BACH1 Binding Links the Genetic Risk for Severe Periodontitis with ST8SIA1.

Genome-wide association studies identified various loci associated with periodontal diseases, but assigning causal alleles remains difficult. Likewise, the generation of biological meaning underlying a statistical association has been challenging. Here, we characterized the genetic association at the gene ST8SIA1 that increases the risk for severe periodontitis in smokers. We used CRISPR/dCas9 activation and RNA-sequencing to identify genetic interaction partners of ST8SIA1 and to determine its function in the cell. We used reporter gene assays to identify regulatory elements at the associated single-nucleotide polymorphisms (SNPs) and to determine effect directions and allele-specific changes of enhancer activity. Antibody electrophoretic mobility shift assays proved allele-specific transcription factor binding at the putative causal SNPs. We found the reported periodontitis risk gene ABCA1 as the top upregulated gene following ST8SIA1 activation. Gene set enrichment analysis showed highest effects on integrin cell surface interactions (area under the curve [AUC] = 0.85; q = 4.9 × 10-6) and cell cycle regulation (AUC = 0.89; q = 1.6 × 10-5). We identified 2 associated repressor elements in the introns of ST8SIA1 that bind the transcriptional repressor BACH1. The putative causative variant rs2012722 decreased BACH1 binding by 40%. We also pinpointed ST8SIA1 as the target gene of the association. ST8SIA1 inhibits cell adhesion with extracellular matrix proteins, integrins, and cell cycle, as well as enhances apoptosis. Likewise, tobacco smoke reportedly results in an inhibition of cell adhesion and a decrease in integrin-positive cells and cell growth. We conclude that impaired ST8SIA1 repression, independently caused by reduced BACH1 binding at the effect T allele, as well as by tobacco smoke, contributes to higher ST8SIA1 levels, and in smokers who carry the effect T allele, both factors would be additive with damaging effects on the gingival barrier integrity. The activity of ST8SIA1 is also linked with the periodontitis risk gene ABCA1.

Water flow paths are hotspots for the dissemination of antibiotic resistance in soil.

Antibiotic resistance genes in soil pose a potential risk for human health. They can enter the soil by irrigation with untreated or insufficiently treated waste water. We hypothesized that water flow paths trigger the formation of antibiotic resistance, since they transport antibiotics, multi-resistant bacteria and free resistance genes through the soil. To test this, we irrigated soil cores once or twice with waste water only, or with waste water added with sulfamethoxazole (SMX) and ciprofloxacin (CIP). The treatments also contained a dye to stain the water flow paths and allowed to sample these separately from unstained bulk soil. The fate of SMX and CIP was assessed by sorption experiments, leachate analyses and the quantification of total and extractable SMX and CIP in soil. The abundance of resistance genes to SMX (sul1 and sul2) and to CIP (qnrB and qnrS) was quantified by qPCR. The sorption of CIP was larger than the dye and SMX. Ciprofloxacin accumulated exclusively in the water flow paths but the resistance genes qnrB and qnrS were not detectable. The SMX concentration in the water flow paths doubled the concentration of the bulk soil, as did the abundance of sul genes, particularly sul1 gene. These results suggest that flow paths do function as hotspots for the accumulation of antibiotics and trigger the formation of resistance genes in soil. Their dissemination also depends on the mobility of the antibiotic, which was much larger for SMX than for CIP.

Immediate effects and outcome of in-utero pulmonary valvuloplasty in fetuses with pulmonary atresia with intact ventricular septum or critical pulmonary stenosis.

