Microorganisms

15 pages, 620 KiB

Open AccessArticle

Host Jumps and Pathogenicity of Botryosphaeriaceae Species on Grapevines (Vitis vinifera) in Chile

by Yadira Hernández, Mauricio Lolas, Karina Elfar, Akif Eskalen, Felipe Gainza-Cortés and Gonzalo A. Díaz

Microorganisms 2025, 13(2), 331; https://doi.org/10.3390/microorganisms13020331 (registering DOI) - 3 Feb 2025

Abstract

Botryosphaeria dieback disease is a significant grapevine trunk disease (GTD) caused by species of Botryosphaeriaceae in Chile and worldwide. Moreover, Botryosphaeriaceae have been described attacking fruit and nut crops in Chile. However, it remains unknown whether fungal isolates from tree hosts have the [...] Read more.

Botryosphaeria dieback disease is a significant grapevine trunk disease (GTD) caused by species of Botryosphaeriaceae in Chile and worldwide. Moreover, Botryosphaeriaceae have been described attacking fruit and nut crops in Chile. However, it remains unknown whether fungal isolates from tree hosts have the potential to infect grapevines in Chile. The aggressiveness and potential cross infection of species of Botryosphaeriaceae collected from crops (grapevines, apples, blueberries, and walnuts), was assessed on grapevines. Plant materials, including nursery cuttings, lignified canes, and green shoots of grapevine cultivars (Cabernet Sauvignon, Syrah, Sauvignon Blanc, Malbec, Aspirant Bouschet, and Merlot), were inoculated with Diplodia mutila, D. seriata, Dothiorella sarmentorum, Lasiodiplodia theobromae, Neofusicoccum arbuti, and N. parvum, under greenhouse and vineyard conditions. Regardless of the origin of the isolates, most species of Botryosphaeriaceae were pathogenic on plant materials, causing necrotic lesions of mean lengths from 11.9 to 86.2 mm using mycelial suspension and from 24.8 to 253.7 mm with mycelial plugs. Notably, Neofusicoccum species were the most aggressive, regardless of host origin. Other less aggressive species included L. theobromae, D. mutila, and D. seriata isolated from apple and walnut. This study highlights the potential of species of Botryosphaeriaceae from alternative fruit hosts as inoculum sources for grapevines in Chile. Full article

(This article belongs to the Special Issue Plant Pathogens: Monitoring, Identification and Biological Control)

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14 pages, 209 KiB

Open AccessCase Report

Use of Cefiderocol in Management of Resistant Gram-Negative Infections in Patients Admitted to a Burn Center

by Lindey C. Lane, Jonathon K. Walker and David M. Hill

Microorganisms 2025, 13(2), 330; https://doi.org/10.3390/microorganisms13020330 (registering DOI) - 3 Feb 2025

Abstract

Cefiderocol is a novel cephalosporin antibiotic approved for urinary tract infections and hospital-acquired or ventilator-associated pneumonias caused by difficult-to-treat Gram-negative pathogens. To date, its use in treating difficult-to-treat Gram-negative infections in burn patients has been minimally described in the literature. Our aim was [...] Read more.

Cefiderocol is a novel cephalosporin antibiotic approved for urinary tract infections and hospital-acquired or ventilator-associated pneumonias caused by difficult-to-treat Gram-negative pathogens. To date, its use in treating difficult-to-treat Gram-negative infections in burn patients has been minimally described in the literature. Our aim was to evaluate cefiderocol use in a population of burn patients initiated on cefiderocol for resistant Gram-negative infections. A retrospective chart review of nine patients was conducted. Two patients were treated for pneumonia; five for bacteremia, three of which had coexisting burn wound infections or pneumonia; one was treated for a burn wound infection alone; and one patient was treated for a simultaneous burn wound infection, pneumonia, and bacteremia. The pathogens treated included the following: multidrug-resistant Pseudomonas aeruginosa, carbapenem-resistant Acinetobacter baumannii, and carbapenem-resistant Enterobacterales. Three isolates were confirmed as New Delhi metallo-beta-lactamase (NDM) producers, though this was likely an underestimate as genetic testing is not routinely performed at our institution and not all the isolates were tested. One of the nine patients in this study succumbed to their infection. Of note, the multidrug-resistant Pseudomonas aeruginosa in this patient tested intermediate to cefiderocol. The patients were treated with cefiderocol for a median of 14 days, most commonly in combination with other antimicrobial therapies. Treatment with cefiderocol appeared to be efficacious in this population of burn patients when other antibiotics routinely used for complicated infections caused by multidrug-resistant (MDR) Gram-negative pathogens showed treatment failure or resistance. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

15 pages, 1030 KiB

Open AccessArticle

Adaptive Resistance of Staphylococcus aureus to Cefquinome Sulfate in an In Vitro Pharmacokinetic Model with Transcriptomic Insights

by Yue Hu, Hao Zhu, Xingbo Zhang, Yuhui Wu, Jingtao Li, Nan Li, Zhanbo Cai and Yuhui Yang

Microorganisms 2025, 13(2), 329; https://doi.org/10.3390/microorganisms13020329 (registering DOI) - 2 Feb 2025

Abstract

Cefquinome sulfate has a strong killing effect against Staphylococcus aureus (S. aureus), but bacterial resistance has become increasingly widespread. Experiments were conducted to investigate the pattern of adaptive resistance of S. aureus to cefquinome sulfate under different dosage regimens by using [...] Read more.

