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Microorganisms, Volume 13, Issue 2 (February 2025) – 213 articles

Cover Story (view full-size image): The gut microbiota has emerged as a critical player in metabolic and liver health, with its influence extending to the pathogenesis and progression of steatotic liver diseases. This review delves into the gut–liver axis, a dynamic communication network linking the gut microbiome and liver through metabolic, immunological, and inflammatory pathways. View this paper
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13 pages, 253 KiB  
Article
The Role of Monocyte Distribution Width (MDW) in the Prediction of Death in Adult Patients with Sepsis
by Dimitrios Theodoridis, Angeliki Tsifi, Emmanouil Magiorkinis, Xenofon Tsamakidis, Apostolos Voulgaridis, Evgenia Moustaferi, Nikoletta Skrepetou, Sotirios Tsifis, Anastasios Ioannidis, Efstathios Chronopoulos and Stylianos Chatzipanagiotou
Microorganisms 2025, 13(2), 427; https://doi.org/10.3390/microorganisms13020427 (registering DOI) - 15 Feb 2025
Abstract
Sepsis is a life-threatening condition; it is a major cause of hospital mortality worldwide and it constitutes a global health problem. This research investigates the use of MDW as a predictor for septic patients. This was a double-center prospective cohort study of adult [...] Read more.
Sepsis is a life-threatening condition; it is a major cause of hospital mortality worldwide and it constitutes a global health problem. This research investigates the use of MDW as a predictor for septic patients. This was a double-center prospective cohort study of adult septic patients. Septic patients were identified and were categorized into two categories: those who improved and those who died. Blood was drawn from the patients three times, on the first, third, and fifth day of their admission to the hospital. MDW was evaluated as a biomarker to predict patient outcome. In addition, existing inflammatory markers were recorded in all patients. The MDW was able to predict patient’s outcome. The average MDW was found to be significantly higher in patients who died in all records. For example, an MDW value of 28.4 on the first day of admission to the hospital was shown to be the best cut-off value in determining fatal outcomes; receiver operating characteristic (ROC) analysis revealed an area under the curve value of 0.71 (95% Confidence Interval-CI: 0.57–0.84) with a sensitivity of 64.7% and a specificity of 88.2%. In conclusion, MDW, in addition to being a marker that can quickly detect sepsis more effectively than other biomarkers, which is proven by numerous studies, could also be used as an indicator to predict patient outcome. This work is an attempt in that direction. Full article
(This article belongs to the Section Medical Microbiology)
17 pages, 2536 KiB  
Review
Omsk Hemorrhagic Fever Virus: A Comprehensive Review from Epidemiology to Diagnosis and Treatment
by Erica Diani, Riccardo Cecchetto, Emil Tonon, Marco Mantoan, Virginia Lotti, Anna Lagni, Asia Palmisano, Pier Paolo Piccaluga and Davide Gibellini
Microorganisms 2025, 13(2), 426; https://doi.org/10.3390/microorganisms13020426 (registering DOI) - 15 Feb 2025
Abstract
Omsk hemorrhagic fever virus (OHFV) is the etiological agent of a poorly studied acute viral disease, causing several epidemic waves observed in the western Siberia regions of Omsk, Kurgan, Novosibirsk, and Tyumen. OHFV is a flavivirus and shares structural and morphological features with [...] Read more.
Omsk hemorrhagic fever virus (OHFV) is the etiological agent of a poorly studied acute viral disease, causing several epidemic waves observed in the western Siberia regions of Omsk, Kurgan, Novosibirsk, and Tyumen. OHFV is a flavivirus and shares structural and morphological features with tick-borne encephalitis (TBE) complex viruses. The disease’s symptoms show high variability, from flu-like symptoms, hyperesthesia, and petechial rush in the upper body to high fever and hemorrhagic manifestations, with a fatality rate of about 1%. The real number of OHFV-infected people is still unknown due to the difficulties in diagnosis and the presence of asymptomatic patients that lead to an underestimation of the total cases. Little is known about the viral infection dynamics at the molecular and cellular levels, the viral involvement in immune escape, cellular pathways alteration, or metabolic influence. It is noteworthy that no clinical trials have currently been performed for effective and specific drug treatments. In this review, we will give an overview of OHFV interactions with humans and animals, diagnostic tools, and drug treatments. We aim to highlight the importance of a frequently undiagnosed or misdiagnosed viral infection that might also even cause severe clinical manifestations such as meningitis and hemorrhage, in order to point out the need to develop new research studies, new diagnostic tools, and new treatments for OHFV. Full article
(This article belongs to the Section Virology)
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15 pages, 498 KiB  
Article
Prevalence and Antimicrobial Resistance of ESBL E. coli in Early Broiler Production Stage and Farm Environment in Lithuania
by Beatrice Kasparaviciene, Aleksandr Novoslavskij, Jurgita Aksomaitiene, Jurate Stankeviciene, Neringa Kasetiene, Romualdas Sinkevicius and Mindaugas Malakauskas
Microorganisms 2025, 13(2), 425; https://doi.org/10.3390/microorganisms13020425 (registering DOI) - 15 Feb 2025
Viewed by 2
Abstract
Escherichia coli, a major opportunistic pathogen in chickens, poses a serious threat to poultry production and public health via potential zoonotic transmission of ESBL-producing strains. Therefore, this study aimed to emphasize broilers as early carriers of ESBL E. coli and provide deeper [...] Read more.
Escherichia coli, a major opportunistic pathogen in chickens, poses a serious threat to poultry production and public health via potential zoonotic transmission of ESBL-producing strains. Therefore, this study aimed to emphasize broilers as early carriers of ESBL E. coli and provide deeper insights into antimicrobial resistance of these bacteria. Prevalence and antimicrobial resistance (MIC) testing of ESBL E. coli in cloacal and environmental samples from one-day-old and five-day-old broilers was conducted on three different growth cycles from a conventional poultry farm in Lithuania. Confirmed prevalence of ESBL E. coli in cloacal samples ranged from 0% to 57.5%, and in environmental swabs from 0% to 25%. All 102 ESBL E. coli isolates were susceptible to meropenem, imipenem, fosfomycin, and colistin. However, 93.14% of the strains were resistant to ceftriaxone (89.06–100%, depending on bacteria isolation source), 97.06% to ciprofloxacin (95.31–100%), and 66.67% to tetracycline (26.09–100%). Additionally, 80.39% of ESBL E. coli strains exhibited multidrug resistance. In total, 23 different antimicrobial resistance profiles were confirmed, with CRO/AMS/AUG/CIP/SXT/TE and CRO/CIP being the most common, detected in 18 of the 102 strains. The detection of widespread antimicrobial-resistant ESBL E. coli in five-day-old broilers emphasizes the need to implement control strategies early in the broiler production cycle. Full article
(This article belongs to the Section Veterinary Microbiology)
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12 pages, 1748 KiB  
Article
First Molecular Survey and Genetic Characterization of Rickettsia spp. in Haemaphysalis hystricis Ticks Infesting Dogs in Taiwan
by Chien-Ming Shih, Xing-Ru Huang, Esmeralda Erazo and Li-Lian Chao
Microorganisms 2025, 13(2), 424; https://doi.org/10.3390/microorganisms13020424 (registering DOI) - 15 Feb 2025
Viewed by 119
Abstract
Rickettsia infection in Haemaphysalis hystricis ticks infesting dogs was first screened in Taiwan by nested-PCR assay targeting the citrate synthase gene (gltA) of Rickettsia. A general infection rate (3.46%) was detected in a total of 1186 examined ticks, and infection [...] Read more.
