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Rossi F, Girardello R, Morais C, Cury AP, Martins LF, da Silva AM, Abdala E, Setubal JC, da Silva Duarte AJ. Plasmid-mediated mcr-1 in carbapenem-susceptible Escherichia coli ST156 causing a blood infection: an unnoticeable spread of colistin resistance in Brazil? Clinics (Sao Paulo) 2017; 72:642-644. [PMID: 29160428 PMCID: PMC5666441 DOI: 10.6061/clinics/2017(10)09] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE We describe an IncX4 pHC891/16mcr plasmid carrying mcr-1 in a colistin-resistant and carbapenem-susceptible E. coli isolate (HC891/16), ST156, which caused a blood infection in a Brazilian patient with gallbladder adenocarcinoma. METHODS Strain HC891/16 was subjected to whole genome sequencing using the MiSeq Platform (Illumina, Inc., USA). Assembly was performed using Mira and ABACAS. RESULTS The isolates showed resistance only to ciprofloxacin, ampicillin and cefoxitin, and whole-genome sequencing revealed the presence of aac(6')Ib-cr and blaTEM1. CONCLUSION Our findings warn of the possible silent dissemination of colistin resistance by carbapenem-susceptible mcr-1 producers, as colistin susceptibility is commonly tested only among carbapenem-resistant isolates.
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Affiliation(s)
- Flavia Rossi
- Divisao Laboratorio Central – LIM03, Setor de Microbiologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | - Raquel Girardello
- Divisao Laboratorio Central – LIM03, Setor de Microbiologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Carlos Morais
- Departamento de Bioquímica, Instituto de Química, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Nucleo de Apoio a Pesquisa em Biologia Computacional e Genomica (NUBIC), Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Ana Paula Cury
- Divisao Laboratorio Central – LIM03, Setor de Microbiologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Edson Abdala
- Instituto do Cancer do Estado de Sao Paulo, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de Sao Paulo, Sao Paulo, SP, BR
- Nucleo de Apoio a Pesquisa em Biologia Computacional e Genomica (NUBIC), Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Alberto José da Silva Duarte
- Divisao Laboratorio Central – LIM03, Setor de Microbiologia, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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103
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Ovejero CM, Delgado-Blas JF, Calero-Caceres W, Muniesa M, Gonzalez-Zorn B. Spread of mcr-1-carrying Enterobacteriaceae in sewage water from Spain. J Antimicrob Chemother 2017; 72:1050-1053. [PMID: 28073965 DOI: 10.1093/jac/dkw533] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/11/2016] [Indexed: 12/11/2022] Open
Abstract
Objectives The mobile colistin resistance gene mcr-1 has been identified worldwide in human and animal sources, while its occurrence in the environment is still largely unknown. The aim of this study was to investigate the presence of mcr-1 -harbouring Enterobacteriaceae in water samples obtained from rivers and waste water treatment plants in the area of Barcelona, Spain. Methods The presence of mcr-1 was detected by PCR. Bacterial identification was performed via MALDI-TOF MS. Resistance to colistin was determined by a broth dilution method. The epidemiological relationship between the positive isolates was assessed with PFGE and ST was determined by MLST. Plasmid characterization was performed by transformation experiments, antimicrobial susceptibility testing and incompatibility group PCR. Results Thirty MDR isolates bearing mcr-1 , 29 Escherichia coli (ST632 and ST479) and 1 Klebsiella pneumoniae (ST526), were identified in sewage from two different waste water treatment plants, whereas the gene was not found in river water. All isolates, including the K. pneumoniae , harboured bla CTX-M-55 and bla TEM-1 . mcr-1 was in all cases associated with an IncI2 plasmid, which only conferred resistance to colistin. mcr-1 was harboured by two predominant E. coli clones that were found in both waste water treatment plants. Conclusions This study showed a high occurrence of mcr-1 in the sewage of Barcelona, mainly due to the dissemination of two E. coli pulsotypes that are circulating in the population. The presence of mcr-1 in the environment is a cause for concern, and suggests high prevalence of mcr-1 in the community.
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Affiliation(s)
- C M Ovejero
- Department of Animal Health and VISAVET, Universidad Complutense de Madrid, Madrid, Spain
| | - J F Delgado-Blas
- Department of Animal Health and VISAVET, Universidad Complutense de Madrid, Madrid, Spain
| | - W Calero-Caceres
- Department of Microbiology, Universitat de Barcelona, Barcelona, Spain
| | - M Muniesa
- Department of Microbiology, Universitat de Barcelona, Barcelona, Spain
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Universidad Complutense de Madrid, Madrid, Spain
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104
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Coates K, Walsh TR, Spencer J, Hinchliffe P. 1.12 Å resolution crystal structure of the catalytic domain of the plasmid-mediated colistin resistance determinant MCR-2. Acta Crystallogr F Struct Biol Commun 2017; 73:443-449. [PMID: 28777086 PMCID: PMC5544000 DOI: 10.1107/s2053230x17009669] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/30/2017] [Indexed: 11/12/2022] Open
Abstract
MCR-2 confers resistance to colistin, a `last-line' antibiotic against extensively resistant Gram-negative pathogens. It is a plasmid-encoded phosphoethanolamine transferase that is closely related to MCR-1. To understand the diversity in the MCR family, the 1.12 Å resolution crystal structure of the catalytic domain of MCR-2 was determined. Variable amino acids are located distant from both the di-zinc active site and the membrane-proximal face. The exceptionally high resolution will provide an accurate starting model for further mechanistic studies.
