scholarly journals Plasmids, Viruses, And Other Circular Elements In Rat Gut

2017 ◽  
Author(s):  
Tue Sparholt Jorgensen ◽  
Martin Asser Hansen ◽  
Zhuofei Xu ◽  
Michael A Tabak ◽  
Soren J. Sorensen ◽  
...  
Keyword(s):  
Anthropogenic Impact ◽  
Antibiotic Resistance Genes ◽  
Falkland Islands ◽  
Bacterial Populations ◽  
Biological Unit ◽  
Circular Dna ◽  
Eukaryotic Species ◽  
Danish Hospital ◽  
Rat Gut ◽  
Rat Cecum

Circular DNA such as plasmids and some viruses is the major source of genetic variation in bacteria and thus has the same important evolutionary function as sexual reproduction in eukaryotic species: It allows dissemination of advantageous traits through bacterial populations. Here, we present the largest collection of novel complete extrachromosomal genetic elements to date, and compare the diversity, distribution, and content of circular sequences from 12 rat cecum samples from the pristine Falkland Islands and Danish hospital sewers, two environments with contrasting anthropogenic impact. Using a validated pipeline, we find 1,869 complete, circular, non-redundant sequences, of which only 114 are previously described. While sequences of similar size from the two environments share general features, the size distribution of the elements between environments differs significantly, with hospital sewer samples hosting larger circular elements than Falkland Island samples, a possible consequence of the massive anthropogenic influence in the hospital sewer environment. Several antibiotic resistance genes have been identified with a notably larger diversity in hospital sewer samples than in Falkland Islands samples in concordance with expectations. Our findings suggest that even though sequences of similar length carry similar traits, the mobilome of rat gut bacteria are affected by human activities in that sewer rats have larger elements and more diverse large elements than pristine island rats. More than 1000 small, novel and not classified small sequences was identified and hint the existence of a biological unit not previously described on a community level.

Complete Genome Sequence of Bacteriophage EFC1 Infecting Enterococcus Faecalis From Chicken

2021 ◽  
Author(s):  
Qi Wang ◽  
Na Liu
Keyword(s):  
Enterococcus Faecalis ◽  
Virulence Genes ◽  
Large Subunit ◽  
Antibiotic Resistance Genes ◽  
Lytic Phage ◽  
High Similarity ◽  
Protein Coding ◽  
Circular Dna ◽  
Intron Structure ◽  
Comparative Phylogenetic Analysis

Abstract In response to Enterococcus faecalis infection of chicken origin, a multi host lytic phage, EFC1 was isolated and characterized the double-stranded circular DNA genome with size of 56099 bp, containing 89 predicted protein coding genes as well as 2 tRNAs involved in intron, structure, transcription, packaging, DNA replication, modification, lysis. Observation of the structure by electron microscopy and comparative phylogenetic analysis of terminase large subunit showed that the phage EFC1 belongs to a new member of Siphoviridae, which is relatively distantly related to its high similarity phages. The phage EFC1 has no relevant virulence genes and antibiotic resistance genes.

scholarly journals The Comprehensive Antibiotic Resistance Database

2013 ◽  
Vol 57 (7) ◽  
pp. 3348-3357 ◽  
Author(s):  
Andrew G. McArthur ◽  
Nicholas Waglechner ◽  
Fazmin Nizam ◽  
Austin Yan ◽  
Marisa A. Azad ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Sequence Data ◽  
Antibiotic Resistance Genes ◽  
Research Database ◽  
Free Living ◽  
Bacterial Populations ◽  
Bioinformatic Tools ◽  
Antibiotic Drug ◽  
Genetics And Genomics ◽  
Living Organisms

ABSTRACTThe field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD;http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.

scholarly journals Compensatory evolution facilitates the acquisition of multiple plasmids in bacteria

2017 ◽  
Author(s):  
Alfonso Santos-Lopez ◽  
Cristina Bernabe-Balas ◽  
Alvaro San Millan ◽  
Rafael Ortega-Huedo ◽  
Andreas Hoefer ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Animal Health ◽  
Antibiotic Resistance Genes ◽  
Multicopy Plasmid ◽  
Bacterial Populations ◽  
Compensatory Evolution ◽  
Evolutionary Forces ◽  
Antimicrobial Resistance Genes ◽  
Biological Cost

AbstractThe coexistence of multicopy plasmids is a common phenomenon. However, the evolutionary forces promoting these genotypes are poorly understood. In this study, we have analyzed multiple ColE1 plasmids (pB1000, pB1005 and pB1006) coexisting within Haemophilus influenzae RdKW20 in all possible combinations. When transformed into the naïve host, each plasmid type presented a particular copy number and produced a specific resistance profile and biological cost, whether alone or coexisting with the other plasmids. Therefore, there was no fitness advantage associated with plasmid coexistence that could explain these common plasmid associations in nature. Using experimental evolution, we showed how H. influenzae Rd was able to completely compensate the fitness cost produced by any of these plasmids. Crucially, once the bacterium has compensated for a first plasmid, the acquisition of new multicopy plasmid(s) did not produced any extra biological cost. We argue therefore that compensatory adaptation pave the way for the acquisition of multiple coexisting ColE1 plasmids.ImportanceAntibiotic resistance is a major concern for human and animal health. Plasmids play a major role in the acquisition and dissemination of antimicrobial resistance genes. In this report we investigate, for the first time, how plasmids are capable to cohabit stably in populations. This coexistence of plasmids is driven by compensatory evolution alleviating the cost of a first plasmid, which potentiates the acquisition of further plasmids at no extra cost. This phenomenon explains the high prevalence of plasmids coexistance in wild type bacteria, which generates multiresistant clones and contributes to the maintenance and spread of antibiotic resistance genes within bacterial populations.

