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Caigoy JC, Nariya H, Shimamoto T, Yan Z, Shimamoto T. ArcAB system promotes biofilm formation through direct repression of hapR transcription in Vibrio cholerae. Microbiol Res 2025; 297:128155. [PMID: 40185028 DOI: 10.1016/j.micres.2025.128155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 03/10/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
Abstract
Vibrio cholerae, the causative agent of cholera, can efficiently adapt its metabolic processes, including biofilm formation, in response to varying respiratory conditions- such as aerobic, microaerobic, and anaerobic- through the ArcAB system. In this study, we elucidate the activation mechanism of V. cholerae ArcB and ArcA and identify ArcB residues H292, D577, and H722, along with ArcA residue D54 as key phosphorylation sites. Furthermore, we demonstrate that the ArcAB system plays a crucial role in regulating biofilm formation under both aerobic and anaerobic conditions. Our findings reveal that the positive regulation of biofilm formation by the ArcAB systems involves the high cell density (HCD) quorum sensing (QS) regulator HapR. Specifically, phosphorylated ArcA represses hapR transcription, thereby promoting biofilm formation under anaerobic condition. This study also highlights an epistatic relationship between ArcA and HapR in biofilm regulation. Overall, our results underscore the critical role of the ArcAB system in the biofilm formation of pathogenic V. cholerae under oxygen-limiting conditions.
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Affiliation(s)
- Jant Cres Caigoy
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Hirofumi Nariya
- Graduate School of Human Life Sciences, Jumonji University, Japan
| | - Toshi Shimamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan
| | - Zhiqun Yan
- Graduate School of Biosphere Science, Hiroshima University, Japan
| | - Tadashi Shimamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, Japan.
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2
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Zhang D, Feng Y, Chu M, Dai Y, Jiang L, Li H. Anti-vibriosis bioactive molecules from marine-derived variant Streptomyces sp. ZZ741A. Nat Prod Res 2025; 39:3031-3042. [PMID: 38486398 DOI: 10.1080/14786419.2024.2321487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/03/2024] [Accepted: 02/13/2024] [Indexed: 05/31/2025]
Abstract
The infection of vibrio is an important cause of huge economic losses in aquaculture industry. At present, antibiotics are mainly used to prevent and reduce the infection of the vibrio, which has accelerated the emergence of multi-drug-resistant strains. New generation alternative anti-vibrio drugs were in urgent to solve this problem. In this study, six compounds (1-6) were isolated from the Streptomyces sp. ZZ741A, a marine-derived Streptomyces variant, including one new compound, 2-carbamoylphenyl isobutyrate (1), five known ones, nocardamine (2), dehydroxynocardamine (3), phenylacetic acid (4), thiophenol (5) and 2,3-dihydroxybenzoic acid (6). The anti-vibriosis assay showed that compounds 2 and 3 had specific inhibition activity against Vibrio vulnificus, Vibrio alginolyticus, and Vibrio parahaemolyticus with the MIC values ranging from 8 to 128 μg/mL. The molecular docking study of their possible mechanism of anti-vibriosis activity showed that the activity might come from the inhibition of Outer membrane protein U (OmpU).
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Affiliation(s)
- Di Zhang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, PR China
| | - Yao Feng
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
| | - Mingyi Chu
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
| | - Yujiang Dai
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
| | - Lu Jiang
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
| | - Huifang Li
- Jiangsu Key Laboratory of Marine Biotechnology/Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, PR China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, PR China
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3
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Wang X, Shi B, Xia C, Hou M, Wang J, Tian A, Shi C, Ma C. Poly-L-lysine functionalized silica membrane-enhanced colorimetric loop-mediated isothermal amplification for sensitive and rapid detection of Vibrio parahaemolyticus. Talanta 2025; 288:127744. [PMID: 39961248 DOI: 10.1016/j.talanta.2025.127744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 02/04/2025] [Accepted: 02/12/2025] [Indexed: 03/05/2025]
Abstract
Traditional detection of foodborne pathogen relies on advanced analyzers, which is inadequate for the rapid control of infections, particularly in resource-limited regions, highlighting the necessity of developing detection systems for point-of-care testing (POCT). Herein, taking Vibrio parahaemolyticus as a detecting target, we reported poly-L-lysine functionalized silica membrane (PL-SM) based loop-mediated isothermal amplification (pLAMP) platform for sensitive on-site detection. This platform utilized PL-SM for DNA capture driven by the electrostatic attraction between protonated amine groups of poly-L-lysine and negatively charged phosphate groups of DNA, followed by introducing a colorimetric indicator calcein for LAMP amplification. After optimization, the colorimetric mode of pLAMP allowed the screening of V. parahaemolyticus with the visual limit of detection (vLOD) of 1 CFU/mL in 50 min, 1000-fold lower than methods based on commercial kits. Validation was performed using 174 seafoods, which was 97 % concordant to those of real-time PCR. Furthermore, an image processing approach was developed based on the analysis of the RGB under UV light. Paired with a smartphone, the objective analytical method could be readily conducted in the field. Thus, we propose a sensitive and visual detection platform, which may play a crucial role in improving testing efficiency and accuracy in food safety, medical diagnostics, and environmental monitoring.
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Affiliation(s)
- Xiujuan Wang
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Binghui Shi
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Cengceng Xia
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Mengnan Hou
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Jingying Wang
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Anning Tian
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, and Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Cuiping Ma
- Sino-UAE International Cooperative Joint Laboratory of Pathogenic Microorganism Rapid Detection, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, Qingdao Key Laboratory of Nucleic Acid Rapid Detection, College of Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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4
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Froschauer K, Svensson SL, Gelhausen R, Fiore E, Kible P, Klaude A, Kucklick M, Fuchs S, Eggenhofer F, Yang C, Falush D, Engelmann S, Backofen R, Sharma CM. Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni. Nat Commun 2025; 16:3078. [PMID: 40159498 PMCID: PMC11955535 DOI: 10.1038/s41467-025-58329-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 03/18/2025] [Indexed: 04/02/2025] Open
Abstract
In contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here, we present a Ribo-seq-based high-resolution translatome map for the major foodborne pathogen Campylobacter jejuni. Besides conventional Ribo-seq, we employed translation initiation site (TIS) profiling to map start codons and also developed a translation termination site (TTS) profiling approach, which revealed stop codons not apparent from the reference genome in virulence loci. Our integrated approach combined with independent validation expanded the small proteome by two-fold, including CioY, a new 34 aa component of the CioAB oxidase. Overall, our study generates a high-resolution annotation of the C. jejuni coding landscape, provided in an interactive browser, and showcases a strategy for applying integrated Ribo-seq to other species to enrich our understanding of small proteomes.
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Affiliation(s)
- Kathrin Froschauer
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, Würzburg, Germany
| | - Sarah L Svensson
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, Würzburg, Germany
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Elisabetta Fiore
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, Würzburg, Germany
| | - Philipp Kible
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, Würzburg, Germany
| | - Alicia Klaude
- Technische Universität Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Martin Kucklick
- Technische Universität Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Daniel Falush
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Susanne Engelmann
- Technische Universität Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Signalling Research Centre CIBSS, University of Freiburg, Freiburg, Germany
| | - Cynthia M Sharma
- University of Würzburg, Institute of Molecular Infection Biology, Department of Molecular Infection Biology II, Würzburg, Germany.