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Affiliation(s)
- Katie Coates
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, England
| | - Timothy R. Walsh
- Department of Medical Microbiology and Infectious Disease, Cardiff Institute of Infection and Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, Wales
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, England
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, England
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105
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Qamar S, Shaheen N, Shakoor S, Farooqi J, Jabeen K, Hasan R. Frequency of colistin and fosfomycin resistance in carbapenem-resistant Enterobacteriaceae from a tertiary care hospital in Karachi. Infect Drug Resist 2017; 10:231-236. [PMID: 28814888 PMCID: PMC5546765 DOI: 10.2147/idr.s136777] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Introduction Management of infections with carbapenem-resistant Enterobacteriaceae (CRE) is challenging. In recent times, agents such as colistin and fosfomycin have been used in combination with other antibiotics to treat such infections. In this study, we aim to seek frequency of colistin and fosfomycin resistance in CRE from Pakistan. Methods This study was conducted at clinical laboratories, Aga Khan University Hospital. In total, 251 CRE were included in the study. Colistin minimum inhibitory concentrations (MICs) were performed using broth microdilution (BMD) method and VITEK® 2 system, whereas fosfomycin susceptibility was performed using Kirby–Bauer method. MIC50 and MIC90 were calculated for colistin and agreement between VITEK and BMD was also calculated. Results Out of 251 strains colistin MIC of ≥4 µg/mL was seen in 40 (15.9%). Of these strains 20 (50%) were Klebsiella pneumoniae. Colistin MIC50 and MIC90 were found to be 0.5 and 16 µg/mL, respectively. BMD and VITEK 2 showed 100% categorical agreement. Essential agreement was 88.5% with kappa score 0.733 indicating strong agreement between VITEK and BMD. 31 out of 251 (12.3%) CREs were resistant to fosfomycin. Conclusion Study shows frequency of colistin and fosfomycin resistance to be 15.9% and 12.3%, respectively. In countries where rate of CREs is high, emerging resistance against these last resort antibiotics is alarming as it leaves clinicians with almost no options to manage such multidrug resistant and extensively drug resistant infections.
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Affiliation(s)
- Salima Qamar
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Najma Shaheen
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Sadia Shakoor
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Joveria Farooqi
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Kauser Jabeen
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
| | - Rumina Hasan
- Clinical Microbiology, Department of Pathology And Laboratory Medicine, Aga Khan University Hospital, Karachi, Pakistan
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ECDC/EFSA/EMA second joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals: Joint Interagency Antimicrobial Consumption and Resistance Analysis (JIACRA) Report. EFSA J 2017; 15:e04872. [PMID: 32625542 PMCID: PMC7009874 DOI: 10.2903/j.efsa.2017.4872] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The second ECDC/EFSA/EMA joint report on the integrated analysis of antimicrobial consumption (AMC) and antimicrobial resistance (AMR) in bacteria from humans and food‐producing animals addressed data obtained by the Agencies’ EU‐wide surveillance networks for 2013–2015. AMC in both sectors, expressed in mg/kg of estimated biomass, were compared at country and European level. Substantial variations between countries were observed in both sectors. Estimated data on AMC for pigs and poultry were used for the first time. Univariate and multivariate analyses were applied to study associations between AMC and AMR. In 2014, the average AMC was higher in animals (152 mg/kg) than in humans (124 mg/kg), but the opposite applied to the median AMC (67 and 118 mg/kg, respectively). In 18 of 28 countries, AMC was lower in animals than in humans. Univariate analysis showed statistically‐significant (p < 0.05) associations between AMC and AMR for fluoroquinolones and Escherichia coli in both sectors, for 3rd‐ and 4th‐generation cephalosporins and E. coli in humans, and tetracyclines and polymyxins and E. coli in animals. In humans, there was a statistically‐significant association between AMC and AMR for carbapenems and polymyxins in Klebsiella pneumoniae. Consumption of macrolides in animals was significantly associated with macrolide resistance in Campylobacter coli in animals and humans. Multivariate analyses provided a unique approach to assess the contributions of AMC in humans and animals and AMR in bacteria from animals to AMR in bacteria from humans. Multivariate analyses demonstrated that 3rd‐ and 4th‐generation cephalosporin and fluoroquinolone resistance in E. coli from humans was associated with corresponding AMC in humans, whereas resistance to fluoroquinolones in Salmonella spp. and Campylobacter spp. from humans was related to consumption of fluoroquinolones in animals. These results suggest that from a ‘One‐health’ perspective, there is potential in both sectors to further develop prudent use of antimicrobials and thereby reduce AMR.
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107
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Tijet N, Faccone D, Rapoport M, Seah C, Pasterán F, Ceriana P, Albornoz E, Corso A, Petroni A, Melano RG. Molecular characteristics of mcr-1-carrying plasmids and new mcr-1 variant recovered from polyclonal clinical Escherichia coli from Argentina and Canada. PLoS One 2017; 12:e0180347. [PMID: 28678874 PMCID: PMC5498056 DOI: 10.1371/journal.pone.0180347] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/14/2017] [Indexed: 11/18/2022] Open
Abstract
We have characterized nine mcr-1-harboring plasmids from clinical Escherichia coli isolates previously described in Argentina and Canada. Three of these plasmids carried a mcr-1-variant called here mcr-1.5. All these E. coli isolates were not clonally related and were recovered in different years and locations. However, their mcr-1-harboring plasmids showed high identity among them and to others characterized in other countries, which strongly suggests that this plasmid-type is playing an important role in spreading this mechanism of resistance to polymyxins.
