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Pan F, Xu Q, Jiang C, Du Q, Yu F, Chen P, Zhang H. Genomic characterisation of bla NDM-5-IncX3 plasmid in an ST4 Klebsiella aerogenes clinical isolate. J Glob Antimicrob Resist 2024; 37:81-85. [PMID: 38460750 DOI: 10.1016/j.jgar.2024.02.011] [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: 02/22/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 03/11/2024] Open
Abstract
OBJECTIVES The dissemination of New Delhi metallo-β-lactamase-5 (NDM-5) among various species of Enterobacterales has attracted serious global attention. Here, we characterise the genomic characterisation of blaNDM-5-IncX3 plasmid (pNDM-KA3) in an ST4 Klebsiella aerogenes (KA3) strain isolated from a neonate with pneumonia. METHODS Antimicrobial susceptibility and multilocus sequence typing was performed for the KA3. The plasmid conjugation assay and plasmid stability of the KA3 (pNDM-KA3) were also analysed. The pNDM-KA3 plasmid was further analysed by whole-genome sequencing and comparative analysis to determine the genetic environment of blaNDM-5. RESULTS The KA3 strain belongs to ST4 and shows high resistance to β-lactam antibiotics, including carbapenems, but is susceptible to ciprofloxacin, amikacin, tigecycline, and colistin. The pNDM-KA3 was successfully transferred to the recipient E. coli J53 and showed strong stability in K. aerogenes. Genomic sequencing revealed that the pNDM-KA3 plasmid was assigned to plasmid incompatibility group X3 with 43367 bp, and a conserved structure sequence of △IS3000-△ISAba125-IS5-blaNDM-5-bleMBL- trpF-dsbC-IS26 was detected upstream and downstream of the blaNDM-5 gene. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. The pNDM-KA3 showed high similarity to blaNDM-5-harbouring plasmids in other species of Enterobacterales, with these plasmids carrying genes for replication (repB), partitioning (parA and parB), stability (hns), and conjugative transfer (virB and virD). CONCLUSIONS Continued monitoring for the dissemination of blaNDM-5 among uncommon Enterobacterales species should be further reinforced.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Xu
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Cong Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qingqing Du
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangyuan Yu
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pengcheng Chen
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China..
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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de Oliveira ÉM, Beltrão EMB, Pimentel MIS, Lopes ACDS. Occurrence of high-risk clones of Klebsiella pneumoniae ST11, ST340, and ST855 carrying the blaKPC-2, blaNDM-1, blaNDM-5, and blaNDM-7 genes from colonized and infected patients in Brazil. J Appl Microbiol 2023; 134:lxad242. [PMID: 37880999 DOI: 10.1093/jambio/lxad242] [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: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023]
Abstract
AIMS Determine which sequence type (ST) clones were carrying the blaKPC, blaNDM, blaVIM, blaIMP, and blaGES genes and their variants in clinical isolates of multidrug-resistant Klebsiella pneumoniae. METHODS AND RESULTS Ten K. pneumoniae isolates were obtained from the colonized and infected patients in a public hospital in the city of Recife-PE, in northeastern Brazil, and were further analyzed. The detection of carbapenem resistance genes and the seven housekeeping genes [for multilocus sequence typing (MLST) detection] were done with PCR and sequencing. The blaKPC and blaNDM genes were detected concomitantly in all isolates, with variants being detected blaNDM-1, blaNDM-5, blaNDM-7, and blaKPC-2. The blaKPC-2 and blaNDM-1 combination being the most frequent. Molecular typing by MLST detected three types of high-risk ST clones, associated with the clonal complex 258, ST11/CC258 in eight isolates, and ST855/CC258 and ST340/CC258 in the other two isolates. CONCLUSIONS These findings are worrying, as they have a negative impact on the scenario of antimicrobial resistance, and show the high genetic variability of K. pneumoniae and its ability to mutate resistance genes and risk of dissemination via different ST clones.
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Affiliation(s)
- Érica Maria de Oliveira
- Departamento de Medicina Tropical, Universidade Federal de Pernambuco-UFPE, Recife, PE 50732-970, Brazil
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Ye J, Jin L, Li Y, Xu H, Lin Y, Zhou T, Zheng B, Wang M, Wang Z. Complete-genome sequencing and comparative genomic characterization of bla NDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections. BMC Genomics 2023; 24:506. [PMID: 37649002 PMCID: PMC10466682 DOI: 10.1186/s12864-023-09579-9] [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: 01/26/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The emergence and wide spread of carbapenemase-producing Enterobacteriaceae (CPE) poses a growing threat to global public health. However, clinically derived carbapenemase-producing Citrobacter causing multiple infections has rarely been investigated. Here we first report the isolation and comparative genomics of two blaNDM-5 carrying Citrobacter freundii (C. freundii) isolates from a patient with bloodstream and urinary tract infections. RESULTS Antimicrobial susceptibility testing showed that both blaNDM-5 carrying C. freundii isolates were multidrug-resistant. Positive modified carbapenem inactivation method (mCIM) and EDTA-carbapenem inactivation method (eCIM) results suggested metallo-carbapenemase production. PCR and sequencing confirmed that both metallo-carbapenemase producers were blaNDM-5 positive. Genotyping and comparative genomics analyses revealed that both isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the blaNDM-5 resistance gene is located on IncX3 plasmid with a length of 46,161 bp, and could successfully be transferred to the recipient Escherichia coli EC600 strain. A conserved structure sequence (ISAba125-IS5-blaNDM-5-trpF-IS26-umuD-ISKox3) was found in the upstream and downstream of the blaNDM-5 gene. CONCLUSIONS The data presented in this study showed that the conjugative blaNDM-5 plasmid possesses a certain ability to horizontal transfer. The dissemination of NDM-5-producing C. freundii isolates should be of close concern in future clinical surveillance. To our knowledge, this is the first study to characterize C. freundii strains carrying the blaNDM-5 gene from one single patient with multiple infections.
