Worst-case scenarios for horizontal gene transfer from Lactococcus lactis carrying heterologous genes to Enterococcus faecalis in the digestive tract of gnotobiotic mice

Increased antibiotic resistance gene abundance linked to intensive bacterial competition in the phyllosphere across an elevational gradient

Antibiotic resistance genes (ARGs) are ancient and widespread in natural habitats, providing survival advantages for microbiomes under challenging conditions. In mountain ecosystems, phyllosphere bacterial communities face multiple stress conditions, and the elevational gradients of mountains represent crucial environmental gradients for studying biodiversity distribution patterns. However, the distribution patterns of ARGs in the phyllosphere along elevational gradients, and their correlation with bacterial community structures, remain poorly understood. Here, we applied metagenomic analyses to investigate the abundance and diversity of ARGs in 88 phyllosphere samples collected from Mount Tianmu, a national natural reserve. Our results showed that the abundance of ARGs in the phyllosphere increased along elevational gradients and was dominated by multidrug resistance and efflux pumps. The composition of bacterial communities, rather than plant traits or abiotic factors, significantly affected ARG abundance. Moreover, increased ARG abundance was correlated with greater phylogenetic overdispersion and a greater proportion of negative associations in the bacterial co-occurrence networks, suggesting that bacterial competition primarily shapes phyllosphere resistomes. These findings constitute a major advance in the biodiversity of phyllosphere resistomes along elevations, emphasizing the significant impact of bacterial community structure and assembly on ARG distribution, and are essential for understanding the emergence of ARGs.

Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives

The emergence of antimicrobial resistant bacteria constitutes an increasing global health concern. Although it is well recognized that the cornerstone underlying this phenomenon is the dissemination of antimicrobial resistance via plasmids and other mobile genetic elements, the antimicrobial resistance transfer routes remain largely uncharted. In this review, we describe different methods for assessing the transfer frequency and host ranges of plasmids within complex microbiomes. The discussion is centered around the critical evaluation of recent advances for monitoring the fate of fluorescently tagged plasmids in bacterial communities through the coupling of fluorescence activated cell sorting and next generation sequencing techniques. We argue that this approach constitutes an exceptional tool for obtaining quantitative data regarding the extent of plasmid transfer, key disseminating taxa, and possible propagation routes. The integration of this information will provide valuable insights on how to develop alternative avenues for fighting the rise of antimicrobial resistant pathogens, as well as the means for constructing more comprehensive risk assessment models.

Contribution of plasmid-encoded peptidase S8 (PrtP) to adhesion and transit in the gut of Lactococcus lactis IBB477 strain

The ability of Lactococcus lactis to adhere to the intestinal mucosa can potentially prolong the contact with the host, and therefore favour its persistence in the gut. In the present study, the contribution of plasmid-encoded factors to the adhesive and transit properties of the L. lactis subsp. cremoris IBB477 strain was investigated. Plasmid-cured derivatives as well as deletion mutants were obtained and analysed. Adhesion tests were performed using non-coated polystyrene plates, plates coated with mucin or fibronectin and mucus-secreting HT29-MTX intestinal epithelial cells. The results indicate that two plasmids, pIBB477a and b, are involved in adhesion of the IBB477 strain. One of the genes localised on plasmid pIBB477b (AJ89_14230), which encodes cell wall-associated peptidase S8 (PrtP), mediates adhesion of the IBB477 strain to bare, mucin- and fibronectin-coated polystyrene, as well as to HT29-MTX cells. Interactions between bacteria and mucus secreted by HT29-MTX cells were further investigated by fluorescent staining and confocal microscopy. Confocal images showed that IBB477 forms dense clusters embedded in secreted mucus. Finally, the ability of IBB477 strain and its ΔprtP deletion mutant to colonise the gastrointestinal tract of conventional C57Bl/6 mice was determined. Both strains were present in the gut for up to 72 h. In summary, adhesion and persistence of IBB477 were analysed by in vitro and in vivo approaches, respectively. Our studies revealed that plasmidic genes encoding cell surface proteins are more involved in the adhesion of IBB477 strain than in the ability to confer a selective advantage in the gut.

Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances

The human microbiome is overly exposed to antibiotics, due, not only to their medical use, but also to their utilization in farm animals and crops. Microbiome composition can be rapidly altered by exposure to antibiotics, with potential immediate effects on health, for instance through the selection of resistant opportunistic pathogens that can cause acute disease. Microbiome alterations induced by antibiotics can also indirectly affect health in the long-term. The mutualistic microbes in the human body interact with many physiological processes, and participate in the regulation of immune and metabolic homeostasis. Therefore, antibiotic exposure can alter many basic physiological equilibria, promoting long-term disease. In addition, excessive antibiotic use fosters bacterial resistance, and the overly exposed human microbiome has become a significant reservoir of resistance genes, contributing to the increasing difficulty in controlling bacterial infections. Here, the complex relationships between antibiotics and the human microbiome are reviewed, with focus on the intestinal microbiota, addressing (1) the effects of antibiotic use on the composition and function of the gut microbiota, (2) the impact of antibiotic-induced microbiota alterations on immunity, metabolism, and health, and (3) the role of the gut microbiota as a reservoir of antibiotic resistances.

Construction and characterization of Enterococcus faecalis CG110/gfp/pRE25*, a tool for monitoring horizontal gene transfer in complex microbial ecosystems

Enterococci are among the most notorious bacteria involved in the spread of antibiotic resistance (ABR) determinants via horizontal gene transfer, a process that leads to increased prevalence of antibiotic-resistant bacteria. In complex microbial communities with a high background of ABR genes, detection of gene transfer is possible only when the ABR determinant is marked. Therefore, the conjugative multiresistance plasmid pRE25, originating from a sausage-associated Enterococcus faecalis, was tagged with a 34-bp random sequence marker spliced by tet(M). The plasmid constructed, designated pRE25(*) , was introduced into E. faecalis CG110/gfp, a strain containing a gfp gene as chromosomal marker. The plasmid pRE25(*) is fully functional compared with its parental pRE25, occurs at one to two copies per chromosome, and can be transferred to Listeria monocytogenes and Listeria innocua at frequencies of 6 × 10(-6) to 8 × 10(-8) transconjugants per donor. The markers on the chromosome and the plasmid enable independent quantification of donor and plasmid, even if ABR genes occur at high numbers in the background ecosystem. Both markers were stable for at least 200 generations, permitting application of the strain in long-running experiments. Enterococcus faecalis CG110/gfp/pRE25(*) is a potent tool for the investigation of horizontal ABR gene transfer in complex environments such as food matrices, biofilms or colonic models.

Molecular investigation of macrolide and Tetracycline resistances in oral bacteria isolated from Tunisian children

OBJECTIVE

This study aims to investigate the antibiotic susceptibility of strains isolated from the oral cavity of Tunisian children.

DESIGN

Strains were isolated from the oral cavity of Tunisian children (60 caries-actives and 30 caries-free). Molecular characterization was assessed by PCR assay to detect erythromycin methylase gene (ermB), macrolide efflux (mefI) and tetracycline resistance genes (tetM and tetO).

RESULTS

A total of 21 species were isolated and identified. Antimicrobial susceptibility revealed that the resistance rate to antibiotics was as follow: erythromycin (22%), tetracycline (15.6%), cefotaxim, (7.3%), trimethoprim-sulfamethoxazol (37.6%), nitrofurantoine (2.8%), pristinamycin (17.4%), quinupristin-dalfopristin (15.6%), and rifampicin (3.7%). The majority of mefI positive strains (31.2%) were isolated from the carious children (n=34) in comparison with 8.25% from the control group (n=9). In addition, frequency of strains caring resistance genes were as follow: 12.84% for ermB, 9.17% for tetM and 27.52% for tetO from the carious children in comparison to 0.092%, 3.67% and 3.67% from the caries free group respectively.