Rickettsia infection in Haemaphysalis hystricis ticks infesting dogs was first screened in Taiwan by nested-PCR assay targeting the citrate synthase gene (gltA) of Rickettsia. A general infection rate (3.46%) was detected in a total of 1186 examined ticks, and infection rates of 3.20%, 3.6%, and 4.27% were detected in females, males, and nymphs, respectively. The monthly prevalence of Rickettsia infection was observed from March to November, and the highest infection was detected in April (6.92%) followed by a higher infection in July (5.56%), October (4.72%), September (3.57%), and May (3.54%). The prevalence of Rickettsia infection in ticks infesting stray dogs (4.15%) is significantly higher than ticks infesting domestic dogs (1.11%) (chi-square test, p = 0.015). Genetic analysis based on the gltA gene sequences from 13 Taiwan specimens, compared with 13 genospecies of Rickettsia strains documented in GenBank, revealed that the genetic identities of these Taiwan strains were phylogenetically affiliated with the genospecies of the transitional group (R. felis) and the spotted fever group (R. aeschlimannii and R. raoultii) of Rickettsia. This study demonstrates the first molecular screening of Rickettsia spp. in H. hystricis ticks infesting dogs in Taiwan. The human pathogenic strain of R. aeschlimannii was first discovered in H. hystricis ticks infesting dogs. Because dogs serve as companion animals to humans, the presence of various Rickettsia species existing in H. hystricis ticks may pose a potential threat to human health in Taiwan. Full article
(This article belongs to the Section Public Health Microbiology)
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17 pages, 1662 KiB  
Article
Enhancing Sorghum Growth: Influence of Arbuscular Mycorrhizal Fungi and Sorgoleone
by Isabela Figueiredo de Oliveira, Maria Lúcia Ferreira Simeone, Ubiraci Gomes de Paula Lana, Cristiane de Carvalho Guimarães and Sylvia Morais de Sousa Tinôco
Microorganisms 2025, 13(2), 423; https://doi.org/10.3390/microorganisms13020423 (registering DOI) - 15 Feb 2025
Viewed by 122
Abstract
The low availability of phosphorus (P) in soil is one of the main constraints on crop production. Plants have developed several strategies to increase P use efficiency, including modifications in root morphology, the exudation of different compounds, and associations with microorganisms such as [...] Read more.
The low availability of phosphorus (P) in soil is one of the main constraints on crop production. Plants have developed several strategies to increase P use efficiency, including modifications in root morphology, the exudation of different compounds, and associations with microorganisms such as arbuscular mycorrhizal fungi (AMF). This study aimed to investigate the effect of sorgoleone compound on AMF colonization and its subsequent impact on P uptake, rhizosphere microbiota, and sorghum growth. The experiment was conducted in a greenhouse using the sorghum genotype P9401, known for low sorgoleone production. Three doses of purified sorgoleone (20 μM, 40 μM, and 80 μM) were added to low-P soil and plants were harvested after 45 days. Treatments included inoculation with the arbuscular mycorrhizal fungi Rhizophagus clarus and a negative control without inoculum. The addition of 40 and 80 μM of sorgoleone did not significantly increase mycorrhization. However, treatment with 20 μM sorgoleone combined with R. clarus inoculation significantly increased total sorghum biomass by 1.6-fold (p ≤ 0.05) compared to the non-inoculated treatment. AMF inoculation influenced only AMF colonization and the fungal microbiota, without affecting the bacterial community, whereas sorgoleone showed no effect on either. The activities of acid and alkaline phosphatases in the rhizospheric soil did not differ significantly among the treatments. Furthermore, the sorghum genes CYP71AM1, associated with sorgoleone biosynthesis, and Sb02g009880, Sb06g002560, Sb06g002540, and Sb03g029970 (related to phosphate transport induced by mycorrhiza) were significantly upregulated (p ≤ 0.05) in fine roots under these conditions. The 20 μM concentration of sorgoleone can enhance AMF colonization in sorghum and promote plant growth under low-P conditions, without significantly altering the microbiota. Full article
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14 pages, 555 KiB  
Article
Urinary Tract Infections Caused by Klebsiella pneumoniae and Prolonged Treatment with Trimethoprim/Sulfamethoxazole
by Rumen Filev, Mila Lyubomirova, Boris Bogov, Alexander Kolevski, Victoria Pencheva, Krasimir Kalinov and Lionel Rostaing
Microorganisms 2025, 13(2), 422; https://doi.org/10.3390/microorganisms13020422 - 14 Feb 2025
Viewed by 240
Abstract
Urinary tract infections (UTIs) are among the most prevalent bacterial infections, with Klebsiella pneumoniae emerging as a significant multidrug-resistant pathogen, particularly in healthcare settings. The frequent utilization of β-lactams and fluoroquinolones has contributed to the reduced clinical application of trimethoprim-sulfamethoxazole (TRS). Nevertheless, this [...] Read more.
Urinary tract infections (UTIs) are among the most prevalent bacterial infections, with Klebsiella pneumoniae emerging as a significant multidrug-resistant pathogen, particularly in healthcare settings. The frequent utilization of β-lactams and fluoroquinolones has contributed to the reduced clinical application of trimethoprim-sulfamethoxazole (TRS). Nevertheless, this reduced use may have preserved its efficacy as a second-line therapy. The aim of this study is to determine whether TRS can be a cost-effective long-term solution for patients with multidrug-resistant K. pneumoniae UTIs. This study evaluated the effectiveness of a structured, long-term TRS regimen in 11 patients with recurrent K. pneumoniae UTIs who had failed at least two prior antibiotic treatments. Patients were carefully selected, and the collected data were analyzed using descriptive analysis. The findings demonstrated microbiological eradication and symptomatic relief in all patients, with only one case of a delayed allergic reaction. All patients had a negative urine microbiology analysis after at least two unsuccessful treatment attempts over a period of 6 to 18 months. These results underscore TRS’s potential as a cost-effective and efficient second-line treatment, particularly in settings with limited therapeutic options. Its affordability, manageable side effect profile, and ability to target biofilm-associated infections further highlight its therapeutic value. Full article
(This article belongs to the Special Issue Urinary Tract Infections and Antibiotic Resistance)
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25 pages, 818 KiB  
Article
Cross-Sectional Assessment on Carbapenem-Resistant Gram-Negative Bacteria Isolated from Patients in Moldova
by Vadim Nirca, Frieder Fuchs, Tessa Burgwinkel, Rocío Arazo del Pino, Ecaterina Zaharcenco, Ralf Matthias Hagen, Sven Poppert, Hagen Frickmann and Paul G. Higgins
Microorganisms 2025, 13(2), 421; https://doi.org/10.3390/microorganisms13020421 - 14 Feb 2025
Viewed by 179
Abstract
Information on the molecular epidemiology and carbapenem resistance mechanisms in Gram-negative bacterial isolates in Moldova is scarce. To close this knowledge gap, carbapenem-resistant Gram-negative bacteria were collected over an 11-month period in a routine diagnostic laboratory in Moldova. Antimicrobial susceptibility was phenotypically and [...] Read more.
Information on the molecular epidemiology and carbapenem resistance mechanisms in Gram-negative bacterial isolates in Moldova is scarce. To close this knowledge gap, carbapenem-resistant Gram-negative bacteria were collected over an 11-month period in a routine diagnostic laboratory in Moldova. Antimicrobial susceptibility was phenotypically and genotypically assessed. Phylogenetic relationships were investigated and multi-locus sequence types were provided. The assessment indicated several clusters of phylogenetically closely related carbapenem-resistant Klebsiella pneumoniae (sequence types ST101, ST395 and ST377), Acinetobacter baumannii (ST2, ST19 and ST78) and Pseudomonas aeruginosa (ST357 and ST654) isolates next to a number of less frequently observed species and sequence types. A phylogenetic relationship to characterized isolates from neighboring Ukraine could be confirmed. Identified carbapenemase genes comprised blaOXA-23, blaOXA-72 and blaGES-11 in A. baumannii, blaKPC-3, blaNDM-1 and blaOXA-48 in K. pneumoniae, as well as blaVIM-2 in Pseudomonas aeruginosa. In conclusion, the assessment suggested the spread of carbapenem-resistant Gram-negative bacteria in Moldova which were partly pre-described from neighboring Ukraine, as well as likely spill-over events, facilitating the regional spread of carbapenem-resistant clones. Several isolates with very high genomic similarity further support the hypothesis of likely regional transmission events driven by several evolutionary successful clonal lineages. Full article
(This article belongs to the Special Issue Combating Antimicrobial Resistance: Innovations and Strategies)
18 pages, 2216 KiB  
Article
Beyond Low Prevalence: Exploring Antibiotic Resistance and Virulence Profiles in Sri Lankan Helicobacter pylori with Comparative Genomics
by Kartika Afrida Fauzia, Jeewantha Rathnayake, Dalla Doohan, Meegahalande Durage Lamawansa, Ricky Indra Alfaray, Saruuljavkhlan Batsaikhan, Bui Hoang Phuc, Langgeng Agung Waskito, Vo Phuoc Tuan, Evariste Tshibangu Kabamba, Shamshul Ansari, Takashi Matsumoto, Junko Akada, Takeshi Matsuhisa and Yoshio Yamaoka
Microorganisms 2025, 13(2), 420; https://doi.org/10.3390/microorganisms13020420 - 14 Feb 2025
Viewed by 222
Abstract
Helicobacter pylori infects at least half the population worldwide, and its highly diverse genomic content correlates with its geographic distribution because of its prolonged relationship with humans. The extremely low infection prevalence alongside low inflammation severity observed in some countries might be caused [...] Read more.
