1
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Gruzdev N, Katz C, Yadid I. Curing of a field strain of Salmonella enterica serovar Infantis isolated from poultry from its highly stable pESI like plasmid. J Microbiol Methods 2024; 222:106959. [PMID: 38782300 DOI: 10.1016/j.mimet.2024.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Salmonella enterica serovar Infantis (S. infantis) is an important emerging pathogen, associated with poultry and poultry products and related to an increasing number of human infections in many countries. A concerning trend among S. infantis isolates is the presence of plasmid-mediated multidrug resistance. In many instances, the genes responsible for this resistance are carried on a megaplasmid known as the plasmid of emerging S. infantis (pESI) or pESI like plasmids. Plasmids can be remarkably stable due to the presence of multiple replicons and post-segregational killing systems (PSKs), which contribute to their maintenance within bacterial populations. To enhance our understanding of S. infantis and its multidrug resistance determinants toward the development of new vaccination strategies, we have devised a new method for targeted plasmid curing. This approach effectively overcomes plasmid addiction by leveraging the temporal overproduction of specific antitoxins coupled with the deletion of the partition region. By employing this strategy, we successfully generated a plasmid-free strain from a field isolate derived from S. infantis 119,944. This method provides valuable tools for studying S. infantis and its plasmid-borne multidrug resistance mechanisms and can be easily adopted for plasmid curing from other related bacteria.
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Affiliation(s)
- Nadya Gruzdev
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Chen Katz
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel
| | - Itamar Yadid
- Migal-Galilee Research Institute, Kiryat-Shmona 1101602, Israel; Tel-Hai College, Upper Galilee 1220800, Israel.
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2
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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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3
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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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4
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Mayorga-Ramos A, Zúñiga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guamán LP. CRISPR-Cas-Based Antimicrobials: Design, Challenges, and Bacterial Mechanisms of Resistance. ACS Infect Dis 2023; 9:1283-1302. [PMID: 37347230 PMCID: PMC10353011 DOI: 10.1021/acsinfecdis.2c00649] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Indexed: 06/23/2023]
Abstract
The emergence of antibiotic-resistant bacterial strains is a source of public health concern across the globe. As the discovery of new conventional antibiotics has stalled significantly over the past decade, there is an urgency to develop novel approaches to address drug resistance in infectious diseases. The use of a CRISPR-Cas-based system for the precise elimination of targeted bacterial populations holds promise as an innovative approach for new antimicrobial agent design. The CRISPR-Cas targeting system is celebrated for its high versatility and specificity, offering an excellent opportunity to fight antibiotic resistance in pathogens by selectively inactivating genes involved in antibiotic resistance, biofilm formation, pathogenicity, virulence, or bacterial viability. The CRISPR-Cas strategy can enact antimicrobial effects by two approaches: inactivation of chromosomal genes or curing of plasmids encoding antibiotic resistance. In this Review, we provide an overview of the main CRISPR-Cas systems utilized for the creation of these antimicrobials, as well as highlighting promising studies in the field. We also offer a detailed discussion about the most commonly used mechanisms for CRISPR-Cas delivery: bacteriophages, nanoparticles, and conjugative plasmids. Lastly, we address possible mechanisms of interference that should be considered during the intelligent design of these novel approaches.
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Affiliation(s)
- Arianna Mayorga-Ramos
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Johana Zúñiga-Miranda
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Saskya E. Carrera-Pacheco
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
| | - Carlos Barba-Ostria
- Escuela
de Medicina, Colegio de Ciencias de la Salud Quito, Universidad San Francisco de Quito USFQ, Quito 170902, Ecuador
| | - Linda P. Guamán
- Centro
de Investigación Biomédica (CENBIO), Facultad de Ciencias
de la Salud Eugenio Espejo, Universidad
UTE, Quito 170527, Ecuador
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5
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Qi Q, Kamruzzaman M, Iredell JR. A Streamlined Approach for Fluorescence Labelling of Low-Copy-Number Plasmids for Determination of Conjugation Frequency by Flow Cytometry. Microorganisms 2023; 11:microorganisms11040878. [PMID: 37110299 PMCID: PMC10144549 DOI: 10.3390/microorganisms11040878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Bacterial conjugation plays a major role in the dissemination of antibiotic resistance and virulence traits through horizontal transfer of plasmids. Robust measurement of conjugation frequency of plasmids between bacterial strains and species is therefore important for understanding the transfer dynamics and epidemiology of conjugative plasmids. In this study, we present a streamlined experimental approach for fluorescence labelling of low-copy-number conjugative plasmids that allows plasmid transfer frequency during filter mating to be measured by flow cytometry. A blue fluorescent protein gene is inserted into a conjugative plasmid of interest using a simple homologous recombineering procedure. A small non-conjugative plasmid, which carries a red fluorescent protein gene with a toxin–antitoxin system that functions as a plasmid stability module, is used to label the recipient bacterial strain. This offers the dual advantage of circumventing chromosomal modifications of recipient strains and ensuring that the red fluorescent protein gene-bearing plasmid can be stably maintained in recipient cells in an antibiotic-free environment during conjugation. A strong constitutive promoter allows the two fluorescent protein genes to be strongly and constitutively expressed from the plasmids, thus allowing flow cytometers to clearly distinguish between donor, recipient, and transconjugant populations in a conjugation mix for monitoring conjugation frequencies more precisely over time.
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Affiliation(s)
- Qin Qi
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
| | - Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW 2145, Australia
- Westmead Hospital, Westmead, Sydney, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
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6
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Maurya AP, Lazdins A, Wilson H, Lloyd GS, Stephens ER, Haines AS, Thomas CM. Iteron control of oriV function in IncP-1 plasmid RK2. Plasmid 2023; 126:102681. [PMID: 36990191 DOI: 10.1016/j.plasmid.2023.102681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023]
Abstract
Replication control of many plasmids is mediated by the balance between the positive and negative effects of Rep protein binding repeated sequences (iterons) associated with the replication origin, oriV. Negative control is thought to be mediated by dimeric Rep protein linking iterons in a process termed "handcuffing". The well-studied oriV region of RK2 contains 9 iterons arranged as a singleton (iteron 1), a group of 3 (iterons 2-4) and a group of 5 (iterons 5-9), but only iterons 5 to 9 are essential for replication. An additional iteron (iteron 10), oriented in the opposite direction, is also involved and reduces copy-number nearly two-fold. Since iterons 1 and 10 share an identical upstream hexamer (5' TTTCAT 3') it has been hypothesised that they form a TrfA-mediated loop facilitated by their inverted orientation. Here we report that contrary to the hypothesis, flipping one or other so they are in direct orientation results in marginally lower rather than higher copy-number. In addition, following mutagenesis of the hexamer upstream of iteron 10, we report that the Logo for the hexamer "upstream" of the regulatory iterons (1 to 4 and 10) differs from that of the essential iterons, suggesting functional differences in their interaction with TrfA.