CONCLUSION

Multi-resistance strains towards macrolides and tetracycline were recorded. The majority of strains carrying antibiotics resistance genes were isolated from the caries active children. The presence of multi-resistant bacteria in the oral cavity can be the major cause of antibiotic prophylaxis failure in dental practise.

Transfer of antibiotic resistance by transformation with eDNA within oral biofilms

We demonstrate that live donor Veillonella dispar cells can transfer the conjugative transposon Tn916 to four different Streptococcus spp. recipients in a multispecies oral consortium growing as a biofilm in a constant depth film fermentor. Additionally, we demonstrate that purified V. dispar DNA can transform Streptococcus mitis to tetracycline resistance in this experimental system. These data show that transfer of conjugative transposon-encoded antibiotic resistance can occur by transformation in addition to conjugation in biofilms.

Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA

We have analyzed the total metagenomic DNA from both human oral and fecal samples derived from healthy volunteers from six European countries to determine the molecular basis for tetracycline and erythromycin resistance. We have determined that tet(M) and tet(W) are the most prevalent tetracycline resistance genes assayed for in the oral and fecal metagenomes, respectively. Additionally, tet(Q), tet(O), and tet(O/32/O) have been shown to be common. We have also shown that erm(B), erm(V), and erm(E) are common erythromycin resistance genes present in these environments. Further, we have demonstrated the ubiquitous presence of the Tn916 integrase in the oral metagenomes and the Tn4451 and Tn1549 integrase genes within the fecal metagenomes.

A probiotic Lactobacillus strain can acquire vancomycin resistance during digestive transit in mice

The present study demonstrates for the first time the transfer of vancomycin resistance (vanA cluster) from enterococci to a Lactobacillusacidophilus commercial strain. Transfers were observed in vitro, but also in vivo in the gut of mice (in the absence of antibiotic pressure) where transconjugants arose at relatively high frequencies and could persist in the digestive environment. Since transfer of vancomycin resistance genes might also take place in the human digestive tract, lactobacilli probiotics should be carefully considered especially in either immunocompromised patients or during antibiotherapy. Acquisition and retransfer of resistance genes should be addressed in the safety evaluation of probiotics.

Delivery of therapeutic proteins to the mucosa using genetically modified microflora

Drug delivery through mucosal surfaces offers a panorama of opportunities. The advantages are clear and include safety, ease of administration and higher social acceptance, although the major disadvantages are drug availability and appropriate drug targeting. Most mucosa are well equipped to manage the presence of bacteria and many are actually permanently colonised with a specific microflora. Such microbiota may become attractive tools for the delivery of a specific niche of protein therapeutics. These proteins can be produced from genetically modified microbes that are common to the mucosa, and their delivery to the host tissues has been demonstrated. This concept is being developed for the delivery of proteins to the intestine, but has also been applied in delivery to the vagina, nose and mouth.

Evidence of vancomycin resistance gene transfer between enterococci of human origin in the gut of mice harbouring human microbiota

OBJECTIVES

Potential intra- and inter-species transfers of vancomycin resistance genes (vanA gene cluster) between Enterococcus strains were evaluated in the gut of heteroxenic mice harbouring a human microbiota.

METHODS

Mice colonized with a stable population of E. faecium 64/3 or E. faecalis JH2-2 recipient strain and harbouring an enterococci-free human microbiota were obtained. Donor strain E. faecium HC-VI2 of clinical origin was administered orogastrically to these mice and transfers were evaluated over time in faecal samples.

RESULTS

Only intraspecies transfers were detected in the digestive tract (DT) of mice harbouring a human microbiota. E. faecium 64/3 transconjugants were detected at several sampling times over the 60 day experiment to levels up to 10(3) cfu/g of faeces, but they did not steadily colonize the DT.

CONCLUSIONS

Here, we show for the first time that transfer of the vanA gene cluster can occur between Enterococcus strains in the DT colonized with a human microbiota and in the absence of selective pressure. The colonization properties of other enterococci transconjugants and the influence of vancomycin intake should be further investigated since transfers in the DT of animals and humans might contribute to emergence and dissemination of new vancomycin-resistant bacteria.