The 64 508 bp IncP-1beta antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1beta group

Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts

Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL₁₂₅ (125 kb) from a human O26:H- EHEC, and pO111-CRL₁₁₅ (115kb) from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3´-conserved segment. Complete sequence analysis showed that pO26-CRL₁₂₅ and pO111-CRL₁₁₅ are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL₁₂₅ but absent in pO111-CRL₁₁₅, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL₁₂₅ imperfect repeats was identified in pO111-CRL₁₁₅ precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3´-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721, encoding resistance to tetracycline, via a region containing the IncP-1α oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons, indicates that homologous recombination events played a key role in the formation of this complex antibiotic resistance gene locus. Comparative sequence analysis of these closely related plasmids reveals aspects of plasmid evolution in pathogenic E. coli from different hosts.

Extended-spectrum β-lactamase producing Escherichia coli in hospital wastewaters and sewage treatment plants in Queensland, Australia

We investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in untreated hospital wastewaters and 2 sewage treatment plants (STPs). A collection of 252 ESBL-producing E. coli isolates from hospital wastewater and STPs were typed and tested for resistance to 17 antimicrobial agents and for the presence of integron-associated integrases (intI gene) and ESBL genes. Eighty-nine percent (n = 176) of the ESBL-producing E. coli strains from hospital wastewater were found in more than 1 sample (common types), with 1 common type accounting for 35% of isolates, found in all samples. These strains were also resistant to up to 9 non-β-lactam antibiotics and showed the same pattern of resistance in all samples. More than 73% of the hospital wastewater isolates possessed SHV-type ESBL as opposed to isolates from STPs that carried only CTX-M-type ESBL genes. The prevalence of the intI gene did not differ between the sources of the isolates. Certain ESBL-producing E. coli were dominant in hospital wastewaters. These strains possessed β-lactamase genes that were different from isolates found in STPs. From a public health point of view, the presence of such a high level of ESBL-producing E. coli strains in hospital wastewaters is of great importance.

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches

Deep sequencing techniques used in metagenomic approaches have greatly advanced the study of microbial communities in various environments. However, one microbial segment that has remained largely unexplored is the natural plasmids residing within microbial environments. Plasmids are perceived as mobile genetic elements that exist extra-chromosomally and occasionally carry accessory genes that confer an advantage to their host in its ecological niche. They are thus thought to play an important evolutionary role in microbial communities by laterally introducing genes and traits into microbial genomes. Despite their importance, technical obstacles still limit the metagenomic study of natural plasmids using deep sequencing techniques. These include low copy number of the plasmids and heterogeneity of microbes in environmental samples, reflected in the low abundance of each individual plasmid. Furthermore, the extracted plasmids usually contain remnants of chromosomal DNA that can potentially interfere with the analysis of unique plasmid traits. We have recently studied the rumen metagenomic plasmid population using a newly developed procedure that successfully overcomes these obstacles. This procedure enables extraction of pure plasmid DNA suited for deep sequencing studies. Here we present a detailed description and characterization of this procedure which could potentially allow the study of plasmids in other environmental niches.

Host range diversification within the IncP-1 plasmid group

Broad-host-range plasmids play a critical role in the spread of antibiotic resistance and other traits. In spite of increasing information about the genomic diversity of closely related plasmids, the relationship between sequence divergence and host range remains unclear. IncP-1 plasmids are currently classified into six subgroups based on the genetic distance of backbone genes. We investigated whether plasmids from two subgroups exhibit a different host range, using two IncP-1γ plasmids, an IncP-1β plasmid and their minireplicons. Efficiencies of plasmid establishment and maintenance were compared using five species that belong to the Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria. The IncP-1β plasmid replicated and persisted in all five hosts in the absence of selection. Of the two IncP-1γ plasmids, both were unable to replicate in alphaproteobacterial host Sphingobium japonicum, and one established itself in Agrobacterium tumefaciens but was very unstable. In contrast, both IncP-1γ minireplicons, which produced higher levels of replication initiation protein than the wild-type plasmids, replicated in all strains, suggesting that poor establishment of the native plasmids is in part due to suboptimal replication initiation gene regulation. The findings suggest that host ranges of distinct IncP-1 plasmids only partially overlap, which may limit plasmid recombination and thus result in further genome divergence.

High prevalence of IncP-1 plasmids and IS1071 insertion sequences in on-farm biopurification systems and other pesticide-polluted environments

Mobile genetic elements (MGEs) are considered as key players in the adaptation of bacteria to degrade organic xenobiotic recalcitrant compounds such as pesticides. We examined the prevalence and abundance of IncP-1 plasmids and IS1071, two MGEs that are frequently linked with organic xenobiotic degradation, in laboratory and field ecosystems with and without pesticide pollution history. The ecosystems included on-farm biopurification systems (BPS) processing pesticide-contaminated wastewater and soil. Comparison of IncP-1/IS1071 prevalence between pesticide-treated and nontreated soil and BPS microcosms suggested that both IncP-1 and IS1071 proliferated as a response to pesticide treatment. The increased prevalence of IncP-1 plasmids and IS1071-specific sequences in treated systems was accompanied by an increase in the capacity to mineralize the applied pesticides. Both elements were also encountered in high abundance in field BPS ecosystems that were in operation at farmyards and that showed the capacity to degrade/mineralize a wide range of chlorinated aromatics and pesticides. In contrast, IS1071 and especially IncP-1, MGE were less abundant in field ecosystems without pesticide history although some of them still showed a high IS1071 abundance. Our data suggest that MGE-containing organisms were enriched in pesticide-contaminated environments like BPS where they might contribute to spreading of catabolic genes and to pathway assembly.

