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Pathogens, Volume 3, Issue 2 (June 2014), Pages 238-498

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Research

Jump to: Review

Open AccessArticle Morphine Attenuates Apically-Directed Cytokine Secretion from Intestinal Epithelial Cells in Response to Enteric Pathogens
Pathogens 2014, 3(2), 249-257; doi:10.3390/pathogens3020249
Received: 26 November 2013 / Revised: 17 March 2014 / Accepted: 20 March 2014 / Published: 2 April 2014
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Abstract
Epithelial cells represent the first line of host immune defense at mucosal surfaces. Although opioids appear to increase host susceptibility to infection, no studies have examined opioid effects on epithelial immune functions. We tested the hypothesis that morphine alters vectorial cytokine secretion [...] Read more.
Epithelial cells represent the first line of host immune defense at mucosal surfaces. Although opioids appear to increase host susceptibility to infection, no studies have examined opioid effects on epithelial immune functions. We tested the hypothesis that morphine alters vectorial cytokine secretion from intestinal epithelial cell (IPEC-J2) monolayers in response to enteropathogens. Both entero-adherent Escherichia coli O157:H7 and entero-invasive Salmonella enterica serovar Typhimurium increased apically-directed IL-6 secretion and bi-directional IL-8 secretion from epithelial monolayers, but only IL-6 secretion evoked by E. coli was reduced by morphine acting through a naloxone-sensitive mechanism. Moreover, the respective type 4 and 5 Toll-like receptor agonists, lipopolysaccharide and flagellin, increased IL-8 secretion from monolayers, which was also attenuated by morphine pretreatment. These results suggest that morphine decreases cytokine secretion and potentially phagocyte migration and activation directed towards the mucosal surface; actions that could increase host susceptibility to some enteric infections. Full article
(This article belongs to the Special Issue Gut Microbiome)
Open AccessArticle Pseudomonas aeruginosa Genome Evolution in Patients and under the Hospital Environment
Pathogens 2014, 3(2), 309-340; doi:10.3390/pathogens3020309
Received: 30 November 2013 / Revised: 26 March 2014 / Accepted: 28 March 2014 / Published: 10 April 2014
Cited by 3 | PDF Full-text (1283 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and [...] Read more.
Pseudomonas aeruginosa is a Gram-negative environmental species and an opportunistic microorganism, establishing itself in vulnerable patients, such as those with cystic fibrosis (CF) or those hospitalized in intensive care units (ICU). It has become a major cause of nosocomial infections worldwide and a serious threat to Public Health because of overuse and misuse of antibiotics that have selected highly resistant strains against which very few therapeutic options exist. Herein is illustrated the intraclonal evolution of the genome of sequential isolates collected in a single CF patient from the early phase of pulmonary colonization to the fatal outcome. We also examined at the whole genome scale a pair of genotypically-related strains made of a drug susceptible, environmental isolate recovered from an ICU sink and of its multidrug resistant counterpart found to infect an ICU patient. Multiple genetic changes accumulated in the CF isolates over the disease time course including SNPs, deletion events and reduction of whole genome size. The strain isolated from the ICU patient displayed an increase in the genome size of 4.8% with major genetic rearrangements as compared to the initial environmental strain. The annotated genomes are given in free access in an interactive web application WallGene  designed to facilitate large-scale comparative analysis and thus allowing investigators to explore homologies and syntenies between P. aeruginosa strains, here PAO1 and the five clinical strains described. Full article
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
Open AccessArticle Application of DNA Aptamers and Quantum Dots to Lateral Flow Test Strips for Detection of Foodborne Pathogens with Improved Sensitivity versus Colloidal Gold
Pathogens 2014, 3(2), 341-355; doi:10.3390/pathogens3020341
Received: 17 February 2014 / Revised: 30 March 2014 / Accepted: 1 April 2014 / Published: 10 April 2014
Cited by 23 | PDF Full-text (909 KB) | HTML Full-text | XML Full-text
Abstract
Preliminary studies aimed at improving the sensitivity of foodborne pathogen detection via lateral flow (LF) test strips by use of high affinity DNA aptamers for capture and reporter functions when coupled to red-emitting quantum dots (Qdot 655) are reported. A variety of [...] Read more.