OBJECTIVE: To assess the immediate effects of fetal pulmonary valvuloplasty on right ventricular (RV) size and function as well as in-utero RV growth and postnatal outcome. METHODS: Patients with pulmonary atresia with intact ventricular septum (PAIVS) or critical pulmonary stenosis (CPS) who underwent fetal pulmonary valvuloplasty at our center between October 2000 and July 2017 were included. Echocardiographic data obtained before and after the procedure were analyzed retrospectively (median interval after intervention, 1 (range, 1-3) days) for ventricular and valvular dimensions and ratios, RV filling time (duration of tricuspid valve (TV) inflow/cardiac cycle length), TV velocity time integral (TV-VTI) × heart rate (HR) and tricuspid regurgitation (TR) velocity. Longitudinal data were collected from only those fetuses followed up in our center. Outcome was assessed using the scoring system as described by Roman et al. for non-biventricular outcome. RESULTS: Thirty-five pulmonary valvuloplasties were performed in our institution on 23 fetuses with PAIVS (n = 15) or CPS (n = 8). Median gestational age at intervention was 28 + 4 (range, 23 + 6 to 32 + 1) weeks. No fetal death occurred. Immediately after successful intervention, RV/left ventricular length (RV/LV) ratio (P ≤ 0.0001), TV/mitral valve annular diameter (TV/MV) ratio (P ≤ 0.001), RV filling time (P ≤ 0.00001) and TV-VTI × HR (P ≤ 0.001) increased significantly and TR velocity (P ≤ 0.001) decreased significantly. In fetuses followed longitudinally to delivery (n = 5), RV/LV and TV/MV ratios improved further or remained constant until birth. Fetuses with unsuccessful intervention (n = 2) became univentricular, all others had either a biventricular (n = 15), one-and-a-half ventricular (n = 3) or still undetermined (n = 3) outcome. Five of nine fetuses with a predicted non-biventricular outcome, in which the procedure was successful, became biventricular, while two of nine had an undetermined circulation. CONCLUSION: In selected fetuses with PAIVS or CPS, in-utero pulmonary valvuloplasty led immediately to larger RV caused by reduced afterload and increased filling, thus improving the likelihood of biventricular outcome even in fetuses with a predicted non-biventricular circulation. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Tigecycline resistance in clinical isolates of Enterococcus faecium is mediated by an upregulation of plasmid-encoded tetracycline determinants tet(L) and tet(M).

OBJECTIVES: Tigecycline represents one of the last-line therapeutics to combat multidrug-resistant bacterial pathogens, including VRE and MRSA. The German National Reference Centre for Staphylococci and Enterococci has received 73 tigecycline-resistant Enterococcus faecium and Enterococcus faecalis isolates in recent years. The precise mechanism of how enterococci become resistant to tigecycline remains undetermined. This study documents an analysis of the role of efflux pumps in tigecycline resistance in clinical isolates of Enterococcus spp. METHODS: Various tigecycline MICs were found for the different isolates analysed. Tigecycline-resistant strains were analysed with respect to genome and transcriptome differences by means of WGS and RT-qPCR. Genes of interest were cloned and expressed in Listeria monocytogenes for verification of their functionality. RESULTS: Detailed comparative whole-genome analyses of three isogenic strains, showing different levels of tigecycline resistance, revealed the major facilitator superfamily (MFS) efflux pump TetL and the ribosomal protection protein TetM as possible drug resistance proteins. Subsequent RT-qPCR confirmed up-regulation of the respective genes. A correlation of gene copy number and level of MIC was inferred from further qPCR analyses. Expression of both tet(L) and tet(M) in L. monocytogenes unequivocally demonstrated the potential to increase tigecycline MICs upon acquisition of either locus. CONCLUSIONS: Our results indicate that increased expression of two tetracycline resistance determinants, a tet(L)-encoded MFS pump and a tet(M)-encoded ribosomal protection protein, is capable of conferring tigecycline resistance in enterococcal clinical isolates.

New antimicrobial contact catalyst killing antibiotic resistant clinical and waterborne pathogens.

Microbial growth on medical and technical devices is a big health issue, particularly when microorganisms aggregate to form biofilms. Moreover, the occurrence of antibiotic-resistant bacteria in the clinical environment is dramatically growing, making treatment of bacterial infections very challenging. In search of an alternative, we studied a novel antimicrobial surface coating based on micro galvanic elements formed by silver and ruthenium with surface catalytic properties. The antimicrobial coating efficiently inhibited the growth of the nosocomial pathogens Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Enterococcus faecium as demonstrated by the growth inhibition on agar surface and in biofilms of antibiotic resistant clinical E. faecalis, E. faecium, and S. aureus isolates. It also strongly reduced the growth of Legionella in a drinking water pipeline and of Escherichia coli in urine. We postulate a mode of action of the antimicrobial material, which is independent of the release of silver ions. Thus, the novel antimicrobial coating could represent an alternative to combat microbial growth avoiding the toxic side effects of high levels of silver ions on eukaryotic cells.

Identification of SagA as a novel vaccine target for the prevention of Enterococcus faecium infections.

