Special Issue "Bacterial Pathogenomics: From Technology to Application"


A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (31 January 2014)

Special Issue Editor

Guest Editor
Dr. Anthony Underwood
Bioinformatics Group | Applied Laboratory and Bio- Informatics Unit, Microbiology Services, Colindale, Public Health England 61 Colindale Avenue, London NW9 5EQ, UK
Website: http://hi.im/antunderwood
E-Mail: anthony.underwood@phe.gov.uk
Phone: 0208 3276466
Interests: pathogen genomics; phylogenomics; virulence; microbiology; public health

Special Issue Information

Dear Colleagues,

The first bacterial genome required a large team and many person years to complete. With current high throughput massively-parallel sequencing technologies it is possible to generate a nearly complete bacterial genome in just a few days. This major revolution opens up huge opportunities, particularly in the ability to compare the whole genomes of many bacterial isolates. This might include trying to answer basic biological questions by looking at genome wide associations and attempting to link genetic features to phenotypic traits. However the questions being asked can also be much more applied, such as using whole genome phylogenies to look for evidence of transmission within a community or hospital or find the source of a disease outbreak.

In this special issue, we invite investigators to submit manuscripts that cover this broad topic. These can include everything from novel uses of current sequencing technology to investigate bacterial genomics, to cutting edge applications of whole genome sequencing to 'real world' scenarios.

We look forward to your contribution.

Dr. Anthony Underwood
Guest Editor


Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues the Article Processing Charge (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Published Papers (15 papers)

by , , , ,  and
Pathogens 2014, 3(2), 417-436; doi:10.3390/pathogens3020417
Received: 1 March 2014; in revised form: 30 April 2014 / Accepted: 4 May 2014 / Published: 9 May 2014
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by ,  and
Pathogens 2014, 3(2), 356-376; doi:10.3390/pathogens3020356
Received: 27 November 2013; in revised form: 4 April 2014 / Accepted: 9 April 2014 / Published: 15 April 2014
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by , , , , , , , ,  and
Pathogens 2014, 3(2), 309-340; doi:10.3390/pathogens3020309
Received: 30 November 2013; in revised form: 26 March 2014 / Accepted: 28 March 2014 / Published: 10 April 2014
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by , ,  and
Pathogens 2014, 3(2), 280-308; doi:10.3390/pathogens3020280
Received: 18 January 2014; in revised form: 22 March 2014 / Accepted: 28 March 2014 / Published: 10 April 2014
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by , , , , , , ,  and
Pathogens 2014, 3(1), 211-237; doi:10.3390/pathogens3010211
Received: 13 December 2013; in revised form: 10 February 2014 / Accepted: 3 March 2014 / Published: 18 March 2014
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by  and
Pathogens 2014, 3(1), 164-184; doi:10.3390/pathogens3010164
Received: 4 December 2013; in revised form: 6 January 2014 / Accepted: 13 February 2014 / Published: 25 February 2014
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by  and
Pathogens 2014, 3(1), 121-148; doi:10.3390/pathogens3010121
Received: 22 November 2013; in revised form: 20 January 2014 / Accepted: 22 January 2014 / Published: 28 January 2014
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by ,  and
Pathogens 2014, 3(1), 93-108; doi:10.3390/pathogens3010093
Received: 26 September 2013; in revised form: 16 December 2013 / Accepted: 7 January 2014 / Published: 21 January 2014
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by , , , , , ,  and
Pathogens 2014, 3(1), 57-72; doi:10.3390/pathogens3010057
Received: 8 November 2013; in revised form: 27 December 2013 / Accepted: 7 January 2014 / Published: 14 January 2014
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by ,  and
Pathogens 2014, 3(1), 36-56; doi:10.3390/pathogens3010036
Received: 30 November 2013; in revised form: 30 December 2013 / Accepted: 7 January 2014 / Published: 13 January 2014
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by  and
Pathogens 2014, 3(1), 25-35; doi:10.3390/pathogens3010025
Received: 27 November 2013; in revised form: 18 December 2013 / Accepted: 7 January 2014 / Published: 9 January 2014
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by ,  and
Pathogens 2013, 2(4), 627-635; doi:10.3390/pathogens2040627
Received: 1 August 2013; in revised form: 19 November 2013 / Accepted: 20 November 2013 / Published: 26 November 2013
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by , , , , , , , ,  and
Pathogens 2013, 2(4), 591-605; doi:10.3390/pathogens2040591
Received: 2 August 2013; in revised form: 16 October 2013 / Accepted: 24 October 2013 / Published: 30 October 2013
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by Jr.
Pathogens 2013, 2(3), 556-570; doi:10.3390/pathogens2030556
Received: 1 August 2013; in revised form: 3 September 2013 / Accepted: 5 September 2013 / Published: 24 September 2013
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by , , , ,  and
Pathogens 2013, 2(3), 544-555; doi:10.3390/pathogens2030544
Received: 17 July 2013; in revised form: 29 August 2013 / Accepted: 2 September 2013 / Published: 10 September 2013
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Review
Title: From Reads to Whole Genome Sequencing, High-Throughput Sequencing in the Fight against Pathogens
Authors: Ségolène Caboche *, Christophe Audebert and David Hot
Affiliation: University of Lille_IFR142, France; Genes Diffusion, France and Institut Pasteur de Lille, France; *E-Mail: segolene.caboche@pasteur-lille.fr (S.G.)
Abstract: The recent progresses of High-Throughput Sequencing (HTS) technologies enable easy and cost-reduced access to whole genome sequencing (WGS) or re-sequencing. This is particularly true for small genome organisms such as bacteria and viruses. HTS associated with adapted, automatic and fast bioinformatic solutions in WGS promises an accurate and timely identification and characterization of pathogen agents. However, so far, it has only been used for posterior studies of circulating pathogen genomes and not yet as a tool of real time genomic identification to help physicians and clinicians in their medical protocol choice. In this review, the already established milestones and those yet to be completed toward this purpose will be described and discussed.
Keywords: HTS; WGS; pathogen outbreak; bioinformatics analysis; analysis pipeline; comparative genomic

