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Thuy TTD, Lu HF, Kuo PY, Lin WH, Lin TP, Lee YT, Duong TTT, Wang MC, Lee YH, Wen LL, Chen YC, Kao CY. Whole-genome-sequence-based characterization of an NDM-5-producing uropathogenic Escherichia coli EC1390. BMC Microbiol 2022; 22:150. [PMID: 35668362 PMCID: PMC9172118 DOI: 10.1186/s12866-022-02562-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Urinary tract infection (UTI) is one of the most common outpatient bacterial infections. In this study, we isolated and characterized an extensively-drug resistant (XDR) NDM-5-producing Escherichia coli EC1390 from a UTI patient by using whole-genome sequencing (WGS) in combination with phenotypic assays. Methods Antimicrobial susceptibility to 23 drugs was determined by disk diffusion method. The genome sequence of EC1390 was determined by Nanopore MinION MK1C platform. Conjugation assays were performed to test the transferability of EC1390 plasmids to E. coli recipient C600. Phenotypic assays, including growth curve, biofilm formation, iron acquisition ability, and cell adhesion, were performed to characterize the function of EC1390 plasmids. Results Our results showed that EC1390 was only susceptible to tigecycline and colistin, and thus was classified as XDR E. coli. A de novo genome assembly was generated using Nanopore 73,050 reads with an N50 value of 20,936 bp and an N90 value of 7,624 bp. WGS analysis showed that EC1390 belonged to the O101-H10 serotype and phylogenetic group A E. coli. Moreover, EC1390 contained 2 conjugative plasmids with a replicon IncFIA (pEC1390-1 with 156,286 bp) and IncFII (pEC1390-2 with 71,840 bp), respectively. No significant difference was observed in the bacterial growth rate in LB broth and iron acquisition ability between C600, C600 containing pEC1390-1, C600 containing pEC1390-2, and C600 containing pEC1390-1 and pEC1390-2. However, the bacterial growth rate in nutrition-limited M9 broth was increased in C600 containing pEC1390-2, and the cell adhesion ability was increased in C600 containing both pEC1390-1 and pEC1390-2. Moreover, these plasmids modulated the biofilm formation under different conditions. Conclusions In summary, we characterized the genome of XDR-E. coli EC1390 and identified two plasmids contributing to the antimicrobial resistance, growth of bacteria in a nutrition-limited medium, biofilm formation, and cell adhesion. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02562-6.
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Affiliation(s)
- Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Hsu-Feng Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung City, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Ping Lin
- Department of Urology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Tzu Lee
- Department of Emergency Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Tran Thi Thuy Duong
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Ming-Cheng Wang
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Hong Lee
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan
| | - Li-Li Wen
- Department of Clinical Laboratory, En Chu Kong Hospital, New Taipei City, Taiwan
| | - Yu-Chen Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, No.155, Sec.2, Linong Street, Taipei, 112, Taiwan.
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Wollenberg KR, Jeffrey BM, Harris MA, Gabrielian A, Hurt DE, Rosenthal A. Patterns of genomic interrelatedness of publicly available samples in the TB portals database. Tuberculosis (Edinb) 2022; 133:102171. [PMID: 35101846 PMCID: PMC8997244 DOI: 10.1016/j.tube.2022.102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 10/19/2022]
Abstract
The TB Portals program is an international collaboration for the collection and dissemination of tuberculosis data from patient cases focused on drug resistance. The central database is a patient-oriented resource containing both patient and pathogen clinical and genomic information. Herein we provide a summary of the pathogen genomic data available through the TB Portals and show one potential application by examining patterns of genomic pairwise distances. Distributions of pairwise distances highlight overall patterns of genome variability within and between Mycobacterium tuberculosis phylogenomic lineages. Closely related isolates (based on whole-genome pairwise distances and time between sample collection dates) from different countries were identified as potential evidence of international transmission of drug-resistant tuberculosis. These high-level views of genomic relatedness provide information that can stimulate hypotheses for further and more detailed research.
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Affiliation(s)
- Kurt R. Wollenberg
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Brendan M. Jeffrey
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael A. Harris
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA,To whom correspondence should be addressed: . Telephone: 301-761-6746
| | - Andrei Gabrielian
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Darrell E. Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
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Loconsole D, Accogli M, Monaco M, Del Grosso M, De Robertis AL, Morea A, Capozzi L, Del Sambro L, Simone A, De Letteriis V, Quarto M, Parisi A, Chironna M. First detection of autochthonous extensively drug-resistant NDM-1 Pseudomonas aeruginosa ST235 from a patient with bloodstream infection in Italy, October 2019. Antimicrob Resist Infect Control 2020; 9:73. [PMID: 32450907 PMCID: PMC7249406 DOI: 10.1186/s13756-020-00734-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Pseudomonas aeruginosa (PA) is one of the most common and serious causes of healthcare-associated bacteremia. The emergence and dissemination of multidrug-resistant (MDR) and extensively drug-resistant (XDR) PA strains pose a major clinical concern. ST235-PA is a high-risk clone which shows a high capacity to acquire antibiotic resistance. Here we describe the first autochthonous New Delhi metallo-β-lactamase (NDM)-producing Pseudomonas aeruginosa ST235 identified in Italy. Case presentation In October 2019, a patient residing in an elderly health care and rehabilitation facility, was hospitalized and died from sepsis caused by an XDR-PA. The strain belonged to the high-risk clone sequence type ST235. Whole genome sequencing (WGS) revealed the presence of genes encoding NDM-1 and multiple β-lactamases, many clinically significant multidrug efflux pump complexes and also the virulence gene ExoU, which is associated with a high cytotoxic phenotype. Conclusions Few strains of NDM-1-PA have been identified worldwide, all belonging to ST235. The combination of ST235 and ExoU is a predictor of highly unfavorable prognosis. The potential spread of these high-risk clones in healthcare settings is worrisome because treatment options are limited. Early identification of high-risk clones could help in outbreaks investigation and infections control.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | | | | | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy.