Cefquinome sulfate has a strong killing effect against Staphylococcus aureus (S. aureus), but bacterial resistance has become increasingly widespread. Experiments were conducted to investigate the pattern of adaptive resistance of S. aureus to cefquinome sulfate under different dosage regimens by using pharmacokinetic-pharmacodynamics (PK-PD) modeling, and the adaptive-resistant bacteria in different states were screened and subjected to transcriptomic sequencing. The results showed that the minimum inhibitory concentration of Staphylococcus aureus under the action of cefquinome sulfate was 0.5 μg/mL, the anti-mutation concentration was 1.6 μg/mL, and the mutation selection window range was 0.5~1.6 μg/mL. In the in vitro pharmacokinetic model to simulate different dosing regimens in the animal body, there are certain rules for the emergence of adaptive drug-resistant bacteria: the intensity of bacterial resistance gradually increased with culture time, and the order of emergence was tolerant bacteria (TO) followed by persistent bacteria (PE) and finally resistant bacteria (RE). The sequence reflected the evolution of adaptive drug resistance. Transcriptome Gene Ontology (GO) analysis revealed that differentially expressed genes were involved in cellular respiration, energy derivation by oxidation of organic compounds, and oxidation–reduction processes. The differentially expressed genes identified functioned in the synthesis of cell membranes, cytoplasm, and intracellular parts. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that 65 genes were differentially expressed after cefquinome sulfate treatment, of which 35 genes were significantly upregulated and 30 genes were significantly downregulated. Five genes, sdhB, sdhA, pdhA, lpdA, and sucC, may be involved in network regulation. This study revealed the cross-regulation of multiple metabolic pathway networks and the targets of network regulation of S. aureus to produce adaptive drug resistance. The results will provide guidance for clinical drug use in animals infected with S. aureus. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

16 pages, 1372 KiB

Open AccessSystematic Review

Post-COVID-19 Small Fiber Neuropathy as a New Emerging Quality of Life-Threatening Disease: A Systematic Review

by Francesca Bandinelli, Marco Di Carlo, Virginia Alba Colantuono, Filippo Nozzoli, Fausto Salaffi, Barbara Chiocchetti, Elena Nucci, Alessandra Mastricci, Eleonora Gherardi and Mirko Manetti

Microorganisms 2025, 13(2), 328; https://doi.org/10.3390/microorganisms13020328 (registering DOI) - 2 Feb 2025

Abstract

Post-acute sequelae of COVID-19 (PASC) syndrome is considered an emergent and diffuse multidisciplinary problem. Compelling evidence suggests that COVID-19 increases symptoms of pre-existent small fiber neuropathy (SFN) and might trigger de novo onset of SFN. In this systematic review, for the first time, [...] Read more.

Post-acute sequelae of COVID-19 (PASC) syndrome is considered an emergent and diffuse multidisciplinary problem. Compelling evidence suggests that COVID-19 increases symptoms of pre-existent small fiber neuropathy (SFN) and might trigger de novo onset of SFN. In this systematic review, for the first time, we provide a comprehensive overview of the clinical and diagnostic features of PASC-SFN, including the accompanying disorders, disease evolution, and possible treatments, described in the recent literature. Following infection, many patients reported a wide range of symptoms and complications, not self-limiting and independent from previous infection severity. SFN begins more frequently with distal limb burning pain and numbness, which accompany other dysautonomia, cognitive, visual, and osteoarticular disorders involving multiple organ systems. In an initial diagnostic suspicion, some tests might be useful as complementary examinations, such as nerve quantitative sensory testing, electromyography, and optic nerve tomography. Otherwise, definite diagnosis is reached with skin biopsy as the gold standard, along with corneal in vivo microscopy when ocular discomfort is present. Being a long-term condition, multiple and dissimilar symptomatic and disease-modifying drugs were employed for the treatment of this condition with the achievement of partial results, including steroids, pregabalin, gabapentin, duloxetine, vitamins, homotaurine and phosphatidylserine, alpha lipoic acid, immunosuppressants, and intravenous immunoglobulin therapy. PASC-SFN is a complex emerging disease and extremely challenging for physicians. At present, the only feasible management of PASC-SFN is represented by a multidisciplinary tailored approach, with future definitive protocols for diagnosis and treatment deemed essential. Full article

