Pathogens

20 pages, 4616 KiB

Open AccessArticle

Novel Techniques to Unravel Causative Bacterial Ecological Shifts in Chronic Urinary Tract Infection

by Catherine C. Y. Chieng, Qingyang Kong, Natasha S. Y. Liou, Mariña Neira Rey, Katie L. Dalby, Neil Jones, Rajvinder Khasriya and Harry Horsley

Pathogens 2025, 14(3), 299; https://doi.org/10.3390/pathogens14030299 - 20 Mar 2025

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Abstract

Chronic urinary tract infection (UTI) presents with protracted lower urinary tract symptoms and elevated urinary leukocyte counts, but its bacterial etiological agents remain obscure. In this cross-sectional investigation, we aimed to unravel the role of the bladder microbiota in chronic UTI pathogenesis by [...] Read more.

Chronic urinary tract infection (UTI) presents with protracted lower urinary tract symptoms and elevated urinary leukocyte counts, but its bacterial etiological agents remain obscure. In this cross-sectional investigation, we aimed to unravel the role of the bladder microbiota in chronic UTI pathogenesis by studying the host immune response. Urine samples were collected from healthy controls (HT), chronic UTI patients who had not initiated treatment (PT) and those undergoing treatment (OT), then sorted into white blood cell (WBC) and epithelial cell (EPC) fractions. Bacteria associated with both fractions were identified by chromogenic agar culture coupled with mass spectrometry and 16S rRNA sequencing. Distinct WBC-exclusive bacteria were observed in the healthy population, but this pattern was less obvious in patients, plausibly due to epithelial shedding and breaching of the urothelial barrier. We also described a bacterial fingerprint guided by Escherichia that was able to stratify patients based on symptom severity. Clustering analyses of mean rank changes revealed highly statistically significant upward and downward ecological shifts in communities of bacteria between the healthy and diseased populations. Interestingly, many of the most abundant genera identified in sequencing remained stable when compared between the study cohorts. We concluded that reshuffling of the urinary microbiome, rather than the activity of a single known urinary pathogen, could drive chronic UTI. Full article

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13 pages, 792 KiB

Open AccessArticle

Clonal Dissemination of NDM-Producing Proteus mirabilis in a Teaching Hospital in Sousse, Tunisia

by Nadia Jaidane, Lamia Tilouche, Saoussen Oueslati, Delphine Girlich, Sana Azaiez, Aymeric Jacquemin, Laurent Dortet, Walid Naija, Abdelhalim Trabelsi, Thierry Naas, Wejdene Mansour and Rémy A. Bonnin

Pathogens 2025, 14(3), 298; https://doi.org/10.3390/pathogens14030298 - 20 Mar 2025

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Abstract

Proteus mirabilis (P. mirabilis) is an opportunistic pathogen involved in urinary tract infections as well as various nosocomial infections. Emerging resistances to beta-lactams in this species complicates potential treatment since it is intrinsically resistant to colistin. Eleven isolates of carbapenem-non-susceptible P. [...] Read more.

Proteus mirabilis (P. mirabilis) is an opportunistic pathogen involved in urinary tract infections as well as various nosocomial infections. Emerging resistances to beta-lactams in this species complicates potential treatment since it is intrinsically resistant to colistin. Eleven isolates of carbapenem-non-susceptible P. mirabilis were identified in Sousse Hospital, Tunisia, from January 2018 to December 2022. MICs were determined and isolates were sequenced to determine their resistomes, sequence types, virulence factors, and their clonal relationships. Susceptibility testing showed that all isolates were resistant to carbapenems, aminoglycosides, fluoroquinolones, chloramphenicol, and the trimethoprim/sulfamethoxazole combination. They remained susceptible to the aztreonam/avibactam combination. All isolates produced NDM-1 carbapenemase and ArmA 16S rRNA methylase. In addition, one isolate co-produced the bla_VEB-6 gene. All isolates belonged to ST135, and phylogenetic analysis revealed that they were closely related. This study described the first outbreak of NDM-1-producing P. mirabilis in Tunisia. Full article

(This article belongs to the Section Bacterial Pathogens)

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8 pages, 652 KiB

Open AccessBrief Report

Ocular Symptoms in Pre- and Perimenopausal Woman Infected with Demodex spp.

by Danuta Kosik-Bogacka, Natalia Łanocha-Arendarczyk, Renata Pilarczyk, Daria Schneider-Matyka, Karolina Kot, Konrad Grzeszczak, Joanna Pyzia and Elżbieta Grochans

Pathogens 2025, 14(3), 297; https://doi.org/10.3390/pathogens14030297 - 20 Mar 2025

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Abstract

The aim of this study was to determine the subjective ocular symptoms in pre- and perimenopausal women infected with Demodex folliculorum and D. brevis. Eyelashes were taken from pre- and perimenopausal women aged from 45 to 69 years (n = 253) and [...] Read more.

The aim of this study was to determine the subjective ocular symptoms in pre- and perimenopausal women infected with Demodex folliculorum and D. brevis. Eyelashes were taken from pre- and perimenopausal women aged from 45 to 69 years (n = 253) and younger women aged from 3 to 40 (n = 204) from the West Pomeranian Voivodeship located in Poland. The prevalence of mites was analyzed according to age and subjective ocular symptoms. Demodex spp. were detected in 75/253 (29.64%) of pre- and perimenopausal women and in 25/204 (12.25%) of younger women. Demodex folliculorum or D. brevis was observed in 72/252 (28.45%) and 1/253 (0.4%) of pre- and perimenopausal women, respectively, but the coinfection of D. folliculorum and D. brevis was noted in 2/253 (0.79%) of women. In young women, only D. folliculorum was detected. Single Demodex spp., multiple parasites, and numerous mites were reported in about 75%, 17%, and 8% of the examined women, respectively. There was a statistically significant relationship between Demodex spp. infestation and the occurrence of dryness of the eyes. Changes occurring in the female body during the pre- and perimenopausal periods lead to an increased incidence of Demodex spp. infestation. Women who report dryness of the eyes should have their eyelashes microscopically examined for Demodex spp. Full article

(This article belongs to the Section Parasitic Pathogens)

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14 pages, 3042 KiB

Open AccessArticle

Detection of Klebsiella pneumoniae in Veterinary and Food Matrices Using Loop-Mediated Isothermal Amplification

by Icía Bermúdez-Fornos, Alberto Cepeda, Alejandro Garrido-Maestu and Alexandre Lamas

Pathogens 2025, 14(3), 296; https://doi.org/10.3390/pathogens14030296 - 19 Mar 2025

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Abstract

Klebsiella pneumoniae is an opportunistic human pathogen of high relevance due to its ability to acquire antibiotic resistance. This pathogen is included, along with Enterococcus faecium, Staphylococcus aureus, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter spp., in the ESKAPE group, [...] Read more.