Invasion of E. coli biofilms by antibiotic resistance plasmids

In spite of the contribution of plasmids to the spread of antibiotic resistance in human pathogens, little is known about the transferability of various drug resistance plasmids in bacterial biofilms. The goal of this study was to compare the efficiency of transfer of 19 multidrug resistance plasmids into Escherichia coli recipient biofilms and determine the effects of biofilm age, biofilm-donor exposure time, and donor-to-biofilm attachment on this process. An E. coli recipient biofilm was exposed separately to 19 E. coli donors, each with a different plasmid, and transconjugants were determined by plate counting. With few exceptions, plasmids that transferred well in a liquid environment also showed the highest transferability in biofilms. The difference in transfer frequency between the most and least transferable plasmid was almost a million-fold. The 'invasibility' of the biofilm by plasmids, or the proportion of biofilm cells that acquired plasmids within a few hours, depended not only on the type of plasmid, but also on the time of biofilm exposure to the donor and on the ability of the plasmid donor to attach to the biofilm, yet not on biofilm age. The efficiency of donor strain attachment to the biofilm was not affected by the presence of plasmids. The most invasive plasmid was pHH2-227, which based on genome sequence analysis is a hybrid between IncU-like and IncW plasmids. The wide range in transferability in an E. coli biofilm among plasmids needs to be taken into account in our fight against the spread of drug resistance.

The detection and sequencing of a broad-host-range conjugative IncP-1β plasmid in an epidemic strain of Mycobacterium abscessus subsp. bolletii

BACKGROUND

An extended outbreak of mycobacterial surgical infections occurred in Brazil during 2004-2008. Most infections were caused by a single strain of Mycobacterium abscessus subsp. bolletii, which was characterized by a specific rpoB sequevar and two highly similar pulsed-field gel electrophoresis (PFGE) patterns differentiated by the presence of a ∼50 kb band. The nature of this band was investigated.

METHODOLOGY/PRINCIPAL FINDINGS

Genomic sequencing of the prototype outbreak isolate INCQS 00594 using the SOLiD platform demonstrated the presence of a 56,267-bp [corrected] circular plasmid, designated pMAB01. Identity matrices, genetic distances and phylogeny analyses indicated that pMAB01 belongs to the broad-host-range plasmid subgroup IncP-1β and is highly related to BRA100, pJP4, pAKD33 and pB10. The presence of pMAB01-derived sequences in 41 M. abscessus subsp. bolletii isolates was evaluated using PCR, PFGE and Southern blot hybridization. Sixteen of the 41 isolates showed the presence of the plasmid. The plasmid was visualized as a ∼50-kb band using PFGE and Southern blot hybridization in 12 isolates. The remaining 25 isolates did not exhibit any evidence of this plasmid. The plasmid was successfully transferred to Escherichia coli by conjugation and transformation. Lateral transfer of pMAB01 to the high efficient plasmid transformation strain Mycobacterium smegmatis mc(2)155 could not be demonstrated.

CONCLUSIONS/SIGNIFICANCE

The occurrence of a broad-host-range IncP-1β plasmid in mycobacteria is reported for the first time. Thus, genetic exchange could result in the emergence of specific strains that might be better adapted to cause human disease.

Broad-host-range IncP-1 plasmids and their resistance potential

The plasmids of the incompatibility (Inc) group IncP-1, also called IncP, as extrachromosomal genetic elements can transfer and replicate virtually in all Gram-negative bacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental bioremediation. Broad-host-range IncP plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to a broad spectrum of antibiotics, heavy metals, and quaternary ammonium compounds used as disinfectants. The backbone of these plasmids carries modules that enable them to effectively replicate, move to a new host via conjugative transfer and to be stably maintained in bacterial cells. The adaptive, resistance, and virulence genes are mainly located on mobile genetic elements integrated between the functional plasmid backbone modules. Environmental studies have demonstrated the wide distribution of IncP-like replicons in manure, soils and wastewater treatment plants. They also are present in strains of pathogenic or opportunistic bacteria, which can be a cause for concern, because they may encode multiresistance. Their broad distribution suggests that IncP plasmids play a crucial role in bacterial adaptation by utilizing horizontal gene transfer. This review summarizes the variety of genetic information and physiological functions carried by IncP plasmids, which can contribute to the spread of antibiotic and heavy metal resistance while also mediating the process of bioremediation of pollutants. Due to the location of the resistance genes on plasmids with a broad-host-range and the presence of transposons carrying these genes it seems that the spread of these genes would be possible and quite hazardous in infection control. Future studies are required to determine the level of risk of the spread of resistance genes located on these plasmids.

Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review

Urban wastewater treatment plants (UWTPs) are among the main sources of antibiotics' release into the environment. The occurrence of antibiotics may promote the selection of antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB), which shade health risks to humans and animals. In this paper the fate of ARB and ARGs in UWTPs, focusing on different processes/technologies (i.e., biological processes, advanced treatment technologies and disinfection), was critically reviewed. The mechanisms by which biological processes influence the development/selection of ARB and ARGs transfer are still poorly understood. Advanced treatment technologies and disinfection process are regarded as a major tool to control the spread of ARB into the environment. In spite of intense efforts made over the last years to bring solutions to control antibiotic resistance spread in the environment, there are still important gaps to fill in. In particular, it is important to: (i) improve risk assessment studies in order to allow accurate estimates about the maximal abundance of ARB in UWTPs effluents that would not pose risks for human and environmental health; (ii) understand the factors and mechanisms that drive antibiotic resistance maintenance and selection in wastewater habitats. The final objective is to implement wastewater treatment technologies capable of assuring the production of UWTPs effluents with an acceptable level of ARB.

Community-wide plasmid gene mobilization and selection

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions.

Inferring the evolutionary history of IncP-1 plasmids despite incongruence among backbone gene trees

Plasmids of the incompatibility group IncP-1 can transfer and replicate in many genera of the Proteobacteria. They are composed of backbone genes that encode a variety of essential functions and accessory genes that have implications for human health and environmental remediation. Although it is well understood that the accessory genes are transferred horizontally between plasmids, recent studies have also provided examples of recombination in the backbone genes of IncP-1 plasmids. As a consequence, phylogeny estimation based on backbone genes is expected to produce conflicting gene tree topologies. The main goal of this study was therefore to infer the evolutionary history of IncP-1 plasmids in the presence of both vertical and horizontal gene transfer. This was achieved by quantifying the incongruence among gene trees and attributing it to known causes such as 1) phylogenetic uncertainty, 2) coalescent stochasticity, and 3) horizontal inheritance. Topologies of gene trees exhibited more incongruence than could be attributed to phylogenetic uncertainty alone. Species-tree estimation using a Bayesian framework that takes coalescent stochasticity into account was well supported, but it differed slightly from the maximum-likelihood tree estimated by concatenation of backbone genes. After removal of the gene that demonstrated a signal of intergroup recombination, the concatenated tree was congruent with the species-tree estimate, which itself was robust to inclusion/exclusion of the recombinant gene. Thus, in spite of horizontal gene exchange both within and among IncP-1 subgroups, the backbone genome of these IncP-1 plasmids retains a detectable vertical evolutionary history.

