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A New Laboratory Workflow Integrating the Free Light Chains Kappa Quotient into Routine CSF Analysis
(2022)
We performed this cohort study to test whether further analysis of intrathecal inflammation can be omitted if the free light chain kappa (FLCκ) quotient is within the reference range in the corresponding quotient diagram. FLCκ concentrations were measured in serum and cerebrospinal fluid (CSF) samples. The intrathecal fraction (IF) of FLCκ was calculated in relation to the hyperbolic reference range. 679 patient samples were used as a discovery cohort (DC). The sensitivity and negative predictive value (NPV) of the FLCκ-IF for the detection of an intrathecal humoral immune response (CSF-specific OCB and/or IF IgG/A/M > 0%) was determined. Based on these data, a diagnostic algorithm was developed and prospectively validated in an independent validation cohort (VC, n = 278). The sensitivity of the FLCκ-IF was 98% in the DC and 97% in the VC with a corresponding NPV of 99%. The use of the FLCκ-IF as a first line analysis would have reduced the Ig and OCB analysis by 62% in the DC and 74% in the VC. The absence of a FLCκ-IF predicts the absence of a humoral intrathecal immune response with a very high NPV of 99%. Thus, integration of our proposed algorithm into routine CSF laboratory analysis could help to reduce analytical efforts.
Abstract
Multiple G‐tracts within the promoter region of the c‐myc oncogene may fold into various G‐quadruplexes with the recruitment of different tracts and guanosine residues for the G‐core assembly. Thermodynamic profiles for the folding of wild‐type and representative truncated as well as mutated sequences were extracted by comprehensive DSC experiments. The unique G‐quadruplex involving consecutive G‐tracts II–V with formation of two one‐nucleotide and one central two‐nucleotide propeller loop, previously proposed to be the biologically most relevant species, was found to be the most stable fold in terms of its Gibbs free energy of formation at ambient temperatures. Its stability derives from its short propeller loops but also from the favorable type of loop residues. Whereas quadruplex folds with long propeller loops are significantly disfavored, a snap‐back loop structure formed by incorporating a 3’‐terminal guanosine into the empty position of a tetrad seems highly competitive based on its thermodynamic stability. However, its destabilization by extending the 3’‐terminus questions the significance of such a species under in vivo conditions.
Für die Bekämpfung bakterieller Infektionen ist das angeborene Immunsystem von essenzieller Bedeutung. Im Rahmen dieser Promotion wurden murine angeborene Immunmechanismen bei systemischer Infektion mit Burkholderia pseudomallei, dem gram-negativen Erreger der Melioidose, sowie pulmonaler Infektion mit dem gram-positiven Erreger Staphylococcus aureus bei genetisch heterogenen BALB/c- und C57BL/6-Mäusen untersucht. Für in vitro-Untersuchungen wurde zunächst im ersten Teil eine Methode zur serumfreien Kultivierung von primären Makrophagen aus murinen Knochenmarkstammzellen unter Verwendung des lipoproteinreduzierten Serumsupplements Panexin® etabliert. Derart kultivierte Makrophagen von BALB/c- und C57BL/6-Mäusen wiesen wichtige Effektor-funktionen wie die Fc-Rezeptor-vermittelte Phagozytose und bakterizide Aktivität auf. Außerdem gelang es, die in der Literatur unter FCS-Bedingungen beschriebenen polarisierten Makrophagen-Phänotypen auch unter serumfreien Bedingungen funktionell nachzuweisen. So wiesen C57BL/6-Makrophagen im Vergleich zu BALB/c-Makrophagen ein deutlich höheres bakterizides Potenzial gegenüber B. pseudomallei auf und produzierten größere Mengen des zytotoxischen Stickoxids, unterschieden sich jedoch nicht in ihrer Fähigkeit, E. coli zu eliminieren. Im zweiten Teil der Arbeit konnte mithilfe dieses standardisierten Zellkultursystems gezeigt werden, dass Caspase-1 bereits in der Frühphase der B. pseudomallei-Infektion