Lateral genetic transfer and the construction of genetic exchange communities

What are the missing pieces needed to stop antibiotic resistance?

As recognized by several international agencies, antibiotic resistance is nowadays one of the most relevant problems for human health. While this problem was alleviated with the introduction of new antibiotics into the market in the golden age of antimicrobial discovery, nowadays few antibiotics are in the pipeline. Under these circumstances, a deep understanding on the mechanisms of emergence, evolution and transmission of antibiotic resistance, as well as on the consequences for the bacterial physiology of acquiring resistance is needed to implement novel strategies, beyond the development of new antibiotics or the restriction in the use of current ones, to more efficiently treat infections. There are still several aspects in the field of antibiotic resistance that are not fully understood. In the current article, we make a non-exhaustive critical review of some of them that we consider of special relevance, in the aim of presenting a snapshot of the studies that still need to be done to tackle antibiotic resistance.

Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger (Meles meles)

Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.

Assessment of a plasmid conjugation procedure to monitor horizontal transfer of an extended-spectrum β-lactamase resistance gene under food chain scenarios

Plasmids are relevant reservoirs of antimicrobial resistance genes (ARGs) which confer adaptive advantages to their host and can be horizontally transferred. The aims of this study were to develop a conjugation procedure to monitor the horizontal transfer of a 193 kb plasmid containing the extended-spectrum β-lactamase production gene bla _CTX-M-14 between two Escherichia coli strains under a range of food chain-related scenarios, including temperature (20-37 °C), pH (5.0-9.0) or the presence of some biocidal agents (benzalkonium chloride, sodium hypochlorite or peracetic acid). The average conjugation rate in LB broth after 18 h at 37 °C was 2.09e-04 and similar rates were observed in a food matrix (cow's milk). The conjugation was reduced at temperatures below 37 °C, at alkaline pH (especially at pH 9.0) or in the presence of benzalkonium chloride. Peracetic acid and sodium hypochlorite slightly increased conjugation rates, which reached 5.59e-04 and 6.77e-03, respectively. The conjugation procedure described can be used to identify risk scenarios leading to an enhanced ARGs transmission via plasmid conjugation, as well as to identify novel intervention strategies impairing plasmid conjugation and tackling antimicrobial resistance.

Selfish, promiscuous and sometimes useful: how mobile genetic elements drive horizontal gene transfer in microbial populations

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In general, transfer is costly to the donor cell while potentially beneficial to the recipients. The diversity and plasticity of cell–MGEs interactions, and those among MGEs, result in complex evolutionary processes where the source, or even the existence of selection for maintaining a function in the genome, is often unclear. For example, MGE-driven HGT depends on cell envelope structures and defense systems, but many of these are transferred by MGEs themselves. MGEs can spur periods of intense gene transfer by increasing their own rates of horizontal transmission upon communicating, eavesdropping, or sensing the environment and the host physiology. This may result in high-frequency transfer of host genes unrelated to the MGE. Here, we review how MGEs drive HGT and how their transfer mechanisms, selective pressures and genomic traits affect gene flow, and therefore adaptation, in microbial populations. The encoding of many adaptive niche-defining microbial traits in MGEs means that intragenomic conflicts and alliances between cells and their MGEs are key to microbial functional diversification.

This article is part of a discussion meeting issue ‘Genomic population structures of microbial pathogens’.

DNA binding by pilins and their interaction with the inner membrane platform of the DNA transporter in Thermus thermophilus

The natural transformation system of Thermus thermophilus has become a model system for studies of the structure and function of DNA transporter in thermophilic bacteria. The DNA transporter in T. thermophilus is functionally linked to type IV pili (T4P) and the major pilin PilA4 plays an essential role in both systems. However, T4P are dispensable for natural transformation. In addition to pilA4, T. thermophilus has a gene cluster encoding the three additional pilins PilA1-PilA3; deletion of the cluster abolished natural transformation but retained T4P biogenesis. In this study, we investigated the roles of single pilins PilA1, PilA2 and PilA3 in natural transformation by mutant studies. These studies revealed that each of these pilins is essential for natural transformation. Two of the pilins, PilA1 and PilA2, were found to bind dsDNA. PilA1 and PilA3 were detected in the inner membrane (IM) but not in the outer membrane (OM) whereas PilA2 was present in both membranes. All three pilins where absent in pilus fractions. This suggests that the pilins form a short DNA binding pseudopilus anchored in the IM. PilA1 was found to bind to the IM assembly platform of the DNA transporter via PilM and PilO. These data are in line with the hypothesis that a DNA binding pseudopilus is connected via an IM platform to the cytosolic motor ATPase PilF.

A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria

In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.

Antibiotic Resistance in Wastewater and Its Impact on a Receiving River: A Case Study of WWTP Brno-Modřice, Czech Republic

Antibiotic resistance has become a global threat in which the anthropogenically influenced aquatic environment represents not only a reservoir for the spread of antibiotic resistant bacteria (ARB) among humans and animals but also an environment where resistance genes are introduced into natural microbial ecosystems. Wastewater is one of the sources of antibiotic resistance. The aim of this research was the evaluation of wastewater impact on the spread of antibiotic resistance in the water environment. In this study, qPCR was used to detect antibiotic resistance genes (ARGs)—blaCTX-M-15, blaCTX-M-32, ampC, blaTEM, sul1, tetM and mcr-1 and an integron detection primer (intl1). Detection of antibiotic resistant Escherichia coli was used as a complement to the observed qPCR results. Our results show that the process of wastewater treatment significantly reduces the abundances of ARGs and ARB. Nevertheless, treated wastewater affects the ARGs and ARB number in the receiving river.

Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?

Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model GammaproteobacteriaEscherichia coli and Salmonella, the regulatory RNA chaperone Hfq appears to play a global role in gene regulation, directly controlling ∼20 to 25% of the entire transcriptome. While the model FirmicutesBacillus subtilis and Staphylococcus aureus encode a Hfq homologue, its role has been significantly depreciated. These bacteria also have marked differences in RNA turnover. E. coli and Salmonella degrade RNA through internal endonucleolytic and 3′→5′ exonucleolytic cleavage that appears to allow transient accumulation of mRNA 3′ UTR cleavage fragments that contain stabilizing 3′ structures. In contrast, B. subtilis and S. aureus are able to exonucleolytically attack internally cleaved RNA from both the 5′ and 3′ ends, efficiently degrading mRNA 3′ UTR fragments. Here, we propose that the lack of 5′→3′ exoribonuclease activity in Gammaproteobacteria has allowed the accumulation of mRNA 3′ UTR ends as the “default” setting. This in turn may have provided a larger pool of unconstrained RNA sequences that has fueled the expansion of Hfq function and small RNA (sRNA) regulation in E. coli and Salmonella. Conversely, the exoribonuclease RNase J may be a significant barrier to the evolution of 3′ UTR sRNAs in B. subtilis and S. aureus that has limited the pool of RNA ligands available to Hfq and other sRNA chaperones, depreciating their function in these model Firmicutes.

