Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates

Antibiotic resistance spread via plasmids is a serious threat to successfully fight infections and makes understanding plasmid transfer in nature crucial to prevent the rise of antibiotic resistance. Studies addressing the dynamics of plasmid conjugation have yet neglected one omnipresent factor: prophages (viruses integrated into bacterial genomes), whose activation can kill host and surrounding bacterial cells. To investigate the impact of prophages on conjugation, we combined experiments and mathematical modelling. Using Escherichia coli , prophage λ and the multidrug-resistant plasmid RP4 we find that prophages can substantially limit the spread of conjugative plasmids. This inhibitory effect was strongly dependent on environmental conditions and bacterial genetic background. Our empirically parameterized model reproduced experimental dynamics of cells acquiring either the prophage or the plasmid well but could only reproduce the number of cells acquiring both elements by assuming complex interactions between conjugative plasmids and prophages in sequential infections. Varying phage and plasmid infection parameters over empirically realistic ranges revealed that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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Conjugative plasmid transfer is limited by prophages but can be overcome by high conjugation rates

10.1101/2021.03.29.437513 ◽

2021 ◽

Author(s):

Claudia Igler ◽

Lukas Schwyter ◽

Daniel Gehrig ◽

Carolin Charlotte Wendling

Keyword(s):

Antibiotic Resistance ◽

Negative Impact ◽

Bacterial Genome ◽

Plasmid Transfer ◽

Conjugative Plasmid ◽

E Coli ◽

Complex Interactions ◽

Infection Dynamics ◽

Infection Parameters ◽

Parameterized Model

AbstractAntibiotic resistance spread via plasmids is a serious threat to successful treatment and makes understanding plasmid transfer in nature crucial to preventing the global rise of antibiotic resistance. However, plasmid dynamics have so far neglected one omnipresent factor: active prophages (phages that are integrated into the bacterial genome), whose activation can kill co-occurring bacteria. To investigate how prophages influence the spread of a multi-drug resistant plasmid, we combined experiments and mathematical modelling. Using E. coli, prophage lambda and the plasmid Rp4 we find that prophages clearly limit the spread of conjugative plasmids. This effect was even more pronounced when we studied this interaction in a ‘phage-friendly’ environment that favoured phage adsorption. Our empirically parameterized model reproduces experimental dynamics in some environments well, but fails to predict them in others, suggesting more complex interactions between plasmid and prophage infection dynamics. Varying phage and plasmid infection parameters over an empirically realistic range suggests that plasmids can overcome the negative impact of prophages through high conjugation rates. Overall, we find that the presence of prophages introduces an additional death rate for plasmid carriers, the magnitude of which is determined in non-trivial ways by the environment, the phage and the plasmid.

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The impact of FDI on environmental technology innovation from the perspective of environmental regulation

E3S Web of Conferences ◽

10.1051/e3sconf/202020602001 ◽

2020 ◽

Vol 206 ◽

pp. 02001

Author(s):

Ziting Wei

Keyword(s):

Environmental Regulation ◽

Technology Innovation ◽

Negative Impact ◽

Positive Impact ◽

Inhibitory Effect ◽

Market Demand ◽

Environmental Technology ◽

Industrial Enterprises ◽

Threshold Regression Model ◽

The Impact

Based on the perspective of environmental regulation, this paper selects panel data of 30 provinces in China from 2011 to 2016, establishes Hansen panel threshold regression model, and investigates the impact of FDI on environmental technology innovation of industrial enterprises in China under the threshold of environmental regulation. The results show that FDI has a significant inhibitory effect on the environmental technological innovation of industrial enterprises; the effect has a significant dual threshold of environmental regulation, with the intensity of environmental regulation across the threshold, the negative impact of FDI gradually weakened; market demand and industry scale have a significant positive impact, the role of technological progress is not significant. The findings of this paper provide a certain reference for the rational use of environmental regulation policies, the maximization of FDI technology spillover, the promotion of environmental technology innovation of industrial enterprises, and the realization of “win-win” of environment and economy.

