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Duran-Bedolla J, Téllez-Sosa J, Bocanegra-Ibarias P, Schilmann A, Bravo-Romero S, Reyna-Flores F, Villa-Reyes T, Barrios-Camacho H. Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase blaNDM and blaKPC resistance genes in hospital wastewater. Appl Environ Microbiol 2024; 90:e0116524. [PMID: 39012101 PMCID: PMC11337798 DOI: 10.1128/aem.01165-24] [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: 06/13/2024] [Accepted: 06/20/2024] [Indexed: 07/17/2024] Open
Abstract
Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the Enterobacteriaceae family. We identified a total of 169 β-lactamase genes; blaTEM in 33.1%, blaCTX-M in 25.4%, blaKPC in 25.4%, blaNDM 8.8%, blaSHV in 5.3%, and blaOXA-48 in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase blaKPC was found in six Citrobacter spp. and E. coli, while blaNDM was detected in two distinct Enterobacter spp. and E. coli. Notably, blaNDM-1 was identified in a 110 Kb IncFII conjugative plasmid in E. cloacae, E. xiangfangensis, and E. coli within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of Enterobacteriaceae carrying a high frequency of carbapenemase blaKPC and blaNDM. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains. IMPORTANCE The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as blaKPC and blaNDM within the Enterobacteriaceae family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.
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Affiliation(s)
- Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico
| | - Juan Téllez-Sosa
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico
| | - Paola Bocanegra-Ibarias
- Facultad de Medicina, Hospital Universitario "Dr. José Eleuterio González", Departamento de Enfermedades Infecciosas, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Astrid Schilmann
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación en Salud Poblacional, Cuernavaca, Morelos, Mexico
| | - Sugey Bravo-Romero
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico
| | - Fernando Reyna-Flores
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico
| | - Tania Villa-Reyes
- Coordinación Nacional de la Red Hospitalaria de Vigilancia Epidemiológica, Dirección General de Epidemiología, Ciudad de México, Mexico
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca, Morelos, Mexico
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2
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Walas N, Slown S, Amato HK, Lloyd T, Bender M, Varghese V, Pandori M, Graham JP. The role of plasmids in carbapenem resistant E. coli in Alameda County, California. BMC Microbiol 2023; 23:147. [PMID: 37217873 DOI: 10.1186/s12866-023-02900-2] [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: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids). RESULTS Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). blaCTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne blaCTX-M-15 gene and an isolate with a plasmid-borne blaCTX-M-15 gene. CONCLUSIONS This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.
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Affiliation(s)
- Nikolina Walas
- School of Public Health, University of California, Berkeley, CA, USA.
| | - Samuel Slown
- School of Public Health, University of California, Berkeley, CA, USA
| | - Heather K Amato
- School of Public Health, University of California, Berkeley, CA, USA
| | - Tyler Lloyd
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Monica Bender
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, USA
| | - Mark Pandori
- Alameda County Public Health Laboratory, Oakland, CA, USA
- Nevada State Public Health Laboratory, Reno, NV, USA
| | - Jay P Graham
- School of Public Health, University of California, Berkeley, CA, USA
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Morgado S, Fonseca E, Vicente AC. Genomics of Klebsiella pneumoniae Species Complex Reveals the Circulation of High-Risk Multidrug-Resistant Pandemic Clones in Human, Animal, and Environmental Sources. Microorganisms 2022; 10:2281. [PMID: 36422351 PMCID: PMC9697336 DOI: 10.3390/microorganisms10112281] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/03/2023] Open
Abstract
The Klebsiella species present a remarkable genetic and ecological diversity, being ubiquitous in nature. In particular, the Klebsiella pneumoniae species complex (KpSC) has emerged as a major public health threat in the world, being an interesting model to assess the risk posed by strains recovered from animals and the environment to humans. We therefore performed a genomic surveillance analysis of the KpSC using every public genome in Brazil, aiming to show their local and global relationships, and the connectivity of antibiotic resistance and virulence considering human, animal, and environmental sources. The 390 genomes from distinct sources encompassed the K. pneumoniae, Klebsiella quasipneumoniae subsp. quasipneumoniae, Klebsiella quasipneumoniae subsp. similipneumoniae, Klebsiella variicola subsp. variicola, Klebsiella variicola subsp. tropica, and Klebsiella grimontii species and subspecies. K. pneumoniae harbored dozens of antibiotic resistance genes, while most of the genomes belong to the high-risk pandemic CC258 occurring in humans, animals, and the environment. In K. pneumoniae ST11, a high prevalence of the virulence determinants yersiniabactin, colibactin, and T6SS was revealed in association with multi-drug resistance (MDR), including carbapenem resistance. A diversity of resistance genes is carried by plasmids, some shared between strains from different STs, regions, and sources. Therefore, here were revealed some factors driving the success of KpSC as a pathogen.