Antibiotic resistance: Time of synthesis in a post-genomic age

Antibiotic resistance has been highlighted by international organizations, including World Health Organization, World Bank and United Nations, as one of the most relevant global health problems. Classical approaches to study this problem have focused in infected humans, mainly at hospitals. Nevertheless, antibiotic resistance can expand through different ecosystems and geographical allocations, hence constituting a One-Health, Global-Health problem, requiring specific integrative analytic tools. Antibiotic resistance evolution and transmission are multilayer, hierarchically organized processes with several elements (from genes to the whole microbiome) involved. However, their study has been traditionally gene-centric, each element independently studied. The development of robust-economically affordable whole genome sequencing approaches, as well as other -omic techniques as transcriptomics and proteomics, is changing this panorama. These technologies allow the description of a system, either a cell or a microbiome as a whole, overcoming the problems associated with gene-centric approaches. We are currently at the time of combining the information derived from -omic studies to have a more holistic view of the evolution and spread of antibiotic resistance. This synthesis process requires the accurate integration of -omic information into computational models that serve to analyse the causes and the consequences of acquiring AR, fed by curated databases capable of identifying the elements involved in the acquisition of resistance. In this review, we analyse the capacities and drawbacks of the tools that are currently in use for the global analysis of AR, aiming to identify the more useful targets for effective corrective interventions.

Plasmid-Mediated Ampicillin, Quinolone, and Heavy Metal Co-Resistance among ESBL-Producing Isolates from the Yamuna River, New Delhi, India

Antibiotic resistance is one of the major current global health crises. Because of increasing contamination with antimicrobials, pesticides, and heavy metals, the aquatic environment has become a hotspot for emergence, maintenance, and dissemination of antibiotic and heavy metal resistance genes among bacteria. The aim of the present study was to determine the co-resistance to quinolones, ampicillin, and heavy metals among the bacterial isolates harboring extended-spectrum β-lactamases (ESBLs) genes. Among 73 bacterial strains isolated from a highly polluted stretch of the Yamuna River in Delhi, those carrying blaCTX-M, blaTEM, or blaSHV genes were analyzed to detect the genetic determinants of resistance to quinolones, ampicillin, mercury, and arsenic. The plasmid-mediated quinolone resistance (PMQR) gene qnrS was found in 22 isolates; however, the qnrA, B, C, and qnrD genes could not be detected in any of the bacteria. Two variants of CMY, blaCMY-2 and blaCMY-42, were identified among eight and seven strains, respectively. Furthermore, merB, merP, merT, and arsC genes were detected in 40, 40, 44, and 24 bacterial strains, respectively. Co-transfer of different resistance genes was also investigated in a transconjugation experiment. Successful transconjugants had antibiotic and heavy metal resistance genes with similar tolerance toward antibiotics and heavy metals as did their donors. This study indicates that the aquatic environment is a major reservoir of bacteria harboring resistance genes to antibiotics and heavy metals and emphasizes the need to study the genetic basis of resistant microorganisms and their public health implications.

Antibiotic Resistance: Moving From Individual Health Norms to Social Norms in One Health and Global Health

Antibiotic resistance is a problem for human health, and consequently, its study had been traditionally focused toward its impact for the success of treating human infections in individual patients (individual health). Nevertheless, antibiotic-resistant bacteria and antibiotic resistance genes are not confined only to the infected patients. It is now generally accepted that the problem goes beyond humans, hospitals, or long-term facility settings and that it should be considered simultaneously in human-connected animals, farms, food, water, and natural ecosystems. In this regard, the health of humans, animals, and local antibiotic-resistance-polluted environments should influence the health of the whole interconnected local ecosystem (One Health). In addition, antibiotic resistance is also a global problem; any resistant microorganism (and its antibiotic resistance genes) could be distributed worldwide. Consequently, antibiotic resistance is a pandemic that requires Global Health solutions. Social norms, imposing individual and group behavior that favor global human health and in accordance with the increasingly collective awareness of the lack of human alienation from nature, will positively influence these solutions. In this regard, the problem of antibiotic resistance should be understood within the framework of socioeconomic and ecological efforts to ensure the sustainability of human development and the associated human-natural ecosystem interactions.

Molecular Serotyping and Antibiotic Resistance Patterns of Escherichia coli Isolated in Hospital Catering Service in Morocco

Escherichia coli is related to foodborne disease and outbreaks worldwide. It mainly affects persons at high risk as newborns, infants, and individuals with impaired immune system in hospitals. Multidrug-resistant E. coli is currently spreading both in community and hospital settings. Our study aims to evaluate the presence of E. coli and the incidence of its antibiotic resistance in samples obtained from various cooked and raw foods (N = 300), food contact surfaces (N = 238), and food handlers (N = 40) in Moroccan hospital catering service. E. coli was identified using API 20E, and the antibiotic resistance patterns were obtained using the agar disk diffusion methods. However, PCR method was used for O157 and H7 typing. The samples analysis showed that 14.33%, 24.16%, and 45% of food, surfaces, and food handlers harbored E. coli, respectively, with the highest rates obtained in raw meats (34.88%) and salads (34.88%). Molecular amplification shows that 14 E. coli isolates carried the flagellar antigen H7, while there are no isolates showing amplification for O157. The high rate of resistance was noted against ampicillin (100%), amoxicillin-clavulanate acid (100%), nalidixic acid (61.62%), and cefotaxime (59.49%), and isolates obtained from food handler's hands showed the highest rates of resistance. None of the isolates are extended-spectrum beta-lactamases producing, while 27.7% of the isolates were metallo-beta-lactams producing. This first study conducted on Moroccan hospital catering services may draw the authorities' attention to the necessity of setting up a surveillance system to monitor the food preparation process and the safety of prepared food in healthcare settings.