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Affiliation(s)
- Nathalie Tijet
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Diego Faccone
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melina Rapoport
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Christine Seah
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
| | - Fernando Pasterán
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Paola Ceriana
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Ezequiel Albornoz
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Alejandro Petroni
- Servicio Antimicrobianos, National and Regional Reference Laboratory in Antimicrobial Resistance, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS “Dr. C. Malbran”, Buenos Aires, Argentina
| | - Roberto G. Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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108
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Corbella M, Mariani B, Ferrari C, Comandatore F, Scaltriti E, Marone P, Cambieri P. Three cases of mcr-1-positive colistin-resistant Escherichia coli bloodstream infections in Italy, August 2016 to January 2017. ACTA ACUST UNITED AC 2017; 22:30517. [PMID: 28449732 PMCID: PMC5404483 DOI: 10.2807/1560-7917.es.2017.22.16.30517] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/20/2017] [Indexed: 11/20/2022]
Abstract
We describe three cases of bloodstream infection caused by colistin-resistant Escherichia coli in patients in a tertiary hospital in Italy, between August 2016 and January 2017. Whole genome sequencing detected the mcr-1 gene in three isolated strains belonging to different sequence types (STs). This occurrence of three cases with mcr-1-positive E. coli belonging to different STs in six months suggests a widespread problem in settings where high multidrug resistance is endemic such as in Italy.
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Affiliation(s)
- Marta Corbella
- SC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,These authors contributed equally to this work
| | - Bianca Mariani
- SC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,These authors contributed equally to this work
| | - Carolina Ferrari
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani"- Università degli Studi di Pavia, Pavia, Italy
| | - Francesco Comandatore
- Centro di Ricerca pediatrico Romeo ed Enrica Invernizzi. Dipartimento di Scienze Biomediche e Cliniche L. Sacco, Università degli Studi di Milano, Milano, Italy
| | - Erika Scaltriti
- Unità di Analisi del Rischio, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Parma, Italy
| | - Piero Marone
- SC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Patrizia Cambieri
- SC Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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109
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In Vitro Study of IS Apl1-Mediated Mobilization of the Colistin Resistance Gene mcr-1. Antimicrob Agents Chemother 2017; 61:AAC.00127-17. [PMID: 28416554 DOI: 10.1128/aac.00127-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/07/2017] [Indexed: 01/03/2023] Open
Abstract
The plasmid-mediated mcr-1 gene encodes a phosphoethanolamine transferase that confers resistance to polymyxins. The mcr-1 gene is associated with insertion sequence ISApl1 (IS30 family). In vitro mobilization assays demonstrated the functionality of the composite transposon structure ISApl1-mcr-1-ISApl1 Transposition generated a 2-bp duplication and occurred in AT-rich DNA regions. This is the first report demonstrating the mobility of the mcr-1 gene by transposition.
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110
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Abstract
The mobile colistin resistance gene mcr-1 has attracted global attention, as it heralds the breach of polymyxins, one of the last-resort antibiotics for the treatment of severe clinical infections caused by multidrug-resistant Gram-negative bacteria. To date, six slightly different variants of mcr-1, and a second mobile colistin resistance gene, mcr-2, have been reported or annotated in the GenBank database. Here, we characterized a third mobile colistin resistance gene, mcr-3. The gene coexisted with 18 additional resistance determinants in the 261-kb IncHI2-type plasmid pWJ1 from porcine Escherichia coli. mcr-3 showed 45.0% and 47.0% nucleotide sequence identity to mcr-1 and mcr-2, respectively, while the deduced amino acid sequence of MCR-3 showed 99.8 to 100% and 75.6 to 94.8% identity to phosphoethanolamine transferases found in other Enterobacteriaceae species and in 10 Aeromonas species, respectively. pWJ1 was mobilized to an E. coli recipient by conjugation and contained a plasmid backbone similar to those of other mcr-1-carrying plasmids, such as pHNSHP45-2 from the original mcr-1-harboring E. coli strain. Moreover, a truncated transposon element, TnAs2, which was characterized only in Aeromonas salmonicida, was located upstream of mcr-3 in pWJ1. This ΔTnAs2-mcr-3 element was also identified in a shotgun genome sequence of a porcine E. coli isolate from Malaysia, a human Klebsiella pneumoniae isolate from Thailand, and a human Salmonella enterica serovar Typhimurium isolate from the United States. These results suggest the likelihood of a wide dissemination of the novel mobile colistin resistance gene mcr-3 among Enterobacteriaceae and aeromonads; the latter may act as a potential reservoir for mcr-3. The emergence of the plasmid-mediated colistin resistance gene mcr-1 has attracted substantial attention worldwide. Here, we examined a colistin-resistant Escherichia coli isolate that was negative for both mcr-1 and mcr-2 and discovered a novel mobile colistin resistance gene, mcr-3. The amino acid sequence of MCR-3 aligned closely with phosphoethanolamine transferases from Enterobacteriaceae and Aeromonas species originating from both clinical infections and environmental samples collected in 12 countries on four continents. Due to the ubiquitous profile of aeromonads in the environment and the potential transfer of mcr-3 between Enterobacteriaceae and Aeromonas species, the wide spread of mcr-3 may be largely underestimated. As colistin has been and still is widely used in veterinary medicine and used at increasing frequencies in human medicine, the continuous monitoring of mobile colistin resistance determinants in colistin-resistant Gram-negative bacteria is imperative for understanding and tackling the dissemination of mcr genes in both the agricultural and health care sectors.
