Fate of free DNA and transformation of the oral bacterium Streptococcus gordonii DL1 by plasmid DNA in human saliva

Integration of Bite Mark Microbiome Analysis with Forensic DNA Profiling: Advancements, Challenges, and Synergistic Approaches

Bite mark analysis plays a pivotal role in forensic investigations, by helping to identify suspects and establish links between individuals and crime scenes. However, traditional bite mark methodologies face significant challenges due to issues with reliability and subjectivity. Recent advances in microbiome analysis, which involves identifying and characterizing the microbial communities found in bite marks, have led to the emergence of a promising tool for forensic investigations. The integration of microbiome analysis with conventional DNA profiling enables more accurate interpretation of bite mark evidence in forensic investigations. This review provides an in-depth look at the integration of bite mark microbiome analysis with forensic DNA profiling. It also addresses the challenges and strategies involved in microbiome-based bite mark analysis for forensic purposes.

Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans

Food consumption allows the entrance of bacteria and their antibiotic resistance (AR) genes into the human oral cavity. To date, very few studies have examined the influence of diet on the composition of the salivary microbiota, and even fewer investigations have specifically aimed to assess the impact of different long-term diets on the salivary resistome. In this study, the saliva of 144 healthy omnivores, ovo-lacto-vegetarians, and vegans were screened by nested PCR for the occurrence of 12 genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and β-lactams. The tet(W), tet(M), and erm(B) genes occurred with the highest frequencies. Overall, no effect of diet on AR gene distribution was seen. Some differences emerged at the recruiting site level, such as the higher frequency of erm(C) in the saliva of the ovo-lacto-vegetarians and omnivores from Bologna and Turin, respectively, and the higher occurrence of tet(K) in the saliva of the omnivores from Bologna. A correlation of the intake of milk and cheese with the abundance of tet(K) and erm(C) genes was seen. Finally, when the occurrence of the 12 AR genes was evaluated along with geographical location, age, and sex as sources of variability, high similarity among the 144 volunteers was seen.

Extensive transmission of microbes along the gastrointestinal tract

The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.

Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis

Horizontal gene transfer (HGT) is a driving force for bacterial evolution that occurs via conjugation, transduction, and transformation. Whereas conjugation and transduction depend on nonbacterial vehicles, transformation is considered a naturally occurring process in which naked DNA molecules are taken up by a competent recipient cell. Here, we report that HGT occurred between two Bacillus subtilis strains cocultured on a minimum medium agar plate for 10 h. This process was almost completely resistant to DNase treatment and appeared to require close proximity between cells. The deletion of comK in the recipient completely abolished gene transfer, indicating that the process involved transformation. This process was also highly efficient, reaching 1.75 × 10⁶ transformants/μg DNA compared to 5.3 × 10³ and 1.86 × 10⁵ transformants/μg DNA for DNA-to-cell transformation by the same agar method and the standard two-step procedure, respectively. Interestingly, when three distantly localized chromosomal markers were selected simultaneously, the efficiency of cell-to-cell transformation still reached 6.26 × 10⁴ transformants/μg DNA, whereas no transformants were obtained when free DNA was used as the donor. Stresses, such as starvation and exposure to antibiotics, further enhanced transformation efficiency by affecting the donor cells, suggesting that stress served as an important signal for promoting this type of HGT. Taken together, our results defined a bona fide process of cell-to-cell natural transformation (CTCNT) in B. subtilis and related species. This finding reveals the previously unrecognized role of donor cells in bacterial natural transformation and improves our understanding of how HGT drives bacterial evolution at a mechanistic level.IMPORTANCE Because DNA is easily prepared, studies of bacterial natural genetic transformation traditionally focus on recipient cells. However, such laboratory artifacts cannot explain how this process occurs in nature. In most cases, competence is only transient and involves approximately 20 to 50 genes, and it is unreasonable for bacteria to spend so many genetic resources on unpredictable and uncertain environmental DNA. Here, we characterized a donor cell-dependent CTCNT process in B. subtilis and related species that was almost completely resistant to DNase treatment and was more efficient than classical natural transformation using naked DNA as a donor, i.e., DNA-to-cell transformation, suggesting that DNA donor cells were also important in the transformation process in natural environments.

