1
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O’Connor L, Heyderman R. The challenges of defining the human nasopharyngeal resistome. Trends Microbiol 2023:S0966-842X(23)00056-2. [DOI: 10.1016/j.tim.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 04/03/2023]
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2
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Wang P, Jiang X, Mu K, Jing Y, Yin Z, Cui Y, Li C, Luo X, Chen F, Yu T, Zhu Z, Sun Y, Chen F, Zhou D. DANMEL: A manually curated reference database for analyzing mobile genetic elements associated with bacterial drug resistance. MLIFE 2022; 1:460-464. [PMID: 38818485 PMCID: PMC10989931 DOI: 10.1002/mlf2.12046] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 06/01/2024]
Abstract
We have developed a manually curated online reference database, DANMEL (http://124.239.252.254/danmel/), that addresses the lack of accurate dissection and annotation of the genetic structures of mobile genetic elements (MGEs) with genes for drug resistance. DANMEL contains accurately annotated and genetically dissected reference MGEs covering 5 categories and 135 subcategories/subfamilies of MGEs. Further, DANMEL provides a detailed guide on how to precisely annotate MGEs. DANMEL also provides SEARCH/BLAST functions to facilitate finding reference MGEs. Overall, DANMEL will aid researchers to conduct in-depth genetic analysis of sequenced bacterial MGEs with drug-resistance genes and further facilitate a better understanding of bacterial MGEs associated with drug resistance at a genomic level.
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Affiliation(s)
- Peng Wang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
- Beijing Institute of Genomics, Chinese Academy of SciencesChina National Center for BioinformationBeijingChina
| | - Kai Mu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Ying Jing
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yujun Cui
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Cuidan Li
- Beijing Institute of Genomics, Chinese Academy of SciencesChina National Center for BioinformationBeijingChina
| | - Xinhua Luo
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Ting Yu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhichen Zhu
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yansong Sun
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Fei Chen
- Beijing Institute of Genomics, Chinese Academy of SciencesChina National Center for BioinformationBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
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3
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Trivedi R, Upadhyay TK, Kausar MA, Saeed A, Sharangi AB, Almatroudi A, Alabdallah NM, Saeed M, Aqil F. Nanotechnological interventions of the microbiome as a next-generation antimicrobial therapy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155085. [PMID: 35398124 DOI: 10.1016/j.scitotenv.2022.155085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/22/2022] [Accepted: 04/03/2022] [Indexed: 06/14/2023]
Abstract
The rise of antimicrobial resistance (AMR) impacts public health due to the diminished potency of existing antibiotics. The microbiome plays an important role in the host's immune system activity and shows the history of exposure to antimicrobials and its manipulation in combating antimicrobial resistance. Advancements in gene technologies, DNA sequencing, and computational biology have emerged as powerful platforms to better understand the relationship between animals and microorganisms (MOs). The past few years have witnessed an increase in the use of nanotechnology, both in industry and in academia, as tools to tackle antimicrobial resistance. New strategies of microbiome manipulation have been developed, such as the use of prebiotics, probiotics, peptides, antibodies, an appropriate diet, phage therapy, and the use of various nanotechnological techniques. Owing to the research outcomes, targeted delivery of antimicrobials with some modifications with nanoparticles can lead to the destruction of resistant microbial cells. In addition, nanoparticles have been studied for their potential antimicrobial effects both in vitro and in vivo. In this review, we highlight key opportunistic areas for applying nanotechnologies with the aim of manipulating the microbiome for the treatment of antimicrobial resistance. Besides providing a detailed review on various nanomaterials, technologies, opportunities, technical needs, and potential approaches for the manipulation of the microbiome to address these challenges, we discuss future challenges and our perspective.
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Affiliation(s)
- Rashmi Trivedi
- Department of Biotechnology, Parul Institute of Applied Sciences and Animal Cell Culture and Immunobiochemistry Lab, Centre of Research for Development, Parul University, Vadodara 391760, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Animal Cell Culture and Immunobiochemistry Lab, Centre of Research for Development, Parul University, Vadodara 391760, India.
| | - Mohd Adnan Kausar
- Department of Biochemistry, College of Medicine, University of Hail, PO Box 2240, Hail, Saudi Arabia
| | - Amir Saeed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, PO Box 2240, Hail, Saudi Arabia
| | - Amit Baran Sharangi
- Department of Plantation Spices Medicinal and Aromatic Crops, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur 741252, India
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Qassim 51431, Saudi Arabia
| | - Nadiyah M Alabdallah
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441 Dammam, Saudi Arabia
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, PO Box 2240, Hail, Saudi Arabia.
| | - Farrukh Aqil
- UofL Health - Brown Cancer Center and Department of Medicine, University of Louisville, Louisville, KY 40202, USA.