Advances in optical mapping for genomic research

Recent advances in optical mapping have allowed the construction of improved genome assemblies with greater contiguity. Optical mapping also enables genome comparison and identification of large-scale structural variations. Association of these large-scale genomic features with biological functions is an important goal in plant and animal breeding and in medical research. Optical mapping has also been used in microbiology and still plays an important role in strain typing and epidemiological studies. Here, we review the development of optical mapping in recent decades to illustrate its importance in genomic research. We detail its applications and algorithms to show its specific advantages. Finally, we discuss the challenges required to facilitate the optimization of optical mapping and improve its future development and application.

Antibiotic Resistance and Epigenetics: More to It than Meets the Eye

The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.

Screening of Metal and Antibiotic Resistance in Beta-lactamase Producing Coliform Bacteria from Hospital Wastewater of Northern India

AIMS

Our exploration work has uncovered the different anti-toxin/metal tolerance and patterns against the heavy metal resistant coliform microscopic organisms from the aquatic waste of the hospital. It might give new routes for the treatment of irresistible ailments particularly by coliform and critical for hazard evaluation as well as hazard management associated with the effluents of the hospital.

BACKGROUND

The higher use of pharmaceuticals, Radionuclides, and other antimicrobial solvents are the major source of metals in hospital wastewater. The hospital aquatic environment has a high content of both organic and inorganic matter with living organisms. Bacteria can resist an antimicrobial agent by producing extracellular enzymes that eliminate antibiotics and metal toxicity. In this study, we covered the existing patent literature in this area. New patents in the areas of topically applied antibiotics and agents that can potentiate the achievement of existing antibiotics may extend their helpful lifetime.

METHODS

Samples were collected from three different Departments of King George Medical University, Lucknow during the month of December to May (2015-16). Isolation and metal tolerance of coliform isolates were done on metal amended plates. The antibiotic sensitivity test was done by disc diffusion method. The plasmid DNA of bacterial isolates was done by the alkaline lysis method. The conjugation study was also performed in wastewater as well as a nutrient medium.

RESULTS

Maximum isolates demonstrated their MICs at 400, 800 and 1600 μg/ml against all the metals, respectively. The high level of resistance was observed against Methicillin (88.32%, 80.60%) followed by penicillin (75%, 76%), Cephradin (59.52%, 28.84%) and least to Gentamycine (1.92%, 5.76) in E. coli and Enterobacter, respectively. Of 70%, 78% E. coli and Enterobacter isolates produce beta-lactamase activity. Six amino acid residues namely, Glu104, Tyr105, Asn132, Asn170, Ala237, and Gly238 of the beta-lactamase were found in the common interaction with the selected drugs. Plasmid DNA size ranged between 48-58.8 kb. The conjugation experiments showed a higher transfer frequency (5.5×10-1 and 3.6×10-1) rate among antibiotics and metals tested.

CONCLUSION

The finding of this study presents a potential health problem as the predominant coliform species have increasingly been associated with outbreaks of hospital infections. It is recommended that hospital waste must be properly treated before its release into the environment.

Networks Consolidate the Core Concepts of Evolution by Natural Selection

Microbiology has unraveled rich evidence of ongoing reticulate evolutionary processes and complex interactions both within and between cells. These phenomena feature real biological networks, which can logically be analyzed using network-based tools. It is thus not surprising that network sciences, a field independent from evolutionary biology and microbiology, have recently pervasively infused their methods into both fields. Importantly, network tools bring forward observations enhancing the understanding of three core evolutionary concepts: variation, fitness, and heredity. Consequently, our work shows how network sciences can enhance evolutionary theory by explaining the evolution by natural selection of a broad diversity of units of selection, while updating the popular figure of Darwin's tree of life with a comprehensive sketch of the networks of evolution.

Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance

Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.

TcpA, a novel Yersinia ruckeri TIR-containing virulent protein mediates immune evasion by targeting MyD88 adaptors

TIR domain-containing protein is an important member for some bacterial pathogens to subvert host defenses. Here we described a fish virulent Yersinia ruckeri SC09 strain that interfered directly with Toll-like receptor (TLR) function by a TIR-containing protein. Firstly, the novel TIR-containing protein was identified by bioinformatics analysis and named as TcpA. Secondly, the toxic effects of TcpA in fish was demonstrated in vivo challenge experiments through knockout mutant and complement mutant of tcpA gene. Thirdly, The study in vitro revealed that TcpA could down-regulate the expression and secretion of IL-6, IL-1β and TNF-α. Finally, we demonstrated that TcpA could inhibit the TLR signaling pathway through interaction with myeloid differentiation factor 88 (MyD88) in experiments such as NF-κB dependent luciferase reporter system, co-immunoprecipitation, GST pull-down and yeast two-hybrid. The study revealed that TcpA was essential for virulence and was able to interact with the TIR adaptor protein MyD88 and inhibit the pre-inflammatory signal of immune cells and promote the intracellular survival of pathogenic Yersinia ruckeri SC09 strain. In conclusion, our results showed that TcpA acted as a new virulence factor in Y. ruckeri could suppress innate immune response and increase virulence by inhibiting TLR and MyD88-mediated specific signaling, highlighting a novel strategy for innate immune evasion in bacteria.

Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands

Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.

Horizontal Gene Transfer and Its Association with Antibiotic Resistance in the Genus Aeromonas spp

The evolution of multidrug resistant bacteria to the most diverse antimicrobials known so far pose a serious problem to global public health. Currently, microorganisms that develop resistant phenotypes to multiple drugs are associated with high morbidity and mortality. This resistance is encoded by a group of genes termed ‘bacterial resistome’, divided in intrinsic and extrinsic resistome. The first one refers to the resistance displayed on an organism without previous exposure to an antibiotic not involving horizontal genetic transfer, and it can be acquired via mutations. The latter, on the contrary, is acquired exclusively via horizontal genetic transfer involving mobile genetic elements that constitute the ‘bacterial mobilome’. This transfer is mediated by three different mechanisms: transduction, transformation, and conjugation. Recently, a problem of public health due to implications in the emergence of multi-drug resistance in Aeromonas spp. strains in water environments has been described. This is derived from the genetic material transfer via conjugation events. This is important, since bacteria that have acquired antibiotic resistance in natural environments can cause infections derived from their ingestion or direct contact with open wounds or mucosal tissue, which in turn, by their resistant nature, makes their eradication complex. Implications of the emergence of resistance in Aeromonas spp. by horizontal gene transfer on public health are discussed.