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Identification of a Novel Conjugative Plasmid in Mycobacteria That Requires Both Type IV and Type VII Secretion

mBio ◽

10.1128/mbio.01744-14 ◽

2014 ◽

Vol 5 (5) ◽

Cited By ~ 39

Author(s):

Roy Ummels ◽

Abdallah M. Abdallah ◽

Vincent Kuiper ◽

Anouar Aâjoud ◽

Marion Sparrius ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Antibiotic Resistance Genes ◽

Conjugative Plasmid ◽

Content Type ◽

Conjugative Plasmids ◽

Type Vii Secretion ◽

Type Iv ◽

Slow Growing

ABSTRACTConjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, includingMycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.IMPORTANCEConjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted thatM. tuberculosisdoes not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred toM. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.

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Detection of Virulence Genes in Multidrug Resistant Enterococci Isolated from Feedlots Dairy and Beef Cattle: Implications for Human Health and Food Safety

BioMed Research International ◽

10.1155/2019/5921840 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13 ◽

Cited By ~ 5

Author(s):

Frank Eric Tatsing Foka ◽

Collins Njie Ateba

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Virulence Genes ◽

Efflux Pump ◽

Health Sector ◽

Multidrug Resistant ◽

North West ◽

The North ◽

Vancomycin Resistant ◽

The Impact

The misuse/abuse of antibiotics in intensive animal rearing and communities led to the emergence of resistant isolates such as vancomycin-resistant enterococci (VREs) worldwide. This has become a major source of concern for the public health sector. The aim of this study was to report the antibiotic resistance profiles and to highlight the presence of virulence genes in VREs isolated from feedlots cattle of the North-West Province of South Africa. 384 faecal samples, 24 drinking troughs water, and 24 soil samples were collected aseptically from 6 registered feedlots. Biochemical and molecular methods were used to identify and categorise the enterococci isolates. Their antibiotic resistance profiles were assessed and genotypic methods were used to determine their antibiotic resistance and their virulence profiles. 527 presumptive isolates were recovered, out of which 289 isolates were confirmed asEnterococcussp. Specifically,E. faecalis(9%),E. faecium(10%),E. durans(69%),E. gallinarum(6%),E. casseliflavus(2%),E. mundtii(2%), andE. avium(2%) were screened after molecular assays.VanA(62%),vanB(17%), andvanC(21%) resistance genes were detected in 176Enterococcussp., respectively. Moreover,tetK(26),tetL(57),msrA/B(111), andmefA(9) efflux pump genes were detected in 138 VRE isolates.Multiple antibiotic resistances were confirmed in all the VRE isolates of this study; the most common antibiotic resistance phenotype wasTETR-AMPR-AMXR-VANR-PENR-LINR-ERYR.CylA,hyl,esp,gelE, andasa1virulence genes were detected in 86 VREs with the exception of vancomycin-resistantE. mundtiiisolates that did not display any virulence factor. Most VRE isolates had more than one virulence genes but the most encountered virulence profile wasgelE-hyl. Potentially pathogenic multidrug resistant VREs were detected in this study; this highlights the impact of extensive usage of antimicrobials in intensive animal rearing and its implications on public health cannot be undermined.

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Impact of antibiotic resistance on outcomes of neutropenic cancer patients withPseudomonas aeruginosabacteraemia (IRONIC study): study protocol of a retrospective multicentre international study

BMJ Open ◽

10.1136/bmjopen-2018-025744 ◽

2019 ◽

Vol 9 (5) ◽

pp. e025744 ◽

Cited By ~ 2

Author(s):

Adaia Albasanz-Puig ◽

Carlota Gudiol ◽

Rocío Parody ◽

Cristian Tebe ◽

Murat Akova ◽

...

Keyword(s):