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4
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Krawczyk B, Wysocka M, Michalik M, Gołębiewska J. Urinary Tract Infections Caused by K. pneumoniae in Kidney Transplant Recipients – Epidemiology, Virulence and Antibiotic Resistance. Front Cell Infect Microbiol 2022; 12:861374. [PMID: 35531341 PMCID: PMC9068989 DOI: 10.3389/fcimb.2022.861374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Urinary tract infections are the most common complication in kidney transplant recipients, possibly resulting in the deterioration of a long-term kidney allograft function and an increased risk of recipient’s death. K. pneumoniae has emerged as one of the most prevalent etiologic agents in the context of recurrent urinary tract infections, especially with multidrug resistant strains. This paper discusses the epidemiology and risk factors associated with urinary tract infections in kidney transplant recipients, multi-drug resistance of K. pneumoniae (ESBL, KPC, NDM), treatment and pathogenesis of K. pneumoniae infections, and possible causes of recurrent UTIs. It also addresses the issue of colonization/becoming a carrier of K. pneumoniae in the gastrointestinal tract and asymptomatic bacteriuria in relation to a symptomatic UTI development and epidemiology.
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Affiliation(s)
- Beata Krawczyk
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
- *Correspondence: Beata Krawczyk,
| | - Magdalena Wysocka
- Department of Molecular Biotechnology and Microbiology, Faculty of Chemistry, Gdańsk University of Technology, Gdańsk, Poland
| | | | - Justyna Gołębiewska
- Department of Nephrology, Transplantology and Internal Medicine, Medical University of Gdańsk, Gdańsk, Poland
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5
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Review and Comparison of Antimicrobial Resistance Gene Databases. Antibiotics (Basel) 2022; 11:antibiotics11030339. [PMID: 35326803 PMCID: PMC8944830 DOI: 10.3390/antibiotics11030339] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however, can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation; however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.
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6
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Maryam L, Usmani SS, Raghava GPS. Computational resources in the management of antibiotic resistance: Speeding up drug discovery. Drug Discov Today 2021; 26:2138-2151. [PMID: 33892146 DOI: 10.1016/j.drudis.2021.04.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/24/2020] [Accepted: 04/12/2021] [Indexed: 01/19/2023]
Abstract
This article reviews more than 50 computational resources developed in past two decades for forecasting of antibiotic resistance (AR)-associated mutations, genes and genomes. More than 30 databases have been developed for AR-associated information, but only a fraction of them are updated regularly. A large number of methods have been developed to find AR genes, mutations and genomes, with most of them based on similarity-search tools such as BLAST and HMMER. In addition, methods have been developed to predict the inhibition potential of antibiotics against a bacterial strain from the whole-genome data of bacteria. This review also discuss computational resources that can be used to manage the treatment of AR-associated diseases.
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Affiliation(s)
- Lubna Maryam
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India
| | - Salman Sadullah Usmani
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi 110020, India.
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7
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de Abreu VAC, Perdigão J, Almeida S. Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview. Front Genet 2021; 11:575592. [PMID: 33537056 PMCID: PMC7848172 DOI: 10.3389/fgene.2020.575592] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/04/2020] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance is a major global public health problem, which develops when pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic recombination between commensal and pathogenic microbes. The resistome is a collection of all ARGs. In microorganisms, the primary method of ARG acquisition is horizontal gene transfer (HGT). Thus, understanding and identifying HGTs, can provide insight into the mechanisms of antimicrobial resistance transmission and dissemination. The use of high-throughput sequencing technologies has made the analysis of ARG sequences feasible and accessible. In particular, the metagenomic approach has facilitated the identification of community-based antimicrobial resistance. This approach is useful, as it allows access to the genomic data in an environmental sample without the need to isolate and culture microorganisms prior to analysis. Here, we aimed to reflect on the challenges of analyzing metagenomic data in the three main approaches for studying antimicrobial resistance: (i) analysis of microbial diversity, (ii) functional gene analysis, and (iii) searching the most complete and pertinent resistome databases.