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Affiliation(s)
- Anand P Maurya
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alessandro Lazdins
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Helen Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Georgina S Lloyd
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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7
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Sundaramoorthy NS, Shankaran P, Gopalan V, Nagarajan S. New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae. Crit Rev Microbiol 2022:1-20. [PMID: 35649163 DOI: 10.1080/1040841x.2022.2080525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.
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Affiliation(s)
- Niranjana Sri Sundaramoorthy
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Prakash Shankaran
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Vidhya Gopalan
- Department of Virology, Kings Institute of Preventative Medicine, Guindy, Chennai, Tamil Nadu, India
| | - Saisubramanian Nagarajan
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
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8
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A novel plasmid entry exclusion system in pKPC_UVA01, a promiscuous conjugative plasmid carrying the
bla
KPC
carbapenemase gene. Antimicrob Agents Chemother 2022; 66:e0232221. [PMID: 35007138 PMCID: PMC8923210 DOI: 10.1128/aac.02322-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conjugative plasmids are the principal mediator in the emergence and spread of antibiotic resistance genes in Enterobacterales. Plasmid entry exclusion (EEX) systems can restrict their transfer into the recipient bacteria carrying closely related plasmids. In this study, we identified and characterized a novel plasmid entry exclusion system in a carbapenem resistance plasmid pKPC_UVA01, which is responsible for widespread dissemination of the blaKPC carbapenemase gene among Enterobacterales in the United States. The identified eex gene in the recipient strain of different Enterobacterales species inhibited the conjugation transfer of pKPC_UVA01 plasmids at a range of 200- to 400-fold, and this inhibition was found to be a dose-dependent function of the EEX protein in recipient cells. The C terminus truncated version of eex or eex with an early termination codon at the C terminus region alleviated the inhibition of conjugative transfer. Unlike the strict specificity of plasmid exclusion by the known EEX protein, the newly identified EEX in the recipient strain could inhibit the transfer of IncP and IncN plasmids. The eex gene from the plasmid pKPC_UVA01 was not required for conjugative transfer but was essential in the donor bacteria for entry exclusion of this plasmid. This was a novel function of a single protein that is essential in both donor and recipient bacteria for the entry exclusion of a plasmid. This eex gene is found to be distributed in multidrug resistance plasmids similar to pKPC_UVA01 in different Enterobacterales species and may contribute to the stability of this plasmid type by controlling its transfer.
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9
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Neil K, Allard N, Roy P, Grenier F, Menendez A, Burrus V, Rodrigue S. High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. Mol Syst Biol 2021; 17:e10335. [PMID: 34665940 PMCID: PMC8527022 DOI: 10.15252/msb.202110335] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 12/15/2022] Open
Abstract
Antibiotic resistance threatens our ability to treat infectious diseases, spurring interest in alternative antimicrobial technologies. The use of bacterial conjugation to deliver CRISPR-cas systems programmed to precisely eliminate antibiotic-resistant bacteria represents a promising approach but requires high in situ DNA transfer rates. We have optimized the transfer efficiency of conjugative plasmid TP114 using accelerated laboratory evolution. We hence generated a potent conjugative delivery vehicle for CRISPR-cas9 that can eliminate > 99.9% of targeted antibiotic-resistant Escherichia coli in the mouse gut microbiota using a single dose. We then applied this system to a Citrobacter rodentium infection model, achieving full clearance within four consecutive days of treatment.
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Affiliation(s)
- Kevin Neil
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Nancy Allard
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Patricia Roy
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Frédéric Grenier
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
| | - Alfredo Menendez
- Département de Microbiologie et d'InfectiologieUniversité de SherbrookeSherbrookeQCCanada
| | - Vincent Burrus
- Département de biologieUniversité de SherbrookeSherbrookeQCCanada
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10
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Wongpayak P, Meesungnoen O, Saejang S, Subsoontorn P. A highly effective and self-transmissible CRISPR antimicrobial for elimination of target plasmids without antibiotic selection. PeerJ 2021; 9:e11996. [PMID: 34567840 PMCID: PMC8428258 DOI: 10.7717/peerj.11996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/27/2021] [Indexed: 01/21/2023] Open
Abstract
The use of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein) for sequence-specific elimination of bacteria or resistance genes is a powerful tool for combating antibiotic resistance. However, this approach requires efficient delivery of CRISPR/Cas DNA cassette(s) into the targeted bacterial population. Compared to phage transduction, plasmid conjugation can deliver DNA to a broader host range but often suffers from low delivery efficiency. Here, we developed multi-plasmid conjugation systems for efficient CRISPR/Cas delivery, target DNA elimination and plasmid replacement. The CRISPR/Cas system, delivered via a broad-host-range R1162 mobilizable plasmid, specifically eliminated the targeted plasmid in recipient cells. A self-transmissible RK2 helper plasmid facilitated the spread of mobilizable CRISPR/Cas. The replacement of the target plasmid with another plasmid from the same compatibility group helped speed up target plasmid elimination especially when the target plasmid was also mobilizable. Together, we showed that up to 100% of target plasmid from the entire recipient population could be replaced even at a low (1:180) donor-to-recipient ratio and in the absence of transconjugant selection. Such an ability to modify genetic content of microbiota efficiently in the absence of selection will be critical for future development of CRISPR antimicrobials as well as genetic tools for in situ microbiome engineering.