Preliminary studies aimed at improving the sensitivity of foodborne pathogen detection via lateral flow (LF) test strips by use of high affinity DNA aptamers for capture and reporter functions when coupled to red-emitting quantum dots (Qdot 655) are reported. A variety of DNA aptamers developed against Escherichia coli, Listeria monocytogenes, and Salmonella enterica were paired in capture and reporter combinations to determine which yielded the strongest detection of their cognate bacteria using a colloidal gold screening system. Several promising sandwich combinations were identified for each of the three bacterial LF strip systems. The best E. coli aptamer-LF system was further studied and yielded a visible limit of detection (LOD) of ~3,000 E. coli 8739 and ~6,000 E. coli O157:H7 in buffer. These LODs were reduced to ~300–600 bacterial cells per test respectively by switching to a Qdot 655 aptamer-LF system. Novel aspects of these assays such as the use of high levels of detergents to avoid quantum dot agglutination and enhance migration in analytical membranes, identification of optimal analytical membrane types, UV-immobilization of capture aptamers, and novel dual biotin/digoxigenin-end labeled aptamer streptavidin-colloidal gold or -Qdot 655 conjugates plus anti-digoxigenin antibody control lines are also discussed. In general, this work provides proof-of-principle for highly sensitive aptamer-Qdot LF strip assays for rapid foodborne pathogen detection. Full article
(This article belongs to the Special Issue Foodborne Pathogens)
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Open AccessArticle Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis
Pathogens 2014, 3(2), 356-376; doi:10.3390/pathogens3020356
Received: 27 November 2013 / Revised: 4 April 2014 / Accepted: 9 April 2014 / Published: 15 April 2014
Cited by 3 | PDF Full-text (2958 KB) | HTML Full-text | XML Full-text
Abstract
The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome network analysis of all available complete bacterial plasmids to determine plasmid associations. A blastp clustering [...] Read more.
The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome network analysis of all available complete bacterial plasmids to determine plasmid associations. A blastp clustering search at 100% aa identity cut-off and sharing at least one gene between plasmids, followed by a multilevel community network analysis revealed that a surprisingly large number of the plasmids were connected by one largest connected component (LCC), with dozens of community sub-groupings. The LCC consisted mainly of Bacilli and Gammaproteobacteria plasmids. Intriguingly, horizontal gene transfer (HGT) was noted between different phyla (i.e., Staphylococcus and Pasteurellaceae), suggesting that Pasteurellaceae can acquire antimicrobial resistance (AMR) genes from closely contacting Staphylococcus spp., which produce the external supplement of V-factor (NAD). Such community network analysis facilitate displaying possible recent HGTs like a class 1 integron, str and tet resistance markers between communities. Furthermore, the distribution of the Inc replicon type and AMR genes, such as the extended-spectrum ß-lactamase (ESBL) CTX-M or the carbapenemases KPC NDM-1, implies that such genes generally circulate within limited communities belonging to typical bacterial genera. Thus, plasmidome network analysis provides a remarkable discriminatory power for plasmid-related HGT and evolution. Full article
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
Open AccessArticle Secretory IgA is Concentrated in the Outer Layer of Colonic Mucus along with Gut Bacteria
Pathogens 2014, 3(2), 390-403; doi:10.3390/pathogens3020390
Received: 29 December 2013 / Revised: 22 April 2014 / Accepted: 24 April 2014 / Published: 29 April 2014
Cited by 13 | PDF Full-text (6307 KB) | HTML Full-text | XML Full-text
Abstract
Antibodies of the secretory IgA (SIgA) class comprise the first line of antigen-specific immune defense, preventing access of commensal and pathogenic microorganisms and their secreted products into the body proper. In addition to preventing infection, SIgA shapes the composition of the gut [...] Read more.