A Yersinia ruckeri TIR Domain-Containing Protein (STIR-2) Mediates Immune Evasion by Targeting the MyD88 Adaptor

TIR domain-containing proteins are essential for bacterial pathogens to subvert host defenses. This study describes a fish pathogen, Yersinia ruckeri SC09 strain, with a novel TIR domain-containing protein (STIR-2) that affects Toll-like receptor (TLR) function. STIR-2 was identified in Y. ruckeri by bioinformatics analysis. The toxic effects of this gene on fish were determined by in vivo challenge experiments in knockout mutants and complement mutants of the stir-2 gene. In vitro, STIR-2 downregulated the expression and secretion of IL-6, IL-1β, and TNF-α. Furthermore, the results of NF-κB-dependent luciferase reporter system, co-immunoprecipitation, GST pull-down assays, and yeast two-hybrid assay indicated that STIR-2 inhibited the TLR signaling pathway by interacting with myeloid differentiation factor 88 (MyD88). In addition, STIR-2 promoted the intracellular survival of pathogenic Yersinia ruckeri SC09 strain by binding to the TIR adaptor protein MyD88 and inhibiting the pre-inflammatory signal of immune cells. These results showed that STIR-2 increased virulence in Y. ruckeri and suppressed the innate immune response by inhibiting TLR and MyD88-mediated signaling, serving as a novel strategy for innate immune evasion.

Alignment-free inference of hierarchical and reticulate phylogenomic relationships

We are amidst an ongoing flood of sequence data arising from the application of high-throughput technologies, and a concomitant fundamental revision in our understanding of how genomes evolve individually and within the biosphere. Workflows for phylogenomic inference must accommodate data that are not only much larger than before, but often more error prone and perhaps misassembled, or not assembled in the first place. Moreover, genomes of microbes, viruses and plasmids evolve not only by tree-like descent with modification but also by incorporating stretches of exogenous DNA. Thus, next-generation phylogenomics must address computational scalability while rethinking the nature of orthogroups, the alignment of multiple sequences and the inference and comparison of trees. New phylogenomic workflows have begun to take shape based on so-called alignment-free (AF) approaches. Here, we review the conceptual foundations of AF phylogenetics for the hierarchical (vertical) and reticulate (lateral) components of genome evolution, focusing on methods based on k-mers. We reflect on what seems to be successful, and on where further development is needed.

Dealing with biofilms of Pseudomonas aeruginosa and Staphylococcus aureus: In vitro evaluation of a novel aerosol formulation of silver sulfadiazine

The risk of infection of skin and soft tissue chronic wounds by gram-negative and gram-positive pathogens growing in biofilms is a major health-care concern. In this study we test a formulation of silver sulfadiazine, vitamin A and lidocaine (AF-SSD) for aerosol administration against biofilms of Pseudomonas aeruginosa and biofilms of methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) strains of Staphylococcus aureus. The aerosol allows the administration of AF-SSD without the direct contact with the wound and avoids contamination of the product after reiterative usage. We evaluated in vitro the anti-biofilm activity of AF-SSD by carrying out different technical approaches such as resazurin assays to measure metabolic activity/viability, crystal violet staining assays to determine biofilm biomass, counting of CFUs and live/dead staining for confocal microscopy analysis. AF-SSD clearly affected biofilm viability, biomass and structure, in the three bacterial strains tested. AF-SSD displayed a strong anti-biofilm effect, showing total bactericidal activity on biofilms of P. aeruginosa at a 400-fold dilution of the product, and after a 100-fold and 10-fold dilution for MRSA and MSSA, respectively. Considering the benefits of aerosol administration, our results support this kind of formulation as a potential improvement over conventional treatments with silver sulfadiazine.

Reconsidering plasmid maintenance factors for computational plasmid design

Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

Tracking the Rules of Transmission and Introgression with Networks

Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.

Phylogenetic Clustering of Genes Reveals Shared Evolutionary Trajectories and Putative Gene Functions

Homologous genes in prokaryotes can be described using phylogenetic profiles which summarize their patterns of presence or absence across a set of genomes. Phylogenetic profiles have been used for nearly twenty years to cluster genes based on measures such as the Euclidean distance between profile vectors. However, most approaches do not take into account the phylogenetic relationships amongst the profiled genomes, and overrepresentation of certain taxonomic groups (i.e., pathogenic species with many sequenced representatives) can skew the interpretation of profiles. We propose a new approach that uses a coevolutionary method defined by Pagel to account for the phylogenetic relationships amongst target organisms, and a hierarchical-clustering approach to define sets of genes with common distributions across the organisms. The clusters we obtain using our method show greater evidence of phylogenetic and functional clustering than a recently published approach based on hidden Markov models. Our clustering method identifies sets of amino-acid biosynthesis genes that constitute cohesive pathways, and motility/chemotaxis genes with common histories of descent and lateral gene transfer.

Suspended Materials in River Waters Differentially Enrich Class 1 Integron- and IncP-1 Plasmid-Carrying Bacteria in Sediments

Aquatic ecosystems are frequently considered as the final receiving environments of anthropogenic pollutants such as pharmaceutical residues or antibiotic resistant bacteria, and as a consequence tend to form reservoirs of antibiotic resistance genes. Considering the global threat posed by the antibiotic resistance, the mechanisms involved in both the formation of such reservoirs and their remobilization are a concern of prime importance. Antibiotic resistance genes are strongly associated with mobile genetic elements that are directly involved in their dissemination. Most mobile genetic element-mediated gene transfers involve replicative mechanisms and, as such, localized gene transfers should participate in the local increase in resistance gene abundance. Additionally, the carriage of conjugative mobile elements encoding cell appendages acting as adhesins has already been demonstrated to increase biofilm-forming capability of bacteria and, therefore, should also contribute to their selective enrichment on surfaces. In the present study, we investigated the occurrence of two families of mobile genetic elements, IncP-1 plasmids and class 1 integrons, in the water column and bank sediments of the Orne River, in France. We show that these mobile elements, especially IncP-1 plasmids, are enriched in the bacteria attached on the suspended matters in the river waters, and that a similar abundance is found in freshly deposited sediments. Using the IncP-1 plasmid pB10 as a model, in vitro experiments demonstrated that local enrichment of plasmid-bearing bacteria on artificial surfaces mainly resulted from an increase in bacterial adhesion properties conferred by the plasmid rather than an improved dissemination frequency of the plasmid between surface-attached bacteria. We propose plasmid-mediated adhesion to particles to be one of the main contributors in the formation of mobile genetic element-reservoirs in sediments, with adhesion to suspended matter working as a selective enrichment process of antibiotic resistant genes and bacteria.

Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia

Background

The nexus between resistance determinants, plasmid type, and clonality appears to play a crucial role in the dissemination and survival of carbapenem-resistant Klebsiella pneumoniae (CRKP). The incidence of infections involving CRKP in Saudi Arabia is increasing and there is a need for detailed molecular profiling of this pathogen for CRKP surveillance and control.