Klebsiella pneumoniae is an opportunistic human pathogen of high relevance due to its ability to acquire antibiotic resistance. This pathogen is included, along with Enterococcus faecium, Staphylococcus aureus, Acinetobacter baumanii, Pseudomonas aeruginosa, and Enterobacter spp., in the ESKAPE group, which consists of the most important bacterial pathogens resistant to antibiotics in clinical setups. Due to the importance of the rapid identification of infection-causative agents, a novel method for the rapid identification of K. pneumoniae was developed in the present work. This novel method was based on loop-mediated isothermal amplification (LAMP) and evaluated in real-time LAMP, as well as in end-point colorimetric LAMP. Additionally, the method was evaluated in two different clinical samples, namely, blood and urine, along with a food sample, namely, milk; four DNA purification protocols were also evaluated (thermal lysis, chelex, magnetic beads, and glass milk). The results revealed differences in the performance of the LAMP assays depending on the specific combination of the matrix–DNA purification protocol. Overall, the protocol reporting the best results in all the matrices was the one based on chelex, with which it was possible to reach an LOD50 below 10 CFU/mL after a short pre-enrichment step of 6 h in TSB. The method demonstrated reliability, sensitivity, and simplicity and could be performed by non-trained personnel thanks to the colorimetric format. Full article

(This article belongs to the Section Bacterial Pathogens)

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Graphical abstract

12 pages, 2093 KiB

Open AccessArticle

The Role of Caspase-1 and Caspase-4 in Modulating Gingival Epithelial Cell Responses to Aggregatibacter actinomycetemcomitans Infection

by Kartheyaene Jayaprakash Demirel, Alessandra Neves Guimaraes and Isak Demirel

Pathogens 2025, 14(3), 295; https://doi.org/10.3390/pathogens14030295 - 18 Mar 2025

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Abstract

Periodontitis is a chronic inflammatory disease characterized by bacterial infection and immune dysregulation. Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a key pathogen linked to disease progression. Caspase-1 and caspase-4 regulate inflammasome activation and cytokine release, yet their roles in gingival epithelial immunity [...] Read more.

Periodontitis is a chronic inflammatory disease characterized by bacterial infection and immune dysregulation. Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) is a key pathogen linked to disease progression. Caspase-1 and caspase-4 regulate inflammasome activation and cytokine release, yet their roles in gingival epithelial immunity remain unclear. The aim of this study was to elucidate the involvement of caspase-1 and caspase-4 in regulating the immune response to A. actinomycetemcomitans infection in gingival epithelial cells. Human gingival epithelial cells (Ca9-22) and caspase-1- and caspase-4-deficient cells were infected with A. actinomycetemcomitans for 24 h. Inflammatory mediator release was analyzed using Olink proteomics. Bacterial colonization and invasion were assessed using fluorescence-based assays and gentamicin protection assays. Caspase-1- and caspase-4-deficient cells showed significantly altered cytokine and chemokine profiles after infection with A. actinomycetemcomitans, showing reduced IL-17C and IL-18 release. We also found an increased release of TGF-α and LIF from caspase-4-deficient cells, along with elevated levels of the chemokines IL-8, CXCL9, and CXCL10. Additionally, both caspase-1- and caspase-4-deficient cells showed increased bacterial colonization and invasion, particularly in caspase-4-deficient cells. These findings suggest that caspase-1 and caspase-4 play distinct yet essential roles in gingival epithelial immunity, regulating cytokine release, barrier integrity, and defense against A. actinomycetemcomitans colonization. Full article

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16 pages, 6026 KiB

Open AccessArticle

Molecular Characterization and Antimicrobial Resistance Evaluation of Listeria monocytogenes Strains from Food and Human Samples

by Annamaria Castello, Vincenzina Alio, Marina Torresi, Gabriella Centorotola, Alexandra Chiaverini, Francesco Pomilio, Ignazio Arrigo, Anna Giammanco, Teresa Fasciana, Marco Francesco Ortoffi, Antonietta Gattuso, Giuseppa Oliveri, Cinzia Cardamone and Antonella Costa

Pathogens 2025, 14(3), 294; https://doi.org/10.3390/pathogens14030294 - 18 Mar 2025

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Abstract

Listeria monocytogenes is an important foodborne pathogen, markedly persistent even in harsh environments and responsible for high hospitalization and mortality rates. The aim of the present study was to detect the strains circulating in Sicily over a five-year period and characterize their antimicrobial [...] Read more.

Listeria monocytogenes is an important foodborne pathogen, markedly persistent even in harsh environments and responsible for high hospitalization and mortality rates. The aim of the present study was to detect the strains circulating in Sicily over a five-year period and characterize their antimicrobial resistance profiles. The key element of this study was the sharing of data among various entities involved in food control and clinical surveillance of listeriosis in order to develop an integrated approach for this pathogen. A total of 128 isolates were analyzed, including 87 food-source strains and 41 clinical specimens. Whole-genome sequencing (WGS) was performed for sequence type (ST) and clonal complex (CC) identification through multilocus sequence typing (MLST) analysis. Antimicrobial resistance was assessed using the Kirby–Bauer method. The majority of strains belonged to serotype IVb (34/41 and 53/87 of clinical and food-source isolates, respectively) and were subtyped as CC2-ST2 (28/34 and 41/53 of clinical and food-source isolates respectively). Most of the isolates were susceptible to the main antimicrobials recommended for treatment of listeriosis. Resistance (R) and intermediate resistance (I) percentages worthy of attention were found against oxacillin (R: 85.9%) and clindamycin (I: 34.6%) in the food-source isolates and trimethoprim/sulfamethoxazole (R: 29.23%) in the clinical isolates. Also, 7.7% of the food-source isolates were multidrug resistant. Our results highlight how the punctual comparison between food and clinical strains is an essential tool for effectively tracking and preventing foodborne outbreaks. Full article

(This article belongs to the Section Bacterial Pathogens)

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25 pages, 914 KiB

Open AccessReview

Unlocking the Interactions Between the Whole-Body Microbiome and HPV Infection: A Literature Review

by Myrto Papamentzelopoulou and Vassiliki C. Pitiriga

Pathogens 2025, 14(3), 293; https://doi.org/10.3390/pathogens14030293 - 18 Mar 2025

Viewed by 513

Abstract

The human microbiome plays a vital role in maintaining human homeostasis, acting as a key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption of the symbiotic relationship between the host and the local microbiota, leading to the [...] Read more.

The human microbiome plays a vital role in maintaining human homeostasis, acting as a key regulator of host immunity and defense mechanisms. However, dysbiotic microbial communities may cause disruption of the symbiotic relationship between the host and the local microbiota, leading to the pathogenesis of various diseases, including viral infections and cancers. One of the most common infectious agents causing cancer is the human papilloma virus (HPV), which accounts for more than 90% of cervical cancers. In most cases, the host immune system is activated and clears HPV, whereas in some cases, the infection persists and can lead to precancerous lesions. Over the last two decades, the advent of next-generation sequencing (NGS) technology and bioinformatics has allowed a thorough and in-depth analysis of the microbial composition in various anatomical niches, allowing researchers to unveil the interactions and the underlying mechanisms through which the human microbiota could affect HPV infection establishment, persistence, and progression. Accordingly, the present narrative review aims to shed light on our understanding of the role of the human microbiome in the context of HPV infection and its progression, mainly to cervical cancer. Furthermore, we explore the mechanisms by which the composition and balance of microbial communities exert potential pathogenic or protective effects, leading to either HPV persistence and disease outcomes or clearance. Special interest is given to how the microbiome can modulate host immunity to HPV infection. Lastly, we summarize the latest findings on the therapeutic efficacy of probiotics and prebiotics in preventing and/or treating HPV infections and the potential of vaginal microbiota transplantation while highlighting the significance of personalized medicine approaches emerging from NGS-based microbiome profiling and artificial intelligence (AI) for the optimal management of HPV-related diseases. Full article

(This article belongs to the Special Issue Oncogenic Viruses: Advances in Molecular Diagnosis, Prevention Strategies and Therapy)

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13 pages, 3504 KiB

Open AccessArticle

Genomic Diversity, Virulome, and Resistome of Streptococcus agalactiae in Northeastern Brazil: Are Multi-Host Adapted Strains Rising?

by Vinicius Pietta Perez, Luciana Roberta Torini, Fernanda Zani Manieri, Suellen Bernardo de Queiroz, Jorhanna Isabelle Araujo de Brito Gomes, Lauro Santos Filho, Eloiza Helena Campana, Celso Jose Bruno de Oliveira, Eduardo Sergio Soares Sousa and Ilana Lopes Baratella Cunha Camargo

Pathogens 2025, 14(3), 292; https://doi.org/10.3390/pathogens14030292 - 17 Mar 2025

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Abstract

Streptococcus agalactiae, known as group B streptococci (GBS), colonizes the digestive and genitourinary tracts and causes neonatal diseases and infections in immunocompromised and elderly individuals. GBS neonatal disease prevention includes intrapartum antibiotic prophylaxis. We characterized 101 GBS isolates obtained from patients in [...] Read more.