Risk Factors ◽

Antibiotic Resistance ◽

Cancer Patients ◽

Case Fatality ◽

International Study ◽

Multidrug Resistant ◽

University Hospital ◽

Personal Privacy ◽

Haematological Patients ◽

The Impact

IntroductionPseudomonas aeruginosa(PA) has historically been one of the major causes of severe sepsis and death among neutropenic cancer patients. There has been a recent increase of multidrug-resistant PA (MDRPA) isolates that may determine a worse prognosis, particularly in immunosuppressed patients. The aim of this study is to establish the impact of antibiotic resistance on the outcome of neutropenic onco-haematological patients with PA bacteraemia, and to identify the risk factors for MDRPA bacteraemia and mortality.Methods and analysisThis is a retrospective, observational, multicentre, international study. All episodes of PA bacteraemia occurring in neutropenic onco-haematological patients followed up at the participating centres from 1 January 2006 to 31 May 2018 will be retrospectively reviewed. The primary end point will be overall case-fatality rate within 30 days of onset of PA bacteraemia. The secondary end points will be to describe the following: the incidence and risk factors for multidrug-resistant and extremely drug-resistant PA bacteraemia (by comparing the episodes due to susceptible PA with those produced by MDRPA), the efficacy of ceftolozane/tazobactam, the rates of persistent bacteraemia and bacteraemia relapse and the risk factors for very early (48 hours), early (7 days) and overall (30 days) case-fatality rates.Ethics and disseminationThe Clinical Research Ethics Committee of Bellvitge University Hospital approved the protocol of the study at the primary site. To protect personal privacy, identifying information of each patient in the electronic database will be encrypted. The processing of the patients’ personal data collected in the study will comply with the Spanish Data Protection Act of 1998 and with the European Directive on the privacy of data. All data collected, stored and processed will be anonymised. Results will be reported at conferences and in peer-reviewed publications.

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Analysis of Antibiotic Resistance Genes in Multidrug-Resistant Acinetobacter sp. Isolates from Military and Civilian Patients Treated at the Walter Reed Army Medical Center

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00778-06 ◽

2006 ◽

Vol 50 (12) ◽

pp. 4114-4123 ◽

Cited By ~ 270

Author(s):

Kristine M. Hujer ◽

Andrea M. Hujer ◽

Edward A. Hulten ◽

Saralee Bajaksouzian ◽

Jennifer M. Adams ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Medical Center ◽

Antibiotic Resistance Genes ◽

Bloodstream Infections ◽

Multidrug Resistant ◽

Walter Reed Army Medical ◽

Army Medical ◽

Starting Point ◽

The Impact

ABSTRACT Military medical facilities treating patients injured in Iraq and Afghanistan have identified a large number of multidrug-resistant (MDR) Acinetobacter baumannii isolates. In order to anticipate the impact of these pathogens on patient care, we analyzed the antibiotic resistance genes responsible for the MDR phenotype in Acinetobacter sp. isolates collected from patients at the Walter Reed Army Medical Center (WRAMC). Susceptibility testing, PCR amplification of the genetic determinants of resistance, and clonality were determined. Seventy-five unique patient isolates were included in this study: 53% were from bloodstream infections, 89% were resistant to at least three classes of antibiotics, and 15% were resistant to all nine antibiotics tested. Thirty-seven percent of the isolates were recovered from patients nosocomially infected or colonized at the WRAMC. Sixteen unique resistance genes or gene families and four mobile genetic elements were detected. In addition, this is the first report of bla OXA-58-like and bla PER-like genes in the U.S. MDR A. baumannii isolates with at least eight identified resistance determinants were recovered from 49 of the 75 patients. Molecular typing revealed multiple clones, with eight major clonal types being nosocomially acquired and with more than 60% of the isolates being related to three pan-European types. This report gives a “snapshot” of the complex genetic background responsible for antimicrobial resistance in Acinetobacter spp. from the WRAMC. Identifying genes associated with the MDR phenotype and defining patterns of transmission serve as a starting point for devising strategies to limit the clinical impact of these serious infections.

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Conjugative delivery of CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci

10.1101/678573 ◽

2019 ◽

Cited By ~ 1

Author(s):

Marinelle Rodrigues ◽

Sara W. McBride ◽

Karthik Hullahalli ◽

Kelli L. Palmer ◽

Breck A. Duerkop

Keyword(s):

Antibiotic Resistance ◽

Enterococcus Faecalis ◽

Resistance Genes ◽

Bacterial Infections ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Conjugative Plasmid ◽