The IncF plasmid pRSB225 isolated from a municipal wastewater treatment plant's on-site preflooder combining antibiotic resistance and putative virulence functions is highly related to virulence plasmids identified in pathogenic E. coli isolates

The IncF antibiotic resistance and virulence plasmid pRSB225, isolated from an unknown bacterium released with the purified wastewater from a municipal sewage treatment plant into the environment has been analysed at the genomic level by pyrosequencing. The 164,550bp plasmid comprises 210 coding sequences (cds). It is composed of three replicons (RepFIA, RepFIB, and RepFII) and encodes further plasmid-specific functions for stable maintenance and inheritance and conjugative plasmid transfer. The plasmid is self-transmissible and shows a narrow host range limited to the family Enterobacteriaceae. The accessory modules of the plasmid mainly comprise genes conferring resistance to ampicillin (bla(TEM-1b)), chloramphenicol (catA1), erythromycin (mphA), kanamycin and neomycin (aphA1), streptomycin (strAB), sulphonamides (sul2), tetracycline (tetA(B)) and trimethoprim (dfrA14), as well as mercuric ions (mer genes). In addition, putative virulence-associated genes coding for iron uptake (iutA/iucABCD, sitABCD, and a putative high-affinity Fe²⁺ uptake system) and for a toxin/antitoxin system (vagCD) were identified on the plasmid. All antibiotic and heavy metal resistance genes are located either on class 1 (Tn10-remnant, Tn4352B) and class 2 transposons (Tn2-remnant, Tn21, Tn402-remnant) or a class 1 integron, whereas almost all putative virulence genes are associated with IS elements (IS1, IS26), indicating that transposition and/or recombination events were responsible for acquisition of the accessory pRSB225 modules. Particular modules of plasmid pRSB225 are related to corresponding segments of different virulence plasmids harboured by pathogenic Escherichia coli strains. Moreover, pRSB225 modules were also detected in entero-aggregative-haemorrhagic E. coli (EAHEC) draft genome sequences suggesting that IncF plasmids related to pRSB225 mediated gene transfer into pathogenic E. coli derivatives.

Accumulation of pharmaceuticals, Enterococcus, and resistance genes in soils irrigated with wastewater for zero to 100 years in central Mexico

Irrigation with wastewater releases pharmaceuticals, pathogenic bacteria, and resistance genes, but little is known about the accumulation of these contaminants in the environment when wastewater is applied for decades. We sampled a chronosequence of soils that were variously irrigated with wastewater from zero up to 100 years in the Mezquital Valley, Mexico, and investigated the accumulation of ciprofloxacin, enrofloxacin, sulfamethoxazole, trimethoprim, clarithromycin, carbamazepine, bezafibrate, naproxen, diclofenac, as well as the occurrence of Enterococcus spp., and sul and qnr resistance genes. Total concentrations of ciprofloxacin, sulfamethoxazole, and carbamazepine increased with irrigation duration reaching 95% of their upper limit of 1.4 µg/kg (ciprofloxacin), 4.3 µg/kg (sulfamethoxazole), and 5.4 µg/kg (carbamazepine) in soils irrigated for 19–28 years. Accumulation was soil-type-specific, with largest accumulation rates in Leptosols and no time-trend in Vertisols. Acidic pharmaceuticals (diclofenac, naproxen, bezafibrate) were not retained and thus did not accumulate in soils. We did not detect qnrA genes, but qnrS and qnrB genes were found in two of the irrigated soils. Relative concentrations of sul1 genes in irrigated soils were two orders of magnitude larger (3.15×10⁻³±0.22×10⁻³ copies/16S rDNA) than in non-irrigated soils (4.35×10⁻⁵±1.00×10⁻⁵ copies/16S rDNA), while those of sul2 exceeded the ones in non-irrigated soils still by a factor of 22 (6.61×10^–4±0.59×10⁻⁴ versus 2.99×10⁻⁵±0.26×10⁻⁵ copies/16S rDNA). Absolute numbers of sul genes continued to increase with prolonging irrigation together with Enterococcus spp. 23S rDNA and total 16S rDNA contents. Increasing total concentrations of antibiotics in soil are not accompanied by increasing relative abundances of resistance genes. Nevertheless, wastewater irrigation enlarges the absolute concentration of resistance genes in soils due to a long-term increase in total microbial biomass.

IncP-1β plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet

The application of toxic triphenylmethane dyes such as crystal violet (CV) in various industrial processes leads to large amounts of dye-contaminated sludges that need to be detoxified. Specific bacteria residing in wastewater treatment plants (WWTPs) are able to degrade triphenylmethane dyes. The objective of this work was to gain insights into the genetic background of bacterial strains capable of CV degradation. Three bacterial strains isolated from a municipal WWTP harboured IncP-1β plasmids mediating resistance to and decolorization of CV. These isolates were assigned to the genera Comamonas and Delftia. The CV-resistance plasmid pKV29 from Delftia sp. KV29 was completely sequenced. In addition, nucleotide sequences of the accessory regions involved in conferring CV resistance were determined for plasmids pKV11 and pKV36 from the other two isolates. Plasmid pKV29 contains typical IncP-1β backbone modules that are highly similar to those of previously sequenced IncP-1β plasmids that confer antibiotic resistance, degradative capabilities or mercury resistance. The accessory regions located between the conjugative transfer (tra) and mating pair formation modules (trb) of all three plasmids analysed share common modules and include a triphenylmethane reductase gene, tmr, that is responsible for decolorization of CV. Moreover, these accessory regions encode other enzymes that are dispensable for CV degradation and hence are involved in so-far-unknown metabolic pathways. Analysis of plasmid-mediated degradation of CV in Escherichia coli by ultra-high-performance liquid chromatography-electrospray ionization-quadrupole-time-of-flight MS revealed that leuco crystal violet was the first degradation product. Michler's ketone and 4-dimethylaminobenzaldehyde appeared as secondary degradation metabolites. Enzymes encoded in the E. coli chromosome seem to be responsible for cleavage of leuco crystal violet. Plasmid-mediated degradation of triphenylmethane dyes such as CV is an option for the biotechnological treatment of sludges contaminated with these dyes.

