Genotyping Cyclospora cayetanensis From Multiple Outbreak Clusters With An Emphasis on a Cluster Linked to Bagged Salad Mix—United States, 2020

Abstract

Cyclosporiasis is a diarrheal illness caused by the food-borne parasite Cyclospora cayetanensis. Annually reported cases have been increasing in the United States prompting development of genotyping tools to aid cluster detection. A recently developed Cyclospora genotyping system based on eight genetic markers was applied to clinical samples collected during the cyclosporiasis peak-period of 2020, facilitating assessment of its epidemiologic utility. While the system performed well and helped inform epidemiological investigations, inclusion of additional markers to improve cluster detection was supported. Consequently, investigations have commenced to identify additional markers to enhance performance.

Verification and Use of the US-FDA BAM 19b Method for Detection of Cyclospora cayetanensis in a Survey of Fresh Produce by CFIA Laboratory

“…Cinar et al [ 18 ] developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples spiked with 200 C. cayetanensis for the typing of isolates; however, the utility of this method is limited if the sample contains multiple isolates of the parasite. A C. cayetanensis genotyping system based on eight genetic markers has been applied to human clinical samples [ 19 ]; however, this approach has not yet been employed successfully for food samples, and additional markers are required to improve cluster detection.…”

Hastening Progress in Cyclospora Requires Studying Eimeria Surrogates

“…Despite such limitations, researchers studying limited supplies of C. cayetanensis have made commendable progress characterizing strains, genomes, and advancing detection. Several C. cayetanensis draft genomes have been characterized and published [ 3 , 4 , 5 , 6 , 7 , 8 , 9 ] and molecular typing efforts have given rise to powerful genotyping tools [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 ] for epidemiological analysis, such as outbreak tracing. As described below, methods such as these and others are now being used to detect C. cayetanensis from various sources of infection.…”

“…Recent progress in DNA-based diagnostics provide exciting, newfound opportunities for surveillance and outbreak tracing. These include assays to amplify, from C. cayetanensis , portions of 18S rDNA [ 54 , 63 , 64 , 65 , 66 , 67 , 68 , 69 ], apicoplast and mitochondrial DNA, and single copy variable nuclear markers suitable for source attribution [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 ]. Bacteriological Analytical Manual (BAM) protocols 19b [ 65 , 66 , 67 , 69 , 70 , 71 ] and 19c [ 72 , 73 ] accurately detect C. cayetanensis in various matrices, such as produce and water and are widely used and validated.…”

“…Such studies could complement established methods such as Multi-locus Sequence Typing (MLST) [ 11 , 14 , 17 , 19 , 20 , 21 ] that have proven useful in source tracing and cluster investigations of C. cayetanensis . Additional innovation might provide more resolution to strengthen these efforts.…”

Cyclospora cayetanensis comprises at least 3 species that cause human cyclosporiasis

“…Prior to the coronavirus disease-2019 (COVID-19) pandemic, annually reported cyclosporiasis cases were increasing in the USA, leading the US Centers for Disease Control and Prevention (CDC) to develop a genotyping system to complement epidemiologic investigations of cyclosporiasis outbreaks (Barratt et al, 2019(Barratt et al, , 2021Nascimento et al, 2020). Early iterations of this system were evaluated on isolates collected during the cyclosporiasis peak period of 2018 (Nascimento et al, 2020), and evaluations continued in 2019 and 2020 (Barratt et al, 2021(Barratt et al, , 2022. These evaluations supported the system's epidemiologic utility as isolates from epidemiologically linked case-patients were typically assigned to the same genetic cluster (Nascimento et al, 2020;Barratt et al, 2021Barratt et al, , 2022.…”