Antibiotic Resistant ◽

Resistance Determinants

AbstractThe innovation of new therapies to combat multidrug-resistant (MDR) bacteria is being outpaced by the continued rise of MDR bacterial infections. Of particular concern are hospital-acquired infections (HAIs) recalcitrant to antibiotic therapies. The Gram-positive intestinal pathobiontEnterococcus faecalisis associated with HAIs and some strains are MDR. Therefore, novel strategies to controlE. faecalispopulations are needed. We previously characterized anE. faecalisType II CRISPR-Cas system and demonstrated its utility in the sequence-specific removal of antibiotic resistance determinants. Here we present work describing the adaption of this CRISPR-Cas system into a constitutively expressed module encoded on a pheromone-responsive conjugative plasmid that efficiently transfers toE. faecalisfor the selective removal of antibiotic resistance genes. Usingin vitrocompetition assays, we show that these CRISPR-Cas-encoding delivery plasmids, or CRISPR-Cas antimicrobials, can reduce the occurrence of antibiotic resistance in enterococcal populations in a sequence-specific manner. Furthermore, we demonstrate that deployment of CRISPR-Cas antimicrobials in the murine intestine reduces the occurrence of antibiotic-resistantE. faecalisby several orders of magnitude. Finally, we show thatE. faecalisdonor strains harboring CRISPR-Cas antimicrobials are immune to uptake of antibiotic resistance determinantsin vivo. Our results demonstrate that conjugative delivery of CRISPR-Cas antimicrobials may be adaptable for future deployment from probiotic bacteria for exact targeting of defined MDR bacteria or for precision engineering of polymicrobial communities in the mammalian intestine.ImportanceCRISPR-Cas nucleic acid targeting systems hold promise for the amelioration of multidrug-resistant enterococci, yet the utility of such tools in the context of the intestinal environment where enterococci reside is understudied. We describe the development of a CRISPR-Cas antimicrobial, deployed on a conjugative plasmid, for the targeted removal of antibiotic resistance genes from intestinalEnterococcus faecalis. We demonstrate that CRISPR-Cas targeting reduces antibiotic resistance ofE. faecalisby several orders of magnitude in the intestine. Although barriers exist that influence the penetrance of the conjugative CRISPR-Cas antimicrobial among target recipientE. faecaliscells, the removal of antibiotic resistance genes inE. faecalisupon uptake of the CRISPR-Cas antimicrobial is absolute. In addition, cells that obtain the CRISPR-Cas antimicrobial are immunized against the acquisition of new antibiotic resistance genes. This study suggests a potential path toward plasmid based CRISPR-Cas therapies in the intestine.

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Estimating the conjugative transfer rate of antibiotic resistance genes: Effect of model structural errors

10.1101/2021.06.29.450325 ◽

2021 ◽

Author(s):

Sulagna Mishra ◽

Thomas U Berendonk ◽

David Kneis

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Rate Constants ◽

Transfer Rate ◽

Antibiotic Resistance Genes ◽

Plasmid Transfer ◽

Transfer Rates ◽

Model Predictions ◽

Mating Conditions ◽

The Impact

The spread of antibiotic resistance genes (ARG) occurs widely through plasmid transfer majorly facilitated via bacterial conjugation. To assess the spread of these mobile ARG, it is necessary to develop appropriate tools to estimate plasmid transfer rates under different environmental conditions. Process-based models are widely used for the estimation of plasmid transfer rate constants. Empirical studies have repeatedly highlighted the importance of subtle processes like delayed growth, the maturation of transconjugants, the physiological cost of plasmid carriage, and the dependence of conjugation on the culture′s growth stage. However, models used for estimating the transfer rates typically neglect them. We conducted virtual mating experiments to quantify the impact of these four typical structural model deficits on the estimated plasmid transfer rate constants. We found that under all conditions, the plasmid cost and the lag phase in growth must be taken into account to obtain unbiased estimates of plasmid transfer rate constants. We observed a tendency towards the underestimation of plasmid transfer rate constants when structurally deficient models were fitted to virtual mating data. This holds for all the structural deficits and mating conditions tested in our study. Our findings might explain an important component of the negative bias in model predictions known as the plasmid paradox. We also discuss other structural deficits that could lead to an overestimation of plasmid transfer rate constants and we demonstrate the impact of ill-fitted parameters on model predictions.

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Enterococcus faecalisCRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine

10.1101/312751 ◽

2018 ◽

Cited By ~ 2

Author(s):

Valerie J. Price ◽

Sara W. McBride ◽

Karthik Hullahalli ◽

Anushila Chatterjee ◽

Breck A. Duerkop ◽

...

