Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany.

BACKGROUND: Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany. METHODS: A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared. RESULTS: WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains. CONCLUSIONS: Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.

Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.

Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency.

Complete Genome Sequence of the Type Strain Citrobacter rodentium DSM 16636.

The type strain Citrobacter rodentium DSM 16636 was characterized in 1995. This species is widely used in rodents to study the virulence of locus-of-enterocyte-effacement-type pathogens, such as enterohemorrhagic Escherichia coli. The type strain had not been sequenced yet. Here, we report the closed genome (5.3 Gbp) and its plasmid (39.3 kbp).

Quantitative studies on roast kinetics for bioactives in coffee.

Quantitative analysis of the bioactives trigonelline (1), N-methylpyridinium (2), caffeine (3), and caffeoylquinic acids (4) in a large set of roasted Arabica (total sample size n = 113) and Robusta coffees (total sample size n = 38) revealed that the concentrations of 1 and 4 significantly correlated with the roasting color (P < 0.001, two tailed), whereas that of 2 significantly correlated inversely with the color (P < 0.001, two tailed). As dark-roasted coffees were rich in N-methylpyridinium whereas light-roasted coffees were rich in trigonelline and caffeoylquinic acids, manufacturing of roast coffees rich in all four bioactives would therefore necessitate blending of two or even more coffees of different roasting colors. Additional experiments on the migration rates during coffee brewing showed that all four bioactives were nearly quantitatively extracted in the brew (>90%) when a water volume/coffee powder ratio of >16 was used.

Bioappearance and pharmacokinetics of bioactives upon coffee consumption.

Habitual consumption of medium amounts of coffee over the whole life-span is hypothesized to reduce the risk to develop diabetes type 2 (DM2) and Alzheimer's disease (AD). To identify putative bioactive coffee-derived metabolites, first, pooled urine from coffee drinkers and non-coffee drinkers were screened by UPLC-HDMS. After statistical data analysis, trigonelline, dimethylxanthines and monomethylxanthines, and ferulic acid conjugates were identified as the major metabolites found after coffee consumption. For quantitative analysis of these markers in body fluids, targeted methods based on stable-isotope dilution and UPLC-MS/MS were developed and applied to plasma samples from a coffee intervention study (n = 13 volunteers) who consumed a single cup of caffeinated coffee brew after a 10-day washout period. Chlorogenic acid-derived metabolites were found to be separated into two groups showing different pharmacokinetic properties. The first group comprised, e.g., ferulic acid and feruloyl sulfate and showed early appearance in the plasma (~1 h). The second group contained particularly chlorogenic acid metabolites formed by the intestinal microflora, appearing late and persisting in the plasma (>6 h). Trigonelline appeared early but persisted with calculated half-life times ~5 h. The plasma levels of caffeine metabolites significantly and progressively increased 2-4 h after coffee consumption and did not reach c max within the time frame of the study. The pharmacokinetic profiles suggest that particularly trigonelline, caffeine, its metabolites, as well as late appearing dihydroferulic acid, feruloylglycine and dihydroferulic acid sulfate formed from chlorogenic acid by the intestinal microflora accumulate in the plasma due to their long half-life times during habitual consumption of several cups of coffee distributed over the day. Since some of these metabolites have been reported to show antioxidant effects in vivo, antioxidant-response-element activating potential, and neuroprotective properties, respectively, some of these key metabolites might account for the inflammation- and DM2/AD risk reducing effects reported for habitual life time consumption of coffee.

2-O-ß-D-Glucopyranosyl-carboxyatractyligenin from Coffea L. inhibits adenine nucleotide translocase in isolated mitochondria but is quantitatively degraded during coffee roasting.

Atractyloside (1) and carboxyatractyloside (2) are well-known inhibitors of the adenine nucleotide translocase (ANT) in mitochondria, thus effectively blocking oxidative phosphorylation. Structurally related derivatives atractyligenin (3), 2-O-ß-D-glucopyranosyl-atractyligenin (4), 3'-O-ß-D-glucopyranosyl-2'-O-isovaleryl-2ß-(2-desoxy-atractyligenin)-ß-D-glucopyranoside (5), and 2-O-ß-D-glucopyranosyl-carboxyatractyligenin (6) were isolated from raw beans of Coffea L. and the impact of 1-6 on ANT activity was evaluated in isolated mitochondria. Among the coffee components, 6 significantly inhibited ANT activity leading to reduced respiration. Quantitative analysis in commercial coffees, experimental roastings of coffee, and model experiments using purified compound 6 consistently revealed a complete degradation during thermal treatment. In comparison, raw coffee extracts were found to contain high levels of 6, which are therefore expected to be present in food products enriched with raw coffee extracts. This implies the necessity of analytically controlling the levels of 6 in raw coffee extracts when used as additives for food products.

