Multidrug-resistant gram-negative organisms: a review of recently approved antibiotics and novel pipeline agents

Background The discovery of antibiotics several decades ago was a defining moment in history. They were used to treat previously incurable diseases and save many lives. However, the use of antibiotics is not benign. Antibiotic resistance occurs due to the natural evolution of bacteria and gene transfer between bacteria via vertical and horizontal routes, resulting in protective mechanisms that render antibacterial agents ineffective. Aim of the review To list and describe current, novel pipeline antibiotics indicated for multidrug-resistant gram-negative bacteria. This review discusses the limited number of novel pipeline drugs available to combat the rapidly increasing number of multidrug-resistant bacteria and the need for initiatives to research and discover more novel antibiotics. Method A search of MEDLINE/PubMed using the search terms antibacterial pipeline OR antibiotic pipeline including publications between 1 January 2018 through 23 January 2020 resulted in 230 items. The results obtained were narrowed by adding the search term AND multi-drug resistant which resulted in 12 items. Then, ClinicalTrials.gov was searched for phase 2-3 "interventional" trials registered between 1 January 2018 and 23 January 2020 with the status "recruiting" or "completed" function and including World Health Organization-defined priority pathogens in the "condition or disease" field. The search process was then completed by introducing the term antibacterial agents in the "other terms" field. The trials search and selection resulted in 13 items. Relevant English-language studies and those conducted in humans were considered. Those drugs belonging to new antibiotic classes or to antibiotic classes already known but with new chemical structure were defined as "novel antibiotics". Results The studies selected and reviewed were those referring to a novel antibiotics. Thus, from MEDLINE/PubMed, we found only 1 item referred to a novel chemical class (Murepavadin n = 1). From ClinicalTrials.gov a total of 4 citations were identified (Ftortiazinon n = 1, Zoliflodacin n = 1, Gepotidacin n = 1, ETX2514 + sulbactam n = 1). Conclusion The antibiotics annually approved by the Food and Drug Administration (FDA) mostly belong to existing classes of antibiotics and have specific indications, limiting their use in many multidrug-resistant infections. There are limited novel drug classes targeting gram-negative infections in the pipeline. Providers must be vigilant with the use of current antibiotics, especially until research and development (R&D) advancements are made.

Defatted safflower seed extract inhibits adipogenesis in 3T3-L1 preadipocytes and improves lipid profiles in C57BL/6J ob/ob mice fed a high-fat diet

In the present study, we hypothesized that defatted safflower seed which is known to be rich in polyphenols might influence adipogenesis and obesity-related disorders, and therefore the anti-adipogenic and hypolipidemic effects of ethanol extract from defatted safflower (Cathamus tinctorius L.) seeds (CSE) were investigated both in cultured 3T3-L1 preadipocytes and in C57BL/6J ob/ob mice fed a high-fat diet. CSE inhibited adipocyte differentiation of 3T3-L1 preadipocytes and decreased expression of the adipogenic transcription factors, SREBP1c and PPARγ, and their target genes. Six-week-old obese (ob/ob) mice were fed a high-fat diet and treated with CSE (50 or 100 mg/kg/day) by oral gavage for 6 weeks. Body fat mass (epididymal and perirenal white adipose tissues) in the CSE-treated groups was significantly lower than that in the high-fat diet control (HFD) group, whereas average daily food intake was not significantly different among the groups. Plasma and hepatic triglyceride levels and plasma low-density lipoprotein cholesterol level were also significantly lower in the CSE groups compared to the HFD group. These results suggest that CSE which decreases body fat mass and improves lipid profiles in plasma and liver, represents a potential treatment option for obesity and associated metabolic disorders, including hyperlipidemia.

Correlation between frictional force and surface roughness of orthodontic archwires

Lateral force microscopy measures the lateral bending of the cantilever depending on the frictional force acting between the tip and surface. The aim of this study was to investigate and compare the relationship between the surface roughness and frictional resistance of four archwire and bracket combinations consisting of the 0.016-inch NiTi and 0.019 × 0.025-inch stainless steel archwires interacting clinically with two representative self-ligating brackets, active-type Clippy-C(®) ceramic self-ligating brackets, and passive-type Damon(®) stainless steel self-ligating brackets, using the lateral force microscopy technique. A 0.016-inch NiTi archwire interacting with passive-type Damon(®) stainless steel self-ligating brackets showed the smoothest surface roughness and the lowest frictional resistance compared to other combinations. The archwires interacting with passive-type Damon(®) stainless steel self-ligating brackets showed significantly lower surface roughness and frictional resistance than those interacting with active-type Clippy-C(®) ceramic self-ligating brackets. The frictional force in the in vivo archwire and bracket system increased with increasing surface roughness of the archwire. This positive correlation suggests that surface roughness can be used as an evaluating marker for estimating the efficiency of orthodontic treatment, rather than the direct measurement of frictional force.