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Affiliation(s)
- Vinicius A C de Abreu
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - José Perdigão
- Laboratório de Bioinformática e Computação de Alto Desempenho (LaBioCad), Faculdade de Computação (FACOMP), Universidade Federal do Pará, Belém, Brazil
| | - Sintia Almeida
- Central de Genômica e Bioinformática (CeGenBio), Núcleo de Pesquisa e Desenvolvimento de Medicamentos (NPDM), Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, Brazil
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8
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Chis AA, Dobrea C, Morgovan C, Arseniu AM, Rus LL, Butuca A, Juncan AM, Totan M, Vonica-Tincu AL, Cormos G, Muntean AC, Muresan ML, Gligor FG, Frum A. Applications and Limitations of Dendrimers in Biomedicine. Molecules 2020; 25:E3982. [PMID: 32882920 PMCID: PMC7504821 DOI: 10.3390/molecules25173982] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/11/2022] Open
Abstract
Biomedicine represents one of the main study areas for dendrimers, which have proven to be valuable both in diagnostics and therapy, due to their capacity for improving solubility, absorption, bioavailability and targeted distribution. Molecular cytotoxicity constitutes a limiting characteristic, especially for cationic and higher-generation dendrimers. Antineoplastic research of dendrimers has been widely developed, and several types of poly(amidoamine) and poly(propylene imine) dendrimer complexes with doxorubicin, paclitaxel, imatinib, sunitinib, cisplatin, melphalan and methotrexate have shown an improvement in comparison with the drug molecule alone. The anti-inflammatory therapy focused on dendrimer complexes of ibuprofen, indomethacin, piroxicam, ketoprofen and diflunisal. In the context of the development of antibiotic-resistant bacterial strains, dendrimer complexes of fluoroquinolones, macrolides, beta-lactamines and aminoglycosides have shown promising effects. Regarding antiviral therapy, studies have been performed to develop dendrimer conjugates with tenofovir, maraviroc, zidovudine, oseltamivir and acyclovir, among others. Furthermore, cardiovascular therapy has strongly addressed dendrimers. Employed in imaging diagnostics, dendrimers reduce the dosage required to obtain images, thus improving the efficiency of radioisotopes. Dendrimers are macromolecular structures with multiple advantages that can suffer modifications depending on the chemical nature of the drug that has to be transported. The results obtained so far encourage the pursuit of new studies.
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Affiliation(s)
| | - Carmen Dobrea
- Preclinical Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, 2A Lucian Blaga St., 550169 Sibiu, Romania; (A.A.C.); (A.M.A.); (L.L.R.); (A.B.); (A.M.J.); (M.T.); (A.L.V.-T.); (G.C.); (A.C.M.); (M.L.M.); (F.G.G.); (A.F.)
| | - Claudiu Morgovan
- Preclinical Department, Faculty of Medicine, “Lucian Blaga” University of Sibiu, 2A Lucian Blaga St., 550169 Sibiu, Romania; (A.A.C.); (A.M.A.); (L.L.R.); (A.B.); (A.M.J.); (M.T.); (A.L.V.-T.); (G.C.); (A.C.M.); (M.L.M.); (F.G.G.); (A.F.)
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9
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Characterization of antibiotic resistance integrons harbored by Romanian Escherichia coli uropathogenic strains. REV ROMANA MED LAB 2020. [DOI: 10.2478/rrlm-2020-0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Because little is known about the integrons which constitute an important means of spreading resistance in bacteria circulating in Romania, this study aimed to detect antibiotic resistance gene cassettes embedded in integrons in a convenient collection of 60 ciprofloxacin-resistant Escherichia coli isolates of various phylogroups, associated with community-acquired urinary tract infections. Characterization of the integrons was accomplished by PCR, restriction fragment length polymorphism typing, and DNA sequencing of each identified type. More than half of the tested E. coli strains were positive for integrons of class 1 (31 strains) or 2 (1 strain). These strains derived more frequently from phylogenetic groups A (15 of 21 strains), B1 (10 of 14 strains), and F (3 of 4 strains), respectively. While 20 strains carried class 1 integrons which could be assigned to nine types, eleven strains carried integrons that lacked the 3’-end conserved segment. The attempts made to characterize the gene cassettes located within the variable region of the various integrons identified in this study revealed the presence of genes encoding resistance to trimethoprim, aminoglycosides, beta-lactams or chloramphenicol. The evidence of transferable resistance determinants already established in the autochthonous E. coli strains highlights the need for improved control of resistance-carrying bacteria.
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10
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Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen ALV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B, Faltyn M, Hernandez-Koutoucheva A, Sharma AN, Bordeleau E, Pawlowski AC, Zubyk HL, Dooley D, Griffiths E, Maguire F, Winsor GL, Beiko RG, Brinkman FSL, Hsiao WWL, Domselaar GV, McArthur AG. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517-D525. [PMID: 31665441 PMCID: PMC7145624 DOI: 10.1093/nar/gkz935] [Citation(s) in RCA: 1179] [Impact Index Per Article: 294.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
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Affiliation(s)
- Brian P Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Tammy T Y Lau
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Kara K Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Mégane Bouchard
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Bachelor of Health Sciences Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Arman Edalatmand
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - William Huynh
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Anna-Lisa V Nguyen
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Bachelor of Health Sciences Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Annie A Cheng
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Sihan Liu
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Sally Y Min
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Anatoly Miroshnichenko
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Hiu-Ki Tran
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Rafik E Werfalli
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Jalees A Nasir
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Martins Oloni
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - David J Speicher
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Alexandra Florescu
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Bachelor of Health Sciences Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Bhavya Singh
- Honours Biology Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Mateusz Faltyn
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Bachelor of Arts & Science Program, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | | | - Arjun N Sharma
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Andrew C Pawlowski
- Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Haley L Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Damion Dooley
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5, British Columbia, Canada
| | - Emma Griffiths
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 1W5, Canada
| | - Geoff L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, B3H 1W5, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - William W L Hsiao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, V6T 2B5, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
- British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, British Columbia, V5Z 4R4, Canada
| | - Gary V Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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11
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Botelho J, Lood C, Partridge SR, van Noort V, Lavigne R, Grosso F, Peixe L. Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain. Emerg Microbes Infect 2019; 8:1186-1194. [PMID: 31381486 PMCID: PMC6713103 DOI: 10.1080/22221751.2019.1648182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Horizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP_PS_41. Average nucleotide identity analyses revealed that FFUP_PS_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP_PS_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.