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

Horizontal gene transfer (HGT) plays a major role in the spread of antibiotic resistance. Of particular concern are Acinetobacter baumannii bacteria, which recently emerged as global pathogens, with nosocomial mortality rates reaching 19-54% (Centers for Disease Control and Prevention, 2013; Joly Guillou, 2005; Talbot et al., 2006). Acinetobacter gains antibiotic resistance remarkably rapidly (Antunes et al., 2014; Joly Guillou, 2005), with multi drug-resistance (MDR) rates exceeding 60% (Antunes et al., 2014; Centers for Disease Control and Prevention, 2013). Despite growing concern (Centers for Disease Control and Prevention, 2013; Talbot et al., 2006), the mechanisms underlying this extensive HGT remain poorly understood (Adams et al., 2008; Fournier et al., 2006; Imperi et al., 2011; Ramirez et al., 2010; Wilharm et al., 2013). Here, we show bacterial predation by Acinetobacter baylyi increases cross-species HGT by orders of magnitude, and we observe predator cells functionally acquiring adaptive resistance genes from adjacent prey. We then develop a population-dynamic model quantifying killing and HGT on solid surfaces. We show DNA released via cell lysis is readily available for HGT and may be partially protected from the environment, describe the effects of cell density, and evaluate potential environmental inhibitors. These findings establish a framework for understanding, quantifying, and combating HGT within the microbiome and the emergence of MDR super-bugs.

Various pathways leading to the acquisition of antibiotic resistance by natural transformation

Natural transformation can lead to exchange of DNA between taxonomically diverse bacteria. In the case of chromosomal DNA, homology-based recombination with the recipient genome is usually necessary for heritable stability. In our recent study, we have shown that natural transformation can promote the transfer of transposons, IS elements, and integrons and gene cassettes, largely independent of the genetic relationship between the donor and recipient bacteria. Additional results from our study suggest that natural transformation with species-foreign DNA might result in the uptake of a wide range of DNA fragments; leading to changes in the antimicrobial susceptibility profile and contributing to the generation of antimicrobial resistance in bacteria.

Bacterial sex in dental plaque

Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

Systemic exposure to Pseudomonal bacteria: a potential link between type 1 diabetes and chronic inflammation

Bacterial endotoxins have been associated with chronic inflammation and the development and progression of diabetic nephropathy. We hypothesized that subjects with high serum lipopolysaccharide activity also carry remains of bacterial DNA in their system. Serum-derived bacterial DNA clones were isolated and identified from 10 healthy controls and 14 patients with type 1 diabetes (T1D) using universal primers targeted to bacterial 16S rDNA. A total of 240 clones representing 35 unique bacterial species were isolated and identified. A significant proportion of the isolated bacteria could be assigned to our living environment. Proteobacteria was by far the most prevalent phylum among the samples. Notably, the patients had significantly higher frequencies of Stenotrophomonas maltophilia clones in their sera compared to the healthy controls. Real-time PCR analysis of S. maltophilia and Pseudomonas aeruginosa flagellin gene copy number in the human leukocyte DNA fraction revealed that the overall Pseudomonal bacterial load was higher in older patients with T1D. Serum IgA- and IgG-antibody levels against Pseudomonal bacteria Delftia acidovorans, P. aeruginosa, and S. maltophilia were also determined in 200 healthy controls and 200 patients with T1D. The patients had significantly higher serum levels of IgA antibodies against all three Pseudomonal bacteria. Additionally, the IgA antibodies against Pseudomonal bacteria correlated significantly with serum C-reactive protein. These findings indicate that recurrent or chronic Pseudomonal exposure may increase susceptibility to chronic inflammation in patients with T1D.

Microbial analysis of bite marks by sequence comparison of streptococcal DNA

Bite mark injuries often feature in violent crimes. Conventional morphometric methods for the forensic analysis of bite marks involve elements of subjective interpretation that threaten the credibility of this field. Human DNA recovered from bite marks has the highest evidentiary value, however recovery can be compromised by salivary components. This study assessed the feasibility of matching bacterial DNA sequences amplified from experimental bite marks to those obtained from the teeth responsible, with the aim of evaluating the capability of three genomic regions of streptococcal DNA to discriminate between participant samples. Bite mark and teeth swabs were collected from 16 participants. Bacterial DNA was extracted to provide the template for PCR primers specific for streptococcal 16S ribosomal RNA (16S rRNA) gene, 16S–23S intergenic spacer (ITS) and RNA polymerase beta subunit (rpoB). High throughput sequencing (GS FLX 454), followed by stringent quality filtering, generated reads from bite marks for comparison to those generated from teeth samples. For all three regions, the greatest overlaps of identical reads were between bite mark samples and the corresponding teeth samples. The average proportions of reads identical between bite mark and corresponding teeth samples were 0.31, 0.41 and 0.31, and for non-corresponding samples were 0.11, 0.20 and 0.016, for 16S rRNA, ITS and rpoB, respectively. The probabilities of correctly distinguishing matching and non-matching teeth samples were 0.92 for ITS, 0.99 for 16S rRNA and 1.0 for rpoB. These findings strongly support the tenet that bacterial DNA amplified from bite marks and teeth can provide corroborating information in the identification of assailants.