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Emergence of the Plasmid-Mediated mcr-1 Gene in Clinical KPC-2-Producing Klebsiella pneumoniae Sequence Type 392 in Brazil. Antimicrob Agents Chemother 2017; 61:AAC.00317-17. [PMID: 28438940 DOI: 10.1128/aac.00317-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Caspar Y, Maillet M, Pavese P, Francony G, Brion JP, Mallaret MR, Bonnet R, Robin F, Beyrouthy R, Maurin M. mcr-1 Colistin Resistance in ESBL-Producing Klebsiella pneumoniae, France. Emerg Infect Dis 2017; 23:874-876. [PMID: 28418313 PMCID: PMC5403025 DOI: 10.3201/eid2305.161942] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report intestinal carriage of an extended-spectrum β-lactamase−producing Klebsiella pneumoniae strain with high-level resistance to colistin (MIC 24 mg/L) in a patient in France who had been hospitalized for fungal meningitis. The strain had the mcr-1 plasmid gene and an inactivated mgrB gene, which are associated with colistin resistance.
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113
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Argudín MA, Deplano A, Meghraoui A, Dodémont M, Heinrichs A, Denis O, Nonhoff C, Roisin S. Bacteria from Animals as a Pool of Antimicrobial Resistance Genes. Antibiotics (Basel) 2017; 6:antibiotics6020012. [PMID: 28587316 PMCID: PMC5485445 DOI: 10.3390/antibiotics6020012] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/12/2017] [Accepted: 06/01/2017] [Indexed: 01/14/2023] Open
Abstract
Antimicrobial agents are used in both veterinary and human medicine. The intensive use of antimicrobials in animals may promote the fixation of antimicrobial resistance genes in bacteria, which may be zoonotic or capable to transfer these genes to human-adapted pathogens or to human gut microbiota via direct contact, food or the environment. This review summarizes the current knowledge of the use of antimicrobial agents in animal health and explores the role of bacteria from animals as a pool of antimicrobial resistance genes for human bacteria. This review focused in relevant examples within the ESC(K)APE (Enterococcus faecium, Staphylococcus aureus, Clostridium difficile (Klebsiella pneumoniae), Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae) group of bacterial pathogens that are the leading cause of nosocomial infections throughout the world.
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Affiliation(s)
- Maria Angeles Argudín
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Ariane Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Alaeddine Meghraoui
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Magali Dodémont
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Amelie Heinrichs
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Olivier Denis
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
- Ecole de Santé Publique, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050 Bruxelles, Belgium.
| | - Claire Nonhoff
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
| | - Sandrine Roisin
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium.
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Abstract
The global rise of multidrug-resistant gram-negative bacteria represents an increasing threat to patient safety. From the first observation of a carbapenem-resistant gram-negative bacteria a global spread of extended-spectrum beta-lactamases and carbapenemases producing Klebsiella pneumoniae has been observed. Treatment options for multidrug-resistant K. pneumoniae are actually limited to combination therapy with some aminoglycosides, tigecycline and to older antimicrobial agents. Unfortunately, the prevalence of colistin-resistant and tigecycline-resistant K. pneumoniae is increasing globally. Infection due to colistin-resistant K. pneumoniae represents an independent risk factor for mortality. Resistance to colistin in K. pneumoniae may be multifactorial, as it is mediated by chromosomal genes or plasmids. The emergence of transmissible, plasmid-mediated colistin resistance is an alarming finding. The absence of new agents effective against resistant Gram-negative pathogens means that enhanced surveillance, compliance with infection prevention procedures, and antimicrobial stewardship programs will be required to limit the spread of colistin-resistant K. pneumoniae.
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Affiliation(s)
- Guido Granata
- Clinical and Research Department, National Institute for Infectious Diseases "L. Spallanzani" - IRCCS, Rome, Italy
| | - Nicola Petrosillo
- Clinical and Research Department, National Institute for Infectious Diseases "L. Spallanzani" - IRCCS, Rome, Italy
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115
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Moraxella Species as Potential Sources of MCR-Like Polymyxin Resistance Determinants. Antimicrob Agents Chemother 2017; 61:AAC.00129-17. [PMID: 28320720 DOI: 10.1128/aac.00129-17] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Plasmid-mediated resistance to polymyxins mediated by the MCR-1/2 determinants has been reported in Enterobacteriaceae worldwide. Using PCR-based and cloning strategies, a series of Moraxella spp. were screened for mcr-like genes. Moraxella spp. that are mainly animal pathogens but may also be human pathogens were identified as potential reservoirs of mcr-like genes.