Methods

The resistance determinants of 71 non-redundant CRKP isolates were investigated by polymerase chain reaction (PCR) and sequencing. Plasmid typing was performed using PCR-based replicon typing and the clonality of isolates was determined by multilocus sequence typing. Capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex PCR. Diversity was calculated using DIVEIN, clonal relationship was determined using eBURST, and phylogenetic analysis was performed using SplitsTree4.

Results

A polyclonal OXA-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by NDM-1 alone in 9/71 (12.7%) isolates. Coproduction of OXA-48 and NDM-1 was observed in 6/71 (8.5%) isolates. Both carbapenemase genes could be transferred into an Escherichia coli recipient. CTX-M-15 was the most abundant extended-spectrum β-lactamase gene detected in 47/71 (66.2%) isolates, whereas clone-specific CTX-M-14 (ST-199 and -709) was found in 15/71 (21%) isolates. Sixty-seven of 71 isolates were positive for one or more plasmid replicons. The replicons detected were: IncFII; IncFIIK; IncFIA; IncFIB; L/M; IncI1; and IncN. FIIK and L/M were predominant, with 69 and 67% positivity, respectively. All isolates were negative for the magA (K1), rmpA, and K2 genes and presented a non-hypermucoviscous phenotype.

Conclusion

A polyclonal CRKP reservoir of sequence types (STs)-37, − 199, and − 152 was observed and ST-152 appeared to be a “frequent carrier” of the NDM-1 gene. ST-199, a singleton not previously reported, showed a sequence diversity suggestive of positive selection. A significant association was evident between resistance determinants and the clonal types of K. pneumoniae: all ST-152 isolates were positive for NDM-1 but negative for OXA-48; ST-199 isolates were positive for OXA-48 but negative for NDM-1; and ST-709 and -199 isolates were positive for CTX-M-14. The incidence of certain clonal types in large numbers predicts an outbreak-like situation and warrants stringent surveillance and infection control.

Electronic supplementary material

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Invasive Methicillin-Resistant Staphylococcus aureus USA500 Strains from the U.S. Emerging Infections Program Constitute Three Geographically Distinct Lineages

USA500 isolates are clonal complex 8 (CC8) Staphylococcus aureus strains closely related to the prominent community- and hospital-associated USA300 group. Despite being relatively understudied, USA500 strains cause a significant burden of disease and are the third most common methicillin-resistant S. aureus (MRSA) strains identified in the U.S. Emerging Infections Program (EIP) invasive S. aureus surveillance. To better understand the genetic relationships of the strains, we sequenced the genomes of 539 USA500 MRSA isolates from sterile site infections collected through the EIP between 2005 and 2013 in the United States. USA500 isolates fell into three major clades principally separated by their distribution across different U.S. regions. Clade C1 strains, found principally in the Northeast, were associated with multiple IS256 insertion elements in their genomes and higher levels of antibiotic resistance. C2 was associated with Southern states, and E1 was associated with Western states. C1 and C2 strains all shared a frameshift in the gene encoding AdsA surface-attached surface protein. We propose that the term "USA500" should be used for CC8 strains sharing a recent common ancestor with the C1, C2, and E1 strains but not in the USA300 group.IMPORTANCE In this work, we have removed some of the confusion surrounding the use of the name "USA500," placed USA500 strains in the context of the CC8 group, and developed a strategy for assignment to subclades based on genome sequence. Our new phylogeny of USA300/USA500 will be a reference point for understanding the genetic adaptations that have allowed multiple highly virulent clonal strains to emerge from within CC8 over the past 50 years.

Diversity Generator Mechanisms Are Essential Components of Biological Systems: The Two Queen Hypothesis

Diversity is widely known to fuel adaptation and evolutionary processes and increase robustness at the population, species and ecosystem levels. The Neo-Darwinian paradigm proposes that the diversity of biological entities is the consequence of genetic changes arising spontaneously and randomly, without regard for their usefulness. However, a growing body of evidence demonstrates that the evolutionary process has shaped mechanisms, such as horizontal gene transfer mechanisms, meiosis and the adaptive immune system, which has resulted in the regulated generation of diversity among populations. Though their origins are unrelated, these diversity generator (DG) mechanisms share common functional properties. They (i) contribute to the great unpredictability of the composition and/or behavior of biological systems, (ii) favor robustness and collectivism among populations and (iii) operate mainly by manipulating the systems that control the interaction of living beings with their environment. The definition proposed here for DGs is based on these properties and can be used to identify them according to function. Interestingly, prokaryotic DGs appear to be mainly reactive, as they generate diversity in response to environmental stress. They are involved in the widely described Red Queen/arms race/Cairnsian dynamic. The emergence of multicellular organisms harboring K selection traits (longer reproductive life cycle and smaller population size) has led to the acquisition of a new class of DGs that act anticipatively to stress pressures and generate a distinct dynamic called the “White Queen” here. The existence of DGs leads to the view of evolution as a more “intelligent” and Lamarckian-like process. Their repeated selection during evolution could be a neglected example of convergent evolution and suggests that some parts of the evolutionary process are tightly constrained by ecological factors, such as the population size, the generation time and the intensity of selective pressure. The ubiquity of DGs also suggests that regulated auto-generation of diversity is a fundamental property of life.

Stable oligonucleotide-functionalized gold nanosensors for environmental biocontaminant monitoring

The global propagation of environmental biocontaminants such as antibiotic resistant pathogens and their antibiotic resistance genes (ARGs) is a public health concern that highlights the need for improved monitoring strategies. Here, we demonstrate the environmental stability and applicability of an oligonucleotide-functionalized gold nanosensor. The mecA ARG was targeted as model biocontaminant due to its presence in clinically-relevant pathogens and to its emergence as an environmental contaminant. mecA-specific nanosensors were tested for antibiotic resistance gene (ARG) detection in ARG-spiked effluent from four wastewater treatment plants (WWTPs). The mecA-specific nanosensors showed stability in environmental conditions and in high ionic strength ([MgCl₂]<50mM), and high selectivity against mismatched targets. Spectrophotometric detection was reproducible with an LOD of 70pM (≈4×10⁷genes/μL), even in the presence of interferences associated with non-target genomic DNA and complex WWTP effluent. This contribution supports the environmental applicability of a new line of cost-effective, field-deployable tools needed for wide-scale biocontaminant monitoring.