Helicobacter pylori infects at least half the population worldwide, and its highly diverse genomic content correlates with its geographic distribution because of its prolonged relationship with humans. The extremely low infection prevalence alongside low inflammation severity observed in some countries might be caused by strains with low virulence potential. Therefore, this study aimed to investigate whole-genome analysis datasets of Sri Lankan H. pylori strains. H. pylori strains were isolated from biopsy specimens and underwent whole-genome sequencing to investigate their antibiotic resistance and virulence potential. The prevalence of H. pylori infection in Sri Lanka is extremely low (1.7% in a previous study), and only six H. pylori strains were successfully isolated from bacterial culture. Antibiotic resistance analysis showed a high prevalence of metronidazole resistance (83.3%, five out of six strains), and investigation of the related genes showed truncation of the rdxA and frxA genes and single-nucleotide polymorphisms in the rdxA, frxA, ribF, omp11, and fur genes. Most virulence genes of the 144 assessed were present, except for the cag pathogenicity island (cagPAI) (absent in four out of six strains), babA/B/C, and tlpB genes. An incomplete type 4 secretion system (tfs) was found in three strains. A pan-genome analysis with non-Sri Lankan H. pylori strains showed that the htpX gene was found only in Sri Lankan strains (p-corrected = 0.0008). A phylogenetic analysis showed that the Sri Lankan strains clustered with strains from hpAsia2 and hpEurope. This comparative genomic study shows that H. pylori strains with low virulence potential are present in countries with a low prevalence of infection and disease severity, indicating a strain-type geographical pattern. The tailored guidelines for screening and treatment strategy for each region are necessary to obtain effective and efficient eradication. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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13 pages, 265 KiB  
Article
Prevalence of Shiga-Toxigenic Escherichia coli in Bovine Manure in the Mid-Atlantic Region of the United States
by Pushpinder K. Litt, Alexis N. Omar, Samantha Gartley, Alyssa Kelly, Thais Ramos, Esmond Nyarko, Tenille Ribeiro de Souza, Michele Jay-Russell, Yuhuan Chen, Peiman Aminabadi, David T. Ingram and Kalmia E. Kniel
Microorganisms 2025, 13(2), 419; https://doi.org/10.3390/microorganisms13020419 - 14 Feb 2025
Viewed by 192
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen and known to reside naturally in cattle. The application of untreated biological soil amendments of animal origin on fresh produce fields results in unique food safety challenges. It is critical to identify farm manure [...] Read more.
Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen and known to reside naturally in cattle. The application of untreated biological soil amendments of animal origin on fresh produce fields results in unique food safety challenges. It is critical to identify farm manure management practices to mitigate pre-harvest pathogen contamination. The objective of this study was to quantify the prevalence and level of STEC in cattle manure in the Mid-Atlantic region of the United States. A total of 161 bovine manure samples were collected from 13 cattle farms between 2016 and 2018. The samples were enriched with non-selective and selective media and quantified following a Most-Probable Number (MPN) assay. Among the recovered STEC isolates, PCR was performed to determine the presence of stx, eae, and rfbE. Clermont PCR was performed to identify phylogenetic groups of isolates. Of the 13 farms, 11 had STEC populations between <1.0 and >5.6 log MPN/g. Farm, humidity, and sampling year significantly (p < 0.05) influenced STEC populations in bovine manure. Of the 108 isolates, 50% were stx+ and 14% eae+. Phylogenetic group analysis revealed that 46% of the isolates belonged to group A, 19% to B1, 7% to B2, and 28% to D. Group D had the highest prevalence of stx+ and eae+ and group B1 had the lowest prevalence. Results suggest STEC geographical distribution in the Mid-Atlantic region is farm-specific, and climatic conditions can be critical for its survival and dissemination. Full article
(This article belongs to the Section Food Microbiology)
11 pages, 3853 KiB  
Article
Molecular and Biological Characterization of an Isolate of Fusarium graminearum dsRNA mycovirus 4 (FgV4) from a New Host Fusarium pseudograminearum
by Guoping Ma, Yueli Zhang, Liguo Ma, Kai Cui, Bo Zhang, Hang Jiang, Kai Qi and Junshan Qi
Microorganisms 2025, 13(2), 418; https://doi.org/10.3390/microorganisms13020418 - 14 Feb 2025
Viewed by 184
Abstract
Wheat Fusarium crown rot (FCR), mainly caused by Fusarium pseudograminearum, is one of the most important diseases. Some mycoviruses are reported to have a hypovirulence trait and considered as a biocontrol agent for plant fungal diseases. In most cases, mycovirus biological effects [...] Read more.
Wheat Fusarium crown rot (FCR), mainly caused by Fusarium pseudograminearum, is one of the most important diseases. Some mycoviruses are reported to have a hypovirulence trait and considered as a biocontrol agent for plant fungal diseases. In most cases, mycovirus biological effects have not been explored clearly. In this study, we identified and characterized a novel isolate of double-stranded RNA (dsRNA) mycovirus, Fusarium graminearum dsRNA mycovirus 4 (FgV4), from a new host, an isolate WC9-2 of F. pseudograminearum. The genome of FgV4-WC9-2 includes two dsRNA segments of 2194 bp and 1738 bp. FgV4-WC9-2 dsRNA1 contains a single open reading frame (ORF1), which encodes a protein of 675 amino acids (aa) and has a conserved RNA-dependent RNA polymerase (RdRp) domain. FgV4-WC9-2 dsRNA2 contains two discontinuous ORFs (ORF2-1 and ORF2-2) that code for hypothetical proteins with unknown function. Biological characteristics research has shown that FgV4-WC9-2 infection did not change the colony morphology, but it could significantly decrease colony growth rate. FgV4-WC9-2 could also reduce the sporulation ability, change the conidia size and reduce the pathogenicity of the host to a certain extent. This study is the first to describe a hypovirulence-associated orthocurvulavirus infecting F. pseudograminearum, which has the potential to assist with FCR disease biological management. Full article
(This article belongs to the Special Issue Diversity and Evolution of Plant and Fungal Viruses)
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16 pages, 5406 KiB  
Article
Microbial Community Structure and Diversity of Endophytic Bacteria and Fungi in the Healthy and Diseased Roots of Angelica sinensis, and Identification of Pathogens Causing Root Rot
by Yaya Cheng, Xiaoyun Zhang, Wenwen Zhang, Jianmei Dong, Yanjun Ma, Aimei Zhang, Fujun Han, Hai Peng and Weibao Kong
Microorganisms 2025, 13(2), 417; https://doi.org/10.3390/microorganisms13020417 - 14 Feb 2025
Viewed by 206
Abstract
Angelica sinensis (Oliv.) Diels is an important traditional Chinese herbal medicine, and its main medicinal part is the root. In recent years, root rot has become one of the bottlenecks hindering the healthy and green development of Angelica cultivation due to the inappropriate [...] Read more.
