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Genomics: Infectious Disease and Host-Pathogen Interaction 3.0
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Genomics: Infectious Disease and Host-Pathogen Interaction 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 November 2024 | Viewed by 4755

Special Issue Editor

Dr. Franklin W.N. Chow

E-Mail Website
Guest Editor
Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong, China
Interests: emerging infectious diseases; host-pathogen interactions; extracellular vesicles; pathogen genomics and evolution; RNA Biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Infectious diseases, which are disorders caused by pathogens such as bacteria, viruses, fungi, or parasites, pose a serious threat to humans, animals, and plants. Pathogens can interact with the host to suppress or evade the host immune systems in order to establish and disseminate the infections.

Unique genome features contribute largely to the events of host–pathogen interactions, governing the virulence level of pathogens and infection severity of the host. With the advancement of NGS and nanopore sequencing, it is now highly cost-effective to pursue genomic and transcriptomic studies. Recent research has shown that host–pathogen interaction can be bi-directionally modulated by small RNAs which come from unique genome loci. Under the current COVID-19 pandemic, there is a surge in the development of SARS-CoV-2 detection methods based on the study of phylogenomics and mutations of viral genomes.

We invite researchers to contribute original research articles and reviews focused on different genomics aspects of i) infectious diseases and ii) host–pathogen interactions.

Topics of interest include, but are not limited to, the following:

  • Genomics and transcriptomics;
  • Phylogenetics and evolution;
  • Small RNA regulations;
  • RNA biology (e.g., Dual-RNA-Seq);
  • Molecular pathogenesis;
  • Molecular detection.

Dr. Franklin W.N. Chow
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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
  • NGS
  • small RNA
  • host-pathogen interaction
  • pathogen detection
  • viruses
  • fungi
  • parasites
  • bacteria
  • evolution

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Related Special Issue

Published Papers (4 papers)