Strain-specific transfer of antibiotic resistance from an environmental plasmid to foodborne pathogens

Pathogens resistant to multiple antibiotics are rapidly emerging, entailing important consequences for human health. This study investigated if the broad-host-range multiresistance plasmid pB10, isolated from a wastewater treatment plant, harbouring amoxicillin, streptomycin, sulfonamide, and tetracycline resistance genes, was transferable to the foodborne pathogens Salmonella spp. or E. coli O157:H7 and how this transfer alters the phenotype of the recipients. The transfer ratio was determined by both plating and flow cytometry. Antibiotic resistance profiles were determined for both recipients and transconjugants using the disk diffusion method. For 14 of the 15 recipient strains, transconjugants were detected. Based on plating, transfer ratios were between 6.8 × 10⁻⁹ and 3.0 × 10⁻² while using flow cytometry, transfer ratios were between <1.0 × 10⁻⁵ and 1.9 × 10⁻². With a few exceptions, the transconjugants showed phenotypically increased resistance, indicating that most of the transferred resistance genes were expressed. In summary, we showed that an environmental plasmid can be transferred into foodborne pathogenic bacteria at high transfer ratios. However, the transfer ratio seemed to be recipient strain dependent. Moreover, the newly acquired resistance genes could turn antibiotic susceptible strains into resistant ones, paving the way to compromise human health.

Characterization of a mobile and multiple resistance plasmid isolated from swine manure and its detection in soil after manure application

AIMS

To isolate and characterize multiple antibiotic resistance plasmids found in swine manure and test for plasmid-associated genetic markers in soil following manure application to an agricultural field.

METHODS AND RESULTS

Plasmids were isolated from an erythromycin enrichment culture that used liquid swine manure as an inoculant. Plasmids were transformed into Escherichia coli DH10β for subsequent characterization. We isolated and DNA sequenced a 22 102-bp plasmid (pMC2) that confers macrolide, and tetracycline resistances, and carries genes predicted to code for mercury and chromium resistance. Conjugation experiments using an pRP4 derivative as a helper plasmid confirm that pMC2 has a functional mobilization unit. PCR was used to detect genetic elements found on pMC2 in DNA extracted from manure amended soil.

CONCLUSIONS

The pMC2 plasmid has a tetracycline-resistant core and has acquired additional resistance genes by insertion of an accessory region (12 762 bp) containing macrolide, mercury and chromium resistance genes, which was inserted between the truncated DDE motifs within the Tn903/IS102 mobile element.

SIGNIFICANCE AND IMPACT OF THE STUDY

  Liquid swine manure used for manure spreading contains multiple antibiotic resistance plasmids that can be detected in soil following manure application.

The complete genome sequences of four new IncN plasmids from wastewater treatment plant effluent provide new insights into IncN plasmid diversity and evolution

The dissemination of antibiotic resistance genes among bacteria often occurs by means of plasmids. Wastewater treatment plants (WWTP) were previously recognized as hot spots for the horizontal transfer of genetic material. One of the plasmid groups that is often associated with drug resistance is the incompatibility group IncN. The aim of this study was to gain insights into the diversity and evolutionary history of IncN plasmids by determining and comparing the complete genome sequences of the four novel multi-drug resistance plasmids pRSB201, pRSB203, pRSB205 and pRSB206 that were exogenously isolated from the final effluent of a municipal WWTP. Their sizes range between 42,875 bp and 56,488 bp and they share a common set of backbone modules that encode plasmid replication initiation, conjugative transfer, and plasmid maintenance and control. All plasmids are transferable at high rates between Escherichia coli strains, but did not show a broad host range. Different genes conferring resistances to ampicillin, streptomycin, spectinomycin, sulfonamides, tetracycline and trimethoprim were identified in accessory modules inserted in these plasmids. Comparative analysis of the four WWTP IncN plasmids and IncN plasmids deposited in the NCBI database enabled the definition of a core set of backbone genes for this group. Moreover, this approach revealed a close phylogenetic relationship between the IncN plasmids isolated from environmental and clinical samples. Phylogenetic analysis also suggests the existence of host-specific IncN plasmid subgroups. In conclusion, IncN plasmids likely contribute to the dissemination of resistance determinants between environmental bacteria and clinical strains. This is of particular importance since multi-drug resistance IncN plasmids have been previously identified in members of the Enterobacteriaceae that cause severe infections in humans.

IncP-1ε Plasmids are Important Vectors of Antibiotic Resistance Genes in Agricultural Systems: Diversification Driven by Class 1 Integron Gene Cassettes

The role of broad-host range IncP-1ε plasmids in the dissemination of antibiotic resistance in agricultural systems has not yet been investigated. These plasmids were detected in total DNA from all of 16 manure samples and in arable soil based on a novel 5′-nuclease assay for real-time PCR. A correlation between IncP-1ε plasmid abundance and antibiotic usage was revealed. In a soil microcosm experiment the abundance of IncP-1ε plasmids was significantly increased even 127 days after application of manure containing the antibiotic compound sulfadiazine, compared to soil receiving only manure, only sulfadiazine, or water. Fifty IncP-1ε plasmids that were captured in E. coli CV601gfp from bacterial communities of manure and arable soil were characterized by PCR and hybridization. All plasmids carried class 1 integrons with highly varying sizes of the gene cassette region and the sul1 gene. Three IncP-1ε plasmids captured from soil bacteria and one from manure were completely sequenced. The backbones were nearly identical to that of the previously described IncP-1ε plasmid pKJK5. The plasmids differed mainly in the composition of a Tn402-like transposon carrying a class 1 integron with varying gene cassettes, IS1326, and in three of the plasmids the tetracycline resistance transposon Tn1721 with various truncations. Diverse Beta- and Gammaproteobacteria were revealed as hosts of one of the IncP-1ε plasmids in soil microcosms. Our data suggest that IncP-1ε plasmids are important vectors for horizontal transfer of antibiotic resistance in agricultural systems.