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Affiliation(s)
- Jianzhong Ye
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Lulu Jin
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, No. 60 Wuning West Road, Dongyang, 322100, Zhejiang Province, China
| | - Yaling Li
- Department of Health Screening Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, Zhejiang, China
| | - Hao Xu
- Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesSchool of Medicine, National Clinical Research Center for Infectious Diseasesthe First Affiliated HospitalZhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou, 310000, Zhejiang Province, China
| | - Yishuai Lin
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Tieli Zhou
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesCollaborative Innovation Center for Diagnosis and Treatment of Infectious DiseasesSchool of Medicine, National Clinical Research Center for Infectious Diseasesthe First Affiliated HospitalZhejiang University, No. 79 Qingchun Road, Shangcheng District, Hangzhou, 310000, Zhejiang Province, China.
| | - Maofeng Wang
- Department of Biomedical Sciences Laboratory, Affiliated Dongyang Hospital of Wenzhou Medical University, No. 60 Wuning West Road, Dongyang, 322100, Zhejiang Province, China.
| | - Zhongyong Wang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, the First Affiliated Hospital of Wenzhou Medical University, Nanbaixiang Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China.
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Behera DU, Dixit S, Gaur M, Mishra R, Sahoo RK, Sahoo M, Behera BK, Subudhi BB, Bharat SS, Subudhi E. Sequencing and Characterization of M. morganii Strain UM869: A Comprehensive Comparative Genomic Analysis of Virulence, Antibiotic Resistance, and Functional Pathways. Genes (Basel) 2023; 14:1279. [PMID: 37372459 DOI: 10.3390/genes14061279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Morganella morganii is a Gram-negative opportunistic Enterobacteriaceae pathogen inherently resistant to colistin. This species causes various clinical and community-acquired infections. This study investigated the virulence factors, resistance mechanisms, functional pathways, and comparative genomic analysis of M. morganii strain UM869 with 79 publicly available genomes. The multidrug resistance strain UM869 harbored 65 genes associated with 30 virulence factors, including efflux pump, hemolysin, urease, adherence, toxin, and endotoxin. Additionally, this strain contained 11 genes related to target alteration, antibiotic inactivation, and efflux resistance mechanisms. Further, the comparative genomic study revealed a high genetic relatedness (98.37%) among the genomes, possibly due to the dissemination of genes between adjoining countries. The core proteome of 79 genomes contains the 2692 core, including 2447 single-copy orthologues. Among them, six were associated with resistance to major antibiotic classes manifested through antibiotic target alteration (PBP3, gyrB) and antibiotic efflux (kpnH, rsmA, qacG; rsmA; CRP). Similarly, 47 core orthologues were annotated to 27 virulence factors. Moreover, mostly core orthologues were mapped to transporters (n = 576), two-component systems (n = 148), transcription factors (n = 117), ribosomes (n = 114), and quorum sensing (n = 77). The presence of diversity in serotypes (type 2, 3, 6, 8, and 11) and variation in gene content adds to the pathogenicity, making them more difficult to treat. This study highlights the genetic similarity among the genomes of M. morganii and their restricted emergence, mostly in Asian countries, in addition to their growing pathogenicity and resistance. However, steps must be taken to undertake large-scale molecular surveillance and to direct suitable therapeutic interventions.
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Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sangita Dixit
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
- Department of Biotechnology & Food Technology, Punjabi University, Patiala 147002, Punjab, India
| | - Rukmini Mishra
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Rajesh Kumar Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Bijay Kumar Behera
- College of Fisheries, Rani Lakshmi Bai Central Agricultural University, Gwalior Road, Jhansi 284003, Uttar Pradesh, India
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
| | - Sutar Suhas Bharat
- Department of Botany, School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar 761211, Odisha, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar 751003, Odisha, India
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Wang D, Zou H, Zhao L, Li Q, Meng M, Li X, Berglund B. High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China. Int J Hyg Environ Health 2023; 250:114159. [PMID: 36989999 DOI: 10.1016/j.ijheh.2023.114159] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Emergence and dissemination of resistance to last-resort antibiotics such as carbapenem and colistin is a growing, global health concern. Wastewater treatment plants (WWTPs) link human activities and the environment, can act as reservoirs and sources for emerging antibiotic resistance, and likely play a large role in antibiotic resistance transmission. The aim of this study was to investigate occurrence and characteristics of colistin- and carbapenem-resistant Escherichia coli (CCREC) in wastewater and sludge samples collected over a one-year period from different functional areas of an urban WWTP in Jinan city, Shandong, China. A total of 8 CCREC were isolated from 168 samples with selective agar and PCR, corresponding to high prevalence of 4.8%, co-harboring carbapenem resistance genes (blaNDM) and colistin resistance gene (mcr-1) and subsequently whole-genome sequenced. Additionally, all isolates were multidrug-resistant by antimicrobial susceptibility testing and carried a variety of antibiotic resistance genes. Two isolates carrying virulence genes associated with avian pathogenic E. coli were identified, one belonging to the high-risk clone O101:H9-ST167. Southern blotting was used to characterize CCREC isolates and plasmids carrying blaNDM-genes or mcr-1 could be transferred to a recipient strain E. coli J53 by in vitro conjugation assays. Resistance to other antibiotic classes were sporadically co-transferred to the transconjugant. Transposition of and mcr-1-carrying element from a transferable IncHI2-plasmid was observed among two CCREC clones isolated within 4 days of each other. The occurrence of multidrug-resistant CCREC capable of transferring their antibiotic resistance genotypes via conjugative plasmids is alarming. WWTPs bring bacteria from different sources together, providing opportunities for horizontal exchange of DNA among compatible hosts. Further dissemination of the colistin-, carbapenem-, or both colistin- and carbapenem resistant E. coli could lead to a serious threat to public health.