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116
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Abstract
Antibiotic resistance is a prevalent problem in public health worldwide. In general, the carbapenem β-lactam antibiotics are considered a final resort against lethal infections by multidrug-resistant bacteria. Colistin is a cationic polypeptide antibiotic and acts as the last line of defense for treatment of carbapenem-resistant bacteria. Very recently, a new plasmid-borne colistin resistance gene, mcr-2, was revealed soon after the discovery of the paradigm gene mcr-1, which has disseminated globally. However, the molecular mechanisms for MCR-2 colistin resistance are poorly understood. Here we show a unique transposon unit that facilitates the acquisition and transfer of mcr-2 Evolutionary analyses suggested that both MCR-2 and MCR-1 might be traced to their cousin phosphoethanolamine (PEA) lipid A transferase from a known polymyxin producer, Paenibacillus Transcriptional analyses showed that the level of mcr-2 transcripts is relatively higher than that of mcr-1 Genetic deletions revealed that the transmembrane regions (TM1 and TM2) of both MCR-1 and MCR-2 are critical for their location and function in bacterial periplasm, and domain swapping indicated that the TM2 is more efficient than TM1. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) confirmed that all four MCR proteins (MCR-1, MCR-2, and two chimeric versions [TM1-MCR-2 and TM2-MCR-1]) can catalyze chemical modification of lipid A moiety anchored on lipopolysaccharide (LPS) with the addition of phosphoethanolamine to the phosphate group at the 4' position of the sugar. Structure-guided site-directed mutagenesis defined an essential 6-residue-requiring zinc-binding/catalytic motif for MCR-2 colistin resistance. The results further our mechanistic understanding of transferable colistin resistance, providing clues to improve clinical therapeutics targeting severe infections by MCR-2-containing pathogens.IMPORTANCE Carbapenem and colistin are the last line of refuge in fighting multidrug-resistant Gram-negative pathogens. MCR-2 is a newly emerging variant of the mobilized colistin resistance protein MCR-1, posing a potential challenge to public health. Here we report transfer of the mcr-2 gene by a unique transposal event and its possible origin. Distribution of MCR-2 in bacterial periplasm is proposed to be a prerequisite for its role in the context of biochemistry and the colistin resistance. We also define the genetic requirement of a zinc-binding/catalytic motif for MCR-2 colistin resistance. This represents a glimpse of transferable colistin resistance by MCR-2.
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117
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MCR-1.6, a New MCR Variant Carried by an IncP Plasmid in a Colistin-Resistant Salmonella enterica Serovar Typhimurium Isolate from a Healthy Individual. Antimicrob Agents Chemother 2017; 61:AAC.02632-16. [PMID: 28264851 DOI: 10.1128/aac.02632-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/20/2017] [Indexed: 11/20/2022] Open
Abstract
In this study, we report a novel mcr-1 gene variant, named mcr-1.6, carried by an IncP plasmid in a colistin-resistant Salmonella enterica serovar Typhimurium isolate from a healthy person. Compared with mcr-1, the mcr-1.6 gene contains two single-nucleotide polymorphisms, one of which results in an arginine to histidine variation (Arg536→His). The plasmid carrying the mcr-1.6 gene was designated pMCR1.6_P053 and is similar to a recently discovered mcr-1-bearing plasmid found in Klebsiella pneumoniae.
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118
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Colistin Resistance Gene mcr-1 and Its Variant in Escherichia coli Isolates from Chickens in China. Antimicrob Agents Chemother 2017; 61:AAC.01204-16. [PMID: 28242671 DOI: 10.1128/aac.01204-16] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/31/2017] [Indexed: 11/20/2022] Open
Abstract
The mcr-1 gene was detected in 5.11% (58/1136) of Escherichia coli isolates of chicken origin from 13 provinces in China. A novel mcr-1 variant, named mcr-1.3, encoding an Ile-to-Val functional variant of MCR-1 was identified in a sequence type 155 (ST155) strain. An mcr-1.3-containing IncI2 plasmid, pHeN867 (60,757 bp), was identified. The transfer of pHeN867 led to a 32-fold increase in the MIC of colistin in the recipient, exhibiting an effect on colistin resistance that was similar to that of mcr-1.
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119
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Sekizuka T, Kawanishi M, Ohnishi M, Shima A, Kato K, Yamashita A, Matsui M, Suzuki S, Kuroda M. Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids. Sci Rep 2017; 7:928. [PMID: 28424528 PMCID: PMC5430464 DOI: 10.1038/s41598-017-01082-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/20/2017] [Indexed: 12/30/2022] Open
Abstract
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan.
| | - Michiko Kawanishi
- Assay Division II, Bacterial Assay Section, National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1 Tokura, Kokubunji-shi, 185-8511, Tokyo, Japan
| | - Mamoru Ohnishi
- Ohnishi Laboratory of Veterinary Microbiology, 10-3-3 Nishirokujyouminami, Shibetsugunnakashibetsu-cho, 086-1106, Hokkaido, Japan
| | - Ayaka Shima
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Kengo Kato
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
| | - Mari Matsui
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Satowa Suzuki
- Department of Bacteriology II, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjyuku-ku, Tokyo, 162-8640, Japan
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120
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Lima Barbieri N, Nielsen DW, Wannemuehler Y, Cavender T, Hussein A, Yan SG, Nolan LK, Logue CM. mcr-1 identified in Avian Pathogenic Escherichia coli (APEC). PLoS One 2017; 12:e0172997. [PMID: 28264015 PMCID: PMC5338808 DOI: 10.1371/journal.pone.0172997] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/13/2017] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance associated with colistin has emerged as a significant concern worldwide threatening the use of one of the most important antimicrobials for treating human disease. Here, we examined a collection (n = 980) of Avian Pathogenic Escherichia coli (APEC) isolated from poultry with colibacillosis from the US and internationally for the presence of mcr-1 and mcr-2, genes known to encode colistin resistance. Included in the analysis was an additional set of avian fecal E. coli (AFEC) (n = 220) isolates from healthy birds for comparative analysis. The mcr-1 gene was detected in a total of 12 isolates recovered from diseased production birds from China and Egypt. No mcr genes were detected in the healthy fecal isolates. The full mcr-1 gene from positive isolates was sequenced using specifically designed primers and were compared with sequences currently described in NCBI. mcr-1 positive isolates were also assessed for phenotypic colistin resistance and extended spectrum beta lactam phenotypes and genotypes. This study has identified mcr-1 in APEC isolates dating back to at least 2010 and suggests that animal husbandry practices could result in a potential source of resistance to the human food chain in countries where application of colistin in animal health is practiced.