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Affiliation(s)
- João Botelho
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Cédric Lood
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Sally R Partridge
- d Centre for Microbiology and Infectious Diseases, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital , Sydney , Australia
| | - Vera van Noort
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,e Institute of Biology, Leiden University , Leiden , The Netherlands
| | - Rob Lavigne
- c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Filipa Grosso
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Luísa Peixe
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
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Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother 2019; 63:AAC.00483-19. [PMID: 31427293 DOI: 10.1128/aac.00483-19] [Citation(s) in RCA: 674] [Impact Index Per Article: 134.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/11/2019] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major public health problem that requires publicly available tools for rapid analysis. To identify AMR genes in whole-genome sequences, the National Center for Biotechnology Information (NCBI) has produced AMRFinder, a tool that identifies AMR genes using a high-quality curated AMR gene reference database. The Bacterial Antimicrobial Resistance Reference Gene Database consists of up-to-date gene nomenclature, a set of hidden Markov models (HMMs), and a curated protein family hierarchy. Currently, it contains 4,579 antimicrobial resistance proteins and more than 560 HMMs. Here, we describe AMRFinder and its associated database. To assess the predictive ability of AMRFinder, we measured the consistency between predicted AMR genotypes from AMRFinder and resistance phenotypes of 6,242 isolates from the National Antimicrobial Resistance Monitoring System (NARMS). This included 5,425 Salmonella enterica, 770 Campylobacter spp., and 47 Escherichia coli isolates phenotypically tested against various antimicrobial agents. Of 87,679 susceptibility tests performed, 98.4% were consistent with predictions. To assess the accuracy of AMRFinder, we compared its gene symbol output with that of a 2017 version of ResFinder, another publicly available resistance gene detection system. Most gene calls were identical, but there were 1,229 gene symbol differences (8.8%) between them, with differences due to both algorithmic differences and database composition. AMRFinder missed 16 loci that ResFinder found, while ResFinder missed 216 loci that AMRFinder identified. Based on these results, AMRFinder appears to be a highly accurate AMR gene detection system.
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Partridge SR, Tsafnat G. Automated annotation of mobile antibiotic resistance in Gram-negative bacteria: the Multiple Antibiotic Resistance Annotator (MARA) and database. J Antimicrob Chemother 2019; 73:883-890. [PMID: 29373760 DOI: 10.1093/jac/dkx513] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/08/2017] [Indexed: 01/26/2023] Open
Abstract
Background Multiresistance in Gram-negative bacteria is often due to acquisition of several different antibiotic resistance genes, each associated with a different mobile genetic element, that tend to cluster together in complex conglomerations. Accurate, consistent annotation of resistance genes, the boundaries and fragments of mobile elements, and signatures of insertion, such as DR, facilitates comparative analysis of complex multiresistance regions and plasmids to better understand their evolution and how resistance genes spread. Objectives To extend the Repository of Antibiotic resistance Cassettes (RAC) web site, which includes a database of 'features', and the Attacca automatic DNA annotation system, to encompass additional resistance genes and all types of associated mobile elements. Methods Antibiotic resistance genes and mobile elements were added to RAC, from existing registries where possible. Attacca grammars were extended to accommodate the expanded database, to allow overlapping features to be annotated and to identify and annotate features such as composite transposons and DR. Results The Multiple Antibiotic Resistance Annotator (MARA) database includes antibiotic resistance genes and selected mobile elements from Gram-negative bacteria, distinguishing important variants. Sequences can be submitted to the MARA web site for annotation. A list of positions and orientations of annotated features, indicating those that are truncated, DR and potential composite transposons is provided for each sequence, as well as a diagram showing annotated features approximately to scale. Conclusions The MARA web site (http://mara.spokade.com) provides a comprehensive database for mobile antibiotic resistance in Gram-negative bacteria and accurately annotates resistance genes and associated mobile elements in submitted sequences to facilitate comparative analysis.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Sydney, Australia
| | - Guy Tsafnat
- Centre for Health Informatics, Australian Institute of Health Innovation, Macquarie University, Sydney, Australia.,Spokade Pty Ltd, Sydney, Australia
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Wyrsch ER, Reid CJ, DeMaere MZ, Liu MY, Chapman TA, Roy Chowdhury P, Djordjevic SP. Complete Sequences of Multiple-Drug Resistant IncHI2 ST3 Plasmids in Escherichia coli of Porcine Origin in Australia. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Roh HJ, Kim BS, Kim A, Kim NE, Lee Y, Chun WK, Ho TD, Kim DH. Whole-genome analysis of multi-drug-resistant Aeromonas veronii isolated from diseased discus (Symphysodon discus) imported to Korea. JOURNAL OF FISH DISEASES 2019; 42:147-153. [PMID: 30350465 DOI: 10.1111/jfd.12908] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/04/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Heyong Jin Roh
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Bo-Seong Kim
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Ahran Kim
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Nam Eun Kim
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Yoonhang Lee
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Won-Kyong Chun
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Tho Diem Ho
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
| | - Do-Hyung Kim
- Department of Aquatic life medicine, Pukyong National University, Busan, Korea
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Exploring Foodborne Pathogen Ecology and Antimicrobial Resistance in the Light of Shotgun Metagenomics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2018; 1918:229-245. [PMID: 30580413 DOI: 10.1007/978-1-4939-9000-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this chapter, applications of shotgun metagenomics for taxonomic profiling and functional investigation of food microbial communities with a focus on antimicrobial resistance (AMR) were overviewed in the light of last data in the field. Potentialities of metagenomic approach, along with the challenges encountered for a wider and routinely use in food safety was discussed.