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Affiliation(s)
- Di Wang
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Qi Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Min Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Björn Berglund
- Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden
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Oktariani AF, Ramona Y, Sudaryatma PE, Dewi IAMM, Shetty K. Role of Marine Bacterial Contaminants in Histamine Formation in Seafood Products: A Review. Microorganisms 2022; 10:microorganisms10061197. [PMID: 35744715 PMCID: PMC9227395 DOI: 10.3390/microorganisms10061197] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Histamine is a toxic biogenic amine commonly found in seafood products or their derivatives. This metabolite is produced by histamine-producing bacteria (HPB) such as Proteus vulgaris, P. mirabilis, Enterobacter aerogenes, E. cloacae, Serratia fonticola, S. liquefaciens, Citrobacter freundii, C. braakii, Clostridium spp., Raoultella planticola, R. ornithinolytica, Vibrio alginolyticus, V. parahaemolyticus, V. olivaceus, Acinetobacter lowffi, Plesiomonas shigelloides, Pseudomonas putida, P. fluorescens, Aeromonas spp., Photobacterium damselae, P. phosphoreum, P. leiognathi, P. iliopiscarium, P. kishitanii, and P. aquimaris. In this review, the role of these bacteria in histamine production in fish and seafood products with consequences for human food poisoning following consumption are discussed. In addition, methods to control their activity in countering histamine production are proposed.
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Affiliation(s)
- Adnorita Fandah Oktariani
- Doctoral Study Program of Biology, Faculty of Mathematics and Natural Sciences, Udayana University, Denpasar 80361, Bali, Indonesia;
- PT. Intimas Surya, Denpasar 80222, Bali, Indonesia
| | - Yan Ramona
- Doctoral Study Program of Biology, Faculty of Mathematics and Natural Sciences, Udayana University, Denpasar 80361, Bali, Indonesia;
- Integrated Laboratory for Biosciences and Biotechnology, Udayana University, Denpasar 80361, Bali, Indonesia
- Correspondence: (Y.R.); (K.S.); Tel.: +62-85101523213 (Y.R.)
| | | | - Ida Ayu Mirah Meliana Dewi
- School of Biology, Faculty of Mathematics and Natural Sciences, Udayana University, Denpasar 80361, Bali, Indonesia;
| | - Kalidas Shetty
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
- Correspondence: (Y.R.); (K.S.); Tel.: +62-85101523213 (Y.R.)
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Shi H, Chen X, Yao Y, Xu J. Morganella morganii
: An unusual analysis of 11 cases of pediatric urinary tract infections. J Clin Lab Anal 2022; 36:e24399. [PMID: 35349730 PMCID: PMC9102756 DOI: 10.1002/jcla.24399] [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: 02/21/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background The increase in rare opportunistic microbial infections caused by Morganella morganii is alarming across the globe. It has been reported that in cases of urinary tract infections (UTIs) caused by M. morganii, however, few studies investigated children. Our study aimed to analyze the risk factors, antimicrobial susceptibility, and clinical characteristics, so as to improve the clinical diagnosis and therapy of M. morganii infection. Methods Between April 1, 2017 and April 1, 2021, 11 cases of pediatric UTIs caused by M. morganii were included in this retrospective study. Medical records were reviewed and analyzed. Results The study population included 10 males and one female between 11 months and 13 years old (mean age: 4 years 9 months). The most common comorbidity was nephrotic syndrome (72.7%, 8/11). Six patients (54.5%) were in the immunosuppressed state due to chemotherapy or immunosuppressant therapy. Ten cases defined as lower UTIs with no specific clinical manifestations had normal or slightly elevated leukocyte counts and procalcitonin (PCT) levels, and normal C‐reactive protein (CRP) levels. One child diagnosed upper UTIs accompanied with fever, high level of leukocyte counts, CRP, and PCT. The M. morganii presented 100% susceptibility to aztreonam, ertapenem, meropenem, piperacillin/tazobactam, cefepime, ceftazidime, cefotetan, ticarcillin/clavulanic acid, and cefoperazone/sulbactam. Almost all patients had good responses to third‐generation cephalosporins antibiotic therapy. Conclusion Clinical vigilance for the possibility of M. morganii in pediatric UTIs in combination with underlying disease or immunosuppression is warranted. Treatment strategies should be proposed according to the clinical condition and the antibiotic susceptibility results.
