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Microorganisms
Special Issues
Genomics and Epidemiology of Clinical Microorganisms
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Genomics and Epidemiology of Clinical Microorganisms

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Medical Microbiology".

Deadline for manuscript submissions: 15 May 2025 | Viewed by 3989

Special Issue Editors

Dr. Addy Cecilia Helguera-Repetto

E-Mail Website
Guest Editor
Departamento de Inmunobioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City 11000, Mexico
Interests: microbiology; molecular epidemiology; molecular diagnosis
Dr. Moises Leon-Juarez

E-Mail Website
Guest Editor
Instituto Nacional de Perinatología, Ciudad de México 11000, Mexico
Interests: viral infection; viral replication; antivirals; vertical viral infections
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to explore the intersection of genomics and epidemiology in understanding the dynamics, evolution, and clinical implications of microorganisms. Contributions to this Special Issue will encompass a broad range of topics, including, but not limited to, the following:

  1. Genomic Characterization of Pathogens: Original research focusing on the genomic analysis of clinically relevant microorganisms, elucidating their genetic diversity, virulence factors, and antibiotic resistance profiles.
  2. Evolutionary Dynamics: Studies investigating the evolutionary trajectories of pathogens within clinical settings, including the emergence of antimicrobial resistance, genetic adaptation to host environments, and evolutionary drivers shaping microbial populations.
  3. Transmission Dynamics and Outbreak Investigations: Research employing genomic epidemiology approaches to track the transmission routes of infectious diseases, investigate outbreak origins, and assess the effectiveness of control measures.
  4. Host–Pathogen Interactions: Investigations into the molecular mechanisms underlying host–pathogen interactions, including the identification of microbial virulence determinants, host immune responses, and genetic factors influencing disease susceptibility.
  5. Bioinformatics and Computational Tools: Development and application of novel bioinformatics tools, computational algorithms, and genomic surveillance platforms for analyzing large-scale microbial genomic datasets and predicting epidemiological trends.
  6. Clinical Implications and Public Health Interventions: Translational research addressing the clinical implications of genomic findings, informing public health policies, and guiding the development of targeted interventions for infectious disease prevention and control.
  7. Emerging Technologies and Methodologies: Reviews or perspectives on emerging technologies (e.g., metagenomics and single-cell sequencing) and methodological advancements in genomic and epidemiological research of clinical microorganisms.

This Special Issue seeks to provide a comprehensive platform for researchers, clinicians, and public health professionals to share their latest findings, methodologies, and insights into the genomics and epidemiology of clinical microorganisms, with the ultimate goal of advancing our understanding of infectious diseases and improving patient outcomes.

Dr. Addy Cecilia Helguera-Repetto
Dr. Moises Leon-Juarez
Guest Editors

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. Microorganisms 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 disease epidemiology
  • pathogen genomics
  • molecular characterization of microorganisms
  • clinical outcomes of infectious diseases
  • virulence determinants
  • antibiotic resistance
  • pathogen gene expression

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (5 papers)