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5
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Huang L, Zhang M, Luo X, Li X, Zhang Y, Lu R. Sublethal Curcumin Exposure Induces Global Gene Expression and Biofilm-Related Phenotypic Changes in Vibrio parahaemolyticus. Curr Microbiol 2025; 82:212. [PMID: 40137992 DOI: 10.1007/s00284-025-04201-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2024] [Accepted: 03/19/2025] [Indexed: 03/29/2025]
Abstract
Vibrio parahaemolyticus, a foodborne pathogen found in marine environments, is susceptible to the antimicrobial effects of curcumin-a lipophilic polyphenolic pigment with diverse biological activities. While sublethal doses of curcumin inhibit behaviors of V. parahaemolyticus, the underlying molecular mechanisms remain poorly characterized. In this study, we aimed to investigate the impact of sublethal doses of curcumin on gene expression and key bacterial processes in V. parahaemolyticus. RNA sequencing (RNA-seq) revealed that sublethal curcumin concentrations significantly suppressed bacterial growth and altered the expression of 788 genes. These differentially expressed genes (DEGs) were associated with critical pathways, including upregulated systems such as polar flagellum, type IV pili, and type VI secretion systems (T6SS1 and T6SS2), as well as downregulated systems such as lateral flagella, exopolysaccharides (EPS), and type III secretion systems (T3SS1 and T3SS2). Notably, most DEGs involved in cyclic di-GMP (c-di-GMP) metabolism were downregulated, while putative porin-related genes were upregulated. Additionally, sublethal curcumin significantly inhibited biofilm formation and swimming motility but enhanced c-di-GMP production in V. parahaemolyticus. This study provides valuable insights into how V. parahaemolyticus adjusts its gene expression in response to sublethal levels of curcumin.
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Affiliation(s)
- Lili Huang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Miaomiao Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xi Luo
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Xue Li
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China
| | - Yiquan Zhang
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China.
| | - Renfei Lu
- Department of Clinical Laboratory, Affiliated Nantong Hospital 3 of Nantong University, Nantong Third People's Hospital, Nantong, 226006, Jiangsu, China.
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6
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Sebastian PJ, Schlesener C, Byrne BA, Miller M, Smith W, Batac F, Goertz CEC, Weimer BC, Johnson CK. Antimicrobial resistance of Vibrio spp. from the coastal California system: discordance between genotypic and phenotypic patterns. Appl Environ Microbiol 2025; 91:e0180824. [PMID: 39898660 PMCID: PMC11921324 DOI: 10.1128/aem.01808-24] [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: 09/23/2024] [Accepted: 12/14/2024] [Indexed: 02/04/2025] Open
Abstract
Antimicrobial resistance in Vibrio species poses risks to both human and marine mammal health. Whole genome sequencing of Vibrio spp. can be utilized to screen for antimicrobial resistance genes and allelic variants to provide mechanistic insights in ways that PCR screening and phenotypic interpretation cannot. Our goals were to (i) characterize antimicrobial resistance patterns of Vibrio spp. pathogens isolated from southern sea otters (Enhydra lutris nereis), northern sea otters (Enhydra lutris kenyoni), and environmental samples from the central California coast using whole genome sequencing, and (ii) compare the presence of antimicrobial resistance genes with phenotypic interpretation from antibiotic susceptibility testing. Unexpectedly, genomic classification identified an understudied species, Vibrio diabolicus, in sea otter and environmental isolates that were previously identified as Vibrio alginolyticus. A total of 489 Vibrio spp. isolates were sequenced, and frequently detected antimicrobial resistance genes included multidrug efflux pumps and genes associated with resistance to ß-lactams and tetracyclines. Genes associated with resistance to fluoroquinolones, aminoglycosides, chloramphenicol, and sulfonamides were uncommon. Sea otter isolates were phenotypically susceptible to tetracycline despite carrying genes tet34 and tet35. Both between- and within-species variations in ampicillin resistance were observed despite the ubiquitous presence of blaCARB genes in V. alginolyticus, V. diabolicus, and Vibrio parahaemolyticus. Discordance between phenotypic and genotypic ampicillin resistance was especially noted for V. parahaemolyticus and was partially attributed to the allelic variation of the blaCARB genes. Tetracyclines and fluoroquinolones, but not ß-lactams, are likely to be effective treatments for vibriosis in sea otters. IMPORTANCE Vibriosis (infection with non-cholera Vibrio spp.) is the most common seafood-borne illness globally, with major impacts on public health, food security, and wildlife health. Potential treatments of antimicrobial-resistant Vibrio spp. in humans, aquaculture, and marine wildlife rehabilitation are complicated by current diagnostic challenges regarding bacterial species identification and interpretation of antimicrobial resistance patterns. Unexpected detection of previously misidentified Vibrio diabolicus in sea otters suggests that a broader taxonomic group of Vibrio infect sea otters than previously described. We also determined that the presence of ß-lactamase genes alone in sea otter isolates does not necessarily correlate with an ampicillin-resistant phenotype, likely due to deleterious amino acid substitutions in certain blaCARB alleles. Continued monitoring of Vibrio spp. phenotypes and genotypes in sea otters is warranted to observe biologically relevant changes in antimicrobial resistance.
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Affiliation(s)
- Peter J. Sebastian
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Cory Schlesener
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Barbara A. Byrne
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Melissa Miller
- Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Marine Wildlife Veterinary Care and Research Center, California Department of Fish and Wildlife, Santa Cruz, California, USA
| | - Woutrina Smith
- Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Francesca Batac
- Marine Wildlife Veterinary Care and Research Center, California Department of Fish and Wildlife, Santa Cruz, California, USA
| | | | - Bart C. Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Christine K. Johnson
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Karen C. Drayer Wildlife Health Center, One Health Institute, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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7
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Lian XQ, Liu GD, Huang MF, Fan QH, Lin ZD. Antimicrobial resistance, virulence factors and phylogenetic profiles of Vibrio parahaemolyticus in the eastern coast of Shenzhen. Front Microbiol 2024; 15:1452942. [PMID: 39588110 PMCID: PMC11586387 DOI: 10.3389/fmicb.2024.1452942] [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: 06/21/2024] [Accepted: 10/23/2024] [Indexed: 11/27/2024] Open
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is a major food-borne pathogen which causes human gastroenteritis. Since the characteristics of V. parahaemolyticus remain unknown, 220 isolates selected from clinical and environmental samples in Dapeng of Shenzhen were tested for the presence of two hemolysin-expressing genes tdh and trh. Among 27 clinical isolates, 26 carrired the tdh gene, and the other one carried both tdh and trh genes, however neither genes were detected in environmental isolates. Meanwhile, antimicrobial susceptibility profiles revealed the isolates with high frequency of resistance to ampicillin (77.73%) and colistin (71.82%) and medium to streptomycin (57.27%). Genetically, by whole genome sequencing (WGS), comparative genomics studies was performed on isolates from various districts and GenBank. Data analysis showed that antimicrobial resistance genes (ARGs) blaCARB, tet(34) and tet(35) were harbored in all genomes and other ARGs was absent in the genomes of 27 clinical isolates. Besides, little regional difference was observed. As for virulence factors, MAM7, T3SS1, T3SS1 secret effector, T3SS2, T3SS2 secret effector, and VpadF were carried by most isolates. Two isolates from other districts were tdh gene positive which clustered with clinical isolates from Dapeng in the same clade, indicating close genetic distance. This study revealed the widely distribution of V. parahaemolyticus in Shenzhen and the diverse ARGs and virulence genes it carried. Furthermore, pathways that pathogen disseminated through were discussed.
