Zilong Zhang

Norovirus is a leading cause of acute gastroenteritis and spreads efficiently in closed, mobile cohorts such as organized travel groups. This case is notable for the real-time detection and genomic confirmation of a cross-border outbreak at a port of entry, including near-identical Norovirus GΙΙ.17[P17] genomes and documented asymptomatic carriage, illustrating the practical value of integrated metagenomic surveillance in border health operations. On July 21, 2024, 26 travelers arrived at Shanghai Port after a 12-day group tour in Europe. Clinical interviews identified 15 individuals (57.7%) with diarrhea, nausea, dizziness, and abdominal pain; no hospitalizations occurred. On-site anal swab testing was negative for SARS-CoV-2, influenza A and B, Vibrio cholerae, and Escherichia coli. RT-qPCR detected Norovirus GII in 10 samples (38.5%), including two asymptomatic individuals. Metagenomic sequencing generated near-complete genomes for all RT-qPCR-positive samples, which were 99.9-100% identical and classified as Norovirus GΙΙ.17[P17], confirming a cross-border outbreak within the travel cohort. Prompt public health response measures were initiated by Shanghai Customs and CDC authorities. This case demonstrates the feasibility and impact of rapid, genomically informed surveillance at the border for detecting and characterizing travel-associated enteric virus outbreaks. The findings underscore the need for robust port-of-entry monitoring, rapid diagnostics, and integrated genomic analysis to mitigate transmission in group travel settings.

Traditional serotyping and multilocus sequence typing (MLST) for Vibrio parahaemolyticus have limitations in resolution and accuracy, particularly for strains with close genetic relationships. The long read length and high sequencing quality of a new type of nanopore sequencer G-seq500 make it possible to type V. parahaemolyticus strains using mtlA, a new identified typing gene for Vibrio. This gene not only offers advantages in cost-effectiveness and speed relative to MLST but also demonstrates comparable resolution. We sequenced the full-length mtlA gene (1,953 bp) of 33 V. parahaemolyticus strains using Geneus G-seq500. A total of 199,658 long reads with an average length of 17,306 bp were produced by one sequencing chip. After recognizing adaptor and barcode, each long read can be split into 12 subreads with mean accuracy of 93.25%, which were then aligned into 64,086 consensus sequences with a mean quality Q35 (sequence accuracy 99.88–99.93%). The final mtlA gene was generated by clustering all the consensus sequencing from same strain, and its accuracy reached 100% with over four consensus sequences clustered together. Then we developed a naming rule based on mtlA clustering of 7,573 mtlA sequences from NCBI together with the 33 mtlA gene sequenced by G-seq500, with the largest cluster composed of 2,321 strains designated as mtlA0001. Our study confirms the high sequencing accuracy of Geneus G-seq500, and the effectiveness of using the full-length mtlA gene for V. parahaemolyticus strain typing and epidemiological surveillance.

Background: Vibrio parahaemolyticus is the predominant etiological agent of seafood-associated foodborne illnesses on a global scale. It is essential to elucidate the mechanisms by which this pathogen disseminates. Given the existing research predominantly concentrates on localized outbreaks, there is a pressing necessity for a comprehensive investigation to capture strains of V. parahaemolyticus cross borders. Results: This study examined the frequency and genetic attributes of imported V. parahaemolyticus strains among travelers entering Shanghai Port, China, between 2017 and 2019.Through the collection of 21 strains from diverse countries and regions, Southeast Asia was pinpointed as a significant source for the emergence of V. parahaemolyticus. Phylogenetic analysis revealed clear delineation between strains originating from human and environmental sources, emphasizing that underlying genome data of foodborne pathogens is essential for environmental monitoring, food safety and early diagnosis of diseases. Furthermore, our study identified the presence of virulence genes (tdh and tlh) and approximately 120 antibiotic resistance-related genes in the majority of isolates, highlighting their crucial involvement in the pathogenesis of V. parahaemolyticus. Conclusions: This research enhanced our comprehension of the worldwide transmission of V. parahaemolyticus and its antimicrobial resistance patterns. The findings have important implications for public health interventions and antimicrobial stewardship strategies, underscoring the necessity for epidemiological surveillance of pathogen at international travel hubs.

The ongoing coronavirus disease 2019 (COVID‐19) pandemic, driven by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), highlights the critical role of genomic surveillance in tracking rapidly spreading viruses and their evolving lineages. The emergence of the SARS‐CoV‐2 tiling array, a comprehensive tool capable of capturing the entire viral genome, has presented a promising avenue for variants. This study introduces the SARS‐CoV‐2 tiling array as a novel method for port inspection. Using next‐generation sequencing as a benchmark, 35 positive samples underwent sequencing through both methodologies, including the Alpha variant (B.1.1.7), Delta variants (AY.120, AY.122, AY.23.1), and Omicron variants (BA.1, BA.2, BA.2.75, BA.4, BA.5, BE.1, BF.7, BN.1, BQ.1, XBB.1) within the sample set. The whole‐genome tiling array demonstrated successful identification of various sublineages of SARS‐CoV‐2. The average sequencing coverage rates were 99.22% (96.82%−99.92%) for the whole‐genome tiling array and 98.56% (92.81%−99.59%) for Illumina sequencing, respectively. The match rates of these two methods ranged from 92.81%−99.59%, with an average rate of 98.56%. Among the benefits of the whole‐genome tiling array are its cost‐effectiveness and equipment simplification, making it particularly suitable for identifying SARS‐CoV‐2 variants in the front‐line inspection department. The aforementioned findings provide valuable insights into the surveillance of COVID‐19 and present a pragmatic solution for improving quarantine measures at entry points.