Usefulness of a Molecular Strategy for the Detection of Bacterial DNA in Patients with Severe Sepsis Undergoing Continuous Renal Replacement Therapy

Interferon-β regulates proresolving lipids to promote the resolution of acute airway inflammation

Acute respiratory distress syndrome is characterized by aberrant inflammatory responses, including polymorphonuclear neutrophil granulocyte dysfunction and hyperactive Toll-like receptor signaling. Timely resolution of bacterial infections depends on efficient removal of neutrophils from the inflamed tissue. Here we show that the antiviral cytokine interferon-β is essential for the resolution of neutrophil-driven airway inflammation by countering Toll-like receptor 9–mediated suppression of phagocytosis, neutrophil apoptosis, and uptake by macrophages. We also report that the beneficial effects of interferon-β are, in part, mediated by production of proresolving lipid mediators, such as 15-epi-lipoxin A₄ and resolvin D1, which act through the lipoxin receptor ALX/FPR2. These findings uncover an interferon-β–initiated ALX/FPR2-centered resolution program as a potential target for facilitating the resolution of airway inflammation.

Aberrant immune responses, including hyperresponsiveness to Toll-like receptor (TLR) ligands, underlie acute respiratory distress syndrome (ARDS). Type I interferons confer antiviral activities and could also regulate the inflammatory response, whereas little is known about their actions to resolve aberrant inflammation. Here we report that interferon-β (IFN-β) exerts partially overlapping, but also cooperative actions with aspirin-triggered 15-epi-lipoxin A₄ (15-epi-LXA₄) and 17-epi-resolvin D1 to counter TLR9-generated cues to regulate neutrophil apoptosis and phagocytosis in human neutrophils. In mice, TLR9 activation impairs bacterial clearance, prolongs Escherichia coli–evoked lung injury, and suppresses production of IFN-β and the proresolving lipid mediators 15-epi-LXA₄ and resolvin D1 (RvD1) in the lung. Neutralization of endogenous IFN-β delays pulmonary clearance of E. coli and aggravates mucosal injury. Conversely, treatment of mice with IFN-β accelerates clearance of bacteria, restores neutrophil phagocytosis, promotes neutrophil apoptosis and efferocytosis, and accelerates resolution of airway inflammation with concomitant increases in 15-epi-LXA₄ and RvD1 production in the lungs. Pharmacological blockade of the lipoxin receptor ALX/FPR2 partially prevents IFN-β–mediated resolution. These findings point to a pivotal role of IFN-β in orchestrating timely resolution of neutrophil and TLR9 activation–driven airway inflammation and uncover an IFN-β–initiated resolution program, activation of an ALX/FPR2-centered, proresolving lipids-mediated circuit, for ARDS.

Roles of neutrophil granule proteins in orchestrating inflammation and immunity

Neutrophil granulocytes form the first line of host defense against invading pathogens and tissue injury. They are rapidly recruited from the blood to the affected sites, where they deploy an impressive arsenal of effectors to eliminate invading microbes and damaged cells. This capacity is endowed in part by readily mobilizable proteins acquired during granulopoiesis and stored in multiple types of cytosolic granules with each granule type containing a unique cargo. Once released, granule proteins contribute to killing bacteria within the phagosome or the extracellular milieu, but are also capable of inflicting collateral tissue damage. Neutrophil-driven inflammation underlies many common diseases. Research over the last decade has documented neutrophil heterogeneity and functional versatility far beyond their antimicrobial function. Emerging evidence indicates that neutrophils utilize granule proteins to interact with innate and adaptive immune cells and orchestrate the inflammatory response. Granule proteins have been identified as important modulators of neutrophil trafficking, reverse transendothelial migration, phagocytosis, neutrophil life span, neutrophil extracellular trap formation, efferocytosis, cytokine activity, and autoimmunity. Hence, defining their roles within the inflammatory locus is critical for minimizing damage to the neighboring tissue and return to homeostasis. Here, we provide an overview of recent advances in the regulation of degranulation, granule protein functions, and signaling in modulating neutrophil-mediated immunity. We also discuss how targeting granule proteins and/or signaling could be harnessed for therapeutic benefits.