(This article belongs to the Special Issue Microbial Infections and Rheumatic Diseases)

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7 pages, 3914 KiB

Open AccessCommunication

Microbial Changes Occurring During Oronasal Fistula Wound Healing

by Steven L. Goudy, Heath L. Bradley, Camillo Anthony Gacasan, Afra Toma, Keerthi Priya Chinniampalayam Sekar, William M. Wuest, Martin Tomov, Vahid Serpooshan, Ahmet Coskun and Rheinallt M. Jones

Microorganisms 2025, 13(2), 327; https://doi.org/10.3390/microorganisms13020327 (registering DOI) - 2 Feb 2025

Abstract

The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By [...] Read more.

The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By contrast, creation of an oro-nasal fistula (ONF), often occurring after surgery to correct a cleft palate, is a significant wound healing challenge. Methods: In this study, we characterized the changes in the oral microbiome of mice following a freshly inflicted wound in the oral palate that results in an open and unhealed ONF. Results: Creation of an ONF in mice significantly lowered oral microbiome alpha diversity, with concurrent blooms of Enterococcus faecalis, Staphylococcus lentus, and Staphylococcus xylosus in the oral cavity. Treatment with oral antibiotics one week before ONF infliction reduced microbiome alpha diversity and prevented E. faecalis, S. lentus, and S. xylosus blooms, but did not impact ONF healing. Conclusions: An ONF in the murine palate leads to a dysbiotic oral microbiome and a bloom of opportunistic pathogens that may prevent ONF healing. Delivery of therapeutics that accelerate ONF healing might restore oral microbiome diversity and inhibit blooms of opportunistic pathogens. Full article

(This article belongs to the Section Microbiomes)

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15 pages, 3252 KiB

Open AccessArticle

Viral Infections in HSCT Recipients with Post-Transplant Lymphoproliferative Disorder: The Role of Torque Teno Virus as a Marker of Immune Functions

by Martyna Pociupany, Carolina Tarabella, Robert Snoeck, Daan Dierickx and Graciela Andrei

Microorganisms 2025, 13(2), 326; https://doi.org/10.3390/microorganisms13020326 (registering DOI) - 2 Feb 2025

Abstract

Monitoring immune function in post-transplant patients is crucial to reduce the risk of viral infections (e.g., cytomegalovirus [CMV] or Epstein–Barr virus [EBV]), which can lead to serious complications such as post-transplant lymphoproliferative disorder (PTLD). Recently, Torque Teno virus (TTV) has attracted interest as [...] Read more.

Monitoring immune function in post-transplant patients is crucial to reduce the risk of viral infections (e.g., cytomegalovirus [CMV] or Epstein–Barr virus [EBV]), which can lead to serious complications such as post-transplant lymphoproliferative disorder (PTLD). Recently, Torque Teno virus (TTV) has attracted interest as a marker of immune function. Thus, we studied the kinetics of common post-transplant viral infections (TTV, EBV, CMV, human herpesvirus-6 [HHV-6], and adenovirus [AdV]) and their association with clinical parameters in 23 HSCT recipients who developed PTLD (PTLD-HSCT) and 25 post-HSCT patients without PTLD (Non-PTLD-HSCT) at three different timepoints: at the time of the transplant (T0), 3 months (T1), and 6 months (T2) post-HSCT. Additionally, 25 healthy donors (HD) were used as the control. EBV, CMV, HHV-6, or AdV infections were found in a few samples, while TTV was found in all of our samples. The highest TTV levels (4.61 [T0], 6.24 [T1] and 6.70 [T2] log₁₀ copies/mL) were seen in PTLD-HSCT patients compared to Non-PTLD-HSCT (3.39 [T0], 4.86 [T1], and 3.75 [T2] log₁₀ copies/mL) and HD (2.25 log₁₀ copies/mL) at all timepoints. Higher TTV levels were also seen in patients with a destructive type of PTLD and in surviving PTLD-HSCT patients compared to deceased ones. TTV kinetics in PTLD patients post-HSCT showed that TTV levels increase with the fall in the host immunocompetence and that by monitoring TTV kinetics, the immune status of the patient can be monitored. Full article

(This article belongs to the Section Virology)

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21 pages, 983 KiB

Open AccessReview

Antimicrobial Potential of Cannabinoids: A Scoping Review of the Past 5 Years

by Maria João Coelho, Maria Duarte Araújo, Márcia Carvalho, Inês Lopes Cardoso, Maria Conceição Manso and Cristina Pina

Microorganisms 2025, 13(2), 325; https://doi.org/10.3390/microorganisms13020325 (registering DOI) - 2 Feb 2025

Abstract

In the scenario of fighting bacterial resistance to antibiotics, natural products have been extensively investigated for their potential antibacterial activities. Among these, cannabinoids—bioactive compounds derived from cannabis—have garnered attention for their diverse biological activities, including anxiolytic, anti-inflammatory, analgesic, antioxidant, and neuroprotective properties. Emerging [...] Read more.

