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Ramos B, Cunha MV. The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124241. [PMID: 38825220 DOI: 10.1016/j.envpol.2024.124241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/28/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.
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Affiliation(s)
- Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c) & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal; Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016, Lisboa, Portugal.
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Buytaers FE, Verhaegen B, Van Nieuwenhuysen T, Roosens NHC, Vanneste K, Marchal K, De Keersmaecker SCJ. Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling. Front Microbiol 2024; 15:1330814. [PMID: 38495515 PMCID: PMC10940517 DOI: 10.3389/fmicb.2024.1330814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Introduction Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone. Methods The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 105 CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed. Results Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases. Discussion This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.
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Affiliation(s)
- Florence E. Buytaers
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | - Tom Van Nieuwenhuysen
- National Reference Laboratory for Foodborne Outbreaks (NRL-FBO) and for Coagulase Positive Staphylococci (NRL-CPS), Foodborne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
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Li Q, Dou L, Zhang Y, Luo L, Yang H, Wen K, Yu X, Shen J, Wang Z. A comprehensive review on the detection of Staphylococcus aureus enterotoxins in food samples. Compr Rev Food Sci Food Saf 2024; 23:e13264. [PMID: 38284582 DOI: 10.1111/1541-4337.13264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 01/30/2024]
Abstract
Staphylococcal enterotoxins (SEs), the major virulence factors of Staphylococcus aureus, cause a wide range of food poisoning and seriously threaten human health by infiltrating the food supply chain at different phases of manufacture, processes, distribution, and market. The significant prevalence of Staphylococcus aureus calls for efficient, fast, and sensitive methods for the early detection of SEs. Here, we provide a comprehensive review of the hazards of SEs in contaminated food, the characteristic and worldwide regulations of SEs, and various detection methods for SEs with extensive comparison and discussion of benefits and drawbacks, mainly including biological detection, genetic detection, and mass spectrometry detection and biosensors. We highlight the biosensors for the screening purpose of SEs, which are classified according to different recognition elements such as antibodies, aptamers, molecularly imprinted polymers, T-cell receptors, and transducers such as optical, electrochemical, and piezoelectric biosensors. We analyzed challenges of biosensors for the monitoring of SEs and conclude the trends for the development of novel biosensors should pay attention to improve samples pretreatment efficiency, employ innovative nanomaterials, and develop portable instruments. This review provides new information and insightful commentary, important to the development and innovation of further detection methods for SEs in food samples.
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Affiliation(s)
- Qing Li
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Leina Dou
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Yingjie Zhang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Huijuan Yang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health safety, College of Veterinary Medicine China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, Beijing, China
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Romano A, Carrella S, Rezza S, Nia Y, Hennekinne JA, Bianchi DM, Martucci F, Zuccon F, Gulino M, Di Mari C, Zaccaria T, Decastelli L. First Report of Food Poisoning Due to Staphylococcal Enterotoxin Type B in Döner Kebab (Italy). Pathogens 2023; 12:1139. [PMID: 37764947 PMCID: PMC10535471 DOI: 10.3390/pathogens12091139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Staphylococcal food poisoning results from the consumption of food contaminated by staphylococcal enterotoxins. In July 2022, the Turin local health board was notified of a suspected foodborne outbreak involving six children who had consumed döner kebab purchased from a takeaway restaurant. The symptoms (vomiting and nausea) were observed 2-3 h later. A microbiological analysis of the food samples revealed high levels (1.5 × 107 CFU/g) of coagulase-positive staphylococci (CPS). The immunoassay detected a contamination with staphylococcal enterotoxins type B (SEB). The whole genome sequencing of isolates from the food matrix confirmed the staphylococcal enterotoxin genes encoding for type B, which was in line with the SEB detected in the food. This toxin is rarely reported in staphylococcal food poisoning, however, because there is no specific commercial method of detection. The involvement of enterotoxin type P (SEP) was not confirmed, though the corresponding gene (sep) was detected in the isolates. Nasal swabs from the restaurant food handlers tested positive for CPS, linking them to the likely source of the food contamination.
