Transfer Of Bacterial DNA Research Articles

Tracing the Sources and Prevalence of Class 1 Integrons, Antimicrobial Resistance, and Trace Elements Using European Honey Bees.

Surveillance of antimicrobial resistance is essential for an effective One Health response. This study explores the efficacy of European honey bees (Apis mellifera) for biomonitoring antimicrobial resistance (AMR) in urban areas. Class 1 integrons (intI1) are investigated as a universal AMR indicator, as well as associated cassette arrays and trace element contaminants at a city-wide scale. Class 1 integrons were found to be pervasive across the urban environment, occurring in 52% (75/144) of the honey bees assessed. The area of waterbodies within the honey bee's foraging radius was associated with intI1 prevalence, indicating an exposure pathway for future investigation to address. Trace element concentrations in honey bees reflected urban sources, supporting the application of this biomonitoring approach. As the first study of intI1 in honey bees, we provide insights into the environmental transfer of bacterial DNA to a keystone species and demonstrate how intI1 biomonitoring can support the surveillance of AMR.

Bacteriophages benefit from generalized transduction.

Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.

CRISPR-Cas-Mediated Phage Resistance Enhances Horizontal Gene Transfer by Transduction.

ABSTRACTA powerful contributor to prokaryotic evolution is horizontal gene transfer (HGT) through transformation, conjugation, and transduction, which can be advantageous, neutral, or detrimental to fitness. Bacteria and archaea control HGT and phage infection through CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) adaptive immunity. Although the benefits of resisting phage infection are evident, this can come at a cost of inhibiting the acquisition of other beneficial genes through HGT. Despite the ability of CRISPR-Cas to limit HGT through conjugation and transformation, its role in transduction is largely overlooked. Transduction is the phage-mediated transfer of bacterial DNA between cells and arguably has the greatest impact on HGT. We demonstrate that in Pectobacterium atrosepticum, CRISPR-Cas can inhibit the transduction of plasmids and chromosomal loci. In addition, we detected phage-mediated transfer of a large plant pathogenicity genomic island and show that CRISPR-Cas can inhibit its transduction. Despite these inhibitory effects of CRISPR-Cas on transduction, its more common role in phage resistance promotes rather than diminishes HGT via transduction by protecting bacteria from phage infection. This protective effect can also increase transduction of phage-sensitive members of mixed populations. CRISPR-Cas systems themselves display evidence of HGT, but little is known about their lateral dissemination between bacteria and whether transduction can contribute. We show that, through transduction, bacteria can acquire an entire chromosomal CRISPR-Cas system, including cas genes and phage-targeting spacers. We propose that the positive effect of CRISPR-Cas phage immunity on enhancing transduction surpasses the rarer cases where gene flow by transduction is restricted.

Origin and Evolution of the Bartonella Gene Transfer Agent.

Gene transfer agents (GTAs) are domesticated bacteriophages that have evolved into molecular machines for the transfer of bacterial DNA. Despite their widespread nature and their biological implications, the mechanisms and selective forces that drive the emergence of GTAs are still poorly understood. Two GTAs have been identified in the Alphaproteobacteria: the RcGTA, which is widely distributed in a broad range of species; and the BaGTA, which has a restricted host range that includes vector-borne intracellular bacteria of the genus Bartonella. The RcGTA packages chromosomal DNA randomly, whereas the BaGTA particles contain a relatively higher fraction of genes for host interaction factors that are amplified from a nearby phage-derived origin of replication. In this study, we compare the BaGTA genes with homologous bacteriophage genes identified in the genomes of Bartonella species and close relatives. Unlike the BaGTA, the prophage genes are neither present in all species, nor inserted into homologous genomic sites. Phylogenetic inferences and substitution frequency analyses confirm codivergence of the BaGTA with the host genome, as opposed to multiple integration and recombination events in the prophages. Furthermore, the organization of segments flanking the BaGTA differs from that of the prophages by a few rearrangement events, which have abolished the normal coordination between phage genome replication and phage gene expression. Based on the results of our comparative analysis, we propose a model for how a prophage may be transformed into a GTA that transfers amplified bacterial DNA segments.

Correlated Mutations and Homologous Recombination Within Bacterial Populations.