An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats

BACKGROUND

Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes.

RESULTS

Plasmid DNA with two resistance genes (nptI and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, were constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. No transformants were identified among 441 tested isolates.

CONCLUSIONS

The analyses showed that extensive ingestion of DNA (100 μg plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit < 1 transformant per 1,1 × 10(8) cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed. This study is consistent with other studies suggesting natural transformation is not detectable in the GIT of mammals.

Integrity of proteins in human saliva after sterilization by gamma irradiation

Microbial contamination of whole human saliva is unwanted for certain in vitro applications, e.g., when utilizing it as a growth substratum for biofilm experiments. The aim of this investigation was to test gamma irradiation for its suitability to sterilize saliva and to investigate the treatment's influence on the composition and integrity of salivary proteins in comparison to filter sterilization. For inhibition of bacterial growth by gamma irradiation, a sterility assurance level of 10(-6) was determined to be reached at a dose of 3.5 kGy. At this dose, the integrity of proteins, as measured by fluorescence, circular dichroism, and gel electrophoretic banding pattern, and the enzymatic activities of salivary amylase and lysozyme were virtually unchanged. Filtration reduced the total protein concentration to about half of its original value and decreased lysozyme activity to about 10%. It can be concluded that irradiation is suitable for sterilizing whole saliva in its native form.

Periodontal pathogens interfere with quorum-sensing-dependent virulence properties in Streptococcus mutans

BACKGROUND AND OBJECTIVE

The mechanism by which periodontal pathogens dominate at disease sites is not yet understood. One possibility is that these late colonizers antagonize the quorum-sensing systems of early colonizers and render those early colonizers less resistant to environmental factors. In this study, we utilized Streptococcus mutans, a well-documented oral Streptococcus with many quorum-sensing-dependent properties, as an example of an earlier colonizer antagonized by periodontal pathogens.

MATERIAL AND METHODS

In this study, S. mutans NG8 and S. mutans LT11 were used in experiments assessing transformation, and S. mutans BM71 was used in experiments investigating bacteriocin production. The effects of the periodontal pathogens Porphyromonas gingivalis and Treponema denticola on these competence-stimulating peptide-dependent properties were evaluated in mixed-broth assays.

RESULTS

Both P. gingivalis (either live bacteria or membrane vesicles) and T. denticola antagonized transformation in S. mutans NG8 and LT11. The production of bacteriocin by S. mutans BM71 was also inhibited by P. gingivalis and T. denticola. Boiling of these late colonizers before addition to the broth cultures abolished their ability to inhibit S. mutans transformation and bacteriocin production. P. gingivalis and T. denticola inactivated S. mutans exogenous competence-stimulating peptide, whereas the boiled bacteria did not.

CONCLUSIONS

This study demonstrated that periodontal pathogens antagonize S. mutans quorum-sensing properties. This may render S. mutans less virulent and less resistant to environmental antibacterial factors.

Risks from GMOs due to horizontal gene transfer

Horizontal gene transfer (HGT) is the stable transfer of genetic material from one organism to another without reproduction or human intervention. Transfer occurs by the passage of donor genetic material across cellular boundaries, followed by heritable incorporation to the genome of the recipient organism. In addition to conjugation, transformation and transduction, other diverse mechanisms of DNA and RNA uptake occur in nature. The genome of almost every organism reveals the footprint of many ancient HGT events. Most commonly, HGT involves the transmission of genes on viruses or mobile genetic elements. HGT first became an issue of public concern in the 1970s through the natural spread of antibiotic resistance genes amongst pathogenic bacteria, and more recently with commercial production of genetically modified (GM) crops. However, the frequency of HGT from plants to other eukaryotes or prokaryotes is extremely low. The frequency of HGT to viruses is potentially greater, but is restricted by stringent selection pressures. In most cases the occurrence of HGT from GM crops to other organisms is expected to be lower than background rates. Therefore, HGT from GM plants poses negligible risks to human health or the environment.