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Affiliation(s)
- Panjaporn Wongpayak
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | | | - Somchai Saejang
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | - Pakpoom Subsoontorn
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
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11
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Wang T, Weiss A, Ha Y, You L. Predicting plasmid persistence in microbial communities by coarse-grained modeling. Bioessays 2021; 43:e2100084. [PMID: 34278591 DOI: 10.1002/bies.202100084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 06/15/2021] [Accepted: 06/17/2021] [Indexed: 11/08/2022]
Abstract
Plasmids are a major type of mobile genetic elements (MGEs) that mediate horizontal gene transfer. The stable maintenance of plasmids plays a critical role in the functions and survival for microbial populations. However, predicting and controlling plasmid persistence and abundance in complex microbial communities remain challenging. Computationally, this challenge arises from the combinatorial explosion associated with the conventional modeling framework. Recently, a plasmid-centric framework (PCF) has been developed to overcome this computational bottleneck. This framework enables the derivation of a simple metric, the persistence potential, to predict plasmid persistence and abundance. Here, we discuss how PCF can be extended to account for plasmid interactions. We also discuss how such model-guided predictions of plasmid fates can benefit from the development of new experimental tools and data-driven computational methods.
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Affiliation(s)
- Teng Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Andrea Weiss
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Yuanchi Ha
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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12
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Kamruzzaman M, Wu AY, Iredell JR. Biological Functions of Type II Toxin-Antitoxin Systems in Bacteria. Microorganisms 2021; 9:microorganisms9061276. [PMID: 34208120 PMCID: PMC8230891 DOI: 10.3390/microorganisms9061276] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
After the first discovery in the 1980s in F-plasmids as a plasmid maintenance system, a myriad of toxin-antitoxin (TA) systems has been identified in bacterial chromosomes and mobile genetic elements (MGEs), including plasmids and bacteriophages. TA systems are small genetic modules that encode a toxin and its antidote and can be divided into seven types based on the nature of the antitoxin molecules and their mechanism of action to neutralise toxins. Among them, type II TA systems are widely distributed in chromosomes and plasmids and the best studied so far. Maintaining genetic material may be the major function of type II TA systems associated with MGEs, but the chromosomal TA systems contribute largely to functions associated with bacterial physiology, including the management of different stresses, virulence and pathogenesis. Due to growing interest in TA research, extensive work has been conducted in recent decades to better understand the physiological roles of these chromosomally encoded modules. However, there are still controversies about some of the functions associated with different TA systems. This review will discuss the most current findings and the bona fide functions of bacterial type II TA systems.
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Affiliation(s)
- Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
- Correspondence: (M.K.); (J.R.I.)
| | - Alma Y. Wu
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia;
- Westmead Hospital, Westmead, NSW 2145, Australia
- Correspondence: (M.K.); (J.R.I.)
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13
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Sklyar T, Kurahina N, Lavrentieva K, Burlaka V, Lykholat T, Lykholat O. Autonomic (Mobile) Genetic Elements of Bacteria and Their Hierarchy. CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721030099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Foley SL, Kaldhone PR, Ricke SC, Han J. Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:e00031-20. [PMID: 33910982 PMCID: PMC8139525 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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Affiliation(s)
- Steven L Foley
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Pravin R Kaldhone
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
- Center for Food Safety and Food Science Department, University of Arkansas, Fayetteville, Arkansas, USA
| | - Steven C Ricke
- Meat Science & Animal Biologics Discovery Program, Department of Animal and Dairy Sciences, University of Wisconsin, Madison, Wisconsin, USA
| | - Jing Han
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
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15
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Molecular characterization of plasmids encoding bla CTX-M from faecal Escherichia coli in travellers returning to the UK from South Asia. J Hosp Infect 2021; 114:134-143. [PMID: 33862156 DOI: 10.1016/j.jhin.2021.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/20/2021] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND The global prevalence of extended-spectrum beta-lactamase-producing Escherichia coli is rising and is dominated by blaCTX-M spread by plasmids. Travellers to South Asia from Western Europe have high rates of acquisition of faecal CTX-M-producing E. coli (CTX-M-EC). AIMS To determine the conjugative ability of CTX-M-EC acquired by healthy volunteers after travel to South Asia, the proportion of travel-acquired CTX-M-EC where blaCTX-M is encoded on a plasmid vs on the bacterial chromosome, and the relatedness of travel-acquired CTX-M-EC plasmids to previously sequenced plasmids. METHODS Faecal samples were collected pre- and post-travel from 23 volunteers who visited South Asia, and CTX-M-EC were cultured. After short- and long-read sequencing, 10 plasmid sequences were identified and compared with previously sequenced plasmids in GenBank. Conjugation to E. coli K-12 was undertaken using filter mating. FINDINGS Thirty-five percent of CTX-M-EC isolates tested transferred the blaCTX-M plasmid by conjugation. Travel-acquired CTX-M-EC carried blaCTX-M on a plasmid in 62% of isolates, whereas 38% of isolates had blaCTX-M on the chromosome. CTX-M-EC plasmids acquired after travel to South Asia had close homology to previously described epidemic plasmids which are widely disseminated in humans, animals and the natural environment. CONCLUSION Globally successful epidemic plasmids are involved in the spread of CTX-M-EC. Targeted strategies may be used to displace such plasmids from the host strain as part of efforts in infection prevention and control in healthcare settings. Bacteria with blaCTX-M plasmids were readily acquired by healthy volunteers, and were carried on return to the UK, providing opportunities for onward dissemination.
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Gama JA, Zilhão R, Dionisio F. Plasmid Interactions Can Improve Plasmid Persistence in Bacterial Populations. Front Microbiol 2020; 11:2033. [PMID: 32983032 PMCID: PMC7487452 DOI: 10.3389/fmicb.2020.02033] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/31/2023] Open
Abstract
It is difficult to understand plasmid maintenance in the absence of selection and theoretical models predict the conditions for plasmid persistence to be limited. Plasmid-associated fitness costs decrease bacterial competitivity, while imperfect partition allows the emergence of plasmid-free cells during cell division. Although plasmid conjugative transfer allows mobility into plasmid-free cells, the rate of such events is generally not high enough to ensure plasmid persistence. Experimental data suggest several factors that may expand the conditions favorable for plasmid maintenance, such as compensatory mutations and accessory genes that allow positive selection. Most of the previous studies focus on bacteria that carry a single plasmid. However, there is increasing evidence that multiple plasmids inhabit the same bacterial population and that interactions between them affect their transmission and persistence. Here, we adapt previous mathematical models to include multiple plasmids and perform computer simulations to study how interactions among them affect plasmid maintenance. We tested the contribution of different plasmid interaction parameters that impact three biological features: host fitness, conjugative transfer and plasmid loss – which affect plasmid persistence. The interaction affecting conjugation was studied in the contexts of intracellular and intercellular interactions, i.e., the plasmids interact when present in the same cell or when in different cells, respectively. First, we tested the effect of each type of interaction alone and concluded that only interactions affecting fitness (epistasis) prevented plasmid extinction. Although not allowing plasmid maintenance, intracellular interactions increasing conjugative efficiencies had a more determinant impact in delaying extinction than the remaining parameters. Then, we allowed multiple interactions between plasmids and concluded that, in a few cases, a combined effect of (intracellular) interactions increasing conjugation and fitness lead to plasmid maintenance. Our results show a hierarchy among these interaction parameters. Those affecting fitness favor plasmid persistence more than those affecting conjugative transfer and lastly plasmid loss. These results suggest that interactions between different plasmids can favor their persistence in bacterial communities.