Streptococcus agalactiae, known as group B streptococci (GBS), colonizes the digestive and genitourinary tracts and causes neonatal diseases and infections in immunocompromised and elderly individuals. GBS neonatal disease prevention includes intrapartum antibiotic prophylaxis. We characterized 101 GBS isolates obtained from patients in João Pessoa, northeastern Brazil, owing to the need to develop and implement vaccines to prevent GBS infections. Capsular types were determined using multiplex-PCR, and antibiotic susceptibility profiles were determined using disc diffusion or the gradient strip method. Clonal diversity was evaluated using pulsed-field gel electrophoresis. Fourteen selected isolates had the genome sequenced and evaluated for virulence and resistance genes. The GBS population had high clonal diversity, with serotype Ia and V prevalence. Among the sequenced isolates, we detected antibiotic resistance genes (ant(6)-Ia, catA8, ermA, ermB, lsaE, lsnuB, mefA/msrD, tetM, tetO, and tetS), several virulence genes, and mobile genetic elements integrated into the chromosome. The most frequent Sequence Type (ST) was ST144, followed by ST196, ST28, ST19, ST12, ST23, ST103, and the new ST1983 (CC103). Phylogenetically, ST103 and ST1983 were distant from the other STs. Our data revealed highly virulent GBS strains in this population and a new ST that could be related to a zoonotic origin. Full article

(This article belongs to the Section Bacterial Pathogens)

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17 pages, 2967 KiB

Open AccessSystematic Review

Can Bacteriophages Be Effectively Utilized for Disinfection in Animal-Derived Food Products? A Systematic Review

by Rafail Fokas, Zoi Kotsiri and Apostolos Vantarakis

Pathogens 2025, 14(3), 291; https://doi.org/10.3390/pathogens14030291 - 16 Mar 2025

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Abstract

Food safety is a paramount public health concern, particularly with the rise of antimicrobial-resistant bacteria. This systematic review explores the efficacy of bacteriophages as a novel and environmentally sustainable approach to controlling multi-resistant and non-resistant bacterial pathogens in animal-derived food products. Following PRISMA [...] Read more.

Food safety is a paramount public health concern, particularly with the rise of antimicrobial-resistant bacteria. This systematic review explores the efficacy of bacteriophages as a novel and environmentally sustainable approach to controlling multi-resistant and non-resistant bacterial pathogens in animal-derived food products. Following PRISMA guidelines, data from multiple studies were synthesized to evaluate bacteriophage applications across diverse food matrices, including beef, poultry, seafood, and dairy. The findings highlight significant variability in bacteriophage efficacy, influenced by factors such as food matrix properties, bacterial strains, and application methods. Phage cocktails and their combination with thermal treatments consistently demonstrated superior bacterial reduction compared to single-phage applications, which yielded variable results. Interestingly, the absence of a clear dose-response relationship underscores the need for a more detailed understanding of phage-host interactions and environmental influences. This review addresses a critical gap in the literature by advocating for matrix-specific, targeted phage applications over generalized approaches. Additionally, it underscores the transformative potential of bacteriophages as sustainable alternatives to chemical disinfectants in modern food safety practices. These insights provide a framework for future research aimed at optimizing bacteriophage efficacy and scaling their application in real-world food production systems. Full article

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15 pages, 1111 KiB

Open AccessArticle

Expanded Gram-Negative Activity of Marinopyrrole A

by Clare F. Euteneuer, Brianna N. Davis, LeeAnna M. Lui, Andrew J. Neville and Paul H. Davis

Pathogens 2025, 14(3), 290; https://doi.org/10.3390/pathogens14030290 - 16 Mar 2025

Viewed by 348

Abstract

The rise of bacterial infections is a global health issue that calls for the development and availability of additional antimicrobial agents. Known for its in vitro effects on Gram-positive organisms, the drug-like small molecule marinopyrrole A was re-examined for the potential of broader [...] Read more.

The rise of bacterial infections is a global health issue that calls for the development and availability of additional antimicrobial agents. Known for its in vitro effects on Gram-positive organisms, the drug-like small molecule marinopyrrole A was re-examined for the potential of broader efficacy against a wider array of microbes. We uncovered selective efficacy against an important subset of Gram-negative bacteria from three genera: Neisseria, Moraxella, and Campylobacter. This susceptibility is correlated with the absence of canonical LPS in these specific Gram-negative species, a phenomenon observed with other hydrophobic anti-microbial compounds. Further, when exposed to molecules which inhibit the LpxC enzyme of the LPS synthesis pathway, previously resistant LPS-producing Gram-negative bacteria showed increased susceptibility to marinopyrrole A. These results demonstrate marinopyrrole A’s efficacy against a broader range of Gram-negative bacteria than previously known, including N. gonorrhea, a species identified as a priority pathogen by the WHO. Full article

(This article belongs to the Section Bacterial Pathogens)

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20 pages, 3764 KiB

Open AccessArticle

A Bibliometric Analysis of HPV-Positive Oropharyngeal Squamous Cell Carcinoma from 2000 to 2023

by Yingying Cui, Wei Li and Binbin Li

Pathogens 2025, 14(3), 289; https://doi.org/10.3390/pathogens14030289 - 15 Mar 2025

Viewed by 411

Abstract

Human-papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV-positive OPSCC) is a distinct disease characterized by unique clinical and molecular features compared to HPV-negative OPSCC. A comprehensive bibliometric analysis of HPV-positive OPSCC research was conducted in this study to identify key trends, research hotspots, and emerging [...] Read more.

Human-papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV-positive OPSCC) is a distinct disease characterized by unique clinical and molecular features compared to HPV-negative OPSCC. A comprehensive bibliometric analysis of HPV-positive OPSCC research was conducted in this study to identify key trends, research hotspots, and emerging frontiers in the field. Data were retrieved from the Web of Science Core Collection database. The distributions of contributors, including countries, institutions, authors, journals, and cooperative networks related to HPV-positive OPSCC, were analyzed and visualized using VOSviewer 1.6.20, CiteSpace 6.3.R1, and the R package Bibliometrix 4.0.0. In addition, the most influential publications and high-frequency keywords were identified and analyzed to discern key topics in this field. A total of 3895 articles and reviews on HPV-positive OPSCC were identified, involving 106 countries, 620 journals, and 18949 authors. The main contributors include the USA (1908 publications), Johns Hopkins University (310 publications), the journal Head and Neck (320 publications), and Erich M. Sturgis (94 publications). The top three keywords are “survival”, “radiotherapy”, and “p16”. There has been a steadily increasing research interest in HPV-positive OPSCC over the last 23 years. Current studies focus on diagnosis, treatment strategies, prognosis, recurrence, and disease surveillance. This bibliometric analysis highlights key contributors and emerging themes, offering insights for future research directions. Full article

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14 pages, 1869 KiB

Open AccessArticle

Molecular Evidence of Raccoon Dog (Nyctereutes procyonoides) as a Natural Definitive Host for Several Sarcocystis Species

by Petras Prakas, Tamara Kalashnikova, Naglis Gudiškis, Donatas Šneideris, Evelina Juozaitytė-Ngugu and Dalius Butkauskas

Pathogens 2025, 14(3), 288; https://doi.org/10.3390/pathogens14030288 - 15 Mar 2025

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Abstract

Sarcocystis parasites infect a wide range of animals, including reptiles, birds, and mammals, and have complex two-host prey–predator life cycle. Sarcocysts are mainly found in the muscles of intermediate hosts, and oocysts sporulate in the intestines of the definitive host. The raccoon dog [...] Read more.