Persistence and reversal of plasmid-mediated antibiotic resistance

In the absence of antibiotic-mediated selection, sensitive bacteria are expected to displace their resistant counterparts if resistance genes are costly. However, many resistance genes persist for long periods in the absence of antibiotics. Horizontal gene transfer (primarily conjugation) could explain this persistence, but it has been suggested that very high conjugation rates would be required. Here, we show that common conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics in Escherichia coli. The notion is applicable to nine plasmids from six major incompatibility groups and mixed populations carrying multiple plasmids. These results suggest that reducing antibiotic use alone is likely insufficient for reversing resistance. Therefore, combining conjugation inhibition and promoting plasmid loss would be an effective strategy to limit conjugation-assisted persistence of antibiotic resistance.

It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.

Characterization of Cefotaxime- and Ciprofloxacin-Resistant Commensal Escherichia coli Originating from Belgian Farm Animals Indicates High Antibiotic Resistance Transfer Rates

Food-producing animals represent one of the sources of antibiotic resistant commensal bacteria. There is an increasing awareness that these bacteria might have the potential to transfer their resistance genes to other (pathogenic) bacteria. In this study, 50 commensal Escherichia coli strains originating from food-producing animals and resistant to the "highest priority, critically important antibiotics" cefotaxime and/or ciprofloxacin, were selected for further characterization. For each strain (i) an antibiogram, (ii) the phylogenetic group, (iii) plasmid replicon type, (iv) presence and identification of integrons, and (v) antibiotic resistance transfer ratios were determined. Forty-five of these strains were resistant to 5 or more antibiotics, and 6 strains were resistant to 10 or more antibiotics. Resistance was most common to ampicillin (100%), sulfamethoxazole, ciprofloxacin (82%), trimethoprim, tetracycline (74%), cefotaxime, (70%) and ceftazidime (62%). Phylogenetic groups A (62%) and B1 (26%) were most common, followed by C (8%) and E (4%). In 43 strains, more than 1 replicon type was detected, with FII (88%), FIB (70%), and I1 (48%) being the most encountered types. Forty strains, positive for integrons, all harbored a class I integron and seven of them contained an additional class II integron. No class III integrons were detected. The antibiotic resistance transfer was assessed by liquid mating experiments. The transfer ratio, expressed as the number of transconjugants per recipient, was between 10^-5 and 10⁰ for cefotaxime resistance and between 10^-7 and 10^-1 for ciprofloxacin resistance. The results of the current study prove that commensal E. coli in food-production animals can be a source of multiple resistance genes and that these bacteria can easily spread their ciprofloxacin and cefotaxime resistance.

What Healthcare Workers Should Know about Environmental Bacterial Contamination in the Intensive Care Unit

Intensive care unit- (ICU-) acquired infections are a major health problem worldwide. Inanimate surfaces and equipment contamination may play a role in cross-transmission of pathogens and subsequent patient colonization or infection. Bacteria contaminate inanimate surfaces and equipment of the patient zone and healthcare area, generating a reservoir of potential pathogens, including multidrug resistant species. Traditional terminal cleaning methods have limitations. Indeed patients who receive a bed from prior patient carrying bacteria are exposed to an increased risk (odds ratio 2.13, 95% confidence intervals 1.62-2.81) of being colonized and potentially infected by the same bacterial species of the previous patient. Biofilm formation, even on dry surfaces, may play a role in reducing the efficacy of terminal cleaning procedures since it enables bacteria to survive in the environment for a long period and provides increased resistance to commonly used disinfectants. No-touch methods (e.g., UV-light, hydrogen peroxide vapour) are under investigation and further studies with patient-centred outcomes are needed, before considering them the standard of terminal cleaning in ICUs. Healthcare workers should be aware of the role of environmental contamination in the ICU and consider it in the broader perspective of infection control measures and stewardship initiatives.

Flipping chromosomes in deep-sea archaea

One of the major mechanisms driving the evolution of all organisms is genomic rearrangement. In hyperthermophilic Archaea of the order Thermococcales, large chromosomal inversions occur so frequently that even closely related genomes are difficult to align. Clearly not resulting from the native homologous recombination machinery, the causative agent of these inversions has remained elusive. We present a model in which genomic inversions are catalyzed by the integrase enzyme encoded by a family of mobile genetic elements. We characterized the integrase from Thermococcus nautili plasmid pTN3 and showed that besides canonical site-specific reactions, it catalyzes low sequence specificity recombination reactions with the same outcome as homologous recombination events on DNA segments as short as 104bp both in vitro and in vivo, in contrast to other known tyrosine recombinases. Through serial culturing, we showed that the integrase-mediated divergence of T. nautili strains occurs at an astonishing rate, with at least four large-scale genomic inversions appearing within 60 generations. Our results and the ubiquitous distribution of pTN3-like integrated elements suggest that a major mechanism of evolution of an entire order of Archaea results from the activity of a selfish mobile genetic element.

Mobile elements (MEs) such as viruses, plasmids and transposons infect most living organisms and often encode recombinases promoting their insertion into cellular genomes. These insertions alter the genome of their host according to two main mechanisms. First, MEs provide new functions to the cell by integrating their own genetic information into the DNA of the host, at one or more locations. Secondly, cellular homologous recombination will act upon multiple integrated copies and produce a variety of large-scale chromosomal rearrangements. If such modifications are advantageous, they will spread into the population by natural selection. Typically, enzymes involved in cellular homologous recombination and the integration of MEs are distinct. We describe here a novel plasmid-encoded archaeal integrase which in addition to site-specific recombination can catalyze low sequence specificity recombination reactions akin to homologous recombination.

Pathogenic Streptococcus strains employ novel escape strategy to inhibit bacteriostatic effect mediated by mammalian peptidoglycan recognition protein

Pathogenic streptococcal species are responsible for some of the most lethal and prevalent animal and human infections. Previous reports have identified a candidate pathogenicity island (PAI) in two highly virulent clinical isolates of Streptococcus suis type 2, a causative agent of high-mortality streptococcal toxic shock syndrome. This PAI contains a type-IVC secretion system C subgroup (type-IVC secretion system) that is involved in the secretion of unknown pathogenic effectors that are responsible for streptococcal toxic shock syndrome caused by highly virulent strains of S. suis. Both virulence protein B4 and virulence protein D4 were demonstrated to be key components of this type-IVC secretion system. In this study, we identify a new PAI family across 3 streptococcal species; Streptococcus genomic island contains type-IV secretion system, which contains a genomic island type-IVC secretion system and a novel PPIase molecule, SP1. SP1 is shown to interact with a component of innate immunity, peptidoglycan recognition protein (PGLYRP-1) and to perturb the PGLYRP-1-mediated bacteriostatic effect by interacting with protein PGLYRP-1. Our study elucidates a novel mechanism by which bacteria escape by components of the innate immune system by secretion of the SP1 protein in pathogenic Streptococci, which then interacts with PGLYRP-1 from the host. Our results provide potential targets for the development of new antimicrobial drugs against bacteria with resistance to innate host immunity.