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.

A genome-wide association study of seed protein and oil content in soybean

BACKGROUND

Association analysis is an alternative to conventional family-based methods to detect the location of gene(s) or quantitative trait loci (QTL) and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Seed protein and oil concentration are quantitative traits which are determined by the interaction among many genes with small to moderate genetic effects and their interaction with the environment. In this study, a genome-wide association study (GWAS) was performed to identify quantitative trait loci (QTL) controlling seed protein and oil concentration in 298 soybean germplasm accessions exhibiting a wide range of seed protein and oil content.

RESULTS

A total of 55,159 single nucleotide polymorphisms (SNPs) were genotyped using various methods including Illumina Infinium and GoldenGate assays and 31,954 markers with minor allele frequency >0.10 were used to estimate linkage disequilibrium (LD) in heterochromatic and euchromatic regions. In euchromatic regions, the mean LD (r2) rapidly declined to 0.2 within 360 Kbp, whereas the mean LD declined to 0.2 at 9,600 Kbp in heterochromatic regions. The GWAS results identified 40 SNPs in 17 different genomic regions significantly associated with seed protein. Of these, the five SNPs with the highest associations and seven adjacent SNPs were located in the 27.6-30.0 Mbp region of Gm20. A major seed protein QTL has been previously mapped to the same location and potential candidate genes have recently been identified in this region. The GWAS results also detected 25 SNPs in 13 different genomic regions associated with seed oil. Of these markers, seven SNPs had a significant association with both protein and oil.

CONCLUSIONS

This research indicated that GWAS not only identified most of the previously reported QTL controlling seed protein and oil, but also resulted in narrower genomic regions than the regions reported as containing these QTL. The narrower GWAS-defined genome regions will allow more precise marker-assisted allele selection and will expedite positional cloning of the causal gene(s).

First Report of Bacterial Leaf Spot of Witloof, Caused by Pseudomonas cichorii in Korea

In August 2011, bacterial leaf spot was observed on witloof (Cichorium intybus L. var. foliosum) grown in a commercial field with 15% incidence in Injae, Korea. Symptoms on leaves included irregular brown to reddish brown spots in the center. Bacterial streaming from the lesions was observed microscopically. Bacterial isolates (BC3286, BC3287, and BC3308-BC3310) were recovered on Trypticase soy agar from lesions surface-sterilized in 70% ethyl alcohol for 30 s. The isolates were gram negative, urease negative, fluorescent on King's B agar, and had aerobic rods with 2 to 6 polar flagella. Pathogenicity tests were separately performed in different greenhouses located in Suwon (National Academy of Agricultural Science) and Chuncheon (Gangwondo Agricultural Research and Extension Services) in Korea. Pathogenicity was confirmed by spray inoculation of healthy, 10-day-old leaves of witloof plants (two plants/isolate) with a suspension of original field isolate (10⁶ CFU/ml). Sterile distilled water was used as negative control. The inoculated plants were incubated in a growth chamber (25°C and 95% relative humidity [RH]) overnight, then transferred to a greenhouse at 23 to 27°C and 60 to 70% RH. Characteristic leaf spot symptoms were observed on inoculated witloof plants 8 days after inoculation. No symptoms were observed on control plants. The bacterium reisolated from the inoculated leaves was confirmed by analyzing sequence of the gyrB gene with direct sequencing method of PCR products using primers gyr-F and gyr-R (2). The sequence of reisolated bacteria shared 100% similarity with inoculated ones. In LOPAT (1) tests, all isolates and the reference strain of Pseudomonas cichorii CFBP2101^T (=BC2595) were levan negative, oxidase positive, potato rot negative, arginine dihydrolase negative, and tobacco hypersensitivity positive, indicative of group III (-, +, -, -, +) of fluorescent pseudomonads. The 16S rRNA (1,408 bp), and gyrB (676 bp) regions were sequenced to aid in identification of the original field isolates as well as P. cichorii CFBP 2101^T (=BC2595) using reported sets of PCR primers, fD1/rP2 and gyr-F/gyr-R, respectively (2,4). Phylogenetic analyses based on partial sequences of the gyrB and the 16S rRNA of Psudomonas spp. available in GenBank, the reference strain of P. cichorii CFBP2101^T (=BC2595), and the witloof field isolates were conducted using the neighbor-joining method with Juke-Cantor model of distance calculation in MEGA version 5.1 (3). The isolates and the reference strain of P. cichorii CFBP2101^T (=BC2595) was clustered in one group with P. cichorii strains in both phylogenetic trees based on the two sequences. Sequences of the 16S rRNA region had a distance index value ranging from 0.000 to 0.001 between the reference strain of P. cichori CFBP2101^T (GenBank JX913784) and the field isolates (JX913785 to JX913789), and ranged from 0.000 to 0.001 within the field isolates. Sequences of the gyrB region had a distance index value ranging 0.029 to 0.033 between the reference strain (JX913790) and the field isolates (JX913791 to JX913795), and ranged from 0.000 to 0.041 within the field isolates. To our knowledge, this is the first report of bacterial leaf spot of witloof caused by P. cihorii in Korea. P. cichorii has a wide host range, and an important economic impact on vegetables. The disease is expected to result in a significant economic impact on root production of witloof in Korea. References: (1) R. A. Lelliott et al. J. Appl. Bacteriol. 29:470, 1966. (2) H. Sawada et al. J. Mol. Evol. 49:627, 1999. (3) K. Tamura et al. Mol. Biol. Evol. 28:2731, 2011. (4) W. G. Weinsburg et al. J. Bacteriol. 173, 697, 1991.