Sarcocystis parasites infect a wide range of animals, including reptiles, birds, and mammals, and have complex two-host prey–predator life cycle. Sarcocysts are mainly found in the muscles of intermediate hosts, and oocysts sporulate in the intestines of the definitive host. The raccoon dog (Nyctereutes procyonoides), native to Asia and invasive in Europe, is a known disease carrier. However, studies on raccoon dogs in the transmission of Sarcocystis are scarce. Between 2019 and 2024, a total of 26 raccoon dog carcasses were collected in Lithuania. The results of a light microscopy examination indicated that 50% of the samples were positive for Sarcocystis spp. sporocysts and sporulated oocysts. Based on nested PCR and sequencing of cox1, 88.5% of the samples were positive for these parasites. Molecular analysis revealed the presence of 11 different Sarcocystis species. Eight species, including S. alces, S. capracanis, S. hjorti, S. iberica, S. linearis, S. morae, S. tenella, and S. venatoria were reported for the first time in raccoon dogs as definitive hosts. The identified Sarcocystis species were linked to intermediate hosts, such as cervids, wild boars, pigs, goats, and sheep. These findings suggest that raccoon dogs play a key role in the spread of Sarcocystis, particularly species infecting cervids. Full article

(This article belongs to the Special Issue Parasitic Diseases in the Contemporary World)

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15 pages, 1798 KiB

Open AccessArticle

Prevalence and Molecular Characterization of Cryptosporidium Species in Diarrheic Children in Cameroon

by Bertrand Sone, Lum Abienwi Ambe, Mireille Nguele Ampama, Constance Ajohkoh, Desmond Che, Julien Alban Nguinkal, Anja Taubert, Carlos Hermosilla and Faustin Kamena

Pathogens 2025, 14(3), 287; https://doi.org/10.3390/pathogens14030287 - 14 Mar 2025

Viewed by 495

Abstract

Cryptosporidiosis remains a major cause of diarrhea-related childhood death, particularly in developing countries. Although effective anti-retroviral therapy has significantly reduced the cryptosporidiosis burden in western nations, the situation in developing countries remains alarming due to limited therapeutic options and a lack of preventive [...] Read more.

Cryptosporidiosis remains a major cause of diarrhea-related childhood death, particularly in developing countries. Although effective anti-retroviral therapy has significantly reduced the cryptosporidiosis burden in western nations, the situation in developing countries remains alarming due to limited therapeutic options and a lack of preventive measures. To better control disease transmission and develop effective prevention strategies, a thorough understanding of the genetic diversity of circulating species is crucial. While cryptosporidiosis has previously been reported in Cameroon, information on the genetic diversity of parasite strains is lacking. In a large cross-sectional study conducted between March 2020 and March 2021 in four regions of Cameroon, Southwest, Littoral, Center and West, a total of 1119 fecal samples of children (n = 1119) were collected and genetically analyzed. This study aimed to assess the genetic diversity of Cryptosporidium strains circulating in this patient cohort in Cameroon. Using modified Ziehl–Neelsen fecal smear staining, an overall prevalence of 8.5% (96/1119) was recorded. PCR analysis revealed a prevalence of 15.4% in the Center, 7.2% in the Littoral, 10.5% in the West, and 13.1% in the Southwest regions. Molecular analysis identified Cryptosporidium. hominis and Cryptosporidium parvum as circulating species, with all subtype families suggesting anthroponotic transmission. No zoonotic subtypes of C. parvum were detected. These findings confirm that cryptosporidiosis transmission in Cameroon is primarily anthroponotic. Nonetheless, much larger epidemiological surveys, including other patient cohorts, are necessary for final confirmation of this statement. Full article

(This article belongs to the Section Parasitic Pathogens)

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19 pages, 3267 KiB

Open AccessArticle

Human Retinal Organoid Model of Ocular Toxoplasmosis

by Liam M. Ashander, Grace E. Lidgerwood, Amanda L. Lumsden, João M. Furtado, Alice Pébay and Justine R. Smith

Pathogens 2025, 14(3), 286; https://doi.org/10.3390/pathogens14030286 - 14 Mar 2025

Viewed by 400

Abstract

The health burden of ocular toxoplasmosis is substantial, and there is an unmet need for safe and curative anti-microbial drugs. One major barrier to research on new therapeutics is the lack of in vitro human-based models beyond two-dimensional cultured cells and tissue explants. [...] Read more.

The health burden of ocular toxoplasmosis is substantial, and there is an unmet need for safe and curative anti-microbial drugs. One major barrier to research on new therapeutics is the lack of in vitro human-based models beyond two-dimensional cultured cells and tissue explants. We aimed to address this research gap by establishing a human retinal organoid model of ocular toxoplasmosis. Retinal organoids, generated from human induced pluripotent stem cells and grown to two stages of organization, were incubated with a suspension of live or heat-killed GT-1 strain T. gondii tachyzoites, or medium without tachyzoites. Both developing (1 month post-isolation) and matured (6 months post-isolation) organoids were susceptible to infection. Spread of live parasites from the margin to the entire organoid over 1 week was indicated by immunolabelling for T. gondii surface antigen 1. This progression was accompanied by changes in the levels of selected tachyzoite transcripts—SAG1, GRA6, and ROP16—and human cytokine transcripts—CCL2, CXCL8, CXCL10, and IL6—in infected versus control conditions. Our human retinal organoid model of ocular toxoplasmosis offers the opportunity for many future lines of study, including tachyzoite interactions with retinal cell populations and leukocyte subsets, parasite stage progression, and disease processes of different T. gondii strains, as well as drug testing. Full article

(This article belongs to the Special Issue Parasitic Diseases in the Contemporary World)

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65 pages, 2112 KiB

Open AccessReview

Exploiting Wolbachia as a Tool for Mosquito-Borne Disease Control: Pursuing Efficacy, Safety, and Sustainability

by Riccardo Moretti, Jue Tao Lim, Alvaro Gil Araujo Ferreira, Luigi Ponti, Marta Giovanetti, Chow Jo Yi, Pranav Tewari, Maria Cholvi, Jacob Crawford, Andrew Paul Gutierrez, Stephen L. Dobson and Perran A. Ross

Pathogens 2025, 14(3), 285; https://doi.org/10.3390/pathogens14030285 - 14 Mar 2025

Viewed by 737

Abstract

Despite the application of control measures, mosquito-borne diseases continue to pose a serious threat to human health. In this context, exploiting Wolbachia, a common symbiotic bacterium in insects, may offer effective solutions to suppress vectors or reduce their competence in transmitting several [...] Read more.

Despite the application of control measures, mosquito-borne diseases continue to pose a serious threat to human health. In this context, exploiting Wolbachia, a common symbiotic bacterium in insects, may offer effective solutions to suppress vectors or reduce their competence in transmitting several arboviruses. Many Wolbachia strains can induce conditional egg sterility, known as cytoplasmic incompatibility (CI), when infected males mate with females that do not harbor the same Wolbachia infection. Infected males can be mass-reared and then released to compete with wild males, reducing the likelihood of wild females encountering a fertile mate. Furthermore, certain Wolbachia strains can reduce the competence of mosquitoes to transmit several RNA viruses. Through CI, Wolbachia-infected individuals can spread within the population, leading to an increased frequency of mosquitoes with a reduced ability to transmit pathogens. Using artificial methods, Wolbachia can be horizontally transferred between species, allowing the establishment of various laboratory lines of mosquito vector species that, without any additional treatment, can produce sterilizing males or females with reduced vector competence, which can be used subsequently to replace wild populations. This manuscript reviews the current knowledge in this field, describing the different approaches and evaluating their efficacy, safety, and sustainability. Successes, challenges, and future perspectives are discussed in the context of the current spread of several arboviral diseases, the rise of insecticide resistance in mosquito populations, and the impact of climate change. In this context, we explore the necessity of coordinating efforts among all stakeholders to maximize disease control. We discuss how the involvement of diverse expertise—ranging from new biotechnologies to mechanistic modeling of eco-epidemiological interactions between hosts, vectors, Wolbachia, and pathogens—becomes increasingly crucial. This coordination is especially important in light of the added complexity introduced by Wolbachia and the ongoing challenges posed by global change. Full article