On the meaning and estimation of plasmid transfer rates for surface-associated and well-mixed bacterial populations

Conjugative plasmid transfer is key to the ability of bacteria to rapidly adapt to new environments, but there is no agreement on a single quantitative measure of the rate of plasmid transfer. Some studies derive estimates of transfer rates from mass-action differential equation models of plasmid population biology. The often-used 'endpoint method' is such an example. Others report measures of plasmid transfer efficiency that simply represent ratios of plasmid-bearing and plasmid-free cell densities and do not correspond to parameters in any mathematical model. Unfortunately, these quantities do not measure the same thing - sometimes differing by orders of magnitude - and their use is often clouded by a lack of specificity. Moreover, they do not distinguish between bulk transfer rates that are only relevant in well-mixed populations and the 'intrinsic' rates between individual cells. This leads to problems for surface-associated populations, which are not well-mixed but spatially structured. We used simulations of a spatially explicit mathematical model to evaluate the effectiveness of these various plasmid transfer efficiency measures when they are applied to surface-associated populations. The simulation results, supported by some experimental findings, showed that these measures can be affected by initial cell densities, donor-to-recipient ratios and initial cell cluster size, and are therefore flawed as universal measures of plasmid transfer efficiency. The simulations also allowed us to formulate some guiding principles on when these estimates are appropriate for spatially structured populations and how to interpret the results. While we focus on plasmid transfer, the general lessons of this study should apply to any measures of horizontal spread (e.g., infection rates in epidemiology) that are based on simple mass-action models (e.g., SIR models in epidemiology) but applied to spatial settings.

Plasmid metagenome reveals high levels of antibiotic resistance genes and mobile genetic elements in activated sludge

The overuse or misuse of antibiotics has accelerated antibiotic resistance, creating a major challenge for the public health in the world. Sewage treatment plants (STPs) are considered as important reservoirs for antibiotic resistance genes (ARGs) and activated sludge characterized with high microbial density and diversity facilitates ARG horizontal gene transfer (HGT) via mobile genetic elements (MGEs). However, little is known regarding the pool of ARGs and MGEs in sludge microbiome. In this study, the transposon aided capture (TRACA) system was employed to isolate novel plasmids from activated sludge of one STP in Hong Kong, China. We also used Illumina Hiseq 2000 high-throughput sequencing and metagenomics analysis to investigate the plasmid metagenome. Two novel plasmids were acquired from the sludge microbiome by using TRACA system and one novel plasmid was identified through metagenomics analysis. Our results revealed high levels of various ARGs as well as MGEs for HGT, including integrons, transposons and plasmids. The application of the TRACA system to isolate novel plasmids from the environmental metagenome, coupled with subsequent high-throughput sequencing and metagenomic analysis, highlighted the prevalence of ARGs and MGEs in microbial community of STPs.

Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes

Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.

The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms

Over the past few decades, degradative plasmids have been isolated from bacteria capable of degrading a variety of both natural and man-made compounds. Degradative plasmids belonging to three incompatibility (Inc) groups in Pseudomonas (IncP-1, P-7, and P-9) have been well studied in terms of their replication, maintenance, and capacity for conjugative transfer. The host ranges of these plasmids are determined by replication or conjugative transfer systems. The host range of IncP-1 is broad, that of IncP-9 is intermediate, and that of IncP-7 is narrow. To understand the behavior of these plasmids and their hosts in various environments, the survivability of inocula, stability or transferability, and efficiency of biodegradation in environments and microcosms have been monitored. The biodegradation and plasmid transfer in various environments have been observed for all three groups, although the kinds of transconjugants differed with the Inc groups. In some cases, the deletion and amplification of catabolic genes acted to reduce the production of toxic catabolic intermediates, or to increase the activity on a particular catabolic pathway. The combination of degradative genes, the plasmid backbone of each Inc group, and the host of the plasmids is key to the degraders adapting to various hosts or to heterogeneous environments.

Increased transfer of a multidrug resistance plasmid in Escherichia coli biofilms at the air-liquid interface

Although biofilms represent a common bacterial lifestyle in clinically and environmentally important habitats, there is scant information on the extent of gene transfer in these spatially structured populations. The objective of this study was to gain insight into factors that affect transfer of the promiscuous multidrug resistance plasmid pB10 in Escherichia coli biofilms. Biofilms were grown in different experimental settings, and plasmid transfer was monitored using laser scanning confocal microscopy and plate counting. In closed flow cells, plasmid transfer in surface-attached submerged biofilms was negligible. In contrast, a high plasmid transfer efficiency was observed in a biofilm floating at the air-liquid interface in an open flow cell with low flow rates. A vertical flow cell and a batch culture biofilm reactor were then used to detect plasmid transfer at different depths away from the air-liquid interface. Extensive plasmid transfer occurred only in a narrow zone near that interface. The much lower transfer frequencies in the lower zones coincided with rapidly decreasing oxygen concentrations. However, when an E. coli csrA mutant was used as the recipient, a thick biofilm was obtained at all depths, and plasmid transfer occurred at similar frequencies throughout. These results and data from separate aerobic and anaerobic matings suggest that oxygen can affect IncP-1 plasmid transfer efficiency, not only directly but also indirectly, through influencing population densities and therefore colocalization of donors and recipients. In conclusion, the air-liquid interface can be a hot spot for plasmid-mediated gene transfer due to high densities of juxtaposed donor and recipient cells.