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF

Bacteria and archaea can exchange genetic material across lineages through processes of lateral genetic transfer (LGT). Collectively, these exchange relationships can be modeled as a network and analyzed using concepts from graph theory. In particular, densely connected regions within an LGT network have been defined as genetic exchange communities (GECs). However, it has been problematic to construct networks in which edges solely represent LGT. Here we apply term frequency-inverse document frequency (TF-IDF), an alignment-free method originating from document analysis, to infer regions of lateral origin in bacterial genomes. We examine four empirical datasets of different size (number of genomes) and phyletic breadth, varying a key parameter (word length k) within bounds established in previous work. We map the inferred lateral regions to genes in recipient genomes, and construct networks in which the nodes are groups of genomes, and the edges natively represent LGT. We then extract maximum and maximal cliques (i.e., GECs) from these graphs, and identify nodes that belong to GECs across a wide range of k. Most surviving lateral transfer has happened within these GECs. Using Gene Ontology enrichment tests we demonstrate that biological processes associated with metabolism, regulation and transport are often over-represented among the genes affected by LGT within these communities. These enrichments are largely robust to change of k.

The influence of the autochthonous wastewater microbiota and gene host on the fate of invasive antibiotic resistance genes

The aim of this study was to assess the fate of invasive antibiotic resistance genes (ARG) discharged in wastewater. With this objective, antibiotic resistant bacteria (ARB) known to harbor specific ARG were inoculated in wastewater (hospital effluent, or municipal raw and treated wastewater) and in ultra-pure sterile water microcosms. Two sets of wastewater ARB isolates were used - set 1, Enterococcus faecalis, Acinetobacter johnsonii, Klebsiella pneumoniae and set 2, Enterococcus faecium, Acinetobacter johnsonii, Escherichia coli. Non-inoculated controls were run in parallel. Samples were collected at the beginning and at the end (15days) of the incubation period and the abundance of the genes 16S rRNA, intI1, bla_TEM and vanA and the bacterial community composition were analyzed. In general, the genes bla_TEM and vanA had lower persistence in wastewater and in ultra-pure water than the genes 16S rRNA or the class 1 integron integrase intI1. This effect was more pronounced in wastewater than in ultra-pure water, evidencing the importance of the autochthonous microbiota on the elimination of invasive ARG. Wastewater autochthonous bacterial groups most correlated with variations of the genes intI1, bla_TEM and vanA were members of the classes Gammaproteobacteria, Bacilli or Bacteroidia. For bla_TEM, but not for vanA, the species of the ARB host was important to determine its fate. These are novel findings on the ecology of ARB in wastewater environments.

Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events

Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable "microbial dark matter." Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat.This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.

Plasmid transfer in biofilms: a perspective on limitations and opportunities

Biofilms dominate microbial life, and their importance for human health and the environment can no longer be dismissed. Nevertheless many of the processes governing this form of microbial growth are still poorly understood. This includes the horizontal exchange of genetic information, which is a major driver in bacterial evolution and rapid adaptation, exemplified by the alarming spread of multi-drug resistance among pathogens mediated by plasmids. Biofilms are often considered hot spot for horizontal gene transfer, yet several studies have shown that plasmid transfer is limited to the outer layers. On the basis of results from decades of research we analyse this paradox and discuss the mechanisms by which biofilm growth can promote the initial transfer of some plasmids, but also limit further plasmid invasion into the population or community. If we want to adequately promote or combat horizontal gene spread in biofilms, we need to gain better insight into the physicochemical and biological mechanisms that control this process.

Close ecological relationship among species facilitated horizontal transfer of retrotransposons

Background

Horizontal transfer (HT) of genetic materials is increasingly being found in both animals and plants and mainly concerns transposable elements (TEs). Many crustaceans have big genome sizes and are thus likely to harbor high TE contents. Their habitat might offer them ample opportunities to exchange genetic materials with organisms that are ecologically close but taxonomically distant to them.

Results

In this study, we analyzed the transcriptome of Pacific white shrimp (Litopenaeus vannamei), an important economic crustacean, to explore traces of HT events. From a collection of newly assembled transcripts, we identified 395 high reliable TE transcripts, most of which were retrotransposon transcripts. One hundred fifty-seven of those transcripts showed highest similarity to sequences from non-arthropod organisms, including ray-finned fishes, mollusks and putative parasites. In total, 16 already known L. vannamei TE families are likely to be involved in horizontal transfer events. Phylogenetic analyses of 10 L. vannamei TE families and their homologues (protein sequences) revealed that L. vannamei TE families were generally more close to sequences from aquatic species. Furthermore, TEs from other aquatic species also tend to group together, although they are often distantly related in taxonomy. Sequences from parasites and microorganisms were also widely present, indicating their possible important roles in HT events. Expression profile analyses of transcripts in two NCBI BioProjects revealed that transcripts involved in HT events are likely to play important roles in antiviral immunity. More specifically, those transcripts might act as inhibitors of antiviral immunity.

Conclusions

Close ecological relationship, especially predation, might greatly facilitate HT events among aquatic species. This could be achieved through exchange of parasites and microorganisms, or through direct DNA flow. The occurrence of HT events may be largely incidental, but the effects could be beneficial for recipients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0767-0) contains supplementary material, which is available to authorized users.

Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics

Horizontal gene transfer (HGT) is a major mechanism responsible for the spread of antibiotic resistance. Conversely, it is often assumed that antibiotics promote HGT. Careful dissection of the literature, however, suggests a lack of conclusive evidence supporting this notion in general. This is largely due to the lack of well-defined quantitative experiments to address this question in an unambiguous manner. In this review, we discuss the extent to which HGT is responsible for the spread of antibiotic resistance and examine what is known about the effect of antibiotics on the HGT dynamics. We focus on conjugation, which is the dominant mode of HGT responsible for spreading antibiotic resistance on the global scale. Our analysis reveals a need to design experiments to quantify HGT in such a way to facilitate rigorous data interpretation. Such measurements are critical for developing novel strategies to combat resistance spread through HGT.

