Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection. In addition, acquisition of cholesterol was identified across the bacterial species. This detailed reference dataset has been established as an open resource to support discovery and translational research.

A246 BALLOON-OCCLUDED RETROGRADE TRANSVENOUS OBLITERATION FOR PRIMARY PROPHYLAXIS OF GASTRIC VARICEAL BLEEDING: A SYSTEMATIC REVIEW

Background

Gastric variceal (GV) bleeding is an infrequent but serioous complication of cirrhosis that is associated with high mortality. Balloon-occluded retrograde transvenous obliteration (BRTO) is an effective treatment to prevent rebleeding from GV. The role of BRTO for primary prophylaxis of GV bleeding has not been established.

Purpose

The aim of the current study is to establish the efficacy and safety of BRTO for primary prophylaxis of GV bleeding.

Method

We searched EMBASE, MEDLINE, and the Cochrane Central Register of Controlled Trials from inception to November 2021. Randomized controlled trials and observational studies involving adults with cirrhosis related GV that had never bled and were treated with BRTO were included. Studies without clinical outcomes or those not reporting primary prophylaxis outcomes separately were excluded. Risk of bias was assessed using the Newcastle-Ottawa scale.

Result(s)

We identified 791 unique citations with 9 eligible studies after a full-text review. A total of 577 patients were included from 9 observational studies (1 prospective, 8 retrospective). Technical success after the first procedure ranged from 82.4-100% (7 studies) and GV eradication on follow-up endoscopy ranged from 88.2-100% (4 studies). GV bleeding occurred in 0-7.3% of patients with follow-up ranging from 15.8-66.2 months (9 studies). Eight studies were considered at high risk of bias due to the lack of a control group or poor comparability between the cohorts.

Conclusion(s)

BRTO appears to be effective for primary prophylaxis of GV bleeding. Further controlled studies are needed before BRTO can be routinely performed for primary prevention of gastric variceal bleeding.

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Disclosure of Interest

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LPS O Antigen Plays a Key Role in Klebsiella pneumoniae Capsule Retention

Despite the importance of encapsulation in bacterial pathogenesis, the biochemical mechanisms and forces that underpin retention of capsule by encapsulated bacteria are poorly understood. In Gram-negative bacteria, there may be interactions between lipopolysaccharide (LPS) core and capsule polymers, between capsule polymers with retained acyl carriers and the outer membrane, and in some bacteria, between the capsule polymers and Wzi, an outer membrane protein lectin. Our transposon studies in Klebsiella pneumoniae B5055 identified additional genes that, when insertionally inactivated, resulted in reduced encapsulation. Inactivation of the gene waaL, which encodes the ligase responsible for attaching the repeated O antigen of LPS to the LPS core, resulted in a significant reduction in capsule retention, measured by atomic force microscopy. This reduction in encapsulation was associated with increased sensitivity to human serum and decreased virulence in a murine model of respiratory infection and, paradoxically, with increased biofilm formation. The capsule in the WaaL mutant was physically smaller than that of the Wzi mutant of K. pneumoniae B5055. These results suggest that interactions between surface carbohydrate polymers may enhance encapsulation, a key phenotype in bacterial virulence, and provide another target for the development of antimicrobials that may avoid resistance issues associated with growth inhibition. IMPORTANCE Bacterial capsules, typically comprised of complex sugars, enable pathogens to avoid key host responses to infection, including phagocytosis. These capsules are synthesized within the bacteria, exported through the outer envelope, and then secured to the external surface of the organism by a force or forces that are incompletely described. This study shows that in the important hospital pathogen Klebsiella pneumoniae, the polysaccharide capsule is retained by interactions with other surface sugars, especially the repeated sugar molecule of the LPS molecule in Gram-negative bacteria known as "O antigen." This O antigen is joined to the LPS molecule by ligation, and loss of the enzyme responsible for ligation, a protein called WaaL, results in reduced encapsulation. Since capsules are essential to the virulence of many pathogens, WaaL might provide a target for new antimicrobial development, critical to the control of pathogens like K. pneumoniae that have become highly drug resistant.

Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016

BACKGROUND

Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji.

METHODS

Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases.

FINDINGS

Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted.

INTERPRETATION

Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries.

FUNDING

This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.

Introduction of a care bundle effectively and sustainably reduces patient-reported surgical site infection in patients undergoing colorectal surgery

BACKGROUND

Surgical site infection (SSI) is one of the most common healthcare-associated infections and is particularly prevalent following colorectal surgery. It is associated with an increase in patient morbidity and healthcare costs. SSI is difficult to monitor as it frequently presents after discharge from hospital, especially if enhanced recovery programmes are in place.

AIM

To develop an effective method for measuring patient-reported 30-day SSI in patients undergoing colorectal resection. To implement a new care bundle capable of delivering a sustainable reduction in SSI.

METHODS

The Public Health England SSI surveillance questionnaire was used. Several data collection methods were tested including postal and telephone-based systems. A new SSI bundle was introduced in our centre incorporating four evidence-based interventions: 2% chlorhexidine skin preparation; repeat-dose antibiotics after 4 h; dual-ring wound protectors; and triclosan-coated sutures for wound closure. System changes were introduced to ensure that the change was sustainable.

FINDINGS

The most reliable method of measuring patient-reported SSI was found to be postal questionnaire with telephone calls made to non-responders. Response rates to the SSI surveillance questionnaire were consistently >75%. Introduction of the new care bundle produced a significant reduction in SSI from 20% to 10% (P ≤ 0.0001) which has been sustained for six years.

CONCLUSION

This is a reliable method for measuring 30-day patient-reported SSI rates. The introduction of this new care bundle has halved the rate of SSI from 20% to 10%.

Bicarbonate-mediated stimulation of RegA, the global virulence regulator from Citrobacter rodentium

The global virulence regulatory protein RegA, an AraC-like regulator, controls the expression of more than 60 genes in the mouse enteric pathogen Citrobacter rodentium. In the presence of bicarbonate, RegA activates the transcription of a number of virulence determinants and inhibits the expression of a series of housekeeping genes. To elucidate the molecular mechanism by which bicarbonate stimulates RegA activity, we carried out biophysical and mutational analyses. Our data indicate that RegA exists as a dimer in solution regardless of bicarbonate concentration. A leucine zipper, located in the region downstream of the N-terminal domain, is responsible for dimerisation. The N-terminal arm itself is involved in modulating the response to bicarbonate, which appears to bind to a region comprising a series of beta-sheets within the N-terminal domain. The presence of bicarbonate relieves the autoinhibition of RegA activity by its N-terminal arm. RegA is the first example of a bacterial virulence regulator that utilises the light switch mechanism, previously described for the Escherichia coli AraC protein, to respond to a gut-associated effector that controls its activity.

Influence of format on in vitro penetration of antibody fragments through porcine cornea

AIM

Antibody fragments, appropriately formulated, can penetrate through the ocular surface and thus have potential as therapeutic agents. The aim was to investigate the influence of protein fragment format on the kinetics and extent of ocular penetration in vitro.

METHODS

Immunoglobulin single chain variable domain fragments of a murine monoclonal antibody with specificity for rat CD4 were engineered with a 20 or 11 amino acid linker by assembly polymerase chain reaction, expressed in Escherichia coli and purified by chromatography. Fab fragments of the parental antibody were prepared by papain digestion. Antibody fragments were formulated with a penetration and a viscosity enhancer and were applied to the surface of perfused pig corneas for up to 10 hours in vitro. Penetration was quantified by flow cytometry on rat thymocytes.

RESULTS

20-mer antibody fragments formed natural monomers and dimers following purification that could be separately isolated, while 11-mer fragments were dimeric. All formats of fragment (20-mer monomers and dimers, 11-mer dimers, Fab) showed penetration through the pig cornea after 6 hours of intermittent topical administration.