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Fu P, Yan G, Li Y, Xie L, Ke Y, Qiu S, Wu S, Shi X, Qin J, Zhou J, Lu G, Yang C, Wang C. Pertussis upsurge, age shift and vaccine escape post-COVID-19 caused by ptxP3 macrolide-resistant Bordetella pertussis MT28 clone in China. Clin Microbiol Infect 2024; 30:1439-1446. [PMID: 39209267 DOI: 10.1016/j.cmi.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 08/12/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVES China has experienced a notable upsurge in pertussis cases post-COVID-19, alongside an age shift to older children, increased vaccine escape, and a notable rise in the prevalence of macrolide-resistant Bordetella pertussis. Here, we present a genomic epidemiological investigation of these events. METHODS We performed a retrospective observational study using culture-positive B pertussis isolated in Shanghai, China, from 2016 to 2024. We analysed strain and pertussis epidemiology dynamics by integrating whole-genome sequencing of 723 strains with antimicrobial susceptibility, transcriptomic profile, and clinical data. We compared the genome sequences of Shanghai strains with 6450 Chinese and global strains. RESULTS From pre-COVID-19 (before December 2019) to post-COVID-19, patients shifted from predominantly infants (90%, 397/442) to a higher proportion of infections in older children (infant: 16%, 132/844), with the share of vaccinated individuals surging from 31% (107/340) to 88% (664/756). The macrolide-resistant Bordetella pertussis prevalence increased from 60% (267/447) to 98% (830/845). The emergence and expansion of a ptxP3-lineage macrolide-resistant clone, MR-MT28, which is uniquely capable of causing substantial infections among older children and vaccinated individuals, was temporally strongly associated with the pertussis upsurge and epidemiological transition. Although MR-MT28 showed increased expression of genes encoding pertussis toxin, it was associated with significantly milder clinical symptoms and a lower hospitalization rate. MR-MT28 likely originated in China around 2016, after acquiring several key mutations, including a novel prn150 allele, and has been detected across multiple regions in China. In addition, 26% (50/195) of MR-MT28 has evolved into predicted Pertactin (PRN)-deficient strains, with an IS481 insertion being the predominant mechanism. DISCUSSION We report that the post-COVID-19 upsurge of pertussis in China is associated with ptxP3-MR-MT28, and provide evidence that pathogen evolution is likely the primary factor driving + pertussis upsurge, age shift, and vaccine escape. MR-MT28 poses a high risk of global spread and warrants global surveillance.
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Affiliation(s)
- Pan Fu
- Laboratory of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gangfen Yan
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yijia Li
- Laboratory of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Li Xie
- The Center for Microbes, Development and Health, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Yuehua Ke
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuxiang Qiu
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuang Wu
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Microbiology Laboratory, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jie Qin
- Laboratory of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinlan Zhou
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoping Lu
- Pediatric Intensive Care Unit, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Chao Yang
- The Center for Microbes, Development and Health, Chinese Academy of Sciences (CAS) Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
| | - Chuanqing Wang
- Laboratory of Microbiology, Department of Clinical Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Nosocomial Infection Control Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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9
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Narayanan KB, Bhaskar R, Han SS. Bacteriophages: Natural antimicrobial bioadditives for food preservation in active packaging. Int J Biol Macromol 2024; 276:133945. [PMID: 39029821 DOI: 10.1016/j.ijbiomac.2024.133945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/21/2024]
Abstract
Developing innovative films and coatings is paramount for extending the shelf life of numerous food products and augmenting the barrier and antimicrobial properties of food packaging materials. Many synthetic chemicals used in active packaging and food storage have the potential to leach into food, posing long-term health risks. It is imperative for active packaging materials to inherently possess biological protective properties to ensure food quality and safety throughout its storage. Bacteriophages, or simply phages, are bacteria-eating viruses that serve as promising natural biocontrol agents and antimicrobial bioadditives in food packaging materials, specifically targeting bacterial foodborne pathogens. These phages are generally recognized as safe (GRAS) by regulatory authorities for food safety applications. They exhibit targeted action against various Gram-positive and -negative foodborne pathogens, including Bacillus spp., Campylobacter spp., Escherichia coli, Listeria monocytogenes, Salmonella spp., Shigella spp., and Vibrio spp., associated with foodborne spoilage and illness without affecting the beneficial microbes. Phage cocktails can be applied directly on food surfaces, incorporated into food packaging materials, or utilized during food processing treatments. Unlike chemical agents, phage activity increases proportionally with the rise in pathogenic bacterial populations. Researchers are exploring various packaging materials to deliver phages with broad host range, stability, and viability ensuring their effectiveness in safeguarding various food systems. The effectiveness of phage immobilization or encapsulation on active food packaging materials depends on various factors, including the characteristics of polymers, the choice of solvents, the type of phage, and its loading efficiency. Factors such as the orientation of phage immobilization on substrates, pH, temperature, exposure to carbohydrates and amino acids, exopolysaccharides, lipopolysaccharides, and metals can also influence phage activity. In this review, we comprehensively discuss the various active packaging systems utilizing bacteriophages as natural biocontrols and antimicrobial bioadditives to reduce the incidence of foodborne illness and enhance consumer confidence in the safety of food products.
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Affiliation(s)
- Kannan Badri Narayanan
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
| | - Rakesh Bhaskar
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea; Research Institute of Cell Culture, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, South Korea.
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10
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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024; 22:543-555. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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11
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Wang S, Sun S, Wang Q, Chen H, Guo Y, Cai M, Yin Y, Ma S, Wang H. PathoTracker: an online analytical metagenomic platform for Klebsiella pneumoniae feature identification and outbreak alerting. Commun Biol 2024; 7:1038. [PMID: 39179660 PMCID: PMC11344050 DOI: 10.1038/s42003-024-06720-6] [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: 01/04/2024] [Accepted: 08/12/2024] [Indexed: 08/26/2024] Open
Abstract
Clinical metagenomics (CMg) Nanopore sequencing can facilitate infectious disease diagnosis. In China, sub-lineages ST11-KL64 and ST11-KL47 Carbapenem-resistant Klebsiella pneumoniae (CRKP) are widely prevalent. We propose PathoTracker, a specially compiled database and arranged method for strain feature identification in CMg samples and CRKP traceability. A database targeting high-prevalence horizontal gene transfer in CRKP strains and a ST11-only database for distinguishing two sub-lineages in China were created. To make the database user-friendly, facilitate immediate downstream strain feature identification from raw Nanopore metagenomic data, and avoid the need for phylogenetic analysis from scratch, we developed data analysis methods. The methods included pre-performed phylogenetic analysis, gene-isolate-cluster index and multilevel pan-genome database and reduced storage space by 10-fold and random-access memory by 52-fold compared with normal methods. PathoTracker can provide accurate and fast strain-level analysis for CMg data after 1 h Nanopore sequencing, allowing early warning of outbreaks. A user-friendly page ( http://PathoTracker.pku.edu.cn/ ) was developed to facilitate online analysis, including strain-level feature, species identifications and phylogenetic analyses. PathoTracker proposed in this study will aid in the downstream analysis of CMg.