Type of Paper: Article
Title: Whole Genome MLST of Staphylococci as a Tool for Clinical Microbiology
Author: Samuel K. Sheppard
Affiliation: Reader in Microbiology and Infectious Disease, Swansea University Senior Research Associate, University of Oxford, Wellcome Trust Fellow, UK; E-Mail: S.K.Sheppard@swansea.ac.uk (S.K.S.)
Abstract: Genome sequencing of bacterial pathogens can provide detailed information about strain variation in relation to important clinical phenotypes such as virulence or susceptibility to treatment, and enhance understanding of disease epidemiology. However the potential of this technology remains largely unrealized in clinical microbiology laboratories, in part because of difficulties in handling population genomic datasets. Here we present a rapid comparative genomics approach based on gene-by-gene analysis of 247 published Staphylococcus aureus and S. epidermidis genomes. We demonstrate the utility of this web accessible analysis platform. First, for basic population genomic analysis including investigation of population structure, variations in the core and accessory genome, and phylogenetic history of lineages – including the relatedness of MLST clonal complexes. Second, for finer scale investigation of clinically important genes such as mecA, which was present in 27% of S. epidermidis and ubiquitous in the S. aureus isolates, and toxin associated genes such as those encoding the PVL toxins and genes responsible for the synthesis of delta- and beta-toxins that were differentially present in the two species. This freely available gene-by-gene analysis pipeline provides a rapid and scalable tool for epidemiological and evolutionary analysis of Staphylococcus, and other bacterial pathogens, and offers the potential for further increasing the use of whole genome sequencing in clinical  microbiology.

