Near-Complete Genome Sequences of Several New Norovirus Genogroup II Genotypes.

We report here the near-complete genome sequences of 13 norovirus strains detected in stool samples from patients with acute gastroenteritis from Bangladesh, Ecuador, Guatemala, Peru, Nicaragua, and the United States that are classified into one existing (genotype II.22 [GII.22]), 3 novel (GII.23, GII.24 and GII.25), and 3 tentative novel (GII.NA1, GII.NA2, and GII.NA3) genotypes

Norovirus Surveillance among Callers to Foodborne Illness Complaint Hotline, Minnesota, USA, 2011–2013

Norovirus is the leading cause of foodborne disease in the United States. During October 2011–January 2013, we conducted surveillance for norovirus infection in Minnesota among callers to a complaint-based foodborne illness hotline who reported diarrhea or vomiting. Of 241 complainants tested, 127 (52.7%) were positive for norovirus

Evaluation of an ensemble-based distance statistic for clustering MLST datasets using epidemiologically defined clusters of cyclosporiasis.

Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis

Comparative Evaluation of Two Commercial Multiplex Panels for Detection of Gastrointestinal Pathogens by Use of Clinical Stool Specimens

Short granite walls accentuating garden axis, walking path crossing garden; The cultural section of the project (Station des Quais), gathers four contemporary gardens inspired by the mood of the river; the Quai des brumes, the Quai des flots, the Quai des hommes and the Quai des vents. At Quai des vents (Wind Dock), tall poles, or "stems," with large white weathervanes attached emerge from the garden, recalling the flight of geese in the wind. Source: Commission de la Capitale Nationale Quebec; http://www.capitale.gouv.qc.ca/ (accessed 7/27/2014

Recurrent outbreaks of cryptosporidiosis associated with calves among students at an educational farm programme, Minnesota, 2003

Enteric illness outbreaks among middle-/high-school students in consecutive semesters of an educational farm programme were investigated with retrospective cohort studies. During the first outbreak, 31/92 (34%) interviewed students were ill. Risk factors included participating in animal science class (RR 8·1, 95% CI 1·2–55·2) and contact with calves (RR 4·2, 95% CI 1·1–16·2). Stool samples from seven students and two calves yielded Cryptosporidium parvum. Students cared for animals in street clothes and practised poor hand washing. During the second outbreak, 37/81 (46%) interviewed animal science students were ill. Risk factors included having visible manure on hands, and wearing coveralls and boots. Stool samples from seven students and eight calves yielded C. parvum. Student hand washing was still inadequate. Coveralls/boots were cleaned infrequently and removed after hand washing. These outbreaks of cryptosporidiosis resulted from calf contact and inadequate hygiene practices. The failure to adequately implement recommended interventions contributed to the second outbreak

Sapovirus Outbreaks in Long-Term Care Facilities, Oregon and Minnesota, USA, 2002–2009

Sapovirus gives new meaning to the phrase “cradle to grave.” Historically, sapovirus has been associated with gastrointestinal illness in children living in group settings such as hospitals, shelters, or refugee camps. But now, sapovirus outbreaks are occurring among elderly residents of long-term care and similar facilities. These elderly residents are especially vulnerable to rapidly transmitted gastrointestinal viruses and serious complications. This virus has been making the rounds in long-term care facilities since 2002, and outbreaks started increasing in 2007. Sapovirus testing should be added to routine diagnostic workups for gastrointestinal infections, regardless of patient age group. Results can be used to develop prevention, control, and treatment guidelines, especially for vulnerable elderly populations

Investigation of US Cyclospora cayetanensis outbreaks in 2019 and evaluation of an improved Cyclospora genotyping system against 2019 cyclosporiasis outbreak clusters.

Cyclosporiasis is an illness characterised by watery diarrhoea caused by the food-borne parasite Cyclospora cayetanensis. The increase in annual US cyclosporiasis cases led public health agencies to develop genotyping tools that aid outbreak investigations. A team at the Centers for Disease Control and Prevention (CDC) developed a system based on deep amplicon sequencing and machine learning, for detecting genetically-related clusters of cyclosporiasis to aid epidemiologic investigations. An evaluation of this system during 2018 supported its robustness, indicating that it possessed sufficient utility to warrant further evaluation. However, the earliest version of CDC's system had some limitations from a bioinformatics standpoint. Namely, reliance on proprietary software, the inability to detect novel haplotypes and absence of a strategy to select an appropriate number of discrete genetic clusters would limit the system's future deployment potential. We recently introduced several improvements that address these limitations and the aim of this study was to reassess the system's performance to ensure that the changes introduced had no observable negative impacts. Comparison of epidemiologically-defined cyclosporiasis clusters from 2019 to analogous genetic clusters detected using CDC's improved system reaffirmed its excellent sensitivity (90%) and specificity (99%), and confirmed its high discriminatory power. This C. cayetanensis genotyping system is robust and with ongoing improvement will form the basis of a US-wide C. cayetanensis genotyping network for clinical specimens

Subtyping Cryptosporidium ubiquitum, a zoonotic pathogen emerging in humans

Cryptosporidium ubiquitum is an emerging zoonotic pathogen. In the past, it was not possible to identify an association between cases of human and animal infection. We conducted a genomic survey of the species, developed a subtyping tool targeting the 60-kDa glycoprotein (gp60) gene, and identified 6 subtype families (XIIa-XIIf) of C. ubiquitum. Host adaptation was apparent at the gp60 locus; subtype XIIa was found in ruminants worldwide, subtype families XIIb-XIId were found in rodents in the United States, and XIIe and XIIf were found in rodents in the Slovak Republic. Humans in the United States were infected with isolates of subtypes XIIb-XIId, whereas those in other areas were infected primarily with subtype XIIa isolates. In addition, subtype families XIIb and XIId were detected in drinking source water in the United States. Contact with C. ubiquitum-infected sheep and drinking water contaminated by infected wildlife could be sources of human infections