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Microorganisms
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The Molecular Epidemiology of Infectious Diseases
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The Molecular Epidemiology of Infectious Diseases

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

Deadline for manuscript submissions: 31 October 2025 | Viewed by 3942

Special Issue Editor

Dr. Jonathan Hon-kwan Chen

E-Mail Website
Guest Editor
Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Hong Kong
Interests: molecular diagnostics; clinical microbiology

Special Issue Information

Dear Colleagues,

Molecular epidemiology of infectious diseases investigates disease transmission by studying the genetic makeup of pathogens, utilising advanced molecular biology techniques. This field has revolutionised epidemiology by enabling detailed investigations into disease spread, outbreak sources, and effective control measures. By analysing the genetic information of pathogens, researchers can trace disease spread, identify outbreak sources and determine the most effective measures to control transmission. Additionally, molecular epidemiology can identify specific virulence factors that contribute to disease severity, leading to the development of targeted treatments and improved patient outcomes.

For this Special Issue of Microorganisms, we welcome original research, short communications, and reviews covering all aspects of molecular epidemiology in infectious diseases. This includes investigations into genotyping and sequencing techniques, studies on disease transmission and outbreak sources, and research on host-pathogen interactions.

Dr. Jonathan Hon-kwan Chen
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. 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

  • molecular epidemiology
  • infectious diseases
  • outbreak investigations
  • transmission
  • genotyping
  • disease control

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Published Papers (6 papers)