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Affiliation(s)
| | | | - Ana Carolina Vicente
- Laboratory of Molecular Genetics of Microorganisms, Oswaldo Cruz Institute, Av. Brasil, 4365—Manguinhos, Rio de Janeiro 21040-900, Brazil
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OXA-48-Like β-Lactamases: Global Epidemiology, Treatment Options, and Development Pipeline. Antimicrob Agents Chemother 2022; 66:e0021622. [PMID: 35856662 PMCID: PMC9380527 DOI: 10.1128/aac.00216-22] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Modern medicine is threatened by the rising tide of antimicrobial resistance, especially among Gram-negative bacteria, where resistance to β-lactams is most often mediated by β-lactamases. The penicillin and cephalosporin ascendancies were, in their turn, ended by the proliferation of TEM penicillinases and CTX-M extended-spectrum β-lactamases. These class A β-lactamases have long been considered the most important. For carbapenems, however, the threat is increasingly from the insidious rise of a class D carbapenemase, OXA-48, and its close relatives. Over the past 20 years, OXA-48 and "OXA-48-like" enzymes have proliferated to become the most prevalent enterobacterial carbapenemases across much of Europe, Northern Africa, and the Middle East. OXA-48-like enzymes are notoriously difficult to detect because they often cause only low-level in vitro resistance to carbapenems, meaning that the true burden is likely underestimated. Despite this, they are associated with carbapenem treatment failures. A highly conserved incompatibility complex IncL plasmid scaffold often carries blaOXA-48 and may carry other antimicrobial resistance genes, leaving limited treatment options. High conjugation efficiency means that this plasmid is sometimes carried by multiple Enterobacterales in a single patient. Producers evade most β-lactam-β-lactamase inhibitor combinations, though promising agents have recently been licensed, notably ceftazidime-avibactam and cefiderocol. The molecular machinery enabling global spread, current treatment options, and the development pipeline of potential new therapies for Enterobacterales that produce OXA-48-like β-lactamases form the focus of this review.
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Surveillance of Antimicrobial Resistance in Hospital Wastewater: Identification of Carbapenemase-Producing Klebsiella spp. Antibiotics (Basel) 2022; 11:antibiotics11030288. [PMID: 35326752 PMCID: PMC8944648 DOI: 10.3390/antibiotics11030288] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 02/01/2023] Open
Abstract
The objective of this study was to investigate the presence and persistence of carbapenemase-producing Klebsiella spp. isolated from wastewater and treated wastewater from two tertiary hospitals in Mexico. We conducted a descriptive cross-sectional study in two hospital wastewater treatment plants, which were sampled in February 2020. We obtained 30 Klebsiella spp. isolates. Bacterial identification was carried out by the Matrix-Assisted Laser Desorption/Ionization-Time of Flight mass spectrometry (MALDI-TOF MS®) and antimicrobial susceptibility profiles were performed using the VITEK2® automated system. The presence of carbapenem resistance genes (CRGs) in Klebsiella spp. isolates was confirmed by PCR. Molecular typing was determined by pulsed-field gel electrophoresis (PFGE). High rates of Klebsiella spp. resistance to cephalosporins and carbapenems (80%) were observed in isolates from treated wastewater from both hospitals. The molecular screening by PCR showed the presence of blaKPC and blaOXA-48-like genes. The PFGE pattern separated the Klebsiella isolates into 19 patterns (A–R) with three subtypes (C1, D1, and I1). Microbiological surveillance and identification of resistance genes of clinically important pathogens in hospital wastewater can be a general screening method for early determination of under-detected antimicrobial resistance profiles in hospitals and early warning of outbreaks and difficult-to-treat infections.
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Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat Microbiol 2022; 7:2054-2067. [PMID: 36411354 PMCID: PMC9712112 DOI: 10.1038/s41564-022-01263-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/10/2022] [Indexed: 11/22/2022]
Abstract
The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.
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Affiliation(s)
- Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ross Booton
- grid.5337.20000 0004 1936 7603Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Teemu Kallonen
- grid.410552.70000 0004 0628 215XDepartment of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Marjorie J. Gibbon
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Natacha Couto
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Virginie Passet
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sebastián López-Fernández
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Carla Rodrigues
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Louise Matthews
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sonia Mitchell
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Reeve
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophia David
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Cristina Merla
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Marta Corbella
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Carolina Ferrari
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Francesco Comandatore
- grid.4708.b0000 0004 1757 2822Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, Milan, Italy
| | - Piero Marone
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Sylvain Brisse
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology, Università di Pavia, Pavia, Italy
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.7737.40000 0004 0410 2071Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Edward J. Feil
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
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Ma Y, Wu X, Li S, Tang L, Chen M, An Q. Proposal for reunification of the genus Raoultella with the genus Klebsiella and reclassification of Raoultella electrica as Klebsiella electrica comb. nov. Res Microbiol 2021; 172:103851. [PMID: 34186167 DOI: 10.1016/j.resmic.2021.103851] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 12/22/2022]
Abstract
The order Enterobacterales was divided into seven families including the family Enterobacteriaceae in 2016. The genus Klebsiella within the family Enterobacteriaceae was divided into two genera Klebsiella and Raoultella in 2001. Here, our phylogenomic analysis shows that the genus Raoultella is nested within the genus Klebsiella. Klebsiella and Raoultella together are monophyletic and share average amino acid identities (AAIs) of 86.9-89.6% above the AAI threshold (86%) for genus delimitation within the family Enterobacteriaceae. Klebsiella and Raoultella share AAIs of 79.9%-85.0% with the other genera within the subfamily "Klebsiella clade", which are in the range of inter-genus AAIs (74‒85%) within the family Enterobacteriaceae. Klebsiella and Raoultella also share six known conserved signature indels. Therefore, we propose to reunify Klebsiella and Raoultella to the single genus Klebsiella and reclassify Raoultella electrica as Klebsiella electrica comb. nov. Our genome-based taxonomic analyses also identified seven potential novel species within the unified genus Klebsiella.
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Affiliation(s)
- Yuanyuan Ma
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Xiuqin Wu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Shuying Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Lie Tang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Mingyue Chen
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Qianli An
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang Province Key Laboratory of Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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