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Affiliation(s)
- João Alves Gama
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Rita Zilhão
- Department of Plant Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Francisco Dionisio
- Department of Plant Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes. Microorganisms 2020; 8:microorganisms8081211. [PMID: 32784449 PMCID: PMC7463591 DOI: 10.3390/microorganisms8081211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
The global spread of antibiotic resistance has posed a serious threat to public healthcare and undermined decades of progress made in the fight against bacterial infections. It has been demonstrated that the lack of novel effective antibiotics and rapid spread of antibiotic resistance genes via horizontal transfer in the ecosystem are mainly responsible for this crisis. Notably, plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) is recognized as the most dominant dissemination pathway of ARGs in humans, animals and environmental settings. Antibiotic selective pressure has always been regarded as one of the crucial contributors to promoting the dissemination of antibiotic resistance through horizontal gene transfer (HGT). However, the roles of exogenous compounds and particularly non-antibiotic drugs in the spread of ARGs are still underappreciated. In this review, we first summarize the major pathways of HGT in bacteria, including conjugation, transformation, transduction and vesiduction. Subsequently, an overview of these compounds capable of promoting the HGT is presented, which guides to the formulation of more reasonable dosing regimens and drug residue standards in clinical practice. By contrast, these compounds that display an inhibition effect on HGT are also highlighted, which provides a unique strategy to minimize the spread of ARGs. Lastly, we discuss the implementations and challenges in bringing these HGT inhibitors into clinical trials.
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18
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Wu AY, Kamruzzaman M, Iredell JR. Specialised functions of two common plasmid mediated toxin-antitoxin systems, ccdAB and pemIK, in Enterobacteriaceae. PLoS One 2020; 15:e0230652. [PMID: 32603331 PMCID: PMC7326226 DOI: 10.1371/journal.pone.0230652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/17/2020] [Indexed: 12/17/2022] Open
Abstract
Toxin-antitoxin systems (TAS) are commonly found on bacterial plasmids and are generally involved in plasmid maintenance. In addition to plasmid maintenance, several plasmid-mediated TAS are also involved in bacterial stress response and virulence. Even though the same TAS are present in a variety of plasmid types and bacterial species, differences in their sequences, expression and functions are not well defined. Here, we aimed to identify commonly occurring plasmid TAS in Escherichia coli and Klebsiella pneumoniae and compare the sequence, expression and plasmid stability function of their variants. 27 putative type II TAS were identified from 1063 plasmids of Klebsiella pneumoniae in GenBank. Among these, ccdAB and pemIK were found to be most common, also occurring in plasmids of E. coli. Comparisons of ccdAB variants, taken from E. coli and K. pneumoniae, revealed sequence differences, while pemIK variants from IncF and IncL/M plasmids were almost identical. Similarly, the expression and plasmid stability functions of ccdAB variants varied according to the host strain and species, whereas the expression and functions of pemIK variants were consistent among host strains. The specialised functions of some TAS may determine the host specificity and epidemiology of major antibiotic resistance plasmids.
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Affiliation(s)
- Alma Y. Wu
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
| | - Muhammad Kamruzzaman
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- * E-mail: (MK); (JI)
| | - Jonathan R. Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, Australia
- Westmead Hospital, Westmead, New South Wales, Australia
- * E-mail: (MK); (JI)
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19
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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20
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Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metab Eng Commun 2020; 10:e00126. [PMID: 32215253 PMCID: PMC7090339 DOI: 10.1016/j.mec.2020.e00126] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/23/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023] Open
Abstract
Genome engineering of non-conventional microorganisms calls for the development of dedicated synthetic biology tools. Pseudomonas putida is a Gram-negative, non-pathogenic soil bacterium widely used for metabolic engineering owing to its versatile metabolism and high levels of tolerance to different types of stress. Genome editing of P. putida largely relies on homologous recombination events, assisted by helper plasmid-based expression of genes encoding DNA modifying enzymes. Plasmid curing from selected isolates is the most tedious and time-consuming step of this procedure, and implementing commonly used methods to this end in P. putida (e.g. temperature-sensitive replicons) is often impractical. To tackle this issue, we have developed a toolbox for both target- and self-curing of plasmid DNA in Pseudomonas species. Our method enables plasmid-curing in a simple cultivation step by combining in vivo digestion of vectors by the I-SceI homing nuclease with synthetic control of plasmid replication, triggered by the addition of a cheap chemical inducer (3-methylbenzoate) to the medium. The system displays an efficiency of vector curing >90% and the screening of plasmid-free clones is greatly facilitated by the use of fluorescent markers that can be selected according to the application intended. Furthermore, quick genome engineering of P. putida using self-curing plasmids is demonstrated through genome reduction of the platform strain EM42 by eliminating all genes encoding β-lactamases, the catabolic ben gene cluster, and the pyoverdine synthesis machinery. Physiological characterization of the resulting streamlined strain, P. putida SEM10, revealed advantageous features that could be exploited for metabolic engineering. Plasmid-curing is the most time-consuming step in genome engineering approaches. We have developed a system for easy target- and self-curing of plasmid DNA. Synthetic control of replication and highly-specific in vivo DNA digestion were used. Plasmid curing with this system displays an efficiency >90% in a 24-h cultivation. Quick genome engineering facilitated genome reduction of P. putida.
