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Wang Q, Wang W, Zhu Q, Shoaib M, Chengye W, Zhu Z, Wei X, Bai Y, Zhang J. The prevalent dynamic and genetic characterization of mcr-1 encoding multi-drug resistant Escherichia coli strains recovered from poultry in Hebei, China. J Glob Antimicrob Resist 2024:S2213-7165(24)00071-7. [PMID: 38795771 DOI: 10.1016/j.jgar.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/03/2024] [Accepted: 04/02/2024] [Indexed: 05/28/2024] Open
Abstract
OBJECTIVES Colistin is known as the last resort antibiotic to treat the infections caused by multi-drug resistant (MDR) foodborne pathogens. The emergence and widespread dissemination of plasmid-mediated colistin resistance gene mcr-1 in the E. coli incurs potential threat to public health. Here, we investigated the epidemiology, transmission dynamics, and genetic characterization of mcr-1 harboring E. coli isolates from poultry origin in Hebei province, China. METHODS A total of 297 fecal samples were collected from the two large poultry farms in Hebei province, China. The samples were processed for E. coli identification by MALDI-TOF-MS and 16S rD4A sequencing. Then, mcr-1 gene harboring E. coli strains were identified by PCR and subjected to antimicrobial susceptibility testing by broth microdilution assay. The genomic characterization of the isolates was done by whole genome sequencing using the various bioinformatics tools, and multi-locus sequence typing (MLST) was done by sequence analysis of the seven housekeeping genes. The conjugation experiment was done to check the transferability of mcr-1 along with the plasmid stability testing. RESULTS A total of six mcr-1 E. coli isolates with MIC of 4 μg/mL were identified from 297 samples (2.02%). The mcr-1 harboring E. coli were identified as MDR and belonged to ST101 (n=4) and ST410 (n=2). The genetic environment of mcr-1 presented its position on IncHI2 plasmid in four isolates and p0111 in two isolates which is rarely reported plasmid type for mcr-1. Moreover, both type of plasmids was transferable to recipient J53, and mcr-1 was flanked by three mobile elements ISApl1, Tn3, and IS26 forming a novel backbone Tn3-IS26-mcr-1- pap2-ISApl1 on p0111 plasmid. The phylogenetic analysis shared a common lineage with mcr-1 harboring isolates from the environment, human and animals which indicate its horizontal spread among the diverse sources, species, and hosts. CONCLUSION This study recommends the one health approach for future surveillance across multiple sources and bacterial species to adopt relevant measures and reduce global resistance crises.
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Affiliation(s)
- Qing Wang
- College of Veterinary Medicine, Gansu Agricultural University, No. 1 Yingmen village, Anning District, Lanzhou, 730070, Gansu Province, P.R.China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Qiqi Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Muhammad Shoaib
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Wang Chengye
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Xiaojuan Wei
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Yubin Bai
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Jiyu Zhang
- College of Veterinary Medicine, Gansu Agricultural University, No. 1 Yingmen village, Anning District, Lanzhou, 730070, Gansu Province, P.R.China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China.
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Mansoor MH, Lu X, Woksepp H, Sattar A, Humak F, Ali J, Li R, Bonnedahl J, Mohsin M. Detection and genomic characterization of Klebsiella pneumoniae and Escherichia coli harboring tet(X4) in black kites (Milvus migrans) in Pakistan. Sci Rep 2024; 14:9054. [PMID: 38643223 PMCID: PMC11032342 DOI: 10.1038/s41598-024-59201-5] [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: 09/27/2023] [Accepted: 04/08/2024] [Indexed: 04/22/2024] Open
Abstract
The emergence of plasmid-mediated tigecycline resistance gene tet(X4) among clinically relevant bacteria has promoted significant concerns, as tigecycline is considered a last-resort drug against serious infections caused by multidrug-resistant bacteria. We herein focused on the isolation and molecular characterization of tet(X4)-positive Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) in wild bird populations with anthropogenic interaction in Faisalabad, Pakistan. A total of 150 birds including black kites (Milvus migrans) and house crows (Corvus splendens) were screened for the presence of tigecycline resistance K. pneumoniae and E. coli. We found two K. pneumoniae and one E. coli isolate carrying tet(X4) originating from black kites. A combination of short- and long-read sequencing strategies showed that tet(X4) was located on a broad host range IncFII plasmid family in K. pneumoniae isolates whereas on an IncFII-IncFIB hybrid plasmid in E. coli. We also found an integrative and conjugative element ICEKp2 in K. pneumoniae isolate KP8336. We demonstrate the first description of tet(X4) gene in the WHO critical-priority pathogen K. pneumoniae among wild birds. The convergence of tet(X4) and virulence associated ICEKp2 in a wild bird with known anthropogenic contact should be further investigated to evaluate the potential epidemiological implications. The potential risk of global transmission of tet(X4)-positive K. pneumoniae and E. coli warrant comprehensive evaluation and emphasizes the need for effective mitigation strategies to reduce anthropogenic-driven dissemination of AMR in the environment.
