Chlorine (Cl-2) gas is a toxic industrial chemical (TIC) that poses a hazard to human health following accidental and/or intentional (e.g. terrorist) release. By using a murine model of sub-lethal Cl-2 exposure we have examined the airway hyper responsiveness, cellular infiltrates, transcriptomic and proteomic responses of the lung. In the "crisis " phase at 2 h and 6 h there is a significant decreases in leukocytes within bronchoalveolar lavage fluid accompanied by an upregulation within the proteome of immune pathways ultimately resulting in neutrophil influx at 24 h. A flip towards "repair " in the transcriptome and proteome occurs at 24 h, neutrophil influx and an associated drop in the lung function persisting until 14 d post-exposure and subsequent "recovery " after 28 days. Collectively, this research provides new insights into the mechanisms of damage, early global responses and processes of repair induced in the lung following the inhalation of Cl-2.

Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop in the large ribosomal subunit, leading to the inhibition of protein translation and cell death. We postulated that this depurination event could be detected using Oxford Nanopore Technologies (ONT) direct RNA sequencing, detecting a change in charge in the ricin loop. In this study, A549 cells were exposed to ricin for 2–24 h in order to induce depurination. In addition, a novel software tool was developed termed RIPpore that could quantify the adenine modification of ribosomal RNA induced by ricin upon respiratory epithelial cells. We provided demonstrable evidence for the first time that this base change detected is specific to RIP activity using a neutralising antibody against ricin. We believe this represents the first detection of depurination in RNA achieved using ONT sequencers. Collectively, this work highlights the potential for ONT and direct RNA sequencing to detect and quantify depurination events caused by ribosome-inactivating proteins such as ricin. RIPpore could have utility in the evaluation of new treatments and/or in the diagnosis of exposure to ricin.

Depurination is a frequent modification to both DNA and RNA, in DNA causing point mutations through misincorporation, in RNA, disabling ribosomes and halting protein synthesis. Some modifications of nucleic acids can be determined by direct sequencing using Oxford Nanopore Technologies (ONT). However, the identification of modifications is often limited by noise and their variety and number. Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop of the large ribosomal subunit. This leaves only a ribose backbone, thus inhibiting protein translation. In humans, biological threat agents and ribosome inactivating proteins, such as ricin and saporin, depurinate base 4605 on the 28S rRNA providing a single defined target to try and identify. We postulated that the depurination event could be detected using ONT direct RNA sequencing through a change in charge in the ricin loop. A software tool was developed, RIPpore, that quantified the adenine modification from direct RNA sequencing data of ribosomal RNA purified from respiratory epithelial cells exposed to ricin. This provided a novel method of directly identifying ricin exposure and a basis for ONT’s utility in detecting lesions in nucleic acids caused by depurination events.

Persister and viable but non-culturable (VBNC) cells are two clonal subpopulations that can survive multidrug exposure via a plethora of putative molecular mechanisms. Here, we combine microfluidics, time-lapse microscopy, and a plasmid-encoded fluorescent pH reporter to measure the dynamics of the intracellular pH of individual persister, VBNC, and susceptible Escherichia coli cells in response to ampicillin treatment. We found that even before antibiotic exposure, persisters have a lower intracellular pH than those of VBNC and susceptible cells. We then investigated the molecular mechanisms underlying the observed differential pH regulation in persister E. coli cells and found that this is linked to the activity of the enzyme tryptophanase, which is encoded by tnaA. In fact, in a ΔtnaA strain, we found no difference in intracellular pH between persister, VBNC, and susceptible E. coli cells. Whole-genome transcriptomic analysis revealed that, besides downregulating tryptophan metabolism, the ΔtnaA strain downregulated key pH homeostasis pathways, including the response to pH, oxidation reduction, and several carboxylic acid catabolism processes, compared to levels of expression in the parental strain. Our study sheds light on pH homeostasis, proving that the regulation of intracellular pH is not homogeneous within a clonal population, with a subset of cells displaying a differential pH regulation to perform dedicated functions, including survival after antibiotic treatment. IMPORTANCE Persister and VBNC cells can phenotypically survive environmental stressors, such as antibiotic treatment, limitation of nutrients, and acid stress, and have been linked to chronic infections and antimicrobial resistance. It has recently been suggested that pH regulation might play a role in an organism's phenotypic survival to antibiotics; however, this hypothesis remains to be tested. Here, we demonstrate that even before antibiotic treatment, cells that will become persisters have a more acidic intracellular pH than clonal cells that will be either susceptible or VBNC upon antibiotic treatment. Moreover, after antibiotic treatment, persisters become more alkaline than VBNC and susceptible E. coli cells. This newly found phenotypic feature is remarkable because it distinguishes persister and VBNC cells that have often been thought to display the same dormant phenotype. We then show that this differential pH regulation is abolished in the absence of the enzyme tryptophanase via a major remodeling of bacterial metabolism and pH homeostasis. These new whole-genome transcriptome data should be taken into account when modeling bacterial metabolism at the crucial transition from exponential to stationary phase. Overall, our findings indicate that the manipulation of the intracellular pH represents a bacterial strategy for surviving antibiotic treatment. In turn, this suggests a strategy for developing persister-targeting antibiotics by interfering with cellular components, such as tryptophanase, that play a major role in pH homeostasis.