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Affiliation(s)
- Nicolle Lima Barbieri
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
| | - Daniel W. Nielsen
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
| | - Yvonne Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
| | - Tia Cavender
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
| | - Ashraf Hussein
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Shi-gan Yan
- School of Bioengineering, Qilu University of Technology, Changqing District, Jinan, Shandong Province, P. R. China
| | - Lisa K. Nolan
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
| | - Catherine M. Logue
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, 1802 University Blvd; VMRI #5 Ames, IA, United States of America
- * E-mail:
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121
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Bustamante P, Iredell JR. Carriage of type II toxin-antitoxin systems by the growing group of IncX plasmids. Plasmid 2017; 91:19-27. [PMID: 28267580 DOI: 10.1016/j.plasmid.2017.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/19/2017] [Accepted: 02/27/2017] [Indexed: 10/20/2022]
Abstract
The stable maintenance of certain plasmids in bacterial populations has contributed significantly to the current worldwide antibiotic resistance (AbR) emergency. IncX plasmids, long underestimated in this regard, have achieved recent notoriety for their roles in transmission of resistance to carbapenem and colistin, the last-line antibiotics for Gram-negative infections. Toxin-antitoxin (TA) systems contribute to stable maintenance of many AbR plasmids, and a few TA systems have been previously described in the IncX plasmids. Here we present an updated overview of the IncX plasmid family and an in silico analysis of the type II TA systems carried in 153 completely sequenced IncX plasmids that are readily available in public databases at time of writing. The greatest number is in the IncX1 subgroup, followed by IncX3 and IncX4, with only a few representatives of IncX2, IncX5 and IncX6. Toxins from the RelE/ParE superfamily are abundant within IncX1 and IncX4 subgroups, and are associated with a variety of antitoxins. By contrast, the HicBA system is almost exclusively encoded by IncX4 plasmids. Toxins from the superfamily CcdB/MazF were also identified, as were less common systems such as PIN-like and GNAT toxins, and plasmids encoding more than one TA system are probably not unusual. Our results highlight the importance of the IncX plasmid group and update previous much smaller studies, and we present for the first time a detailed analysis of type II TA systems in these plasmids.
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Affiliation(s)
- Paula Bustamante
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia.
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122
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Pragasam AK, Shankar C, Veeraraghavan B, Biswas I, Nabarro LEB, Inbanathan FY, George B, Verghese S. Molecular Mechanisms of Colistin Resistance in Klebsiella pneumoniae Causing Bacteremia from India-A First Report. Front Microbiol 2017; 7:2135. [PMID: 28119670 PMCID: PMC5220082 DOI: 10.3389/fmicb.2016.02135] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023] Open
Abstract
Colistin has long been a reserve drug used for the treatment of carbapenem resistant Klebsiella pneumoniae. Carbapenem resistance in K. pneumoniae has been increasing and is as high as 44% in India. Although a reserve agent, with rise in rates of resistance to carbapenems, the usage of colistin has increased over the years leading to slow emergence of resistance. Colistin resistance is mainly mediated by the alteration in the LPS of bacterial outer membrane with the addition of L-Ara4-N and PEtN molecules. These alterations are mediated by mutations in several genes involved in lipidA modifications and most commonly mutations in mgrB gene has been reported. Recently there is emergence of plasmid mediated resistance due to mcr-1 and mcr-2 genes which poses a threat for the rapid global spread. This study aims at characterizing eight colistin resistant K. pneumoniae from bacteremia by whole genome sequencing. Eight K. pneumoniae were isolated from blood culture during 2013 and 2014 at the Department of Clinical Microbiology, Christian Medical College, India. Antimicrobial susceptibility testing was performed and minimum inhibitory concentration (MIC) was determined for colistin and polymyxin B by broth-micro dilution method. Whole genome sequencing was performed using Ion Torrent and the genome of all eight isolates was analyzed. The eight isolates were resistant to all the antimicrobials expect tigecycline. MIC of colistin and polymyxin B were ranged from 4 to 1024 μg/ml and 0.5 to 2048 μg/ml respectively. Multiple mutations were observed in the chromosomal genes involved in lipid A modifications. mcr-1 and mcr-2 gene was absent in all the isolates. The most significant were mutations in mgrB gene. Among the eight isolates, four, three and one were belonged to sequence types ST 231, ST14 and ST147 respectively. Seven isolates had blaOXA-48 like, one co-expressed blaNDM-1 and blaOXA-48 like genes leading to carbapenem resistance. Overall, multiple numbers of alterations have been observed. This includes silent mutations, point mutations, insertions and/or deletions. Mutations in mgrB gene is responsible for resistance to colistin in this study. Due to emergence of resistance to reserve drugs, there is a need for combination therapies for carbapenem resistant K. pneumoniae and colistin must be judiciously used.