IFNγ-unabhängig für die bakterizide Potenz der Makrophagen erforderlich ist, die Caspase-1-Aktivität andererseits im gleichen Zeitraum jedoch eine Zunahme des zytotoxischen Erregereffektes verursacht. Durch die gestörte intrazelluläre Erregerelimination unmittelbar nach Infektion kam es im weiteren zeitlichen Verlauf zur Zunahme des erregerabhängigen Zelltodes, für den in der Literatur allerdings ursächlich auch das Fehlen verzögerter Caspase-1-abhängiger protektiver Effekte diskutiert wird. Weiterhin konnte gezeigt werden, dass Caspase-1 eine essenzielle Bedeutung für die in vivo-Resistenz und Generierung der inflammatorischen Zytokinantwort hat, welche zur Überwindung der akuten Infektion beiträgt. Während die Caspase-1-Expression bei unterschiedlich empfänglichen BALB/c- und C57BL/6-Makrophagen nach Infektion vergleichbar war, könnte die gesteigerte IL-1β-Produktion bei resistenteren C57BL/6-Makrophagen darauf hinweisen, dass unterschiedliche Aktivitäten des Enzyms in Mausstämmen mit unterschiedlichen genotypischen Eigenschaften den Verlauf der murinen Melioidose beeinflussen. Im letzten Teil dieser Dissertation wurde erstmals am Beispiel von BALB/c- und C57BL/6-Mäusen ein vergleichendes S. aureus-Pneumoniemodell entwickelt, bei dem BALB/c-Mäuse neben einer höheren Empfänglichkeit auch eine verminderte Fähigkeit aufwiesen, den Erreger aus der Lunge zu eliminieren. Während neutrophile Granulozyten für das Überleben erforderlich waren und die Organkeimzahlen signifikant zu reduzieren vermochten, steigerten Makrophagen die Mortalität, ohne jedoch Einfluss auf die Bakterienelimination zu haben. Für diese Mortalitätszunahme könnte eine überschießende Zytokinantwort mit der Folge eines Zytokinschocks verantwortlich sein. Schließlich wurde gezeigt, dass das bakterielle sae-Regulon, welches die Expression verschiedener bakterieller Proteine steuert, sowohl für die Virulenz, als auch für die intrapulmonale Persistenz des Erregers in diesem Infektionsmodell von entscheidender Bedeutung ist. Die zu beobachtenden Unterschiede in Mortalität und Organkeimzahlen belegen zugleich, dass das etablierte Mausmodell eine für die Untersuchung bakterieller Virulenzfaktoren ausreichende Sensitivität aufweist.
Coagulase-negative staphylococci (CoNS) are common opportunistic pathogens, but also ubiquitous human and animal commensals. Infection-associated CoNS from healthcare environments are typically characterized by pronounced antimicrobial resistance (AMR) including both methicillin- and multidrug-resistant isolates. Less is known about AMR patterns of CoNS colonizing the general population. Here we report on AMR in commensal CoNS recovered from 117 non-hospitalized volunteers in a region of Germany with a high livestock density. Among the 69 individuals colonized with CoNS, 29 had reported contacts to either companion or farm animals. CoNS were selectively cultivated from nasal swabs, followed by species definition by 16S rDNA sequencing and routine antibiotic susceptibility testing. Isolates displaying phenotypic AMR were further tested by PCR for presence of selected AMR genes. A total of 127 CoNS were isolated and Staphylococcus epidermidis (75%) was the most common CoNS species identified. Nine isolates (7%) were methicillin-resistant (MR) and carried the mecA gene, with seven individuals (10%) being colonized with at least one MR-CoNS isolate. While resistance against gentamicin, phenicols and spectinomycin was rare, high resistance rates were found against tetracycline (39%), erythromycin (33%) and fusidic acid (24%). In the majority of isolates, phenotypic resistance could be associated with corresponding AMR gene detection. Multidrug-resistance (MDR) was observed in 23% (29/127) of the isolates, with 33% (23/69) of the individuals being colonized with MDR-CoNS. The combined data suggest that MR- and MDR-CoNS are present in the community, with previous animal contact not significantly influencing the risk of becoming colonized with such isolates.