Angelica sinensis (Oliv.) Diels is an important traditional Chinese herbal medicine, and its main medicinal part is the root. In recent years, root rot has become one of the bottlenecks hindering the healthy and green development of Angelica cultivation due to the inappropriate application of chemical fertilizers, pesticides, plant growth regulators, and continuous cropping. In this study, high-throughput sequencing technology was adopted to reveal the differences in the community structure and diversity of endophytic bacteria and fungi in the roots of healthy and diseased A. sinensis. The results showed that the diversity index of endophytic bacterial communities was significantly higher in healthy root than in diseased Angelica root systems. There was a significant difference in endophytic fungal community diversity only at the m1 sampling site. There was a significant difference in the β-diversity of bacterial communities, but not of fungi. In terms of community composition, Proteobacteria was the dominant phylum of bacteria, and Sphingobium and Pseudomonas were the dominant genera; Ascomycota and Basidiomycota were the dominant phyla of fungi, and Plectosphaerella, Paraphoma, and Fusarium were the dominant genera. In addition, the relative abundance of the genera Sphingobium and Pseudomonas was higher in healthy roots, while Fusarium was higher in diseased samples. Among the five pathogens isolated from diseased root, four strains were Fusarium sp., and one was Paraphoma chrysanthemicola, which is reported for the first time. Our findings indicate that the endophyte community structure of A. sinensis infected with root rot changed significantly compared with healthy plants, and Fusarium is an important pathogenic factor, which provides a valuable microbiological basis for the targeted biocontrol of Angelica root rot. Full article
(This article belongs to the Section Plant Microbe Interactions)
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17 pages, 1413 KiB  
Article
Spatial Landscape Structure Influences Cross-Species Transmission in a Rabies-like Virus Model
by Norma Rocio Forero-Muñoz, Gabriel Dansereau, Francois Viard, Emily Acheson, Patrick Leighton and Timothée Poisot
Microorganisms 2025, 13(2), 416; https://doi.org/10.3390/microorganisms13020416 - 14 Feb 2025
Viewed by 210
Abstract
In this study, we simulated biologically realistic agent-based models over neutral landscapes to examine how spatial structure affects the spread of a rabies-like virus in a two-species system. We built landscapes with varying autocorrelation levels and simulated disease dynamics using different transmission rates [...] Read more.
In this study, we simulated biologically realistic agent-based models over neutral landscapes to examine how spatial structure affects the spread of a rabies-like virus in a two-species system. We built landscapes with varying autocorrelation levels and simulated disease dynamics using different transmission rates for intra- and interspecies spread. The results were analysed based on combinations of spatial landscape structures and transmission rates, focusing on the median number of new reservoir and spillover cases. We found that both spatial landscape structures and viral transmission rates are key factors in determining the number of infected simulated agents and the epidemiological week when the highest number of cases occurs. While isolated habitat patches with elevated carrying capacity pose significant risks for viral transmission, they may also slow the spread compared to more connected patches, depending on the modelled scenario. This study highlights the importance of spatial landscape structure and viral transmission rates in cross-species spread. Our findings have implications for disease control strategies and suggest that future research should also focus on how landscape factors interact with pathogen dynamics, especially in those locations where susceptible agents could be more in contact with pathogens with high transmission rates. Full article
(This article belongs to the Special Issue Rabies Virus: Infections, Reservoirs and Vectors)
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23 pages, 7087 KiB  
Article
Enhanced Leaching of Lepidolite by Acidophilic Microorganisms Under Mechanical Activation
by Jingna Li, Mengyuan Wang, Ruiyong Zhang, Hongchang Liu, Shiyun Huang, Yang Liu, Rui Liao, Arevik Vardanyan, Jinlan Xia and Jun Wang
Microorganisms 2025, 13(2), 415; https://doi.org/10.3390/microorganisms13020415 - 13 Feb 2025
Viewed by 376
Abstract
In recent years, mechanical activation technology has been extensively applied as a pretreatment process to increase the leaching efficiency in hydrometallurgical mineral processing. However, studies on its application in the lepidolite bioleaching process are limited. Therefore, the effects of mechanical activation on lithium [...] Read more.
In recent years, mechanical activation technology has been extensively applied as a pretreatment process to increase the leaching efficiency in hydrometallurgical mineral processing. However, studies on its application in the lepidolite bioleaching process are limited. Therefore, the effects of mechanical activation on lithium extraction by an acidophilic iron/sulfur-oxidizing microbial community under different nutrient conditions were evaluated in this study. The solution behavior, phase morphology, and compositional evolution, and microbial community structure succession under eutrophic conditions with exogenous pyrite as the energy substrate and oligotrophic conditions, were investigated. The results revealed that mechanical activation significantly influences the microbial community structure and the interrelationship between microbial activity and mineral phase decomposition and transformation by altering the physical and chemical properties of lepidolite. The best leaching effect was observed in the eutrophic bioleaching groups, followed by the oligotrophic groups at all mechanical activation times. Notably, at a rotation speed of 200 r/min, a material-to-ball mass ratio of 1:20, and an activation time of 150 min, the maximum leaching rates of lithium under eutrophic and oligotrophic conditions were 24.9% and 20.8%, respectively, which were 20.0% and 17.9% higher than those of the nonactivated group. The phase and composition analyses indicated that the dissolution of lithium silicate minerals occurs through a combination of protic acid corrosion, the complexation/electrostatic interactions of extracellular polymeric substances, and the complexation of secondary minerals. These results indicate that the leaching effect is closely related to the pretreatment of mechanical activation, the energy substrates, and the microbial community structure, and this has important reference value for the optimization of the bioleaching process of lepidolite. Full article
(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)
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9 pages, 623 KiB  
Communication
Phenotypic Ultra-Rapid Antimicrobial Susceptibility Testing for Ceftazidime–Avibactam: In Support of Antimicrobial Stewardship
by Inês Martins-Oliveira, Blanca Pérez-Viso, Rosário Gomes, David Abreu, Ana Silva-Dias, Rafael Cantón and Cidália Pina-Vaz
Microorganisms 2025, 13(2), 414; https://doi.org/10.3390/microorganisms13020414 - 13 Feb 2025
Viewed by 246
Abstract
Ceftazidime–avibactam (CZA) is a potent broad-spectrum drug combination covering extended-spectrum β-lactamases, AmpC, and carbapenemases of class A and D, OXA-48-type producers. Rapid antimicrobial susceptibility testing is crucial for the timely de-escalation/escalation of therapy. We evaluate CZA susceptibility using the CE-IVD FASTgramneg kit (FASTinov [...] Read more.
Ceftazidime–avibactam (CZA) is a potent broad-spectrum drug combination covering extended-spectrum β-lactamases, AmpC, and carbapenemases of class A and D, OXA-48-type producers. Rapid antimicrobial susceptibility testing is crucial for the timely de-escalation/escalation of therapy. We evaluate CZA susceptibility using the CE-IVD FASTgramneg kit (FASTinov®), a ground-breaking 2 h assay, based on flow cytometry technology for antimicrobial susceptibility testing. The assay involved rapid bacterial extraction and purification from positive blood cultures (PBCs), followed by a 1 h 37 °C incubation and flow cytometry analysis (Cytoflex, Beckman-Coulter). The susceptibility report was generated using a proprietary software and interpreted using EUCAST and CLSI 2024 criteria. Sensitivity and specificity were calculated against a reference standardized method (disk diffusion) according to ISO20776-2:2021. Overall, 135 Enterobacterales and 73 Pseudomonas aeruginosa isolates were studied. Thirty-four isolates were resistant to CZA, including six P. aeruginosa and 28 Enterobacterales (24 metallo-beta-lactamase producers, three KPC variants, and one co-producing KPC+NDM). Sensitivity and specificity reached 100% when using EUCAST and CLSI criteria compared with the reference method. The FASTinov ultra-rapid susceptibility assay for CZA demonstrated excellent results, potentially enabling de-escalation/escalation even before the second dose. Combining the speed of a molecular assay with the comprehensive information of a phenotypic test offers valuable insights for treatment decisions. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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22 pages, 2642 KiB  
Article
Molecular Insights into Cell-Mediated Immunity in Atypical Non-Ulcerated Cutaneous Leishmaniasis
by Luís Fábio S. Batista, Carmen M. Sandoval Pacheco, Gabriela V. Araujo Flores, Frederico M. Ferreira, André N. A. Gonçalves, Wilfredo H. Sosa-Ochoa, Vânia L. R. da Matta, Claudia M. C. Gomes, Concepción Zúniga, Carlos E. P. Corbett, Daniel C. Jeffares, Helder I. Nakaya, Fernando T. Silveira and Márcia D. Laurenti
Microorganisms 2025, 13(2), 413; https://doi.org/10.3390/microorganisms13020413 - 13 Feb 2025
Viewed by 310
Abstract
Leishmania (Leishmania) infantum chagasi infections range from asymptomatic (AS) to severe visceral leishmaniasis (VL). One of the manifestations is an atypical non-ulcerated cutaneous leishmaniasis (NUCL), which occurs in some locations of Central America with few cases of VL. We conducted a [...] Read more.
