Dataset Information

Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020.

ABSTRACT: We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900-2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.

SUBMITTER: Faleye TOC

PROVIDER: S-EPMC8472758 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:On 10 August 2016, the Maricopa County Department of Public Health identified culture-confirmed Salmonella enterica serotype Javiana isolates from two persons who reported eating at a seafood restaurant; seven additional cases were reported by 15 August. We investigated to identify a source and prevent further illness. We interviewed persons with laboratory-reported Salmonella Javiana infection. Pulsed-field gel electrophoresis (PFGE) and whole genome sequencing of isolates were performed. A case was defined as diarrheal illness in a person during July to September 2016; confirmed cases had Salmonella Javiana isolate yielding outbreak-related PFGE patterns; probable cases had diarrheal illness and an epidemiologic link to a confirmed case. Case finding was performed (passive surveillance and identification of ill meal companions). A case-control study assessed risk factors for Salmonella Javiana infection among restaurant diners; control subjects were chosen among meal companions. No restaurant workers reported illness. Foods were reportedly cooked according to the Food Code. Food and environmental samples were collected and cultured; Salmonella Javiana with an indistinguishable PFGE pattern was isolated from portioned repackaged raw shrimp, halibut, and a freezer door handle. We identified 50 Salmonella Javiana cases (40 confirmed and 10 probable); illness onset range was from 22 July to 17 September 2016. Isolates from 40 patients had highly related PFGE patterns. Thirty-three (73%) of 45 patients interviewed reported eating at the restaurant. Among 21 case patients and 31 control subjects, unfried cooked shrimp was associated with illness (odds ratio, 6.7; 95% confidence interval, 1.8 to 24.9; P = 0.004). Among restaurant diners, laboratory and case-control evidence indicated shrimp as the possible outbreak source; poor thermal inactivation of Salmonella on shrimp is theorized as a possible cause. Cross-contamination might have prolonged this outbreak; however, the source was not identified and highlights limitations that can arise during these types of investigations.

Project description:Campylobacter is a leading cause of gastroenteritis across the globe caused by the ingestion of contaminated food, water, or contact with animals carrying Campylobacter bacteria. The resulting disease, campylobacteriosis, is usually self-limiting, but cases may develop post-infectious sequelae (PIS) such as gastrointestinal disorders, neurological disorders, and joint disorders. The objective of this study was to estimate a crude incidence rate for PIS among Campylobacter cases in Maricopa County, Arizona, USA and to determine the feasibility of conducting a larger scale study to understand chronic outcomes from campylobacteriosis and salmonellosis.The pilot study spanned from August 1, 2016, to August 31, 2017. During this time, cases of campylobacteriosis were reported to the Maricopa County Department of Public Health and interviewed by public health students at the University of Arizona. Initial interviews were conducted using a routine enteric surveillance questionnaire, and eligible cases were recruited and consented into the pilot study. Follow-up with a questionnaire occurred 4 to 6 weeks from the date of each case's initial interview. Data analysis was conducted using STATA SE 14 and included chi-squared tests to determine differences in demographics, symptoms, and exposures between those enrolled in the study and those eligible but not enrolled during the study period and feasibility metrics for the study including enrollment rates, response rates, time to interview, and reasons for non-enrollment. Crude rates with 95% confidence intervals were calculated to estimate PIS.Of the routine surveillance cases, 102 (36%) enrolled into the pilot study. Of enrolled participants, 68.6% completed the follow-up questionnaire. Most enrolled participants were non-Hispanic White, male, and aged 60?+?years. Over half (52.8%, 95% CI 41.1%, 64.5%) of cases experienced PIS approximately 4 to 6 weeks after acute onset of campylobacteriosis.Results from this pilot study indicate that a larger study is feasible. The larger study will identify the true incidence of PIS and improve the management of patient health among ethnically diverse populations.

Project description:Background:Zika virus (ZIKV) is an emerging mosquito-borne disease that can cause severe birth defects if contracted congenitally. Since late 2015, there has been a large increase in the number of travel-related cases of Zika virus infection in Canada. Objective:The objective of this study was to describe the epidemiology of travel-related Zika cases in Canada from October 2015 to June 2017 and review them in the context of the international outbreak in the Americas. Methods:Zika virus infections were confirmed by polymerase chain reaction (PCR) detection of viral RNA and/or the serological identification of ZIKV-specific antibodies in serum. Cases of ZIKV infection were identified by provincial and territorial health authorities, and reported on a regular basis to the Public Health Agency of Canada (PHAC). Case information requested included date of illness onset, age category, sex, pregnancy status, and location(s) and dates of travel. Estimates for the monthly number of Canadians travelling outside of Canada to other countries in the Americas were obtained from Statistics Canada and the International Air Transport Association (IATA). Data to produce the epidemic curves of autochthonous cases for each region of the Americas were extracted from country-specific epidemic curves on the Pan American Health Organization website. Results:As of June 7, 2017, 513 laboratory confirmed cases and two Zika-related birth/fetal anomalies were reported across all 10 provinces. Illness in Canadian travellers generally coincided with outbreak intensity in the country of exposure rather than travel volume. There has been no evidence of autochthonous (local) transmission in Canada. Currently, cases are on the decline both in Canada and internationally. Conclusion:The surge in Canadian ZIKV infections in 2016 was directly related to the incursion and spread of ZIKV into the Americas. Although cases are now on the decline worldwide, it remains to be seen whether a resurgence of cases in previously affected or new areas will occur. Both outbreak intensity and seasonality of ZIKV transmission should be monitored over time in order to inform the timing of public health education campaigns, as some may turn out to be more effective in the off-peak travel season when the risk of disease transmission may be higher. Ongoing education and awareness among travellers, particularly for pregnant women and those planning pregnancies, is still indicated.

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Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020.

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