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Affiliation(s)
- Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Shuai Ma
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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12
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Zhou H, Lu Z, Liu X, Bie X, Cui X, Wang Z, Sun X, Yang J. Characterization and transmission of plasmid-mediated multidrug resistance in foodborne Vibrio parahaemolyticus. Front Microbiol 2024; 15:1437660. [PMID: 39144225 PMCID: PMC11322368 DOI: 10.3389/fmicb.2024.1437660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/19/2024] [Indexed: 08/16/2024] Open
Abstract
Objectives The purpose of this study was to determine the structural features and transferability of the multidrug-resistance (MDR) plasmid, and resistance phenotypes for the tested antimicrobials in foodborne Vibrio parahaemolyticus. Methods Plasmids were isolated from a V. parahaemolyticus strain of seafood origin, then sequenced using the Illumina NovaSeq 6000 and PacBio Sequel II sequencing platforms to obtain the complete genome data. Characterization of the MDR plasmid pVP52-1, including determination of antimicrobial resistance genes (ARGs), plasmid incompatibility groups, and transferability, was carried out. Results V. parahaemolyticus strain NJIFDCVp52 contained two circular chromosomes and two circular plasmids (pVP52-1 and pVP52-2). Plasmid typing indicated that pVP52-1 belonged to the incompatibility group IncA/C2 and the sequence type pST3. pVP52-1 carried 12 different ARGs, an IS110-composite transposon consisting of aac(6')-Ib-cr, qnrVC1, aac(6')-Ib, dfrA14, and the IS26-mphA-IS6100 unit flanked by inverted sequences of IS5075 and IS4321. pVP52-2 carried no ARGs. A plasmid elimination assay showed that only pVP52-1 and its ARGs were lost, the loss of resistance to several antimicrobials, causing a change from the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-trimethoprim/sulfamethoxazole resistance pattern to the ampicillin resistance pattern. In accordance, a conjugation transfer assay showed that only pVP52-1 and its ARGs were horizontally transferred, leading to increased antimicrobial resistance in Escherichia coli strain EC600, causing a change from the ampicillin-nalidixic acid resistance pattern to the ampicillin-ampicillin/sulbactam-cefazolin-cefoxitin-ceftazidime-cefotaxime-imipenem-nalidixic acid-chloramphenicol-tetracycline-trimethoprim/sulfamethoxazole-azithromycin resistance pattern. Further transferability experiments revealed that pVP52-1 could be transferred to other enterobacterial strains of E. coli and Salmonella. Discussion This study emphasizes the urgent need for continued surveillance of resistance plasmids and changes in antimicrobial resistance profiles among the V. parahaemolyticus population.
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Affiliation(s)
- Haibo Zhou
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinmei Liu
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Xiaomei Bie
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xinping Cui
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zuwei Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaojie Sun
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
| | - Jun Yang
- Key Laboratory of Detection and Traceability Technology of Foodborne Pathogenic Bacteria for Jiangsu Province Market Regulation, Nanjing Institute for Food and Drug Control, Nanjing, China
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13
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Fu P, Li Y, Qin J, Xie L, Yang C, Wang C. Molecular epidemiology and genomic features of Bordetella parapertussis in Shanghai, China, 2017-2022. Front Microbiol 2024; 15:1428766. [PMID: 39044958 PMCID: PMC11263204 DOI: 10.3389/fmicb.2024.1428766] [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: 05/07/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024] Open
Abstract
Background Pertussis is a highly contagious respiratory illness mainly caused by Bordetella pertussis (BP). Bordetella parapertussis (BPP) can induce symptoms compatible with pertussis, but has been underdiagnosed and underreported. The current pertussis vaccines offer low protection against BPP. Herein, we aim to reveal the epidemiology and genomic evolution of BPP in Shanghai, China. Methods Children diagnosed with BPP infection from January 2017 to December 2022 in Shanghai, China were enrolled. We performed antimicrobial susceptibility testing (AST), multiple locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing (WGS) analysis. A total of 260 international BPP genomes were chosen for comparison to investigate the genomic diversity and phylogenetic characteristics of Chinese strains within a global context. Results Sixty patients were diagnosed with BPP infection by culture, with the positive ratio of 3.5‰ (60/17337) for BPP in nasopharyngeal swap samples. The average age of patients was 4.5 ± 0.3 years. BPPs contained four MLVA types including MT6 (65.0%), MT4 (26.7%), untype-1 (6.7%) and MT5 (1.7%), and none of strains showed resistance to macrolides. All strains carried virulence genotype of ptxP37/ptxA13/ptxB3/ptxC3/ptxD3/ptxE3/fim2-2/fim3-10. MT4 and MT5 strains carried prn54, whereas MT6 and untype-1 BPPs expressed prn101. We identified two outbreaks after 2020 caused by MT4 and MT6 strains, each corresponding to distinct WGS-based phylogenetic lineages. The MT4-lineage is estimated to have originated around 1991 and has since spread globally, being introduced to China between 2005 and 2010. In contrast, the MT6-lineage was exclusively identified in China and is inferred to have originated around 2002. Conclusion We revealed the genomic diversity of BPPs circulating in Shanghai, China, and reported the outbreaks of MT6 and MT4 BPPs after 2020. This is the first report on the emergence and regional outbreak of MT6 BPPs in the world, indicating that continuous surveillance on BPPs are thus required.
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Affiliation(s)
- Pan Fu
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Nosocomial Infection Control Department, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yijia Li
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jie Qin
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Li Xie
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Chao Yang
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Chuanqing Wang
- Laboratory of Microbiology, Department of Clinical Laboratory, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
- Nosocomial Infection Control Department, Children’s Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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14
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Olymon K, Yadav M, Teronpi V, Kumar A. Unravelling the genomic secrets of bacterial fish pathogens: a roadmap to aquaculture sustainability. Mol Biol Rep 2024; 51:364. [PMID: 38407655 DOI: 10.1007/s11033-024-09331-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
In the field of aquaculture, bacterial pathogens pose significant challenges to fish health and production. Advancements in genomic technologies have revolutionized our understanding of bacterial fish pathogens and their interactions with their host species. This review explores the application of genomic approaches in the identification, classification, and characterization of bacterial fish pathogens. Through an extensive analysis of the literature, we have compiled valuable data on 79 bacterial fish pathogens spanning 13 different phyla, encompassing their whole genome sequences. By leveraging high-throughput sequencing techniques, researchers have gained valuable insights into the genomic makeup of these pathogens, enabling a deeper understanding of their virulence factors and mechanisms of host interaction. Furthermore, genomic approaches have facilitated the discovery of potential vaccine and drug targets, opening up new avenues for the development of effective interventions against fish pathogens. Additionally, the utilization of genomics in fish disease resistance and control in aquaculture has shown promising results, enabling the identification of genetic markers associated with disease resistance traits. This review highlights the significant contributions of genomics to the field of fish pathogen research and underscores its potential for improving disease management strategies and enhancing the sustainability of aquaculture practices.