Antibiotic resistance is increasing worldwide making it necessary to search for alternative antimicrobials. Sodium bituminosulfonate is a long-known substance, whose antimicrobial inhibitory activity has recently been re-evaluated. However, to the best of our knowledge, the bactericidal mode of action of this substance has not been systematically characterized. The aim of this study was to investigate the in vitro bactericidal activity of sodium bituminosulfonate by determining the minimal bactericidal concentrations (MBC), as well as the rapidity of bactericidal effect by time-kill curves. Clinical isolates of methicillin-susceptible (MSSA, n = 20) and methicillin-resistant (mecA/mecC-MRSA, n = 20) Staphylococcus aureus were used to determine MBC by a broth microdilution method. Sodium bituminosulfonate (Ichthyol® light) was tested in double-dilution concentration steps ranging from 0.03 g/L to 256 g/L. For time-kill analysis, two reference and two clinical S. aureus strains were tested with different concentrations of sodium bituminosulfonate (1× minimal inhibitory concentration (MIC), 2× MIC, 4× MIC, 16× MIC and 256× MIC). For MSSA isolates, MBC50, MBC90 and the MBC range were 0.5 g/L, 1.0 g/L and 0.125–1.0 g/L; (MBC/MIC ratio)50, (MBC/MIC ratio)90 and the range of the MBC/MIC ratio were 4, 4 and 1–8, respectively. Among MRSA isolates, MBC50, MBC90 and the MBC range amounted to 0.5 g/L, 1.0 g/L and 0.06–1.0 g/L; (MBC/MIC ratio)50, (MBC/MIC ratio)90 and the range of the MBC/MIC ratio were 2, 4 and 1–8, respectively. Time-kill kinetics revealed a bactericidal effect after 30 min for sodium bituminosulfonate concentrations of 16× MIC and 256× MIC. The bactericidal activity against MSSA and MRSA was demonstrated for sodium bituminosulfonate. The killing was very rapid with the initial population reduced by 99.9% after only short incubation with concentrations of 16× MIC and higher.
The worldwide distribution and prevalence of melioidosis, an infectious disease caused by the soil-dwelling Gram-negative bacterium Burkholderia pseudomallei, is unknown. In Vietnam, sporadic cases of melioidosis have been reported for decades, but clinical and epidemiological data for the indigenous population are still scarce. In this study, we reviewed clinical and demographic data of patients with culture-proven melioidosis diagnosed at a single large referral hospital in Hanoi between November 1997 and December 2005. The clinical manifestations of melioidosis with fatal septicaemia as the most common presentation, a high rate of underlying diseases and a peak of cases admitted during the wet season were similar to studies from other endemic areas. The geographical origin of melioidosis patients shows that melioidosis exists in at least 18 northern provinces. The characterization of clinical B. pseudomallei strains by multilocus sequence typing identified 17 different sequence types (STs), ten of which have (as yet) not been found outside Vietnam. Several of these STs presumably were generated through recent evolutionary events in this rapidly diversifying bacterial species, and thus restricted geographic distribution may be a consequence of limited time passed since emergence. In order to define the distribution of the bacterium in the environment, our study also aimed to develop a more sensitive culture method for the detection of B. pseudomallei from soil samples in endemic areas compared to the currently used culture method based on soil dispersion in water. Our newly developed protocol involving soil dispersion in a polyethylene glycol and sodium deoxycholate solution increased the yield of viable B. pseudomallei from soil samples. Comparative testing of soil samples from Northeast Thailand covering a wide range of B. pseudomallei concentrations demonstrated a significantly higher recovery (p < 0.0001) of B. pseudomallei colony forming units by the new method compared to the conventional method. Our data indicate that using the detergents polyethylene glycol and sodium deoxycholate not only results in a higher recovery of viable B. pseudomallei, but also results in a shift in the bacterial species recovered from soil samples. Molecular methods based on