Abstract Motivation A fundamental problem for disease treatment is that while antibiotics are a powerful counter to bacteria, they are ineffective against viruses. Often, bacterial and viral infections are confused due to their similar symptoms and lack of rapid diagnostics. With many clinicians relying primarily on symptoms for diagnosis, overuse and misuse of modern antibiotics are rife, contributing to the growing pool of antibiotic resistance. To ensure an individual receives optimal treatment given their disease state and to reduce over-prescription of antibiotics, the host response can in theory be measured quickly to distinguish between the two states. To establish a predictive biomarker panel of disease state (viral/bacterial/no-infection), we conducted a meta-analysis of human blood infection studies using machine learning. Results We focused on publicly available gene expression data from two widely used platforms, Affymetrix and Illumina microarrays as they represented a significant proportion of the available data. We were able to develop multi-class models with high accuracies with our best model predicting 93% of bacterial and 89% viral samples correctly. To compare the selected features in each of the different technologies, we reverse-engineered the underlying molecular regulatory network and explored the neighbourhood of the selected features. The networks highlighted that although on the gene-level the models differed, they contained genes from the same areas of the network. Specifically, this convergence was to pathways including the Type I interferon Signalling Pathway, Chemotaxis, Apoptotic Processes and Inflammatory/Innate Response. Availability Data and code are available on the Gene Expression Omnibus and github. Supplementary information Supplementary data are available at Bioinformatics online.

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A fundamental problem for disease treatment is that while antibiotics are a powerful counter to bacteria, they are ineffective against viruses. To ensure a given individual receives optimal treatment given their disease state and to reduce over-prescription of antibiotics leading to antimicrobial resistance, the host response can be measured to distinguish between the two states. To establish a predictive biomarker panel of disease state we conducted a meta-analysis of human blood infection studies using Machine Learning (ML). We focused on publicly available gene expression data from two widely used platforms, Affymetrix and Illumina microarrays, and integrated over 2000 samples for each platform to develop optimal gene panels. On average our models predicted 80% of bacterial and 85% viral samples correctly by class of infection type. For our best performing model, identified with an evolutionary algorithm, 93% of bacterial and 89% of viral samples were classified correctly. To enable comparison between the two differing microarray platforms, we reverse engineered the underlying molecular regulatory network and overlay the identified models. This revealed that although the exact gene-level overlap between models generated from the two technologies was relatively low, both models contained genes in the same areas of the network, indicating that the same functional changes in host biology were being detected, providing further confidence in the robustness of our models. Specifically, this convergence was to pathways including the Type I interferon Signalling Pathway, Chemotaxis, Apoptotic Processes, and Inflammatory / Innate Response. Amongst and related to these pathways we found three genes, IFI27, LY6E , and CD177 , particularly prevalent throughout our analysis. Author summary Bacterial and viral disease require specific treatments, and whilst there are various treatment options for specific infection types, rapid diagnosis and identification of the optimal treatment remains challenging. Even in wealthier countries with developed healthcare systems, unnecessary prescription of antibiotics to patients with viral infections is causing phenomena such as multi-drug resistent bacteria. One way to distinguish a viral from bacterial infection is to measure an individual’s responses, for example by measuring the expression of particular genes in a blood sample, as different types of infections trigger different types of responses. In our study we analysed thousands of previously collected data sets from human blood, where individuals had either viral, bacterial or no infection (control). We used machine learning to identify “signatures” – small sets of genes that are indicative of the type of infection (if any) carried by an individual. Within data sets we used two different technology platforms had been used to collect data. We demonstrated that their gene-level signatures do not overlap perfectly when derived from the different platforms, the biological networks from which those genes were derived, however, had a high overlap – giving confidence that our models are robust against technology artefacts or bias. We have identified a small set of genes that serve as strong biomarkers of infection status in humans. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was also supported by the Chem-Bio Diagnostics program contract HDTRA1-12-D-0003-0023 from the Department of Defense Chemical and Biological Defense program through the Defense Threat Reduction Agency (DTRA). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The publication used already available data. Therefore no additional approval was required. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data is available at the following Gene expression Omnibus IDs: GSE49954, GSE50628, GSE54992, GSE25504, GSE66099, GSE69606, GSE6269, GSE18090, GSE28750, GSE34205, GSE52428, GSE95104, GSE17156, GSE30550, GSE29385, GSE32707, GSE37250, GSE40396, GSE60244, GSE64456, GSE68310.