CONCLUSION

Antibody fragments of different shapes and sizes can penetrate the cornea after topical administration, thereby increasing the potential of this class of proteins for topical ophthalmic use.

Identification of vaccine candidate antigens from a genomic analysis of Porphyromonas gingivalis

Porphyromonas gingivalis is a key periodontal pathogen which has been implicated in the etiology of chronic adult periodontitis. Our aim was to develop a protein based vaccine for the prevention and or treatment of this disease. We used a whole genome sequencing approach to identify potential vaccine candidates. From a genomic sequence, we selected 120 genes using a series of bioinformatics methods. The selected genes were cloned for expression in Escherichia coli and screened with P. gingivalis antisera before purification and testing in an animal model. Two of these recombinant proteins (PG32 and PG33) demonstrated significant protection in the animal model, while a number were reactive with various antisera. This process allows the rapid identification of vaccine candidates from genomic data.

Isolation of recombinant protective Helicobacter pylori antigens

A total of seven clones producing both new and previously described Helicobacter pylori proteins were isolated from a library of H. pylori genomic DNA. The screening approach by which these proteins were detected relied on the use of antisera raised in mice vaccinated with Helicobacter felis sonicate plus cholera toxin, a regimen which protects mice from H. pylori challenge. This strategy was designed to maximize the possibility of obtaining antigens which might be capable of conferring protection from H. pylori infection. Two of the clones were shown to encode the urease enzyme and the heat shock protein HspB, which have already been identified as protective antigens. The other five clones were sequenced, protein coding regions were deduced, and these sequences were amplified by PCR for incorporation into Escherichia coli expression vectors. The proteins produced from these expression systems were purified to allow testing for protective efficacy in an H. pylori mouse model. All five proteins were able to facilitate the clearance of a challenge with H. pylori, as judged by an assay of gastric urease activity and light microscopy on stomach sections. These results clearly indicate that the screening strategy has successfully identified candidate vaccine antigens.

Enhanced secretory ability for the human factor VIII light chain produced in baculovirus-infected insect cells

The light and truncated heavy chains of human factor VIII, expressed separately in baculovirus-infected insect cells, exhibited different secretory behaviour when compared with each other and with a biologically active fusion molecule of the truncated heavy and light chains. The light chain was very efficiently secreted into culture medium, as judged by high extracellular protein levels and the absence of evidence for light chain retention within cells. Alternatively, proteins containing the heavy chain sequence were poorly secreted and appeared to be sequestered within cells, suggesting that regions within the heavy chain are responsible for the low levels of secreted protein which have generally been observed for recombinant factor VIII.

Expression of biologically active human factor VIII using a baculovirus vector

Factor VIII is a complex, plasma glycoprotein involved in the process of blood coagulation. Production of the recombinant molecule has largely been confined to mammalian cell systems which have, in general, proven to be inefficient producers of factor VIII. The use of a baculovirus expression system may provide increased levels of this glycoprotein, although it is not certain that insect cell-derived factor VIII will be biologically active. The N-linked glycosylation patterns in insect cells, until recently thought to be less complex than in mammalian cells, may influence activity and/or secretory ability. To this end we engineered a B domain-deleted factor VIII cDNA sequence for expression in Spodoptera frugiperda cells. The construct retained the native signal sequence to allow secretion of recombinant protein into the culture medium. Initial studies revealed the production of secreted factor VIII, and this protein was shown to possess coagulation activity. The presence of N-linked oligosaccharide residues was demonstrated, the glycosylated molecule being of a similar size to that expressed in mammalian cells.