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Affiliation(s)
- Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Laura Friis
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Justine Turlin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
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21
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Lazdins A, Maurya AP, Miller CE, Kamruzzaman M, Liu S, Stephens ER, Lloyd GS, Haratianfar M, Chamberlain M, Haines AS, Kreft JU, Webber MA, Iredell J, Thomas CM. Potentiation of curing by a broad-host-range self-transmissible vector for displacing resistance plasmids to tackle AMR. PLoS One 2020; 15:e0225202. [PMID: 31940351 PMCID: PMC6961859 DOI: 10.1371/journal.pone.0225202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/29/2019] [Indexed: 12/21/2022] Open
Abstract
Plasmids are potent vehicles for spread of antibiotic resistance genes in bacterial populations and often persist in the absence of selection due to efficient maintenance mechanisms. We previously constructed non-conjugative high copy number plasmid vectors that efficiently displace stable plasmids from enteric bacteria in a laboratory context by blocking their replication and neutralising their addiction systems. Here we assess a low copy number broad-host-range self-transmissible IncP-1 plasmid as a vector for such curing cassettes to displace IncF and IncK plasmids. The wild type plasmid carrying the curing cassette displaces target plasmids poorly but derivatives with deletions near the IncP-1 replication origin that elevate copy number about two-fold are efficient. Verification of this in mini IncP-1 plasmids showed that elevated copy number was not sufficient and that the parB gene, korB, that is central to its partitioning and gene control system, also needs to be included. The resulting vector can displace target plasmids from a laboratory population without selection and demonstrated activity in a mouse model although spread is less efficient and requires additional selection pressure.
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Affiliation(s)
- Alessandro Lazdins
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Anand Prakash Maurya
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Claire E. Miller
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Muhammad Kamruzzaman
- University of Sydney, Centre for Infectious Disease & Microbiology, Westmead Institute of Medical Research, Westmead, New South Wales, Australia
| | - Shuting Liu
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Elton R. Stephens
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Georgina S. Lloyd
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Mona Haratianfar
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Melissa Chamberlain
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Anthony S. Haines
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Jan-Ulrich Kreft
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Mark. A. Webber
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
| | - Jonathan Iredell
- University of Sydney, Centre for Infectious Disease & Microbiology, Westmead Institute of Medical Research, Westmead, New South Wales, Australia
| | - Christopher M. Thomas
- Institute of Microbiology & Infection and School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England, United Kingdom
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22
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Ramadan Mohamed E, Ali MY, Waly NGFM, Halby HM, Abd El-Baky RM. The Inc FII Plasmid and its Contribution in the Transmission of blaNDM-1 and blaKPC-2 in Klebsiella pneumoniae in Egypt. Antibiotics (Basel) 2019; 8:antibiotics8040266. [PMID: 31847288 PMCID: PMC6963397 DOI: 10.3390/antibiotics8040266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 12/25/2022] Open
Abstract
The emergence of blaKPC-2 and blaNDM-1 producing Klebsiella pneumoniae represents a great problem in many Egyptian hospitals. One hundred and twenty-six K. pneumoniae isolates from patients admitted to Assiut University Hospital were identified by an API20E kit. Carbapenemase-producing K. pneumoniae (CPKP) was detected by the modified carbapenem inactivation method (mCIM), the EDTA-modified carbapenem inactivation method (eCIM), and an E-test. Based on the polymerase chain reaction, all isolates were negative for bla-VIM-1 and bla-IMP-1, fifteen of these isolates were positive for both blaKPC-2 and blaNDM-1, two isolates were positive for blaKPC-2 only, and twenty-eight isolates were positive for bla-NDM-1 only. Although one isolate was positive for the string test, all CPKP isolates were negative for capsular genes. Only 71.1% of CPKP transferred their plasmids to their corresponding transconjugants (E. coli J53). The resistance patterns of the clinical isolates and their transconjugates were similar, except for 12 isolates, which showed differences with their transconjugates in the resistance profile of four antibiotics. Molecular typing of the plasmids based on replicon typing showed that Inc FIIK and FII plasmids predominated in isolates and their transconjugants carrying blaKPC-2 and/or blaNDM-1. Conjugative Inc FII plasmids play an important role in the spread of CPKP, and their recognition is essential to limit their spread.
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Affiliation(s)
- Eman Ramadan Mohamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 11651, Egypt; (E.R.M.); (M.Y.A.); (H.M.H.)
| | - Mamdouh Yones Ali
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 11651, Egypt; (E.R.M.); (M.Y.A.); (H.M.H.)
| | - Nancy G F M Waly
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Hamada Mohamed Halby
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Assuit 11651, Egypt; (E.R.M.); (M.Y.A.); (H.M.H.)
| | - Rehab Mahmoud Abd El-Baky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Deraya University, Minia 61519, Egypt
- Correspondence: ; Tel.: +20-1092487412
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23
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Blázquez J, Rodríguez-Beltrán J, Matic I. Antibiotic-Induced Genetic Variation: How It Arises and How It Can Be Prevented. Annu Rev Microbiol 2019; 72:209-230. [PMID: 30200850 DOI: 10.1146/annurev-micro-090817-062139] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
By targeting essential cellular processes, antibiotics provoke metabolic perturbations and induce stress responses and genetic variation in bacteria. Here we review current knowledge of the mechanisms by which these molecules generate genetic instability. They include production of reactive oxygen species, as well as induction of the stress response regulons, which lead to enhancement of mutation and recombination rates and modulation of horizontal gene transfer. All these phenomena influence the evolution and spread of antibiotic resistance. The use of strategies to stop or decrease the generation of resistant variants is also discussed.
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Affiliation(s)
- Jesús Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), 28049 Madrid, Spain; .,Unidad de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen del Rocio, 41013 Seville, Spain.,Red Española de Investigacion en Patologia Infecciosa, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Ivan Matic
- Faculté de Médecine Paris Descartes, INSERM 1001, CNRS, Université Paris-Descartes-Sorbonne Paris Cité, 75014 Paris, France;
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24
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Mutai WC, Waiyaki PG, Kariuki S, Muigai AWT. Plasmid profiling and incompatibility grouping of multidrug resistant Salmonella enterica serovar Typhi isolates in Nairobi, Kenya. BMC Res Notes 2019; 12:422. [PMID: 31311578 PMCID: PMC6636098 DOI: 10.1186/s13104-019-4468-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Plasmids harbour antibiotic resistance genes which contribute to the emergence of multidrug resistant pathogens. We detected the presence of plasmids in multidrug resistant Salmonella enterica serovar Typhi (S. Typhi) isolates from our previous study and consequently determined their incompatibility groups and possibility of conjugation transmission. Plasmids were extracted from 98 multidrug resistant S. Typhi isolates based on alkaline lysis technique. Plasmid incompatibility grouping was established by PCR replicon typing using 18 pairs of primers to amplify FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F and FIIA replicons. Antibiotic resistance phenotypes were conjugally transferred from S. Typhi isolates with plasmids to Escherichia coli K12F strain devoid of plasmids. RESULTS Approximately 79.6% of the MDR S. Typhi isolates were related to the existence of plasmids. We detected 93.6% of plasmids belonging to incompatibility (Inc) group HI1. The other incompatibility groups identified included IncFIC (16.7%), IncP (1.3%), and IncI1 (1.3%) which appeared together with Inc HI1. MDR S. Typhi isolated carried a homologous plasmid of incompatibility group HI1 most of which transferred the resistance phenotypes of ampicillin, tetracycline and chloramphenicol to the transconjugants.