In the scenario of fighting bacterial resistance to antibiotics, natural products have been extensively investigated for their potential antibacterial activities. Among these, cannabinoids—bioactive compounds derived from cannabis—have garnered attention for their diverse biological activities, including anxiolytic, anti-inflammatory, analgesic, antioxidant, and neuroprotective properties. Emerging evidence suggests that cannabinoids may also possess significant antimicrobial properties, with potential applications in enhancing the efficacy of conventional antimicrobial agents. Therefore, this review examines evidence from the past five years on the antimicrobial properties of cannabinoids, focusing on underlying mechanisms such as microbial membrane disruption, immune response modulation, and interference with microbial virulence factors. In addition, their synergistic potential, when used alongside standard therapies, underscores their promise as a novel strategy to address drug resistance, although further research and clinical trials are needed to validate their therapeutic use. Overall, cannabinoids offer a promising avenue for the development of innovative treatments to combat drug-resistant infections and reduce the reliance on traditional antimicrobial agents. Full article

(This article belongs to the Special Issue Antimicrobial Effects of Bioactive Compounds: Phytoproducts-Based Fight against Pathogens)

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24 pages, 2047 KiB

Open AccessArticle

Engineering the Marine Pseudoalteromonas haloplanktis TAC125 via the pMEGA Plasmid Targeted Curing Using PTasRNA Technology

by Angelica Severino, Concetta Lauro, Marzia Calvanese, Christopher Riccardi, Andrea Colarusso, Marco Fondi, Ermenegilda Parrilli and Maria Luisa Tutino

Microorganisms 2025, 13(2), 324; https://doi.org/10.3390/microorganisms13020324 (registering DOI) - 2 Feb 2025

Abstract

Marine bacteria that have adapted to thrive in extreme environments, such as Pseudoalteromonas haloplanktis TAC125 (PhTAC125), offer a unique biotechnological potential. The discovery of an endogenous megaplasmid (pMEGA) raises questions about its metabolic impact and functional role in that strain. This [...] Read more.

Marine bacteria that have adapted to thrive in extreme environments, such as Pseudoalteromonas haloplanktis TAC125 (PhTAC125), offer a unique biotechnological potential. The discovery of an endogenous megaplasmid (pMEGA) raises questions about its metabolic impact and functional role in that strain. This study aimed at streamlining the host genetic background by curing PhTAC125 of the pMEGA plasmid using a sequential genetic approach. We combined homologous recombination by exploiting a suicide vector, with the PTasRNA gene-silencing technology interfering with pMEGA replication machinery. This approach led to the construction of the novel PhTAC125 KrPL² strain, cured of the pMEGA plasmid, which exhibited no significant differences in growth behavior, though showcasing enhanced resistance to oxidative stress and a reduced capacity for biofilm formation. These findings represent a significant achievement in developing our understanding of the role of the pMEGA plasmid and the biotechnological applications of PhTAC125 in recombinant protein production. This opens up the possibility of exploiting valuable pMEGA genetic elements and further advancing the genetic tools for PhTAC125. Full article

(This article belongs to the Special Issue Cold-Adapted Bacteria and Marine Bacteria)

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10 pages, 598 KiB

Open AccessReview

Balancing Nature and Nurture: The Role of Biocontrol Agents in Shaping Plant Microbiomes for Sustainable Agriculture

by Suzana Moussa and Lilach Iasur Kruh

Microorganisms 2025, 13(2), 323; https://doi.org/10.3390/microorganisms13020323 (registering DOI) - 2 Feb 2025

Abstract

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with [...] Read more.

Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with plants; certain conditions favor beneficial bacteria, and others support pathogens. In this mini-review, we focus on an additional factor influencing plant microbiomes and their surrounding environments: the use of biocontrol agents. The increasing application of microbial inoculants and their metabolites as biocontrol strategies in agriculture has created a critical knowledge gap about the effects of introducing non-native bacterial species into natural plant ecosystems. The inoculation of plants and their environments with exogenous biocontrol microorganisms has the potential to alter microbial community diversity and composition, presenting both opportunities and challenges for sustainable agricultural practices. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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19 pages, 11266 KiB

Open AccessArticle

Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase (RdRp) Region and VP1 Gene in Sapovirus GI.1 and GI.2

by Fuminori Mizukoshi, Ryusuke Kimura, Tatsuya Shirai, Asumi Hirata-Saito, Eri Hiraishi, Kosuke Murakami, Yen Hai Doan, Hiroyuki Tsukagoshi, Nobuhiro Saruki, Takeshi Tsugawa, Kana Kidera, Yoshiyuki Suzuki, Naomi Sakon, Kazuhiko Katayama, Tsutomu Kageyama, Akihide Ryo and Hirokazu Kimura

Microorganisms 2025, 13(2), 322; https://doi.org/10.3390/microorganisms13020322 (registering DOI) - 1 Feb 2025

Abstract

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using [...] Read more.

