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Genomics: Infectious Disease and Host-Pathogen Interaction

Medicine and Health

Genomics: Infectious Disease and Host-Pathogen Interaction

F. Wang and N. Chow

Dive into this Special Issue of the International Journal of Molecular Sciences where Franklin Wang and Ngai Chow explore the cutting-edge applications of genomics in combating infectious diseases! Discover twelve original research articles and three reviews that delve into vital topics such as biofilms, diagnostics, and innovative vaccine development.

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Playback language: English
Introduction
Infectious diseases, caused by bacteria, viruses, fungi, and parasites, pose a significant threat. Pathogens interact with hosts, influencing infection establishment, spread, and immune evasion. Genomic features like mutations and specific genes heavily impact host-pathogen interactions, determining virulence, resistance, and disease severity. Next-generation sequencing (NGS) and nanopore sequencing have made genomic, transcriptomic, metagenomic, and small RNA research more accessible and cost-effective. Recent research reveals a bidirectional interaction between pathogen virulence genes and host defense mechanisms. Improving viral detection methods through phylogenomics and mutation analysis is crucial in microbiology. This special issue examines these interactions across various pathogens and hosts.
Literature Review
The special issue incorporates twelve original research articles and three reviews focusing on biofilm formation, diagnostics, vaccine development, and host-pathogen interactions. These studies utilize genomic, transcriptomic, and microbiomic data to provide novel insights into infectious disease mechanisms.
Methodology
The methodology varies across the twelve original articles and three reviews included in this special issue. Specific methodologies are described for each individual study within the special issue and are not summarized here. However, the overall methodological approaches involve techniques such as whole genome sequencing, RNA sequencing, metagenomics, metatranscriptomics, and various bioinformatics analyses. For instance, some studies utilize whole-genome random mutagenesis to identify genes associated with bacterial responses to environmental stimuli, while others employ comparative genomics to analyze the evolution of viral strains. Transcriptomic approaches analyze gene expression changes in host cells following pathogen infection. Microbiomic studies used DNA and RNA sequencing to identify microbial communities in various environments. Several studies used specific assays for viral detection and analyses of specific gene expression to study host-pathogen interactions.
Key Findings
Key findings across the studies included in this special issue are diverse but interconnected. Regarding biofilm formation, research on *Acinetobacter baumannii* showed that sub-minimum inhibitory concentrations of imipenem and colistin induced biofilm-specific antibiotic resistance and virulence genes, increasing antibiotic tolerance. Surprisingly, the SARS-CoV-2 spike protein and mouse coronavirus inhibited biofilm formation by *Streptococcus pneumoniae* and *Staphylococcus aureus*, suggesting a potential link to secondary pneumonia in COVID-19 patients. In diagnostics, FTA cards proved highly effective for releasing nucleic acids from African swine fever virus (ASFV) and influenza A virus (IAV), simplifying diagnostic procedures. A novel vaccination strategy using genetically modified trypanosomes showed promise in protecting against prion diseases. In host-pathogen interactions, studies revealed novel Ebola virus-derived microRNAs that might target host genes and that serial passaging of influenza A virus induced mutations altering viral evolution. Analysis of porcine circovirus type 4 (PCV4) suggested a potential link to mink circovirus (MiCV). Research on wheat stripe rust identified SNPs associated with avirulence genes, and a database was created for studying alfalfa-bacterial stem blight interactions. A transcriptomic study of *Leishmania infantum* revealed that low virulence might be linked to alterations in phagocytosis and signal transduction pathways in canine macrophages. Finally, a comparative study showed that DNA sequencing is better for identifying bacteria and DNA viruses in pepper fruits, while mRNA sequencing is superior for fungi and RNA viruses.
Discussion
The findings in this special issue highlight the power of genomics in understanding infectious diseases. The studies demonstrate how genomic techniques can reveal mechanisms of pathogenicity, antibiotic resistance, and host immune evasion. The findings on biofilm formation, particularly the unexpected inhibitory effect of SARS-CoV-2 spike protein, warrant further investigation. The development of improved diagnostic tools based on FTA cards and the novel vaccination strategy offers promising avenues for combating infectious diseases. The identification of novel viral microRNAs and the analysis of viral evolution underscore the dynamic nature of host-pathogen interactions. The database developed for studying plant-pathogen interactions provides a valuable resource for future research. Overall, the findings emphasize the need for integrative, multi-omics approaches to understand the complexity of infectious diseases and to develop effective control strategies.
Conclusion
This special issue successfully showcases the diverse applications of genomics in infectious disease research. The studies highlight the importance of understanding biofilm formation, developing advanced diagnostics, designing effective vaccines, and elucidating the intricate mechanisms of host-pathogen interactions. Future research should focus on expanding the use of these techniques to investigate a broader range of pathogens and host organisms, further integrating multi-omics approaches, and translating these findings into effective prevention and treatment strategies.
Limitations
The limitations of this special issue are primarily those inherent in the individual studies it contains. The generalizability of findings from in vitro or model organism studies to human populations may be limited. Furthermore, the scope of this special issue, while broad, does not encompass all facets of infectious disease genomics. The specific limitations of each individual study are not summarized here, but should be considered when interpreting the results of each study.
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