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Affiliation(s)
- Huixuan Shi
- Department of Pediatrics The First Affiliated Hospital of Xiamen University Xiamen China
- Pediatric Key Laboratory of Xiamen Xiamen China
- Institute of Pediatrics School of Medicine Xiamen University Xiamen China
| | - Xianrui Chen
- Department of Pediatrics The First Affiliated Hospital of Xiamen University Xiamen China
- Pediatric Key Laboratory of Xiamen Xiamen China
- Institute of Pediatrics School of Medicine Xiamen University Xiamen China
| | - Yonghua Yao
- Department of Pediatrics The First Affiliated Hospital of Xiamen University Xiamen China
- Pediatric Key Laboratory of Xiamen Xiamen China
- Institute of Pediatrics School of Medicine Xiamen University Xiamen China
| | - Jinping Xu
- Department of Pediatrics The First Affiliated Hospital of Xiamen University Xiamen China
- Pediatric Key Laboratory of Xiamen Xiamen China
- Institute of Pediatrics School of Medicine Xiamen University Xiamen China
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Jing Y, Yin Z, Wang P, Guan J, Chen F, Wang L, Li X, Mu X, Zhou D. A Genomic and Bioinformatics View of the Classification and Evolution of Morganella Species and Their Chromosomal Accessory Genetic Elements Harboring Antimicrobial Resistance Genes. Microbiol Spectr 2022; 10:e0265021. [PMID: 35196820 PMCID: PMC8865565 DOI: 10.1128/spectrum.02650-21] [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: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 11/20/2022] Open
Abstract
In this study, draft-genome sequencing was conducted for 60 Chinese Morganella isolates, and furthermore, 12 of them were fully sequenced. Then, a total of 166 global sequenced Morganella isolates, including the above 60, were collected to perform average nucleotide identity-based genomic classification and core single nucleotide polymorphism-based phylogenomic analysis. A genome sequence-based species classification scheme for Morganella was established, and accordingly, the two conventional Morganella species were redefined as two complexes and further divided into four and two genospecies, respectively. At least 88 acquired antimicrobial resistance genes (ARGs) were disseminated in these 166 isolates and were prevalent mostly in the isolates from hospital settings. IS26/IS15DI, IS10 and IS1R, and Tn3-, Tn21-, and Tn7-subfamily unit transposons were frequently presented in these 166 isolates. Furthermore, a detailed sequence comparison was applied to 18 Morganella chromosomal accessory genetic elements (AGEs) from the fully sequenced 12 isolates, together with 5 prototype AGEs from GenBank. These 23 AGEs were divided into eight different groups belonging to composite/unit transposons, transposable prophages, integrative and mobilizable elements, and integrative and conjugative elements, and they harbored at least 52 ARGs involved in resistance to 15 categories of antimicrobials. Eleven of these 23 AGEs acquired large accessory modules, which exhibited complex mosaic structures and contained many antimicrobial resistance loci and associated ARGs. Integration of ARG-containing AGEs into Morganella chromosomes would contribute to the accumulation and dissemination of ARGs in Morganella and enhance the adaption and survival of Morganella under complex and diverse antimicrobial selection pressures. IMPORTANCE This study presents a comprehensive genomic epidemiology analysis on global sequenced Morganella isolates. First, a genome sequence-based species classification scheme for Morganella is established with a higher resolution and accuracy than those of the conventional scheme. Second, the prevalence of accessory genetic elements (AGEs) and associated antimicrobial resistance genes (ARGs) among Morganella isolates is disclosed based on genome sequences. Finally, a detailed sequence comparison of eight groups of 23 AGEs (including 19 Morganella chromosomal AGEs) reveals that Morganella chromosomes have evolved to acquire diverse AGEs harboring different profiles of ARGs and that some of these AGEs harbor large accessory modules that exhibit complex mosaic structures and contain a large number of ARGs. Data presented here provide a deeper understanding of the classification and evolution of Morganella species and also those of ARG-containing AGEs in Morganella at the genomic scale.
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Affiliation(s)
- Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jiayao Guan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingling Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xinyue Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaofei Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Xiang G, Lan K, Cai Y, Liao K, Zhao M, Tao J, Ma Y, Zeng J, Zhang W, Wu Z, Yu X, Liu Y, Lu Y, Xu C, Chen L, Tang YW, Chen C, Jia W, Huang B. Clinical Molecular and Genomic Epidemiology of Morganella morganii in China. Front Microbiol 2021; 12:744291. [PMID: 34650543 PMCID: PMC8507844 DOI: 10.3389/fmicb.2021.744291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: Ongoing acquisition of antimicrobial resistance genes has made Morganella morganii a new clinical treatment challenge. Understanding the molecular epidemiology of M. morganii will contribute to clinical treatment and prevention. Methods: We undertook a 6-year clinical molecular epidemiological investigation of M. morganii from three tertiary hospitals in China since 2014. Antimicrobial susceptibility testing was performed using a VITEK-2 system. All isolates were screened for β-lactam and plasmid-mediated quinolone resistance genes by PCR. Isolates carrying carbapenem-resistant genes were subjected to whole-genome sequencing (WGS). The variation and evolution of these mobile genetic elements (MGEs) were then systematically analyzed. Results: Among all M. morganii isolates (n = 335), forty (11.9%) were recognized as multidrug resistant strains. qnrD1, aac(6′)-Ib-cr, blaTEM–104, and blaCTX–M–162 were the top four most prevalent resistance genes. Notably, phylogenomic and population structure analysis suggested clade 1 (rhierBAPS SC3 and SC5) associated with multiple resistance genes seemed to be widely spread. WGS showed a blaOXA–181-carrying IncX3 plasmid and a Proteus genomic island 2 variant carrying blaCTX–M–3, aac(6′)-Ib-cr coexisted in the same multidrug resistant strain zy_m28. Additionally, a blaIMP–1-carrying IncP-1β type plasmid was found in the strain nx_m63. Conclusion: This study indicates a clade of M. morganii is prone to acquire resistance genes, and multidrug resistant M. morganii are increasing by harboring a variety of MGEs including two newly discovered ones in the species. We should be vigilant that M. morganii may bring more extensive and challenging antimicrobial resistance issue.