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Affiliation(s)
- Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Valentina Teronpi
- Department, of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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15
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Ren F, Li Y, Zhang M, Chen W, Chen W, Chen H. Photocatalytic inactivation mechanism of nano-BiPO 4 against Vibrio parahaemolyticus and its application in abalone. Food Res Int 2024; 177:113806. [PMID: 38225110 DOI: 10.1016/j.foodres.2023.113806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/26/2023] [Accepted: 12/02/2023] [Indexed: 01/17/2024]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus) is the main pathogenic bacteria in seafood that can cause serious food-borne illness. The annual incidence of V. parahaemolyticus infection in the United States exceeds 45,000 cases, indicating there are potential shortcomings in seafood sterilization techniques. Meanwhile, the ongoing emergence of antibiotic-resistant strains highlights the urgent need for novel bacteriostatic strategies to eliminate V. parahaemolyticus. Nano-BiPO4 is a semiconductor with high H2O2 production efficiency and has potential for photocatalytic bacterial inactivation. But the effectiveness and mechanism of BiPO4 photocatalytic inactivation of V. parahaemolyticus has not been reported. In this study, nano-BiPO4 synthesized in pure water (P1) was found to exhibit optimal H2O2 production efficiency (1203 μmol h-1g-1) and antibacterial activity (in 0.8 g/L). Under UV light irradiation, P1 induced alterations in bacterial cell morphology, elevation in intracellular levels of ROS, H2O2, O2-, GSSG and MDA, and reduction in GSH level. Meanwhile, metabolomic analysis revealed that P1 stimulates the arginine biosynthesis, TCA cycle and alanine, aspartate and glutamate metabolism. These abnormal changes in the oxidative stress indicators and metabolic pathways proved that the bacterial damage was related to the H2O2 produced by nano-BiPO4 photocatalysis. Moreover, sliced abalone and hemolysis assay were used to demonstrate the applicability and biosafety of P1. This study provides theoretical support for exploring nano-BiPO4 as a bacterial inhibitor against V. parahaemolyticus.
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Affiliation(s)
- Fei Ren
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - You Li
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Ming Zhang
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China.
| | - Wenxue Chen
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China.
| | - Weijun Chen
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
| | - Haiming Chen
- Hainan University-HSF/LWL Collaborative Innovation Laboratory, College of Food Sciences & Engineering, Hainan University, 58 People Road, Haikou 570228, PR China
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16
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EFSA Panel on Biological Hazards (BIOHAZ), Koutsoumanis K, Allende A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Herman L, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Fox E, Gosling R(B, Gil BM, Møretrø T, Stessl B, da Silva Felício MT, Messens W, Simon AC, Alvarez‐Ordóñez A. Persistence of microbiological hazards in food and feed production and processing environments. EFSA J 2024; 22:e8521. [PMID: 38250499 PMCID: PMC10797485 DOI: 10.2903/j.efsa.2024.8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
Listeria monocytogenes (in the meat, fish and seafood, dairy and fruit and vegetable sectors), Salmonella enterica (in the feed, meat, egg and low moisture food sectors) and Cronobacter sakazakii (in the low moisture food sector) were identified as the bacterial food safety hazards most relevant to public health that are associated with persistence in the food and feed processing environment (FFPE). There is a wide range of subtypes of these hazards involved in persistence in the FFPE. While some specific subtypes are more commonly reported as persistent, it is currently not possible to identify universal markers (i.e. genetic determinants) for this trait. Common risk factors for persistence in the FFPE are inadequate zoning and hygiene barriers; lack of hygienic design of equipment and machines; and inadequate cleaning and disinfection. A well-designed environmental sampling and testing programme is the most effective strategy to identify contamination sources and detect potentially persistent hazards. The establishment of hygienic barriers and measures within the food safety management system, during implementation of hazard analysis and critical control points, is key to prevent and/or control bacterial persistence in the FFPE. Once persistence is suspected in a plant, a 'seek-and-destroy' approach is frequently recommended, including intensified monitoring, the introduction of control measures and the continuation of the intensified monitoring. Successful actions triggered by persistence of L. monocytogenes are described, as well as interventions with direct bactericidal activity. These interventions could be efficient if properly validated, correctly applied and verified under industrial conditions. Perspectives are provided for performing a risk assessment for relevant combinations of hazard and food sector to assess the relative public health risk that can be associated with persistence, based on bottom-up and top-down approaches. Knowledge gaps related to bacterial food safety hazards associated with persistence in the FFPE and priorities for future research are provided.
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17
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Peng Y, Xue P, Wang R, Shang H, Yao B, Zheng Z, Yan C, Chen W, Xu J. Engineering of an adaptive tandem CRISPR/Cas12a molecular amplifier permits robust analysis of Vibrio parahaemolyticus. Talanta 2024; 266:125061. [PMID: 37567119 DOI: 10.1016/j.talanta.2023.125061] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/31/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Seeking new molecular diagnostic method for pathogenic bacteria detection is of utmost importance for ensuring food safety and protecting human health. Herein, we have engineered an adaptive tandem CRISPR/Cas12a molecular amplifier specifically designed for robust analysis of vibrio parahaemolyticus (V. parahaemolyticus), one of the most harmful pathogens. Our strategy involves the integration of three crucial processes: recombinase polymerase amplification (RPA) for copy number amplification, terminal deoxynucleotidyl transferase (TdT) for template-free strand elongation, and CRISPR/Cas12a-mediated trans-cleavage of a reporter molecule. By combining these processes, the target genomic DNA extracted from V. parahaemolyticus is able to activate many CRISPR/Cas12a units (CRISPR/Cas12an) simultaneously, resulting in a greatly amplified target signal to indicate the presence and concentration of V. parahaemolyticus. This unique model offers more advantages compared to traditional amplification models that use one RPA amplicon to activate one CRISPR/Cas12a unit. Under optimized conditions, our method enables the detection of target V. parahaemolyticus within a linear range of 1 × 102-1 × 107 CFU/mL, with an impressive limit of detection as low as 12.4 CFU/mL. It is conceivable that the adaptive tandem CRISPR/Cas12a molecular amplifier could be adapted as routine diagnostic kits in future for in-field detection of pathogens.
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Affiliation(s)
- Yubo Peng
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Pengpeng Xue
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Renjing Wang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Huijie Shang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China
| | - Bangben Yao
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China; Anhui Province Institute of Product Quality Supervision & Inspection, Hefei, 230051, China
| | - Zhi Zheng
- Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China
| | - Chao Yan
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China.
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, PR China; Key Laboratory for Agricultural Products Processing of Anhui Province, Hefei University of Technology, Hefei, 230009, PR China.