Background: A fundamental problem for disease treatment is that while antibiotics are a powerful counter to bacteria, they are ineffective against viruses. Without proper identification equipment, medical practitioners can unnecessarily prescribe antibiotics to patients without bacterial infections, leaving the source disease untreated and fostering anti-microbial resistance (AMR). This was highlighted by two defence organisations, the Defence Threat Reduction Agency (DTRA) and Defence Science Technology Laboratories (DSTL) as particularly hazardous for soldiers without access to proper means of diagnosis. Suitably, work was commissioned as a basis to assist in the design of a future, portable diagnosis device that could differentially diagnosis disease state based on profiles of gene expressions. Methods and materials: We conducted a meta-analysis of human blood infection studies using Machine Learning (ML) driven biomarker discovery to obtain a panel of genes enabling differential diagnosis of disease state. We performed our meta-analysis on GEO gene expression data, all from open source microarray human blood infection studies. Our analysis was divided into six distinct phases: (1) Data gathering, (2) Pre-processing (consisting of a novel multi-stage batch correction pipeline), (3) Feature Selection (using a genetically inspired search algorithm), (4) Functional Enrichment Analysis, (5) Inferring Interaction Networks and clustering genes, and (6) finally Out-of-Sample Testing for validation. Results: We present an optimal panel of genes, as well as some similarly performing alternatives, which are robust and generalisable, enabling technology-independent differential diagnosis of disease state. We also provide direct insight into the underlying gene interaction networks which control response to disease, and subsequently the key groups of genes important for diagnosis, verified by two parallel analyses on cohorts using Affymetrix and Illumina RNA Microarray. Conclusion: We presented several panels of genes which when taken together are indicated to perform well on both discovery data and out of sample testing (on different microarray manufacturers). While there was some inconsistency between manufacturer gene lists, we still observed high convergence around four gene groups, most prominently the Interferon Stimulated Genes (ISGs). These sets have altered expressions between bacterial, viral, and control disease states, and when taken together provide a predictive baseline for differential diagnosis on gene expression alone.

Highly virulent bacterial pathogens cause acute infections which are exceptionally difficult to treat with conventional antibiotic therapies alone. Understanding the chain of events that are triggered during an infection of a host has the potential to lead to new therapeutic strategies. For the first time, the transcriptomic responses within the lungs of Balb/C mice have been compared during an acute infection with the intracellular pathogens Burkholderia pseudomallei, Francisella tularensis and Yersinia pestis. Temporal changes were determined using RNAseq and a bioinformatics pipeline; expression of protein was also studied from the same sample. Collectively it was found that early transcriptomic responses within the infected host were associated with the (a) slowing down of critical cellular functions, (b) production of circulatory system components, (c) lung tissue integrity, and (d) intracellular regulatory processes. One common molecule was identified, Errfi1 (ErbB receptor feedback inhibitor 1); upregulated in response to all three pathogens and a potential novel marker of acute infection. Based upon the pro-inflammatory responses observed, we sought to synchronise each infection and report that 24 h p.i. of B. pseudomallei infection closely aligned with 48 h p.i. of infection with F. tularensis and Y. pestis. Post-transcriptional modulation of RANTES expression occurred across all pathogens, suggesting that these infections directly or indirectly modulate cell trafficking through chemokine expression/detection. Collectively, this unbiased NGS approach has provided an in-depth characterisation of the host transcriptome following infection with these highly virulent pathogens ultimately aiding in the development of host-directed therapies as adjuncts or alternatives to antibiotic treatment.

