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Kabwe M, Dashper S, Tucci J. The Microbiome in Pancreatic Cancer-Implications for Diagnosis and Precision Bacteriophage Therapy for This Low Survival Disease. Front Cell Infect Microbiol 2022; 12:871293. [PMID: 35663462 PMCID: PMC9160434 DOI: 10.3389/fcimb.2022.871293] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
While the mortality rates for many cancers have decreased due to improved detection and treatments, that of pancreatic cancer remains stubbornly high. The microbiome is an important factor in the progression of many cancers. Greater understanding of the microbiome in pancreatic cancer patients, as well as its manipulation, may assist in diagnosis and treatment of this disease. In this report we reviewed studies that compared microbiome changes in pancreatic cancer patients and non-cancer patients. We then identified which bacterial genera were most increased in relative abundance across the oral, pancreatic, duodenal, and faecal tissue microbiomes. In light of these findings, we discuss the potential for utilising these bacteria as diagnostic biomarkers, as well as their potential control using precision targeting with bacteriophages, in instances where a causal oncogenic link is made.
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Affiliation(s)
- Mwila Kabwe
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
| | - Stuart Dashper
- Melbourne Dental School, University of Melbourne, Melbourne, VIC, Australia
| | - Joseph Tucci
- Department of Rural Clinical Sciences, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Bendigo, VIC, Australia
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2
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Huang C, Feng C, Liu X, Zhao R, Wang Z, Xi H, Ou H, Han W, Guo Z, Gu J, Zhang L. The Bacteriophage vB_CbrM_HP1 Protects Crucian Carp Against Citrobacter braakii Infection. Front Vet Sci 2022; 9:888561. [PMID: 35601403 PMCID: PMC9120918 DOI: 10.3389/fvets.2022.888561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Citrobacter braakii is an opportunistic pathogen that induces aquatic infections in fish and turtles. In this study, a bacteriophage that infects C. braakii, named vB_CbrM_HP1, was isolated from sewage. This phage belongs to Myoviridae family, Ounavirinae subfamily, Mooglevirus genus. We also used the phage to treat crucian carp infection caused by C. braakii for the first time. vB_CbrM_HP1 was relatively stable at temperatures ranging from 4 to 60°C and pH values ranging from 3 to 11 but float slightly. When the multiplicities of infection (MOI) was 0.0001, the titer reached a maximum of 4.20 × 1010 PFU/ml. As revealed from the results of whole genomic sequence analysis, the total length of vB_CbrM_HP1 was 89335 bp, encoding 135 ORFs, 9 of which were <75% similar to the known sequences in NCBI. The phage vB_CbrM_HP1 showed a highly efficient bactericidal effect against C. braakii both in vitro and in vivo. In vitro, vB_CbrM_HP1 was capable of effectively killing bacteria (the colony count decreased by 4.7 log units at 5 h). In vivo, administration of vB_CbrM_HP1 (1 × 109 PFU) effectively protected crucian carp against fatal infection caused by C. braakii. Phage treatment reduced the levels of inflammatory factors. All these results demonstrated the potential of vB_CbrM_HP1 as an alternative treatment strategy for infections caused by C. braakii.
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Affiliation(s)
- Chunzheng Huang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Chao Feng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiao Liu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Rihong Zhao
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zijing Wang
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hengyu Xi
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongda Ou
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenyu Han
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zhimin Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Changchun, China
- *Correspondence: Zhimin Guo
| | - Jingmin Gu
- State Key Laboratory for Zoonotic Diseases, Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Jingmin Gu
| | - Lei Zhang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
- Lei Zhang
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Mizuno CM, Luong T, Cederstrom R, Krupovic M, Debarbieux L, Roach DR. Isolation and Characterization of Bacteriophages That Infect Citrobacter rodentium, a Model Pathogen for Intestinal Diseases. Viruses 2020; 12:E737. [PMID: 32650458 PMCID: PMC7412075 DOI: 10.3390/v12070737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/30/2020] [Accepted: 07/07/2020] [Indexed: 12/22/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a major pathogen for diarrheal diseases among children. Antibiotics, when used appropriately, are effective; however, their overuse and misuse have led to the rise of antibiotic resistance worldwide. Thus, there are renewed efforts into the development of phage therapy as an alternative antibacterial therapy. Because EPEC in vivo models have shortcomings, a surrogate is used to study the mouse pathogen Citrobacter rodentium in animal models. In this study, two new phages CrRp3 and CrRp10, which infect C. rodentium, were isolated and characterized. CrRp3 was found to be a new species within the genus Vectrevirus, and CrRp10 is a new strain within the species Escherichia virus Ime09, in the genus Tequatrovirus. Both phages appear to have independently evolved from E. coli phages, rather than other Citrobacter spp. phages. Neither phage strain carries known genes associated with bacterial virulence, antibiotic resistance, or lysogeny. CrRp3 is more potent, having a 24-fold faster adsorption rate and shorter lytic cycle when compared to the same properties of CrRp10. However, a lysis curve analysis revealed that CrRp10 prevented growth of C. rodentium for 18 h, whereas resistance developed against CrRp3 within 9 h. We also show that hypoxic (5% oxygen) conditions decreased CrRp3 ability to control bacterial densities in culture. In contrast, low oxygen conditions did not affect CrRp10 ability to replicate on C. rodentium. Together, CrRp10 is likely to be the better candidate for future phage therapy investigations.