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1153] [Impact Index Per Article: 192.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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19
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Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. Clin Infect Dis 2018; 67:161-170. [PMID: 29340588 PMCID: PMC6030810 DOI: 10.1093/cid/ciy027] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk. Methods We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Results K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type [ST] 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital. Conclusions The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.
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Affiliation(s)
- Claire L Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mirjana Mirceta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kerrie M Watson
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Victoria, Australia
| | | | - Denis W Spelman
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
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Beg AZ, Khan AU. Genome analyses of blaNDM-4 carrying ST 315 Escherichia coli isolate from sewage water of one of the Indian hospitals. Gut Pathog 2018; 10:17. [PMID: 29849769 PMCID: PMC5968484 DOI: 10.1186/s13099-018-0247-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 05/19/2018] [Indexed: 12/03/2022] Open
Abstract
Background Emergence of carbapenem resistant Escherichia coli pathovars and their environmental dissemination are alarming problems. E. coli isolated from sewage water of hospital setting conferred a high resistance towards β-lactams, particularly towards carbapenem. This prompted us to perform whole genome sequence analysis to investigate the antimicrobial determinants, pathogenicity status and mobile genetic elements associated with resistance genes. Results To the best of our knowledge this is the first report of ST 315 carrying NDM-4 from India. The genome analysis has revealed the unknown characteristics associated with this sequence type (ST 315) like resistance and virulence factors. Based on virulence markers, its pathotype was identified as ExPEC. Furthermore, a mobile plasmid with multiple β-lactamases genes and clinically relevant resistance markers was detected. Phylogenetic analysis of Inc F plasmids sequences carrying ESBLs and NDM variants, revealed un-relatedness in these plasmids due to their varying size and backbone sequences. Conclusions Presence of carbapenem resistant E. coli ST 315 with high level antibiotic resistance, near hospital environment is an alarming situation in context to its spread. WGS based analyses have provided details on virulence and resistance status which could overcome the lack of information available on ST 315, globally. This could further help in its quick detection and control in clinical settings. Electronic supplementary material The online version of this article (10.1186/s13099-018-0247-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ayesha Z Beg
- Medical Microbiology and Molecular Biology, Laboratory Interdisciplinary, Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002 India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology, Laboratory Interdisciplinary, Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002 India
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21
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Kim A, Lim Y, Kim N, Luan Nguyen T, Roh HJ, Park CI, Han HJ, Jung SH, Cho MY, Kim DH, Smith P. A Comparison of Genotypic and Phenotypic Methods for Analyzing the Susceptibility to Sulfamethoxazole and Trimethoprim in Edwardsiella piscicida. Microb Drug Resist 2018; 24:1226-1235. [PMID: 29437540 DOI: 10.1089/mdr.2017.0137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In a study of 39 isolates of Edwardsiella piscicida made from Korean aquaculture sites, sul genes were detected in 16 isolates and dfr genes in 19. Ten isolates were shown to contain both sul and dfr genes. MIC and disc diffusion zones assays were performed to measure the phenotypic susceptibilities of the 39 isolates. Normalized resistance interpretation was applied to these data to categorize isolates as either fully susceptible or as manifesting reduced susceptibility. The standard CLSI protocols specify the use of a mixture of sulfamethoxazole/trimethoprim (20:1) in both MIC and disc diffusion tests. Using the CLSI MIC protocol, 100% of the isolates containing dfr genes, but only 75% of the isolates containing sul genes, were categorized as manifesting reduced susceptibility. Using the CLSI disc diffusion protocol, only 58% of the isolates containing dfr genes and 69% of those containing sul genes were categorized as manifesting reduced susceptibility. When the single agent trimethoprim was substituted for the combined mixture in both the MIC and disc diffusion protocols, 100% of the dfr-positive isolates were categorized as NWT. When the single-agent sulfamethoxazole was substituted, the analysis of the MIC characterized 100% and the disc zone data 94% of the sul-positive isolates as manifesting reduced susceptibility. It is argued that the use of trimethoprim and sulfamethoxazole as single agents in phenotypic susceptibility tests would provide more meaningful data than the currently recommended use of these two agents combined.