Antibodies of the secretory IgA (SIgA) class comprise the first line of antigen-specific immune defense, preventing access of commensal and pathogenic microorganisms and their secreted products into the body proper. In addition to preventing infection, SIgA shapes the composition of the gut microbiome. SIgA is transported across intestinal epithelial cells into gut secretions by the polymeric immunoglobulin receptor (pIgR). The epithelial surface is protected by a thick network of mucus, which is composed of a dense, sterile inner layer and a loose outer layer that is colonized by commensal bacteria. Immunofluorescence microscopy of mouse and human colon tissues demonstrated that the SIgA co-localizes with gut bacteria in the outer mucus layer. Using mice genetically deficient for pIgR and/or mucin-2 (Muc2, the major glycoprotein of intestinal mucus), we found that Muc2 but not SIgA was necessary for excluding gut bacteria from the inner mucus layer in the colon. Our findings support a model whereby SIgA is anchored in the outer layer of colonic mucus through combined interactions with mucin proteins and gut bacteria, thus providing immune protection against pathogens while maintaining a mutually beneficial relationship with commensals. Full article
(This article belongs to the Special Issue Gut Microbiome)
Open AccessArticle Antibiofilm Effect of Octenidine Hydrochloride on Staphylococcus aureus, MRSA and VRSA
Pathogens 2014, 3(2), 404-416; doi:10.3390/pathogens3020404
Received: 20 March 2014 / Revised: 23 April 2014 / Accepted: 28 April 2014 / Published: 6 May 2014
Cited by 6 | PDF Full-text (848 KB) | HTML Full-text | XML Full-text
Abstract
Millions of indwelling devices are implanted in patients every year, and staphylococci (S. aureus, MRSA and vancomycin-resistant S. aureus (VRSA)) are responsible for a majority of infections associated with these devices, thereby leading to treatment failures. Once established, [...] Read more.
Millions of indwelling devices are implanted in patients every year, and staphylococci (S. aureus, MRSA and vancomycin-resistant S. aureus (VRSA)) are responsible for a majority of infections associated with these devices, thereby leading to treatment failures. Once established, staphylococcal biofilms become resistant to antimicrobial treatment and host response, thereby serving as the etiological agent for recurrent infections. This study investigated the efficacy of octenidine hydrochloride (OH) for inhibiting biofilm synthesis and inactivating fully-formed staphylococcal biofilm on different matrices in the presence and absence of serum protein. Polystyrene plates and stainless steel coupons inoculated with S. aureus, MRSA or VRSA were treated with OH (zero, 0.5, one, 2 mM) at 37 °C for the prevention of biofilm formation. Additionally, the antibiofilm effect of OH (zero, 2.5, five, 10 mM) on fully-formed staphylococcal biofilms on polystyrene plates, stainless steel coupons and urinary catheters was investigated. OH was effective in rapidly inactivating planktonic and biofilm cells of S. aureus, MRSA and VRSA on polystyrene plates, stainless steel coupons and urinary catheters in the presence and absence of serum proteins. The use of two and 10 mM OH completely inactivated S. aureus planktonic cells and biofilm (>6.0 log reduction) on all matrices tested immediately upon exposure. Further, confocal imaging revealed the presence of dead cells and loss in biofilm architecture in the OH-treated samples when compared to intact live biofilm in the control. Results suggest that OH could be applied as an effective antimicrobial to control biofilms of S. aureus, MRSA and VRSA on appropriate hospital surfaces and indwelling devices. Full article
(This article belongs to the Special Issue Biofilm-Based Nosocomial Infections) Print Edition available
Open AccessArticle Transcriptional Profiling of a Cross-Protective Salmonella enterica serovar Typhimurium UK-1 dam Mutant Identifies a Set of Genes More Transcriptionally Active Compared to Wild-Type, and Stably Transcribed across Biologically Relevant Microenvironments
Pathogens 2014, 3(2), 417-436; doi:10.3390/pathogens3020417
Received: 1 March 2014 / Revised: 30 April 2014 / Accepted: 4 May 2014 / Published: 9 May 2014
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Abstract
Vaccination with Salmonella enterica serovar Typhimurium lacking DNA adenine methyltransferase confers cross-protective immunity against multiple Salmonella serotypes. The mechanistic basis is thought to be associated with the de-repression of genes that are tightly regulated when transiting from one microenvironment to another. This [...] Read more.