Gene transfer events and their occurrence in selected environments

Genes encoding virulence determinants are transferred between species in many different environments. In this review we describe gene transfer events to and from different species of bacteria, from bacteria to plants, and from plants to bacteria. Examples of the setting for these transfer events include: the GI tract, the rumen, the oral cavity, and in food matrixes. As a case study, the flux of virulence factors from E.coli O157:H7 is described as an example of gene flow in the environment.

Genetically Engineered Plants and Foods: A Scientist's Analysis of the Issues (Part I)

Through the use of the new tools of genetic engineering, genes can be introduced into the same plant or animal species or into plants or animals that are not sexually compatible-the latter is a distinction with classical breeding. This technology has led to the commercial production of genetically engineered (GE) crops on approximately 250 million acres worldwide. These crops generally are herbicide and pest tolerant, but other GE crops in the pipeline focus on other traits. For some farmers and consumers, planting and eating foods from these crops are acceptable; for others they raise issues related to safety of the foods and the environment. In Part I of this review some general and food issues raised regarding GE crops and foods will be addressed. Responses to these issues, where possible, cite peer-reviewed scientific literature. In Part II to appear in 2009, issues related to environmental and socioeconomic aspects of GE crops and foods will be covered.

Lack of detectable DNA uptake by bacterial gut isolates grown in vitro and by Acinetobacter baylyi colonizing rodents in vivo

Biological risk assessment of food containing recombinant DNA has exposed knowledge gaps related to the general fate of DNA in the gastrointestinal tract (GIT). Here, a series of experiments is presented that were designed to determine if genetic transformation of the naturally competent bacterium Acinetobacter baylyi BD413 occurs in the GIT of mice and rats, with feed-introduced bacterial DNA containing a kanamycin resistance gene (nptII). Strain BD413 was found in various gut locations in germ-free mice at 10(3)-10(5) CFU per gram GIT content 24-48 h after administration. However, subsequent DNA exposure of the colonized mice did not result in detectable bacterial transformants, with a detection limit of 1 transformant per 10(3)-10(5) bacteria. Further attempts to increase the likelihood of detection by introducing weak positive selection with kanamycin of putative transformants arising in vivo during a 4-week-long feeding experiment (where the mice received DNA and the recipient cells regularly) did not yield transformants either. Moreover, the in vitro exposure of actively growing A. baylyi cells to gut contents from the stomach, small intestine, cecum or colon contents of rats (with a normal microbiota) fed either purified DNA (50 microg) or bacterial cell lysates did not produce bacterial transformants. The presence of gut content of germfree mice was also highly inhibitory to transformation of A. baylyi, indicating that microbially-produced nucleases are not responsible for the sharp 500- to 1,000,000-fold reduction of transformation frequencies seen. Finally, a range of isolates from the genera Enterococcus, Streptococcus and Bifidobacterium spp. was examined for competence expression in vitro, without yielding any transformants. In conclusion, model choice and methodological constraints severely limit the sample size and, hence, transfer frequencies that can be measured experimentally in the GIT. Our observations suggest the contents of the GIT shield or adsorb DNA, preventing detectable exposure of feed-derived DNA fragments to competent bacteria.

Competence-induced fratricide in streptococci

Competence for natural genetic transformation in Streptococcus pneumoniae is controlled by the extracellular concentration of the competence-stimulating peptide (CSP), an exported peptide pheromone. Upon entering the competent state, pneumococci start transcribing a number of CSP-responsive genes, termed the early and late competence (com) genes. Some of the proteins encoded by these com genes are absolutely required for DNA uptake and transformation, but most of them are dispensable. This finding indicates that the majority of CSP-regulated proteins in S. pneumoniae is involved in processes unrelated to natural genetic transformation. Recently, however, it became clear that the biological role of a few of the dispensable proteins might be linked to the transformation process. Although these proteins are not needed for transformation per se, they constitute a killing mechanism that could be used by competent cells to acquire DNA from non-competent pneumococci. This mechanism, termed fratricide, has so far only been described for pneumococci. In this manuscript, we review evidence that suggests the conservation of fratricide as well as the independent evolution of its genetic control and of its effectors in several species of the genus Streptococcus, and discuss its possible biological significance in relation to natural transformation.

