Microorganisms最新文献

{"title":"Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin.","authors":"Li Dai, Xiaolong Hao, Tong Niu, Zhen Liu, Yanmei Wang, Xiaodong Geng, Qifei Cai, Juan Wang, Yongyu Ren, Fangming Liu, Hongen Liu, Zhi Li","doi":"10.3390/microorganisms13092173","DOIUrl":"10.3390/microorganisms13092173","url":null,"abstract":"<p><p>The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (<i>p</i> < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (<i>p</i> < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (<i>p</i> < 0.05) but the lowest soil water content (<i>p</i> < 0.05). Microbial diversity indices indicated that Pielou's evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioprospecting of Goat Rumen Microbiota for Optimum Cellulase Enzyme Production to Support Sustainable Bioenergy Systems.","authors":"Kgodiso J Rabapane, Tonderayi S Matambo","doi":"10.3390/microorganisms13092170","DOIUrl":"10.3390/microorganisms13092170","url":null,"abstract":"<p><p>This study reports the isolation and optimization of cellulase-producing bacteria from the gastrointestinal tract of South African goats for the pretreatment of lignocellulosic biomass in bioenergy applications. Among the isolates, three strains, <i>Bacillus</i> KC50, <i>Bacillus</i> KC70, and <i>Proteus mirabilis</i> KC94, were identified by 16S rDNA sequencing. To our knowledge, this is the first report of cellulolytic optimization in <i>P. mirabilis</i> derived from goat rumen. Enzyme production was optimized under varying pH, temperature, and incubation conditions. <i>P. mirabilis</i> KC94 exhibited robust enzyme activity at pH 7 and 35 °C, with stability across a broader range than the <i>Bacillus</i> strains. Peak activity occurred at 84 h of incubation, reflecting strain-specific metabolic adaptation. The presence of organic solvents and surfactants inhibited enzyme activity, whereas mild oxidative stress induced by H₂O₂ stimulated cellulase production. Amplification of GH39, GH45, and GH48 genes revealed KC94's strong genetic potential for efficient lignocellulose degradation. These findings highlight the biotechnological potential of rumen-derived cellulolytic bacteria, particularly <i>P. mirabilis</i> KC94, for advancing sustainable bioenergy systems.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472465/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic and Transcriptomic Profiling of a Highly Virulent <i>Plesiomonas shigelloides</i> Strain: Insights into Pathogenicity and Host Immune Response.","authors":"Zhixiu Wang, Shaoxuan Gu, Wen Lv, Jiayi Chen, Min Xue, Suli Liu, Jiaming Mao, Guohong Chen","doi":"10.3390/microorganisms13092168","DOIUrl":"10.3390/microorganisms13092168","url":null,"abstract":"<p><p><i>Plesiomonas shigelloides</i>, a Gram-negative bacterium prevalent in aquatic environments and also frequently isolated from livestock and poultry, was investigated through integrated whole-genome sequencing and functional analyses. We deciphered the pathogenic mechanisms of <i>P. shigelloides</i> CA-HZ1, a highly virulent strain isolated from a novel piscine host, revealing a complete genome assembly with a 3.49 Mb circular chromosome and 311 kb plasmid housing 3247 predicted protein-encoding genes. Critical genomic features included 496 virulence factors and 225 antibiotic resistance genes. Pathogenicity analysis indicated that <i>P. shigelloides</i> was responsible for disease outbreaks. Antimicrobial susceptibility tests showed resistance to various drugs, such as kanamycin, erythromycin, and penicillin. Histopathological examination showed significant alterations in the infected hosts. Quantitative real-time PCR (qRT-PCR) was carried out to analyze immune-related gene (IL-6, IL-1β, IL-21, STAT1, and HSP70) levels in liver and intestinal tissues, demonstrating the potent immunity triggered by <i>P. shigelloides</i> infection. An analysis of the liver transcriptome revealed that <i>P. shigelloides</i> has the potential to influence the cellular composition, molecular functions, and biological processes. Collectively, this study describes the genomic basis underlying both the pathogenic potential and hypervirulence of <i>P. shigelloides</i> CA-HZ1, establishing a foundational framework for investigating its broad host tropism and immune response.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12473095/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-Time PCR Test (Flora Select™) for Assessing the Effectiveness of Bacterial Vaginosis Treatment During Pregnancy.","authors":"Hajime Ota, Shigeki Shimada, Yuta Kobayashi, Tatsuya Yoshiwara, Osamu Yoshino, Yoshiyuki Fukushi, Shinichiro Wada, Soromon Kataoka, Hideto Yamada","doi":"10.3390/microorganisms13092169","DOIUrl":"10.3390/microorganisms13092169","url":null,"abstract":"<p><p>Preterm birth is a major cause of perinatal mortality and morbidity in newborns, and its risk is increased by bacterial vaginosis (BV) during pregnancy. This multicenter prospective cohort study aimed to evaluate whether Flora select™ (FS), a newly developed real-time polymerase chain reaction test, is clinically useful for assessing the effectiveness of BV treatment during pregnancy. The vaginal microbiome characterized by relative dominance rates of <i>Lactobacillus</i> ≤ low (<50%), together with a positive test for <i>Gardnerella</i>, <i>Prevotella</i>, or <i>Atopobium</i> species, was defined as BV-FS A criterion. The vaginal microbiome characterized by <i>Lactobacillus</i> medium (50%≤, <80%), together with positive tests for <i>Gardnerella</i> plus either <i>Prevotella</i> species or <i>Atopobium</i> species, was defined as BV-FS B criterion. This study