Type of Paper: Article
Title: Integrons in the Commensal Flora as a Reservoir for Transmission of Antibiotic Resistance Genes to Pathogens
Author: Knut Rudi
Affiliation: Norwegian University of Life Sciences, Department of Chemistry, Biotechnology and Food Science, P.O. Box 5003, NO-1432 Aas, Norway; E-Mail: knut.rudi@umb.no (K.R.)
Abstract: Antibiotics have revolutionized treatment of bacterial infections. Unfortunately, the use of antibiotics has been over-emphasized, resulting in the spread of antibiotic resistance genes. Integrons residing in transposons or genome islands have served as a main vector for this spread. These integrons consist of several genes acquired from different microbes and are expressed by a strong promoter. The genes in the integrons can be related to both resistance to antibiotics and host-microbe interaction. Integrons in pathogenic bacteria have been extensively investigated, while integrons in the commensal flora have not yet gained much attention. This review will mainly focus on integrons in the commensal flora and the potential of their transfer to pathogens. Information on the integrons residing in the commensal flora can potentially aid in controlling the spread of antibiotic resistance genes to pathogens, and as a consequence the spread of multi-resistant infections. This review will give an appraisal on a very important, but often overlooked aspect of the microbiota as a reservoir for antibiotic resistant genes in integrons and genome plasticity of microbes. With the accumulated information on the role of commensals in genetic transfer of integrons, in the future, this knowledge can be used to curb the spread of antibiotic resistance genes.

Type of Paper: Article
Title: Comprehensive Analysis of Prokaryotes in Environmental Water Using Whole Genome Amplification and DNA Microarray
Author: Koichi Suzuki
Affiliation: Department of Microbiology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan; E-Mail: koichis@nih.go.jp (K.S.)
Abstract: Environmental water contains a microflora consisted of high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, an approach other than cultivation is needed to identify prokaryotes in environmental water. To establish a simplified protocol to detect prokaryotes in environmental water, a novel DNA microarray was developed. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. To evaluate this DNA microarray, one liter of environmental water samples were collected from seven sites in Japan and whole DNA was extracted and uniformly amplified using whole genome amplification (WGA). DNA was labeled with Cy3-conjugated 16S rRNA specific primers and subjected to microarray analysis. The microarray successfully identified indigenous and pathogenic bacteria, and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.

Type of Paper: Review
Title: Live Genomics for Pathogen Monitoring in Public Health Systems
Authors: Giuseppe D'Auria 1,*, Maria Victoria Schneider 2 and Andrés Moya 1
Affiliations: 1 Joint Unit of Research in Genomics and Health Center for Public Health Research (FISABIO-CSISP), Valencia, Spain
2 The Genome Analysis Centre, Norwich Research Park, Norwich, UK; *E-Mail: dauria_giu@gva.es (G.D.A.)
Abstract: Whole genome analysis based on next generation sequencing represents now an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Thus, pathogenic organisms of interest could be tracked at genomic level monitoring all-at-one its expansion, pathogenicity, resistance to antibiotics, virulence and persistence factors, mobile elements, adaptation features, etc. not only in a world-wide context but, probably more useful, at a local context behind a recurrent or emergency outbreak event. In this paper we review the state of the art in infection diagnostics and propose an actuation protocol based on a “streaming approach” going from pathogens genome sequencing trough results formatting, comparative analysis and data mining. Thus, genomics data of target pathogens populate relational databases where automatic data-mining pipelines allows extracting differential data of interest such as virulence, resistance persistence factors, SNPs and InDels profiles. Such analytical protocol allows responding in short time to the needs of locally circumscribed outbreaks providing causes of resistance and genetic tracking elements for rapid detection and monitoring actuations for present or future occurrences.

Type of Paper: Review
Title: Genomic and Global Approaches to Unraveling How Hypermutable Sequences Influence Bacterial Pathogenesis
Authors: Fadil A. Bidmos and Christopher D. Bayliss *
Affiliation: Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK; *E-Mail: cdb12@le.ac.uk (C.D.B.)
Abstract: Rapid adaptation to fluctuations in the host mileau contributes to the host persistence and virulence of bacterial pathogens. Adaptation is frequently mediated by hypermutable sequences in bacterial pathogens. Early bacterial genomic studies identified the multiplicity and potential for virulence-associated functions of these hypermutable sequences. Thus simple sequence repeat tracts and site-specific recombination were found to control capsular type, lipopolysaccharide structure, pilin diversity and expression of outer membrane proteins. We review how the population diversity inherent in these mechanisms of localised hypermutation is now being unlocked by investigation of model systems and clinical samples. A contrast is presented between the problematical nature of analysing simple sequence repeats in next generation sequencing data and in simpler, pragmatic PCR-based approaches. Specific examples are presented of the potential relevance of this localized hypermutation to meningococcal pathogenesis. This leads us to speculate on the future prospects for unraveling how hypermutable mechanisms may contribute to transmission, spread and persistence of bacterial pathogens.