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Affiliation(s)
- Agila K Pragasam
- Department of Clinical Microbiology, Christian Medical College Vellore, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College Vellore, India
| | | | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Centre Kansas, KS, USA
| | - Laura E B Nabarro
- Department of Clinical Microbiology, Christian Medical College Vellore, India
| | | | - Biju George
- Department of Haematology, Christian Medical College Vellore, India
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123
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How should we respond to the emergence of plasmid-mediated colistin resistance in humans and animals? Int J Infect Dis 2017; 54:77-84. [DOI: 10.1016/j.ijid.2016.11.415] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/08/2016] [Accepted: 11/22/2016] [Indexed: 01/29/2023] Open
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124
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High resolution crystal structure of the catalytic domain of MCR-1. Sci Rep 2016; 6:39540. [PMID: 28000749 PMCID: PMC5175174 DOI: 10.1038/srep39540] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/24/2016] [Indexed: 01/07/2023] Open
Abstract
The newly identified mobile colistin resistant gene (mcr-1) rapidly spread among different bacterial strains and confers colistin resistance to its host, which has become a global concern. Based on sequence alignment, MCR-1 should be a phosphoethanolamine transferase, members of the YhjW/YjdB/YijP superfamily and catalyze the addition of phosphoethanolamine to lipid A, which needs to be validated experimentally. Here we report the first high-resolution crystal structure of the C-terminal catalytic domain of MCR-1 (MCR-1C) in its native state. The active pocket of native MCR-1C depicts unphosphorylated nucleophilic residue Thr285 in coordination with two Zinc ions and water molecules. A flexible adjacent active site loop (aa: Lys348-365) pose an open conformation compared to its structural homologues, suggesting of an open substrate entry channel. Taken together, this structure sets ground for further study of substrate binding and MCR-1 catalytic mechanism in development of potential therapeutic agents.
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125
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Epidemiology of infections caused by polymyxin-resistant pathogens. Int J Antimicrob Agents 2016; 48:614-621. [DOI: 10.1016/j.ijantimicag.2016.09.025] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/22/2016] [Accepted: 09/24/2016] [Indexed: 11/18/2022]
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126
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Gao R, Hu Y, Li Z, Sun J, Wang Q, Lin J, Ye H, Liu F, Srinivas S, Li D, Zhu B, Liu YH, Tian GB, Feng Y. Dissemination and Mechanism for the MCR-1 Colistin Resistance. PLoS Pathog 2016; 12:e1005957. [PMID: 27893854 PMCID: PMC5125707 DOI: 10.1371/journal.ppat.1005957] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/26/2016] [Indexed: 01/08/2023] Open
Abstract
Polymyxins are the last line of defense against lethal infections caused by multidrug resistant Gram-negative pathogens. Very recently, the use of polymyxins has been greatly challenged by the emergence of the plasmid-borne mobile colistin resistance gene (mcr-1). However, the mechanistic aspects of the MCR-1 colistin resistance are still poorly understood. Here we report the comparative genomics of two new mcr-1-harbouring plasmids isolated from the human gut microbiota, highlighting the diversity in plasmid transfer of the mcr-1 gene. Further genetic dissection delineated that both the trans-membrane region and a substrate-binding motif are required for the MCR-1-mediated colistin resistance. The soluble form of the membrane protein MCR-1 was successfully prepared and verified. Phylogenetic analyses revealed that MCR-1 is highly homologous to its counterpart PEA lipid A transferase in Paenibacili, a known producer of polymyxins. The fact that the plasmid-borne MCR-1 is placed in a subclade neighboring the chromosome-encoded colistin-resistant Neisseria LptA (EptA) potentially implies parallel evolutionary paths for the two genes. In conclusion, our finding provids a first glimpse of mechanism for the MCR-1-mediated colistin resistance. Colistin is an ultimate line of refuge against fatal infections by multidrug-resistant Gram-negative pathogens. The plasmid-mediated transfer of the mobile colistin resistance gene (mcr-1) represents a novel mechanism for antibacterial drug resistance, and also poses new threats to public health. However, the mechanistic aspects of the MCR-1 colistin resistance are not fully understood. Here we report comparative genomics of two new mcr-1-harbouring plasmids isolated from the human gut microbiota. Genetic studies determined that both the transmembrane region and a substrate-binding motif are essential for its function. Phylogenetic analyses revealed that MCR-1 is highly homologous to the PEA lipid A transferase in Paenibacillus, a known producer of polymyxins. The fact that the plasmid-borne MCR-1 is placed in a subclade neighboring the chromosome-encoded colistin-resistant Neisseria LptA potentially implies parallel evolutionary paths for the two genes. Our results reveal mechanistic insights into the MCR-1-mediated colistin resistance.