Culture-Dependent and Sequencing Methods Revealed the Absence of a Bacterial Community Residing in the Urine of Healthy Cats

A growing number of studies suggest that the lower urinary tract of humans and dogs can harbor a urinary microbiota. Nevertheless, a certain concern has developed that the microbiota reported could be due to unaccounted contamination, especially in low-biomass samples. The aim of this study was to investigate the bacterial community which populates the urine of healthy cats using two approaches: a culture-dependent approach which consisted of the expanded quantitative urine culture (EQUC) techniques capable of identifying live bacteria not growing in standard urine cultures, and a culture-independent approach which consisted of 16S ribosomal RNA next generation sequencing (16S rRNA NGS) capable of identifying bacterial DNA and exploring microbial diversity with high resolution. To avoid confounding factors of possible bacterial contamination, the urine was sampled using ultrasound-guided cystocentesis, and several sample controls and negative controls were analyzed. The urine sampled from the 10 cats included in the study showed no bacterial growth in the EQUC procedure. Although several reads were successfully originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and the negative control, and no taxa were statistically accepted as non-contaminant. Taken together, the results obtained allowed stating that no viable bacteria were present in the urine of healthy cats without lower urinary tract disease and urinary tract infections, and that the bacterial DNA detected was of contaminant origin.

Neutrophil heterogeneity and fate in inflamed tissues: implications for the resolution of inflammation

Neutrophils are polymorphonuclear leukocytes that play a central role in host defense against infection and tissue injury. They are rapidly recruited to the inflamed site and execute a variety of functions to clear invading pathogens and damaged cells. However, many of their defense mechanisms are capable of inflicting collateral tissue damage. Neutrophil-driven inflammation is a unifying mechanism underlying many common diseases. Efficient removal of neutrophils from inflammatory loci is critical for timely resolution of inflammation and return to homeostasis. Accumulating evidence challenges the classical view that neutrophils represent a homogeneous population and that halting neutrophil influx is sufficient to explain their rapid decline within inflamed loci during the resolution of protective inflammation. Hence, understanding the mechanisms that govern neutrophil functions and their removal from the inflammatory locus is critical for minimizing damage to the surrounding tissue and for return to homeostasis. In this review, we briefly address recent advances in characterizing neutrophil phenotypic and functional heterogeneity and the molecular mechanisms that determine the fate of neutrophils within inflammatory loci and the outcome of the inflammatory response. We also discuss how these mechanisms may be harnessed as potential therapeutic targets to facilitate resolution of inflammation.

15-Epi-LXA4 and 17-epi-RvD1 restore TLR9-mediated impaired neutrophil phagocytosis and accelerate resolution of lung inflammation

Timely resolution of bacterial infections critically depends on phagocytosis of invading pathogens by polymorphonuclear neutrophil granulocytes (PMNs), followed by PMN apoptosis and efferocytosis. Here we report that bacterial DNA (CpG DNA) and mitochondrial DNA impair phagocytosis and attenuate phagocytosis-induced apoptosis in human PMNs through Toll-like receptor 9 (TLR9)-mediated release of neutrophil elastase and proteinase 3 and subsequent down-regulation of the complement receptor C5aR. Consistently, CpG DNA delays pulmonary clearance of Escherichia coli in mice and suppresses PMN apoptosis, efferocytosis, and generation of proresolving lipid mediators, thereby prolonging lung inflammation evoked by E. coli Genetic deletion of TLR9 renders mice unresponsive to CpG DNA. We also show that aspirin-triggered 15-epi-lipoxin A₄ (15-epi-LXA₄) and 17-epi-resolvin D1 (17-epi-RvD1) through the receptor ALX/FPR2 antagonize cues from CpG DNA, preserve C5aR expression, restore impaired phagocytosis, and redirect human PMNs to apoptosis. Treatment of mice with 15-epi-LXA₄ or 17-epi-RvD1 at the peak of inflammation accelerates clearance of bacteria, blunts PMN accumulation, and promotes PMN apoptosis and efferocytosis, thereby facilitating resolution of E. coli-evoked lung injury. Collectively, these results uncover a TLR9-mediated endogenous mechanism that impairs PMN phagocytosis and prolongs inflammation, and demonstrate both endogenous and therapeutic potential for 15-epi-LXA₄ and 17-epi-RvD1 to restore impaired bacterial clearance and facilitate resolution of acute lung inflammation.

Toll-like receptor 9 signaling regulates tissue factor and tissue factor pathway inhibitor expression in human endothelial cells and coagulation in mice

Supplemental Digital Content is available in the text.