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Research

Jump to: Review

25 pages, 3665 KiB  
Article
Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing E. coli (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA
by Molly M. Leeper, Morgan N. Schroeder, Taylor Griswold, Mohit Thakur, Krittika Krishnan, Lee S. Katz, Kelley B. Hise, Grant M. Williams, Steven G. Stroika, Sung B. Im, Rebecca L. Lindsey, Peyton A. Smith, Jasmine Huffman, Alyssa Kelley, Sara Cleland, Alan J. Collins, Shruti Gautam, Eishita Tyagi, Subin Park, João A. Carriço, Miguel P. Machado, Hannes Pouseele, Dolf Michielsen and Heather A. Carletonadd Show full author list remove Hide full author list
Microorganisms 2025, 13(6), 1310; https://doi.org/10.3390/microorganisms13061310 - 4 Jun 2025
Abstract
Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, and outbreak investigation of STEC. In this study, we [...] Read more.
Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, and outbreak investigation of STEC. In this study, we applied three WGS-based subtyping methods, high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multi-locus sequence typing using chromosome-associated loci [wgMLST (chrom)], and core genome multi-locus sequence typing (cgMLST), to isolate sequences from 11 STEC outbreaks. For each outbreak, we evaluated the concordance between subtyping methods using pairwise genomic differences (number of SNPs or alleles), linear regression models, and tanglegrams. Pairwise genomic differences were highly concordant between methods for all but one outbreak, which was associated with international travel. The slopes of the regressions for hqSNP vs. allele differences were 0.432 (cgMLST) and 0.966 wgMLST (chrom); the slope was 1.914 for cgMLST vs. wgMLST (chrom) differences. Tanglegrams comprised of outbreak and sporadic sequences showed moderate clustering concordance between methods, where Baker’s Gamma Indices (BGIs) ranged between 0.35 and 0.99 and Cophenetic Correlation Coefficients (CCCs) were ≥0.88 across all outbreaks. The K-means analysis using the Silhouette method showed the clear separation of outbreak groups with average silhouette widths ≥0.87 across all methods. This study validates the use of cgMLST for the national surveillance of STEC illness clusters using the PulseNet 2.0 system and demonstrates that hqSNP or wgMLST can be used for further resolution. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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15 pages, 1820 KiB  
Article
Assess the Variability and Robustness of an Aluminum-Based Adsorption–Precipitation Method for Virus Detection in Wastewater Samples
by Lorena Casado-Martín, Marta Hernández, José M. Eiros, Antonio Valero and David Rodríguez-Lázaro
Microorganisms 2025, 13(6), 1186; https://doi.org/10.3390/microorganisms13061186 - 23 May 2025
Viewed by 389
Abstract
Wastewater-based molecular epidemiology enables the surveillance of both symptomatic and asymptomatic individuals in a non-invasive, cost-effective, rapid, and early-detection manner. The use of wastewater analysis to monitor the prevalence of viral pathogens in a given population has increased significantly since the COVID-19 pandemic. [...] Read more.
Wastewater-based molecular epidemiology enables the surveillance of both symptomatic and asymptomatic individuals in a non-invasive, cost-effective, rapid, and early-detection manner. The use of wastewater analysis to monitor the prevalence of viral pathogens in a given population has increased significantly since the COVID-19 pandemic. These studies typically involve three main steps: viral concentration, nucleic acid extraction, and DNA/RNA quantification. However, the absence of a standardized methodology remains a major limitation, hindering result comparability across studies. Among the available viral concentration techniques, aluminum-based adsorption–precipitation is one of the most commonly used due to its simplicity, efficiency, and low cost. This study evaluates the robustness and variability of the viral concentration and nucleic acid extraction steps by implementing different process controls in wastewater samples across 122 independent experiments. Additionally, correlations between viral recovery efficiencies and relevant physicochemical parameters were also analyzed (n = 600). The results indicate that, despite the overall robustness of the method, the concentration step exhibits the highest variability (CV = 53.82%), which accounted for 53.73% of the overall variability. In addition, our results show that, on average, 0.65 logarithmic units were lost during the viral concentration step. Furthermore, viral recovery rates were influenced by seasonality and sample characteristics, while no significant correlation was observed with pH or conductivity. These findings highlight the importance of process controls, confirming the robustness of the methodology, and identifying key parameters that should be considered in future studies for improved data interpretation. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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15 pages, 2639 KiB  
Article
Neisseria gonorrhoeae—Susceptibility Trends and Basic Molecular Mapping of Isolates Collected in Israel in 2016–2022
by Zeev Dveyrin, Tal Alon, Andrei Makhon, Israel Nissan, Zohar Mor and Efrat Rorman
Microorganisms 2025, 13(4), 750; https://doi.org/10.3390/microorganisms13040750 - 26 Mar 2025
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Abstract
Neisseria gonorrhoeae (NG) is a globally significant sexually transmitted infection (STI) with increasing antimicrobial resistance (AMR), posing a serious threat to public health. Between 2016 and 2022, the Israeli National NG Reference Center (INNGRC) comprehensively analyzed NG isolates in Israel to determine AMR [...] Read more.
Neisseria gonorrhoeae (NG) is a globally significant sexually transmitted infection (STI) with increasing antimicrobial resistance (AMR), posing a serious threat to public health. Between 2016 and 2022, the Israeli National NG Reference Center (INNGRC) comprehensively analyzed NG isolates in Israel to determine AMR patterns and sequence types (STs). Antimicrobial susceptibility testing (AST) was performed on 1205 NG isolates using E-test gradient strips, and NG-MAST analysis was conducted on 279 isolates via Sanger sequencing and whole genome sequencing (WGS). Surveillance revealed high resistance rates to ciprofloxacin (54.4%), azithromycin (41.3%), tetracycline, and benzylpenicillin, while all isolates remained susceptible to ceftriaxone and spectinomycin. Multi-drug resistance (MDR) was observed in 8.6% of isolates, and 3% were classified as extensively drug-resistant (XDR). NG-MAST analysis identified 72 distinct STs, with ST292, ST4269, and ST5441 being the most prevalent. ST19665 and ST11461 predominated in 2022, while ST292, ST5441, and ST16169 were more abundant in 2018. The findings highlight the increasing prevalence of AMR in NG in Israel and underscore the importance of continuous surveillance and molecular characterization by reference laboratories like the INNGRC to inform treatment strategies and public health interventions, ultimately reducing the burden of this critical STI. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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21 pages, 2426 KiB  
Article
Molecular Epidemiology of Salmonella enterica Serotype Dublin Isolated from 2011 to 2022 from Veal and Dairy Cattle in Pennsylvania
by Manoj K. Sekhwal, Lingling Li, Traci Pierre, Tammy Matthews, Erin Luley, Deepanker Tewari, Suresh V. Kuchipudi, Bhushan Jayarao and Maurice Byukusenge
Microorganisms 2025, 13(2), 400; https://doi.org/10.3390/microorganisms13020400 - 12 Feb 2025
Viewed by 1107
Abstract
The emergence of Salmonella enterica serotype Dublin (S. Dublin) presents significant challenges to animal and human health. We analyzed 109 S. Dublin isolates from bovine submissions to the Penn State Animal Diagnostic Laboratory between 2011 and 2022. Using whole genome sequencing, [...] Read more.
The emergence of Salmonella enterica serotype Dublin (S. Dublin) presents significant challenges to animal and human health. We analyzed 109 S. Dublin isolates from bovine submissions to the Penn State Animal Diagnostic Laboratory between 2011 and 2022. Using whole genome sequencing, we assessed their phenotypic and genotypic resistance patterns and correlated these traits with case histories and pathology reports. Core-genome analysis identified cgSTs with similar allelic profiles between our isolates and those from the U.S. and Canada, while some cgSTs were unique to our study. Histopathologic findings suggest a predominance of respiratory and gastroenteric/hepatic lesions, aligning with the histopathological case definition for S. Dublin infection. Critically, all isolates were multidrug-resistant, particularly to ampicillin (87%), ceftiofur (89%), chlortetracycline (94%), oxytetracycline (94%), enrofloxacin (17%), florfenicol (94%), sulfadimethoxine (97%), and trimethoprim (20%). Plasmid genomic analysis unveiled distinct plasmid types including virulence, resistance, and hybrid plasmids, carrying unique compositions of virulence genes and antimicrobial resistance. These findings underscore the importance of managing calf movement to control the introduction and dissemination of new cgSTs in Pennsylvania and potentially nationwide. Furthermore, they emphasize the urgent need to mitigate S. Dublin transmission, combat antimicrobial resistance, and enhance surveillance efforts to effectively protect animal and human health. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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13 pages, 1724 KiB  
Article
A Novel Genotype of Orientia tsutsugamushi in Human Cases of Scrub Typhus from Southeastern India
by Krishnamoorthy Nallan, Bhuvaneshwari Chinnathambi Kalidoss, Eunice Swarna Jacob, Samyuktha Krishnasamy Mahadevan, Steny Joseph, Ramkumar Ramalingam, Govindarajan Renu, Balaji Thirupathi, Balajinathan Ramasamy, Bhavna Gupta, Manju Rahi and Paramasivan Rajaiah
Microorganisms 2025, 13(2), 333; https://doi.org/10.3390/microorganisms13020333 - 4 Feb 2025
Viewed by 1126
Abstract
Scrub typhus is a mite-borne, re-emerging public health problem in India, particularly in Tamil Nadu, South India. More than 40 serotypes of Orientia tsutsugamushi have been documented worldwide. However, the information on the circulation of its molecular sub-types in India is scanty. A [...] Read more.
Scrub typhus is a mite-borne, re-emerging public health problem in India, particularly in Tamil Nadu, South India. More than 40 serotypes of Orientia tsutsugamushi have been documented worldwide. However, the information on the circulation of its molecular sub-types in India is scanty. A retrospective study was conducted among serologically confirmed cases of scrub typhus. DNA isolated from blood was screened by a nested polymerase chain reaction (nPCR) targeting the GroEL and the 56 kDa type-specific antigen (TSA) genes. Out of 59 samples, 14 partial fragments of GroEL and the twelve 56 kDa genes were PCR-amplified and DNA-sequenced. The neighbor-joining (NJ) analysis indicated three distinct phylogenetic clades, including a novel genotype designated as Ot-Thanjavur-Tamil Nadu (Ot-TJTN, 9 nos. 64.3%); Karp-like (4 nos. 28.6%); and Kuroki-Gilliam type (1 no. 7.1%). Also, phylogenetic analysis of twelve 56 kDa variable domains (VDΙ-ΙΙΙ) of TSA gene sequences revealed a distinctive new genotypic cluster of eight samples (66.6%), and the remaining four (33.4%) were Karp-like genotypes. The Simplot analysis for the similarity and event of recombination testing elucidated the existence of the new genotype of the Ot-TJTN cluster, which was undescribed so far, in the Kato and TA716 lineages. The significant findings recommend further studies to understand the ongoing transmission dynamics of different O. tsutsugamushi strains in vector mites, rodent hosts, and humans in this region. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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Review