Embedded elements in the IncPβ plasmids R772 and R906 can be mobilized and can serve as a source of diverse and novel elements

IncP plasmids are important contributors to bacterial adaptation. Their phenotypic diversity is due largely to accessory regions located in one or two specific parts of the plasmid. The accessory regions are themselves diverse, as judged from sequenced plasmids mostly isolated from non-clinical sources. To further understand the diversity, evolutionary history and functional attributes of the accessory regions, we compared R906 and R772, focusing on the oriV–trfA accessory region. These IncPβ plasmids were from porcine and clinical sources, respectively. We found that the accessory regions formed potentially mobile elements, Tn510 (from R906) and Tn511 (from R772), that differed internally but had identical borders. Both elements appeared to have evolved from a TnAO22-like mer transposon that had inserted into an ancestral IncPβ plasmid and then accrued additional transposable elements and genes from various proteobacteria. Structural comparisons suggested that Tn510 (and a descendent in pB10), Tn511 and the mer element in pJP4 represent three lineages that evolved from the same widely dispersed IncPβ carrier. Functional studies on Tn511 revealed that its mer module is inactive due to a merT mutation, and that its aphAI region is prone to deletion. More significantly, we showed that by providing a suitable transposase gene in trans, the defective Tn510 and Tn511 could transpose intact or in part, and could also generate new elements (stable cointegrates and novel transposons). The ingredients for assisted transposition events similar to those observed here occur in natural microcosms, providing non-self-mobile elements with avenues for dispersal to new replicons and for structural diversification. This work provides an experimental demonstration of how the complex embedded elements uncovered in IncP plasmids and in other plasmid families may have been generated.

The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination

Plasmids are important members of the bacterial mobile gene pool, and are among the most important contributors to horizontal gene transfer between bacteria. They typically harbour a wide spectrum of host beneficial traits, such as antibiotic resistance, inserted into their backbones. Although these inserted elements have drawn considerable interest, evolutionary information about the plasmid backbones, which encode plasmid related traits, is sparse. Here we analyse 25 complete backbone genomes from the broad-host-range IncP-1 plasmid family. Phylogenetic analysis reveals seven clades, in which two plasmids that we isolated from a marine biofilm represent a novel clade. We also found that homologous recombination is a prominent feature of the plasmid backbone evolution. Analysis of genomic signatures indicates that the plasmids have adapted to different host bacterial species. Globally circulating IncP-1 plasmids hence contain mosaic structures of segments derived from several parental plasmids that have evolved in, and adapted to, different, phylogenetically very distant host bacterial species.

Plasmids are present in many bacteria and are often transferred between different species causing horizontal gene transfer. By comparing the sequences of 25 plasmid DNA backbones, the authors show that homologous recombination is prevalent in plasmids and that the plasmids have adapted to persist in different host bacteria.

Accumulation of sulfonamide resistance genes in arable soils due to repeated application of manure containing sulfadiazine

Two soils were amended three times with pig manure. The abundance of sulfonamide resistance genes was determined by quantitative PCR 2 months after each application. In both soils treated with sulfadiazine-containing manure, the numbers of copies of sul1 and sul2 significantly increased compared to numbers after treatments with antibiotic-free manure or a control and accumulated with repeated applications.

Persistence and dissemination of the multiple-antibiotic-resistance plasmid pB10 in the microbial communities of wastewater sludge microcosms

Plasmid-mediated dissemination of antibiotic resistance genes is widely recognized to take place in many environmental compartments but remains difficult to study in a global perspective because of the complexity of the environmental matrices considered and the lack of exhaustive tools. In this report, we used a molecular approach based on quantitative PCR to monitor the fate of the antibiotic resistance plasmid pB10 and its donor host in microbial communities collected from various wastewater treatment plant (WWTP) sludges and maintained in microcosms under different conditions. In aerated activated sludge microcosms, pB10 did not persist because of an apparent loss of the donor bacteria. The persistence of the donor bacteria noticeably increased in non-aerated activated sludge microcosms or after amending antibiotics (sulfamethoxazole or amoxicillin) at sub-inhibitory concentrations, but the persistence of the donor bacteria did not stimulate the dissemination of pB10. The dissemination of the plasmid appeared as an increasing plasmid to donor ratio in microcosm setups with microbial communities collected in anaerobic digesters or the spatially organized communities from fixed biofilm reactors. As a whole, the data collected suggest that some WWTP processes, more than others, may sustain microbial communities that efficiently support the dissemination of the multiple-antibiotic-resistance plasmid pB10.

Sequencing and comparative analysis of IncP-1α antibiotic resistance plasmids reveal a highly conserved backbone and differences within accessory regions

Although IncP-1 plasmids are important for horizontal gene transfer among bacteria, in particular antibiotic resistance spread, so far only three plasmids from the subgroup IncP-1α have been completely sequenced. In this study we doubled this number. The three IncP-1α plasmids pB5, pB11 and pSP21 were isolated from bacteria of two different sewage treatment plants and sequenced by a combination of next-generation and capillary sequencing technologies. A comparative analysis including the previously analysed IncP-1α plasmids RK2, pTB11 and pBS228 revealed a highly conserved plasmid backbone (at least 99.9% DNA sequence identity) comprising 54 core genes. The accessory elements of the plasmid pB5 constitute a class 1 integron interrupting the parC gene and an IS6100 copy inserted into the integron. In addition, the tetracycline resistance genes tetAR and the ISTB11-like element are located between the klc operon and the trfA-ssb operon. Plasmid pB11 is loaded with a Tn5053-like mercury resistance transposon between the parCBA and parDE operons and contains tetAR that are identical to those identified in plasmid pB5 and the insertion sequence ISSP21. Plasmid pSP21 harbours an ISPa7 element in a Tn402 transposon including a class 1 integron between the partitioning genes parCBA and parDE. The IS-element ISSP21 (99.89% DNA sequence identity to ISSP21 from pB11), inserted downstream of the tetR gene and a copy of ISTB11 (identical to ISTB11 on pTB11) inserted between the genes pncA and pinR. On all three plasmids the accessory genes are almost always located between the backbone modules confirming the importance of the backbone functions for plasmid maintenance. The striking backbone conservation among the six completely sequenced IncP-1α plasmids is in contrast to the much higher diversity within the IncP-1β subgroup.