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Affiliation(s)
- Guoxiu Xiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Translational Medicine Research Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Kai Lan
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Kang Liao
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mei Zhao
- Department of Laboratory Medicine, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Jia Tao
- Department of Laboratory Medicine, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yi Ma
- Department of Clinical Laboratory, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianming Zeng
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Weizheng Zhang
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Zhongwen Wu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuyang Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yang Lu
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Caixia Xu
- Translational Medicine Research Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - Yi-Wei Tang
- Medical and Scientific Affairs, Cepheid, Sunnyvale, CA, United States
| | - Cha Chen
- Department of Laboratory Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Wei Jia
- Department of Laboratory Medicine, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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10
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Huang J, Zhang S, Zhao Z, Chen M, Cao Y, Li B. Acquisition of a Stable and Transferable bla NDM-5-Positive Plasmid With Low Fitness Cost Leading to Ceftazidime/Avibactam Resistance in KPC-2-Producing Klebsiella pneumoniae During Treatment. Front Cell Infect Microbiol 2021; 11:658070. [PMID: 34354959 PMCID: PMC8329419 DOI: 10.3389/fcimb.2021.658070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The emergence and prevalence of carbapenem-resistant Enterobacteriaceae (CRE) have drawn worldwide attention. Ceftazidime/avibactam (CAZ/AVI) gives us a valuable alternative strategy to treat CRE infections. Unfortunately, CAZ/AVI resistance could occur during CAZ/AVI treatment. The CAZ/AVI-resistant Carbapenem-resistant Klebsiella pneumoniae (CR-KP) (KP137060) and earlier CAZ/AVI-susceptible isolate (KP135194) from the same hospitalized patient were collected at Fujian Medical University Union Hospital between October and November 2019. In this study, CAZ/AVI MICs of CAZ/AVI-susceptible and -resistant isolates (KP135194 and KP137060) were 4 mg/L and 128 mg/L, respectively; and the two isolates had the same antibiotic resistance pattern to other carbapenems. Two strains were then submitted for whole-genome sequencing and bioinformatic analysis. ompK36 was not detected in two isolates. No mutation was observed in bla KPC-2, ompK35 and ompK37 in this study and there was no significant difference of the expression in bla KPC-2, ompK35 and ompK37 between the two isolates (p>0.05). Two isolates were sequence type 11 and harbored bla KPC-2, bla SHV-182 and bla TEM-1B. Compared with KP135194, KP137060 harbored an additional bla NDM-5 positive plasmid. bla NDM-5 gene could be successfully transferred into E. coli J53 at a conjugation frequency of 1.14×10-4. Plasmid stability testing showed that bla KPC-2- and bla NDM-5-harboring plasmids were still stably maintained in the hosts. Growth assay and growth competition experiments showed there was no significant difference in fitness cost between two CR-KP isolates. Our study described the acquisition of a bla NDM-5-harboring plasmid leading to resistance to ceftazidime/avibactam in KPC-2-producing Klebsiella pneumoniae during treatment. This phenomenon deserves further exploration.
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Affiliation(s)
- Jiangqing Huang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Shengcen Zhang
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zhichang Zhao
- Department of Pharmacy, Fujian Medical University Union Hospital, Fuzhou, China
| | - Min Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou, China
| | - Yingping Cao
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
| | - Bin Li
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, China
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11
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ODFM, an omics data resource from microorganisms associated with fermented foods. Sci Data 2021; 8:113. [PMID: 33879798 PMCID: PMC8058077 DOI: 10.1038/s41597-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 03/23/2021] [Indexed: 11/08/2022] Open
Abstract
ODFM is a data management system that integrates comprehensive omics information for microorganisms associated with various fermented foods, additive ingredients, and seasonings (e.g. kimchi, Korean fermented vegetables, fermented seafood, solar salt, soybean paste, vinegar, beer, cheese, sake, and yogurt). The ODFM archives genome, metagenome, metataxonome, and (meta)transcriptome sequences of fermented food-associated bacteria, archaea, eukaryotic microorganisms, and viruses; 131 bacterial, 38 archaeal, and 28 eukaryotic genomes are now available to users. The ODFM provides both the Basic Local Alignment Search Tool search-based local alignment function as well as average nucleotide identity-based genetic relatedness measurement, enabling gene diversity and taxonomic analyses of an input query against the database. Genome sequences and annotation results of microorganisms are directly downloadable, and the microbial strains registered in the archive library will be available from our culture collection of fermented food-associated microorganisms. The ODFM is a comprehensive database that covers the genomes of an entire microbiome within a specific food ecosystem, providing basic information to evaluate microbial isolates as candidate fermentation starters for fermented food production.
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12
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Rahman A, Bhuiyan OF, Sadique A, Afroze T, Sarker M, Momen AMI, Alam J, Hossain A, Khan I, Rahman KF, Kamruzzaman M, Shams F, Ahsan GU, Hossain M. Whole genome sequencing provides genomic insights into three Morganella morganii strains isolated from bovine rectal swabs in Dhaka, Bangladesh. FEMS Microbiol Lett 2021; 367:5780225. [PMID: 32129839 DOI: 10.1093/femsle/fnaa043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/03/2020] [Indexed: 12/17/2022] Open
Abstract
Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae tribe of the Morganellaceae family, is an unusual opportunistic pathogen mainly responsible for nosocomial and urinary tract infections. While cattle have long been established as a source of a few zoonotic pathogens, no such data has been recorded for M. morganii despite its ubiquitous presence in nature and a number of animal hosts. In this study, draft genomes were produced of three M. morganii isolates from Bangladeshi cattle. The three isolates, named B2, B3 and B5, possessed an average genome size of 3.9 Mp, a GC% of ∼51% and pan and core genomes of 4637 and 3812 genes, respectively. All strains were bearers of the qnrD1 carrying plasmid Col3M and possessed roughly similar virulence profiles and prophage regions. The strains also carried genes that were unique when compared with other publicly available M. morganii genomes. Many of these genes belonged to metabolic pathways associated with adaptation to environmental stresses and were predicted in silico to be borne in genomic islands. The findings of this study expand on the current understanding of M. morganii''s genomic nature and its adaptation in cattle.