scholarly journals Architecture of the outer-membrane core complex from a conjugative type IV secretion system

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Himani Amin ◽  
Aravindan Ilangovan ◽  
Tiago R. D. Costa
Keyword(s):  
Outer Membrane ◽  
Antibiotic Resistance Genes ◽  
Secretion System ◽  
Core Complex ◽  
Bacterial Populations ◽  
E Coli ◽  
Membrane Complex ◽  
Type Iv ◽  
Membrane Spanning ◽  
Inner Membrane Complex

AbstractConjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation.

scholarly journals Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

mBio ◽  
2015 ◽  
Vol 6 (3) ◽  
Author(s):  
Hong Xue ◽  
Otto X. Cordero ◽  
Francisco M. Camas ◽  
William Trimble ◽  
Folker Meyer ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Antibiotic Resistance Genes ◽  
Host Population ◽  
Bacterial Populations ◽  
In The Wild ◽  
Host Phylogeny ◽  
High Fraction ◽  
Extensive Exchange

ABSTRACTAlthough plasmids and other episomes are recognized as key players in horizontal gene transfer among microbes, their diversity and dynamics among ecologically structured host populations in the wild remain poorly understood. Here, we show that natural populations of marineVibrionaceaebacteria host large numbers of families of episomes, consisting of plasmids and a surprisingly high fraction of plasmid-like temperate phages. Episomes are unevenly distributed among host populations, and contrary to the notion that high-density communities in biofilms act as hot spots of gene transfer, we identified a strong bias for episomes to occur in free-living as opposed to particle-attached cells. Mapping of episomal families onto host phylogeny shows that, with the exception of all phage and a few plasmid families, most are of recent evolutionary origin and appear to have spread rapidly by horizontal transfer. Such high eco-evolutionary turnover is particularly surprising for plasmids that are, based on previously suggested categorization, putatively nontransmissible, indicating that this type of plasmid is indeed frequently transferred by currently unknown mechanisms. Finally, analysis of recent gene transfer among plasmids reveals a network of extensive exchange connecting nearly all episomes. Genes functioning in plasmid transfer and maintenance are frequently exchanged, suggesting that plasmids can be rapidly transformed from one category to another. The broad distribution of episomes among distantly related hosts and the observed promiscuous recombination patterns show how episomes can offer their hosts rapid assembly and dissemination of novel functions.IMPORTANCEPlasmids and other episomes are an integral part of bacterial biology in all environments, yet their study is heavily biased toward their role as vectors for antibiotic resistance genes. This study presents a comprehensive analysis of all episomes within several coexisting bacterial populations ofVibrionaceaefrom the coastal ocean and represents the largest-yet genomic survey of episomes from a single bacterial family. The host population framework allows analysis of the eco-evolutionary dynamics at unprecedented resolution, yielding several unexpected results. These include (i) discovery of novel, nonintegrative temperate phages, (ii) revision of a class of episomes, previously termed “nontransmissible,” as highly transmissible, and (iii) surprisingly high evolutionary turnover of episomes, manifest as frequent birth, spread, and loss.

scholarly journals Quantitative Occurrence of Antibiotic Resistance Genes among Bacterial Populations from Wastewater Treatment Plants Using Activated Sludge

2019 ◽  
Vol 9 (3) ◽  
pp. 387 ◽  
Author(s):  
Adriana Osińska ◽  
Ewa Korzeniewska ◽  
Monika Harnisz ◽  
Sebastian Niestępski
Keyword(s):  
Antibiotic Resistance ◽  
Wastewater Treatment ◽  
Activated Sludge ◽  
Wastewater Treatment Plants ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Treated Wastewater ◽  
Beta Lactams ◽  
Treatment Technology ◽  
Bacterial Populations

Wastewater treatment plants (WWTPs) are an important reservoir in the development of drug resistance phenomenon and they provide a potential route of antibiotic resistance gene (ARGs) dissemination in the environment. The aim of this study was to assess the role of WWTPs in the spread of ARGs. Untreated and treated wastewater samples that were collected from thirteen Polish WWTPs (applying four different modifications of activated sludge–based treatment technology) were analyzed. The quantitative occurrence of genes responsible for the resistance to beta-lactams and tetracyclines was determined using the real-time PCR method. Such genes in the DNA of both the total bacterial population and of the E. coli population were analyzed. Among the tested genes that are responsible for the resistance to beta-lactams and tetracyclines, blaOXA and blaTEM and tetA were dominant, respectively. This study found an insufficient reduction in the quantity of the genes that are responsible for antibiotic resistance in wastewater treatment processes. The results emphasize the need to monitor the presence of genes determining antibiotic resistance in the wastewater that is discharged from treatment plants, as they can help to identify the hazard that treated wastewater poses to public health.