Dextran sulfate and heparin sulfate inhibit platelet-activating factor-induced pulmonary edema

We tested the hypothesis that dextran sulfate and heparin sulfate inhibit platelet-activating factor- (PAF) induced pulmonary edema in the isolated perfused guinea pig lung via a charge-dependent mechanism. Dextran sulfate prevented the changes in pulmonary capillary pressure (Ppc, 7.8 +/- 0.9 vs. 14.0 +/- 0.7 cmH2O), lung weight gain (dW, +0.48 +/- 0.29 vs. +8.41 +/- 2.07 g), and pulmonary edema formation or wet-to-dry weight ratio [(W-D)/D, 6.5 +/- 0.3 vs. 13.2 +/- 2.6] occurring 60 min after PAF infusion (10(-11) M) into an isolated lung. The unsulfated form of dextran had no protective effect [Ppc, dW, and (W-D)/D, 11.9 +/- 1.4 cmH2O, +5.33 +/- 2.18 g, and 11.2 +/- 3.2, respectively]. The unrelated anionic compound, heparin sulfate, also inhibited the PAF response [Ppc, dW, and (W-D)/D, 7.0 +/- 0.5 cmH2O, +0.61 +/- 0.32 g, and 6.1 +/- 0.2, respectively], whereas the partially desulfated form of heparin was not effective in inhibiting PAF-induced edema [Ppc, dW, and (W-D)/D, 15.1 +/- 0.7 cmH2O, +6.07 +/- 1.58 g, and 10.0 +/- 1.2, respectively]. When the metachromatic dye crystal violet was used as an indicator of charge interactions, the sulfated compounds interacted with PAF in vitro. The data indicate that PAF-induced pulmonary edema is inhibited by sulfated polysaccharides, possibly via a charge interaction between negatively charged compounds and PAF.

Protein kinase inhibitor prevents pulmonary edema in response to H2O2

We investigated the effect of H2O2 (92 microM) in isolated guinea pig lungs perfused with a buffered Ringer solution. Pulmonary arterial pressure (Ppa), pulmonary capillary pressure (Ppc), and change in lung weight (delta W) were recorded at 0 min and at 15, 30, and 60 min after the H2O2. The capillary filtration coefficient (Kfc) was measured at 0 and 30 min. The perfusion of H2O2 increased the Ppa, Ppc, delta W, and Kfc. The thromboxane synthetase inhibitor Dazoxiben, or the vasodilator papaverine, prevented the increases in Ppa and Ppc. The protein kinase C (PKC) inhibitor H7 [1-(5-isoquinolinesulfonyl)-2-methylpiperazine dihydrochloride] prevented the increases in Ppa, Ppc, delta W, and Kfc, whereas the inactive isoquinoline HA1004 [N-(2-guanidinoethyl)-5-isoquinolinesulfonamide hydrochloride] had little effect on the H2O2 response. H2O2 increased the number of stress fibers and disrupted the peripheral band of cultured confluent endothelial cells, changes that were prevented with pretreatment with H7. PKC may mediate the increases in vascular permeability and pulmonary edema that occur in response to H2O2.

Myxobacteria exert partial control of damping-off and root disease in container-grown tree seedlings

Many tree seedlings for reforestation are now being produced in small discreet containers. On these seedlings, losses and stunting from root pathogens occur widely and unpredictably. Some myxobacteria of the group Cytophaga which produce powerful extracellular proteolytic and chitinolytic enzymes were introduced into fumigated or non-fumigated peat before or after sowing seeds of four species of conifer. They actively colonized the rhizosphere of the developing seedlings without affecting seedling development. In subsequent inoculation tests with pathogenic fungi, there was significantly less mortality, chlorosis, and stunting, than in checks without myxobacteria.

Evidence on intracellular sites of terminal synthesis of carotenoids in Mucor hiemalis Wehm

Evidence is presented from cell fractionation and analysis, suggesting that the sites of carotenoid synthesis and accumulation in Mucor hiemalis Wehm. are the dissolved protein fraction and the free and bound lipid fractions, respectively. Quantitative characterization of carotenoids in various fractions indicates that terminal synthesis follows the Porter–Lincoln sequence.