Broad-host-range plasmids in treated wastewater effluent and receiving streams

The occurrence of broad-host-range (BHR) plasmid amplicons belonging to incompatibility (Inc) groups IncA/C, IncN, IncP, and IncW in two wastewater treatment plant (WWTP) effluents and effluent-receiving streams in Northwest Arkansas, Mud Creek and Spring Creek, was determined. Community DNA captured on filter membranes and plasmid DNA extracted from antibiotic-resistant Escherichia coli isolated from Mud Creek was used for polymerase chain reaction at amplification of partial gene sequences specific to BHR plasmids. IncP plasmid amplicons were detected in effluent and downstream sites in both streams, while IncN and IncW plasmid amplicons were detected in Spring Creek in effluent and downstream but not upstream. IncA/C plasmid amplicons, in contrast, were detected at all sites, including upstream in most samples in Spring Creek and in one sample from Mud Creek. One IncP and two IncN were the only BHR plasmid amplicons found in 85 screened antibiotic-resistant E. coli isolates, and were detected only in isolates from effluent and downstream samples. Broad-host-range plasmids frequently carry antibiotic-resistance genes and can facilitate horizontal transfer of those genes. While BHR plasmids have been detected in WWTPs, WWTPs do not target these genetic elements for destruction. This study indicates that BHR plasmids are in WWTP effluent and are introducing BHR plasmids into streams. Additionally, species other than E. coli may be better targets as indicator bacteria for future studies of the impact of treated effluent on environmental dissemination of BHR plasmids.

Variation in permissiveness for broad-host-range plasmids among genetically indistinguishable isolates of Dickeya sp. from a small field plot

Phytopathogenic populations need genetic flexibility to adapt to continually improving plant defences. The gene pool transferred by broad-host-range plasmids provides genetic variation for the population. However, a population has to balance this benefit with the risk of acquiring deleterious foreign DNA. This could be achieved by modulating the ratio of individuals with high or low permissiveness to broad-host-range plasmids. We investigated whether plasmid uptake varied among genetically indistinguishable isolates of Dickeya sp. from a 400 m(2) field plot. The transfer frequencies of broad-host-range IncP-1 plasmids from Escherichia coli to Dickeya differed significantly among isolates. The transfer frequencies for plasmids pTH10 and pB10 of the divergent alpha- and beta-subgroups of IncP-1, respectively, correlated well. Strains that differed in permissiveness for these plasmids by orders of magnitude were not distinguishable by other phenotypic traits analysed, by genomic fingerprints or hrpN gene sequences. Such strains were isolated in close vicinity and from different plots of the field, indicating a reasonably fast genetic mechanism of switching between low and high permissiveness.

Network analyses structure genetic diversity in independent genetic worlds

DNA flows between chromosomes and mobile elements, following rules that are poorly understood. This limited knowledge is partly explained by the limits of current approaches to study the structure and evolution of genetic diversity. Network analyses of 119,381 homologous DNA families, sampled from 111 cellular genomes and from 165,529 phage, plasmid, and environmental virome sequences, offer challenging insights. Our results support a disconnected yet highly structured network of genetic diversity, revealing the existence of multiple "genetic worlds." These divides define multiple isolated groups of DNA vehicles drawing on distinct gene pools. Mathematical studies of the centralities of these worlds' subnetworks demonstrate that plasmids, not viruses, were key vectors of genetic exchange between bacterial chromosomes, both recently and in the past. Furthermore, network methodology introduces new ways of quantifying current sampling of genetic diversity.

Monitoring the dissemination of the broad-host-range plasmid pB10 in sediment microcosms by quantitative PCR

Studying the transfer of specific mobile genetic elements in complex environmental matrices remains difficult because suitable molecular tools are not yet available to back up classical culture-dependent approaches. In this report, we show that quantitative PCR could be used to monitor the dissemination of the broad-host-range plasmid pB10 in sediment microcosms. This approach lies in the differential measurement of the host and plasmid DNAs used to inoculate the microcosms, using a particular design of quantitative PCR primers/probes where we took advantage of the mosaic aspect of the bacterial genomes to achieve a highly specific quantitative PCR detection system.

Accounting for mating pair formation in plasmid population dynamics

Plasmids are important vehicles for horizontal gene transfer and rapid adaptation in bacteria, including the spread of antibiotic resistance genes. Conjugative transfer of a plasmid from a plasmid-bearing to a plasmid-free bacterial cell requires contact and attachment of the cells followed by plasmid DNA transfer prior to detachment. We introduce a system of differential equations for plasmid transfer in well-mixed populations that accounts for attachment, DNA transfer, and detachment dynamics. These equations offer advantages over classical mass-action models that combine these three processes into a single "bulk" conjugation rate. By decomposing the process of plasmid transfer into its constituent parts, this new model provides a framework that facilitates meaningful comparisons of plasmid transfer rates in surface and liquid environments. The model also allows one to account for experimental and environmental effects such as mixing intensity. To test the adequacy of the model and further explore the effects of mixing on plasmid transfer, we performed batch culture experiments using three different plasmids and a range of different mixing intensities. The results show that plasmid transfer is optimized at low to moderate shaking speeds and that vigorous shaking negatively affects plasmid transfer. Using reasonable assumptions on attachment and detachment rates, the mathematical model predicts the same behavior.

Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics

To detect plasmid-borne antibiotic-resistance genes in wastewater treatment plant (WWTP) bacteria, 192 resistance-gene-specific PCR primer pairs were designed and synthesized. Subsequent PCR analyses on total plasmid DNA preparations obtained from bacteria of activated sludge or the WWTP's final effluents led to the identification of, respectively, 140 and 123 different resistance-gene-specific amplicons. The genes detected included aminoglycoside, beta-lactam, chloramphenicol, fluoroquinolone, macrolide, rifampicin, tetracycline, trimethoprim and sulfonamide resistance genes as well as multidrug efflux and small multidrug resistance genes. Some of these genes were only recently described from clinical isolates, demonstrating genetic exchange between clinical and WWTP bacteria. Sequencing of selected resistance-gene-specific amplicons confirmed their identity or revealed that the amplicon nucleotide sequence is very similar to a gene closely related to the reference gene used for primer design. These results demonstrate that WWTP bacteria are a reservoir for various resistance genes. Moreover, detection of about 64 % of the 192 reference resistance genes in bacteria obtained from the WWTP's final effluents indicates that these resistance determinants might be further disseminated in habitats downstream of the sewage plant.