direct bacterial nucleic acid extraction from environmental samples and subsequent amplification have the potential to overcome many restrictions of traditional microbiological approaches. Moreover, culture-dependent methods require special expertise in recognizing B. pseudomallei colony morphologies. Thus, a highly sensitive culture-independent DNA-based method that allows direct quantification of B. pseudomallei from soil is needed, particularly in diagnostic laboratories outside endemic areas. We therefore aimed to establish a protocol for B. pseudomallei soil DNA isolation, purification and quantification by qPCR targeting a type three secretion system 1 single copy gene. This assay was validated using 40 soil samples from Northeast Thailand that underwent parallel bacteriological culture. All 26 samples that were B. pseudomallei-positive by direct culture were B. pseudomallei qPCR-positive, with a median of 1.84 x 104 genome equivalents (range 3.65 x 102 to 7.85 x 105) per gram of soil. This was 10.6 fold (geometric mean; range 1.1 to 151.3) higher than the bacterial count as defined by culture. Moreover, the qPCR detected B. pseudomallei in seven samples (median 36.9 genome equivalents per g soil; range 9.4 to 47.3), which were negative on direct culture. These seven positives were reproduced using a nested PCR targeting a second, independent B. pseudomallei-specific sequence. Two samples were direct culture and qPCR negative but nested PCR positive. Five samples were negative by both PCR methods and culture. In conclusion, this is the first report on a series of cases describing clinical and epidemiological features of melioidosis and corresponding Burkholderia pseudomallei strains from northern Vietnam. Moreover, our newly developed culture-based and PCR-based methods provide highly specific and sensitive tools for the quantitative environmental surveillance of B. pseudomallei.
Summary
Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5‐enolpyruvyl‐shikimate‐3‐phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate‐resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate‐sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia.
Ziel dieser Arbeit war die funktionelle Charakterisierung von zwei putativen Virulenzgenen von Burkholderia pseudomallei. Es wurde ein klassischer LysR-Typ Transkriptionsregulator (BPSL0117) mittels Tn5 Mutagenese als wichtiger Virulenzfaktor gefunden und mit verschiedenen in vitro, in vivo und weiterer molekularer Methoden wie gelfreie Proteomics untersucht. Daneben wurde ein hypothetisches Protein (BPSS1528 = bapA) mit unbekannter Funktion aus einen Typ-III-Sekretionssystem gezielt deletiert und funktionell beschrieben. Diese Mutante wies letztlich keine eingeschränkte Virulenz im Vergleich zum Wildtypstamm aus.
Staphylococcus aureus has acquired resistance to antibiotics since their first use. The S. aureus protein NorA, an efflux pump belonging to the major facilitator superfamily (MFS), contributes to resistance to fluoroquinolones (e.g., ciprofloxacin), biocides, dyes, quaternary ammonium compounds, and antiseptics. Different compounds have been identified as potential efflux pump inhibitors (EPIs) of NorA that result in increased intracellular concentration of antibiotics, restoring their antibacterial activity and cell susceptibility. However, none of the currently known EPIs have been approved for clinical use, probably due to their toxicity profiles. In the present study, we screened approved drugs for possible efflux pump inhibition. By screening a compound library of approximately 1200 different drugs, we identified nilotinib, a tyrosine kinase inhibitor, as showing the best efflux pump inhibitory activity, with a fractional inhibitory concentration index of 0.1875, indicating synergism with ciprofloxacin, and a minimum effective concentration as low as 0.195 μM. Moreover, at 0.39 μM, nilotinib, in combination with 8 μg/mL of ciprofloxacin, led to a significant reduction in biofilm formation and preformed mature biofilms. This is the first description of an approved drug that can be used as an efflux pump inhibitor and to reduce biofilms formation at clinically achievable concentrations.