Human sapovirus (HuSaV) is a significant cause of gastroenteritis. This study aims to analyze the evolutionary dynamics of the RNA-dependent RNA polymerase (RdRp) and capsid (VP1) genes of the HuSaV GI.1 and GI.2 genotypes between 1976 and 2020. Using bioinformatics tools such as the Bayesian phylogenetics software BEAST 2 package (v.2.7.6), we constructed time-scale evolutionary trees based on the gene sequences. Most of the recent common ancestors (MRCAs) of the RdRp region and VP1 gene in the present HuSaV GI.1 diverged around 1930 and 1933, respectively. The trees of the HuSaV GI.1 RdRp region and VP1 gene were divided into two clusters. Further, the MRCAs of the RdRp region and VP1 gene in HuSaV GI.2 diverged in 1960 and 1943, respectively. The evolutionary rates were higher for VP1 gene in HuSaV GI.1 than that in HuSaV GI.2, furthermore, were higher in GI.1 Cluster B than GI.1 Cluster A. In addition, a steep increase was observed in the time-scaled genome population size of the HuSaV GI.1 Cluster B. These results indicate that the HuSaV GI.1 Cluster B may be evolving more actively than other genotypes. The conformational B-cell epitopes were predicted with a higher probability in RdRp for GI.1 and in VP1 for GI.2, respectively. These results suggest that the RdRp region and VP1 gene in HuSaV GI.1 and GI.2 evolved uniquely. These findings suggest unique evolutionary patterns in the RdRp region and VP1 gene of HuSaV GI.1 and GI.2, emphasizing the need for a ‘One Health’ approach to better understand and combat this pathogen. Full article

(This article belongs to the Special Issue Microbial Evolutionary Genomics and Bioinformatics)

15 pages, 3603 KiB

Open AccessArticle

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 (registering DOI) - 1 Feb 2025

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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12 pages, 1942 KiB

Open AccessArticle

Association of Longitudinal Oral Microbiome Activity and Pediatric Concussion Recovery

by Justin Ceasar, Deepika Pugalenthi Saravanan, Brennen A. Harding and Steven D. Hicks

Microorganisms 2025, 13(2), 320; https://doi.org/10.3390/microorganisms13020320 (registering DOI) - 1 Feb 2025

Abstract

Mild traumatic brain injury (mTBI) results in a constellation of symptoms commonly referred to as a concussion. It is unclear why certain individuals experience persistent symptoms. Given the growing evidence linking the microbiome with cognition and inflammation, we examined whether longitudinal microbiome patterns [...] Read more.

Mild traumatic brain injury (mTBI) results in a constellation of symptoms commonly referred to as a concussion. It is unclear why certain individuals experience persistent symptoms. Given the growing evidence linking the microbiome with cognition and inflammation, we examined whether longitudinal microbiome patterns were associated with concussion symptoms. A cohort study of 118 children (aged 7–21 years) was conducted. Symptoms were assessed at three timepoints post-injury (4, 11, and 30 days) using the Post-Concussion Symptom Inventory. Saliva microbial activity was measured at each timepoint using RNA sequencing. A linear mixed model assessed the relationship between microbial activity and symptom burden while controlling for age, sex, and days post-mTBI. The participants’ mean age was 16 (±3) years. The symptom burden decreased across all three timepoints (25 ± 22, 13 ± 17, and 5 ± 12). The longitudinal symptom burden was associated with elevated activity of Lactobacillus (F = 5.47; adj. p = 0.020) and Saccharomyces (F = 6.79; adj. p = 0.020) and reduced activity of Micrococcus (F = 7.94, adj. p = 0.015). These results do not establish a causative relationship, or support the use of microbial measures as a concussion test. Further studies are needed to explore the role of the gut–brain axis in mTBI. Full article

(This article belongs to the Special Issue Oral Microbes and Human Health)

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19 pages, 8414 KiB

Open AccessArticle

Mechanisms Driving Seasonal Succession and Community Assembly in Sediment Microbial Communities Across the Dali River Basin, the Loess Plateau, China

by Xin Chen, Jing Li, Guoce Xu, Kang Fang, Shun Wan, Bin Wang and Fengyou Gu

Microorganisms 2025, 13(2), 319; https://doi.org/10.3390/microorganisms13020319 (registering DOI) - 1 Feb 2025

Abstract

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used [...] Read more.