Longer resistance of some DNA traits from BT176 maize to gastric juice from gastrointestinal affected patients

The presence of antibiotic resistance marker genes in genetically engineered plants is one of the most controversial issues related to Genetically Modified Organism (GMO)-containing food, raising concern about the possibility that these markers could increase the pool of antibiotic resistance genes. This study investigates the in vitro survival of genes bla and cryIA(b) of maize Bt176 in human gastric juice samples. Five samples of gastric juice were collected from patients affected by gastro-esophageal reflux or celiac disease and three additional samples were obtained by pH modification with NaHCO3. DNA was extracted from maize Bt176 and incubated with samples of gastric juices at different times. The survival of the target traits (bla gene, whole 1914 bp gene cry1A(b), and its 211 bp fragment) was determined using PCR. The stability of the target genes was an inverse function of their lengths in all the samples. Survival in samples from untreated subjects was below the normal physiological time of gastric digestion. On the contrary, survival time in samples from patients under anti-acid drug treatment or in samples whose pH was modified, resulted strongly increased. Our data indicate the possibility that in particular cases the survival time could be so delayed that, as a consequence, some traits of DNA could reach the intestine. In general, this aspect must be considered for vulnerable consumers (people suffering from gastrointestinal diseases related to altered digestive functionality, physiological problems or drug side-effects) in the risk analysis usually referred to healthy subjects.

Degradation of transgenic DNA from genetically modified soya and maize in human intestinal simulations

The inclusion of genetically modified (GM) foods in the human diet has caused considerable debate. There is concern that the transfer of plant-derived transgenes to the resident intestinal microflora could have safety implications. For these gene transfer events to occur, the nucleic acid would need to survive passage through the gastrointestinal tract. The aim of the present study was to evaluate the rate at which transgenes, contained within GM soya and maize, are degraded in gastric and small bowel simulations. The data showed that 80 % of the transgene in naked GM soya DNA was degraded in the gastric simulations, while no degradation of the transgenes contained within GM soya and maize were observed in these acidic conditions. In the small intestinal simulations, transgenes in naked soya DNA were degraded at a similar rate to the material in the soya protein. After incubation for 30 min, the transgenes remaining in soya protein and naked DNA were 52 (SEM 13·1) % AND 34 (sem 17·5) %, respectively, and at the completion of the experiment (3 h) these values were 5 % and 3 %, respectively. In contrast to the soya transgene, the maize nucleic acid was hydrolysed in the small intestinal simulations in a biphasic process in which approximately 85 % was rapidly degraded, while the rest of the DNA was cleaved at a rate similar to that in the soya material. Guar gum and tannic acid, molecules that are known to inhibit digestive enzymes, did not influence the rate of transgene degradation in soya protein. In contrast guar gum reduced the rate of transgene degradation in naked soya DNA in the initial stages, but the polysaccharide did not influence the amount of nucleic acid remaining at the end of the experiment. Tannic acid reduced the rate of DNA degradation throughout the small bowel simulations, with 21 (sem 5·4) % and 2 (sem 1·8) % of the naked soya DNA remaining in the presence and absence of the phenolic acid, respectively. These data indicate that some transgenes in GM foods may survive passage through the small intestine.

Transgenic maize in the presence of ampicillin modifies the metabolic profile and microbial population structure of bovine rumen fluidin vitro

Recently, transgenic crops have been considered as possible donors of transgenes that could be taken up by micro-organisms under appropriate conditions. In anin vitrorumen simulation system, effects of ampicillin on microbial communities growing either on rumen contents with transgenic maize carrying a gene that confers resistance to ampicillin or its isogenic counterpart as substrates were examined continuously over 13 d. Rate of production of SCFA was measured to determine functional changes in the rumen model and single-strand conformational polymorphism was used to detect alterations in structure of the microbial community. Rumen contents treated with ampicillin displayed a marked decrease in the rate of production of SCFA and diversity of the microbial community was reduced severely. In the presence of transgenic maize, however, the patterns of change of rumen micro-organisms and their metabolic profiles were different from that of rumen fluid incorporating maize bred conventionally. Recovery of propionate production was observed both in the rumen fluid fed transgenic and conventional maize after a delay of several days but recovery occurred earlier in fermenters fed transgenic maize. Alterations in the microbial population structures resulting from the ampicillin challenge were not reversed during the experimental run although there was evidence of adaptation of the microbial communities over time in the presence of the antibiotic, showing that populations with different microbial structures could resume a pre-challenge metabolic profile following the introduction of ampicillin, irrespective of the source of the plant material in the growth medium.