Sulfur mustard (HD) is a vesicating and alkylating agent widely used on the battlefield during World War I and more recently in the Iran-Iraq War. It targets the eyes, skin, and lungs, producing skin burns, conjunctivitis, and compromised respiratory function; early acute effects lead to long-term consequences. However, it is the effects on the lungs that drive morbidity and eventual mortality. The temporal postexposure response to HD within lung tissue raises the question of whether toxicity is driven by the alkylating properties of HD on critical homeostatic pathways. We have established an anesthetized swine model of inhaled HD vapor exposure to investigate the toxic effects of HD 12 h postexposure. Large white female swine were anesthetized and instrumented prior to exposure to air, 60 (sublethal) or 100 μg·kg-1 (∼LD40) doses of HD (10 min). Physiological parameters were continuously assessed. Data indicate that exposure to 100 μg·kg-1 HD lowered arterial blood oxygenation and increased shunt fraction and lavage protein compared with those of air-exposed controls and the 60 μg·kg-1 dose of HD. Histopathology showed an increased total pathology score between the 100 μg·kg-1 HD group and air-exposed controls. Principal component analysis of differentially expressed genes demonstrated a distinct and separable response of inhaled HD between air-exposed controls and the 60 and 100 μg·kg-1 doses of HD. Canonical pathway analysis demonstrated changes in acute phase response signaling, aryl hydrocarbon receptor signaling, NRF-2 mediated oxidative stress, and zymosterol biosynthesis in the 60 and 100 μg·kg-1 HD dose group. Transcriptional changes also indicated alterations in immune response, cancer, and cell signaling and metabolism canonical pathways. The 100 μg·kg-1 dose group also showed significant changes in cholesterol biosynthesis. Taken together, exposure to inhaled HD had a significant effect on physiological responses coinciding with acute changes in gene expression and lung histopathology. In addition, transcriptomics support the observed beneficial effects of N-acetyl-l-cysteine for treatment of acute inhalation HD exposure.

The bronchial epithelium provides protection against pathogens from the inhaled environment through the formation of a highly-regulated barrier. In order to understand the pulmonary diseases melioidosis and tularemia caused by Burkholderia thailandensis and Fransicella tularensis, respectively, the barrier function of the human bronchial epithelium were analysed. Polarised 16HBE14o- or differentiated primary human bronchial epithelial cells (BECs) were exposed to increasing multiplicities of infection (MOI) of B. thailandensis or F. tularensis Live Vaccine Strain and barrier responses monitored over 24–72 h. Challenge of polarized BECs with either bacterial species caused an MOI- and time-dependent increase in ionic permeability, disruption of tight junctions, and bacterial passage from the apical to the basolateral compartment. B. thailandensis was found to be more invasive than F. tularensis. Both bacterial species induced an MOI-dependent increase in TNF-α release. An increase in ionic permeability and TNF-α release was induced by B. thailandensis in differentiated BECs. Pretreatment of polarised BECs with the corticosteroid fluticasone propionate reduced bacterial-dependent increases in ionic permeability, bacterial passage, and TNF-α release. TNF blocking antibody Enbrel® reduced bacterial passage only. BEC barrier properties are disrupted during respiratory bacterial infections and targeting with corticosteroids or anti-TNF compounds may represent a therapeutic option.

Members of the Burkholderia species can cause a range of severe, often fatal, respiratory diseases. A variety of in vitro models of infection have been developed in an attempt to elucidate the mechanism by which Burkholderia spp. gain entry to and interact with the body. The majority of studies have tended to focus on the interaction of bacteria with phagocytic cells with a paucity of information available with regard to the lung epithelium. However, the lung epithelium is becoming more widely recognized as an important player in innate immunity and the early response to infections. Here we review the complex relationship between Burkholderia species and epithelial cells with an emphasis on the most pathogenic species, Burkholderia pseudomallei and Burkholderia mallei. The current gaps in knowledge in our understanding are highlighted along with the epithelial host-pathogen interactions that offer potential opportunities for therapeutic intervention.

Francisella tularensis inhalation results in bacterial interaction with numerous lung cell types, including those of the epithelium. This work investigates a three-dimensional cell-culture system to characterise the epithelial response to E tularensis. Immortalised human pneumocytes (A549s) grown in rotating-wall vessel (RWV) bioreactors display an in vivo-like phenotype, which has been confirmed to be driven by specific transcriptional events (8454 genes, p <= 0.05). These data support the RWV model as a more in vivo-like culture system to investigate the lung epithelium, compared to monolayer counterparts. RWV-cultured A549s were infected with E tularensis SchuS4 and LVS and intracellular replication mapped over 22 h compared to monolayer cells. The RWV-cultured A549s were more resistant to SchuS4 and LVS infection (p <= 0.05). Transcriptomics identified 2086 genes (p <= 0.05) as candidates for host pathogen interactions which result in the observed increase in resistance of the RWV-cultured A549 cells. Gene and pathway analysis identified processes involved in MMP modulation, endocytosis, mucin production and the complement pathway amongst others. The role of these pathways during infection was further characterised using chemical inhibitors. This work has revealed several new hypotheses worthy of further testing in order to understand the epithelial host response to E tularensis infection. (C) 2014 Published by Elsevier Masson SAS on behalf of Institut Pasteur.