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Affiliation(s)
- Winnie C Mutai
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya.
| | - Peter G Waiyaki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Anne W T Muigai
- School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
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25
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A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance. Sci Rep 2019; 9:9872. [PMID: 31285520 PMCID: PMC6614396 DOI: 10.1038/s41598-019-46318-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/26/2019] [Indexed: 11/16/2022] Open
Abstract
Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems on low-copy-number plasmids. Thousands of TA loci have since been identified on chromosomes, plasmids and mobile elements in bacteria and archaea with diverse roles in bacterial physiology and in maintenance of genetic elements. Here, we identified and characterised a plasmid mediated type II TA system in Enterobacteriaceae as a member of the ParDE super family. This system (hereafter, ParDEI) is distributed among IncI and IncF-type antibiotic resistance and virulence plasmids found in avian and human-source Escherichia coli and Salmonella. It is found that ParDEI is a plasmid stability and stress response module that increases tolerance of aminoglycoside, quinolone and β-lactam antibiotics in E. coli by ~100–1,000-fold, and thus to levels beyond those achievable in the course of antibiotic therapy for human infections. ParDEI also confers a clear survival advantage at 42 °C and expression of the ParEI toxin in trans induces the SOS response, inhibits cell division and promotes biofilm formation. This transmissible high-level antibiotic tolerance is likely to be an important factor in the success of the IncI and IncF plasmids which carry it and the important pathogens in which these are resident.
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26
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Düzgün AÖ, Saral A. Next-generation sequencing of plasmid carrying blaOXA-48 in Klebsiella pneumoniae from Turkey. Acta Microbiol Immunol Hung 2019; 66:261-272. [PMID: 30803252 DOI: 10.1556/030.66.2019.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A carbapenem-resistant Klebsiella pneumoniae strain was isolated in Turkey in 2012 and blaNDM-1 and blaOXA-48 genes were observed in this strain. The aim of this study was to investigate transferability of plasmid bearing blaOXA-48 in K. pneumoniae and to use whole-genome sequencing in order to understand the genetic context of plasmid. K. pneumoniae strain was used as donor in conjugation experiments. Antibiotic susceptibility profile of selected transconjugant was determined. Plasmid was isolated from transconjugant colony and was named as pKPT. Complete sequencing of the pKPT was conducted using a next-generation sequencing. Annotation of the contigs was performed using the Geneious R9, followed by finding open reading frames (ORFs) with selected web-based tools. BLAST analysis was performed at the NCBI BLAST server to determine genes showing more than 90% similarity with these ORFs. Results of antibiotic susceptibility test showed that transconjugant colony was resistant to ampicillin/sulbactam, piperacillin, and piperacillin/tazobactam. The pKPT plasmid had a length of 45,217 bp and an average G + C content of 49%. Blast analysis revealed that pKPT was included in the IncL/M incompatibility group. The pKPT was found to contain blaOXA-48 within Tn1999.2 transposon without any other antibiotic resistance gene.
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Affiliation(s)
- Azer Özad Düzgün
- 1 Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gümüşhane University, Gümüşhane, Turkey
- 2 Medicinal Plants, Traditional Medicine Practice and Research Center, Gümüşhane University, Gümüşhane, Turkey
| | - Ayşegül Saral
- 3 Department of Nutrition and Dietetics, Faculty of Health Sciences, Artvin Coruh University, Artvin, Turkey
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27
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Raymond B. Five rules for resistance management in the antibiotic apocalypse, a road map for integrated microbial management. Evol Appl 2019; 12:1079-1091. [PMID: 31297143 PMCID: PMC6597870 DOI: 10.1111/eva.12808] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Resistance to new antimicrobials can become widespread within 2-3 years. Resistance problems are particularly acute for bacteria that can experience selection as both harmless commensals and pathogenic hospital-acquired infections. New drugs, although welcome, cannot tackle the antimicrobial resistance crisis alone: new drugs must be partnered with more sustainable patterns of use. However, the broader experience of resistance management in other disciplines, and the assumptions on which resistance rests, is not widely appreciated in clinical and microbiological disciplines. Improved awareness of the field of resistance management could improve clinical outcomes and help shape novel solutions. Here, the aim is to develop a pragmatic approach to developing a sustainable integrated means of using antimicrobials, based on an interdisciplinary synthesis of best practice, recent theory and recent clinical data. This synthesis emphasizes the importance of pre-emptive action and the value of reducing the supply of genetic novelty to bacteria under selection. The weight of resistance management experience also cautions against strategies that over-rely on the fitness costs of resistance or low doses. The potential (and pitfalls) of shorter courses, antibiotic combinations and antibiotic mixing or cycling are discussed in depth. Importantly, some of variability in the success of clinical trials of mixing approaches can be explained by the number and diversity of drugs in a trial, as well as whether trials encompass single wards or the wider transmission network that is a hospital. Consideration of the importance of data, and of the initially low frequency of resistance, leads to a number of additional recommendations. Overall, reduction in selection pressure, interference with the transmission of problematic genotypes and multidrug approaches (combinations, mixing or cycling) are all likely to be required for sustainability and the protection of forthcoming drugs.