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Affiliation(s)
- Ahran Kim
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Yunjin Lim
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Nameun Kim
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Thanh Luan Nguyen
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Heyong Jin Roh
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Chan-Il Park
- 2 Department of Marine Biology & Aquaculture, College of Marine Science, Gyeongsang National University , Tongyeong, Republic of Korea
| | - Hyun-Ja Han
- 3 Pathology Research Division, National Institute of Fisheries Science , Busan, Republic of Korea
| | - Sung-Hee Jung
- 3 Pathology Research Division, National Institute of Fisheries Science , Busan, Republic of Korea
| | - Mi-Young Cho
- 3 Pathology Research Division, National Institute of Fisheries Science , Busan, Republic of Korea
| | - Do-Hyung Kim
- 1 Department of Aquatic Life Medicine, College of Fisheries Science, Pukyong National University , Busan, Republic of Korea
| | - Peter Smith
- 4 Department of Microbiology, School of Natural Sciences, National University of Ireland , Galway, Ireland
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Identification of beta-Lactamases and beta-Lactam-Related Proteins in Human Pathogenic Bacteria using a Computational Search Approach. Curr Microbiol 2017; 74:915-920. [DOI: 10.1007/s00284-017-1265-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
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McArthur AG, Tsang KK. Antimicrobial resistance surveillance in the genomic age. Ann N Y Acad Sci 2016; 1388:78-91. [PMID: 27875856 DOI: 10.1111/nyas.13289] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/30/2016] [Accepted: 10/05/2016] [Indexed: 12/31/2022]
Abstract
The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings. To do so, efforts must be focused toward exploiting the advancements of genome sequencing and information technology. Currently, AMR bioinformatics software and databases reflect different scopes and functions, each with its own strengths and weaknesses. A review of the available tools reveals common approaches and reference data but also reveals gaps in our curated data, models, algorithms, and data-sharing tools that must be addressed to conquer the limitations and areas of unmet need within the AMR research field before DNA sequencing can be fully exploited for AMR surveillance and improved clinical outcomes.
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Affiliation(s)
- Andrew G McArthur
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
| | - Kara K Tsang
- M. G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, Hamilton, Canada
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Adu-Oppong B, Gasparrini AJ, Dantas G. Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. Ann N Y Acad Sci 2016; 1388:42-58. [PMID: 27768825 DOI: 10.1111/nyas.13257] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/16/2016] [Accepted: 08/22/2016] [Indexed: 02/07/2023]
Abstract
Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.
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Affiliation(s)
- Boahemaa Adu-Oppong
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrew J Gasparrini
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, Missouri.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
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25
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Gillings MR, Paulsen IT, Tetu SG. Genomics and the evolution of antibiotic resistance. Ann N Y Acad Sci 2016; 1388:92-107. [DOI: 10.1111/nyas.13268] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Sasha G. Tetu
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
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Pereira MB, Wallroth M, Kristiansson E, Axelson-Fisk M. HattCI: Fast and Accurate attC site Identification Using Hidden Markov Models. J Comput Biol 2016; 23:891-902. [PMID: 27428829 DOI: 10.1089/cmb.2016.0024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Integrons are genetic elements that facilitate the horizontal gene transfer in bacteria and are known to harbor genes associated with antibiotic resistance. The gene mobility in the integrons is governed by the presence of attC sites, which are 55 to 141-nucleotide-long imperfect inverted repeats. Here we present HattCI, a new method for fast and accurate identification of attC sites in large DNA data sets. The method is based on a generalized hidden Markov model that describes each core component of an attC site individually. Using twofold cross-validation experiments on a manually curated reference data set of 231 attC sites from class 1 and 2 integrons, HattCI showed high sensitivities of up to 91.9% while maintaining satisfactory false-positive rates. When applied to a metagenomic data set of 35 microbial communities from different environments, HattCI found a substantially higher number of attC sites in the samples that are known to contain more horizontally transferred elements. HattCI will significantly increase the ability to identify attC sites and thus integron-mediated genes in genomic and metagenomic data. HattCI is implemented in C and is freely available at http://bioinformatics.math.chalmers.se/HattCI .
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Affiliation(s)
- Mariana Buongermino Pereira
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Mikael Wallroth
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
| | - Erik Kristiansson
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden .,2 Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Marina Axelson-Fisk
- 1 Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg , Gothenburg, Sweden
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Wyrsch ER, Roy Chowdhury P, Chapman TA, Charles IG, Hammond JM, Djordjevic SP. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis. Front Microbiol 2016; 7:843. [PMID: 27379026 PMCID: PMC4908116 DOI: 10.3389/fmicb.2016.00843] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/22/2016] [Indexed: 11/18/2022] Open
Abstract
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.
