Website: https://vjfc.nifc.gov.vn/
Website: https://vjfc.nifc.gov.vn/
Salmonella spp. are among the major causative agents of foodborne illness. Conventional microbiological methods are effective for pathogen detection and isolation but have limited ability to assess the genetic relatedness among isolates recovered from different samples. This study applied Nanopore whole-genome sequencing to assess the genetic relatedness among Salmonella spp. isolates recovered during a bánh mì associated foodborne outbreak in Vietnam. A total of 16 outbreak-associated samples, including food and clinical specimens, were tested for common microbiological hazards and bacterial toxins relevant to foodborne outbreak investigations. Ten of the 16 samples were positive for Salmonella spp. The recovered Salmonella isolates were subjected to whole-genome sequencing and bioinformatics analysis to assess read quality, genome assembly characteristics, serotype, multilocus sequence type, plasmid profile, and antimicrobial resistance-associated genes. All ten isolates were identified as Salmonella enterica serovar Enteritidis, belonged to sequence type ST11, and showed highly similar genetic profiles. Single nucleotide polymorphism (SNP) analysis revealed pairwise distances of 0 - 6 SNPs, with several food isolates showing identical SNP profiles to isolates recovered from clinical specimens. These findings indicate a close genetic relationship between the food and clinical isolates and provide genomic evidence supporting the epidemiological hypothesis of a common exposure source in the outbreak.
Salmonella spp., foodborne outbreak, bánh mì, Nanopore sequencing, genetic relatedness, whole genome sequencing.
[1]. Centers for Disease Control and Prevention (CDC), “About Salmonella infection,” October 4, 2024. [Online]. Available: https://www.cdc.gov/salmonella/about/ [Accessed July 1, 2026].
[2]. World Health Organization (WHO), “Salmonella (non-typhoidal),” February 20, 2018. [Online]. Available: https://www.who.int/news-room/fact-sheets/detail/salmonella-(non-typhoidal) [Accessed July 1, 2026].
[3]. Vietnamnet, “More than 310 people suffered from Phuong bread poisoning, 273 cases were hospitalized.” [Online]. Available: https://vietnamnet.vn/313-nguoi-ngo-doc-sau-an-banh-mi-phuong-2193143.html [Accessed July 1, 2026].
[4]. Vietnam Food Administration, “Update on the situation of food poisoning cases in Long Khanh City,” May 8, 2024. [Online]. Available: https://vfa.gov.vn/tin-tuc/cap-nhat-tinh-hinh-vu-ngo-doc-thuc-pham-tren-dia-ban-thanh-pho-long-khanh.html [Accessed July 1, 2026].
[5]. Sai Gon Giai Phong, “Suspected bread poisoning case in Dong Thap: 25/36 samples were positive for Salmonella sp.,” June 20, 2026. [Online]. Available: https://www.sggp.org.vn/vu-nghi-ngo-doc-banh-mi-o-dong-thap-2536-mau-benh-pham-duong-tinh-voi-salmonella-sp-post858348.html [Accessed July 1, 2026].
[6]. Nhan Dan, “Bread poisoning case in Vung Tau: More than 54% of patient samples are positive for Salmonella bacteria,” March 9, 2026. [Online]. Available: https://nhandan.vn/vu-ngo-doc-banh-mi-o-vung-tau-hon-54-mau-benh-nhan-duong-tinh-voi-vi-khuan-salmonella-post947250.html [Accessed July 1, 2026].
[7]. Centers for Disease Control and Prevention (CDC), “Multistate Foodborne Outbreaks: Investigation Steps,” November 21, 2025. [Online]. Available: https://www.cdc.gov/foodborne-outbreaks/outbreakbasics/investigation-steps.html [Accessed July 1, 2026].
[8]. U.S. Food and Drug Administration (FDA), “Examples of How FDA Has Used Whole Genome Sequencing of Foodborne Pathogens For Regulatory Purposes.” [Online]. Available:
https://www.fda.gov/food/whole-genome-sequencing-wgs-program/examples-how-fda-has-used-wholegenome-sequencing-foodborne-pathogens-regulatory-purposes [Accessed July 1, 2026].
[9]. J. Quick, P. Ashton, S. Calus, et al., “Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella,” Genome Biology, vol. 16, p. 114, 2015.
[10]. Y. Lin, L. Yang, S. Qiu, et al., “Rapid identification and source tracing of a Salmonella Typhimurium outbreak in China by metagenomic and whole-genome sequencing,” Foodborne Pathogens and Disease, vol. 19, no. 4, pp. 259–265, 2022.
[11]. T. L. Taylor, J. D. Volkening, E. DeJesus, et al., “Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology,” Scientific Reports, vol. 9, p. 16350, 2019.
[12]. X. Wu, H. Luo, C. Ge, et al., “Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection,” Frontiers in Microbiology, vol. 13, p. 1073057, 2023.
[13]. S. Rheman, S. Hossain, M. S. Sarker, et al., “Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh,” Frontiers in Microbiology, vol. 15, p. 1329620, 2024.
[14]. B. Bogaerts, A. Van den Bossche, B. Verhaegen, et al., “Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens,” Journal of Clinical Microbiology, vol. 62, no. 5, p. e01576-23, 2024.
[15]. Oxford Nanopore Technologies, “Dorado,” August 9, 2026. [Online]. Available: https://github.com/nanoporetech/dorado [Accessed August 13, 2026].
[16]. M. Kolmogorov, J. Yuan, Y. Lin, and P. A. Pevzner, “Assembly of long, error-prone reads using repeat graphs,” Nature Biotechnology, vol. 37, no. 5, pp. 540–546, 2019.
[17]. EPI2ME, “wf-bacterial-genomes,” July 23, 2026. [Online]. Available: https://github.com/epi2melabs/wf-bacterial-genomes [Accessed August 13, 2026].
[18]. Oxford Nanopore Technologies, “Medaka,” August 7, 2026. [Online]. Available: https://github.com/nanoporetech/medaka [Accessed August 13, 2026].
[19]. O. Schwengers, L. Jelonek, M. A. Dieckmann, S. Beyvers, J. Blom, and A. Goesmann, “Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification,” Microbial Genomics, vol. 7, no. 11, p. 000685, 2021.
[20]. V. Bortolaia, R. S. Kaas, E. Ruppe, et al., “ResFinder 4.0 for predictions of phenotypes from genotypes, The Journal of Antimicrobial Chemotherapy, vol. 75, no. 12, pp. 3491–3500, 2020.
[21]. J. Robertson and J. H. E. Nash, “MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies,” Microbial Genomics, vol. 4, no. 8, p. e000206, 2018.
[22]. R. S. Kaas, P. Leekitcharoenphon, F. M. Aarestrup, and O. Lund, “Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms,” PLoS One, vol. 9, no. 8, p. e104984, 2014.
[23]. Saltykova, V. Wuyts, W. Mattheus, et al., “Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:-,” PLoS One, vol. 13, no. 2, p. e0192504, 2018.
[24]. H. H. Mostafa, “An evolution of Nanopore next-generation sequencing technology: implications for medical microbiology and public health,” Journal of Clinical Microbiology, vol. 62, no. 5, p. e00246-24, 2024.
[25]. C. Nadon, I. Van Walle, P. Gerner-Smidt, et al., “PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance,” Euro Surveillance, vol. 22, no. 23, p. 30544, 2017