Urinary N-methylpyridinium and trigonelline as candidate dietary biomarkers of coffee consumption.

SCOPE: In order to validate the in vivo function of putatively healthy molecules in foods, human intervention studies are required. As the subject's compliance concerning intake or abstinence of a given food is considered mandatory to be monitored by biomarkers, the objective was to identify analytical markers for coffee consumption. METHODS AND RESULTS: Urine samples collected from coffee drinkers were compared with those of non-coffee drinkers using hydrophilic liquid interaction chromatography (HILIC)/time-of-flight mass spectrometry-based metabolite profiling. Two urinary molecules, found to be contributing most to the dissimilarities between both groups, were identified as N-methylpyridinium (NMP) and trigonelline and their suitability as coffee-specific biomarkers was validated by means of a coffee intervention study. After the volunteers (five females and four males) consumed a single dose of coffee, morning urine was collected for 10 days while staying abstinent from any coffee. HILIC-MS/MS-stable isotope dilution analysis (SIDA) revealed elevated urinary concentrations of trigonelline and NMP for up to 48 (p=0.001) and 72 h (p=0.002), respectively, after coffee consumption when compared with non-coffee drinkers. CONCLUSION: Analysis of urinary NMP allows to check for coffee consumption within a period of 3 days and is proposed as a dietary biomarker which might be used as an analytical probe to control compliance in human intervention studies on coffee.

Development of a hydrophilic liquid interaction chromatography-high-performance liquid chromatography-tandem mass spectrometry based stable isotope dilution analysis and pharmacokinetic studies on bioactive pyridines in human plasma and urine after coffee consumption.

The paper reports on the development of an accurate hydrophilic liquid interaction chromatography tandem mass spectrometry (HILIC-MS/MS) based stable isotope dilution analysis for the simultaneous quantitation of the food-derived bioactive pyridines trigonelline, nicotinic acid, nicotinamide, and N-methylpyridinium, as well as their key metabolites nicotinamide-N-oxide, N-methylnicotinamide, N-methyl-2-pyridone-5-carboxamide, N-methyl-4-pyridone-5-carboxamide, and N-methyl-2-pyridone-5-carboxylic acid in human plasma and urine. Precision of the stable isotope dilution analysis (SIDA) was 1.9% and 11.9% relative standard deviation (n = 6), and accuracy was between 92.4% and 113.0%. The lower limit of quantitation (LLOQ) was 50 fmol (10 pmol/mL) injected onto the column for all analytes with the exception of N-methyl-2-pyridone-5-carboxylic acid and N-methyl-2-pyridone-5-carboxamide, for which an LLOQ of 100 fmol (20 pmol/mL) was found. The method was applied to monitor the plasma appearance and urinary excretion and to determine pharmacokinetic parameters of the bioactive pyridines as well as their metabolites in a clinical human intervention study with healthy volunteers (six women, seven men) after oral administration of 350 mL of a standard coffee beverage. Trigonelline plasma levels increased from 160 nmol/L to maximum concentrations of 5479 (males) or 6547 nmol/L (females), and N-methylpyridinium plasma levels raised from virtually complete absence to maximum values of 777 (females) or 804 nmol/L (males) within 2-3 and 1-2 h after coffee consumption, respectively. The high plasma levels of N-methylpyridinium found after coffee consumption clearly demonstrate for the first time that this cation is entering the vascular system, which is the prerequisite for biological in vivo effects claimed for that compound. In contrast, the coffee intervention did not significantly influence the plasma concentrations of N-methyl-2-pyridone-5-carboxamide and N-methyl-4-pyridone-5-carboxamide, the major niacin metabolites. Within 8 h after coffee intervention, an urinary excretion of 57.4 +/- 6.9% of trigonelline and 69.1 +/- 6.2% of N-methylpyridinium was found for the male volunteers, whereas females excreted slightly less with 46.2 +/- 7.4% and 61.9 +/- 12.2% of these pyridines.