Leishmania (Leishmania) infantum chagasi infections range from asymptomatic (AS) to severe visceral leishmaniasis (VL). One of the manifestations is an atypical non-ulcerated cutaneous leishmaniasis (NUCL), which occurs in some locations of Central America with few cases of VL. We conducted a transcriptomic analysis of cell-mediated immunity (CMI) on blood samples from NUCL, AS, VL patients from Amapala, Honduras, and healthy controls. RNA-seq revealed a similar perturbation of gene expression in NUCL and AS. Eight gene signatures of CMI were found in NUCL involved in CD8+ T lymphocyte infiltration, reactive oxygen species generation, PD-1 receptor ligand, inflammasome assembly, chemotaxis, complement receptor and suppressor immune cell infiltration. NUCL was distinguished from VL by its up-regulation of differently expressed genes (DEGs) related to T lymphocyte exhaustion, adhesion and transmigration of leukocytes, and down-regulation of oxidative stress genes. In contrast, VL exhibited up-regulated DEGs involved in antigen cross-presentation, and similar to VL from Brazil, down-regulated DEGs involved in innate immunity. Corroborating the transcriptome findings, both the Leishmanin skin test, and the immunopathology of NUCL skin lesion defined NUCL as a proinflammatory condition, intermediate between the AS and VL clinical outcomes. That condition may be the underlying element for the benign nature of the NUCL. Full article
(This article belongs to the Special Issue Microbial Infections and Host Immunity)
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17 pages, 2640 KiB  
Article
Descriptive Comparative Transcriptomic Analysis of Genotype IV SHEV ORF3-Expressing HepG2 Cells
by Hanwei Jiao, Chi Meng, Fengyuan Jiao, Gengxu Zhou, Lingjie Wang, Shengping Wu, Cailiang Fan, Jixiang Li, Liting Cao, Yu Zhao and Yichen Luo
Microorganisms 2025, 13(2), 412; https://doi.org/10.3390/microorganisms13020412 - 13 Feb 2025
Viewed by 225
Abstract
Background: Swine hepatitis E (HEV) is a zoonotic infectious disease caused by the swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is a key virulence factor in swine HEV, playing a crucial role in the release of viral particles, the modulation [...] Read more.
Background: Swine hepatitis E (HEV) is a zoonotic infectious disease caused by the swine hepatitis E virus (SHEV). Open reading frame 3 (ORF3) is a key virulence factor in swine HEV, playing a crucial role in the release of viral particles, the modulation of the host innate immune response, and regulation of autophagy and apoptosis, etc. However, its main function and pathogenic mechanism remain incompletely understood. Results: In our study, adenoviruses ADV4-ORF3 and ADV4-GFP were successfully constructed and mediated the overexpression of enhanced green fluorescent protein (EGFP)-ORF3 and EGFP in HepG2 cells. A total of 217 differentially expressed messenger RNAs (mRNAs) were screened by high-throughput sequencing, and 27 statistically significant differentially expressed genes were screened for further quantitative real-time reverse transcription (qRT-PCR) verification by functional enrichment (Gene Ontology [GO] and Kyoto Encyclopedia of Genes and Genomes [KEGG]). They are mainly involved in six pathways: the cellular response to unfolded protein, inflammatory response, cytokine activity, TNF signaling pathway, influenza A, and pathways in cancer. In a comparative analysis of transcriptome and mRNA expression profiles of lncRNA sequencing, the results showed that 3 mRNAs of GPX1, MDM4, and CLDN and 39 transcripts overlapped and have been identified. Conclusions: Eight differential genes, HSPA1A, HSPA1B, PLD3, RELA, GPI, SAMHD1, RPS6KA4, and PIK3CB, were successfully verified. Comparing and analyzing the results of the two sequencing methods indicated that the 3 mRNAs of GPX1, MDM4, and CLDN and 39 transcripts overlapped and have been identified in SHEV ORF3-expressing HepG2 cells, which has laid a genetic foundation for the physiological function and mechanism of SHEV ORF3. Full article
(This article belongs to the Section Virology)
23 pages, 1674 KiB  
Article
Emerging Bluetongue Virus Serotype 4 in the Balearic Islands, Spain (2021): Outbreak Investigations and Experimental Infection in Sheep
by David Romero-Trancón, Marta Valero-Lorenzo, María José Ruano, Paloma Fernández-Pacheco, Elena García-Villacieros, Cristina Tena-Tomás, Ana López-Herranz, Jorge Morales, Bartolomé Martí, Miguel Ángel Jiménez-Clavero, Germán Cáceres-Garrido, Montserrat Agüero and Rubén Villalba
Microorganisms 2025, 13(2), 411; https://doi.org/10.3390/microorganisms13020411 - 13 Feb 2025
Viewed by 333
Abstract
Bluetongue is an infectious, non-contagious, arthropod-borne viral disease of ruminants caused by bluetongue virus (BTV), producing severe impacts on livestock. Historically, Southern Europe has suffered multiple incursions of different BTV serotypes with serious consequences. In 2021, BTV re-emerged in the Balearic Islands (Spain) [...] Read more.
Bluetongue is an infectious, non-contagious, arthropod-borne viral disease of ruminants caused by bluetongue virus (BTV), producing severe impacts on livestock. Historically, Southern Europe has suffered multiple incursions of different BTV serotypes with serious consequences. In 2021, BTV re-emerged in the Balearic Islands (Spain) after 16 years free of the disease, causing a large outbreak that mainly affected sheep, as well as cattle and goats. A novel emerging strain of BTV serotype 4 (BTV-4) was identified via preliminary molecular characterization as the etiological culprit of the epizootic. This study delineates the outbreak in the Balearic Islands in 2021, encompassing field-based clinical observations and laboratory findings. Additionally, an experimental infection was conducted in sheep using the novel BTV-4 strain to assess its virulence, pathogenicity, and laboratory diagnostic characteristics. The in vivo characterization was conducted concurrently with the virulent and widely disseminated BTV-4 RNM 2020 strain that has precipitated significant outbreaks in the Mediterranean region in recent years. Both strains exhibited analogous pathogenic potential in sheep and yielded equivalent outcomes in diagnostic parameters. Furthermore, the impact of the novel BTV-4 strain is discussed. Full article
(This article belongs to the Special Issue Pandemics and Infectious Diseases)
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16 pages, 17329 KiB  
Article
Listeria monocytogenes Modulates Macrophage Inflammatory Responses to Facilitate Its Intracellular Survival by Manipulating Macrophage-Derived Exosomal ncRNAs
by Jian Jiao, Zhongmei Ma, Nengxiu Li, Fushuang Duan, Xuepeng Cai, Yufei Zuo, Jie Li, Qingling Meng and Jun Qiao
Microorganisms 2025, 13(2), 410; https://doi.org/10.3390/microorganisms13020410 - 13 Feb 2025
Viewed by 269
Abstract
Exosomes are nanoscale vesicles secreted by cells that play vital regulatory roles in intercellular communication and immune responses. Listeria monocytogenes (L. Monocytogenes, LM) is a notable Gram-positive intracellular parasitic bacterium that infects humans and diverse animal species. However, the specific [...] Read more.
Exosomes are nanoscale vesicles secreted by cells that play vital regulatory roles in intercellular communication and immune responses. Listeria monocytogenes (L. Monocytogenes, LM) is a notable Gram-positive intracellular parasitic bacterium that infects humans and diverse animal species. However, the specific biological function of exosomes secreted by macrophages during L. Monocytogenes infection (hereafter EXO-LM) remains elusive. Here, we discovered that EXO-LM stimulated the secretion of inflammation-associated cytokines by macrophages, facilitating the intracellular survival of L. monocytogenes within macrophages. Transcriptomic analysis shows that EXO-LM significantly upregulates immune recognition and inflammation-related signaling pathways in macrophages. Furthermore, a ceRNA regulatory network comprising exosomal ncRNAs and macrophage RNAs was constructed through EXO-LM transcriptome sequencing. Utilizing bioinformatics and dual-luciferase reporter assays, we identified two potential binding sites between lncRNA Rpl13a-213 and miR-132-3p. Cell transfection experiments demonstrated that Rpl13a-213 overexpression augmented pro-inflammatory cytokine expression in macrophages, in contrast to the suppression by miR-132-3p overexpression. The decrease in Rpl13a-213 upon EXO-LM stimulation enhances miR-132-3p expression, dampening the inflammatory response in macrophages and aiding L. monocytogenes intracellular survival. This study unveils the immunomodulatory function of exosomal ncRNAs originating from macrophages, which provides fresh perspectives into the mechanisms underlying macrophage inflammatory response regulation by L. monocytogenes-infected cell-derived exosomes. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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10 pages, 1394 KiB  
Article
The Role of Quantitative Real-Time PCR in the Invasive Pulmonary Aspergillosis Diagnosis: A Retrospective Study
by Laura Trovato, Maddalena Calvo, Concetta Ilenia Palermo and Guido Scalia
Microorganisms 2025, 13(2), 409; https://doi.org/10.3390/microorganisms13020409 - 13 Feb 2025
Viewed by 259
Abstract
Invasive pulmonary aspergillosis (IPA) reports significant mortality rates among critically ill patients. A prompt microbiological diagnosis is essential to establish a coherent antifungal treatment. Despite its low sensitivity and prolonged turn-around time, culture represents the conventional diagnostic technique. Additionally, galactomannan detection may support [...] Read more.