Vaccination with Salmonella enterica serovar Typhimurium lacking DNA adenine methyltransferase confers cross-protective immunity against multiple Salmonella serotypes. The mechanistic basis is thought to be associated with the de-repression of genes that are tightly regulated when transiting from one microenvironment to another. This de-repression provides a potential means for the production of a more highly expressed and stable antigenic repertoire capable of inducing cross-protective immune responses. To identify genes encoding proteins that may contribute to cross-protective immunity, we used a Salmonella Typhimurium DNA adenine methyltransferase mutant strain (UK-1 dam mutant) derived from the parental UK-1 strain, and assessed the transcriptional profile of the UK-1 dam mutant and UK-1 strain grown under conditions that simulate the intestinal or endosomal microenvironments encountered during the infective process. As expected, the transcriptional profile of the UK-1 dam mutant identified a set of genes more transcriptionally active when compared directly to UK-1, and stably transcribed in biologically relevant culture conditions. Further, 22% of these genes were more highly transcribed in comparison to two other clinically-relevant Salmonella serovars. The strategy employed here helps to identify potentially conserved proteins produced by the UK-1 dam mutant that stimulate and/or modulate the development of cross-protective immune responses toward multiple Salmonella serotypes. Full article
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
Open AccessArticle Pyrosequencing Reveals the Predominance of Pseudomonadaceae in Gut Microbiome of a Gall Midge
Pathogens 2014, 3(2), 459-472; doi:10.3390/pathogens3020459
Received: 1 April 2014 / Revised: 13 May 2014 / Accepted: 3 June 2014 / Published: 11 June 2014
Cited by 4 | PDF Full-text (670 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of [...] Read more.
Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654 high quality sequences of the V3 hypervariable region of the 16S rRNA gene were obtained through 454-pyrosequencing. From these sequences, 311 operational taxonomic units (OTUs) were obtained at the >97% similarity cutoff. In the gut of 1st instar, otu01, a member of Pseudomonas, was predominant, representing 90.2% of total sequences. otu13, an unidentified genus in the Pseudomonadaceae family, represented 1.9% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 2nd instar, otu01 and otu13 decreased to 85.5% and 1.5%, respectively. otu04, a member of Buttiauxella, represented 9.7% of total sequences. The remaining OTUs were each less than 1%. In the gut of the 3rd instar, otu01 and otu13 further decreased to 29.0% and 0%, respectively. otu06, otu08, and otu16, also three members of the Pseudomonadaceae family were 13.2%, 8.6%, and 2.3%, respectively. In addition, otu04 and otu14, two members of the Enterobacteriaceae family, were 4.7% and 2.5%; otu18 and otu20, two members of the Xanthomonadaceae family, were 1.3% and 1.2%, respectively; otu12, a member of Achromobacter, was 4.2%; otu19, a member of Undibacterium, was 1.4%; and otu9, otu10, and otu15, members of various families, were 6.1%, 6.3%, and 1.9%, respectively. The investigation into dynamics of Pseudomonas, the most abundant genera, revealed that its population level was at peak in freshly hatched or 1 day larvae as well as in later developmental stages, thus suggesting a prominent role for this bacterium in Hessian fly development and in its interaction with host plants. This study is the first comprehensive survey on bacteria associated with the gut of a gall midge, and provides a foundation for future studies to elucidate the roles of gut microbes in Hessian fly virulence and biology. Full article
(This article belongs to the Special Issue Gut Microbiome)
Open AccessArticle Antimicrobial Activity of Selected Phytochemicals against Escherichia coli and Staphylococcus aureus and Their Biofilms
Pathogens 2014, 3(2), 473-498; doi:10.3390/pathogens3020473
Received: 4 May 2014 / Revised: 4 June 2014 / Accepted: 5 June 2014 / Published: 18 June 2014
Cited by 6 | PDF Full-text (397 KB) | HTML Full-text | XML Full-text
Abstract
Bacteria can be resistant to multiple antibiotics and we are fast approaching a time when antibiotics will not work on some bacterial infections. New antimicrobial compounds are urgently necessary. Plants are considered the greatest source to obtain new antimicrobials. This study aimed [...] Read more.