Infections caused by multiresistant Gram-positive bacteria represent a major health burden in the community as well as in hospitalized patients. Enterococci, especially Enterococcus faecium, are well-known pathogens of hospitalized patients and are frequently linked with resistance against multiple antibiotics, which compromises effective therapy. Rabbit immune serum raised against heat-killed E. faecium E155, a HiRECC clone, was used in an opsonophagocytic assay, an inhibition assay and a mouse bacteraemia model to identify targets of opsonic and protective antibodies. Serum against whole heat-killed bacteria was opsonic and recognized a protein of about 72 kDa that was abundantly secreted. This protein, identified as SagA by LC-ES-MS/MS, was expressed in Escherichia coli and purified. Rabbit serum raised against the purified protein showed opsonic killing activity that was inhibited by almost 100% using 100 µg purified protein ml(-1). In a mouse bacteraemia model, a statistically significant reduction of the colony counts in blood was shown with immune rabbit serum compared with preimmune serum using the homologous and a heterologous vancomycin-resistant enterococci (VRE) strain. These results indicate that SagA could be used as a promising vaccine target to treat and/or prevent VRE bacteraemia.

Conjugative plasmids in multi-resistant bacterial isolates from Indian soil.

AIMS: Determination of heavy metal and antibiotic resistance and presence of conjugative plasmids in bacteria isolated from soil irrigated with wastewater. METHODS AND RESULTS: Composite soil samples were collected from Ghaziabad, Uttar Pradesh, India. Forty different bacteria were selected from nutrient agar and characterized by morphological, cultural and biochemical tests. All the isolates were tested for their resistance to different heavy metals and antibiotics. The DNA derived from multiple metal and antibiotic-resistant bacterial isolates was PCR amplified and plasmid-specific sequences (IncP, IncN, IncW, IncQ and pMV158-type) were analysed by dot blot hybridization. All isolates gave PCR products with trfA2 and oriT primers of the IncP group. These PCR products also hybridized with the RP4-derived probes. However, the samples were negative for all the other investigated plasmids as proved by PCR and dot blots. CONCLUSIONS: The presence of conjugative/mobilizable IncP plasmids in the isolates indicates that these bacteria have gene-mobilizing capacity with implications for potential dissemination of introduced recombinant DNA. SIGNIFICANCE AND IMPACT OF THE STUDY: The detection of IncP plasmids in all the bacterial isolates is another proof for the prevalence of these plasmids. We propose that IncP plasmids are mainly responsible for the spread of multi-resistant bacteria in these soils.

A survey on biotechnological potential and safety of the novel Enterococcus species of dairy origin, E. italicus.

The biotechnological and safety properties of the novel enterococcal species of dairy origin, Enterococcus italicus, were investigated. The strains of the species showed technological characteristics related to their use as adjunct cultures in the production of artisanal cheeses. They were susceptible or poorly resistant to several clinical relevant antibiotics. Moreover, E. italicus strains were associated with low virulence profiles, as verified by screening for the presence of 33 different genes encoding antibiotic resistance and known virulence factors in the genus Enterococcus. From the data obtained, we deduce that the presence of E. italicus strains in cheeses results in a low health risk and that within the species new safe adjunct cultures for the dairy industry could be found.

Application of culture-independent methods to assess the bacteria removal efficiency of subsurface flow constructed wetlands.

The bacteriologic treatment efficiency of vertical and horizontal subsurface flow constructed wetlands (SFCWs) was analysed in two multistage wastewater treatment systems by culture dependent and independent methods. When assessed with standard cultivation procedures, bacteria removal efficiency of the vertical and horizontal SFCWs was similar. However, microscopic enumerations of the wastewater bacteria after DNA staining revealed a completely different removal pattern: bacteria removal efficiency of the horizontal SFCWs was in general low and erratic, whereas the vertical SFCWs displayed high bacteria removal rates. The discrepancies in the results obtained by bacteria enumeration and cultivation was due to a strong decrease in bacterial culturability after treatment by the horizontal SFCWs, leading to overestimation of the real bacterial concentrations in these effluents. Additionally, a PCR based approach for the detection of the enteropathogenic bacteria Campylobacter jejuni and Yersinia enterocolitica was tested in the wastewater samples. The methods were specific and reproducible in the analysed samples and could be carried out within 12 h, proving very adequate as an alternative to cultivation. This work recommends a review of the current standard methodology for wastewater quality surveillance, as well as of the design of SFCW.

