Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs

Yang, Chao; Li, Yinghui; Jiang, Min; Wang, Lei; Jiang, Yixiang; Hu, Lulu; Shi, Xiaolu; He, Long; Cai, Rui; Wu, Shuang; Qiu, Yaqun; Lu, Linying; Zuo, Le; Chen, Qiongcheng; Wu, Yarong; Martı́nez-Urtaza, Jaime; Wan, Chengsong; Yang, Ruifu; Cui, Yu‐Jun; Hu, Qinghua

doi:10.1038/s41564-022-01182-0

Cited by 31 publications

(20 citation statements)

References 41 publications

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“…Foodborne diseases, caused by Salmonella and many other pathogens, are critical and sustaining threats to global public health ( 1 , 2 ). Improved control of foodborne bacterial transmission requires various aspects of investment, such as investigation of epidemiological prevalence, detection of contaminated point, and bacterial typing.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

et al. 2022

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In public health field, high-resolution and efficient typing of the bacterial pathogen is essential, considering source-tracking and risk assessment are fundamental issues. Currently, there are no recommendations for applying molecular characterization methods for Salmonella along the food chain, and a systematic in-field investigation comparing subtyping methods in the context of routine surveillance was partially addressed.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

et al. 2022

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“…SNP distances between viral genomes were calculated based on concatenated SNPs using snp-dists (https://github.com/tseemann/snp-dists). 20…”

Section: Methodsmentioning

confidence: 99%

“…SNP distances between viral genomes were calculated based on concatenated SNPs using snp-dists (https://github.com/tseemann/snp-dists). 20 To determine SARS-CoV-2 lineage abundance in wastewater, we first performed quality control, alignment and primer sequence trimming using MGI MetargetCOVID software. In brief, sequencing reads were aligned to the reference sequence (MN908947.3) with BWA mem, and reads with hard or soft clips >10 were filtered using the SAMclip method.…”

Section: Sequencing and Analysismentioning

confidence: 99%

Longitudinal wastewater surveillance addressed public health priorities during the transition from “dynamic COVID-zero” to “opening up” in China: a population-based study

et al. 2023

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Background Wastewater surveillance provides real-time, cost-effective monitoring of SARS-CoV-2 transmission. We developed the first city-level wastewater warning system in mainland China, located in Shenzhen. Our study aimed to reveal cryptic transmissions under the "dynamic COVID-zero" policy and characterize the dynamics of the infected population and variant prevalence, and then guide the allocation of medical resources during the transition to "opening up" in China. Methods In this population-based study, a total of 1,204 COVID-19 cases were enrolled to evaluate the contribution of Omicron variant-specific faecal shedding rates in wastewater. After that, wastewater samples from up to 334 sites distributed in communities and port areas in two districts of Shenzhen covering 1.74 million people were tested daily to evaluate the sensitivity and specificity of this approach and were validated against daily SARS-CoV-2 screening. After the public health policy was switched to "opening up" in December 7, 2022, we conducted wastewater surveillance at wastewater treatment plants and pump stations covering 3.55 million people to estimate infected populations using model prediction and detect the relative abundance of SARS-CoV-2 lineages using wastewater sequencing. Findings In total, 82.4% of SARS-CoV-2 Omicron cases tested positive for faecal viral RNA within the first four days after the diagnosis, which was far more than the proportion of the ancestral variant. A total of 27,759 wastewater samples were detected from July 26 to November 30 in 2022, showing a sensitivity of 73.8% and a specificity of 99.8%. We further found that wastewater surveillance played roles in providing early warnings and revealing cryptic transmissions in two communities. Based on the above results, we employed a prediction model to monitor the daily number of infected individuals in Shenzhen during the transition to "opening up" in China, with over 80% of the population infected in both Futian District and Nanshan District. Notably, the prediction of the daily number of hospital admission was consistent with the actual number. Further sequencing revealed that the Omicron subvariant BA.5.2.48 accounted for the most abundant SARS-CoV-2 RNA in wastewater, and BF.7.14 and BA.5.2.49 ranked second and third, respectively, which was consistent with the clinical sequencing. Interpretation This study provides a scalable solution for wastewater surveillance of SARS-CoV-2 to provide real-time monitoring of the new variants, infected populations and facilitate the precise prediction of hospital admission. This novel framework could be a One Health system for the surveillance of other infectious and emerging pathogens with faecal shedding and antibiotic resistance genes in the future. Funding Sanming Project of Medicine in Shenzhen, Shenzhen Key Medical Discipline Construction Fund.

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“…No statistical methods were used to determine sample size, and there were no data excluded from the analyses. The experiments were not randomized ( Yang et al, 2022 ). FSS isolated 129 Salmonella strains from food samples (mainly livestock meat and poultry meat).…”

Section: Methodsmentioning

confidence: 99%

Population dynamics and antimicrobial resistance of Salmonella Derby ST40 from Shenzhen, China

et al. 2022

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Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the most common serotypes responsible for salmonellosis in humans and animals. The two main sequence types (ST) observed in China are ST40 and ST71, with ST40 presently being the most common in Shenzhen. Recent years have seen an increasing number of cases of salmonella caused by ST40 S. Derby, but the epidemiology is not clear. We gathered 314 ST40 S. Derby isolates from food and patient samples for 11 years in Shenzhen; 76 globally prevalent representative strains were also collected. Whole-genome sequencing (WGS) combined with drug resistance phenotyping was used to examine population structural changes, inter-host associations, drug resistance characteristics, and the food-transmission risks of ST40 S. Derby in Shenzhen over this period. The S. enterica evolutionary tree is divided into five clades, and the strains isolated in Shenzhen were primarily concentrated in Clades 2, 4, and 5, and thus more closely related to strains from Asian (Thailand and Vietnam) than European countries. Our 11-year surveillance of S. Derby in Shenzhen showed that Clades 2, 4, and 5 are now the dominant epidemic branches, and branches 2 and 5 are heavily multi-drug resistant. The main resistance pattern is ampicillin-tetracycline-ciprofloxacin-chloramphenicol-nalidixic acid-streptomycin-sulfamethoxazole/trimethoprim. This may lead to a trend of increasing resistance to ST40 S. Derby in Shenzhen. Using a segmentation of ≤3 SNP among clone clusters, we discovered that Clades 2 and 4 contained multiple clonal clusters of both human- and food-derived strains. The food-derived strains were mainly isolated from pig liver, suggesting this food has a high risk of causing disease outbreaks in Shenzhen.

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Outbreak dynamics of foodborne pathogen Vibrio parahaemolyticus over a seventeen year period implies hidden reservoirs

Cited by 31 publications

References 41 publications

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

Comprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella

Longitudinal wastewater surveillance addressed public health priorities during the transition from “dynamic COVID-zero” to “opening up” in China: a population-based study

Population dynamics and antimicrobial resistance of Salmonella Derby ST40 from Shenzhen, China

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