Bacteria can be resistant to multiple antibiotics and we are fast approaching a time when antibiotics will not work on some bacterial infections. New antimicrobial compounds are urgently necessary. Plants are considered the greatest source to obtain new antimicrobials. This study aimed to assess the antimicrobial activity of four phytochemicals—7-hydroxycoumarin (7-HC), indole-3-carbinol (I3C), salicylic acid (SA) and saponin (SP)—against Escherichia coli and Staphylococcus aureus, either as planktonic cells or as biofilms. These bacteria are commonly found in hospital-acquired infections. Some aspects on the phytochemicals mode of action, including surface charge, hydrophobicity, motility and quorum-sensing inhibition (QSI) were investigated. In addition, the phytochemicals were combined with three antibiotics in order to assess any synergistic effect. 7-HC and I3C were the most effective phytochemicals against E. coli and S. aureus. Both phytochemicals affected the motility and quorum-sensing (QS) activity, which means that they can play an important role in the interference of cell-cell interactions and in biofilm formation and control. However, total biofilm removal was not achieved with any of the selected phytochemicals. Dual combinations between tetracycline (TET), erythromycin (ERY) and ciprofloxacin (CIP) and I3C produced synergistic effects against S. aureus resistant strains. The overall results demonstrates the potential of phytochemicals to control the growth of E. coli and S. aureus in both planktonic and biofilm states. In addition, the phytochemicals demonstrated the potential to act synergistically with antibiotics, contributing to the recycling of old antibiotics that were once considered ineffective due to resistance problems. Full article
(This article belongs to the Special Issue Biofilm-Based Nosocomial Infections) Print Edition available

Review

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Open AccessReview Integrons in the Intestinal Microbiota as Reservoirs for Transmission of Antibiotic Resistance Genes
Pathogens 2014, 3(2), 238-248; doi:10.3390/pathogens3020238
Received: 24 December 2013 / Revised: 13 March 2014 / Accepted: 13 March 2014 / Published: 31 March 2014
Cited by 5 | PDF Full-text (265 KB) | HTML Full-text | XML Full-text
Abstract
The human intestinal microbiota plays a major beneficial role in immune development and resistance to pathogens. The use of antibiotics, however, can cause the spread of antibiotic resistance genes within the resident intestinal microbiota. Important vectors for this are integrons. This review [...] Read more.
The human intestinal microbiota plays a major beneficial role in immune development and resistance to pathogens. The use of antibiotics, however, can cause the spread of antibiotic resistance genes within the resident intestinal microbiota. Important vectors for this are integrons. This review therefore focuses on the integrons in non-pathogenic bacteria as a potential source for the development and persistence of multidrug resistance. Integrons are a group of genetic elements which are assembly platforms that can capture specific gene cassettes and express them. Integrons in pathogenic bacteria have been extensively investigated, while integrons in the intestinal microbiota have not yet gained much attention. Knowledge of the integrons residing in the microbiota, however, can potentially aid in controlling the spread of antibiotic resistance genes to pathogens. Full article
(This article belongs to the Special Issue Gut Microbiome)
Open AccessReview High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology
Pathogens 2014, 3(2), 258-279; doi:10.3390/pathogens3020258
Received: 20 November 2013 / Revised: 28 February 2014 / Accepted: 20 March 2014 / Published: 2 April 2014
Cited by 7 | PDF Full-text (331 KB) | HTML Full-text | XML Full-text
Abstract
The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic [...] Read more.
The recent progresses of high-throughput sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. HTS associated with adapted, automatic and fast bioinformatics solutions for sequencing applications promises an accurate and timely identification and characterization of pathogenic agents. Many studies have demonstrated that data obtained from HTS analysis have allowed genome-based diagnosis, which has been consistent with phenotypic observations. These proofs of concept are probably the first steps toward the future of clinical microbiology. From concept to routine use, many parameters need to be considered to promote HTS as a powerful tool to help physicians and clinicians in microbiological investigations. This review highlights the milestones to be completed toward this purpose. Full article
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Open AccessReview Leptospiral Pathogenomics
Pathogens 2014, 3(2), 280-308; doi:10.3390/pathogens3020280
Received: 18 January 2014 / Revised: 22 March 2014 / Accepted: 28 March 2014 / Published: 10 April 2014
Cited by 10 | PDF Full-text (2226 KB) | HTML Full-text | XML Full-text
Abstract
Leptospirosis, caused by pathogenic spirochetes belonging to the genus Leptospira, is a zoonosis with important impacts on human and animal health worldwide. Research on the mechanisms of Leptospira pathogenesis has been hindered due to slow growth of infectious strains, poor transformability, [...] Read more.