(This article belongs to the Special Issue Surveillance and Control Strategies to Fight Mosquito-Borne Diseases)

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15 pages, 711 KiB

Open AccessArticle

Epidemiological and Clinical Characteristics of Adult RSV Infections: A Retrospective Analysis at University Hospital Center Zagreb (2022–2024)

by Antonio Perčinić, Tara Vuletić, Nina Lizzul, Andrea Vukić Dugac, Ana Gverić Grginić, Irena Tabain, Dragan Jurić and Ana Budimir

Pathogens 2025, 14(3), 284; https://doi.org/10.3390/pathogens14030284 - 14 Mar 2025

Viewed by 341

Abstract

Respiratory syncytial virus (RSV) is a significant cause of respiratory infections in adults, particularly among older adults and individuals with chronic diseases. While traditionally linked to pediatric populations, RSV’s impact on adults, especially the elderly, is increasingly recognized but remains understudied in many [...] Read more.

Respiratory syncytial virus (RSV) is a significant cause of respiratory infections in adults, particularly among older adults and individuals with chronic diseases. While traditionally linked to pediatric populations, RSV’s impact on adults, especially the elderly, is increasingly recognized but remains understudied in many regions. This retrospective study, conducted at the University Hospital Center Zagreb from October 2022 to April 2024, is the first to analyze RSV-positive adults in Croatia. Using RT-PCR testing, we evaluated clinical and epidemiological characteristics in both hospitalized and outpatient populations, focusing on those aged > 65 years. Among 2631 tested individuals, the RSV prevalence was 5.25%, with older adults experiencing the most severe outcomes, including pneumonia, COPD exacerbation, and intensive care admissions. Seasonal analysis confirmed a winter peak in RSV cases, while chronic conditions such as cardiovascular and respiratory diseases were strongly associated with higher complication rates. These findings demonstrate that older adults with comorbidities bear the greatest burden of RSV infection, highlighting the need for the early identification of high-risk patients. By providing detailed insights into RSV-related outcomes in this population, this study supports the development of targeted prevention and management strategies to reduce the burden of RSV in vulnerable groups. Full article

(This article belongs to the Special Issue Emerging and Neglected Pathogens in the Balkans)

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5 pages, 134 KiB

Open AccessEditorial

Emergence and Control of African Swine Fever

by Lauro Velazquez-Salinas

Pathogens 2025, 14(3), 283; https://doi.org/10.3390/pathogens14030283 - 14 Mar 2025

Viewed by 328

Abstract

African swine fever (ASF) is a highly lethal and contagious viral disease found in domestic pigs, wild boars, and wild suids, and it has significant economic consequences [...] Full article

(This article belongs to the Special Issue Emergence and Control of African Swine Fever)

10 pages, 881 KiB

Open AccessCommunication

Retrospective Epidemiological Analysis of Influenza A Infections in a Single Hospital in Korea (2007–2024): Age, Sex, and Seasonal Patterns

by Jeong Su Han, Hyeong Ho Kim, Jae-Sik Jeon, Yoo Na Chung and Jae Kyung Kim

Pathogens 2025, 14(3), 282; https://doi.org/10.3390/pathogens14030282 - 14 Mar 2025

Viewed by 344

Abstract

Influenza A is a respiratory virus that causes high infection rates and mortality worldwide, particularly affecting high-risk groups such as children, older adults, and individuals with chronic conditions. This retrospective study was conducted at a single tertiary hospital in Korea to analyze the [...] Read more.

Influenza A is a respiratory virus that causes high infection rates and mortality worldwide, particularly affecting high-risk groups such as children, older adults, and individuals with chronic conditions. This retrospective study was conducted at a single tertiary hospital in Korea to analyze the epidemiological characteristics of influenza A infections from 2007 to 2024, focusing on age, sex, and seasonal variations. Using multiplex real-time PCR data from 23,284 individuals, we found that the overall positivity rate for influenza A was 5.6%, with seasonal fluctuations showing the highest rate in winter (14.0%) and the lowest in summer (0.5%). Age-based analysis revealed significantly higher positivity rates in older adults (7.9%) and adults (7.6%) than in children (5.0%) and infants (3.1%). No significant differences were observed in positivity rates between sexes (male: 5.43%, female: 5.76%, p = 0.428). These findings provide essential insights into the regional and seasonal patterns of influenza A, emphasizing the importance of targeted vaccination strategies, adaptive public health interventions, and continuous surveillance for effective prevention and outbreak control management. Full article

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17 pages, 3678 KiB

Open AccessArticle

Impact of Human Body Temperature on Stress Tolerance and Transcriptome of Cronobacter sakazakii

by Siqi Li, Yuanyuan Wang, Yahao Yang, Xinlu Yu, Jiajia Liu, Meiling Jiang, Jing Zhang, Ge Yun, Yufei Han, Heng Wang, Qiong Xie and Gukui Chen

Pathogens 2025, 14(3), 281; https://doi.org/10.3390/pathogens14030281 - 14 Mar 2025

Viewed by 342

Abstract

Cronobacter sakazakii is a food-borne pathogen that can thrive in various environments, including the human body. The human body’s physiological temperature exceeds that of the environment (22–30 °C), necessitating adaptations to heat stress during this transition. Managing heat stress is crucial when transitioning [...] Read more.

Cronobacter sakazakii is a food-borne pathogen that can thrive in various environments, including the human body. The human body’s physiological temperature exceeds that of the environment (22–30 °C), necessitating adaptations to heat stress during this transition. Managing heat stress is crucial when transitioning from the environment to the human body. In this study, we explored the effect of human body temperature on the growth of planktonic C. sakazakii, as well as its acid resistance, osmotic stress resistance, autoaggregation, and cell surface hydrophobicity. Our study demonstrated that human body temperature facilitated the growth, acid resistance, and osmotic resistance of C. sakazakii, compared to 28 °C. The relationship between human body temperature and phenotypes was studied by comparing gene expression at human and environmental temperatures (37 to 28 °C) using high-throughput sequencing. The results revealed up-regulation in the expression of 626 genes, including genes involved in arginine and proline metabolism, carbon fixation pathways, and nitrogen metabolism. Further analysis showed that human body temperature is essential for the environmental stress resistance of C. sakazakii. It boosts denitrification, betaine transport, and universal stress proteins, supporting membrane integrity and osmoprotectant transport. This study enhances our understanding of the strategies employed by C. sakazakii during its adaptation to the human body. Full article

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10 pages, 202 KiB

Open AccessArticle

Clinical Characteristics, Neuroimaging Findings and Long-Term Sequelae in Children with Congenital Cytomegalovirus Infection: A Single Centre Study

by Ivana Valenčak, Lorna Stemberger Marić, Maja Vrdoljak Pažur, Snježana Židovec Lepej, Nenad Šuvak and Goran Tešović

Pathogens 2025, 14(3), 280; https://doi.org/10.3390/pathogens14030280 - 14 Mar 2025

Viewed by 357

Abstract

Congenital cytomegalovirus infection is the most common congenital infection worldwide and an important cause of neurodevelopmental delay and sensorineural hearing loss. Neuroimaging represents the best prognostic marker in cCMV infection. The aim of this study was to establish the role of cranial ultrasound [...] Read more.