Inferring the rate of homologous recombination within a bacterial population remains a key challenge in quantifying the basic parameters of bacterial evolution. Due to the high sequence similarity within a clonal population, and unique aspects of bacterial DNA transfer processes, detecting recombination events based on phylogenetic reconstruction is often difficult, and estimating recombination rates using coalescent model-based methods is computationally expensive, and often infeasible for large sequencing data sets. Here, we present an efficient solution by introducing a set of mutational correlation functions computed using pairwise sequence comparison, which characterize various facets of bacterial recombination. We provide analytical expressions for these functions, which precisely recapitulate simulation results of neutral and adapting populations under different coalescent models. We used these to fit correlation functions measured at synonymous substitutions using whole-genome data on Escherichia coli and Streptococcus pneumoniae populations. We calculated and corrected for the effect of sample selection bias, i.e., the uneven sampling of individuals from natural microbial populations that exists in most datasets. Our method is fast and efficient, and does not employ phylogenetic inference or other computationally intensive numerics. By simply fitting analytical forms to measurements from sequence data, we show that recombination rates can be inferred, and the relative ages of different samples can be estimated. Our approach, which is based on population genetic modeling, is broadly applicable to a wide variety of data, and its computational efficiency makes it particularly attractive for use in the analysis of large sequencing datasets.

Detection and identification methods and new tests as developed and used in the framework of COST873 for bacteria pathogenic to stone fruits and nuts: Tumorigenic Agrobacterium spp.

SUMMARY Crown gall, caused by bacteria belonging to different species of the genus Agrobacterium, is one of the most serious diseases affecting nursery production of fruit trees and nuts. From a practical point of view, determination if the soil of fields designated for nursery plantations is free from tumour-inducing agrobacteria is very important. During the infection process, after transfer of bacterial DNA to the plant cell, the presence of bacteria is no longer required for gall development. Therefore, infections caused by Agrobacterium remain difficult to detect although many methods are available for diagnosis of crown gall and identification of agrobacteria. In the present minireview, methods for isolation, identification and detection of tumorigenic agrobacteria developed within COST873 are described and ready-touse protocols based on both classical or molecular methods are provided.

Can microbes on skin help linking persons and crimes?

Linking persons to crimes through DNA analysis is a well-established approach for more than 25 years. While enormous numbers of cases all over the world have been solved based on DNA, there is still need for additional tools for improvement in physical evidence choice and collection. Unfortunately not all samples collected from crime scenes, are suitable for linking persons to crimes due to the quantity and quality of the human DNA collected. Recent studies have shown personality of bacterial community on human body surface that may open new perspectives for forensics. The aim of the study was evaluation of variability of bacterial communities on skin of palm and fingers between and within individuals as well as transfer of bacterial DNA during contact to the object and persistence of community parameters during storage. Four volunteers were recruited and samples collected during 5 days and afterwards once per week during 1 month in the morning and in the afternoon by swabbing of palm and fingers after holding sterile object for 1 min with persons dominant hand. The samples were also collected from the handled objects, except the first object, in which surface was quartered and sampled by quarter zone with 1-week interval after storing the object at room temperature. DNA was extracted and metagenomic analysis of bacterial community using 16S rRNA gene hypervariable regions was performed on Roche/454 platform. Our preliminary results are promising however foresee need for more elaborative studies to be able to implement this approach into the routine practice.

BifidobacteriumandLactobacillusDNA in the human placenta

Bifidobacteria and lactobacilli are part of the human normal intestinal microbiota and may possibly be transferred to the placenta. It was hypothesized that intestinal bacteria or their components are present in the placenta and that the foetus may be exposed to them. We investigated the presence of bifidobacteria and lactobacilli and their DNA in the human placenta. We studied 34 human placentae (25 vaginal and nine caesarean deliveries) for the presence Bifidobacterium spp. and Lactobacillus rhamnosus. Cultivation was used for the detection of viable cells and genus and species-specific PCR for the detection of DNA. No bifidobacteria or lactobacilli were found by cultivation. Bifidobacterial DNA was detected in 33 and L. rhamnosus DNA in 31 placenta samples. DNA from intestinal bacteria was found in most placenta samples. The results suggest that horizontal transfer of bacterial DNA from mother to foetus may occur via placenta. Bacterial DNA contains unmethylated CpG oligodeoxynucleotide motifs which induce immune effects. Specific CpG motifs activate Toll-like receptor 9 and subsequently trigger Th-1-type immune responses. Although the newborn infant is considered immunologically immature, exposure by bacterial DNA may programme the infant's immune development during foetal life earlier than previously considered.