Horizontal gene transfer in metal and radionuclide contaminated soils

The horizontal transfer of genes encoded on mobile genetic elements (MGEs) such as plasmids and phage and their associated hitchhiking elements (transposons, integrons, integrative and conjugative elements, and insertion sequences) rapidly accelerate genome diversification of microorganisms, thereby affecting their physiology, metabolism, pathogenicity,and ecological character. The analyses of completed prokaryotic genomes reveal that horizontal gene transfer (HGT) continues to be an important factor contributing to the innovation of microbial genomes. Indeed, microbial genomes are remarkably dynamic and a considerable amount of genetic information is inserted or deleted by HGT mechanisms. Thus, HGT and the vast pool of MGEs provide microbial communities with an unparalleled means by which to respond rapidly to changing environmental conditions and exploit new ecological niches. Metals and radionuclide contamination in soils, the subsurface, and aquifers poses a serious challenge to microbial growth and survival because these contaminants cannot be transformed or biodegraded into non-toxic forms as often occurs with organic xenobiotic contaminants. In this chapter we present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contributions of HGT to adaptation for survival in mixed waste sites.

Persistence mechanisms of conjugative plasmids

Are plasmids selfish parasitic DNA molecules or an integrated part of the bacterial genome? This chapter reviews the current understanding of the persistence mechanisms of conjugative plasmids harbored by bacterial cells and populations. The diversity and intricacy of mechanisms affecting the successful propagation and long-term continued existence of these extra-chromosomal elements is extensive. Apart from the accessory genetic elements that may provide plasmid-harboring cells a selective advantage, special focus is placed on the mechanisms conjugative plasmids employ to ensure their stable maintenance in the host cell. These importantly include the ability to self-mobilize in a process termed conjugative transfer, which may occur across species barriers. Other plasmid stabilizing mechanisms include the multimer resolution system, active partitioning, and post-segregational-killing of plasmid-free cells. Finally, various molecular adaptations of plasmids to better match the genetic background of their bacterial host cell will be described.

Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes

Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the ‘evolutionary history’ of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed δ-distance, has been commonly used to measure differences in dinucleotide composition, or ‘genomic signature’, between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance–covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the δ-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host.

Diversity of IncP-9 plasmids of Pseudomonas

IncP-9 plasmids are important vehicles for degradation and resistance genes that contribute to the adaptability of Pseudomonas species in a variety of natural habitats. The three completely sequenced IncP-9 plasmids, pWW0, pDTG1 and NAH7, show extensive homology in replication, partitioning and transfer loci (an approximately 25 kb region) and to a lesser extent in the remaining backbone segments. We used PCR, DNA sequencing, hybridization and phylogenetic analyses to investigate the genetic diversity of 30 IncP-9 plasmids as well as the possibility of recombination between plasmids belonging to this family. Phylogenetic analysis of rep and oriV sequences revealed nine plasmid subgroups with 7-35 % divergence between them. Only one phenotypic character was normally associated with each subgroup, except for the IncP-9beta cluster, which included naphthalene- and toluene-degradation plasmids. The PCR and hybridization analysis using pWW0- and pDTG1-specific primers and probes targeting selected backbone loci showed that members of different IncP-9 subgroups have considerable similarity in their overall organization, supporting the existence of a conserved ancestral IncP-9 sequence. The results suggested that some IncP-9 plasmids are the product of recombination between plasmids of different IncP-9 subgroups but demonstrated clearly that insertion of degradative transposons has occurred on multiple occasions, indicating that association of this phenotype with these plasmids is not simply the result of divergent evolution from a single successful ancestral degradative plasmid.

Novel insertion sequence- and transposon-mediated genetic rearrangements in genomic island SGI1 of Salmonella enterica serovar Kentucky

Salmonella genomic island 1 (SGI1) is an integrative mobilizable element that harbors a multidrug resistance (MDR) gene cluster. Since its identification in epidemic Salmonella enterica serovar Typhimurium DT104 strains, variant SGI1 MDR gene clusters conferring different MDR phenotypes have been identified in several S. enterica serovars and classified as SGI1-A to -O. A study was undertaken to characterize SGI1 from serovar Kentucky strains isolated from travelers returning from Africa. Several strains tested were found to contain the partially characterized variant SGI1-K, recently described in a serovar Kentucky strain isolated in Australia. This variant contained only one cassette array, aac(3)-Id-aadA7, and an adjacent mercury resistance module. Here, the uncharacterized part of SGI1-K was sequenced. Downstream of the mer module similar to that found in Tn21, a mosaic genetic structure was found, comprising (i) part of Tn1721 containing the tetracycline resistance genes tetR and tet(A); (ii) part of Tn5393 containing the streptomycin resistance genes strAB, IS1133, and a truncated tnpR gene; and (iii) a Tn3-like region containing the tnpR gene and the beta-lactamase bla(TEM-1) gene flanked by two IS26 elements in opposite orientations. The rightmost IS26 element was shown to be inserted into the S044 open reading frame of the SGI1 backbone. This variant MDR region was named SGI1-K1 according to the previously described variant SGI1-K. Other SGI1-K MDR regions due to different IS26 locations, inversion, and partial deletions were characterized and named SGI1-K2 to -K5. Two new SGI1 variants named SGI1-P1 and -P2 contained only the Tn3-like region comprising the beta-lactamase bla(TEM-1) gene flanked by the two IS26 elements inserted into the SGI1 backbone. Three other new variants harbored only one IS26 element inserted in place of the MDR region of SGI1 and were named SGI1-Q1 to -Q3. Thus, in serovar Kentucky, the SGI1 MDR region undergoes recombinational and insertional events of transposon and insertion sequences, resulting in a higher diversity of MDR gene clusters than previously reported and consequently a higher diversity of MDR phenotypes.

Adaptive plasmid evolution results in host-range expansion of a broad-host-range plasmid

Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this "long-term host range" can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range.

Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations

In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p(+)) cells as low as 10(-7). To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p(+) fraction increased to 13%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids.

Metagenomics and the niche concept

The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.