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Research

16 pages, 3573 KiB  
Article
Local Genomic Surveillance of Invasive Streptococcus pyogenes in Eastern North Carolina (ENC) in 2022–2023
by Weihua Huang, John E. Markantonis, Changhong Yin, Joseph R. Pozdol, Kimberly P. Briley and John T. Fallon
Int. J. Mol. Sci. 2024, 25(15), 8179; https://doi.org/10.3390/ijms25158179 - 26 Jul 2024
Viewed by 863
Abstract
The recent increase in Group A Streptococcus (GAS) incidences in several countries across Europe and some areas of the Unites States (U.S.) has raised concerns. To understand GAS diversity and prevalence, we conducted a local genomic surveillance in Eastern North Carolina (ENC) in [...] Read more.
The recent increase in Group A Streptococcus (GAS) incidences in several countries across Europe and some areas of the Unites States (U.S.) has raised concerns. To understand GAS diversity and prevalence, we conducted a local genomic surveillance in Eastern North Carolina (ENC) in 2022–2023 with 95 isolates and compared its results to those of the existing national genomic surveillance in the U.S. in 2015–2021 with 13,064 isolates. We observed their epidemiological changes before and during the COVID-19 pandemic and detected a unique sub-lineage in ENC among the most common invasive GAS strain, ST28/emm1. We further discovered a multiple-copy insertion sequence, ISLgar5, in ST399/emm77 and its single-copy variants in some other GAS strains. We discovered ISLgar5 was linked to a Tn5801-like tetM-carrying integrative and conjugative element, and its copy number was associated with an ermT-carrying pRW35-like plasmid. The dynamic insertions of ISLgar5 may play a vital role in genome fitness and adaptation, driving GAS evolution relevant to antimicrobial resistance and potentially GAS virulence. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction 3.0)
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16 pages, 1613 KiB  
Article
Genomic Landscape of Susceptibility to Severe COVID-19 in the Slovenian Population
by Anja Kovanda, Tadeja Lukežič, Aleš Maver, Hana Vokač Križaj, Mojca Čižek Sajko, Julij Šelb, Matija Rijavec, Urška Bidovec-Stojković, Barbara Bitežnik, Boštjan Rituper, Peter Korošec and Borut Peterlin
Int. J. Mol. Sci. 2024, 25(14), 7674; https://doi.org/10.3390/ijms25147674 - 12 Jul 2024
Viewed by 883
Abstract
Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings [...] Read more.
Determining the genetic contribution of susceptibility to severe SARS-CoV-2 infection outcomes is important for public health measures and individualized treatment. Through intense research on this topic, several hundred genes have been implicated as possibly contributing to the severe infection phenotype(s); however, the findings are complex and appear to be population-dependent. We aimed to determine the contribution of human rare genetic variants associated with a severe outcome of SARS-CoV-2 infections and their burden in the Slovenian population. A panel of 517 genes associated with severe SARS-CoV-2 infection were obtained by combining an extensive review of the literature, target genes identified by the COVID-19 Host Genetic Initiative, and the curated Research COVID-19 associated genes from PanelApp, England Genomics. Whole genome sequencing was performed using PCR-free WGS on DNA from 60 patients hospitalized due to severe COVID-19 disease, and the identified rare genomic variants were analyzed and classified according to the ACMG criteria. Background prevalence in the general Slovenian population was determined by comparison with sequencing data from 8025 individuals included in the Slovenian genomic database (SGDB). Results show that several rare pathogenic/likely pathogenic genomic variants in genes CFTR, MASP2, MEFV, TNFRSF13B, and RNASEL likely contribute to the severe infection outcomes in our patient cohort. These results represent an insight into the Slovenian genomic diversity associated with a severe COVID-19 outcome. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction 3.0)
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18 pages, 704 KiB  
Article
Distribution of papA and papG Variants among Escherichia coli Genotypes: Association with Major Extraintestinal Pathogenic Lineages
by Valentina Fernández-Yáñez, Patricio Suazo, Claudia Hormazábal, Valentina Ibaceta, Mauricio Arenas-Salinas, Roberto M. Vidal, Francisco Silva-Ojeda, Carolina Arellano, Ignacio Muñoz and Felipe Del Canto
Int. J. Mol. Sci. 2024, 25(12), 6657; https://doi.org/10.3390/ijms25126657 - 17 Jun 2024
Cited by 1 | Viewed by 904
Abstract
The pyelonephritis-associated fimbria (P fimbria) is one of the most recognized adhesion determinants of extraintestinal pathogenic Escherichia coli strains (ExPECs). Twelve variants have been described for the gene encoding the P fimbria major structural subunit PapA and three variants for the gene encoding [...] Read more.
The pyelonephritis-associated fimbria (P fimbria) is one of the most recognized adhesion determinants of extraintestinal pathogenic Escherichia coli strains (ExPECs). Twelve variants have been described for the gene encoding the P fimbria major structural subunit PapA and three variants for the gene encoding the adhesin subunit PapG. However, their distribution among the ExPEC diversity has not been comprehensively addressed. A complete landscape of that distribution might be valuable for delineating basic studies about the pathogenicity mechanisms of ExPECs and following up on the evolution of ExPEC lineages, particularly those most epidemiologically relevant. Therefore, we performed a massive descriptive study to detect the papA and papG variants along different E. coli genotypes represented by genomic sequences contained in the NCBI Assembly Refseq database. The most common papA variants were F11, F10, F48, F16, F12, and F7-2, which were found in significant association with the most relevant ExPEC genotypes, the phylogroups B2 and D, and the sequence types ST95, ST131, ST127, ST69, ST12, and ST73. On the other hand, the papGII variant was by far the most common followed by papGIII, and both were also found to have a significant association with common ExPEC genotypes. We noticed the presence of genomes, mainly belonging to the sequence type ST12, harboring two or three papA variants and two papG variants. Furthermore, the most common papA and papG variants were also detected in records representing strains isolated from humans and animals such as poultry, bovine, and dogs, supporting previous hypotheses of potential cross-transmission. Finally, we characterized a set of 17 genomes from Chilean uropathogenic E. coli strains and found that ST12 and ST73 were the predominant sequence types. Variants F7-1, F7-2, F8, F9, F11, F13, F14, F16, and F48 were detected for papA, and papGII and papGIII variants were detected for papG. Significant associations with the sequence types observed in the analysis of genomes contained in the NCBI Assembly Refseq database were also found in this collection in 16 of 19 cases for papA variants and 7 of 9 cases for the papG variants. This comprehensive characterization might support future basic studies about P fimbria-mediated ExPEC adherence and future typing or epidemiological studies to monitor the evolution of ExPECs producing P fimbria. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction 3.0)
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20 pages, 2280 KiB  
Article
Reprogramming in Candida albicans Gene Expression Network under Butanol Stress Abrogates Hyphal Development
by Rajesh Anand, Mohammad Kashif, Awadhesh Pandit, Ram Babu and Agam P. Singh
Int. J. Mol. Sci. 2023, 24(24), 17227; https://doi.org/10.3390/ijms242417227 - 7 Dec 2023
Cited by 1 | Viewed by 1515
Abstract
Candida albicans is the causative agent of invasive fungal infections. Its hyphae-forming ability is regarded as one of the important virulence factors. To unravel the impact of butanol on Candida albicans, it was placed in O+ve complete human serum with butanol [...] Read more.
Candida albicans is the causative agent of invasive fungal infections. Its hyphae-forming ability is regarded as one of the important virulence factors. To unravel the impact of butanol on Candida albicans, it was placed in O+ve complete human serum with butanol (1% v/v). The Candida transcriptome under butanol stress was then identified by mRNA sequencing. Studies including electron microscopy demonstrated the inhibition of hyphae formation in Candida under the influence of butanol, without any significant alteration in growth rate. The numbers of genes upregulated in the butanol in comparison to the serum alone were 1061 (20 min), 804 (45 min), and 537 (120 min). Candida cells exhibited the downregulation of six hypha-specific transcription factors and the induction of four repressor/regulator genes. Many of the hypha-specific genes exhibited repression in the medium with butanol. The genes related to adhesion also exhibited repression, whereas, among the heat-shock genes, three showed inductions in the presence of butanol. The fungal-specific genes exhibited induction as well as repression in the butanol-treated Candida cells. Furthermore, ten upregulated genes formed the core stress gene set in the presence of butanol. In the gene ontology analysis, enrichment of the processes related to non-coding RNA, ribosome biosynthesis, and metabolism was observed in the induced gene set. On the other side, a few GO biological process terms, including biofilm formation and filamentous growth, were enriched in the repressed gene set. Taken together, under butanol stress, Candida albicans is unable to extend hyphae and shows growth by budding. Many of the genes with perturbed expression may have fitness or virulence attributes and may provide prospective sites of antifungal targets against C. albicans. Full article
(This article belongs to the Special Issue Genomics: Infectious Disease and Host-Pathogen Interaction 3.0)
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