Effects of a brief Qigong-based stress reduction program (BQSRP) in a distressed Korean population: a randomized trial

Background

Distressed individuals in Korea may benefit from the practice of mind–body exercises such as Qigong. However, the effectiveness of such techniques needs to be investigated.

Methods

Fifty participants who were eligible to this study were randomized into a group receiving a 4-week intervention of a brief Qigong-based stress reduction program (BQSRP) or a wait-list control group. Before and after the intervention period, saliva samples were collected and questionnaires were completed on perceived stress, anxiety, “Hwa-Byung” (anger syndrome), and quality of life. Salivary cortisol has emerged in mind-body therapy research as an easy-to-collect, relatively inexpensive, biologic marker of stress. Salivary corisol were collected to evaluate physiological effect of BQSRP. Between-group comparisons of change from baseline to study completion were analyzed by analysis of covariance for the Perceived Stress Scale and independent two sample t-tests for other measures.

Results

Compared with the control group, the BQSRP intervention group displayed significantly larger decreases in Perceived Stress Scale scores (p = 0.0006), State Anxiety scores (p = 0.0028), Trait Anxiety scores (p < 0.0001), personality subscale scores of the Hwa-Byung Scale (p = 0.0321), symptoms scores of the Hwa-Byung Scale (p = 0.0196), and a significantly larger increase in World Health Organization Quality of Life Abbreviated version scores (ps < .05). Salivary cortisol levels were not changed.

Conclusions

The BQSRP appears to be effective in reducing stress perception, anxiety, anger, and improving quality of life (KCT0000056).

High-throughput SNP discovery and assay development in common bean

BACKGROUND

Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery.

RESULTS

Using a multi-tier reduced representation library we discovered a total of 3,487 SNPs of which 2,795 contained sufficient flanking genomic sequence for SNP assay development. Using Sanger sequencing to determine the validation rate of these SNPs, we found that 86% are likely to be true SNPs. Furthermore, we designed a GoldenGate assay which contained 1,050 of the 3,487 predicted SNPs. A total of 827 of the 1,050 SNPs produced a working GoldenGate assay (79%).

CONCLUSIONS

Through combining two next generation sequencing techniques we have developed a method that allows high-throughput SNP discovery in any diploid organism without the need of a whole genome sequence or the creation of normalized cDNA libraries. The need to only perform one 454 run and one GA sequencer run allows high-throughput SNP discovery with sufficient sequence for assay development to be performed in organisms, such as common bean, which have limited genomic resources.