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Research

15 pages, 3603 KiB  
Article
Drug Resistance Mutations (DRMs) for Long-Acting Injectable Cabotegravir and Rilpivirine (CAB/RPV LAI) in the HIV-1 Subtype A6 Epidemic in Poland
by Andrzej Załęski, Agnieszka Lembas, Tomasz Dyda, Joanna Osińska, Joanna Jabłońska, Justyna Stempkowska-Rejek, Justyna Orzechowska and Alicja Wiercińska-Drapało
Microorganisms 2025, 13(2), 321; https://doi.org/10.3390/microorganisms13020321 - 1 Feb 2025
Viewed by 420
Abstract
HIV subtype A6 with the L74I polymorphism, which increases the risk of cabotegravir/rilpivirine treatment failure, causes more and more infections in Poland. In this multicenter, observational, cross-sectional study (2023–2024), we analyzed viral subtypes and drug-resistance mutations to drugs used for long-acting injectable antiretroviral [...] Read more.
HIV subtype A6 with the L74I polymorphism, which increases the risk of cabotegravir/rilpivirine treatment failure, causes more and more infections in Poland. In this multicenter, observational, cross-sectional study (2023–2024), we analyzed viral subtypes and drug-resistance mutations to drugs used for long-acting injectable antiretroviral treatment and pre-exposure prophylaxis. Among 357 people with HIV, 247 (69%) were Polish nationals, and 102 (29%) were from former Soviet Union countries. Of the 357 people included, 159 (45%) had subtype B, and 177 (50%) had subtype A6 infections, with 165 (87%) of the latter characterized by the L74I polymorphism. Subtype A6 was more frequent in women (66% vs. 46% in men, p < 0.05) and among people from former Soviet countries (77% vs. 39% in Polish nationals, p < 0.05). About 40% of people had either drug-resistance mutations for cabotegravir/rilpivirine or HIV A6 subtype with the L74I polymorphism; 4.5% had both of these conditions. Compared to subtype B infections, subtype A6 infections were characterized by more frequent major transmitted drug-resistance mutations for non-nucleoside reverse transcriptase inhibitors (8.5% vs. 1.9%, p = 0.007) and rilpivirine (5.1% vs. 0.6%, p = 0.016). Due to the frequent occurrence of the L74I polymorphism and drug-resistance mutations in HIV A6 subtype infection, about 40% of people with HIV in Poland may be at risk of long-acting injectable treatment failure. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
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19 pages, 2655 KiB  
Article
Advancing Understanding of Escherichia coli Pathogenicity in Preterm Neonatal Sepsis
by Oscar Villavicencio-Carrisoza, Orly Grobeisen-Duque, Ana Laura Garcia-Correa, Irma Eloisa Monroy-Muñoz, Graciela Villeda-Gabriel, Irma Elena Sosa-González, Hector Flores-Herrera, Ricardo Figueroa-Damian, Jorge Francisco Cerna-Cortes, Sandra Rivera-Gutierrez, Isabel Villegas-Mota, Veronica Zaga-Clavellina and Addy Cecilia Helguera-Repetto
Microorganisms 2025, 13(2), 219; https://doi.org/10.3390/microorganisms13020219 - 21 Jan 2025
Viewed by 493
Abstract
Neonatal sepsis is a major cause of mortality in preterm infants, with Escherichia coli as one of the leading pathogens. Few studies have examined the interplay between virulence factors, resistance profiles, phylogroups, and clinical outcomes in this population. We analyzed 52 E. coli [...] Read more.
Neonatal sepsis is a major cause of mortality in preterm infants, with Escherichia coli as one of the leading pathogens. Few studies have examined the interplay between virulence factors, resistance profiles, phylogroups, and clinical outcomes in this population. We analyzed 52 E. coli strains isolated from 49 preterm neonates diagnosed with sepsis at a tertiary-level hospital in Mexico. Strains underwent phylogenetic classification, virulence gene profiling, and antimicrobial resistance testing. PFGE was used to assess genetic relatedness and outbreak clusters. Clinical data were correlated with molecular findings. Phylogroups A and B2 accounted for 46% of strains. Phylogroup A exhibited notable virulence, with high prevalence of the pathogenicity island described in virulent extra-intestinal E. coli strains (PAI), aerobactin siderophore receptor AerJ (iutA), and yersiniabactin siderophore receptor (fyuA) genes, alongside significant resistance profiles. PFGE identified two dominating branches. Branch A, comprising phylogroups A and B2, displayed high resistance and was prevalent in the neonatal intensive care unit. Branch C, with phylogroups A and D, showed less multidrug resistance but was significantly associated with maternal chorioamnionitis. This study redefines E. coli pathogenicity in neonatal sepsis, highlighting the virulence of traditionally non-pathogenic phylogroups. High virulence strains were associated with more severe outcomes. These findings underscore the need for enhanced strategies in targeted prevention, improved diagnostics, and tailored treatments for high-risk preterm populations. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