Invasive pulmonary aspergillosis (IPA) reports significant mortality rates among critically ill patients. A prompt microbiological diagnosis is essential to establish a coherent antifungal treatment. Despite its low sensitivity and prolonged turn-around time, culture represents the conventional diagnostic technique. Additionally, galactomannan detection may support the diagnostic process. Ultimate generation methods, such as the real-time polymerase chain reaction (Real-Time PCR), integrated the diagnostic procedure to improve the overall laboratory effectiveness, especially regarding a quantitative Aspergillus spp. DNA detection. Herein, we propose a retrospective analysis where a quantitative real-time PCR was performed on respiratory samples belonging to patients with or without probable pulmonary aspergillosis. The study enrolled 62 samples, whose PCR results were compared to culture and galactomannan indexes. Additionally, clinical and general data were collected for all the patients. The qPCR assay reported 100% sensitivity and negative predictive value, while specificity reached 59.2% and the positive predictive value was 76.1%. Moreover, IPA patients reported fungal DNA loads higher than 103 in a logarithmic scale, while non-aspergillosis episodes reported a maximum level of 103. We hypothesized a future possibility to define a specific cut-off in distinguishing colonization from infection cases, requiring further investigations and speculations about IPA patients and respiratory samples. Full article
(This article belongs to the Collection Feature Papers in Medical Microbiology)
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16 pages, 281 KiB  
Review
Effect of the Darolac® (Oralis SB®) Probiotic Formulation on Oral Health: A Narrative Review
by Lya Blais, Noémie Auclair-Ouellet, Annie Tremblay and Sylvie Binda
Microorganisms 2025, 13(2), 408; https://doi.org/10.3390/microorganisms13020408 - 13 Feb 2025
Viewed by 317
Abstract
Gingivitis and periodontitis are prevalent periodontal conditions associated with dysbiosis of the oral cavity, which leads to inflammation and bleeding of gums, loss of tooth attachment, and degradation of the underlying bone structure. The standard adjunctive treatment for periodontal conditions, chlorhexidine mouthwash, is [...] Read more.
Gingivitis and periodontitis are prevalent periodontal conditions associated with dysbiosis of the oral cavity, which leads to inflammation and bleeding of gums, loss of tooth attachment, and degradation of the underlying bone structure. The standard adjunctive treatment for periodontal conditions, chlorhexidine mouthwash, is effective but is associated with several side effects. Probiotics have been explored as an alternative solution that promotes oral health by restoring homeostasis in the oral cavity. This review presents a summary of clinical trials using the Darolac® (Oralis SB®) probiotic formulation (Lactobacillus acidophilus Rosell®-52, Lactobacillus rhamnosus Rosell®-11, Bifidobacterium longum Rosell®-175 and Saccharomyces boulardii CNCM I-1079) as a mouthwash to support the maintenance of oral health or the restoration of its balance. In reviewed studies, Darolac® is compared to a placebo or other common solutions for periodontal conditions, including chlorhexidine mouthwash. Studies show that Darolac® is as effective or even superior to other available solutions, which supports its use as an effective adjuvant to oral health. The effects of Darolac® on the reduction in oral pathogens and markers of oral dysbiosis are reviewed, and the association between periodontitis, inflammation, and systemic diseases, as well as their implications and the use of probiotics in the periodontal field, are discussed. Full article
(This article belongs to the Special Issue Beneficial Microorganisms and Antimicrobials: 2nd Edition)
2 pages, 453 KiB  
Correction
Correction: Karayannis et al. Screening of New Industrially Important Bacterial Strains for 1,3-Propanediol, 2,3-Butanediol and Ethanol Production through Biodiesel-Derived Glycerol Fermentations. Microorganisms 2023, 11, 1424
by Dimitris Karayannis, Gabriel Vasilakis, Ioannis Charisteidis, Alexandros Litinas, Eugenia Manolopoulou, Effie Tsakalidou and Seraphim Papanikolaou
Microorganisms 2025, 13(2), 407; https://doi.org/10.3390/microorganisms13020407 - 13 Feb 2025
Viewed by 146
Abstract
In the original publication [...] Full article
(This article belongs to the Section Microbial Biotechnology)
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32 pages, 2048 KiB  
Systematic Review
Antimicrobial Lock Therapy in Clinical Practice: A Scoping Review
by Aniello Alfieri, Sveva Di Franco, Maria Beatrice Passavanti, Maria Caterina Pace, Vittorio Simeon, Paolo Chiodini, Sebastiano Leone and Marco Fiore
Microorganisms 2025, 13(2), 406; https://doi.org/10.3390/microorganisms13020406 - 13 Feb 2025
Viewed by 307
Abstract
Antimicrobial lock therapy (ALT) prevents microbial colonization in central vein catheters and treats existing catheter-related bloodstream infections (CRBSIs); the ALT assessment involves several key considerations. First, identifying which patients are suitable candidates is crucial. Additionally, understanding the clinical contexts in which is utilised [...] Read more.
Antimicrobial lock therapy (ALT) prevents microbial colonization in central vein catheters and treats existing catheter-related bloodstream infections (CRBSIs); the ALT assessment involves several key considerations. First, identifying which patients are suitable candidates is crucial. Additionally, understanding the clinical contexts in which is utilised provides insight into its applications. Examining when ALT has been employed and analyzing trends in its use over time can highlight its evolving role in patient care. Equally important is understanding how ALT is administered, including the specific agents used. Lastly, determining whether there is sufficient existing literature is essential to evaluate the feasibility of conducting future systematic reviews. This study is a scoping review adhered to the PRISMA-ScR guidelines and followed a five-stage methodological framework. Of the 1024 studies identified, 336 were included in the analysis. Findings highlight the widespread use of ethanol and taurolidine for CRBSIs prevention and the concurrent use of ALT with systemic antimicrobials to treat CRBSIs without catheter removal. ALT improves clinical outcomes, including post-infection survival and catheter retention. From our analysis, we have concluded that both an umbrella review of systematic reviews and a network meta-analysis comparing lock solutions can provide clearer guidance for clinical practice. Full article
(This article belongs to the Special Issue State-of-the-Art Medical Microbiology in Italy (2023, 2024))
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19 pages, 848 KiB  
Article
Antimicrobial Stewardship and Infection Prevention and Control in the Veneto Region, Northeastern Italy: Governance Models, Resources, and Key Challenges Across Hospital and Community Settings—Findings from the ARCO Project
by Paola Anello, Stefano Vianello, Vincenzo Baldo, Enrica Frasson, Umberto Gallo, Roberta Rampazzo, Milvia Marchiori, Mara Carraro, Sara Marchiori, Marta Pigozzo, Vinicio Manfrin, Annarita Mazzariol, Paola De Ambrosis, Davide Gentili, Michele Tonon, Romina Cazzaro, Giovanna Scroccaro, Francesca Russo and Daniele Mengato
Microorganisms 2025, 13(2), 405; https://doi.org/10.3390/microorganisms13020405 - 13 Feb 2025
Viewed by 338
Abstract
Antimicrobial resistance represents a global health challenge, with Italy among the most affected countries in Europe. In response, the Veneto Region developed governance models to enhance antimicrobial stewardship (AMS) and infection prevention in both hospital and community settings. This study assessed the implementation [...] Read more.