Antimicrobial resistance in Enterococcus spp. and Escherichia coli isolated from poultry feed and feed ingredients

Poultry feed is at the start of the food safety chain in the "farm-to-fork" model, and might serve as a source of antimicrobial resistant bacteria present in poultry meat. Antimicrobial resistance was investigated in 1137 enterococci and 163 Escherichia coli strains recovered from 23 samples of commercial broiler feed and 66 samples of raw feeding materials taken over half a year timespan. Enumeration of enterococci and E. coli were also performed using traditional plating and fluorescent in situ hybridisation methods. Viable enterococci were detected in all feed samples and in 66% of samples of separate feed ingredients, while E. coli was present in 50% and 32% of feed and raw feeding materials, respectively. The median values (50th percentile) for plate and FISH counts for feeds were, respectively, 2.70 log CFU/g and 5.52 log cells/g for enterococci, and 0.15 log CFU/g and 6.00 log cells/g for E. coli. Among enterococci recovered from feed ingredients, resistance to rifampicin, erythromycin, nitrofurantoin, tetracycline, and ciprofloxacin was found in 59.8%, 21.6%, 21.2%, 18.0% and 6.9% of the isolates, respectively. A considerable proportion of the enterococci isolates obtained from broiler feed displayed resistance to tetracycline (69.1%), rifampicin (58.5%), erythromycin (52.9%) and nitrofurantoin (36.2%). Lower percentage of resistance was observed to chloramphenicol (4.6%), ciprofloxacin (3.9%), vancomycin (1.9%) and ampicillin (1.2%). Among E. coli recovered from feed ingredients and poultry feeds, resistance to ampicillin, tetracycline and streptomycin was found in 22.9%, 27.6% and 19.0% and in 22.4%, 41.4% and 17.0% of the isolates, respectively. These data show that feedstuffs and poultry feeds are extensively contaminated by resistant enterococci and, in a lesser extent, by E. coli, thus leading to their introduction in the farm environment.

Leaf-feeding larvae of Manduca sexta (Insecta, Lepidoptera) drastically reduce copy numbers of aadA antibiotic resistance genes from transplastomic tobacco but maintain intact aadA genes in their feces

The objective of this study was to evaluate the effect of insect larval feeding on the fate and genetic transformability of recombinant DNA from a transplastomic plant. Leaves of tobacco plants with an aadA antibiotic resistance gene inserted into their chloroplast genome were incubated with larvae of the tobacco hornworm Manduca sexta (Lepidoptera). The specifically designed Acinetobacter strain BD413 pBAB(2) was chosen to analyze the functional integrity of the aadA transgene for natural transformation after gut passages. No gene transfer was detected after simultaneous feeding of leaves and the Acinetobacter BD413 pBAB(2) as a recipient, even though 15% of ingested Acinetobacter BD413 cells could be recovered as viable cells from feces 6 h after feeding. Results with real-time PCR indicated that an average of 98.2 to 99.99% of the aadA gene was degraded during the gut passage, but the range in the number of aadA genes in feces of larvae fed with transplastomic leaves was enormous, varying from 5 x 10(6) to 1 x 10(9) copies.g(-1). DNA extracted from feces of larvae fed with transplastomic leaves was still able to transform externally added competent Acinetobacter BD413 pBAB(2) in vitro. Transformation frequencies with concentrated feces DNA were in the same range as those found with leaves (10(-4)-10(-6) transformants per recipient) or purified plasmid DNA (10(-3)-10(-7)). The presence of functionally intact DNA was also qualitatively observed after incubation of 30 mg freshly shed feces directly with competent Acinetobacter BD413 pBAB(2), demonstrating that aadA genes in feces have a potential to undergo further horizontal gene transfer under environmental conditions.

Impact environnemental des cultures transgéniques

L’adoption à grande échelle des cultures transgéniques depuis dix ans a soulevé de nombreuses questions quant aux impacts possibles de ces nouvelles lignées végétales sur les écosystèmes agricoles et naturels. Des questions ont été soulevées, en particulier, sur le devenir des transgènes dans le milieu et sur une possible « pollution » du patrimoine génétique des organismes vivants à l’échelle des écosystèmes. Après une énumération des impacts environnementaux associés aux végétaux transgéniques, cet article de synthèse dresse un aperçu des connaissances actuelles sur le devenir – ou la migration – des transgènes dans le milieu. Les phénomènes d’hybridation et d’introgression génique en direction d’espèces ou de lignées apparentées sont d’abord abordés, après quoi sont considérés les phénomènes de transfert horizontal des transgènes en direction d’organismes non apparentés. Un article complémentaire publié dans ce même numéro traite de l’impact environnemental des protéines recombinantes encodées par les transgènes (Michaud 2005).