Objective:

Bacterial DNA (CpG DNA) persists in tissues and blood under pathological conditions that are associated with enhanced intravascular coagulation. Toll-like receptor 9 recognizes CpG DNA and elicits innate and adoptive immunity, yet the impact of CpG DNA on coagulation has not been studied. In this study, we investigated the effects of CpG DNA on the expression and activity of tissue factor, a key initiator of coagulation and tissue factor pathway inhibitor in human coronary artery endothelial cells and on coagulation in mice.

Design:

Controlled in vitro and in vivo studies.

Setting:

University research laboratory.

Subjects:

Cultured human coronary artery endothelial cell, wild-type mice, and TLR9-deficient mice.

Interventions:

Human coronary artery endothelial cell was challenged with CpG DNA, and tissue factor and tissue factor pathway inhibitor expression and activity were assessed. In mice, the effects of CpG DNA on bleeding time and plasma levels of thrombin-antithrombin complexes and tissue factor were measured.

Measurements and Main Results:

We found that CpG DNA, but not eukaryotic DNA, evoked marked nuclear factor-κB-mediated increases in tissue factor expression at both messenger RNA and protein levels, as well as in tissue factor activity. Conversely, CpG DNA significantly reduced tissue factor pathway inhibitor transcription, secretion, and activity. Inhibition of Toll-like receptor 9 with a telomere-derived Toll-like receptor 9 inhibitory oligonucleotide or transient Toll-like receptor 9 knockdown with small interfering RNA attenuated human coronary artery endothelial cell responses to CpG DNA. In wild-type mice, CpG DNA shortened the bleeding time parallel with dramatic increases in plasma thrombin-antithrombin complex and tissue factor levels. Pretreatment with inhibitory oligonucleotide or anti-tissue factor antibody or genetic deletion of TLR9 prevented these changes, whereas depleting monocytes with clodronate resulted in a modest partial inhibition.

Conclusions:

Our findings demonstrate that bacterial DNA through Toll-like receptor 9 shifted the balance of tissue factor and tissue factor pathway inhibitor toward procoagulant phenotype in human coronary artery endothelial cells and activated blood coagulation in mice. Our study identifies Toll-like receptor 9 inhibitory oligonucleotides as potential therapeutic agents for the prevention of coagulation in pathologies where bacterial DNA may abundantly be present.

Transfer of low-molecular weight single-stranded DNA through the membrane of a high-flux dialyzer

PURPOSE

Microbial contamination is often present in dialysate used for hemodialysis. Small single-stranded bacterial DNA sequences are capable of activating human inflammatory pathways, through mechanisms that include the Toll-like-receptor 9, and dialysis patients frequently show severe inflammation. Since these molecules have been found in dialysate and in patients' bloodstreams, we studied the potential of low-molecular weight DNA sequences, of the same structure as found in bacteria, to cross from the dialyzer circuit to the blood circuit of a dialysis filter.

METHODS

The mass transfer of DNA fragments across a high-flux dialyzer was evaluated with an in vitro dialysis model, in both conventional dialysis and pure convection mode. Measurement of DNA was performed by HPLC.

RESULTS

In dialysis mode, these mass transfer coefficients were calculated for different single-stranded DNA chain lengths: 5-bases = 28.5%, 9-bases = 20.5%, 20-bases = 9.4%, 35-bases = 2.4%, 50-bases and 100-bases, no transfer detected. In convection mode, these sieving coefficients were calculated: 5-bases = 1.0, 9-bases = 1.0, 20-bases = 0.68, 35-bases = 0.40, 50-bases = 0.17, 100-bases, no convective transfer detected. The physical size of DNA molecules could be the major factor that influences their movement through dialyzer pores.

CONCLUSIONS

This study establishes that significant transfer across the dialyzer may occur with single-stranded DNA in the size range of 20-bases or less. These findings need to be confirmed with an in vitro whole blood model and with clinical investigations. Previous studies have described the clinical benefits of achieving high-purity dialysate. Precautions are warranted to minimize the presence of these DNA compounds in fluids utilized for hemodialysis treatment.