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Gkentzi D, Tsintoni A, Christopoulou I, Mamalis I, Paliogianni F, Assimakopoulos SF, Marangos M, Dimitriou G. Extensively-drug resistant Acinetobacter baumannii bacteremia in neonates: effective treatment with the combination of colistin and ampicillin/sulbactam. J Chemother 2020; 32:103-106. [PMID: 31992156 DOI: 10.1080/1120009x.2020.1716478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Acinetobacter baumannii has evolved as a major pathogen of outbreaks in the healthcare setting with increased morbidity and mortality. In neonates, treatment can be quite challenging due to the resistance profile of A. baumannii as well as limited data on pharmakokinetics and pharmakodynamics of antibiotics in this age group. We present an outbreak of eight cases of extensively-drug resistant (XDR) A. baumannii bacteremias successfully managed with the combination of colistin with high dose ampicillin/sulbactam.
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Affiliation(s)
- Despoina Gkentzi
- Department of Pediatrics, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Asimina Tsintoni
- Department of Pediatrics, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Irini Christopoulou
- Department of Pediatrics, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Ilias Mamalis
- Department of Pediatrics, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Fotini Paliogianni
- Department of Microbiology, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Stelios F Assimakopoulos
- Department of Infectious Diseases, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Markos Marangos
- Department of Infectious Diseases, University General Hospital of Patras, Patras Medical School, Rio, Greece
| | - Gabriel Dimitriou
- Department of Pediatrics, University General Hospital of Patras, Patras Medical School, Rio, Greece
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Wollenberg K, Harris M, Gabrielian A, Ciobanu N, Chesov D, Long A, Taaffe J, Hurt D, Rosenthal A, Tartakovsky M, Crudu V. A retrospective genomic analysis of drug-resistant strains of M. tuberculosis in a high-burden setting, with an emphasis on comparative diagnostics and reactivation and reinfection status. BMC Infect Dis 2020; 20:17. [PMID: 31910804 PMCID: PMC6947865 DOI: 10.1186/s12879-019-4739-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/27/2019] [Indexed: 12/01/2022] Open
Abstract
Background Recurrence of drug-resistant tuberculosis (DR-TB) after treatment occurs through relapse of the initial infection or reinfection by a new drug-resistant strain. Outbreaks of DR-TB in high burden regions present unique challenges in determining recurrence status for effective disease management and treatment. In the Republic of Moldova the burden of DR-TB is exceptionally high, with many cases presenting as recurrent. Methods We performed a retrospective analysis of Mycobacterium tuberculosis from Moldova to better understand the genomic basis of drug resistance and its effect on the determination of recurrence status in a high DR-burden environment. To do this we analyzed genomes from 278 isolates collected from 189 patients, including 87 patients with longitudinal samples. These pathogen genomes were sequenced using Illumina technology, and SNP panels were generated for each sample for use in phylogenetic and network analysis. Discordance between genomic resistance profiles and clinical drug-resistance test results was examined in detail to assess the possibility of mixed infection. Results There were clusters of multiple patients with 10 or fewer differences among DR-TB samples, which is evidence of person-to-person transmission of DR-TB. Analysis of longitudinally collected isolates revealed that many infections exhibited little change over time, though 35 patients demonstrated reinfection by divergent (number of differences > 10) lineages. Additionally, several same-lineage sample pairs were found to be more divergent than expected for a relapsed infection. Network analysis of the H3/4.2.1 clade found very close relationships among 61 of these samples, making differentiation of reactivation and reinfection difficult. There was discordance between genomic profile and clinical drug sensitivity test results in twelve samples, and four of these had low level (but not statistically significant) variation at DR SNPs suggesting low-level mixed infections. Conclusions Whole-genome sequencing provided a detailed view of the genealogical structure of the DR-TB epidemic in Moldova, showing that reinfection may be more prevalent than currently recognized. We also found increased evidence of mixed infection, which could be more robustly characterized with deeper levels of genomic sequencing.
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Affiliation(s)
- Kurt Wollenberg
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Michael Harris
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrei Gabrielian
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nelly Ciobanu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Moldova.,Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Alyssa Long
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica Taaffe
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Darrell Hurt
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael Tartakovsky
- Office of Cyber Infrastructure & Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeriu Crudu
- Microbiology and Morphology Laboratory, Institute of Phthisiopneumology, Chisnau, Moldova
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