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Affiliation(s)
- Ethan R Wyrsch
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
| | - Piklu Roy Chowdhury
- The ithree Institute, University of Technology Sydney, SydneyNSW, Australia; NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, SydneyNSW, Australia
| | - Toni A Chapman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Ian G Charles
- Institute of Food Research, Norwich Research Park Norwich, UK
| | - Jeffrey M Hammond
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Sydney NSW, Australia
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Sydney NSW, Australia
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Abstract
The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".
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Bakour S, Sankar SA, Rathored J, Biagini P, Raoult D, Fournier PE. Identification of virulence factors and antibiotic resistance markers using bacterial genomics. Future Microbiol 2016; 11:455-66. [PMID: 26974504 DOI: 10.2217/fmb.15.149] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In recent years, the number of multidrug-resistant bacteria has increased rapidly and several epidemics were signaled in different regions of the world. Faced with this situation that presents a major global public health concern, the development and the use of new and rapid technologies is more than urgent. The use of the next-generation sequencing platforms by microbiologists and infectious disease specialists has allowed great progress in the medical field. Here, we review the usefulness of whole-genome sequencing for the detection of virulence and antibiotic resistance associated genes.
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Affiliation(s)
- Sofiane Bakour
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Senthil Alias Sankar
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Jaishriram Rathored
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Philippe Biagini
- UMR CNRS 7268 Equipe "Emergence et coévolution virale," Etablissement Français du Sang Alpes-Méditerranée et Aix-Marseille Université, 27 Boulevard Jean Moulin, 13005 Marseille
| | - Didier Raoult
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| | - Pierre-Edouard Fournier
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), UM 63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
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Sabirova JS, Xavier BB, Coppens J, Zarkotou O, Lammens C, Janssens L, Burggrave R, Wagner T, Goossens H, Malhotra-Kumar S. Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS. J Antimicrob Chemother 2016; 71:1501-9. [PMID: 26968884 DOI: 10.1093/jac/dkw003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/30/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). METHODS All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). RESULTS All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212-0.849) (P = 0.007). CONCLUSIONS This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.
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Affiliation(s)
- Julia S Sabirova
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Basil Britto Xavier
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Jasmine Coppens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Olympia Zarkotou
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Christine Lammens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Lore Janssens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
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Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient. Gene 2016; 578:105-11. [DOI: 10.1016/j.gene.2015.12.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/08/2015] [Indexed: 01/11/2023]
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Abstract
The unrestricted use of antibiotics has resulted in rapid acquisition of antibiotic resistance (AR) and spread of multidrug-resistant (MDR) bacterial pathogens. With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. However, due to the absence of a centralized platform for AR gene resources, availability, consistency, and accuracy of information vary considerably across different databases. In this article, we explore existing AR gene data resources in order to make them more visible to the clinical microbiology community, to identify their limitations, and to propose potential solutions.
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Rowe W, Verner-Jeffreys DW, Baker-Austin C, Ryan JJ, Maskell DJ, Pearce GP. Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2016; 73:1541-1549. [PMID: 27054725 DOI: 10.2166/wst.2015.634] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aquatic environment has been implicated as a reservoir for antimicrobial resistance genes (ARGs). In order to identify sources that are contributing to these gene reservoirs, it is crucial to assess effluents that are entering the aquatic environment. Here we describe a metagenomic assessment for two types of effluent entering a river catchment. We investigated the diversity and abundance of resistance genes, mobile genetic elements (MGEs) and pathogenic bacteria. Findings were normalised to a background sample of river source water. Our results show that effluent contributed an array of genes to the river catchment, the most abundant being tetracycline resistance genes tetC and tetW from farm effluents and the sulfonamide resistance gene sul2 from wastewater treatment plant (WWTP) effluents. In nine separate samples taken across 3 years, we found 53 different genes conferring resistance to seven classes of antimicrobial. Compared to the background sample taken up river from effluent entry, the average abundance of genes was three times greater in the farm effluent and two times greater in the WWTP effluent. We conclude that effluents disperse ARGs, MGEs and pathogenic bacteria within a river catchment, thereby contributing to environmental reservoirs of ARGs.
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Affiliation(s)
- Will Rowe
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK E-mail:
| | | | | | - Jim J Ryan
- Environment, Health and Safety, GlaxoSmithKline, Ware, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK E-mail:
| | - Gareth P Pearce
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK E-mail:
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fosI Is a New Integron-Associated Gene Cassette Encoding Reduced Susceptibility to Fosfomycin. Antimicrob Agents Chemother 2015; 60:686-8. [PMID: 26552984 DOI: 10.1128/aac.02437-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
In this work, we demonstrate that the fosI gene encodes a predicted small protein with 134 amino acids and determines reduced susceptibility to fosfomycin. It raised the MIC from 0.125 to 6 μg/ml when the pBRA100 plasmid was introduced into Escherichia coli TOP10 and to 16 μg/ml when the gene was cloned into the pBC_SK(-) vector and expressed in E. coli TOP10.