Genotypic comparison of bacteria recovered from human bite marks and teeth using arbitrarily primed PCR

AIMS

This study assessed, for forensic purposes, the feasibility of genotypically matching oral streptococci recovered from recent human bite marks with those from the teeth of the biter.

METHODS AND RESULTS

Streptococci were isolated from the incisors of eight volunteers. Arbitrarily primed PCR (AP-PCR) distinguished 106 streptococcal genotypes among the participants, each harbouring at least eight distinct strains. In a crime simulation, a sample from an experimental bite mark was analysed by an experimenter unaware of its origin. The bacteria were unambiguously matched to the biter by comparing the amplicon profiles with those from the eight participants. In contrast, bacteria from an additional bite mark (not generated by one of the original participants) could not be matched to any of the eight participants. Between 20 and 78% of catalogued bacterial genotypes were recovered 12 months later from each participant. Throughout the study period, none of the bacterial genotypes were shared between participants.

CONCLUSIONS

Streptococci isolated from recent bite marks can be catalogued by AP-PCR and matched to the teeth responsible for the bite.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study provides 'proof of concept' that genotypic analysis of streptococci from bite marks may provide valuable forensic evidence in situations where the perpetrator's DNA cannot be recovered.

Bt176 corn in poultry nutrition: physiological characteristics and fate of recombinant plant DNA in chickens

A genetically modified Bt176 corn hybrid, which contains an insecticidal protein against the European corn borer, and its conventional, nonmodified counterpart were evaluated in 4 separate trials to verify substantial equivalence in feeding value and animal performance. Thirty-six individually kept laying hens and 3 replicates of 94 broiler chickens each, assigned to 12 cages, were fed 2 different hen and broiler diets containing either 60% conventional or 60% Bt176 corn. The nutrient compositions of the 2 corn hybrids and the 2 corn diets revealed no major differences. Furthermore, metabolism and performance data revealed no significant differences between the birds that received the conventional, nonmodified corn, and those that received the modified corn diets. The detection of the genetic modification, by PCR, in feed obtained from insect-resistant Bt corn, in tissues and products from animals fed Bt corn is described. In all evaluated chicken tissues of muscle, liver, and spleen, the corn-chloroplast ivr gene fragment was amplified. It can be deduced from these findings and from other studies that the transfer of DNA fragments into the body is a normal process that takes place constantly. Nevertheless, no recombinant plant DNA fragments such as recombinant bla or cry1A(b) fragments could be found. Bt-gene specific constructs from the Bt corn were not detected in any of the poultry samples, neither in organs, meat, nor eggs.

Experimental methods for assaying natural transformation and inferring horizontal gene transfer

The observation of frequent lateral acquisitions of genes in sequenced bacterial genomes has spurred experimental investigations to elucidate the factors governing ongoing gene transfer processes in bacteria. The uptake of naked DNA by natural transformation is known to occur in a wide range of bacterial species and in some archaea. We describe a series of protocols designed to dissect the natural genetic transformability of individual bacterial strains under conditions that progress from standard in vitro conditions to purely in situ, or natural, conditions. One of the most important factors in ensuring the success of any transformation assay system is the use of a sensitive, effective, and distinguishable selection regimen. Detailed template protocols for assaying bacterial transformation in vitro are presented using the naturally competent bacterium Acinetobacter baylyi strain BD413 as a model. Factors increasing the complexity of the assay systems are included in the following section describing the incorporation of components of natural systems to the in vitro models, such as in soil and water microcosm experiments. We then present template protocols for the transformation of bacteria in modified natural systems, such as in the presence of host tissues and extracts or in the greenhouse. Clear and ecologically meaningful demonstrations of in situ natural transformation are most desirable but are also the most complex and challenging. Because of the highly variable nature of these experiments, we include a discussion of important factors that should be considered when designing such experiments. Some advantages and disadvantages of the experimental systems with regard to resolving the hypotheses tested are included in each section.