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18
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Fang GY, Liu XQ, Mu XJ, Huang BW, Jiang YJ. Distinct increase in antimicrobial resistance genes among Vibrio parahaemolyticus in recent decades worldwide. CHEMOSPHERE 2023; 340:139905. [PMID: 37611759 DOI: 10.1016/j.chemosphere.2023.139905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/18/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Vibrio parahaemolyticus is a common pathogen, and has emerged with multiple antimicrobial resistance (AMR). However, few studies have conducted large-scale investigations of AMR and virulence trends of V. parahaemolyticus worldwide. This study longitudinally monitored antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) trends of 1540 V. parahaemolyticus isolates isolated from 1951 to 2021. The number of ARGs in V. parahaemolyticus isolates distinctly increased over the years (P = 5.9e-10), while the number of VFGs decreased significantly (P < 2.2e-16). However, the number of VFGs of isolates isolated from humans has not changed significantly over the years (R = 0.013, P = 0.74), suggesting that the pathogenic risk to humans has not been reduced. Besides, mobile genetic elements are important contributors to ARGs in V. parahaemolyticus (R = 0.34, P < 2.2e-16), but have no promoting effect on VFGs (P = 0.50). The structural equation model illustrated that the human development index promoted the consumption of antibiotics, thereby indirectly promoting an increase in the AMR of the V. parahaemolyticus isolates. Finally, the random forest was performed to predict the ARG and VFG risks of global terrestrial V. parahaemolyticus isolates, and successfully map these threats with over 80% accuracy. This study aimed to evaluate the global risks posed by AMR and virulence, which helps to develop methods specifically targeting V. parahaemolyticus to mitigate these threats.
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Affiliation(s)
- Guan-Yu Fang
- College of Food and Health, Zhejiang A&F University, Hangzhou, 311300, PR China.
| | - Xing-Quan Liu
- College of Food and Health, Zhejiang A&F University, Hangzhou, 311300, PR China
| | - Xiao-Jing Mu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China; Suzhou Precision Biotechco., Ltd, Suzhou, 215000, PR China
| | - Bing-Wen Huang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China
| | - Yu-Jian Jiang
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, PR China
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19
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Ji JS, Xia Y, Liu L, Zhou W, Chen R, Dong G, Hu Q, Jiang J, Kan H, Li T, Li Y, Liu Q, Liu Y, Long Y, Lv Y, Ma J, Ma Y, Pelin K, Shi X, Tong S, Xie Y, Xu L, Yuan C, Zeng H, Zhao B, Zheng G, Liang W, Chan M, Huang C. China's public health initiatives for climate change adaptation. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 40:100965. [PMID: 38116500 PMCID: PMC10730322 DOI: 10.1016/j.lanwpc.2023.100965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/01/2023] [Accepted: 11/01/2023] [Indexed: 12/21/2023]
Abstract
China's health gains over the past decades face potential reversals if climate change adaptation is not prioritized. China's temperature rise surpasses the global average due to urban heat islands and ecological changes, and demands urgent actions to safeguard public health. Effective adaptation need to consider China's urbanization trends, underlying non-communicable diseases, an aging population, and future pandemic threats. Climate change adaptation initiatives and strategies include urban green space, healthy indoor environments, spatial planning for cities, advance location-specific early warning systems for extreme weather events, and a holistic approach for linking carbon neutrality to health co-benefits. Innovation and technology uptake is a crucial opportunity. China's successful climate adaptation can foster international collaboration regionally and beyond.
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Affiliation(s)
- John S. Ji
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Yanjie Xia
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Linxin Liu
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Weiju Zhou
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Renjie Chen
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National School of Public Health, Health Commission Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Guanghui Dong
- Department of Occupational and Environmental Health, School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Qinghua Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Jingkun Jiang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Haidong Kan
- School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National School of Public Health, Health Commission Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Tiantian Li
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Li
- Public Meteorological Service Centre, China Meteorological Administration, Beijing, China
| | - Qiyong Liu
- National Institute of Infectious Diseases at China, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanxiang Liu
- Public Meteorological Service Centre, China Meteorological Administration, Beijing, China
| | - Ying Long
- School of Architecture, Tsinghua University, Beijing, China
| | - Yuebin Lv
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jian Ma
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Yue Ma
- School of Architecture, Tsinghua University, Beijing, China
| | - Kinay Pelin
- School of Climate Change and Adaptation, University of Prince Edward Island, Prince Edward Island, Canada
| | - Xiaoming Shi
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shilu Tong
- National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Queensland University of Technology, Brisbane, Australia
| | - Yang Xie
- School of Economics and Management, Beihang University, Beijing, China
| | - Lei Xu
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Changzheng Yuan
- School of Public Health, Zhejiang University, Hangzhou, China
| | - Huatang Zeng
- Shenzhen Health Development Research and Data Management Center, Shenzhen, China
| | - Bin Zhao
- Department of Building Science, School of Architecture, Tsinghua University, Beijing, China
| | - Guangjie Zheng
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Wannian Liang
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Margaret Chan
- Vanke School of Public Health, Tsinghua University, Beijing, China
| | - Cunrui Huang
- Vanke School of Public Health, Tsinghua University, Beijing, China
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20
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She Y, Jiang Y, Luo M, Duan X, Xie L, Yang C, Xu L, Fu Y, Lv Z, Cai R, Li Y, Qiu Y, Hu L, Shi X, Wang L, Wu S, Chen Q, Jiang M, Hu Q. Emergence of chromosomally located bla CTX-M-14b and qnrS1 in Salmonella enterica serotype Kentucky ST198 in China. Int J Antimicrob Agents 2023; 62:106896. [PMID: 37343807 DOI: 10.1016/j.ijantimicag.2023.106896] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/23/2023]
Abstract
Highly fluoroquinolone-resistant Salmonella enterica serotype Kentucky has become widespread in recent years, largely associated with the spread of sequence type 198 (ST198), which often leads to multidrug resistance. Research on the genomic epidemiology of Salmonella Kentucky in China is currently uncommon. In this study, we analysed the genomic epidemiology and antimicrobial resistance characteristics of Salmonella Kentucky ST198 collected from foodborne disease surveillance in Shenzhen, China, during 2010-2021, using whole-genome sequencing and antibiotic susceptibility testing. In addition, 158 global Salmonella Kentucky ST198 genomes were included for comparison. Among 8559 Salmonella isolates, 43 Salmonella Kentucky ST198 isolates were detected during 2010-2021. The global Salmonella Kentucky ST198 evolutionary tree was divided into five clades, with Shenzhen isolates distributed in clades 198.1, 198.2-1 and 198.2-2, mainly clustered with Chinese strains. Strains in clade 198.2 dominated in Shenzhen and all of them showed multidrug resistance. Nine strains showed high resistance to ceftriaxone, which was associated with blaCTX-M-14b in clade 198.2-1, which was demonstrated to be located on the chromosome. Fifteen strains showed high resistance to ciprofloxacin, which was associated with carriage of qnrS1 in clade 198.2-2. qnrS1 was first located on an IncHI2 plasmid and then transferred into the chromosome. Here we report the genomic and antimicrobial resistance characterisation of Salmonella Kentucky ST198 in Shenzhen. Of particular concern, we identified for the first time a clade 198.2-1 isolate carrying blaCTX-M-14b as well as chromosomally located qnrS1 in clade 198.2-2 of Salmonella Kentucky ST198 in China, highlighting the necessity of surveillance of clade 198.2.