Congenital cytomegalovirus infection is the most common congenital infection worldwide and an important cause of neurodevelopmental delay and sensorineural hearing loss. Neuroimaging represents the best prognostic marker in cCMV infection. The aim of this study was to establish the role of cranial ultrasound and brain magnetic resonance imaging in the development of long-term sequelae in symptomatic and asymptomatic children with cCMV infection. Of the 47 children enrolled in the study, 25 (53.1%) were classified as symptomatic at birth. In 27/47 patients, SNHL was diagnosed with a similar proportion among the symptomatic and asymptomatic at birth (51.8% and 48.1%, respectively; p = 1.0). Thirty case patients had available data on follow-up. Neurological sequelae were more frequently seen in patients with symptomatic cCMV, but only cerebral abnormalities seen on initial MRI results had a consequential link with the later development of motor (OR 17.5; 95% Cl: 2667, 114,846; p = 0.002) and speech disorders (OR 15; 95% Cl: 2477, 90,843; p = 0.02). Although not statistically significant, hearing deterioration was more frequent in children with abnormal MRI results (OR 5; 95% Cl: 0.846, 29,567; p = 0.121). Neuroimaging abnormalities, as identified through both cranial ultrasound (CrUS) and MRI, are critical prognostic indicators for long-term sequelae, applicable to both symptomatic and asymptomatic children. Full article

(This article belongs to the Special Issue Emerging and Neglected Pathogens in the Balkans)

14 pages, 1945 KiB

Open AccessArticle

The Effect of Helicobacter pylori Gene Combinations of cagA, cagE, virB11, vacA, and babA on the Outcome of Gastric Disease in a Southern Moroccan Population

by Mariama Barhoine, Fatima Moustaoui, Omayma Hammani, Mohamed Aghrouch, Zohra Lemkhente, Zineb Belhabib, Zineb Bajaddoub, Anass Touyar, Nourdin Aqoudad, Bouchra Rherissi, Nadia El Kadmiri, Youssef Idaghdour, Fatima Boubrik and Ahmed Belmouden

Pathogens 2025, 14(3), 279; https://doi.org/10.3390/pathogens14030279 - 14 Mar 2025

Viewed by 453

Abstract

Helicobacter pylori (H. pylori) possess an arsenal of virulence genes that makes them the main etiological factor in gastric diseases. In this study, 120 southern Moroccan patients who were dyspeptic were profiled to investigate the potential association between disease severity and [...] Read more.

Helicobacter pylori (H. pylori) possess an arsenal of virulence genes that makes them the main etiological factor in gastric diseases. In this study, 120 southern Moroccan patients who were dyspeptic were profiled to investigate the potential association between disease severity and the combination of multiple virulence genes. Gastric biopsies were taken from patients, followed by histopathological evaluation and genotyping of H. pylori using PCR. H. pylori was detected in 58.3% of cases, and genotypes were distributed as follows: oipA (94.3%), cagA (62.9%), virB11 (60%), babA (55.7%), dupA (54.3%), cagE (51.4%), iceA1 (31.4%), iceA2 (45.7%), vacA s2m2 (47.1%), vacA s1m1 (30%), and vacA s1m2 (7.1%). Statistically significant associations with males were observed for the cagA, cagE, and virB11 genes and multiple strain infections. Multivariate analysis revealed an association between cagE and heightened neutrophil activity, with an odds ratio (OR) of 4.99 (p = 0.03). The gene combination [cagA (+), cagE (+), virB11 (+), vacA s1m1, and babA (+)] emerged as a predictive factor for gastric cancer (OR = 11.10, p = 0.046), while the combination [cagA (-), cagE (-), virB11 (-), vacA s2m2, babA (+)] was associated with gastric atrophy (OR = 10.25, p = 0.016). Age (≤40 years) (OR = 5.87, p = 0.013) and moderate to severe bacterial density (OR = 15.38, p = 0.017) were identified as predictive factors for follicular gastritis. These findings underscore the significance of multigene profiling as a prognostic marker and emphasize the importance of age and sex in preventing adverse outcomes in severe gastric diseases. Full article

(This article belongs to the Section Bacterial Pathogens)

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15 pages, 538 KiB

Open AccessReview

Comprehensive Insights into Highly Pathogenic Avian Influenza H5N1 in Dairy Cattle: Transmission Dynamics, Milk-Borne Risks, Public Health Implications, Biosecurity Recommendations, and One Health Strategies for Outbreak Control

by Henrietta Owusu and Yasser M. Sanad

Pathogens 2025, 14(3), 278; https://doi.org/10.3390/pathogens14030278 - 13 Mar 2025

Viewed by 941

Abstract

Highly pathogenic avian influenza (HPAI) H5N1 has been traditionally linked to poultry and wild birds, which has recently become a serious concern for dairy cattle, causing outbreaks all over the United States. The need for improved surveillance, biosecurity protocols, and interagency collaboration is [...] Read more.

Highly pathogenic avian influenza (HPAI) H5N1 has been traditionally linked to poultry and wild birds, which has recently become a serious concern for dairy cattle, causing outbreaks all over the United States. The need for improved surveillance, biosecurity protocols, and interagency collaboration is highlighted by the discovery of H5N1 in dairy herds in several states and its human transmission. The epidemiology, transmission dynamics, and wide-ranging effects of H5N1 in cattle are reviewed in this paper, with particular attention paid to the disease’s effects on agricultural systems, public health, and animal health. Nonspecific clinical symptoms, such as decreased milk production and irregular milk consistency, are indicative of infection in dairy cows. Alarmingly, significant virus loads have been discovered in raw milk, raising worries about potential zoonotic transmission. The dangers of viral spillover between species are further highlighted by cases of domestic cats experiencing severe neurological symptoms after ingesting raw colostrum and milk from infected cows. Even though human cases remain rare, and they are mostly related to occupational exposure, constant attention is required due to the possibility of viral adaptability. The necessity of a One Health approach that integrates environmental, animal, and human health efforts is further supported by the broad occurrence of H5N1 across multiple species. For early detection, containment, and mitigation, cooperation between veterinary clinics, public health organizations, and agricultural stakeholders is crucial. Controlling the outbreak requires stringent movement restrictions, regular testing of dairy cows in reference labs, and adherence to biosecurity procedures. This review highlights the importance of thorough and coordinated efforts to manage H5N1 in dairy cattle by combining existing knowledge and pointing out gaps in surveillance and response strategies. Additionally, it sheds light on the potential risk of consumption of cow’s milk contaminated with H5N1 virus by humans and other companion animals like cats. In the face of this changing threat, proactive monitoring, strict biosecurity protocols, and cross-sector cooperation are crucial for reducing financial losses and protecting human and animal health. Full article

(This article belongs to the Special Issue Epidemiology and Molecular Pathogenesis of Antimicrobial Resistance and Virulence for Foodborne Pathogens: 2nd Edition)

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20 pages, 5010 KiB

Open AccessArticle

Metronidazole Activation by a Deeply Entangled Dimeric Malic Enzyme in Entamoeba histolytica

by Arindam Chakrabarty, Debajyoti Dutta, Mithu Baidya, Anirudha Dutta, Amit Kumar Das and Sudip K. Ghosh

Pathogens 2025, 14(3), 277; https://doi.org/10.3390/pathogens14030277 - 13 Mar 2025

Viewed by 641

Abstract

Metronidazole is the preferred drug for treating amoebiasis caused by Entamoeba histolytica. Its antiamoebic activity is primarily attributed to activation by various reductases. This study reports an alternative activation pathway in E. histolytica mediated by the decarboxylating malic enzyme. Functional characterization of [...] Read more.