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Bharathan S, Sundaramoorthy NS, Chandrasekaran H, Rangappa G, ArunKumar G, Subramaniyan SB, Veerappan A, Nagarajan S. Sub lethal levels of platinum nanoparticle cures plasmid and in combination with carbapenem, curtails carbapenem resistant Escherichia coli. Sci Rep 2019; 9:5305. [PMID: 30923328 PMCID: PMC6438982 DOI: 10.1038/s41598-019-41489-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Drug resistance traits are rapidly disseminated across bacteria by horizontal gene transfer, especially through plasmids. Plasmid curing agents that are active both in vitro and in vivo will resensitize Multi Drug Resistant (MDR) bacteria to antimicrobial agents. Pectin capped platinum nanoparticles (PtNPs) at sub MIC (20 µM) concentration was effective, in causing loss of Extended Spectrum Beta Lactamase (ESBL) harboring plasmid as evidenced by, absence of plasmid in agarose gel and by a concomitant (16-64 fold) drop in MIC for cell wall inhibitors ceftriaxone and meropenem, in carbapenem resistant Escherichia coli (CREC). Interestingly, the plasmid cured strain exhibited small colony morphology and displayed slower growth both in vitro and in vivo. Complementation of cured strain with plasmid from the wild type strain restored resistance towards meropenem and ceftriaxone. Relative to wild type, plasmid cured strain displayed 50% reduction in biofilm formation. Plasmid curing also occurred in vivo in infected zebrafish with curing efficiency of 17% for nanoparticle + meropenem treatment. PtNPs + meropenem reduced bioburden of CREC in infected zebrafish by 2.4 log CFU. Mechanistic studies revealed that nanoparticle interacted with cell surface and perturbed inner membrane integrity. PtNPs did not induce ROS, yet it caused plasmid DNA cleavage, as evidenced by gyrase inhibition assay. Our study for the first time reveals that PtNPs as plasmid curing agent can resensitize MDR bacteria to selective antimicrobial agents in vivo.
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Affiliation(s)
- Subhashree Bharathan
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Niranjana Sri Sundaramoorthy
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Harini Chandrasekaran
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Gagana Rangappa
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - GaneshPrasad ArunKumar
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Siva Bala Subramaniyan
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Anbazhagan Veerappan
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India.
| | - Saisubramanian Nagarajan
- Center for Research in Infectious Diseases, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India.
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29
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Buckner MMC, Ciusa ML, Piddock LJV. Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing. FEMS Microbiol Rev 2018; 42:781-804. [PMID: 30085063 PMCID: PMC6199537 DOI: 10.1093/femsre/fuy031] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/25/2018] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global problem hindering treatment of bacterial infections, rendering many aspects of modern medicine less effective. AMR genes (ARGs) are frequently located on plasmids, which are self-replicating elements of DNA. They are often transmissible between bacteria, and some have spread globally. Novel strategies to combat AMR are needed, and plasmid curing and anti-plasmid approaches could reduce ARG prevalence, and sensitise bacteria to antibiotics. We discuss the use of curing agents as laboratory tools including chemicals (e.g. detergents and intercalating agents), drugs used in medicine including ascorbic acid, psychotropic drugs (e.g. chlorpromazine), antibiotics (e.g. aminocoumarins, quinolones and rifampicin) and plant-derived compounds. Novel strategies are examined; these include conjugation inhibitors (e.g. TraE inhibitors, linoleic, oleic, 2-hexadecynoic and tanzawaic acids), systems designed around plasmid incompatibility, phages and CRISPR/Cas-based approaches. Currently, there is a general lack of in vivo curing options. This review highlights this important shortfall, which if filled could provide a promising mechanism to reduce ARG prevalence in humans and animals. Plasmid curing mechanisms which are not suitable for in vivo use could still prove important for reducing the global burden of AMR, as high levels of ARGs exist in the environment.
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Affiliation(s)
- Michelle M C Buckner
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
| | - Maria Laura Ciusa
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
| | - Laura J V Piddock
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, The University of Birmingham B15 2TT, UK
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Graf FE, Palm M, Warringer J, Farewell A. Inhibiting conjugation as a tool in the fight against antibiotic resistance. Drug Dev Res 2018; 80:19-23. [DOI: 10.1002/ddr.21457] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 02/03/2023]
Affiliation(s)
- Fabrice E. Graf
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Martin Palm
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
| | - Anne Farewell
- Department of Chemistry and Molecular Biology; University of Gothenburg; Gothenburg Sweden
- Centre for Antibiotic Resistance Research (CARe); University of Gothenburg; Gothenburg Sweden
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31
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Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context. Trends Microbiol 2018; 26:978-985. [PMID: 30049587 DOI: 10.1016/j.tim.2018.06.007] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 12/29/2022]
Abstract
Antibiotic-resistant infections are an urgent problem in clinical settings because they sharply increase mortality risk in critically ill patients. The horizontal spread of antibiotic resistance genes among bacteria is driven by bacterial plasmids, promoting the evolution of resistance. Crucially, particular associations exist between resistance plasmids and bacterial clones that become especially successful in clinical settings. However, the factors underlying the success of these associations remain unknown. Recent in vitro evidence reveals (i) that plasmids produce fitness costs in bacteria, and (ii) that these costs are alleviated over time through compensatory mutations. I argue that plasmid-imposed costs and subsequent compensatory adaptation may determine the success of associations between plasmids and bacteria in clinical settings, shaping the in vivo evolution of antibiotic resistance.
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32
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Marquez-Ortiz RA, Haggerty L, Olarte N, Duarte C, Garza-Ramos U, Silva-Sanchez J, Castro BE, Sim EM, Beltran M, Moncada MV, Valderrama A, Castellanos JE, Charles IG, Vanegas N, Escobar-Perez J, Petty NK. Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance. Genome Biol Evol 2018; 9:1725-1741. [PMID: 28854628 PMCID: PMC5554438 DOI: 10.1093/gbe/evx115] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/21/2022] Open
Abstract
Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes.
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Affiliation(s)
- Ricaurte Alejandro Marquez-Ortiz
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Leanne Haggerty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Jesus Silva-Sanchez
- Instituto Nacional de Salud Pública (INSP), CISEI, Cuernavaca, Morelos, México
| | - Betsy E Castro
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Eby M Sim
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Mauricio Beltran
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - María V Moncada
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | | | - Jaime E Castellanos
- Grupo de Patogénesis Infecciosa, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Ian G Charles
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Natasha Vanegas
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia.,The ithree Institute, University of Technology Sydney, New South Wales, Australia
| | - Javier Escobar-Perez
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, D.C., Colombia
| | - Nicola K Petty
- The ithree Institute, University of Technology Sydney, New South Wales, Australia
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Abstract
Plasmids are highly useful tools for studying living cells and for heterologous expression of genes and pathways in cell factories. Standardized tools and operating procedures for handling such DNA vectors are core principles in synthetic biology. Here, we describe protocols for molecular cloning and exchange of genetic parts in the Standard European Vectors Architecture (SEVA) vector system. Additionally, to facilitate rapid testing and iterative bioengineering using different vector designs, we provide a one-step protocol for a universal CRISPR-Cas9-based plasmid curing system (pFREE) and demonstrate the application of this system to cure SEVA constructs (all vectors are available at SEVA/Addgene).