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Affiliation(s)
- Yiying She
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Miaomiao Luo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Xiangke Duan
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Xie
- University of South China, Hengyang, China
| | - Chao Yang
- Institute Pasteur of Shanghai Chinese Academy of Sciences, Shanghai, China
| | - Liangcai Xu
- Shenzhen Futian District Center for Disease Control and Prevention, Shenzhen, China
| | - Yulin Fu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ziquan Lv
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lulu Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuang Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China.
| | - Qinghua Hu
- School of Public Health, Shanxi Medical University, Taiyuan, China; Shenzhen Center for Disease Control and Prevention, Shenzhen, China; Shenzhen Research Center for Communicable Disease Control and Prevention, Chinese Academy of Medical Sciences, Shenzhen, China.
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21
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Gu R, Duan Y, Li Y, Luo Z. Fiber-Optic-Based Biosensor as an Innovative Technology for Point-of-Care Testing Detection of Foodborne Pathogenic Bacteria To Defend Food and Agricultural Product Safety. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37432923 DOI: 10.1021/acs.jafc.3c02067] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Food safety is a concerning issue globally. Foodborne-pathogenic-bacteria-derived foodborne disease outbreaks have increased the threat to human health. The accurate and rapid detection of foodborne bacteria is of great significance for food safety. A fiber-optic-based biosensor has emerged as a powerful technique for the point-of-care testing of foodborne bacteria in food and agricultural products. This Perspective discusses the opportunities and challenges of fiber-optic-based biosensors for foodborne bacteria detection. The corresponding solution strategies to promote the application of this innovative technology in food and agricultural product detection for food safety and human health are also discussed and proposed.
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Affiliation(s)
- Ronghui Gu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Guiyang 550025, Guizhou, People's Republic of China
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, Guizhou, People's Republic of China
- National & Local Joint Engineering Research Center for the Exploitation of Homology Resources of Medicine and Food, Guizhou University, Guiyang 550025, Guizhou, People's Republic of China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, Sichuan, People's Republic of China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
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22
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Zhao B, Lees JA, Wu H, Yang C, Falush D. Genealogical inference and more flexible sequence clustering using iterative-PopPUNK. Genome Res 2023; 33:988-998. [PMID: 37253539 PMCID: PMC10519404 DOI: 10.1101/gr.277395.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
Bacterial genome data are accumulating at an unprecedented speed due to the routine use of sequencing in clinical diagnoses, public health surveillance, and population genetics studies. Genealogical reconstruction is fundamental to many of these uses; however, inferring genealogy from large-scale genome data sets quickly, accurately, and flexibly is still a challenge. Here, we extend an alignment- and annotation-free method, PopPUNK, to increase its flexibility and interpretability across data sets. Our method, iterative-PopPUNK, rapidly produces multiple consistent cluster assignments across a range of sequence identities. By constructing a partially resolved genealogical tree with respect to these clusters, users can select a resolution most appropriate for their needs. We showed the accuracy of clusters at all levels of similarity and genealogical inference of iterative-PopPUNK based on simulated data and obtained phylogenetically concordant results in real data sets from seven bacterial species. Using two example sets of Escherichia/Shigella and Vibrio parahaemolyticus genomes, we show that iterative-PopPUNK can achieve cluster resolutions ranging from phylogroup down to sequence typing (ST). The iterative-PopPUNK algorithm is implemented in the "PopPUNK_iterate" program, available as part of the PopPUNK package.
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Affiliation(s)
- Bin Zhao
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton CB10 1SD, United Kingdom
| | - Hongjin Wu
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China;
| | - Daniel Falush
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China;
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23
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Hassan M, Mohd Ali MR, Zamri HF, Nor Amdan NA, Azmai MNA, Maniam S, Mohamed Alipiah N, Hashim R. Distribution, Prevalence, and Antibiotic Susceptibility Profiles of Infectious Noncholera Vibrio Species in Malaysia. J Trop Med 2023; 2023:2716789. [PMID: 37274080 PMCID: PMC10238136 DOI: 10.1155/2023/2716789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/05/2023] [Accepted: 05/06/2023] [Indexed: 06/06/2023] Open
Abstract
Background The noncholera Vibrio spp. which cause vibriosis are abundantly found in our water ecosystem. These bacteria could negatively affect both humans and animals. To date, there is a paucity of information available on the existence and pathogenicity of this particular noncholera Vibrio spp. in Malaysia in comparison to their counterpart, Vibrio cholera. Methods In this study, we extracted retrospective data from Malaysian surveillance database. Analysis was carried out using WHONET software focusing noncholera Vibrio spp. including Vibrio parahaemolyticus, Vibrio vulnificus, Vibrio fluvialis, Vibrio alginolyticus, Vibrio hollisae (Grimontia hollisae), Vibrio mimicus, Vibrio metschnikovii, and Vibrio furnissii. Results Here, we report the first distribution and prevalence of these species isolated in Malaysia together with the antibiotic sensitivity profile based on the species. We found that V. parahaemolyticus is the predominant species isolated in Malaysia. Noticeably, across the study period, V. fluvialis is becoming more prevalent, as compared to V. parahaemolyticus. In addition, this study also reports the first isolation of pathogenic V. furnissii from stool in Malaysia. Conclusion These data represent an important step toward understanding the potential emergence of noncholera Vibrio spp. outbreaks.
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Affiliation(s)
- Murnihayati Hassan
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Mohammad Ridhuan Mohd Ali
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Hana Farizah Zamri
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Nur Asyura Nor Amdan
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Mohammad Noor Amal Azmai
- Aquatic Animal Health & Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Saraswathiy Maniam
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
| | - Norfarrah Mohamed Alipiah
- Aquatic Animal Health & Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Rohaidah Hashim
- Bacteriology Unit, Infectious Disease Research Center (IDRC), Institute for Medical Research (IMR), National Institutes of Health (NIH) Complex, Ministry of Health Malaysia, Setia Alam, 40170 Shah Alam, Kuala Lumpur, Selangor, Malaysia
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24
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Searching pathogenic bacteria in the rare biosphere of the ocean. Curr Opin Biotechnol 2023; 80:102894. [PMID: 36680847 DOI: 10.1016/j.copbio.2023.102894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/21/2023]
Abstract
Harmful marine bacteria, such as Vibrio or Aeromonas species, typically exist at low abundance in ocean environments but represent a reservoir from which epidemics can arise. Particularly, Vibrio strains and their associated infections are on the rise globally due to increasing sea surface temperature representing an emergent threat for human and animal health also being responsible for large economic losses in the aquaculture industry worldwide. New technological approaches are needed to improve strategies targeting these pathogens. This review discusses new approaches based on improved sampling strategies and novel analytical methods offering increased accuracy, high throughput, and informativeness to study and detect microbial pathogens in the marine environment. Detecting and characterizing ultra-low-abundance pathogenic strains can serve as a critical tool in risk management and outbreak prevention of diseases caused by emerging marine pathogens.