Metronidazole is the preferred drug for treating amoebiasis caused by Entamoeba histolytica. Its antiamoebic activity is primarily attributed to activation by various reductases. This study reports an alternative activation pathway in E. histolytica mediated by the decarboxylating malic enzyme. Functional characterization of this NADPH-dependent enzyme reveals that it is secreted into the extracellular milieu and may play a role in E. histolytica adhesion to human enteric cells. Structural analysis of the E. histolytica malic enzyme (EhME) demonstrates that the protein forms a strict dimer, with the protomers interlocked by a unique knot structure formed by two polypeptide chains. This distinctive structural feature closely aligns EhME with its prokaryotic counterparts. In conclusion, our findings reveal that E. histolytica harbors a deeply entangled dimeric malic enzyme that contributes to metronidazole susceptibility, sharing structural similarities with bacterial malic enzymes. Full article

(This article belongs to the Section Parasitic Pathogens)

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Graphical abstract

16 pages, 272 KiB

Open AccessArticle

A 10-Year Study of Neonatal Sepsis from Tuen Mun Hospital, Hong Kong

by Pascoe Lee, Eugene Sin, Kam-Tong Yip and Kenneth Ng

Pathogens 2025, 14(3), 276; https://doi.org/10.3390/pathogens14030276 - 13 Mar 2025

Viewed by 361

Abstract

Background: Neonatal sepsis is a major cause of infant mortality, and it accounts for a significant consumption of antimicrobials in paediatrics. This is the first comprehensive study on neonatal sepsis in Hong Kong. Methods: From 2014 to 2023, all neonates admitted to a [...] Read more.

Background: Neonatal sepsis is a major cause of infant mortality, and it accounts for a significant consumption of antimicrobials in paediatrics. This is the first comprehensive study on neonatal sepsis in Hong Kong. Methods: From 2014 to 2023, all neonates admitted to a single institution with culture-proven infections from the blood and/or cerebrospinal fluid were selected and reviewed retrospectively. The infecting organisms, their antibiotic nonsusceptibility pattern, and the concordance of empirical antimicrobial therapy with the microbiological profiles were described and were further compared between infants of normal/low birth weight (≥1.5 kg) and very low/extremely low birth weight (<1.5 kg), early-onset sepsis (<72 h), and late-onset sepsis (4–28 days), the first and the second 5-year periods (2014–2018 vs. 2019–2023). Results: After contaminants were excluded, there were 118 affected neonates with 125 organisms identified. Fifty-nine were male. Thirty-four were very low/extremely low birth weight infants, and twenty-eight infants had early-onset sepsis. Patient demographics and the microbiology findings did not differ between the first 5 years and the latter 5 years. However, the incidence of neonatal sepsis was significantly lower in the latter 5 years (3.23 vs. 1.61 per 1000 live births, p < 0.001), the period that coincided with the COVID-19 pandemic. Escherichia coli was the most common Gram-negative pathogen. Streptococcus agalactiae and Streptococcus bovis group infections were more common in early-onset sepsis, while coagulase-negative Staphylococcus and non-E. coli Gram-negative pathogens were more likely to occur in late-onset sepsis. In very low/extremely low birth weight infants, the rate of cefotaxime or ceftriaxone nonsusceptibility among Gram-negative isolates was higher (p = 0.01), and concordance of empirical antimicrobial therapy was lower (p = 0.006). Conclusions: Management of neonatal sepsis remains challenging, and there is a need for optimising antimicrobial therapy, especially in preterm patients. Antepartum screening with intrapartum antibiotic prophylaxis is effective in reducing the risk of early-onset sepsis associated with S. agalactiae, while stringent infection control measures are important for the prevention of late-onset sepsis. Full article

26 pages, 4568 KiB

Open AccessArticle

Insights into Functions of Universal Stress Proteins Encoded by Genomes of Gastric Cancer Pathogen Helicobacter pylori and Related Bacteria

by Raphael D. Isokpehi, Shaneka S. Simmons, Angela U. Makolo, Antoinesha L. Hollman, Solayide A. Adesida, Olabisi O. Ojo and Amos O. Abioye

Pathogens 2025, 14(3), 275; https://doi.org/10.3390/pathogens14030275 - 13 Mar 2025

Viewed by 432

Abstract

The genes that encode the universal stress protein (USP) family domain (pfam00582) aid the survival of bacteria in specific host or habitat-induced stress conditions. Genome sequencing revealed that the genome of Helicobacter pylori, a gastric cancer pathogen, typically contains one USP gene, [...] Read more.

The genes that encode the universal stress protein (USP) family domain (pfam00582) aid the survival of bacteria in specific host or habitat-induced stress conditions. Genome sequencing revealed that the genome of Helicobacter pylori, a gastric cancer pathogen, typically contains one USP gene, while related helicobacters have one or two distinct USP genes. However, insights into the functions of Helicobacteraceae (Helicobacter and Wolinella) USP genes are still limited to inferences from large-scale genome sequencing. Thus, we have combined bioinformatics and visual analytics approaches to conduct a more comprehensive data investigation of a set of 1045 universal stress protein sequences encoded in 1014 genomes including 785 Helicobacter pylori genomes. The study generated a representative set of 183 USP sequences consisting of 180 Helicobacter sequences, two Wolinella succinogenes sequences, and a sequence from a related campylobacteria. We used the amino acid residues and positions of the 12 possible functional sites in 1030 sequences to identify 25 functional sites patterns for guiding studies on functional interactions of Helicobacteraceae USPs with ATP and other molecules. Genomic context searches and analysis identified USP genes of gastric and enterohepatic helicobacters that are adjacent or in operons with genes for proteins responsive to DNA-damaging oxidative stress (ATP-dependent proteases: ClpS and ClpA); and DNA uptake proteins (natural competence for transformation proteins: ComB6, ComB7, ComB8, ComB9, ComB10, ComBE, and conjugative transfer signal peptidase TraF). Since transcriptomic evidence indicates that oxidative stress and the presence of virulence-associated genes regulate the transcription of H. pylori USP gene, we recommend further research on Helicobacter USP genes and their neighboring genes in oxidative stress response and virulence of helicobacters. To facilitate the reuse of data and research, we produced interactive analytics resources of a dataset composed of values for variables including phylogeography of H. pylori strains, protein sequence features, and gene neighborhood. Full article

(This article belongs to the Section Bacterial Pathogens)

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20 pages, 6831 KiB

Open AccessArticle

Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation

by Gustavo E. Olivos-Ramirez, Luis F. Cofas-Vargas, Tobias Madl and Adolfo B. Poma

Pathogens 2025, 14(3), 274; https://doi.org/10.3390/pathogens14030274 - 12 Mar 2025

Viewed by 1281

Abstract

We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of [...] Read more.

We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of each variant were characterized by analyzing their distributions within a selected space of collective variables (CVs), such as inter-domain distances between the receptor-binding domain (RBD) and the N-terminal domain (NTD). Our primary focus was to identify conformational states relevant to potential structural transitions and to determine the set of native contacts (NCs) that stabilize these conformations. The results reveal that genetically more distant variants, such as XBB.1.5, BA.1, and JN.1, tend to adopt more compact conformational states compared to the WT. Additionally, these variants exhibit novel NC profiles, characterized by an increased number of specific contacts distributed among ionic, polar, and nonpolar residues. We further analyzed the impact of specific mutations, including T478K, N500Y, and Y504H. These mutations not only enhance interactions with the human host receptor but also alter inter-chain stability by introducing additional NCs compared to the WT. Consequently, these mutations may influence the accessibility of certain protein regions to neutralizing antibodies. Overall, these findings contribute to a deeper understanding of the structural and functional variations among S protein variants. Full article

(This article belongs to the Section Viral Pathogens)

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20 pages, 3280 KiB

Open AccessArticle

Molecular Survey of Anaplasmataceae Agents, Rickettsia spp., Bartonella spp., and Piroplasmids in Ectoparasites from Cave-Dwelling Bats in Mainland Portugal

by Gustavo Seron Sanches, Luísa Rodrigues, Estefania Torrejón, Ricardo Bassini-Silva, Ana Cláudia Calchi, Daniel Antônio Braga Lee, Paulo Vitor Cadina Arantes, Eder Barbier, Darci Moraes Barros-Battesti, Gustavo Graciolli, Rosangela Zacarias Machado, Sandra Antunes, Ana Domingos and Marcos Rogério André

Pathogens 2025, 14(3), 273; https://doi.org/10.3390/pathogens14030273 - 12 Mar 2025

Viewed by 497

Abstract

Bats and their ectoparasites play a crucial role in understanding the ecology and transmission of vector-borne pathogens, yet these dynamics remain poorly studied in Portugal. This study aimed to investigate the molecular occurrence of vector-borne bacteria (Anaplasma spp., Bartonella spp., Ehrlichia spp., [...] Read more.