Interactions between Francisella tularensis and the host are slowly being elucidated. Microarray technology was used to further characterise the response of Balb/c mice after inhalation of the virulent F. tularensis, SchuS4. The validated array data revealed changes in expression of 476 genes across a 96 h time course following infection (p ≤ 0.05). These data confirm down-regulation of the toll-like receptor pathway (TLR3, 4, 5, 7 and 8), and the induction of IFN-γ inducible genes (T-cell specific GTPase, β2 microglobulin and interleukin 21). The overall response appears to be two staged with an initial up-regulation of genes involved in apoptosis, TNFα production and antigen presentation. This is followed by a large alteration of expression at 96 h as the host succumbs to infection. A key regulatory time-point has been identified at 24 h post challenge, where several transcriptional events may predicate the progression of infection; these include transcriptional regulators of inflammation and proteolytic pathways. Pathway analysis indicates a novel role for cell-cell adhesion and extracellular matrix modulation in infection. Transcripts representing cellular junctions, focal adhesion and adherens junctions changed following infection. Additionally, aspects of extracellular matrix remodelling have been confirmed at the protein level, suggesting an important role of the respiratory epithelium in host response to F. tularensis warranting further study.

The toxin ricin has been shown to cause inflammatory lung damage, leading to pulmonary oedema and, at higher doses, mortality. In order to understand the genetic basis of this inflammatory cascade a custom microarray platform (1509 genes) directed towards immune and inflammatory markers was used to investigate the temporal expression profiles of genes in a Balb/c mouse model of inhalational ricin exposure. To facilitate examination of those genes involved in both inflammatory cascades and wound repair the dose which was investigated was sub-lethal across a 96-h time course. Histopathology of the lung was mapped across the time course and genetic responses considered in the context of overall lung pathology. Six hundred and eighty-five genes were found to be statistically significantly different compared to controls, across the time course and these genes have been investigated in the context of their biological function in ricin poisoning. As well as confirming key inflammatory markers associated with ricin intoxication (TNFalpha and IL1beta) several pathways that are altered in expression were identified following pulmonary exposure to ricin. These genes included those involved in cytokine-cytokine signalling cascades (IL1, IL1r, IL1r2, Ccl 4, 6, 10), focal adhesion (Fn1, ICAM1) and tissue remodelling (VEGF, Pim1). Furthermore, the observed alteration in expression of matrix metalloproteinases (MMPs) and their inhibitors (TIMPs) indicates a key role in membrane integrity and cellular adhesion in ricin poisoning. Data captured using this transcriptomic approach could be used to develop a specific approach to the treatment of inhalational ricin exposure. This work was conducted as part of a wider programme of work to compare a number of militarily relevant lung damaging agents, with a view to establishing a rational basis for the identification of more generic medical countermeasures.

A previously characterised amplified ELISA for ricin (sensitivity limit approximately 200 pg mL(-1)) has been employed to quantify ricin following a novel recovery method from selected tissues. Tissue samples from rats dosed by pulmonary instillation or orally with ricin were homogenised and treated with an elution buffer to extract ricin. This is the first time that ex vivo recovery of ricin post exposure following pulmonary or oral challenge has been achieved using clinically acceptable sampling methods, with promise in terms of diagnosis for the timely implementation of therapy.The toxin was detected and quantified using the ELISA in conjunction with pure ricin standards. Extracts from tissues sampled, including lung, blood, liver and spleen tested positive for ricin with maximum yield in lung associated fractions for pulmonary dosing and liver tissue for oral administration. This indicates the potential of lavage and blood sampling for timely diagnosis of ricin poisoning by pulmonary and oral routes, respectively.Time course analysis at 24 and 48 h also indicated the progression of ricin from surfaces of the lung into the lung tissue. Inter-subject variation was observed in the case of oral dosing, with data for ricin-treated and vehicle control tissues not statistically different in all samples. In addition the oral toxicity of the crude ricin administered was found to be higher than expected in the rat, based upon published information and an unpublished in house murine study. Crown Copyright (c) 2006 Published by Elsevier Ireland Ltd. All rights reserved.