Microorganisms are instrumental in river ecosystems and participate in biogeochemical cycles. It is thought that dynamic hydrological processes in rivers influence microbial community assembly, but the seasonal succession and community assembly of river sediments on the Loess Plateau remain unclear. This study used high-throughput sequencing technology (16S and ITS) and the neutral community model to analyze seasonal succession and the assembly processes associated with microbial communities in the Dali River, a tributary of the Yellow River on the Loess Plateau. The results showed that sediment bacterial and fungal community diversity indexes in non-flood season were 1.03–3.15 times greater than those in flood season. There were obvious variations between non-flood and flood seasons in sediment microorganisms. The similarities among all, abundant, and rare microbial communities decreased as geographical distance increased. Proteobacteria (52.5–99.6%) and Ascomycota (22.0–34.2%) were the primary microbial phyla in all, abundant, and rare microbial communities. Sediment ammonia nitrogen, water temperature, and sediment organic carbon significantly affected (p < 0.05) the structure of all, abundant, and rare sediment microorganism communities. The ecological networks for the bacterial community of non-flood season and fungal community of flood season had complex topological parameters. The bacterial community in river sediments was driven by deterministic processes, while the fungal community was dominated by stochastic processes. These results expanded understanding about sediment microbial community characteristics in rivers on the Loess Plateau and provided insights into the assembly processes and the factors driving microbial communities in river networks. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 4781 KiB

Open AccessArticle

Molecular Epidemiology of Dengue Viruses in Lao People’s Democratic Republic, 2020–2023

by Cécile Troupin, Kedkeo Intavong, Somphavanh Somlor, Souksakhone Viengphouthong, Sitsana Keosenhom, Thep Aksone Chindavong, Phaithong Bounmany, Longthor Vachouaxiong, Thonglakhone Xaybounsou, Chittaphone Vanhnollat, Phonepadith Khattignavong, Darouny Phonekeo, Bouaphanh Khamphaphongphane, Phonepadith Xangsayarath, Vincent Lacoste, Philippe Buchy and Gary Wong

Microorganisms 2025, 13(2), 318; https://doi.org/10.3390/microorganisms13020318 (registering DOI) - 1 Feb 2025

Abstract

Dengue fever is a widespread mosquito-borne viral disease caused by infections with dengue virus (DENV). Since its initial detection in 1979, the disease has posed a significant public health threat to the Lao People’s Democratic Republic (Lao PDR). Surveillance is crucial for understanding [...] Read more.

Dengue fever is a widespread mosquito-borne viral disease caused by infections with dengue virus (DENV). Since its initial detection in 1979, the disease has posed a significant public health threat to the Lao People’s Democratic Republic (Lao PDR). Surveillance is crucial for understanding the circulation of DENV in endemic regions and identifying potential hot spots with higher-than-expected case numbers of dengue fever. In this study, we present the results from our surveillance activities in the Lao PDR spanning 2020–2023. While quarantine restrictions from the COVID-19 pandemic posed substantial disruptions to performing DENV surveillance, over 8800 samples were tested during this period, with a positive rate of close to 60%. Cases were reported from all three regions (northern, Central, and southern) of the Lao PDR. Three circulating serotypes (DENV-1, DENV-2, and DENV-4) were detected, with DENV-1 dominant in 2021 and 2022, while DENV-2 was dominant in 2020 and 2023. Phylogenetic analyses suggest that the genotypes of DENV-1, DENV-2, and DENV-4 were closely related to corresponding isolates from neighboring countries. These findings provide an update on the nature of DENV cases detected in the Lao PDR and underscore the critical importance of sustaining a robust surveillance network to track infections. Full article

(This article belongs to the Special Issue Epidemiology of Hemorrhagic Fever Viruses)

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22 pages, 1817 KiB

Open AccessArticle

The Characterization of Lactic Acid Bacteria Strains as Components of a Biopreparation for Chickens for Slaughter

by Daria Zamojska, Justyna Rosicka-Kaczmarek, Ewa Macierzyńska-Piotrowska and Adriana Nowak

Microorganisms 2025, 13(2), 317; https://doi.org/10.3390/microorganisms13020317 (registering DOI) - 1 Feb 2025

Abstract

Since 2022, the European Union has banned the use of antibiotics in animal production. We conducted studies to characterize Lactiplantibacillus plantarum (47, AN8, and OK-B) and Ligilactobacillus salivarius (AN9) and evaluate their potential to create a biopreparation based on fermented whey for chickens. [...] Read more.