Bats and their ectoparasites play a crucial role in understanding the ecology and transmission of vector-borne pathogens, yet these dynamics remain poorly studied in Portugal. This study aimed to investigate the molecular occurrence of vector-borne bacteria (Anaplasma spp., Bartonella spp., Ehrlichia spp., and Rickettsia spp.) and protozoa (Babesia spp. and Theileria spp.) in ectoparasites of cave-dwelling bats. Bats were sampled from two caves in Portugal, and their ectoparasites included wing mites (Spinturnix myoti), ticks (Ixodes simplex), and bat flies (Penicillidia conspicua and Nycteribia schmidlii). Molecular analyses revealed the presence of Bartonella spp. in S. myoti and N. schmidlii. Phylogenetic inference based on the gltA gene positioned the detected genotypes close to those previously reported in bats and Nycteribiidae flies in Europe, Asia, and Africa. Notably, no DNA from Anaplasmataceae, Rickettsia spp., or piroplasmids was detected. The prevalence of S. myoti was high, with all examined bats being infested, showing notable differences in ectoparasite diversity concerning sex and cave-specific location. These findings suggest that host behavior, environmental conditions, and ectoparasite lifecycles play critical roles in shaping pathogen transmission dynamics. This study advances the understanding of bat ectoparasite–pathogen interactions in a region with limited data and highlights the need for continued research to assess the zoonotic potential and ecological impacts of the Bartonella genotypes detected herein. Full article

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13 pages, 1850 KiB

Open AccessArticle

Acid Tolerance of Coxiella burnetii Is Strain-Specific and Might Depend on Stomach Content

by Katharina Sobotta, Jan Schulze-Luehrmann, Martha Ölke, Katharina Boden and Anja Lührmann

Pathogens 2025, 14(3), 272; https://doi.org/10.3390/pathogens14030272 - 12 Mar 2025

Viewed by 773

Abstract

Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella (C.) burnetii. Human infections occur mainly via inhalation, but infections via the oral route have been observed. Gastric acidic conditions (pH 2–4) are the first defense mechanism [...] Read more.

Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella (C.) burnetii. Human infections occur mainly via inhalation, but infections via the oral route have been observed. Gastric acidic conditions (pH 2–4) are the first defense mechanism to limit food-associated infections. In this study, we tested the ability of C. burnetii to survive extremely acidic conditions (pH 2–3) to assess the risk of oral infection in humans. We treated different C. burnetii strains with different pH values and calculated the recovery rate by counting colony-forming units. The analysis of an additional eight C. burnetii strains showed that some strains are acid-resistant, while others are not. Importantly, the presence of pepsin, an endopeptidase and the main digestive enzyme in the gastrointestinal tract, increases the survival rate of C. burnetii. Similarly, the presence of milk might also increase the survival rate. These results suggest that oral infections by C. burnetii are possible and depend on the bacterial strain and the stomach microenvironment. Consequently, the digestive infection route of C. burnetii could play a role in the transmission of the pathogen. Full article

(This article belongs to the Special Issue Coxiella burnetii: The Host Immune Response, Host-Pathogen Interaction and Pathogenesis)

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12 pages, 268 KiB

Open AccessBrief Report

Development of a Simple and Accurate Molecular Protocol Using 16SrRNA for Species-Specific Identification of Achromobacter spp.

by Giulia Maria Saitta, Laura Veschetti, Rebecca Feletti, Angela Sandri, Marzia Boaretti, Paola Melotti, Maria Carelli, Maria M. Lleò, Giovanni Malerba and Caterina Signoretto

Pathogens 2025, 14(3), 271; https://doi.org/10.3390/pathogens14030271 - 12 Mar 2025

Viewed by 396

Abstract

The Achromobacter genus comprises 22 species and various genogroups. Some species with higher virulence or antibiotic resistance are more likely to cause chronic infections in people with cystic fibrosis (CF). Current identification methods often fail to accurately distinguish between the species or result [...] Read more.

The Achromobacter genus comprises 22 species and various genogroups. Some species with higher virulence or antibiotic resistance are more likely to cause chronic infections in people with cystic fibrosis (CF). Current identification methods often fail to accurately distinguish between the species or result in misidentifications due to biochemical similarities. This study aims to develop an accurate qPCR protocol for species-level identification that is applicable in clinical diagnostic laboratories. Whole-genome sequencing of clinical isolates from different Achromobacter species identified species-specific single-nucleotide polymorphisms (SNPs) in two 16S gene regions. Based on these SNPs, two sets of primers and qPCR probes were designed to generate unique identification profiles. Thermal profiles were optimized, and qPCR was performed on serial bacterial DNA dilutions to determine the detection limit (LOD). Four probes successfully identified three species: A. xylosoxidans, A. dolens, and A. insuavis. Two additional probes were designed for novel genotypes unrelated to publicly available sequences. The LOD ranged from 0.005 pg/µL to 1 pg/µL. Combined probes achieved 100% sensitivity, with specificity ranging from 97.95% to 100%. This qPCR protocol enables accurate species identification, overcoming the limitations of current methods, and represents a reliable tool for clinical diagnostics. Full article

13 pages, 235 KiB

Open AccessArticle

The Prevalence of Toxoplasmosis in Bulgaria for the Period 2014–2023, with a Focus on Pregnant Women

by Iskra Rainova, Rumen Harizanov, Mihaela Videnova, Nina Tsvetkova, Raina Borisova, Eleonora Kaneva and Yana Todorova

Pathogens 2025, 14(3), 270; https://doi.org/10.3390/pathogens14030270 - 11 Mar 2025

Viewed by 445

Abstract

The specificity of the life cycle of T. gondii, the causative agent of toxoplasmosis, determines its relevance in some patient groups; especially in women of childbearing age. The objective of this study was to ascertain the prevalence of this parasitic infection in [...] Read more.

The specificity of the life cycle of T. gondii, the causative agent of toxoplasmosis, determines its relevance in some patient groups; especially in women of childbearing age. The objective of this study was to ascertain the prevalence of this parasitic infection in Bulgaria between 2014 and 2023, focusing on pregnant women and those applying for an in vitro procedure or after an abortion. During the period, 115,053 individuals were tested for toxoplasmosis in the country, with an average seropositivity rate of 16.96%. At the NRL for the Diagnosis of Parasitic Diseases, ELISA tests were utilized to ascertain specific Toxoplasma IgG, IgM, and IgA antibodies, IgG avidity, and PCR to substantiate the DNA of the parasite. Between 2014 and 2023, the laboratory conducted tests on 631 pregnant women, and 161 women applying for in vitro fertilization or after an abortion. In 24.7% of pregnant women, data demonstrated the presence of IgG antibodies only, and Toxoplasma IgG and IgM or IgG, IgM, and IgA antibodies were found in 16.6% and 8% of women, respectively. In the subset of individuals examined after an abortion or for an in vitro procedure, IgG was detected in 28%, IgG and IgM in 13%, and IgG, IgM, and IgA antibodies in 3.7%. Seroprevalence rises with increasing age, but does not show any dynamic compared to our previous studies. Our results show a higher seropositivity for toxoplasmosis in pregnant women in Bulgaria than in neighboring countries. Full article

(This article belongs to the Special Issue Toxoplasmosis in Immunocompromised and Immunocompetent Host: Recent Updates About the Epidemiology, Diagnosis, Clinical Manifestations and Management)

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