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Affiliation(s)
| | - Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Hanna Woksepp
- Department of Development and Public Health, Kalmar County Hospital, 391 85, Kalmar, Sweden
- Department of Chemistry and Biomedical Sciences, Linnaeus University, 392 31, Kalmar, Sweden
| | - Amna Sattar
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Farwa Humak
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Jabir Ali
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, People's Republic of China
| | - Jonas Bonnedahl
- Department of Biomedical and Clinical Sciences, Linköping University, 581 83, Linköping, Sweden.
- Department of Infectious Diseases, Region Kalmar County, 391 85, Kalmar, Sweden.
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan.
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Li M, Zhang H, Zhang W, Cao Y, Sun B, Jiang Q, Zhang Y, Liu H, Guo W, Chang C, Zhou N, Lv C, Guo C, Guo X, Shang J, Huang S, Zhu Y. One global disseminated 193 kb high-risk hybrid plasmid harboring tet(X4), mcr or bla NDM threatening public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 876:162807. [PMID: 36921865 DOI: 10.1016/j.scitotenv.2023.162807] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 05/10/2023]
Abstract
In Shanghai, the prevalence of tet(X4) and tet(X4)-carrying plasmid from food-producing -animal Enterobacteriales has not been intensively investigated. Here, five tet(X4)-positive swine-origin E. coli strains were characterized among 652 food-producing-animal E. coli isolates in Shanghai during 2018-2021 using long-term surveillance among poultry, swine and cattle, antimicrobial susceptibility testing, and tet(X4)-specific PCR. A combination of short- and long-read sequencing technologies demonstrated that the five strains with 4 STs carried a nearly identical 193 kb tet(X4)-bearing plasmid (p193k-tetX4) belonging to the same IncFIA(HI1)/IncHI1A/IncHIB plasmid family (p193k). Surprisingly, 34 of the 151 global tet(X4)-positive plasmids was the p193k members and exclusively pandemic in China. Other p193k members harboring many critically important ARGs (mcr or blaNDM) with particular genetic environment are widespread throughout human-animal-environmental sources, with 33.77 % human origin. Significantly, phylogenetic analysis of 203 p193k-tetX4 sequences revealed that human- and animal-origin plasmids clustered within the same phylogenetic subgroups. The largest lineage (173/203) comprised 161 E. coli, 6 Klebsiella, 3 Enterobacter, 2 Citrobacter, and 1 Leclercia spp. from animals (n = 143), humans (n = 18), and the environment (n = 9). Intriguingly, the earliest 2015 E. coli strain YA_GR3 from Malaysian river water and 2016 S. enterica Chinese clinical strain GX1006 in another lineage demonstrated that p193k-tetX4 have been widely spread from S. enterica or E. coli to other Enterobacterales. Furthermore, 180 E. coli p193k-tetX4 strains were widespread cross-sectorial transmission among food animals, pets, migratory birds, human and ecosystems. Our findings proved the extensive transmission of the high-risk p193k harboring crucial ARGs across multiple interfaces and species. Therefore, one-health-based systemic surveillance of these similar high-risk plasmids across numerous sources and bacterial species is extremely essential.
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Affiliation(s)
- Min Li
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Haoran Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Wengang Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Ying Cao
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Bingqing Sun
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Qin Jiang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Yu Zhang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China
| | - Haodong Liu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - WenNan Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Cheng Chang
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Nan Zhou
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Chao Lv
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Chaoyi Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China
| | - Jun Shang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China.
| | - Shixin Huang
- Shanghai Center for Animal Disease Prevention and Control, Shanghai Institute for Veterinary Drugs and Feeds Control, Shanghai 201103, China.
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, China.