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25
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Transcriptome Analysis Reveals the Effect of Low NaCl Concentration on Osmotic Stress and Type III Secretion System in Vibrio parahaemolyticus. Int J Mol Sci 2023; 24:ijms24032621. [PMID: 36768942 PMCID: PMC9916905 DOI: 10.3390/ijms24032621] [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: 11/24/2022] [Revised: 01/02/2023] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Vibrio parahaemolyticus is a moderately halophilic foodborne pathogen that is mainly distributed in marine and freshwater environments. The transition of V. parahaemolyticus between aquatic ecosystems and hosts is essential for infection. Both freshwater and host environments have low salinity. In this study, we sought to further investigate the effects of low salinity (0.5% NaCl) on the fitness and virulence of V. parahaemolyticus. We found that V. parahaemolyticus could survive in Luria-Bertani (LB) and M9 mediums with different NaCl concentrations, except for the M9 medium containing 9% NaCl. Our results further showed that V. parahaemolyticus cultured in M9 medium with 0.5% NaCl had a higher cell density than that cultured at other NaCl concentrations when it entered the stationary phase. Therefore, we compared the transcriptomes of V. parahaemolyticus wild type (WT) cultured in an M9 medium with 0.5% and 3% NaCl at the stationary phase using RNA-seq. A total of 658 genes were significantly differentially expressed in the M9 medium with 0.5% NaCl, including regulators, osmotic adaptive responses (compatible solute synthesis systems, transporters, and outer membrane proteins), and virulence factors (T3SS1 and T6SS1). Furthermore, a low salinity concentration in the M9 medium induced the expression of T3SS1 to mediate the cytotoxicity of V. parahaemolyticus to HeLa cells. Similarly, low salinity could also induce the secretion of the T3SS2 translocon protein VPA1361. These factors may result in the high pathogenicity of V. parahaemolyticus in low-salinity environments. Taken together, these results suggest that low salinity (0.5% NaCl) could affect gene expression to mediate fitness and virulence, which may contribute to the transition of V. parahaemolyticus between aquatic ecosystems and the host.
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26
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Fu P, Zhou J, Yang C, Nijiati Y, Zhou L, Yan G, Lu G, Zhai X, Wang C. Molecular Evolution and Increasing Macrolide Resistance of Bordetella pertussis, Shanghai, China, 2016-2022. Emerg Infect Dis 2023; 30:29-38. [PMID: 38146984 PMCID: PMC10756392 DOI: 10.3201/eid3001.221588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023] Open
Abstract
Resurgence and spread of macrolide-resistant Bordetella pertussis (MRBP) threaten global public health. We collected 283 B. pertussis isolates during 2016-2022 in Shanghai, China, and conducted 23S rRNA gene A2047G mutation detection, multilocus variable-number tandem-repeat analysis, and virulence genotyping analysis. We performed whole-genome sequencing on representative strains. We detected pertussis primarily in infants (0-1 years of age) before 2020 and older children (>5-10 years of age) after 2020. The major genotypes were ptxP1/prn1/fhaB3/ptxA1/ptxC1/fim2-1/fim3-1 (48.7%) and ptxP3/prn2/fhaB1/ptxA1/ptxC2/fim2-1/fim3-1 (47.7%). MRBP increased remarkably from 2016 (36.4%) to 2022 (97.2%). All MRBPs before 2020 harbored ptxP1, and 51.4% belonged to multilocus variable-number tandem-repeat analysis type (MT) 195, whereas ptxP3-MRBP increased from 0% before 2020 to 66.7% after 2020, and all belonged to MT28. MT28 ptxP3-MRBP emerged only after 2020 and replaced the resident MT195 ptxP1-MRBP, revealing that 2020 was a watershed in the transformation of MRBP.
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Affiliation(s)
| | | | - Chao Yang
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Yaxier Nijiati
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Lijun Zhou
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Gangfen Yan
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Guoping Lu
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Xiaowen Zhai
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
| | - Chuanqing Wang
- National Children's Medical Center, Shanghai, China (P. Fu, J. Zhou, Y. Nijiati, L. Zhou, G. Yan, G. Lu, X. Zhai, C. Wang)
- Chinese Academy of Sciences, Shanghai (C. Yang)
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27
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Luo M, She Y, Jiang Y, Xie L, Yang C, Qiu Y, Cai R, Li Y, Xu L, Hu L, Wang L, Wu S, Chen Q, Shi X, Jiang M, Hu Q. Population dynamics and antimicrobial resistance of Salmonella Derby ST40 from Shenzhen, China. Front Microbiol 2022; 13:1065672. [PMID: 36605513 PMCID: PMC9808032 DOI: 10.3389/fmicb.2022.1065672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
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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Affiliation(s)
- Miaomiao Luo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yiying She
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Xie
- School of Public Health, University of South China, Hengyang, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Liangcai Xu
- Shenzhen Futian District Center for Disease Control and Prevention, Shenzhen, China
| | - Lulu Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuang Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China,Min Jiang,
| | - Qinghua Hu
- School of Public Health, Shanxi Medical University, Taiyuan, China,Shenzhen Center for Disease Control and Prevention, Shenzhen, China,*Correspondence: Qinghua Hu,
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28
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Abstract
High-resolution and efficient typing for the bacterial pathogen is essential for tracking the sources, detecting or diagnosing variants, and conducting a risk assessment. However, a systematic in-field investigation of Salmonella along the food chain has not been documented. This study assessed 12 typing methods, such as antimicrobial-resistance (AMR) gene profile typing, Core Genome Multilocus Sequence Typing (cgMLST), and CRISPR multi-virulence locus sequence typing (CRISPR-MVLST), to evaluate their effectiveness for use in routine monitoring of foodborne Salmonella transmission along the poultry production chain. During 2015-16, a total of 1,064 samples were collected from poultry production chain, starting from breeding farms and slaughterhouses to the markets of Zhejiang province in China. A total of 61 consecutive unique Salmonella isolates recovered from these samples were selected for genome sequencing and further comparative typing analysis. Traditional typing methods, including serotyping, AMR phenotype-based typing, as well as modern genotyping approaches, were evaluated and compared by their discrimination index (DI). The results showed that the serotyping method identified nine serovars. The gold standard cgMLST method indicated only 18 different types (DI = 0.8541), while the CRISPR-MVLST method detected 30 types (DI = 0.9628), with a higher DI than all examined medium-resolution WGS-based genotyping methods. We demonstrate that the CRISPR-MVLST might be used as a tool with high discriminatory power, comparable ease of use, ability of tracking the source of Salmonella strains along the food chain and indication of genetic features especially virulence genes. The available methods with different purposes and laboratory expertise were also illustrated to assist in rational implementation. IMPORTANCE 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. Using 1,064 samples along a poultry production chain with a considerable level of Salmonella contamination, we collected representative isolates for genome sequencing and comparative analysis by using 12 typing techniques, particularly with whole-genome sequence (WGS) based methods and a recently invented CRISPR multi-virulence locus sequence typing (CRISPR-MVLST) method. CRISPR-MVLST is identified as a tool with higher discriminatory power compared with medium-resolution WGS-based typing methods, comparable ease of use and proven ability of tracking Salmonella isolates. Besides, we also offer recommendations for rational choice of subtyping methods to assist in better implementation schemes.
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