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15 pages, 638 KiB  
Article
Association of Single-Nucleotide Variants in ACE2 with the Persistence of Positive qPCR Test for SARS-CoV-2 in Healthcare Professionals During the First Wave of the COVID-19 Pandemic
by Karina Jiménez-Gil, Jorge Alberto Cerón-Albarrán, Melissa Daniella Gonzalez-Fernandez, Rosalba Sevilla-Montoya, Alberto Hidalgo-Bravo, Javier Angeles-Martínez, Daniel Montes-Herrera, Oscar Villavicencio-Carrisoza, Carmen Selene García-Romero, José Esteban Muñoz-Medina and Irma Eloisa Monroy-Muñoz
Microorganisms 2024, 12(12), 2560; https://doi.org/10.3390/microorganisms12122560 - 12 Dec 2024
Viewed by 586
Abstract
The persistence of qPCR positivity for SARS-CoV-2 in individuals who recovered from COVID-19 raised several questions regarding viral transmission, with a special interest in healthcare professionals who may pose a risk of transmitting SARS-CoV-2. This issue highlights the necessity for identifying the genetic [...] Read more.
The persistence of qPCR positivity for SARS-CoV-2 in individuals who recovered from COVID-19 raised several questions regarding viral transmission, with a special interest in healthcare professionals who may pose a risk of transmitting SARS-CoV-2. This issue highlights the necessity for identifying the genetic risk factors associated with persistent SARS-CoV-2 infection. A promising target for achieving this goal is the angiotensin-converting enzyme 2 (ACE2) gene, which has been associated with clinical characteristics of COVID-19 infection, such as severity. The analysis of samples from the first wave of the COVID-19 pandemic represents the initial response of the immune human system against this new virus, without the effect of vaccination or the presence of multiple strains. The aim of this study was to analyze the association of genetic variants in ACE2 with persistent SARS-CoV-2 infection. We conducted a case–control study, including 151 healthcare workers who tested positive for SARS-CoV-2 by qPCR during the first wave of the COVID-19 pandemic, and who were followed up until their results were negative. ACE2 was sequenced through Sanger sequencing. The sequence was compared against a reference sequence and variants identified. Four ACE2 variants were associated with persistent SARS-CoV-2 qPCR positivity. Three of the variants with an effect on the resulting protein were associated with increased risk of persistent SARS-CoV-2 qPCR positivity, NG_012575.2:g.35481 C>T, NG_012575.2:g.35483 G>T and NG_012575.2:g.35498 G>T. On the other hand, the rs2285666 (NG_012575.2:g.14934 G>A) was associated with a higher risk for persistent SARS-CoV-2 qPCR positivity in women and rs4646150 (NG_012575.2:g.25701 G>A) in men. The NG_012575.2:g.35498 G>T variant represents an amino acid change with a possibly harmful effect on ACE2 function. Our results suggest that ACE2 variants might be useful for identifying the population at higher risk for developing persistent SARS-CoV-2-positive qPCR results. This knowledge can be helpful for designing health policies for protecting healthcare professionals and, in consequence, users of health services. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
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13 pages, 279 KiB  
Article
Occurrence of Aggregatibacter actinomycetemcomitans and Its JP2 Genotype in a Cohort of 220 Western Australians with Unstable Periodontitis
by Nabil Khzam, Omar Kujan, Dorte Haubek and Leticia Algarves Miranda
Microorganisms 2024, 12(11), 2354; https://doi.org/10.3390/microorganisms12112354 - 18 Nov 2024
Cited by 1 | Viewed by 721
Abstract
Aim: The main purpose of the present study was to investigate the carrier rate of Aggregatibacter actinomycetemcomitans and its JP2 genotype in a cohort of 200 Western Australians diagnosed with periodontitis. Materials and Methods: In this descriptive cross-sectional study, 220 consecutive patients with [...] Read more.