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Affiliation(s)
- Rongsui Gao
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yongfei Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhencui Li
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Qingjing Wang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jingxia Lin
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Huiyan Ye
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Swaminath Srinivas
- Department of Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - Defeng Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
| | - Guo-Bao Tian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- * E-mail:
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127
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Caniaux I, van Belkum A, Zambardi G, Poirel L, Gros MF. MCR: modern colistin resistance. Eur J Clin Microbiol Infect Dis 2016; 36:415-420. [DOI: 10.1007/s10096-016-2846-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/08/2016] [Indexed: 11/24/2022]
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128
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Occurrence of mcr-1 in Colistin-Resistant Salmonella enterica Isolates Recovered from Humans and Animals in Italy, 2012 to 2015. Antimicrob Agents Chemother 2016; 60:7532-7534. [PMID: 27697756 DOI: 10.1128/aac.01803-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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129
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Field D, Seisling N, Cotter PD, Ross RP, Hill C. Synergistic Nisin-Polymyxin Combinations for the Control of Pseudomonas Biofilm Formation. Front Microbiol 2016; 7:1713. [PMID: 27833601 PMCID: PMC5080341 DOI: 10.3389/fmicb.2016.01713] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023] Open
Abstract
The emergence and dissemination of multi-drug resistant pathogens is a global concern. Moreover, even greater levels of resistance are conferred on bacteria when in the form of biofilms (i.e., complex, sessile communities of bacteria embedded in an organic polymer matrix). For decades, antimicrobial peptides have been hailed as a potential solution to the paucity of novel antibiotics, either as natural inhibitors that can be used alone or in formulations with synergistically acting antibiotics. Here, we evaluate the potential of the antimicrobial peptide nisin to increase the efficacy of the antibiotics polymyxin and colistin, with a particular focus on their application to prevent biofilm formation of Pseudomonas aeruginosa. The results reveal that the concentrations of polymyxins that are required to effectively inhibit biofilm formation can be dramatically reduced when combined with nisin, thereby enhancing efficacy, and ultimately, restoring sensitivity. Such combination therapy may yield added benefits by virtue of reducing polymyxin toxicity through the administration of significantly lower levels of polymyxin antibiotics.
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Affiliation(s)
- Des Field
- School of Microbiology, University College Cork Cork, Ireland
| | - Nynke Seisling
- School of Microbiology, University College Cork Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research CentreCork, Ireland; APC Microbiome Institute, University College CorkCork, Ireland
| | - R P Ross
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome Institute, University College CorkCork, Ireland
| | - Colin Hill
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome Institute, University College CorkCork, Ireland
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Plasmid with Colistin Resistance Gene mcr-1 in Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains Isolated from Pig Slurry in Estonia. Antimicrob Agents Chemother 2016; 60:6933-6936. [PMID: 27572412 DOI: 10.1128/aac.00443-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/25/2016] [Indexed: 01/23/2023] Open
Abstract
A plasmid carrying the colistin resistance gene mcr-1 was isolated from a pig slurry sample in Estonia. The gene was present on a 33,311-bp plasmid of the IncX4 group. mcr-1 is the only antibiotic resistance gene on the plasmid, with the other genes mainly coding for proteins involved in conjugative DNA transfer (taxA, taxB, taxC, trbM, and the pilX operon). The plasmid pESTMCR was present in three phylogenetically very different Escherichia coli strains, suggesting that it has high potential for horizontal transfer.
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Wyres KL, Holt KE. Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. Trends Microbiol 2016; 24:944-956. [PMID: 27742466 DOI: 10.1016/j.tim.2016.09.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/06/2016] [Accepted: 09/20/2016] [Indexed: 02/05/2023]
Abstract
Antimicrobial-resistant Klebsiella pneumoniae (Kp) has emerged as a major global public health problem. While resistance can occur across a broad range of Kp clones, a small number have become globally distributed and commonly cause outbreaks in hospital settings. Here we describe recent comparative genomics investigations that have shed light on Kp population structure and the evolution of antimicrobial-resistant clones. These studies provide the basic framework within which genomic epidemiology and evolution can be understood, but have merely scratched the surface of what can and should be explored. We assert that further large-scale comparative and functional genomics studies are urgently needed to better understand the biology of this clinically important bacterium.
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Affiliation(s)
- Kelly L Wyres
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.
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mcr-1 is borne by highly diverse Escherichia coli isolates since 2004 in food-producing animals in Europe. Clin Microbiol Infect 2016; 23:51.e1-51.e4. [PMID: 27615718 DOI: 10.1016/j.cmi.2016.08.033] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 08/30/2016] [Accepted: 08/31/2016] [Indexed: 11/21/2022]
Abstract
OBJECTIVES In November 2015, a plasmid-mediated colistin resistance, MCR-1, was described in animals, food and humans in China, and it was considered as a potential emerging threat to public health. Therefore, we screened for the mcr-1 gene a European collection of colistin-resistant Escherichia coli (n=218) and Salmonella spp. (n=74) isolated from diseased food-producing animals between 2004 and 2014 and characterized the mcr-1-positive clones. METHODS Screening for mcr-1 gene was performed by PCR on isolates for which inhibition diameter was <15 mm around a 50 μg disk of colistin. Positive E. coli isolates were then characterized by phylogrouping, multilocus sequence typing and pulsed-field gel electrophoresis typing. Antibiotic susceptibility was determined by disk diffusion testing or by broth microdilution. RESULTS Among the collection, 42 E. coli and three Salmonella spp. were positive for mcr-1, with continuous detection since 2004 mainly from bovine and swine digestive infections. Most of the mcr-1-positive strains were resistant to amoxicillin and cotrimoxazole but remained susceptible to cephalosporins, carbapenems and piperacillin/tazobactam. All but one isolate were resistant to colistin, with a minimum inhibitory concentration of >2 mg/L. Most of the mcr-1-positive E. coli belonged to the phylogroup A with two prevalent clonal complexes, CC10 and CC165, in which sequence type 10 and sequence type 100 were overrepresented and pulsed-field gel electrophoresis typing revealed a high diversity of pulsotypes. CONCLUSIONS MCR-1 was detected yearly in European food-producing animal since 2004 with a high diversity of pulsotypes supporting the dissemination of mcr-1 via plasmids.
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