Expression of the mobM gene of the streptococcal plasmid pMV158 in Lactococcus lactis subsp. lactis.

The streptococcal plasmid pMV158 is not auto-transferable, but it can be mobilised between bacteria by the use of functions supplied by plasmids of the pIP501/pAM beta 1 family. Plasmid pMV158 encodes a protein, MobM, which is involved in its mobilisation. This process initiates when MobM specifically cleaves supercoiled pMV158 plasmid DNA at the origin of transfer, oriT. Plasmid pMV158 has been transferred to Lactococcus lactis by conjugation aided by plasmid pAM beta 1. In the lactococcal host, MobM-mediated specific pMV158-relaxed molecules were detected. The intracellular amount of MobM has been quantified by immunoblot analyses and shown to be about 3500 molecules per cell. In the same host, we have mapped the initiation point of transcription of mobM. Transcription of this gene is directed from a promoter with an extended--10 region which overlaps with the pMV158-oriT.

Mobilisation of the streptococcal plasmid pMV158: interactions of MobM protein with its cognate oriT DNA region.

The streptococcal plasmid pMV158 encodes the relaxase protein, MobM, involved in its mobilisation. Purified MobM protein specifically cleaved supercoiled or single-stranded DNA containing the plasmid origin of transfer, oriT. Gel retardation and DNase I footprinting assays performed with DNA fragments containing the plasmid oriT provided evidence for specific binding of MobM by oriT DNA. Dissection of the MobM-binding sequence revealed that the oriT region protected by MobM spanned 28 nucleotides, and includes an inversely repeated sequence, termed IR2. MobM exhibits a high degree of similarity with the mob gene product of the Streptococcus ferus plasmid pVA380-1. Although the origins of transfer of pMV158 and pVA380-1 show 20% sequence divergence in a 24-bp sequence included in their oriT regions, the pMV158 MobM was able to cleave a supercoiled derivative of pVA380-1 in vitro.

In vivo definition of the functional origin of leading strand replication on the lactococcal plasmid pFX2.

The lactococcal plasmid pFX2 belongs to a family of plasmids, whose prototype is the streptococcal plasmid pMV158, that replicates by the rolling circle mechanism. Determination of the nucleotide sequence of the repX gene of pFX2 allowed us to make some minor corrections in the published sequence, and to show that the repX gene is identical to the rep gene of plasmid pWV01. We have established pFX2 in Escherichia coli and in Streptococcus pneumoniae. In the latter host, we have defined in vivo the nick site introduced by the RepX protein. Plasmid pFX2 and the pMV158 derivative pLS1 exhibit a moderate degree of incompatibility in S. pneumoniae. Cloning of the double strand origin (dso) of pFX2 into a high-copy-number plasmid that is compatible with the pMV158 replicon led to an increase in incompatibility toward pLS1. Plasmids pFX2 and pLS1 exhibit homologies in their Rep proteins and in their dso sequences, but not in their negative control elements. Thus, the observed incompatibility indicates that cross-recognition of Rep proteins and dso takes place.

Determination of specific DNA strand discontinuities with nucleotide resolution in exponentionally growing bacteria harboring rolling circle-replicating plasmids.

Plasmid replication by the rolling circle mechanism and conjugative transfer of plasmids require the generation of a specific strand discontinuity in the DNA. In both processes cleavage at the so-called nic site is catalyzed by plasmid-encoded proteins. The strand discontinuities at the conjugative origins of transfer of plasmid pE194 and pMV158 were determined in Bacillus subtilis and Streptococcus pneumoniae, respectively, with a recently developed runoff DNA synthesis assay. The positions of intracellular cleavage within the respective transfer origins were shown to coincide with the site predicted for pE194 and with the nic site determined in vitro for pMV158. For pMV158, the influence of a mutation in the S. pneumoniae polA gene on the efficiency of replication was investigated. In addition, the nic site within the double-stranded origin of the-rolling circle-replicating plasmid pMV158 in S. pneumoniae as well as that of pFX2 in Escherichia coli was mapped with nucleotide resolution.

Specific cleavage of chromosomal and plasmid DNA strands in gram-positive and gram-negative bacteria can be detected with nucleotide resolution.