Aim: The main purpose of the present study was to investigate the carrier rate of Aggregatibacter actinomycetemcomitans and its JP2 genotype in a cohort of 200 Western Australians diagnosed with periodontitis. Materials and Methods: In this descriptive cross-sectional study, 220 consecutive patients with periodontitis, aged 18 years and older, were recruited to a specialist periodontal practice in Perth City. Every patient included in this study contributed three different intra-oral samples. Periodontal, radiographical, and microbiological assessments were performed. The samples were analysed using a polymerase chain reaction for the detection of Aggregatibacter actinomycetemcomitans and its JP2 genotype using the primers and conditions described previously. A Chi-square test and logistic regression analysis were performed to evaluate the results. Results: The prevalence of Aggregatibacter actinomycetemcomitans was 28.18%. The carrier rates of A. actinomycetemcomitans in the unstimulated saliva, cheek swabs, and pooled subgingival plaque samples were 21.80%, 19.50%, and 17.70%, respectively. There was a significant correlation between the severe form of periodontitis (stage IV, grade C) and younger age (p = 0.004), positive family history of periodontitis (p < 0.001), oral hygiene method (p < 0.001), and irregular dental visit attendance (p < 0.001). The binary logistic regression analysis revealed that having severe periodontitis risk increased almost three times in those who were young (OR: 2.812) and came from a family with a history of periodontal disease (OR: 3.194). However, the risk of severe periodontitis was five times higher in those patients with tooth loss due to periodontal disease (OR: 5.071). The highly leukotoxic JP2 genotype of Aggregatibacter actinomycetemcomitans was not detected. Conclusions: This study of a Western Australian cohort confirmed the low presence of Aggregatibacter actinomycetemcomitans and the complete absence of its JP2 genotype. Young age, family history of periodontal disease, lack of flossing, irregular dental visits, and tooth loss due to periodontitis were identified as potential risk factors for periodontitis stage IV, grade C in this cohort. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
13 pages, 2487 KiB  
Article
A Genome-Focused Investigation Reveals the Emergence of a Mycobacterium tuberculosis Strain Related to Multidrug-Resistant Tuberculosis in the Amazon Region of Brazil
by Emilyn Costa Conceição, Johannes Loubser, Arthur Emil dos Santos Guimarães, Abhinav Sharma, Liliana Kokusanilwa Rutaihwa, Anzaan Dippenaar, Richard Steiner Salvato, Ricardo José de Paula Souza e Guimarães, Maria Cristina da Silva Lourenço, Wandyra Araújo Barros, Ninarosa Calzavara Cardoso, Robin Mark Warren, Sebastien Gagneux, Beatriz Gilda Jegerhorn Grinsztejn, Philip Noel Suffys and Karla Valéria Batista Lima
Microorganisms 2024, 12(9), 1817; https://doi.org/10.3390/microorganisms12091817 - 2 Sep 2024
Viewed by 1229
Abstract
A previous study in Pará, Northern Brazil, described a strain of Mycobacterium tuberculosis with a unique genotype (SIT2517/T1) associated with multidrug-resistant tuberculosis (MDR-TB). To improve our understanding of MDR-TB transmission dynamics of these strains within this region, we performed phenotypic and genotypic drug [...] Read more.
A previous study in Pará, Northern Brazil, described a strain of Mycobacterium tuberculosis with a unique genotype (SIT2517/T1) associated with multidrug-resistant tuberculosis (MDR-TB). To improve our understanding of MDR-TB transmission dynamics of these strains within this region, we performed phenotypic and genotypic drug susceptibility testing (pDST/gDST), 24-loci mycobacterial interspersed repetitive units (MIRU-VNTR) genotyping, whole-genome sequencing (WGS) and geo-epidemiology analysis. Of the 28 SIT2517/T1 isolates, 19 (67.9%) could be genotyped by 24-loci MIRU-VNTR and 15 by WGS. All belonged to sublineage 4.1.1.3, distinct from other representative Lineage 4 isolates identified in Brazil. The MDR phenotype determined by pDST was confirmed by gDST, the latter also demonstrating the presence of additional mutations conferring pre-extensively drug-resistance (pre-XDR). Discrepancies between gDST and pDST were observed for pyrazinamide and fluoroquinolones. Thirteen out of 15 isolates analyzed by WGS were clustered when applying a 12 single nucleotide polymorphisms (SNPs) cutoff. The SIT2517/T1 isolates were distributed across the metropolitan regions of Belém and Collares municipalities, showing no geographic clustering. WGS-transmission network analysis revealed a high likelihood of direct transmission and the formation of two closely linked transmission chains. This study highlights the need to implement TB genomic surveillance in the Brazilian Amazon region. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
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