Since 2022, the European Union has banned the use of antibiotics in animal production. We conducted studies to characterize Lactiplantibacillus plantarum (47, AN8, and OK-B) and Ligilactobacillus salivarius (AN9) and evaluate their potential to create a biopreparation based on fermented whey for chickens. The following methods were used: lactic acid bacteria (LAB) culture and storage, crystal violet staining, Koch’s plate method, Caco-2 cell culture, hydrophobicity test, and spectrophotometric measurements. All bacteria showed weak adhesion to polystyrene and collagen, and the L. plantarum species demonstrated weak adhesion to mucus. All bacteria showed strong adhesion to the intestinal epithelial cell line Caco-2. LAB showed strong autoaggregation and coaggregation with E. coli ATCC10536. The highest affinity for xylene was exhibited by L. salivarius AN9 (above 30%) while, for chloroform, the highest affinity was exhibited by L. plantarum OK-B (approx. 95%); the affinity for n-hexadecane for all strains was below 20%. The highest survival in the presence of bile salts (0.3%) was demonstrated by L. plantarum 47 (above 54%). The effect of low pH resulted in decreased viability for all strains. Significant differences were demonstrated in the concentration of lactic acid between MRS and whey medium after culturing LAB. These results will aid in qualifying these strains for further research to create a functional feed for chickens. Full article

(This article belongs to the Special Issue Microorganisms in Functional Foods)

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13 pages, 1418 KiB

Open AccessArticle

QuantiFERON^® Monitor Test as a Potential Tool for Stratifying Patients by Infection Risk and Tailoring Follow-Up Care in Lung Transplant Recipients: A Single-Center Retrospective Experience

by Paolo Solidoro, Antonio Curtoni, Filippo Patrucco, Eleonora Russo, Francesca Sidoti, Giorgia Piccinini, Alessandro Bondi, Paolo Valesella, Mattia Genco, Massimo Boffini, Rocco Francesco Rinaldo and Cristina Costa

Microorganisms 2025, 13(2), 316; https://doi.org/10.3390/microorganisms13020316 (registering DOI) - 1 Feb 2025

Abstract

Background: Lung transplantation is a life-saving option for patients with end-stage respiratory diseases, but risk of infections remains critical for ensuring long-term organ function. This study aimed to assess immune recovery in lung transplant recipients by measuring IFN-γ levels using the QuantiFERON Monitor [...] Read more.

Background: Lung transplantation is a life-saving option for patients with end-stage respiratory diseases, but risk of infections remains critical for ensuring long-term organ function. This study aimed to assess immune recovery in lung transplant recipients by measuring IFN-γ levels using the QuantiFERON Monitor Test (QFM). Results were correlated with episodes of infection and organ rejection to explore the assay’s predictive potential. Methods: A retrospective study was conducted on 15 lung transplant recipients at the Lung Transplant Centre of Turin (Città della Salute e della Scienza di Torino, Italy) between December 2019 and January 2023. Patients were divided into a High Infection (HI) group (with >3 infections) and Low Infection (LI) group (with ≤3 infections). QFM assays were performed after 18 months post-transplant. Results: HI patients had lower QFM levels compared to LI (68.84 ± 21.98 vs. 380.54 ± 104.64 UI/mL, p = 0.033). A QFM value <89.5 UI/mL was associated with increased infection risk (p < 0.05). Patients with lower QFM levels also exhibited higher rates of MRSA bacteremia during hospitalization (50% HI vs. 0% LI, p = 0.04). No differences were observed in acute or chronic rejection rates, but LI patients showed more frequent alveolar neutrophilia at the fourth month post-transplant (0% HI vs. 55.5% LI, p = 0.04). Conclusion: lower QFM values were associated with higher infection risk, highlighting the assay’s potential for immune monitoring. In this study, a QFM value of 89.5 UI/mL showed good predictive accuracy for infections beyond 18 months. Further studies are needed to refine QFM’s role in post-transplant care. Full article

(This article belongs to the Special Issue Pneumonia: New Diagnostic and Therapeutic Options)

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26 pages, 1303 KiB

Open AccessReview

The Urogenital System Microbiota: Is It a New Gamechanger in Urogenital Cancers?

by Gülfem Ece, Ahmet Aktaş, Ayse Caner, İmran Sağlık, Tuğba Kula Atik, Özlem Ulusan Bağcı, Fulya Bayındır Bilman, Hadiye Demirbakan, Seda Güdül Havuz, Esra Kaya, Özlem Koyuncu Özyurt, Gülay Yetkin and Orçun Zorbozan

Microorganisms 2025, 13(2), 315; https://doi.org/10.3390/microorganisms13020315 (registering DOI) - 1 Feb 2025

Abstract

The human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and [...] Read more.