scholarly journals Evolution of satellite plasmids can stabilize the maintenance of newly acquired accessory genes in bacteria

2019 ◽  
Author(s):  
Xue Zhang ◽  
Daniel E. Deatherage ◽  
Hao Zheng ◽  
Stratton J. Georgoulis ◽  
Jeffrey E. Barrick
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Antibiotic Resistance Genes ◽  
New Host ◽  
Bacterial Populations ◽  
Evolutionary Pathway ◽  
Bacterial Gene ◽  
Accessory Genes ◽  
A Cell ◽  
Incq Plasmids

AbstractPlasmids play a principal role in the spread of antibiotic resistance and other traits by horizontal gene transfer in bacteria. However, newly acquired plasmids generally impose a fitness burden on a cell, and they are lost from a population rapidly if there is not selection to maintain a unique function encoded on the plasmid. Mutations that ameliorate this fitness cost can sometimes eventually stabilize a plasmid in a new host, but they typically do so by inactivating some of its novel accessory genes. In this study, we identified an additional evolutionary pathway that can prolong the maintenance of newly acquired genes encoded on a plasmid. We discovered that propagation of an RSF1010-based IncQ plasmid inEscherichia colioften generated ‘satellite plasmids’ with spontaneous deletions of accessory genes and genes required for plasmid replication. These smaller plasmid variants are nonautonomous genetic parasites. Their presence in a cell drives down the copy number of full-length plasmids, which reduces the burden from the accessory genes without eliminating them entirely. The evolution of satellite plasmids may be favored relative to other plasmid fates because they give a more immediate fitness advantage to a cell’s progeny and because the organization of IncQ plasmids makes them particularly prone to certain deletions during replication. Satellite plasmids also evolved inSnodgrassella alvicolonizing the honey bee gut, suggesting that this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature.Significance StatementPlasmids are multicopy DNA elements found in bacteria that replicate independently of a cell’s chromosome. The spread of plasmids carrying antibiotic-resistance genes to new bacterial pathogens is a challenge for treating life-threatening infections. Often plasmids or their accessory genes encoding unique functions are lost soon after transfer into a new cell because they impose a fitness burden. We report that a family of transmissible plasmids can rapidly evolve ‘satellite plasmids’ that replicate as genetic parasites of the original plasmid. Satellite plasmid formation reduces the burden from the newly acquired genes, which may enable them to survive intact for longer after transfer into a new cell and thereby contribute to the spread of antibiotic resistance and other traits within bacterial populations.

scholarly journals Freshwater Viral Metagenome Reveals Novel and Functional Phage-borne Antibiotic Resistance Genes

2019 ◽  
Author(s):  
Kira Moon ◽  
Ilnam Kang ◽  
Kwang Seung Park ◽  
Jeong Ho Jeon ◽  
Kihyun lee ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Viral Metagenomics ◽  
The Novel ◽  
Multidrug Efflux ◽  
Bacterial Populations ◽  
Host Interactions ◽  
E Coli ◽  
Catalytic Kinetics

Abstract BackgroundAntibiotic resistance developed by bacteria is a significant threat to global health. Antibiotic resistance genes (ARGs) spread across different bacterial populations through multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages. ARGs carried by bacteriophages are considered especially threatening due to their prolonged persistence in the environment, fast replication rates, and ability to infect phylogenetically remote bacterial hosts. Several studies employing qPCR and viral metagenomics have shown that viral fraction and viral sequence reads in clinical and environmental samples carry many ARGs. However, only a few ARGs have been found in viral contigs assembled from metagenome reads, with most of these genes lacking effective antibiotic resistance phenotypes. Owing to the wide application of viral metagenomics, nevertheless, different classes of ARGs are being continuously found in viral metagenomes acquired from diverse environments. As such, the presence and functionality of ARGs encoded by bacteriophages remain up for debate.ResultsWe evaluated ARGs excavated from viral contigs recovered from urban surface water viral metagenome data. In virome reads and contigs, diverse ARGs, including polymyxin resistance genes, multidrug efflux proteins, and β-lactamases, were identified. In particular, the novel β-lactamases blaHRV-1 and blaHRVM-1 found in this study had unique sequences, forming distinct clades of Class A and subclass B3 β-lactamases, respectively. Minimum inhibitory concentration analyses for E. coli strains harboring blaHRV-1 and blaHRVM-1 and catalytic kinetics of purified HRV-1 and HRVM-1 showed reduced susceptibility to penicillin, narrow- and extended-spectrum cephalosporins, and carbapenems. These genes were also found in bacterial metagenomes, indicating that they were harbored by actively infecting phages.ConclusionOur results showed that viruses in the environment carry as-yet-unreported functional ARGs, albeit in small quantities. We thereby suggest that environmental bacteriophages could be reservoirs of widely variable, unknown ARGs that could be disseminated via virus-host interactions.

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