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Affiliation(s)
- Aura Rahman
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Omar Faruk Bhuiyan
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Abdus Sadique
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Tamanna Afroze
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Mrinmoy Sarker
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Abdul Mueed Ibne Momen
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Jahidul Alam
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh
| | - Arman Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Imran Khan
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Kazi Fahmida Rahman
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | | | - Fariza Shams
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Gias U Ahsan
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Public Health, North South University, Dhaka, Bangladesh
| | - Maqsud Hossain
- NSU Genome Research Institute (NGRI), North South University, Dhaka, Bangladesh.,Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
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13
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Pan F, Xu Q, Zhang H. Emergence of NDM-5 Producing Carbapenem-Resistant Klebsiella aerogenes in a Pediatric Hospital in Shanghai, China. Front Public Health 2021; 9:621527. [PMID: 33718321 PMCID: PMC7947282 DOI: 10.3389/fpubh.2021.621527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Background: Carbapenem-resistant Klebsiella aerogenes (CRKA) has posed a serious threat for clinical anti-infective therapy. However, the molecular characteristics of CRKA in Shanghai are rarely reported. Objective: This study aimed to investigate the resistance profiles, dissemination mechanism, and molecular characteristics of CRKA strains isolated from children in a pediatric hospital, Shanghai. Method: Fifty CRKA isolates were collected in 2019. Antimicrobial susceptibility of the strains was determined by broth microdilution method. The β-lactamases and outer membrane porin genes were characterized by polymerase chain reaction (PCR). Conjugation experiments were performed to determine the transferability of the plasmids. The plasmids were typed based on their incompatibility group using the PCR-based replicon typing method. Multilocus sequence typing (MLST) and enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) were performed for the genetic relationship. Results: All CRKA strains showed high level of resistance to cephalosporins and carbapenems, but still susceptible to aminoglycosides, colistin, and tigecycline. Forty five of fifty isolates carried blaNDM−5 genes (45/50, 90%), alongside with other β-Lactamase genes including blaCTX−M−1, blaTEM−1, and blaSHV−11 being detected. Loss of ompK35 and ompK36 genes were observed in 14% (7/50) and 28% (14/50), respectively, with 5 isolates lacking both ompK35 and ompK36. MLST analysis demonstrated that the majority of isolates belonged to ST4 (47/50, 94%) and ERIC-PCR fingerprinting was performed to identify NDM-5-producing isolates with approximately or more than 80% similarity levels. Plasmids carrying blaNDM−5 were successfully transferred to the E. coli recipient and plasmid typing showed that IncX3 were the prevalent among CRKA isolates. Conclusions: Our finding revealed the emergence of NDM-5 producing CRKA belonging to ST4 among children in Shanghai. Further attention should be paid to control the horizontal spread of the Class B carbapenemases like NDM in children.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qi Xu
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
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14
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Zhao Q, Berglund B, Zou H, Zhou Z, Xia H, Zhao L, Nilsson LE, Li X. Dissemination of bla NDM-5 via IncX3 plasmids in carbapenem-resistant Enterobacteriaceae among humans and in the environment in an intensive vegetable cultivation area in eastern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116370. [PMID: 33460870 DOI: 10.1016/j.envpol.2020.116370] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/21/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
The environment of a large-scale vegetable production area can be exposed to antibiotic residues and antibiotic-resistant bacteria (ARB) via animal manure and irrigation with contaminated water, which can facilitate the dissemination of ARB. However, the occurrence of ARB in plantation areas and their dissemination in this environment remain largely unexplored. In total, 382 samples including those from vegetable (n = 106), soil (n = 87), well water (n = 24), river water (n = 20), river sediments (n = 20), farmer feces (n = 58) and farmer hands (n = 67) were collected in 2019 from a large-scale cultivation area in Shandong, China. Selective agar plates were used to screen for carbapenem-resistant Enterobacteriaceae (CRE) and whole-genome sequencing and Southern blotting were used to characterise isolates and mobile genetic elements carrying carbapenem resistance determinants. A total of nine NDM-5-producing isolates of Escherichia coli, Klebsiella pneumoniae, and Citrobacter spp. were identified from environmental sources and human feces, all of which were multidrug-resistant. Single nucleotide polymorphism analysis suggested clonal transmission of carbapenem-resistant Citrobacter sedlakii within greenhouse soils in the area. Eight of the isolates carried closely related or identical IncX3 plasmids carrying blaNDM-5, which were shown to be conjugative via filter mating experiments, indicating the highly transmissible nature of this genetic element. Isolates of E. coli and Citrobacter freundii were detected in the feces of local farm workers and contained similar IncX3 plasmids with blaNDM-5 environmental isolates, suggesting a potential risk of CRE transfer from the work environment to the farm workers. Thus, further research is required to investigate the potential health risks associated with environmental exposure to CRE in vegetable cultivation areas.