The human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and carcinogenesis. Studies suggest that alterations in this microbiota contribute to the development and progression of genitourinary cancers, emphasizing the concept of oncobiome, which refers to microbial genetic contributions to cancer. Similarly, gut microbiota can influence hormone levels and systemic inflammation, impacting cancers such as cervical and prostate cancer. Advanced studies indicate that microbial communities in genitourinary cancers have distinct profiles that may serve as diagnostic biomarkers or therapeutic targets. Dysbiosis of the urinary microbiota correlates with bladder and kidney cancer. Additionally, gut microbiota influence the effectiveness of cancer treatments. However, further research is necessary to clarify causality, the role of microbial metabolites, and hormonal regulation. The aim of this review is to understand that these dynamics present opportunities for innovative cancer diagnostics and therapies, highlighting the need for integration of microbiology, oncology, and genomics to explore the role of microbiota in genitourinary cancers. For this, a comprehensive search of relevant databases was conducted, applying specific inclusion and exclusion criteria to identify studies examining the association between microbiota and urogenital cancers. Research into the mechanisms by which microbiota influence urogenital cancers may pave the way for new diagnostic and therapeutic approaches, ultimately improving patient outcomes. Full article

(This article belongs to the Special Issue Microbiota in Human Health and Disease)

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8 pages, 993 KiB

Open AccessCommunication

Emergence of NDM-7-Producing Klebsiella quasipneumoniae subs. simillipneumoniae ST138 in a Hospital from the Northern Region of Brazil

by Amália R. F. Lobato, Mikhail J. S. Souza, Emanoele S. Pereira, Thalyta B. Cazuza, Artur Silva, Rafael A. Baraúna and Danielle M. Brasiliense

Microorganisms 2025, 13(2), 314; https://doi.org/10.3390/microorganisms13020314 (registering DOI) - 1 Feb 2025

Abstract

Clinical emergent bacterial pathogens are a great threat to the global health system, chiefly Gram-negative carbapenem-resistant Enterobacterales and the Klebsiella pneumoniae species complex. Here, we present the molecular and phenotypic characterization of Klebsiella quasipneumoniae subs. similipneumoniae IEC57090 strain, belonging to ST138 and showing [...] Read more.

Clinical emergent bacterial pathogens are a great threat to the global health system, chiefly Gram-negative carbapenem-resistant Enterobacterales and the Klebsiella pneumoniae species complex. Here, we present the molecular and phenotypic characterization of Klebsiella quasipneumoniae subs. similipneumoniae IEC57090 strain, belonging to ST138 and showing a multidrug resistance phenotype. The bla_NDM-7 present in one of the two resistance plasmids carried by the isolate, the antibiotic resistance genes fosA, oqxAB, and acrR, and gene mutations on porins ompK36 and ompK37, both associated with cephalosporin and carbapenem resistance, were detected. Virulence factors such as the clusters of type I and III fimbria, type IV pili genes, and genes associated with the K1 capsule, siderophore production, and multiple mobile genetic elements (MGE) were predicted. The emergence of silent pathogens in clinical environments highlights the importance of active research on new threads that may compromise the last resources of antimicrobials, such as carbapenems, specifically on mobile genetic elements containing carbapenemases in emergent pathogens, which can spread these antimicrobial resistance elements. This study reinforces that molecular biology vigilance can prevent outbreaks and help to better understand antimicrobial resistance and pathogens in clinical environment dynamics. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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12 pages, 8454 KiB

Open AccessArticle

IL-6–Caspase 3 Axis Plays an Important Role in Enteritis Caused by Legionella pneumophila Pulmonary Infection

by Dahui Zhao, Xuefeng Duan, Li Zhu, Min Fang, Tian Qin and Yuhai Bi

Microorganisms 2025, 13(2), 313; https://doi.org/10.3390/microorganisms13020313 (registering DOI) - 1 Feb 2025

Abstract

Background: Since Legionella pneumophila (Lp) is widely present in natural and artificial water environments, it has a high potential risk of outbreak. Diarrhea caused by Lp pulmonary infection is an important symptom of Legionnaires’ disease (LD); however, the underlying mechanism of the diarrhea [...] Read more.

Background: Since Legionella pneumophila (Lp) is widely present in natural and artificial water environments, it has a high potential risk of outbreak. Diarrhea caused by Lp pulmonary infection is an important symptom of Legionnaires’ disease (LD); however, the underlying mechanism of the diarrhea has not yet been revealed. This not only has a negative impact on clinical diagnosis and treatment, but may also cause misdiagnosis. Methods: In the present study, a mouse model of enteritis caused by pulmonary infection of Lp was established. By using this mouse model, we explored the underlying mechanisms of the enteritis caused by Lp pulmonary infection. Results: The results indicated that the systemic inflammatory response played a very important role in the enteritis phenotype caused by a strong-virulence strain of Lp. Furthermore, we found that the expression of Bcl-2 was downregulated by IL-6 through the p53 signaling pathway, thereby activating the caspase 3 of intestinal epithelial cells (IECs), causing the apoptosis of IECs, and ultimately leading to the enteritis phenotype. Conclusions: The IL-6–caspase 3 axis plays an important role in enteritis caused by Lp pulmonary infection. Full article

(This article belongs to the Section Medical Microbiology)

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