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Affiliation(s)
- Ida Lauritsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Se Hyeuk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Rodriguez MD, Paul Z, Wood CE, Rice KC, Triplett EW. Construction of Stable Fluorescent Reporter Plasmids for Use in Staphylococcus aureus. Front Microbiol 2017; 8:2491. [PMID: 29312199 PMCID: PMC5735104 DOI: 10.3389/fmicb.2017.02491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/30/2017] [Indexed: 12/15/2022] Open
Abstract
Here, the genes encoding three different fluorescent proteins were cloned into the stably maintained Staphylococcus aureus shuttle vector pKK30. The resulting plasmids were transformed into two S. aureus strains; SH1000 and RN4220. Stability assays illustrated that the three recombinant plasmids retained near 100% maintenance in vitro for 160 generations. S. aureus strain SH1000 expressing green fluorescent protein was then inoculated in an ovine model and in vivo stability for 6 days was demonstrated. In essence, these reporter plasmids represent a useful set of tools for dynamic imaging studies in S. aureus. These three reporter plasmids are available through BEI Resources.
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Affiliation(s)
- Michelle D. Rodriguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Zubin Paul
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Charles E. Wood
- Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Kelly C. Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Eric W. Triplett
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
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35
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Wang CM, Zhao FL, Zhang L, Chai XY, Meng QG. Synthesis and Antibacterial Evaluation of a Series of 11,12-Cyclic Carbonate Azithromycin-3-O-descladinosyl-3-O-carbamoyl Glycosyl Derivatives. Molecules 2017; 22:molecules22122146. [PMID: 29207567 PMCID: PMC6149787 DOI: 10.3390/molecules22122146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/27/2017] [Indexed: 11/16/2022] Open
Abstract
A novel series of 11,12-cyclic carbonate azithromycin-3-O-descladinosyl-3-O-carbamoyl glycosyl derivatives were designed, synthesized, and evaluated for their antibacterial activities in vitro. Most of these compounds had significant antibacterial activity against seven kinds of susceptible strains. In particular, compound G1 exhibited the most potent activity against methicillin-resistant Streptococcus pneumoniae 943 (MIC: 1 μg/mL), Staphylococcus pneumoniae 746 (MIC: 2 μg/mL), Streptococcus pyogenes 447 (MIC: 8 μg/mL), and Escherichia coli 236 (MIC: 32 μg/mL), which were two-, four-, four-, four-, and eight-fold stronger activity than azithromycin, respectively. Additionally, compound G2 exhibited improved activity against methicillin-resistant Staphylococcus aureus MRSA-1 (MIC: 8 μg/mL), Streptococcus pneumoniae 943 (MIC: 2 μg/mL), Staphylococcus pneumoniae 746 (MIC: 2 μg/mL), and Escherichia coli 236 (MIC: 32 μg/mL), which were two-, two-, four-, and eight-fold better activity than azithromycin, respectively. As for methicillin-resistant Staphylococcus aureus MRSA-1, compound G6 presented the most excellent activity (MIC: 4 μg/mL), showing four-fold higher activity than azithromycin (MIC: 16 μg/mL) and erythromycin (MIC: 16 μg/mL). However, compared with other compounds, compounds G7 and G8 with the disaccharide side chain were observed the lower activity against seven strains.
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Affiliation(s)
- Chao-Ming Wang
- School of Pharmacy, Key Laboratory ofMolecular Pharmacology and Drug Evaluation,Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Feng-Lan Zhao
- School of Pharmacy, Key Laboratory ofMolecular Pharmacology and Drug Evaluation,Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 30 Qingquan Road, Yantai 264005, China.
| | - Lei Zhang
- School of Pharmacy, Key Laboratory ofMolecular Pharmacology and Drug Evaluation,Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 30 Qingquan Road, Yantai 264005, China.
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
| | - Xiao-Yun Chai
- Department of Organic Chemistry, College of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
| | - Qing-Guo Meng
- School of Pharmacy, Key Laboratory ofMolecular Pharmacology and Drug Evaluation,Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, 30 Qingquan Road, Yantai 264005, China.
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36
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Lauritsen I, Porse A, Sommer MOA, Nørholm MHH. A versatile one-step CRISPR-Cas9 based approach to plasmid-curing. Microb Cell Fact 2017; 16:135. [PMID: 28764701 PMCID: PMC5540278 DOI: 10.1186/s12934-017-0748-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/22/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Plasmids are widely used and essential tools in molecular biology. However, plasmids often impose a metabolic burden and are only temporarily useful for genetic engineering, bio-sensing and characterization purposes. While numerous techniques for genetic manipulation exist, a universal tool enabling rapid removal of plasmids from bacterial cells is lacking. RESULTS Based on replicon abundance and sequence conservation analysis, we show that the vast majority of bacterial cloning and expression vectors share sequence similarities that allow for broad CRISPR-Cas9 targeting. We have constructed a universal plasmid-curing system (pFREE) and developed a one-step protocol and PCR procedure that allow for identification of plasmid-free clones within 24 h. While the context of the targeted replicons affects efficiency, we obtained curing efficiencies between 40 and 100% for the plasmids most widely used for expression and engineering purposes. By virtue of the CRISPR-Cas9 targeting, our platform is highly expandable and can be applied in a broad host context. We exemplify the wide applicability of our system in Gram-negative bacteria by demonstrating the successful application in both Escherichia coli and the promising cell factory chassis Pseudomonas putida. CONCLUSION As a fast and freely available plasmid-curing system, targeting virtually all vectors used for cloning and expression purposes, we believe that pFREE has the potential to eliminate the need for individualized vector suicide solutions in molecular biology. We envision the application of pFREE to be especially useful in methodologies involving multiple plasmids, used sequentially or simultaneously, which are becoming increasingly popular for genome editing or combinatorial pathway engineering.
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Affiliation(s)
- Ida Lauritsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Andreas Porse
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Morten O. A. Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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