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Affiliation(s)
- Qian Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Björn Berglund
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85, Linköping, Sweden; State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ziyu Zhou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiyu Xia
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lennart E Nilsson
- Department of Biomedical and Clinical Sciences, Linköping University, 581 85, Linköping, Sweden
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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15
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Singh AK, Das S, Kumar S, Gajamer VR, Najar IN, Lepcha YD, Tiwari HK, Singh S. Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli. Front Microbiol 2020; 11:581072. [PMID: 33224119 PMCID: PMC7674312 DOI: 10.3389/fmicb.2020.581072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/18/2020] [Indexed: 12/25/2022] Open
Abstract
Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.
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Affiliation(s)
- Ashish Kumar Singh
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Saurav Das
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Santosh Kumar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Varsha Rani Gajamer
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Ishfaq Nabi Najar
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Yangchen D. Lepcha
- State Institute of Rural Development (SIRD), Government of Sikkim, Gangtok, India
| | - Hare Krishna Tiwari
- Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Samer Singh
- Centre of Experimental Medicine and Surgery (CEMS), Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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16
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Yin D, Lin Y, Li Z, Ma H, Lu L, Wang K, Yang L, Du X, Li P, Qi K, Song H. Characterization of a Novel NDM-5-Harboring Plasmid from a Carbapenem-Resistant Escherichia coli Isolate from China. Infect Drug Resist 2020; 13:3929-3935. [PMID: 33173318 PMCID: PMC7646509 DOI: 10.2147/idr.s277997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
Background A carbapenem-resistant Escherichia coli (sequence type 5415) strain was isolated from a male patient through routine surveillance in 2018 in Guangzhou, China. Materials and Methods Bacteria were isolated from a sputum culture and identified by using the Vitek 2 compact system. The blaNDM-5 gene was amplified and confirmed by sequencing. Antimicrobial susceptibility testing was determined by a Vitek 2 compact system. The blaNDM-5 gene was located by Southern blotting. Whole-genome sequencing was carried out using both Illumina MiSeq and Oxford Nanopore MinION. Results S1-PFGE and Southern blotting showed that the bla NDM-5 gene was located on a novel 66-kb IncFII [F2:A-:B-] plasmid. Conjugation assays revealed that the bla NDM-5-bearing plasmid was self-transferrable. Genomic sequencing and comparative analysis suggested that plasmid p2947-NDM5 likely originated from a combination of an IncFII-type backbone and the bla NDM-5 flanking genetic elements. Conclusion This is the first report of an ST5414 E. coli strain expressing an NDM-5 β-lactamase. This study highlights the genetic complexity of bla NDM-5 carrying plasmids and the urgent need for continuous active monitoring.
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Affiliation(s)
- Dongdong Yin
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control College of Animal Science and Technology, Anhui Agricultural University, Hefei, People's Republic of China
| | - Yanfeng Lin
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Zhonghong Li
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,College of Environmental and Chemical Engineering, Nanchang Hangkong University, Nanchang, People's Republic of China
| | - Hui Ma
- The Sixth Medical Center of PLA General Hospital, Beijing, People's Republic of China
| | - Lanfen Lu
- Department of Laboratory Diagnosis, Sun Yat-Sen University Affiliated Zhongshan Hospital, Zhongshan, People's Republic of China
| | - Kaiying Wang
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Lang Yang
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China.,Institute for Disease Control and Prevention, AMMS, Beijing, People's Republic of China
| | - Xinying Du
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
| | - Peng Li
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control College of Animal Science and Technology, Anhui Agricultural University, Hefei, People's Republic of China
| | - Hongbin Song
- Center for Disease Control and Prevention of PLA, Beijing, People's Republic of China
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17
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Taggar G, Attiq Rheman M, Boerlin P, Diarra MS. Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment. Antibiotics (Basel) 2020; 9:antibiotics9100693. [PMID: 33066205 PMCID: PMC7602032 DOI: 10.3390/antibiotics9100693] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (blaKPC), class B (blaIMP, blaVIM, blaNDM), and class D (blaOXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.
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Affiliation(s)
- Gurleen Taggar
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Muhammad Attiq Rheman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Moussa Sory Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Correspondence:
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Shao C, Hao Y, Wang Y, Jiang M, Jin Y. Genotypic and Phenotypic Characterization of bla NDM-7-Harboring IncX3 Plasmid in a ST11 Klebsiella pneumoniae Isolated From a Pediatric Patient in China. Front Microbiol 2020; 11:576823. [PMID: 33123108 PMCID: PMC7566911 DOI: 10.3389/fmicb.2020.576823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 09/07/2020] [Indexed: 01/08/2023] Open
Abstract
NDM-7, a variant of New Delhi metallo-beta-lactamases (NDM), has the highest carbapenem-hydrolyzing activity. NDM-7-producing enterobacteria have been reported in many countries. In this study, we reported NDM-7 production in ST11 Klebsiella pneumoniae isolated from a boy hospitalized in the pediatric intensive care unit of a teaching hospital in China. The isolate exhibited resistance to β-lactam antimicrobials, quinolones, and trimethoprim/sulfamethoxazole, and it harbored bla NDM- 7, bla CTX-M- 15, qnrA, qnrB, and qnrS. The serotype of the isolated K. pneumoniae was assigned as K1, and it contained three virulence genes, including kfuBC, uge, and fim. The bla NDM- 7 gene was located on a conjugative IncX3 plasmid designated as pB14NDM-7. This plasmid was fully sequenced and compared with the available bla NDM- 7-harboring IncX3 plasmids. pB14NDM-7 contained a conserved genetic context of ISkox3-umuD-IS26-ΔTn125-IS5-ΔTn125-IS3000-ΔTn2. pB14NDM-7 showed 99% nucleotide identity and the same genetic context with three bla NDM- 7-harboring IncX3 plasmids obtained from Escherichia coli in China. Our results indicate that IncX3 plasmid may contribute to the prevalence of bla NDM- 7 in China. The high prevalence of NDM variants worldwide highlights the critical need for careful monitoring and control of the rapid dissemination of bla NDM.