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Affiliation(s)
- Angelo Romano
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Simona Carrella
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Sara Rezza
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Yacine Nia
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Jacques Antoine Hennekinne
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Université Paris-Est, 94700 Maisons-Alfort, France
| | - Daniela Manila Bianchi
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Francesca Martucci
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Fabio Zuccon
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
| | - Margherita Gulino
- Azienda Sanitaria Locale TO5 di Chieri, Carmagnola, Moncalieri e Nichelino—Dipartimento di Prevenzione SC Igiene degli Alimenti e della Nutrizione, 10042 Nichelino, Italy
| | - Carmela Di Mari
- Azienda Sanitaria Locale TO5 di Chieri, Carmagnola, Moncalieri e Nichelino—Dipartimento di Prevenzione SC Igiene degli Alimenti e della Nutrizione, 10042 Nichelino, Italy
| | - Teresa Zaccaria
- SC Microbiologia e Virologia Azienda Ospedaliero-Universitaria, Città Della Salute e Della Scienza di Torino, 10126 Turin, Italy
| | - Lucia Decastelli
- National Reference Laboratory for Coagulase Positive Staphylococci including S. aureus, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d’Aosta, 10148 Turin, Italy
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Guo Y, Yu X, Wang J, Hua D, You Y, Wu Q, Ji Q, Zhang J, Li L, Hu Y, Wu Z, Wei X, Jin L, Meng F, Yang Y, Hu X, Long L, Hu S, Qi H, Ma J, Bei W, Yan X, Wang H, He Z. A food poisoning caused by ST7 Staphylococcal aureus harboring sea gene in Hainan province, China. Front Microbiol 2023; 14:1110720. [PMID: 37007521 PMCID: PMC10060626 DOI: 10.3389/fmicb.2023.1110720] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
ST7 Staphylococcus aureus is highly prevalent in humans, pigs, as well as food in China; however, staphylococcal food poisoning (SFP) caused by this ST type has rarely been reported. On May 13, 2017, an SFP outbreak caused by ST7 S. aureus strains occurred in two campuses of a kindergarten in Hainan Province, China. We investigated the genomic characteristics and phylogenetic analysis of ST7 SFP strains combined with the 91 ST7 food-borne strains from 12 provinces in China by performing whole-genome sequencing (WGS). There was clear phylogenetic clustering of seven SFP isolates. Six antibiotic genes including blaZ, ANT (4′)-Ib, tetK, lnuA, norA, and lmrS were present in all SFP strains and also showed a higher prevalence rate in 91 food-borne strains. A multiple resistance plasmid pDC53285 was present in SFP strain DC53285. Among 27 enterotoxin genes, only sea and selx were found in all SFP strains. A ФSa3int prophage containing type A immune evasion cluster (sea, scn, sak, and chp) was identified in SFP strain. In conclusion, we concluded that this SFP event was caused by the contamination of cakes with ST7 S. aureus. This study indicated the potential risk of new emergencing ST7 clone for SFP.
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Affiliation(s)
- Yahui Guo
- Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
| | - Xiaojie Yu
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Jixiao Wang
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - De Hua
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Yuanhai You
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Qingbo Wu
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Qinglong Ji
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jianzhong Zhang
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Liefei Li
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Yuan Hu
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Zhonghui Wu
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Xiaoyue Wei
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Lianqun Jin
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Fanliang Meng
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Yuhua Yang
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xiaofeng Hu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lijin Long
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Heyuan Qi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Juncai Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenwen Bei
- Hainan Provincial Center for Disease Control and Prevention, Haikou, China
| | - Xiaomei Yan
- Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
- *Correspondence: Xiaomei Yan,
| | - Haibin Wang
- Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
- Beijing Chaoyang District Center for Disease Control and Prevention, Beijing, China
- Haibin Wang,
| | - Zilong He
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Zilong He,
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Sri Prabakusuma A, Zhu J, Shi Y, Ma Q, Zhao Q, Yang Z, Xu Y, Huang A. Prevalence and antimicrobial resistance profiling of Staphylococcus aureus isolated from traditional cheese in Yunnan, China. 3 Biotech 2022; 12:1. [PMID: 34926114 PMCID: PMC8639989 DOI: 10.1007/s13205-021-03072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023] Open
Abstract
The prevalence of staphylococcal infection and the emergence of multidrug resistance of Staphylococcus aureus (S. aureus) are major concerns in food safety and public health. This study aimed to investigate the prevalence of S. aureus isolated from traditional Chinese Rubing and Rushan cheese, antimicrobial resistance profiles, genomic characteristics, and predict antimicrobial resistance genes (ARGs). From 124 samples, 18 of 62 (29.03%) of Rubing and 5 of 62 (8.06%) of Rushan cheese were confirmed to be S. aureus positive by standard culture-based methods. Twenty-three coagulase-positive staphylococci isolates were grouped into 16 clusters by pulsed-field gel electrophoresis and subjected to routine susceptibility testing to 12 antibiotics. Those isolates exhibited high resistance to penicillin (100%), erythromycin, trimethoprim-sulphamethoxazole (34.78%), oxacillin, clindamycin, and cefoxitin (21.74%). Multidrug-resistant (MDR) S. aureus was found in 34.78% (8 of 23) of isolates. Further, S. aureus strain DC.RB_015 isolated from Rubing cheese, recognized as the most resistant to six antibiotics, was selected for whole-genome sequencing (WGS), continued with in silico approaches. S. aureus DC.RB_015 had a single chromosome size of 2,794,578 bp and a plasmid size of 22,961 bp. The strain harbored 18 predicted ARGs, including eight efflux pump genes (mepA, tet(K), arlR, arlS, norA, mgrA, tet(38), LmrS), one peptidoglycan biosynthesis gene (bacA), two β-lactams resistance genes (mecA, blaZ), and seven genes conferring other antimicrobial resistance (APH(3')-IIIa, aad(6), ErmB, SAT-4, mecR1, GlpT, murA). The results of this study expand the knowledge of S. aureus strain DC.RB_015, increase food safety awareness, and will be helpful in establishing therapeutic therapy. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03072-4.
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Affiliation(s)
- Adhita Sri Prabakusuma
- Department of Food Technology, Faculty of Industrial Technology, Universitas Ahmad Dahlan, Yogyakarta, 55166 Indonesia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Jingjing Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Qingwen Ma
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Qiong Zhao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Zushun Yang
- Yunnan Center for Disease Control and Prevention (CDC), Kunming, 650100 Yunnan China
| | - Yan Xu
- Yunnan Center for Disease Control and Prevention (CDC), Kunming, 650100 Yunnan China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
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