Antimicrobial resistance represents a global health challenge, with Italy among the most affected countries in Europe. In response, the Veneto Region developed governance models to enhance antimicrobial stewardship (AMS) and infection prevention in both hospital and community settings. This study assessed the implementation of these models and explored strategies for improvement. A survey targeting hospital medical and district health management, hospital pharmacies, and primary care pharmaceutical departments was conducted to evaluate governance adherence, resource allocation, training, and reporting practices. Findings were analyzed by a focus group comprising regional experts, infectious disease specialists, microbiologists, and policymakers, which identified critical gaps and proposed actionable recommendations. Results revealed disparities in AMS implementation between hospital and community care, with key challenges including limited multidisciplinary collaboration, inconsistent resource distribution, and gaps in training. The focus group emphasized the need for stronger governance, standardized protocols, and improved communication to address these shortcomings. This study underscores significant gaps and opportunities within the Veneto Region’s healthcare system and provides a framework for enhancing AMS and infection prevention strategies, bridging the divide between hospital and community care to combat antimicrobial resistance effectively. Full article
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20 pages, 2827 KiB  
Article
Sheep-Derived Lactobacillus johnsonii M5 Enhances Immunity and Antioxidant Capacity, Alleviates Diarrhea, and Improves Intestinal Health in Early-Weaned Lambs
by Zhuo Wang, Yuwei Zhao, Dingkun Fan, Jixian Zhang, Qiyu Diao and Kai Cui
Microorganisms 2025, 13(2), 404; https://doi.org/10.3390/microorganisms13020404 - 13 Feb 2025
Viewed by 318
Abstract
The early weaning of lambs frequently leads to weakened immunity, impaired intestinal function, and increased susceptibility to intestinal disease. Lactobacillus plays a role in regulating immunity, enhancing antioxidant capacity, and maintaining intestinal health. This study aims to isolate a strain of Lactobacillus with [...] Read more.
The early weaning of lambs frequently leads to weakened immunity, impaired intestinal function, and increased susceptibility to intestinal disease. Lactobacillus plays a role in regulating immunity, enhancing antioxidant capacity, and maintaining intestinal health. This study aims to isolate a strain of Lactobacillus with favorable probiotic properties from sheep feces and investigate its effects on the intestinal health of early-weaned lambs. In this study, the growth characteristics, acid production capacity, bacteriostatic capacity, bile salt tolerance, gastrointestinal fluid tolerance, self-coagulation capacity, and surface hydrophobicity of Lactobacillus isolated from sheep feces were analyzed for in vitro probiotic properties. Lactobacilli with strong probiotic properties were used for in vivo validation. A total of 72 Hu lambs were allocated into four groups: a ewe-reared group (ER), early-weaning group (EW), low-dose Lactobacillus group (LL), and high-dose Lactobacillus group (HL). Early weaning was performed in the EW, LL, and HL groups at the age of 28 days. Lactobacillus johnsonii M5 (L. johnsonii M5), isolated from sheep feces, exhibited strong probiotic properties in vitro. Feeding EW lambs with a low dose of L. johnsonii M5 significantly reduced their diarrhea rate (p < 0.05). Its supplementation increased the levels of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) and total antioxidant capacity (T-AOC) in serum and jejunal mucosa and decreased levels of malondialdehyde (MDA) (p < 0.05). Compared to the EW group, serum immunoglobulin G (IgG) levels were significantly increased in the LL group (p < 0.05). Compared to the EW group, feeding with L. johnsonii M5 increased the content of anti-inflammatory cytokines, while reducing the content of pro-inflammatory cytokines in serum and jejunal mucosa (p < 0.05). Feeding early-weaned lambs with L. johnsonii M5 also decreased jejunal crypt depth and increased occludin and claudin-1 in jejunal mucosa (p < 0.05). These findings indicate that feeding early-weaned lambs with L. johnsonii M5 enhances their immunity and antioxidant capacity, improving intestinal health, and mitigates diarrhea in early-weaned lambs. Full article
(This article belongs to the Section Veterinary Microbiology)
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10 pages, 1135 KiB  
Case Report
Visceral Leishmaniasis in a 25-Year-Old Female Kidney Transplant Recipient from a Non-Endemic Region: A Case Report from Romania
by Alin Gabriel Mihu, Mariana Patiu, Delia Monica Dima, Daniela Adriana Oatis, Cristina Mihaela Cismaru, Rodica Lighezan and Tudor Rares Olariu
Microorganisms 2025, 13(2), 403; https://doi.org/10.3390/microorganisms13020403 - 12 Feb 2025
Viewed by 420
Abstract
Visceral leishmaniasis is a rare parasitic infection in non-endemic regions such as Romania. We report the case of a 25-year-old female kidney transplant recipient from Cluj County, Romania, who developed persistent bicytopenia with anemia and thrombocytopenia. Despite no history of travel outside Cluj [...] Read more.
Visceral leishmaniasis is a rare parasitic infection in non-endemic regions such as Romania. We report the case of a 25-year-old female kidney transplant recipient from Cluj County, Romania, who developed persistent bicytopenia with anemia and thrombocytopenia. Despite no history of travel outside Cluj County and being the only organ recipient from the same donor to experience signs and symptoms, she was diagnosed with visceral leishmaniasis. The second bone marrow aspirate performed revealed Leishmania amastigotes. She was quickly sent to Victor Babes Infectious Disease Hospital in Bucharest for additional tests and treatment. The kidney function of the patient was maintained. This case highlights the importance of considering leishmaniasis in immunosuppressed patients presenting with unexplained cytopenia, even in non-endemic regions. This is the first documented case of visceral leishmaniasis in a kidney transplant recipient in Romania. The present report could serve as a foundation for future educational programs targeted toward informing both healthcare providers and patients about the risks, diagnosis, and management of leishmaniasis in immunosuppressed individuals in non-endemic regions. Full article
(This article belongs to the Special Issue Research on Leishmania and Leishmaniasis: Second Edition)
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32 pages, 24926 KiB  
Article
Histopathological and Proteomics Analysis of Shrimp Litopenaeus vannamei Infected with Ecytonucleospora hepatopenaei
by Ping Ni, Yingyao Ma, Bingxin Shi and Mengqiang Wang
Microorganisms 2025, 13(2), 402; https://doi.org/10.3390/microorganisms13020402 - 12 Feb 2025
Viewed by 245
Abstract
Ecytonucleospora hepatopenaei (EHP) is a microsporidian pathogen that primarily infects the hepatopancreas of Litopenaeus vannamei. Previous studies on EHP detection primarily focused on histology, in situ hybridization (ISH), and PCR, mainly concentrating on hepatopancreatic infections, with limited research on extra-hepatopancreatic tissues. This [...] Read more.
Ecytonucleospora hepatopenaei (EHP) is a microsporidian pathogen that primarily infects the hepatopancreas of Litopenaeus vannamei. Previous studies on EHP detection primarily focused on histology, in situ hybridization (ISH), and PCR, mainly concentrating on hepatopancreatic infections, with limited research on extra-hepatopancreatic tissues. This study investigates the pathogenic mechanisms of EHP infection in L. vannamei through molecular quantification, histopathology, and proteomics analysis. RT-qPCR was employed to examine the infection differences across various tissues at the molecular level, revealing that the hepatopancreas, stomach, midgut, muscle, gills, and antennal glands are susceptible tissues. Pathological analysis, combining H&E staining, Masson’s trichrome staining, and immunohistochemistry, identified the EHP-targeted sites at the tissue level. Masson’s staining effectively highlighted fibrosis, unveiling the histopathological characteristics of chronic EHP infection, while immunohistochemistry enhanced the specificity of EHP localization. The pathological features of EHP infection were primarily characterized by inflammation, cell degeneration and necrosis, and the accumulation of microsporidia in the cytoplasm. Proteomics analysis was used to interpret the histopathological findings, revealing significant enrichment of pathways related to inflammation, immune regulation, metabolism, and apoptosis regulation. These findings provide new insights into the infection mechanisms and tissue tropism of EHP. Full article
(This article belongs to the Special Issue Aquatic Microorganisms and Their Application in Aquaculture)
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24 pages, 7701 KiB  
Review
The Role of Active Packaging in the Defense Against Foodborne Pathogens with Particular Attention to Bacteriophages
by Rajesh V. Wagh, Ruchir Priyadarshi, Ajahar Khan, Zohreh Riahi, Jeyakumar Saranya Packialakshmi, Pavan Kumar, Sandeep N. Rindhe and Jong-Whan Rhim
Microorganisms 2025, 13(2), 401; https://doi.org/10.3390/microorganisms13020401 - 12 Feb 2025
Viewed by 456
Abstract
The increasing demand for food safety and the need to combat emerging foodborne pathogens have driven the development of innovative packaging solutions. Active packaging, particularly those incorporating antimicrobial agents, has emerged as a promising approach to enhance food preservation and safety. Among these [...] Read more.