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Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data. PLoS One 2015. [PMID: 26197475 PMCID: PMC4510569 DOI: 10.1371/journal.pone.0133492] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Results Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR’s application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. Conclusions We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR is effective in detecting antimicrobial resistance genes in metagenomic and isolate sequencing data from both environmental metagenomes and sequencing data from clinical isolates.
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Saha SB, Uttam V, Verma V. u-CARE: user-friendly Comprehensive Antibiotic resistance Repository of Escherichia coli. J Clin Pathol 2015; 68:648-51. [PMID: 25935546 DOI: 10.1136/jclinpath-2015-202927] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/14/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND AND AIMS Despite medical advancements, Escherichia coli-associated infections remain a major public health concern and although an abundant information about E. coli and its antibiotic resistance mechanisms is available, no effective tool exists that integrates gene and genomic data in context to drug resistance, thus raising a need to develop a repository that facilitates integration and assimilation of factors governing drug resistance in E. coli. DESCRIPTIONS User-friendly Comprehensive Antibiotic resistance Repository of Escherichia coli (u-CARE) is a manually curated catalogue of 52 antibiotics with reported resistance, 107 genes, transcription factors and single nucleotide polymorphism (SNPs) involved in multiple drug resistance of this pathogen. Each gene page provides detailed information about its resistance mechanisms, while antibiotic page consists of summary, chemical description and structural descriptors with links to external public databases like GO, CDD, DEG, Ecocyc, KEGG, Drug Bank, PubChem and UniProt. Moreover, the database integrates this reductive information to holistic data such as strain-specific and segment-specific pathogenic islands and operons. In addition, the database offers rich user interface for the visualisation and retrieval of information using various search criteria such as sequence, keyword, image and class search. CONCLUSIONS u-CARE is aimed to cater to the needs of researchers working in the field of antimicrobial drug resistance with minimal knowledge of bioinformatics. This database is also intended as a guide book to medical practitioners to avoid use of antibiotics against which resistance has already been reported in E. coli. The database is available from: http://www.e-bioinformatics.net/ucare.
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Affiliation(s)
- Saurav B Saha
- Department of Computational Biology and Bioinformatics, JSBB, SHIATS Allahabad, Uttar Pradesh, India
| | - Vishwas Uttam
- Department of Computational Biology and Bioinformatics, JSBB, SHIATS Allahabad, Uttar Pradesh, India
| | - Vivek Verma
- Clinical Vaccine R&D Center, Chonnam National University Hwasun Hospital, Jeonnam, South Korea
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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Diene SM, Rolain JM. Investigation of antibiotic resistance in the genomic era of multidrug-resistant Gram-negative bacilli, especially Enterobacteriaceae, Pseudomonas and Acinetobacter. Expert Rev Anti Infect Ther 2013; 11:277-96. [PMID: 23458768 DOI: 10.1586/eri.13.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The increase and spread of multidrug-resistant (MDR) Gram-negative bacteria, including Enterobacteriaceae, Pseudomonas and Acinetobacter species, have become major concerns worldwide. Although the frequent misuse of antibiotic drugs has greatly contributed to worldwide antibiotic resistance by causing a large dispersal of resistance determinants, recent studies demonstrate that these resistance determinants could have emerged from ancient or environmental sources. Moreover, during the last 10 years, we have been witnessing the emergence and development of technologies for high-throughput sequencing, coinciding with an exponential increase in the number of bacterial genomes sequenced. These sequencing technologies allow a complete study of MDR bacterial genomes and are the best way to investigate the genetic determinants of antimicrobial resistance. Accordingly, studies using genome sequencing to decipher resistance determinants in Enterobacteriaceae, Pseudomonas and Acinetobacter species have demonstrated several advantages including, among others: an exhaustive identification of resistance determinants from any clinical, epidemiological or environmental MDR bacterium; identification of the acquisition mechanisms for resistance determinants exchanged between bacterial species through mobile genetic elements and elucidation and understanding, in record time (less than 1 week), of some critical or epidemic events caused by particular pathogenic bacteria. Therefore, it is clear today that the bacterial genome sequencing approach has revolutionized all fields of scientific research and represents a powerful tool to explore the world of microorganisms.
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Affiliation(s)
- Seydina M Diene
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, 27 Bd Jean Moulin 13385 Marseille Cedex 05, France
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Abstract
The field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD; http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.
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40
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A novel gene cassette potentially conferring resistance to aminoglycosides. Antimicrob Agents Chemother 2013; 56:4566-7. [PMID: 22826289 DOI: 10.1128/aac.00625-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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