On a weekly or bi-weekly basis , RNA from all positive samples is extracted and sequenced . The sequencing approach here , derived from the ARTIC network protocol , utilizes NEB reagents and variant avoidant VarSkip Short primers . This approach is compatible with multiple sequencing platforms , which provides additional sample processing flexibility based on how quickly the sequencing results are needed . Patient results are reported to state health labs as required , and sequence data is anonymized before submission to NCBI SRA , NCBI Genbank , and GISAID . Furthermore , the testing and sequencing data are used to inform workplace safety measures and continually monitor for potential work-place transmission events . Ultimately , workplace SARS-CoV-2 viral surveillance has the dual benefit of promoting employee safety and minimizing disruptions to business operations . Current and future efforts for workplace viral surveillance efforts can also be expanded to include additional respiratory viruses , such as influenza and RSV .

Presenter : Betsy Young , eyoung @ neb . com

Outbreak of Carbapenem-producing Pseudomonas aeruginosa at an Ophthalmology Clinic , Los Angeles County

S . Bharula , K . Yong , J . Mephors , A . Clarke , J . Garrigues , P . Hemarajata , Z . Rubin , N . Green ; Los Angeles County Public Health Laboratory

In May 2022 , our department identified transmission of VIM + Pseudomonas aeruginosa in an ophthalmology setting from Public Health reporting of resistant Pseudomonas . Four patients were involved . All were hospitalized and either had lost sight permanently or suffered severely diminished vision in the infected eye ( s ). Investigation of the four cases found that all patients were seen at the same ophthalmology clinic . The clinic performed exams using tonometers with reusable tips and provided non-prescription dry eye drops to patients . A retrospective review of reported VIM + Pseudomonas aeruginosa from clinical laboratories and hospitals from our jurisdiction did not identify additional cases . Isolates from corneal scrapings were sent to the public health laboratory for whole genome sequencing . Genomic analysis of the 4 VIM + Pseudomonas isolates showed that all shared the same MLST ( type 1203 ), had predicted serogroup O2 , and harbored the blaVIM-80 and blaGES-9 combination of carbapenem resistance genes . There were only 1-6 SNP differences among the patient Pseudomonas isolates suggesting relatedness . In addition to carbapenem resistance , genes were identified conferring resistance to other antibiotic classes including aminoglycosides , cephalosporins , macrolides , chloroamphenicol , fosfomycin , tetracyclines , and sulfonamides . A site visit with environmental sampling by Public Health was conducted at the ophthalmology clinic . Environmental microbiology testing at CDC revealed the presence of P . aeruginosa in a bathroom sink sample and in samples obtained from a tonometer cleaning system . Isolate sequencing in our laboratory showed that none of the three recovered environmental Pseudomonas isolates genetically matched patient isolates . Although infection control gaps were identified at the clinic including improper disinfection of the tonometer cleaning system , no exact mechanism of transmission was identified . In January 2023 , an Epi-X alert was issued . CDC is now investigating this as a multi-state outbreak now involving more than 50 patients in 11 states for VIM + P . aeruginosa with the same MLST type , serotype , and unique resistance genes combination as initially identified in our laboratory . Artificial tear eye drops are being investigated as possible common source of infection .

Presenter : Nicole Green , nicgreen @ ph . lacounty . gov

Potential Transmission Dynamics of blaKPC in an Ongoing Outbreak Response Involving Multiple Bacterial Genera

J . Dale , B . Craft , L . Tourdot , S . O ’ Malley , A . Beaudoin , P . Snippes ; Minnesota Department of Health

Increased antimicrobial use , insufficient infection prevention and control , and larger than normal burdens on the healthcare system during the COVID-19 pandemic contributed to significant increases in antimicrobial resistant ( AR ) organisms . Surveillance to detect AR threats declined early in the pandemic amid focus on the COVID-19 response , but both reactive and proactive surveillance efforts are again increasing . The Minnesota Department of Health ( MDH ) initiated point prevalence surveys ( PPS ) in March 2022 at long-term care facility A ( LTCF-A ) upon identification of a clinical Klebsiella oxytoca isolate harboring the carbapenemase gene blaKPC . During March – December 2022 , a total of 160 residents were screened in multiple rounds of colonization PPS and 13 tested positive for blaKPC using the GeneXpert Cepheid Carba-R assay . Culture-based methods successfully isolated a total of 15 organisms harboring blaKPC from 10 / 13 residents ; 2 additional organisms were obtained from clinical cultures . The predominant blaKPC-positive species identified was K . oxytoca ( 7 ). Six additional species of bacteria harboring blaKPC were detected including Escherichia coli ( 2 ), Enterobacter cloacae complex ( 1 ), Citrobacter amalonaticus complex ( 1 ), Citrobacter freundii complex ( 1 ), Klebsiella pneumoniae ( 2 ), and Raoultella ornithinolytica ( 1 ). Whole genome sequencing results suggest three separate introductions of K . oxytoca based on single nucleotide polymorphism ( SNP ) analysis demonstrating two distinct clusters ( Cluster 1 : 14-27 SNPs ; Cluster 2 : 2-5 SNPs ) separated by approximately four months based on specimen collection dates . The 2 E . coli were isolated from different residents approximately 3 months apart and are 30 SNPs different , suggesting relatedness . Two residents had multiple blaKPC organisms isolated from a single rectal swab ; K . oxytoca and E . cloacae complex from patient 1 , and K . oxytoca , C . freundii complex , and R . ornithinolytica from patient 2 . All 17 organisms harbored the blaKPC-4 gene variant , but short-read sequencing is insufficient to determine whether a common extrachromosomal element harboring blaKPC exists across multiple bacterial genera . It is therefore unclear whether the 6 non-K . oxytoca organisms were introduced into the facility harboring the carbapenemase gene or if they acquired blaKPC-4 through horizontal gene transfer ( HGT ) in LTCF-A . Long-read sequencing methods and simplified bioinformatics workflows would inform elucidation of the transmission dynamics within patients 1 and 2 , and in LTCF-A . Understanding the impact of HGT in outbreak scenarios would aid epidemiological response and prevention . The aim of future work at the MDH Public Health Laboratory is to develop sequencing and bioinformatics workflows that enable predictive assessment of HGT events to aid in outbreak response .

Presenter : Jennifer Dale , jennifer . dale @ state . mn . us