Artemisia capillaris inhibits lipid accumulation in 3T3-L1 adipocytes and obesity in C57BL/6J mice fed a high fat diet

The purpose of the current study was to determine the effect of the Artemisia capillaris ethyl acetate (ACE) fraction on diet-induced obesity and to elucidate the underlying mechanism. The ACE fraction treatment decreased the leptin level and fat accumulation in cultured 3T3-L1 adipocytes through the free fatty acids released in the medium. The ACE fraction significantly suppressed the expression of peroxisome proliferator-activated receptor-gamma in cultured 3T3-L1 adipocytes. To determine the effect of the ACE fraction on C57BL/6J male mice, the mice were separated into six groups: normal control (N), N plus 0.1 g/kg body weight ACE (NB), high fat control group (HF), HF plus 0.05 g/kg of body weight ACE (HFA), HF plus 0.1 g/kg of body weight ACE (HFB), and HF plus 0.03 g/kg of body weight rosiglitazone (RG) groups. We speculate that the HFB group exhibits a lipid-lowering effect via increased mitochondrial beta-oxidation, of which the rate-limiting enzyme is carnitine palmitoyl transferase I, the activity of which was significantly increased. Also, the activity of fatty acid synthase, a key enzyme of fatty acid synthesis, was markedly suppressed (19%) in the HFB group, as compared to the HF group, and glycerol-3-phosphate dehydrogenase activity, which is very useful in studying adipogenic differentiation in vitro, was markedly suppressed (30%) in the HFB group compared with the HF group. Furthermore, the HFB group showed lowered hepatic lipid droplet accumulation and adipose tissue weight and size. We suggest that 0.1 g of the ACE fraction/kg of body weight may exert an anti-obesity effect in C57BL/6J mice by enhancing lipid metabolism.

A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis

The first genetic transcript map of the soybean genome was created by mapping one SNP in each of 1141 genes in one or more of three recombinant inbred line mapping populations, thus providing a picture of the distribution of genic sequences across the mapped portion of the genome. Single-nucleotide polymorphisms (SNPs) were discovered via the resequencing of sequence-tagged sites (STSs) developed from expressed sequence tag (EST) sequence. From an initial set of 9459 polymerase chain reaction primer sets designed to a diverse set of genes, 4240 STSs were amplified and sequenced in each of six diverse soybean genotypes. In the resulting 2.44 Mbp of aligned sequence, a total of 5551 SNPs were discovered, including 4712 single-base changes and 839 indels for an average nucleotide diversity of Theta= 0.000997. The analysis of the observed genetic distances between adjacent genes vs. the theoretical distribution based upon the assumption of a random distribution of genes across the 20 soybean linkage groups clearly indicated that genes were clustered. Of the 1141 genes, 291 mapped to 72 of the 112 gaps of 5-10 cM in the preexisting simple sequence repeat (SSR)-based map, while 111 genes mapped in 19 of the 26 gaps >10 cM. The addition of 1141 sequence-based genic markers to the soybean genome map will provide an important resource to soybean geneticists for quantitative trait locus discovery and map-based cloning, as well as to soybean breeders who increasingly depend upon marker-assisted selection in cultivar improvement.

Quantitative determination of amygdalin epimers from armeniacae semen by liquid chromatography

D-amygdalin and its conversion product, neoamygdalin, were quantitatively analyzed on reverse-phase, high-performance liquid chromatography with an optimized eluent of 10 mM sodium phosphate buffer (pH 3.1) containing 8.5% acetonitrile. Linearity between concentrations and detector responses was obtained in the range from 0.05 to 0.5 mM. The detection limits for D-amygdalin and neoamygdalin were approximately 5 microM per injected amount. Armeniacae semen contains not only amygdalin but also emlusin, which is an enzyme that hydrolyzes amygdalin. When extracting amygdalin from a whole piece of armeniacae semen in boiling water, there was almost no influence of emulsin; which increased the extraction efficiency. However, conversion of d-amygdalin into neoamygdalin at high temperature was found. In this report, we solved this problem by using 4% citric acid as an extractant. This solution also prevented the extraction process from being affected by emulsin. In addition, the extraction efficiency remained the same as that when methanol was used as an extractant, regardless of the cutting size.

Reverse-phase HPLC separation of D-amygdalin and neoamygdalin and optimum conditions for inhibition of racemization of amygdalin

In boiling aqueous solution, D-amygdalin usually begins to convert into neoamygdalin in 3 min and more than 30% of the initial D-amygdalin is found as neoamygdalin after 30 min. In this report, we establish methods for simple HPLC analysis and the inhibition of D-amygdalin conversion. D-Amygdalin and its conversion product, neoamygdalin, were clearly separated on reverse-phase column chromatography by an optimized eluent of 10 mM sodium phosphate buffer (pH 3.8) containing 6% acetonitrile. Linearity for analyzing D-amygdalin and neoamygdalin was observed in the range from 0.05 to 0.5 mM. The detection limits for D-amygdalin and neoamygdalin were ca. 5 microM per injected amount. We found that D-amygdalin conversion was completely inhibited by adding 0.05% citric acid to the aqueous solution before boiling. To prevent the loss of pharmaceutical potency of Tonin, we applied this method to measure the conversion rate of D-amygdalin. We confirmed that D-amygdalin conversion in Tonin is effectively inhibited by acidic boiling solution with 0.1% citric acid.