The increasing demand for food safety and the need to combat emerging foodborne pathogens have driven the development of innovative packaging solutions. Active packaging, particularly those incorporating antimicrobial agents, has emerged as a promising approach to enhance food preservation and safety. Among these agents, bacteriophages (phages) have gained significant attention due to their specificity, efficacy, and natural origin. This manuscript explores the role of active packaging in protecting against foodborne pathogens, with a particular focus on bacteriophages. The review overviews recent advances in antimicrobials in food packaging, followed by a detailed discussion of bacteriophages, including their classification, mode of action, multidisciplinary applications, and their use as antimicrobial agents in active food packaging. The manuscript also highlights commercially available bacteriophage-based products and addresses the challenges and limitations associated with their integration into packaging materials. Despite their potential, issues such as stability, regulatory hurdles, and consumer acceptance remain critical considerations. In conclusion, bacteriophages represent a promising tool in active packaging for enhancing food safety, but further research and innovation are needed to overcome existing barriers and fully realize their potential in the food industry. Full article
(This article belongs to the Special Issue Latest Review Papers in Food Microbiology 2024)
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21 pages, 2426 KiB  
Article
Molecular Epidemiology of Salmonella enterica Serotype Dublin Isolated from 2011 to 2022 from Veal and Dairy Cattle in Pennsylvania
by Manoj K. Sekhwal, Lingling Li, Traci Pierre, Tammy Matthews, Erin Luley, Deepanker Tewari, Suresh V. Kuchipudi, Bhushan Jayarao and Maurice Byukusenge
Microorganisms 2025, 13(2), 400; https://doi.org/10.3390/microorganisms13020400 - 12 Feb 2025
Viewed by 506
Abstract
The emergence of Salmonella enterica serotype Dublin (S. Dublin) presents significant challenges to animal and human health. We analyzed 109 S. Dublin isolates from bovine submissions to the Penn State Animal Diagnostic Laboratory between 2011 and 2022. Using whole genome sequencing, [...] Read more.
The emergence of Salmonella enterica serotype Dublin (S. Dublin) presents significant challenges to animal and human health. We analyzed 109 S. Dublin isolates from bovine submissions to the Penn State Animal Diagnostic Laboratory between 2011 and 2022. Using whole genome sequencing, we assessed their phenotypic and genotypic resistance patterns and correlated these traits with case histories and pathology reports. Core-genome analysis identified cgSTs with similar allelic profiles between our isolates and those from the U.S. and Canada, while some cgSTs were unique to our study. Histopathologic findings suggest a predominance of respiratory and gastroenteric/hepatic lesions, aligning with the histopathological case definition for S. Dublin infection. Critically, all isolates were multidrug-resistant, particularly to ampicillin (87%), ceftiofur (89%), chlortetracycline (94%), oxytetracycline (94%), enrofloxacin (17%), florfenicol (94%), sulfadimethoxine (97%), and trimethoprim (20%). Plasmid genomic analysis unveiled distinct plasmid types including virulence, resistance, and hybrid plasmids, carrying unique compositions of virulence genes and antimicrobial resistance. These findings underscore the importance of managing calf movement to control the introduction and dissemination of new cgSTs in Pennsylvania and potentially nationwide. Furthermore, they emphasize the urgent need to mitigate S. Dublin transmission, combat antimicrobial resistance, and enhance surveillance efforts to effectively protect animal and human health. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
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14 pages, 4154 KiB  
Article
Molecular Evolution of the Fusion (F) Genes in Human Parainfluenza Virus Type 2
by Tatsuya Shirai, Fuminori Mizukoshi, Ryusuke Kimura, Rina Matsuoka, Mitsuru Sada, Kazuya Shirato, Haruyuki Ishii, Akihide Ryo and Hirokazu Kimura
Microorganisms 2025, 13(2), 399; https://doi.org/10.3390/microorganisms13020399 - 12 Feb 2025
Viewed by 348
Abstract
Human parainfluenza virus type 2 (HPIV2) is a clinically significant respiratory pathogen, which highlights the necessity of studies on its molecular evolution. This study investigated the evolutionary dynamics, phylodynamics, and structural characteristics of the HPIV2 fusion (F) gene using a comprehensive [...] Read more.
Human parainfluenza virus type 2 (HPIV2) is a clinically significant respiratory pathogen, which highlights the necessity of studies on its molecular evolution. This study investigated the evolutionary dynamics, phylodynamics, and structural characteristics of the HPIV2 fusion (F) gene using a comprehensive dataset spanning multiple decades and geographic regions. Phylogenetic analyses revealed two distinct clusters of HPIV2 F gene sequences, which were estimated to have diverged from a common ancestor approximately a century ago. Cluster 1 demonstrated a higher evolutionary rate and genetic diversity compared to the more stable cluster 2. Bayesian Skyline Plot analyses indicated a significant increase in the effective population size of the F gene between 2005 and 2015; potentially linked to enhanced diagnostic and surveillance capabilities. Structural modeling identified conserved conformational epitopes predominantly in the apex and stalk regions of the F protein. These findings underscore the evolutionary constraints and antigenic landscape of the HPIV2 F protein. Full article
(This article belongs to the Section Public Health Microbiology)
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13 pages, 3021 KiB  
Article
Predictive Value of Direct Disk Diffusion Testing from Positive Blood Cultures for Detection of Antimicrobial Nonsusceptibility
by Tammy Ting-Yan Wong, Chung-Ho Lee, Hester Wing-Sum Luk, Cindy Wing-Sze Tse and Pak-Leung Ho
Microorganisms 2025, 13(2), 398; https://doi.org/10.3390/microorganisms13020398 - 12 Feb 2025
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Abstract
Antibiotic resistance poses a significant global threat, particularly in the context of bloodstream infections. Early antimicrobial susceptibility testing plays a crucial role in guiding clinicians to optimize treatment and enhance patient outcomes. Direct disk diffusion testing (dDDT), utilizing positive blood culture broth as [...] Read more.
Antibiotic resistance poses a significant global threat, particularly in the context of bloodstream infections. Early antimicrobial susceptibility testing plays a crucial role in guiding clinicians to optimize treatment and enhance patient outcomes. Direct disk diffusion testing (dDDT), utilizing positive blood culture broth as an inoculum, provides results one day earlier than the standard method using bacterial colonies. This retrospective study evaluated the ability of dDDT to predict nonsusceptibility to commonly used antibiotics. From January 2021 to December 2023, a total of 1473 blood cultures positive for a single pathogen (Enterobacterales, Pseudomonas aeruginosa, Staphylococcus aureus, β-hemolytic streptococci, or Enterococcus spp.) were examined. The results of dDDT were compared against the standard disk diffusion method as the reference standard. A total of 9754 organism–antibiotic pairs were analyzed. The positive predictive values were more than 98% for clinically significant resistant phenotypes, including ceftriaxone, ceftazidime, cefepime, and meropenem nonsusceptibility in Enterobacterales, ceftazidime and meropenem nonsusceptibility in P. aeruginosa, and cefoxitin resistance in S. aureus. Overall, sensitivities exceeded 98% for the majority of organism–antibiotic pairs, with specificities ranging from 88.4% to 100%. Categorical agreement was high at 97.9%, ranging from 88.8% to 100% across organism groups. The overall rates of major error and very major error were very low, at 0.2% and 0.04%, respectively, and ranged from 0% to 1.5% and 0% to 0.04%, respectively, across organism groups. In conclusion, dDDT is a reliable and expedient method for detecting antibiotic nonsusceptibility, making it a valuable tool for the timely management of bloodstream infections caused by resistant organisms. Full article
(This article belongs to the Section Medical Microbiology)
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