The relevance of gene transfer to the safety of food and feed derived from genetically modified (GM) plants

In 2000, the thematic network ENTRANSFOOD was launched to assess four different topics that are all related to the testing or assessment of food containing or produced from genetically modified organisms (GMOs). Each of the topics was linked to a European Commission (EC)-funded large shared cost action (see http://www.entransfood.com). Since the exchange of genetic information through horizontal (lateral) gene transfer (HGT) might play a more important role, in quantity and quality, than hitherto imagined, a working group dealing with HGT in the context of food and feed safety was established. This working group was linked to the GMOBILITY project (GMOBILITY, 2003) and the results of the deliberations are laid down in this review paper. HGT is reviewed in relation to the potential risks of consuming food or feed derived from transgenic crops. First, the mechanisms for obtaining transgenic crops are described. Next, HGT mechanisms and its possible evolutionary role are described. The use of marker genes is presented in detail as a special case for genes that may pose a risk. Furthermore, the exposure to GMOs and in particular to genetically modified (GM) deoxyribonucleic acid (DNA) is discussed as part of the total risk assessment. The review finishes off with a number of conclusions related to GM food and feed safety. The aim of this paper is to provide a comprehensive overview to assist risk assessors as well as regulators and the general public in understanding the safety issues related to these mechanisms.

Persistence of DNA studied in different ex vivo and in vivo rat models simulating the human gut situation

This study aimed to evaluate the possibility of DNA sequences from genetically modified plants to persist in the gastrointestinal (GI) tract. PCR analysis and transformation assays were used to study DNA persistence and integrity in various ex vivo and in vivo systems using gnotobiotic rats. DNA studied was either plasmid DNA, naked plant DNA or plant DNA embedded in maize flour. Ex vivo experiments performed by incubating plant DNA in intestinal samples, showed that DNA is rapidly degraded in the upper part of the GI tract whereas degradation is less severe in the lower part. In contrast, plasmid DNA could be recovered throughout the GI tract when intestinal samples were taken up to 5 h after feeding rats with plasmid. Furthermore, DNA isolated from these intestinal samples was able to transform electro-competent Escherichia coli, showing that the plasmid was still biologically active. The results indicate that ingested DNA may persist in the GI tract and consequently may be present for uptake by intestinal bacteria.

Marker rescue studies of the transfer of recombinant DNA to Streptococcus gordonii in vitro, in foods and gnotobiotic rats

A plasmid marker rescue system based on restoration of the nptII gene was established in Streptococcus gordonii to study the transfer of bacterial and transgenic plant DNA by transformation. In vitro studies revealed that the marker rescue efficiency depends on the type of donor DNA. Plasmid and chromosomal DNA of bacteria as well as DNA of transgenic potatoes were transferred with efficiencies ranging from 8.1 x 10(-6) to 5.8 x 10(-7) transformants per nptII gene. Using a 792-bp amplification product of nptII the efficiency was strongly decreased (9.8 x 10(-9)). In blood sausage, marker rescue using plasmid DNA was detectable (7.9 x 10(-10)), whereas in milk heat-inactivated horse serum (HHS) had to be added to obtain an efficiency of 2.7 x 10(-11). No marker rescue was detected in extracts of transgenic potatoes despite addition of HHS. In vivo transformation of S. gordonii LTH 5597 was studied in monoassociated rats by using plasmid DNA. No marker rescue could be detected in vivo, although transformation was detected in the presence of saliva and fecal samples supplemented with HHS. It was also shown that plasmid DNA persists in rat saliva permitting transformation for up to 6 h of incubation. It is suggested that the lack of marker rescue is due to the absence of competence-stimulating factors such as serum proteins in rat saliva.

Assessing the survival of transgenic plant DNA in the human gastrointestinal tract

The inclusion of genetically modified (GM) plants in the human diet has raised concerns about the possible transfer of transgenes from GM plants to intestinal microflora and enterocytes. The persistence in the human gut of DNA from dietary GM plants is unknown. Here we study the survival of the transgene epsps from GM soya in the small intestine of human ileostomists (i.e., individuals in which the terminal ileum is resected and digesta are diverted from the body via a stoma to a colostomy bag). The amount of transgene that survived passage through the small bowel varied among individuals, with a maximum of 3.7% recovered at the stoma of one individual. The transgene did not survive passage through the intact gastrointestinal tract of human subjects fed GM soya. Three of seven ileostomists showed evidence of low-frequency gene transfer from GM soya to the microflora of the small bowel before their involvement in these experiments. As this low level of epsps in the intestinal microflora did not increase after consumption of the meal containing GM soya, we conclude that gene transfer did not occur during the feeding experiment.