Development of quantitative extraction method of amygdalin without enzymatic hydrolysis from tonin(Persicae Semen) by high performance liquid chromatography

Tonin(Persicae Semen) is the herb medicine that contains amygdalin as a major ingredient. Amygdalin in water is decomposed into benzaldehyde, HCN, and glucose by emulsin, a hydrolysis enzyme in tonin. A useful and practical method for the optimum extraction condition of amygdalin without enzymatic hydrolysis is required. The extraction yield of amygdalin of natural formula tonin was 0.1% from crude powders, 1.4% from small pieces, 3.5% from half pieces and 2.4% from whole pieces. The extraction yield of amygdalin of outer shell-eliminated tonin was 0.3% from crude powders, 1.4% from small pieces, and 3.5% from half pieces and whole pieces respectively. The extraction yield of amygdalin was most high when using the size larger than half.

Reliability of intraoperative transesophageal echocardiography during Tetralogy of Fallot repair

There is limited information available concerning the accuracy of intraoperative transesophageal echocardiography (TEE) in predicting the extent of residual abnormalities after recovery from surgical repair of tetralogy of Fallot. Therefore, we investigated differences between the results of final postbypass TEE and those of postrecovery (mean, 6 days after surgery) transthoracic echocardiography in a total of 28 consecutive pediatric patients who underwent repair of tetralogy of Fallot with biplane or multiplane TEE. Both postbypass and postrecovery echocardiographic examinations included measurements of the right ventricle (RV)-main pulmonary artery (PA) and the main PA-branch PA peak instantaneous gradients, the degree of pulmonary valvar insufficiency, and color Doppler interrogation of the ventricular septum for residual defects. The RV-main PA gradient did not change significantly: 15 +/- 13 vs 18 +/- 14 mmHg (postbypass versus postrecovery, mean +/- SD). None of the patients had a decrease of > or = 10 mmHg; and only one patient had an increase of > or = 15 mmHg. There also was no change in the degree of pulmonary insufficiency (3.0 +/- 1.2 versus 3.1 +/- 1.1, using a scale of 0 to 4). Only one of the seven very small (< or = 2 mm) residual ventricular septal defects was not discovered during postbypass TEE. However, postrecovery transthoracic echocardiography detected significant branch PA stenosis (peak gradient, > or = 15 mmHg) in five patients (18%) that was not detected during postbypass TEE (P < 0.03). Of the branch PA stenoses that were not detected during TEE, four were left and one was right.

CONCLUSIONS

Postbypass TEE after tetralogy of Fallot repair reliably predicts residual postrecovery hemodynamic abnormalities, except for branch PA stenosis.

Variables controlling contrast generation in a urinary bladder model

An ultrasound system has been developed to generate microbubbles in vivo for use as ultrasound contrast agent. Possible application include diagnosis of reflux in the urinary tract. In experiments designed to elucidate the contrast microbubble generation process, acoustic bursts (at 1.8 MHz, 125 ms) were propagated through a latex rubber balloon, modeled after a rabbit urinary bladder, containing fluids of various air and carbon dioxide saturations and concentrations of cavitation nuclei (0.198-micron-diam polystyrene particles). The peak rarefactional pressure threshold for contrast microbubble generation, as visualized with a diagnostic ultrasound system, decreased approximately a factor of 2 for increasing particle concentration from 10(8) to 10(10) particles/cc, with the lowest threshold of 5.24 MPa. For samples with gas saturations below 50% and 10(10) particles/cc, the average thresholds were at least twice as high as those of more saturated fluids (with mean threshold for saturated fluids of 6.45 MPa), and samples containing CO2 had considerably lower thresholds than respective under-saturations in air. At a fixed pressure amplitude, echogenicity tended to increase with both increasing particle concentration and gas saturation; this was more favorable for samples containing CO2. Even in a restricted-nuclei environment such as the urinary bladder, generation of vaporous cavitation should be possible; however, subsequently, abundant gas is needed to grow vaporous bubbles to persistent and imageable sizes, to assist in the diagnosis of urinary reflux.