A sensitive and precise in vitro technique for detecting DNA strand discontinuities produced in vivo has been developed. The procedure, a form of runoff DNA synthesis on molecules released from lysed bacterial cells, mapped precisely the position of cleavage of the plasmid pMV158 leading strand origin in Streptococcus pneumoniae and the site of strand scission, nic, at the transfer origins of F and the F-like plasmid R1 in Escherichia coli. When high frequency of recombination strains of E. coli were examined, DNA strand discontinuities at the nic positions of the chromosomally integrated fertility factors were also observed. Detection of DNA strand scission at the nic position of F DNA in the high frequency of recombination strains, as well as in the episomal factors, was dependent on sexual expression from the transmissable element, but was independent of mating. These results imply that not only the transfer origins of extrachromosomal F and F-like fertility factors, but also the origins of stably integrated copies of these plasmids, are subject to an equilibrium of cleavage and ligation in vivo in the absence of DNA transfer.

Comparison of ccd of F, parDE of RP4, and parD of R1 using a novel conditional replication control system of plasmid R1.

A number of plasmid-encoded gene systems are thought to stabilize plasmids by killing plasmid-free cells (also termed post-segregational killing or plasmid addiction). Here we analyse the mechanisms of plasmid stabilization by ccd of F, parDE of RP4 and parD of R1, and compare them to hok/sok of R1. To induce synchronous plasmid loss we constructed a novel plasmid replication-arrest system, which possesses the advantage that plasmid replication can be completely arrested by the addition of IPTG, a non-metabolizable inducer. Using isogenic plasmid constructions we have found, for the first time, consistent correlation between the effect on steady-state loss rates and the effect on cell proliferation in the plasmid replication-arrest assay for all three systems. The parDE system had the most pronounced effect both on plasmid stabilization and on plasmid retention after replication arrest. In contrast, ccd and parD both exhibited weaker effects than anticipated from previously published results. Thus, our results indicate that the function and efficiencies of some of the systems should be reconsidered. Our results are consistent with the previously postulated hypothesis that ccd and parDE act by killing plasmid-free segregants, whereas parD seems to act by inhibiting cell division of plasmid-free segregants.

Analysis of the multimer resolution system encoded by the parCBA operon of broad-host-range plasmid RP4.

The broad-host-range plasmid RP4 encodes a highly efficient partitioning function, termed par, that is capable of stabilizing plasmids in a variety of Gram-negative bacteria independently of the nature of the replicon. The mechanism responsible for plasmid stabilization by this locus appears to be a complex system which includes a site-specific recombination system mediating resolution of plasmid multimers. In this report we present a detailed study on this multimer resolution system (mrs). The parA gene encodes two forms of a resolvase capable of catalysing site-specific recombination between specific sites situated in the promoter region of the parCBA operon. The two ParA proteins that are produced as a result of independent translation initiation at two different start codons within the same open reading frame were overexpressed in Escherichia coli and partially purified. Both forms of the enzyme are able to recombine a supercoiled cointegrate substrate containing two cis-acting elements with the same orientation in an in vitro resolution assay. ParA-mediated, site-specific recombination was found to be independent of any other gene product encoded by the RP4 par locus in vitro and in vivo. The DNA-binding sites for the ParA resolvase were determined using DNase I protection experiments. The results identified three binding sites within the mrs cis-acting region. Both the biochemical properties of the ParA protein and the organization of the cis-acting recombination site revealed a high degree of similarity to the site-specific recombination systems of Tn3-like transposable elements suggesting an evolutionary relationship.

Stability of r-microbes: stabilization of plasmid vectors by the partitioning function of broad-host-range plasmid RP4.

The genes for biosynthesis of the biodegradable polymer poly-beta-hydroxybutyric acid (PHB) cloned from Alcaligenes eutrophus H16 were used for synthesis of PHB with recombinant Escherichia coli strains. It was recognized that the PHB-biosynthesis genes cause segregational instability to the plasmids used as vectors. Recombinant PHB-plasmids are rapidly lost from host cells and plasmid-free cells occur at high rates, even under conditions of selection for the plasmids. Cloning the partitioning region of plasmid RP4 onto such plasmids resulted in a high degree of stabilization. These par-stabilized recombinant PHB-plasmids could be maintained quite efficiently in batch cultivation experiments in the absence of any selection pressure.