Leptospirosis, caused by pathogenic spirochetes belonging to the genus Leptospira, is a zoonosis with important impacts on human and animal health worldwide. Research on the mechanisms of Leptospira pathogenesis has been hindered due to slow growth of infectious strains, poor transformability, and a paucity of genetic tools. As a result of second generation sequencing technologies, there has been an acceleration of leptospiral genome sequencing efforts in the past decade, which has enabled a concomitant increase in functional genomics analyses of Leptospira pathogenesis. A pathogenomics approach, by coupling of pan-genomic analysis of multiple isolates with sequencing of experimentally attenuated highly pathogenic Leptospira, has resulted in the functional inference of virulence factors. The global Leptospira Genome Project supported by the U.S. National Institute of Allergy and Infectious Diseases to which key scientific contributions have been made from the international leptospirosis research community has provided a new roadmap for comprehensive studies of Leptospira and leptospirosis well into the future. This review describes functional genomics approaches to apply the data generated by the Leptospira Genome Project towards deepening our knowledge of virulence factors of Leptospira using the emerging discipline of pathogenomics. Full article
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
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Open AccessReview Mouse Models of Hepatitis B Virus Infection Comprising Host-Virus Immunologic Interactions
Pathogens 2014, 3(2), 377-389; doi:10.3390/pathogens3020377
Received: 6 March 2014 / Revised: 9 April 2014 / Accepted: 11 April 2014 / Published: 23 April 2014
Cited by 4 | PDF Full-text (543 KB) | HTML Full-text | XML Full-text
Abstract
Hepatitis B virus (HBV) infection is one of the most prevalent infectious diseases associated with various human liver diseases, including acute, fulminant and chronic hepatitis; liver cirrhosis; and hepatocellular carcinoma. Despite the availability of an HBV vaccine and the development of antiviral [...] Read more.
Hepatitis B virus (HBV) infection is one of the most prevalent infectious diseases associated with various human liver diseases, including acute, fulminant and chronic hepatitis; liver cirrhosis; and hepatocellular carcinoma. Despite the availability of an HBV vaccine and the development of antiviral therapies, there are still more than 350 million chronically infected people worldwide, approximately 5% of the world population. To understand the virus biology and pathogenesis in HBV-infected patients, several animal models have been developed to mimic hepatic HBV infection and the immune response against HBV, but the narrow host range of HBV infection and lack of a full immune response spectrum in animal models remain significant limitations. Accumulating evidence obtained from studies using a variety of mouse models that recapitulate hepatic HBV infection provides several clues for understanding host-virus immunologic interactions during HBV infection, whereas the determinants of the immune response required for HBV clearance are poorly defined. Therefore, adequate mouse models are urgently needed to elucidate the mechanism of HBV elimination and identify novel targets for antiviral therapies. Full article
(This article belongs to the Special Issue Animal Model to Study Viral Immunity)
Open AccessReview WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?
Pathogens 2014, 3(2), 437-458; doi:10.3390/pathogens3020437
Received: 24 April 2014 / Revised: 30 May 2014 / Accepted: 3 June 2014 / Published: 11 June 2014
Cited by 7 | PDF Full-text (264 KB) | HTML Full-text | XML Full-text
Abstract
Recent advances in DNA sequencing technologies have the potential to transform the field of clinical and public health microbiology, and in the last few years numerous case studies have demonstrated successful applications in this context. Among other considerations, a lack of user-friendly [...] Read more.
Recent advances in DNA sequencing technologies have the potential to transform the field of clinical and public health microbiology, and in the last few years numerous case studies have demonstrated successful applications in this context. Among other considerations, a lack of user-friendly data analysis and interpretation tools has been frequently cited as a major barrier to routine use of these techniques. Here we consider the requirements of microbiology laboratories for the analysis, clinical interpretation and management of bacterial whole-genome sequence (WGS) data. Then we discuss relevant, existing WGS analysis tools. We highlight many essential and useful features that are represented among existing tools, but find that no single tool fulfils all of the necessary requirements. We conclude that to fully realise the potential of WGS analyses for clinical and public health microbiology laboratories of all scales, we will need to develop tools specifically with the needs of these laboratories in mind. Full article

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