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Affiliation(s)
- Carolina M. Mizuno
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Tiffany Luong
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
| | - Robert Cederstrom
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Laurent Debarbieux
- Department of Microbiology, Institut Pasteur, 75015 Paris, France; (C.M.M.); (M.K.); (L.D.)
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; (T.L.); (R.C.)
- Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
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Deepthi KG, Jayasudha R, Girish RN, Manikandan P, Ram R, Narendran V, Prabagaran SR. Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries. Exp Eye Res 2018; 174:1-12. [PMID: 29772229 DOI: 10.1016/j.exer.2018.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/18/2018] [Accepted: 05/10/2018] [Indexed: 10/16/2022]
Abstract
The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the predominant pathogens for early predisposition.
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Affiliation(s)
| | | | - Rameshan Nair Girish
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Palanisamy Manikandan
- Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu, India
| | - Rammohan Ram
- Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu, India
| | - Venkatapathy Narendran
- Aravind Eye Hospital and Postgraduate Institute of Ophthalmology, Coimbatore, Tamil Nadu, India
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Oliveira H, Pinto G, Oliveira A, Oliveira C, Faustino MA, Briers Y, Domingues L, Azeredo J. Characterization and genome sequencing of a Citrobacter freundii phage CfP1 harboring a lysin active against multidrug-resistant isolates. Appl Microbiol Biotechnol 2016; 100:10543-10553. [PMID: 27683211 DOI: 10.1007/s00253-016-7858-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/29/2016] [Accepted: 09/13/2016] [Indexed: 01/26/2023]
Abstract
Citrobacter spp., although frequently ignored, is emerging as an important nosocomial bacterium able to cause various superficial and systemic life-threatening infections. Considered to be hard-to-treat bacterium due to its pattern of high antibiotic resistance, it is important to develop effective measures for early and efficient therapy. In this study, the first myovirus (vB_CfrM_CfP1) lytic for Citrobacter freundii was microbiologically and genomically characterized. Its morphology, activity spectrum, burst size, and biophysical stability spectrum were determined. CfP1 specifically infects C. freundii, has broad host range (>85 %; 21 strains tested), a burst size of 45 PFU/cell, and is very stable under different temperatures (-20 to 50 °C) and pH (3 to 11) values. CfP1 demonstrated to be highly virulent against multidrug-resistant clinical isolates up to 12 antibiotics, including penicillins, cephalosporins, carbapenems, and fluroquinoles. Genomically, CfP1 has a dsDNA molecule with 180,219 bp with average GC content of 43.1 % and codes for 273 CDSs. The genome architecture is organized into function-specific gene clusters typical for tailed phages, sharing 46 to 94 % nucleotide identity to other Citrobacter phages. The lysin gene encoding a predicted D-Ala-D-Ala carboxypeptidase was also cloned and expressed in Escherichia coli and its activity evaluated in terms of pH, ionic strength, and temperature. The lysine optimum activity was reached at 20 mM HEPES, pH 7 at 37 °C, and was able to significantly reduce all C. freundii (>2 logs) as well as Citrobacter koseri (>4 logs) strains tested. Interestingly, the antimicrobial activity of this enzyme was performed without the need of pretreatment with outer membrane-destabilizing agents. These results indicate that CfP1 lysin is a good candidate to control problematic Citrobacter infections, for which current antibiotics are no longer effective.