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Shi J, Zhu H, Liu C, Xie H, Li C, Cao X, Shen H. Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates. Front Microbiol 2023; 13:1105401. [PMID: 36741897 PMCID: PMC9889832 DOI: 10.3389/fmicb.2022.1105401] [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: 11/22/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Objective The worldwide dissemination of colistin-resistant Escherichia coli (E. coli) endangers public health. This study aimed to better understand the global genomic epidemiology of E. coli isolates carrying mobilized colistin resistance (mcr) genes, providing information to assist in infection and prevention. Methods Escherichia coli genomes were downloaded from NCBI, and mcr was detected using BLASTP. Per software was used to extract information on hosts, resources, collection data, and countries of origin from GenBank. Sequence types (STs), prevalence of plasmids, antimicrobial resistance genes (ARG), and virulence factors (VF) in these genomes were analyzed. Statistical analyses were performed to assess the relationships between mcr, ARGs, plasmids, and STs. Results In total, 778 mcr-positive isolates were identified. Four mcr variants were detected, with mcr-1 (86.1%) being the most widespread, followed by mcr-9 (5.7%), mcr-5 (4.4%), and mcr-3 (3.0%). Multiple ARGs were identified, with bla CTX-M (53.3%), fosA (28.8%), qnr (26.1%), bla NDM (19.8%), and aac (6')-Ib-cr (14.5%) being the most common. Overall, 239 distinct STs were identified, of which ST10 (13.8%) was the most prevalent. A total of 113 different VFs were found, terC (99.9%) and gad (83.0%) were most frequently detected. Twenty types of plasmids were identified; IncFIB (64.1%), IncX (42.3%), and IncX (42.3%) were the most common replicons. IncI2 and IncX4 were frequently detected in mcr-1-positive isolates, whereas IncFII, IncI1-I, and IncHI2 were dominant plasmids in mcr-3, mcr-5, and mcr-9-positive isolates, respectively. A higher frequency of ARGs and VFs was observed among ST156 and ST131 isolates. Conclusion Our data indicated that more than half of the mcr-positive E. coli strains carried endemic ARGs and VFs. ST10 and ST156 isolates deserved further attention, given the rapid transmission of ST10 and the convergence of ARGs and VFs in ST156.
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Affiliation(s)
- Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hong Zhu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Xiaoli Cao,
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,Han Shen,
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Xu J, Guo H, Li L, He F. Molecular epidemiology and genomic insights into the transmission of carbapenem-resistant NDM-producing Escherichia coli. Comput Struct Biotechnol J 2023; 21:847-855. [PMID: 36698971 PMCID: PMC9842800 DOI: 10.1016/j.csbj.2023.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/05/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Escherichia coli is a leading cause of nosocomial infections. Carbapenem-resistant E. coli (CREC), which has been frequently isolated in recent years because of the widespread use of carbapenems, poses a significant challenge to clinical anti-infection treatment. In this study, a total of 27 CREC strains were identified from a set of 795 E. coli isolates collected over a two-year period from a tertiary hospital in China. Whole-genome sequencing revealed that 17 strains carried the bla NDM-5 gene, 5 strains carried the bla NDM-1 gene, 1 strain carried the bla NDM-7 gene, and the remaining 4 strains carried the bla KPC-2 gene. All 23 NDM-producing E. coli strains were resistant to all antibiotics except tigecycline, colistin, and cefiderocol. Nine different sequence types (STs) were identified, with ST410 and ST167 being the most prevalent. All of the bla NDM genes were located on conjugatable plasmids. We identified five different plasmid replicon types ranging in size from 20 kb to 200 kb, with the IncX3-type plasmid, 46 kb in size, being a key factor in facilitating the horizontal transmission of the bla NDM gene in E. coli. The structure surrounding the bla NDM gene was relatively conserved and mainly contained the following structures: IS3000-ISAbal25-IS5-bla NDM-ble MBL-trpF-dsbC-IS26. However, the plasmid backbone structure was highly variable, which indicates that the bla NDM gene has already spread horizontally among different types of plasmids. In addition, we discovered two copies of the bla NDM-5 gene in a single plasmid (pEC29-NDM-5), with an identical structure around the gene and the complete sequence of the class 1 integron. Our findings detail the prevalence of CREC in a tertiary hospital in China, and the emergence of multiple copies of the bla NDM-5 gene on a single plasmid needs our attention.
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Affiliation(s)
- Juan Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang 310013, China
| | - Hao Guo
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Lirong Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
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