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Pathogens
Special Issues
Characterizing Infectious Diseases Using a 'Total Infectome' Approach
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Characterizing Infectious Diseases Using a 'Total Infectome' Approach

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 4130

Special Issue Editor

Prof. Dr. Mang Shi

E-Mail Website
Guest Editor
Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
Interests: virus evolution; metagenomics; meta-transcriptomics; macroevolution; pathogen discovery; virology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The recent deployment of microbial discovery technology has revolutionized the field of infectious diseases. On the one hand, the number of potential pathogens discovered has increased exponentially, and on the other hand, it becomes more and more clear that the characterization of infections by the interaction of multiple microbial organisms, such that the “one disease, one pathogen” paradigm, does not easily capture the diversity and complexity of the pathogens involved. Indeed, with modern next-generation-sequencing-based metagenomic approaches, we are able to reveal all types of microbial “key players” simultaneously in the event of infection, which includes viral, bacterial, and eukaryotic pathogens, namely, the “total infectome”, such that we can comprehensively characterize induvial roles of each pathogens as well as their interactions that contribute to the development of disease. For example, in diagnosis, we may consider the cause of an infectious disease based on a panel of co-infecting pathogens rather than individual infectious agents. Or, in the case of pathogen hunting in wild animals, to simultaneously reveal all types of agents relevant for human infection.

Therefore, the aim of this Special Issue is to bring together a series of articles (both reviews and original research) that use the “total infectome” approach to characterize a variety of infectious diseases in humans, animals, as well as other organisms, with the purpose to better reveal the enormous diversity, complex interactions, potential clinical manifestations, and epidemiological impact of different types of pathogens.

Potential topics include, but are not limited to:

  • Pathogen discovery in diseased human, animals and other organisms;
  • Role of diverse microbial pathogens in infectious diseases;
  • Evolution and diversity of microbes;
  • Interaction of microbial pathogens;
  • Methodology in “total infectome” characterization;
  • Future perspectives for pathogen discovery and characterization.

Prof. Dr. Mang Shi
Guest Editor

Manuscript Submission Information

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. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short 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 thoroughly refereed through a single-blind 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 monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • infectious diseases
  • total infectome
  • pathogen discovery and characterization
  • evolution and diversity of microbes
  • microbial pathogens

Published Papers (2 papers)

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Research

20 pages, 3614 KiB  
Article
Metatranscriptomic Sequencing of Medically Important Mosquitoes Reveals Extensive Diversity of RNA Viruses and Other Microbial Communities in Western Australia
by Binit Lamichhane, Craig Brockway, Kimberly Evasco, Jay Nicholson, Peter J. Neville, Avram Levy, David Smith and Allison Imrie
Pathogens 2024, 13(2), 107; https://doi.org/10.3390/pathogens13020107 - 25 Jan 2024
Cited by 1 | Viewed by 1310
Abstract
Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from [...] Read more.
Mosquitoes harbor a wide diversity of microorganisms, including viruses that are human pathogens, or that are insect specific. We used metatranscriptomics, an unbiased high-throughput molecular approach, to describe the composition of viral and other microbial communities in six medically important mosquito species from across Western Australia: Aedes vigilax, Culex annulirostris, Cx. australicus, Cx. globocoxitus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. We identified 42 viral species, including 13 novel viruses, from 19 families. Culex mosquitoes exhibited a significantly higher diversity of viruses than Aedes mosquitoes, and no virus was shared between the two genera. Comparison of mosquito populations revealed a heterogenous distribution of viruses between geographical regions and between closely related species, suggesting that geography and host species may play a role in shaping virome composition. We also detected bacterial and parasitic microorganisms, among which Wolbachia bacteria were detected in three members of the Cx. pipiens complex, Cx. australicus, Cx. pipiens biotype molestus, and Cx. quinquefasciatus. In summary, our unbiased metatranscriptomics approach provides important insights into viral and other microbial diversity in Western Australian mosquitoes that vector medically important viruses. Full article
(This article belongs to the Special Issue Characterizing Infectious Diseases Using a 'Total Infectome' Approach)
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16 pages, 2464 KiB  
Article
Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization
by Linlin Xie, Liangjun Chen, Xinran Li, Junying Zhou, Hongpan Tian, Jin Zhao, Zhiqiang Li and Yirong Li
Pathogens 2023, 12(7), 944; https://doi.org/10.3390/pathogens12070944 - 17 Jul 2023
Cited by 4 | Viewed by 2292
Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower [...] Read more.
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower respiratory tract during viral infection. However, both bacterial and fungal microbiota in the lung of COVID-19 patients remained to be explored. Methods: In this study, we conducted nanopore sequencing analyses of the lower respiratory tract samples from 38 COVID-19 patients and 26 non-COVID-19 pneumonia controls. Both bacterial and fungal microbiome diversities and microbiota abundances in the lung were compared. Results: Our results revealed significant differences in lung microbiome between COVID-19 patients and non-COVID-19 controls, which were strongly associated with SARS-CoV-2 infection and clinical status. COVID-19 patients exhibited a notably higher abundance of opportunistic pathogens, particularly Acinetobacter baumannii and Candida spp. Furthermore, the potential pathogens enriched in COVID-19 patients were positively correlated with inflammation indicators. Conclusions: Our study highlights the differences in lung microbiome diversity and composition between COVID-19 patients and non-COVID-19 patients. This may contribute to predicting co-pathogens and selecting optimal treatments for respiratory infections caused by SARS-CoV-2. Full article
(This article belongs to the Special Issue Characterizing Infectious Diseases Using a 'Total Infectome' Approach)
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