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26 pages, 750 KiB  
Review
Advances in Wastewater-Based Epidemiology for Pandemic Surveillance: Methodological Frameworks and Future Perspectives
by Weihe Zhu, Daxi Wang, Pengsong Li, Haohao Deng and Ziqing Deng
Microorganisms 2025, 13(5), 1169; https://doi.org/10.3390/microorganisms13051169 - 21 May 2025
Viewed by 307
Abstract
Wastewater-based epidemiology (WBE) has emerged as a transformative approach for community-level health monitoring, particularly during the COVID-19 pandemic. This review critically examines the methodological framework of WBE systems through the following three core components: (1) sampling strategies that address spatial–temporal variability in wastewater [...] Read more.
Wastewater-based epidemiology (WBE) has emerged as a transformative approach for community-level health monitoring, particularly during the COVID-19 pandemic. This review critically examines the methodological framework of WBE systems through the following three core components: (1) sampling strategies that address spatial–temporal variability in wastewater systems, (2) comparative performance of different platforms in pathogen detection, and (3) predictive modeling integrating machine learning approaches. We systematically analyze how these components collectively overcome the limitations of conventional surveillance methods through early outbreak detection, asymptomatic case identification, and population-level trend monitoring. While highlighting technical breakthroughs in viral concentration methods and variant tracking through sequencing, the review also identifies persistent challenges, including data standardization, cost-effectiveness concerns in resource-limited settings, and ethical considerations in public health surveillance. Drawing insights from global implementation cases, we propose recommendations for optimizing each operational phase and discuss emerging applications beyond pandemic response. This review highlights WBE as an indispensable tool for modern public health, whose methodological refinements and cross-disciplinary integration are critical for transforming pandemic surveillance from reactive containment to proactive population health management. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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