Keyword(s):

Antibiotic Resistance ◽

Enterococcus Faecalis ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Conjugative Plasmids ◽

Resistance Plasmids ◽

The Impact ◽

Mammalian Intestine

AbstractCRISPR-Cas systems are barriers to horizontal gene transfer (HGT) in bacteria. Little is known about CRISPR-Cas interactions with conjugative plasmids, and studies investigating CRISPR-Cas/plasmid interactions inin vivomodels relevant to infectious disease are lacking. These are significant gaps in knowledge because conjugative plasmids disseminate antibiotic resistance genes among pathogensin vivo, and it is essential to identify strategies to reduce the spread of these elements. We use enterococci as models to understand the interactions of CRISPR-Cas with conjugative plasmids.Enterococcus faecalisis a native colonizer of the mammalian intestine and harbors pheromone-responsive plasmids (PRPs). PRPs mediate inter- and intraspecies transfer of antibiotic resistance genes. We assessedE. faecalisCRISPR-Cas anti-PRP activity in the mouse intestine and under varyingin vitroconditions. We observed striking differences in CRISPR-Cas efficiencyin vitroversusin vivo. With few exceptions, CRISPR-Cas blocked intestinal PRP dissemination, whilein vitro, the PRP frequently escaped CRISPR-Cas defense. Our results further the understanding of CRISPR-Cas biology by demonstrating that standardin vitroexperiments do not adequately model thein vivoanti-plasmid activity of CRISPR-Cas. Additionally, our work identifies several variables that impact the apparentin vitroanti-plasmid activity of CRISPR-Cas, including planktonic versus biofilm settings, different donor/recipient ratios, production of a plasmid-encoded bacteriocin, and the time point at which matings are sampled. Our results are clinically significant because they demonstrate that barriers to HGT encoded by normal human microbiota can have significant impacts onin vivoantibiotic resistance dissemination.ImportanceCRISPR-Cas is a type of immune system encoded by bacteria that is hypothesized to be a natural impediment to the spread of antibiotic resistance genes. In this study, we directly assessed the impact of CRISPR-Cas on antibiotic resistance dissemination in the mammalian intestine and under varyingin vitroconditions. We observed a robust effect of CRISPR-Cas onin vivobut notin vitrodissemination of antibiotic resistance plasmids in the native mammalian intestinal colonizerEnterococcus faecalis. We conclude that standard laboratory experiments currently do not appropriately model thein vivoconditions where antibiotic resistance dissemination occurs betweenE. faecalisstrains. Moreover, our results demonstrate that CRISPR-Cas encoded by native members of the mammalian intestinal microbiota can block the spread of antibiotic resistance plasmids.

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Antibiotic Resistance Conferred by a Conjugative Plasmid and a Class I Integron in Vibrio cholerae O1 El Tor Strains Isolated in Albania and Italy

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.43.3.693 ◽

1999 ◽

Vol 43 (3) ◽

pp. 693-696 ◽

Cited By ~ 66

Author(s):

Vincenzo Falbo ◽

Alessandra Carattoli ◽

Fabio Tosini ◽

Cristina Pezzella ◽

Anna Maria Dionisi ◽

...

Keyword(s):

Antibiotic Resistance ◽

Vibrio Cholerae ◽

Molecular Basis ◽

Gene Cassette ◽

Multidrug Resistant ◽

Conjugative Plasmid ◽

Class 1 Integron ◽

Class 1 ◽

Vibrio Cholerae O1 ◽

El Tor

ABSTRACT Multidrug-resistant Vibrio cholerae O1 El Tor strains isolated during the 1994 outbreak of cholera in Albania and Italy were characterized for the molecular basis of antibiotic resistance. All strains were found to be resistant to tetracycline, streptomycin, spectinomycin, trimethoprim, sulfathiazole, and the vibriostatic compound O/129 (2,4-diamino-6,7-diisopropylteridine). Resistance genes were self-transferable by a conjugative plasmid of about 60 MDa, with the exception of spectinomycin resistance, which was conferred by theaadA1 gene cassette located in the bacterial chromosome within a class 1 integron. The resistance to trimethoprim and O/129 was conferred by the dfrA1 gene, which was present on the plasmid. Although the dfrA1 gene is known to be borne on an integron cassette, class 1, 2, or 3 intI genes were not detected as part of the plasmid DNA from the strains studied.

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