Exploring lateral genetic transfer among microbial genomes using TF-IDF

Many microbes can acquire genetic material from their environment and incorporate it into their genome, a process known as lateral genetic transfer (LGT). Computational approaches have been developed to detect genomic regions of lateral origin, but typically lack sensitivity, ability to distinguish donor from recipient, and scalability to very large datasets. To address these issues we have introduced an alignment-free method based on ideas from document analysis, term frequency-inverse document frequency (TF-IDF). Here we examine the performance of TF-IDF on three empirical datasets: 27 genomes of Escherichia coli and Shigella, 110 genomes of enteric bacteria, and 143 genomes across 12 bacterial and three archaeal phyla. We investigate the effect of k-mer size, gap size and delineation of groups on the inference of genomic regions of lateral origin, finding an interplay among these parameters and sequence divergence. Because TF-IDF identifies donor groups and delineates regions of lateral origin within recipient genomes, aggregating these regions by gene enables us to explore, for the first time, the mosaic nature of lateral genes including the multiplicity of biological sources, ancestry of transfer and over-writing by subsequent transfers. We carry out Gene Ontology enrichment tests to investigate which biological processes are potentially affected by LGT.

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF

Lateral genetic transfer (LGT) plays an important role in the evolution of microbes. Existing computational methods for detecting genomic regions of putative lateral origin scale poorly to large data. Here, we propose a novel method based on TF-IDF (Term Frequency-Inverse Document Frequency) statistics to detect not only regions of lateral origin, but also their origin and direction of transfer, in sets of hierarchically structured nucleotide or protein sequences. This approach is based on the frequency distributions of k-mers in the sequences. If a set of contiguous k-mers appears sufficiently more frequently in another phyletic group than in its own, we infer that they have been transferred from the first group to the second. We performed rigorous tests of TF-IDF using simulated and empirical datasets. With the simulated data, we tested our method under different parameter settings for sequence length, substitution rate between and within groups and post-LGT, deletion rate, length of transferred region and k size, and found that we can detect LGT events with high precision and recall. Our method performs better than an established method, ALFY, which has high recall but low precision. Our method is efficient, with runtime increasing approximately linearly with sequence length.

The Prehistory of Antibiotic Resistance

Antibiotic resistance is a global problem that is reaching crisis levels. The global collection of resistance genes in clinical and environmental samples is the antibiotic "resistome," and is subject to the selective pressure of human activity. The origin of many modern resistance genes in pathogens is likely environmental bacteria, including antibiotic producing organisms that have existed for millennia. Recent work has uncovered resistance in ancient permafrost, isolated caves, and in human specimens preserved for hundreds of years. Together with bioinformatic analyses on modern-day sequences, these studies predict an ancient origin of resistance that long precedes the use of antibiotics in the clinic. Understanding the history of antibiotic resistance is important in predicting its future evolution.

Regulation of genetic flux between bacteria by restriction-modification systems

Restriction-modification (R-M) systems are often regarded as bacteria's innate immune systems, protecting cells from infection by mobile genetic elements (MGEs). Their diversification has been recently associated with the emergence of particularly virulent lineages. However, we have previously found more R-M systems in genomes carrying more MGEs. Furthermore, it has been suggested that R-M systems might favor genetic transfer by producing recombinogenic double-stranded DNA ends. To test whether R-M systems favor or disfavor genetic exchanges, we analyzed their frequency with respect to the inferred events of homologous recombination and horizontal gene transfer within 79 bacterial species. Genetic exchanges were more frequent in bacteria with larger genomes and in those encoding more R-M systems. We created a recognition target motif predictor for Type II R-M systems that identifies genomes encoding systems with similar restriction sites. We found more genetic exchanges between these genomes, independently of their evolutionary distance. Our results reconcile previous studies by showing that R-M systems are more abundant in promiscuous species, wherein they establish preferential paths of genetic exchange within and between lineages with cognate R-M systems. Because the repertoire and/or specificity of R-M systems in bacterial lineages vary quickly, the preferential fluxes of genetic transfer within species are expected to constantly change, producing time-dependent networks of gene transfer.

Bacteriophages affect evolution of bacterial communities in spatially distributed habitats: a simulation study

Background

Bacteriophages are known to be one of the driving forces of bacterial evolution. Besides promoting horizontal transfer of genes between cells, they may induce directional selection of cells (for instance, according to more or less resistance to phage infection). Switching between lysogenic and lytic pathways results in various types of (co)evolution in host-phage systems. Spatial (more generally, ecological) organization of the living environment is another factor affecting evolution. In this study, we have simulated and analyzed a series of computer models of microbial communities evolving in spatially distributed environments under the pressure of phage infection.

Results

We modeled evolving microbial communities living in spatially distributed flowing environments. Non-specific nutrient supplied in the only spatial direction, resulting in its non-uniform distribution in environment. We varied the time and the location of initial phage infestation of cells as well as switched chemotaxis on and off. Simulations were performed with the Haploid evolutionary constructor software (http://evol-constructor.bionet.nsc.ru/).

Conclusion

Simulations have shown that the spatial location of initial phage invasion may lead to different evolutionary scenarios. Phage infection decreases the speciation rate by more than one order as far as intensified selection blocks the origin of novel viable populations/species, which could carve out potential ecological niches. The dependence of speciation rate on the invasion node location varied on the time of invasion. Speciation rate was found to be lower when the phage invaded fully formed community of sedentary cells (at middle and late times) at the species-rich regions. This is especially noticeable in the case of late-time invasion.

Our simulation study has shown that phage infection affects evolution of microbial community slowing down speciation and stabilizing the system as a whole. This influencing varied in its efficiency depending on spatially-ecological factors as well as community state at the moment of phage invasion.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0620-4) contains supplementary material, which is available to authorized users.

Genome Analysis of Phage SMSAP5 as Candidate of Biocontrol for Staphylococcus aureus

In this study, we reported the morphogenetic analysis and genome sequence by genomic analysis of the newly isolated staphylococcal phage SMSAP5 from soil of slaughterhouses for cattle. Based on transmission electron microscopy evident morphology, phage SMSAP5 belonged to the Siphoviridae family. Phage SMSAP5 had a double-stranded DNA genome with a length of 45,552 bp and 33 % G+C content. Bioinformatics analysis of the phage genome revealed 43 open reading frames. A blastn search revealed that its nucleotide sequence shared a high degree of similarity with that of the Staphylococcus phage tp310-2. In conclusion, this study is the first report to show the morphological features and the complete genome sequence of the phage SMSAP5 from soil of slaughterhouses for cattle.