Ultrasound-mediated DNA transfer for bacteria

In environmental microbiology, the most commonly used methods of bacterial DNA transfer are conjugation and electroporation. However, conjugation requires physical contact and cell–pilus–cell interactions; electroporation requires low-ionic strength medium and high voltage. These limitations have hampered broad applications of bacterial DNA delivery. We have employed a standard low frequency 40 kHz ultrasound bath to successfully transfer plasmid pBBR1MCS2 into Pseudomonas putida UWC1, Escherichia coli DH5α and Pseudomonas fluorescens SBW25 with high efficiency. Under optimal conditions: ultrasound exposure time of 10 s, 50 mM CaCl2, temperature of 22°C, plasmid concentration of 0.8 ng/µl, P. putida UWC1 cell concentration of 2.5 × 109 CFU (colony forming unit)/ml and reaction volume of 500 µl, the efficiency of ultrasound DNA delivery (UDD) was 9.8 ± 2.3 × 10−6 transformants per cell, which was nine times more efficient than conjugation, and even four times greater than electroporation. We have also transferred pBBR1MCS2 into E. coli DH5α and P. fluorescens SBW25 with efficiencies of 1.16 ± 0.13 × 10−6 and 4.33 ± 0.78 × 10−6 transformants per cell, respectively. Low frequency UDD can be readily scaled up, allowing for the application of UDD not only in laboratory conditions but also on an industrial scale.

An assessment of the risks associated with the use of antibiotic resistance genes in genetically modified plants: report of the Working Party of the British Society for Antimicrobial Chemotherapy.

Development of genetically modified (GM) plants is contentious, in part because bacterial antibiotic resistance (AR) genes are used in their construction and often become part of the plant genome. This arouses concern that cultivation of GM plants might provide a reservoir of AR genes that could power the evolution of new drug-resistant bacteria. We have considered bacterial DNA transfer systems (conjugation, transduction and transformation) and mechanisms of recombination (homologous recombination, transposition, site-specific recombination and DNA repair) that together might productively transfer AR genes from GM plants to bacterial cells, but are unable to identify a credible scenario whereby new drug-resistant bacteria would be created. However, we cannot entirely rule out the possibility of rare transfer events that involve novel mechanisms. Hence, we also considered if occasional transfers of AR genes (bla(TEM), aph(3'), aadA) from GM plants into bacteria would pose a threat to public health. These AR genes are common in many bacteria and each is found on mobile genetic elements that have moved extensively between DNA molecules and bacterial cells. This gene mobility has already severely compromised clinical use of antibiotics to which resistance is conferred. Accordingly, the argument that occasional transfer of these particular resistance genes from GM plants to bacteria would pose an unacceptable risk to human or animal health has little substance. We conclude that the risk of transfer of AR genes from GM plants to bacteria is remote, and that the hazard arising from any such gene transfer is, at worst, slight.

Genome plasticity: insertion sequence elements, transposons and integrons, and DNA rearrangement.

Living organisms are defined by the genes they possess. Control of expression of this gene set, both temporally and in response to the environment, determines whether an organism can survive changing conditions and can compete for the resources it needs to reproduce. Bacteria are no exception; changes to the genome will, in general, threaten the ability of the microbe to survive, but acquisition of new genes may enhance its chances of survival by allowing growth in a previously hostile environment. For example, acquisition of an antibiotic resistance gene by a bacterial pathogen can permit it to thrive in the presence of an antibiotic that would otherwise kill it; this may compromise clinical treatments. Many forces, chemical and genetic, can alter the genetic content of DNA by locally changing its nucleotide sequence. Notable for genetic change in bacteria are transposable elements and site-specific recombination systems such as integrons. Many of the former can mobilize genes from one replicon to another, including chromosome-plasmid translocation, thus establishing conditions for interspecies gene transfer. Balancing this, transposition activity can result in loss or rearrangement of DNA sequences. This chapter discusses bacterial DNA transfer systems, transposable elements and integrons, and the contributions each makes towards the evolution of bacterial genomes, particularly in relation to bacterial pathogenesis. It highlights the variety of phylogenetically distinct transposable elements, the variety of transposition mechanisms, and some of the implications of rearranging DNA, and addresses the effects of genetic change on the fitness of the microbe.

Recombinant DNA Made Easy II. Gene, Gene, Who's Got the Gene?

In a previous article (Thomson 1988) students were introduced to a rather simple laboratory study involving the intercellular transfer of bacterial DNA that codes for the resistance to antibiotics. The results of that study merely demonstrated that such a transfer can occur. In this article, students will be able to determine not only that DNA can be transferred between bacteria, they should be able to predict the type of DNA transferred; that is, whether it is chromosomal or extra chromosomal DNA in the form of a plasmid. In addition, from the data obtained, the students should be able to determine which bacterium functioned as the donor (male) or perhaps whether both bacteria donated genes to each other.

Bacterial nucleic acid synthesis in plants following bacterial contact.

After plants have been in contact with a suspension of bacteria one finds in plant cells self replicating bacterial DNA and replicating molecules formed of bacterial DNA combined with plant DNA. Moreover newly synthesized bacterial RNA appears in the host cell. These phenomena seem to be due to a transfer of bacterial DNA into plant cells.