Enzymatic treatment of specimens before DNA extraction directly influences molecular detection of infectious agents

INTRODUCTION

Biological samples, pharmaceuticals or food contain proteins, lipids, polymers, ammoniums and macromolecules that alter the detection of infectious agents by DNA amplification techniques (PCR). Moreover the targeted DNA has to be released from the complex cell walls and the compact nucleoprotein matrixes and cleared from potential inhibitors. The goal of the present work was to assess the efficiency of enzymatic pretreatments on infectious agents to make DNA available for further extraction and amplification.

METHODS

Staphylococcus epidermidis, Streptococcus mitis, Propionibacterium acnes, Escherichia coli, Pseudomonas aeruginosa, Candida albicans, Aspergillus niger and Fusarium solani were mixed with an internal control virus and treated with: 1) proteinase K; 2) lyticase and 3) lyticase followed by proteinase K. DNAs was manually extracted using the QIAmp DNA Mini kit or the MagNA Pure Compact automate. DNA extraction yields and the inhibitors were assessed with a phocid Herpesvirus. Bacterial detection was performed using TaqMan real-time PCR and yeasts and filamentous Fungi with HRM (real-time PCR followed by high-resolution melting analysis).

RESULTS

Viral DNA was released, extracted and detected using manual and automatic methods without pre enzymatic treatments. Either the manual or the automatic DNA extraction systems did not meet the sensitivity expectations if enzymatic treatments were not performed before: lyticase for Fungi and Proteinase K for Bacteria. The addition of lyticase and proteinase K did not improve results. For Fungi the detection after lyticase was higher than for Proteinase K, for which melting analysis did not allow fungal specification.

DISCUSSION

Columns and magnetic beads allowed collecting DNA and separate PCR inhibitors. Detection rates cannot be related to DNA-avidity of beads or to elution but to the lack of proteolysis.

Toll-like receptor 9 signaling delays neutrophil apoptosis by increasing transcription of Mcl-1

Neutrophils detect bacterial constituents, including bacterial DNA (CpG DNA), which elicits innate immunity and prolongs the functional life span of neutrophils through suppression of apoptosis. Both the anti-apoptotic protein Mcl-1 and activation of NF-κB have been implicated in neutrophil survival, but there is no evidence that these are linked in neutrophils. We hypothesized that CpG DNA could simultaneously activate these pathways. High purity CpG DNA (0.4–3.2 µg/ml) extended the life span of human neutrophils in vitro by delaying apoptosis through altering the rate of Mcl-1 turnover. CpG DNA slightly decreased Mcl-1 protein level in the presence of cyclohexmide and the proteasome inhibitor MG132 had little effect on Mcl-1 expression in CpG DNA-treated neutrophils. In contrast, CpG DNA evoked rapid increases in DNA binding by NF-κB/p65 and Mcl-1 mRNA. NF-κB inhibitors and the telomere-derived TLR9 inhibitory oligonucleotide 5′-TTT AGG GTT AGG GTT AGG G-3′ markedly reduced Mcl-1 protein levels and subsequently abrogated suppression of apoptosis by CpG DNA. Furthermore, CpG DNA attenuated the decreases in Mcl-1 in both cell lysate and nucleus of neutrophils undergoing spontaneous apoptosis and increased Mcl-1 translocation to the mitochondria, leading to preservation of mitochondrial transmembrane potential. These results demonstrate that CpG DNA through toll-like receptor 9 links two survival signaling pathways by delaying apoptosis through induction of NF-κB-mediated Mcl-1 gene transcription and promoting Mcl-1 translocation to the mitochondria.

Screening for bacteremia in sepsis and renal failure using hemofilters for renal replacement therapy

BACKGROUND

In patients with sepsis and renal failure, extracorporeal blood flow during renal replacement therapy may lead to the deposition of bacteria on artificial membranous surfaces, which might be suitable for the detection of pathogens. We studied whether discarded dialysis hemofilters can be used for the detection of bacteremia in patients with sepsis and renal failure.

METHODS

Hemofilters of 16 ICU patients with sepsis were sampled. The hemofilters were incubated with soy broth and dehisced under sterile conditions. Samples were plated on blood agar and analyzed. Patient's characteristics were assessed.

RESULTS

Despite the use of antibiotics in 87.5 % (14/16), a true positive detection rate of 31.3 % (5/16) for bacteremia was found by using cultures from hemofilters. The overall true positive rate of blood cultures was significantly lower (10.7 %, 8/75, p = 0.048). Bacteria detected in hemofilters were similar to those found in blood cultures or by cultures from other sources of infection in 80 % (4/5).