Type of Paper: Article
Whole-Proteome and 16S rRNA Analyses of Pathogenic Strains of Alphaproteobacteria
Yunyun Zhou 1, Douglas R. Call 1,2 and Shira L. Broschat 1,2,3,*

School of Electrical Engineering and Computer Science, Washington State University, Pullman, WA, USA
Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA
3 Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, USA; *E-Mail: cdb12@le.ac.uk (C.D.B.)
Thousands of whole-genome and whole-proteome sequences have been made available through advances in sequencing technology, and millions more will become available in the coming years. This wealth of genetic information does and will provide numerous opportunities for learning, among which is a greater understanding of relationships among species. Researchers have used 16S rRNA and other techniques to study the evolutionary origins of bacteria, but these techniques do not give insight into the sharing of genes among bacteria via horizontal transfer. In this work we use an open source software program called pClust to cluster proteins from whole proteomes of twelve Alphaproteobacteria and compare the results with their established 16S rRNA phylogeny. We obtain dendrograms using orthologous protein clusters and using a simple 16S rRNA technique. The results differ significantly only in one respect: the animal pathogen Rickettsia typhi is clustered with the three remaining animal pathogens using the whole proteomes rather than as a singlet cluster using the 16S rRNA genes. We conclude that whole-proteome analysis can give insight into relationships among species beyond their established phylogenies, perhaps reflecting the effects of horizontal gene transfer and potentially providing insight into the functions of shared genes by means of shared phenotypes.
whole-proteome sequences; alphaproteobacteria; bacterial pathogens; bacterial phenotypes; pClust


Type of Paper: Article
On the limits of bacterial lifestyle predictions based on genome content
Eudes Barbosa 1,3*, Richard Röttger 2 , Vasco Azevedo1 and Jan Baumbach 3

Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
2 Max Planck Institute for Informatics, Saarbrücken, Germany
3 Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark; E-Mails: eudesgvb@ufmg.br (E.B.); vasco@icb.ufmg.br (V.A.); roettger@mpi-inf.mpg.de (R.R.); jbaumbac@imada.sdu.dk (J.B.)
Actinobacterial species occupy various niches in diverse habitats. Hence, we may assume the existence of lifestyle-specific genomic features. Here, we study the genomic repertoire of 89 actinobacteria classified into four life styles, the pathogenicity classes HP (human pathogens), AP (animal pathogens), OP (opportunistic pathogens), and NP (non-pathogen). Our aim is to investigate the level of their genome specificity by identifying class-specific gene sets. We hypothesize: (H1) Pathogens (HPs, APs, OPs) possess specific pathogenicity genes not existing in NPs. (H2) Animal and human pathogens cannot be distinguished due to an observation bias, i.e. the diversity of AP hosts, and the assumption that HPs might also be APs although never having been identified as such. Additionally, (H3) there is no intrinsic genomic characteristic of opportunistic pathogens (OPs) compared to HPs and APs, as the interplay between host and pathogen as well as small mutations might play a more dominant role. To study these hypotheses, we implemented a bioinformatics pipeline that combines evolutionary sequence analysis (BLAST and Transitivity Clustering) with statistical learning methods (R software package). Essentially, we present orthologous gene sets that computationally distinguish pathogens from NPs (H1). We further show a limited differentiating repertoire for HP from AP (H2), and for OP from HP&AP (H3). In conclusion, we give evidence and illustrate the limitation we face when trying to deduce a certain microbial lifestyle from genomic content, at least in the case of actinobacterial pathogenicity.
Bacterial lifestyle; Actinobacteria; Pathogenicity

Last update: 23 December 2013

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