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Affiliation(s)
- Chunhong Shao
- Clinical Laboratory of Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yingying Hao
- Clinical Laboratory of Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yong Wang
- Clinical Laboratory of Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Meijie Jiang
- Clinical Laboratory of Taian City Central Hospital, Tai'an, China
| | - Yan Jin
- Clinical Laboratory of Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Palmieri N, Hess C, Hess M, Alispahic M. Sequencing of five poultry strains elucidates phylogenetic relationships and divergence in virulence genes in Morganella morganii. BMC Genomics 2020; 21:579. [PMID: 32831012 PMCID: PMC7446228 DOI: 10.1186/s12864-020-07001-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/17/2020] [Indexed: 12/31/2022] Open
Abstract
Background M. morganii is a bacterium frequently associated with urinary infections in humans. While many human strains are sequenced, only the genomes of few poultry strains are available. Here, we performed a detailed characterization of five highly resistant Morganella morganii strains isolated in association with Escherichia coli from diseased domestic Austrian poultry flocks, namely geese, turkeys and chicken layers. Additionally, we sequenced the genomes of these strains by NGS and analyzed phylogenetic clustering, resistance and virulence genes in the context of host-specificity. Results Two strains were identified to be Extended Spectrum Beta Lactamase (ESBL) and one as AmpC beta-lactamases (AMP-C) phenotype, while two were ESBL negative. By integrating the genome sequences of these five poultry strains with all the available M. morganii genomes, we constructed a phylogenetic tree that clearly separates the Morganella genus into two clusters (M1 and M2), which approximately reflect the proposed subspecies classification (morganii and sibonii). Additionally, we found no association between phylogenetic structure and host, suggesting interspecies transmission. All five poultry strains contained genes for resistance to aminocoumarins, beta-lactams, colistin, elfamycins, fluoroquinolones, phenicol, rifampin and tetracycline. A comparative genomics analysis of virulence genes showed acquisition of novel virulence genes involved in secretion system and adherence in cluster M2. We showed that some of these genes were acquired by horizontal gene transfer from closely related Morganellaceae species and propose that novel virulence genes could be responsible for expansion of tissue tropism in M. morganii. Finally, we detected variability in copy number and high sequence divergence in toxin genes and provided evidence for positive selection in insecticidal toxins genes, likely reflecting host-related adaptations. Conclusions In summary, this study describes i) the first isolation and characterization of M. morganii from goose and turkey, ii) a large-scale genetic analysis of M. morganii and an attempt to generate a global picture of the M. morganii intraspecific phylogenetic structure.
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Affiliation(s)
- Nicola Palmieri
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria
| | - Merima Alispahic
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinärplatz 1, 1210, Vienna, Austria.
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The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel) 2020; 9:antibiotics9040186. [PMID: 32316342 PMCID: PMC7235769 DOI: 10.3390/antibiotics9040186] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and can be encoded by both chromosomal and plasmid-mediated genes. These enzymes represent the most potent β-lactamases, which hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillin, and aztreonam. The major issues associated with carbapenemase production are clinical due to compromising the activity of the last resort antibiotics used for treating serious infections, and epidemiological due to their dissemination into various bacteria across almost all geographic regions. Carbapenemase-producing Enterobacteriaceae have received more attention upon their first report in the early 1990s. Currently, there is increased awareness of the impact of nonfermenting bacteria, such as Acinetobacter baumannii and Pseudomonas aeruginosa, as well as other Gram-negative bacteria that are carbapenemase-producers. Outside the scope of clinical importance, carbapenemases are also detected in bacteria from environmental and zoonotic niches, which raises greater concerns over their prevalence, and the need for public health measures to control consequences of their propagation. The aims of the current review are to define and categorize the different families of carbapenemases, and to overview the main lines of their spread across different bacterial groups.
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Shrestha S, Tada T, Sherchan JB, Uchida H, Hishinuma T, Oshiro S, Morioka S, Kattel H, Kirikae T, Sherchand JB. Highly multidrug-resistant Morganella morganii clinical isolates from Nepal co-producing NDM-type metallo-β-lactamases and the 16S rRNA methylase ArmA. J Med Microbiol 2020; 69:572-575. [PMID: 32100711 DOI: 10.1099/jmm.0.001160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Morganella morganii can harbour extended-spectrum β-lactamases and carbapenemases, resulting in increased resistance to multiple antibiotics and a high mortality rate. This study describes the emergence of highly multidrug-resistant clinical isolates of M. morganii from Nepal co-producing NDM-type metallo-β-lactamases, including NDM-1 and NDM-5, and the 16S rRNA methylase ArmA. This is the first report of M. morganii clinical isolates from Nepal co-producing NDM-1/-5 and ArmA. It is important to establish infection control systems and effective treatments against multidrug-resistant M. morganii.
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Affiliation(s)
- Shovita Shrestha
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Jatan B Sherchan
- Department of Medical Microbiology, Kathmandu University School of Medical Sciences, Dhulikhel, Nepal
| | - Hiroki Uchida
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tomomi Hishinuma
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satoshi Oshiro
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | | | - Hari Kattel
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Jeevan B Sherchand
- Department of Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
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