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Affiliation(s)
- Hugo Oliveira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Graça Pinto
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ana Oliveira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carla Oliveira
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | | | - Yves Briers
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, Box 2462, 3001, Leuven, Belgium.,Department of Applied Biosciences, Ghent University, Valentin Vaerwijckweg 1, 9000, Ghent, Belgium
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Joana Azeredo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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Hamdi S, Rousseau GM, Labrie SJ, Kourda RS, Tremblay DM, Moineau S, Slama KB. Characterization of Five Podoviridae Phages Infecting Citrobacter freundii. Front Microbiol 2016; 7:1023. [PMID: 27446058 PMCID: PMC4925675 DOI: 10.3389/fmicb.2016.01023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Citrobacter freundii causes opportunistic infections in humans and animals, which are becoming difficult to treat due to increased antibiotic resistance. The aim of this study was to explore phages as potential antimicrobial agents against this opportunistic pathogen. We isolated and characterized five new virulent phages, SH1, SH2, SH3, SH4, and SH5 from sewage samples in Tunisia. Morphological and genomic analyses revealed that the five C. freundii phages belong to the Caudovirales order, Podoviridae family, and Autographivirinae subfamily. Their linear double-stranded DNA genomes range from 39,158 to 39,832 bp and are terminally redundant with direct repeats between 183 and 242 bp. The five genomes share the same organization as coliphage T7. Based on genomic comparisons and on the phylogeny of the DNA polymerases, we assigned the five phages to the T7virus genus but separated them into two different groups. Phages SH1 and SH2 are very similar to previously characterized phages phiYeO3-12 and phiSG-JL2, infecting, respectively, Yersinia enterocolitica and Salmonella enterica, as well as sharing more than 80% identity with most genes of coliphage T7. Phages SH3, SH4, and SH5 are very similar to phages K1F and Dev2, infecting, respectively, Escherichia coli and Cronobacter turicensis. Several structural proteins of phages SH1, SH3, and SH4 were detected by mass spectrometry. The five phages were also stable from pH 5 to 10. No genes coding for known virulence factors or integrases were found, suggesting that the five isolated phages could be good candidates for therapeutic applications to prevent or treat C. freundii infections. In addition, this study increases our knowledge about the evolutionary relationships within the T7virus genus.
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Affiliation(s)
- Sana Hamdi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Geneviève M Rousseau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Simon J Labrie
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Rim S Kourda
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
| | - Denise M Tremblay
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie, et de Bioinformatique and PROTEO, Faculté des Sciences et de Génie, Félix d'Hérelle Reference Center for Bacterial Viruses, and GREB, Faculté de Médecine Dentaire, Université Laval Québec City, QC, Canada
| | - Karim B Slama
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis-El ManarTunis, Tunisie; Département de Biotechnologie, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El-ManarTunis, Tunisie
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7
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Zhao X, Huang S, Zhao J, He X, Li E, Li H, Liu W, Zou D, Wei X, Wang X, Dong D, Yang Z, Yan X, Shen Z, Yuan J. Characterization of phiCFP-1, a virulent bacteriophage specific for Citrobacter freundii. J Med Virol 2015; 88:895-905. [PMID: 26455439 DOI: 10.1002/jmv.24401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2015] [Indexed: 12/14/2022]
Abstract
Citrobacter freundii, a Gram-negative bacterium, causes many opportunistic infections. Bacteriophage phiCFP-1 was isolated and characterized by its ability to lyse the multidrug-resistant clinical C. freundii strain P10159. Transmission electron microscopy showed that the phage has an icosahedral head and a short tail, making it a Podoviridae family member. In a single-step growth experiment, phiCFP-1 exhibited an eclipse period of 20 min and a burst size of 100 particles per cell. Its genome assembled as a circular molecule when genomic sequencing was completed. However, based on genome content and organization, it was categorized as a classic T7-related phage, and such phages are known to have linear genomes with direct terminal repeats. With the quick and simple method established herein, the 38,625-bp linear double-stranded DNA with 229-bp direct terminal repeats was accurately identified. The genome contained 43 putative open reading frames and no tRNA genes. Using a proteomics-based approach, seven viral and two host proteins from purified phiCFP-1 particles were identified. Comparative genomics and recombination analyzes revealed close genetic relatedness among phiCFP-1, phiYeO3-12/vB_YenP_AP5 (from Yersinia enterocolitica O3), and phiSG-JL2 (from Salmonella enterica).
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Affiliation(s)
- Xiangna Zhao
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Simo Huang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Jiangtao Zhao
- Emergency Department, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoming He
- College of Food Science and Engineering, Northwest A and F University, Yangling, China
| | - Erna Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Huan Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Wei Liu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Dayang Zou
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Xuesong Wang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Derong Dong
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Zhan Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Xiabei Yan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
| | - Zhiqiang Shen
- Tianjin Institute of Health and Environmental Medicine, Key Laboratory of Risk Assessment and Control for Environment and Food Safety, Tianjin, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, China
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