CONCLUSIONS

Cultures from used hemofilters of patients with sepsis and renal failure provide the opportunity to identify pathogenic microorganisms as an add-on approach. Further studies should investigate whether this method is applicable in clinical practice to enhance the sensitivity of microbiological diagnostics.

Cutaneous Infection of Nocardia Altamirensis: The First Case Report

We report the first case of Nocardia altamirensis cutaneous infection in an immunocompetent host. A 53-year-old male, with no predisposing factors, presented with a suppurative papular nodule on the dorsum of his left foot. N. altamirensis was identified by sequencing the 16S ribosomal RNA (rRNA), and treatment with amikacin led to complete resolution of the clinical picture. We believe that cutaneous nocardiosis should be kept in mind as a possible cause of serious complications also in immunocompetent hosts considering a nonspecific clinical picture and misdiagnosis of the infection as well as the poor response to empirical antimicrobial therapy.

Bacterial DNA activates endothelial cells and promotes neutrophil adherence through TLR9 signaling

TLR9 detects bacterial DNA (CpG DNA) and elicits both innate and adoptive immunity. Recent evidence indicates that TLR9 is expressed in more diverse cell types than initially thought. In this study, we report that HUVECs constitutively express TLR9 and selectively recognize unmethylated CpG motifs in bacterial DNA and synthetic immune stimulatory CpG oligodeoxynucleotides. HUVECs respond to CpG DNA with rapid phosphorylation of IkappaB-alpha and NF-kappaB-mediated gene transcription and surface expression of the adhesion molecules ICAM-1 and E-selectin independent of MAPK signaling. The telomere-derived TLR9 inhibitory oligonucleotide 5'-TTT AGG GTT AGG GTT AGG G-3', agents that block endosomal acidification such as chloroquine and bafilomycin A, and NF-kappaB inhibitors abrogated CpG DNA-induced signaling. HUVEC activation by CpG DNA led to markedly enhanced neutrophil adhesion under nonstatic conditions that was further enhanced when neutrophils were stimulated with CpG DNA. The adhesive interactions were blocked by Abs against CD18 and, to a lesser degree, by anti-E-selectin and anti-L-selectin Abs. Our findings demonstrate that bacterial DNA promotes beta(2) integrin and E-selectin-mediated HUVEC-neutrophil adherence, and indicate the ability of CpG DNA to initiate and/or maintain the inflammatory response.

Advances in the microbiological diagnosis of sepsis

Accurate diagnostic tests are essential for the correct identification of etiologic agents causing sepsis. Conventional microbiology cultures are time consuming and may even yield negative results in many cases of septic shock. In this manner, molecular-based technologies are emerging as promising tests for use into routine clinical laboratories. In this review, we discuss current available molecular methods for bacteremia diagnosis in adult and pediatric patients with suspected or confirmed sepsis. Results of studies using polymerase chain reaction, real-time polymerase chain reaction, and complementary DNA/oligonucleotide microarrays are described and discussed into the current scenario. These new methodologies are able to detect even small amounts of bacterial DNA directly from blood specimens and show increased sensitivity and specificity for detecting many infectious agents associated with sepsis. Despite some limitations presented by nucleic acid-based techniques, these genotypic tests can be useful along with traditional microbiology diagnostics.

Adrenal insufficiency in liver disease - what is the evidence?

Recently, treatment with corticosteroids in the setting of septic shock and adrenal insufficiency has been shown to decrease mortality. In septic patients, a blunted response to adrenal stimulation identifies patients with a poorer prognosis who may benefit from corticosteroid supplementation. This condition has been termed relative adrenal insufficiency (RAI). Given the similarities between septic shock and liver failure, a number of groups have now studied the incidence of RAI in various forms of liver disease. Although different definitions of RAI exist, the current literature suggests that RAI is common, being seen in 33% of acute liver failure patients and up to 65% of patients with chronic liver disease and sepsis. The finding that RAI can exist in the absence of sepsis and may be as high as 92% of patients undergoing liver transplantation using a steroid free protocol has led one group to propose the term hepatoadrenal syndrome. The purpose of this review is to summarise the existing evidence for adrenal insufficiency in liver disease, to examine the possibility that adrenal dysfunction in liver disease may have a separate pathogenesis to that observed in sepsis and to provide insight into the potential areas for further research into this condition.