enrolled 25 pregnant women with classical BV (Nugent score ≥ 7) at initial examinations, and they met the BV-FS A (<i>n</i> = 23) and BV-FS B (<i>n</i> = 2) criteria. No woman with classical BV had a missed diagnosis of molecular BV. Treatments with metronidazole vaginal tablets resulted in the improvement of 88.0% (22/25) of classical BV, 65.2% (15/23) of BV-FS A, and 50.0% (1/2) of BV-FS B cases, whereas positive rates of <i>Ureaplasma</i> species in women with classical BV increased by 42.9%. Although most classical BV cases were cured following metronidazole treatments, a considerable proportion still harbored molecular BV detected by FS. Although the Nugent scoring system revealed that 80.0% (20/25) of women with classical BV (Nugent score ≥ 7) were sufficiently cured as BV-negative (Nugent scores 0-3), 5 (25%) of the 20 cured cases still met the BV-FS A/B criteria. FS particularly detected <i>Ureaplasma</i> species in 9 (45%) of the 20 cured cases. It could identify pregnant women who require additional treatments for residual molecular BV and <i>Ureaplasma</i> species. Therefore, the FS test may be clinically useful for assessing the vaginal microbiome and evaluating the effectiveness of BV treatments.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12473051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Omicron Wave in Tunisia: Dynamic, Diversity, and Phylogenetic Analyses.","authors":"Yasmine Chaari, Sondes Haddad-Boubaker, Haifa Khemiri, Wasfi Fares, Anissa Chouikha, Cesare Camma, Alessio Lorusso, Hanen Smaoui, Khaoula Meftah, Ouafa Kallala, Abdelhalim Trabelsi, Amel Chtourou, Awatef Taktak, Olfa Bahri, Manel Hamdoun, Yassine Chaabouni, Henda Touzi, Amel Sadraoui, Zina Meddeb, Nissaf Ben Alaya, Mariem Gdoura, Henda Triki","doi":"10.3390/microorganisms13092162","DOIUrl":"10.3390/microorganisms13092162","url":null,"abstract":"<p><p>The SARS-CoV-2 Omicron variant has exhibited a rapid progression around the world, but its molecular insights in North Africa remain understudied. This study characterizes the genetic diversity, dynamics, and evolutionary trends of the Omicron variant in Tunisia over a 33-month period (December 2021-August 2024). In total, 928 high-quality whole-genome sequences were considered in this study, of which 559 were retrieved from the GISAID database and 369 were generated in our laboratory. Phylogenetic analysis of the dominant subvariants (BA.1, BA.2, and BA.5) was performed using IQ-TREE. BA.2 was the predominant subvariant (38%), followed by BA.1 (24.0%), Omicron recombinants (19%), and BA.5 (18%). BA.2 diversified into JN, KP, and BN sub-lineages. Recombinants were dominated by XBB (98.8%), primarily including EG.4, XBB.1.5, and XBB.2.3.11, with rare detection of XDK and XDQ. Phylogenetic analysis revealed local clusters in BA.1, BA.2, and BA.5 alongside imported strains. Tunisia's Omicron wave was mainly driven by BA.2 and its recombinants, with evidence of localized viral evolution and sporadic introductions. The detection of rare recombinants underlines the importance of integrating regional genomic surveillance with epidemiological data in order to help guide future public health strategies.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12473128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of Drug Resistance Mutations in <i>Mycobacterium tuberculosis</i> Isolates from Moroccan Patients Using Deeplex Targeted Next-Generation Sequencing.","authors":"Said Laatri, Safaa El Kassimi, El Mehdi Bentaleb, My Driss El Messaoudi, Joy Irobi, Bouchra Belkadi, Abdelkarim Filali-Maltouf, Hassan Ait Benhassou","doi":"10.3390/microorganisms13092163","DOIUrl":"10.3390/microorganisms13092163","url":null,"abstract":"<p><p>Tuberculosis (TB) is a major public health concern worldwide and in Morocco, particularly considering the increasing burden of drug-resistant <i>Mycobacterium tuberculosis</i> (MTB) strains. In this study, we report the first nationwide molecular characterization of MTB clinical isolates using the Deeplex-MycTB targeted next-generation sequencing (tNGS) assay. A total of 71 culture-derived DNA samples from Moroccan TB patients were analyzed to detect resistance-associated mutations across 18 genes and to determine phylogenetic lineages. Of the 68 interpretable samples, 75% harbored either confirmed or uncharacterized mutations linked to drug resistance. Among these, 78% were classified as multidrug-resistant TB (MDR-TB) including 25.5% that met the criteria for pre-extensively drug-resistant TB (pre-XDR-TB). Mutations were most frequently identified in <i>rpoB</i>, <i>katG</i>, <i>inhA</i>, and <i>pncA</i>, consistent with resistance to rifampicin, isoniazid, and pyrazinamide. Phylogenetic analysis revealed a predominance of Lineage 4.3 (Euro-American) with a high representation of the LAM9 and T clades, some of which showed associations with specific resistance profiles. These findings highlight the utility of tNGS as a powerful tool for rapid resistance detection and molecular surveillance, with potential implications for guiding individualized treatment and informing national TB control strategies in Morocco.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145175977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Water Parameters Predicting the Seasonal and Spatial Dynamics of the Vibrio Harveyi- and Splendidus-Clade Pathogens.","authors":"Karagan Royer, Andrei L Barkovskii","doi":"10.3390/microorganisms13092167","DOIUrl":"10.3390/microorganisms13092167","url":null,"abstract":"<p><p><i>Vibrio</i> species of the Harveyi and Splendidus clades are the causative agents of vibriosis, resulting in mortality rates of up to 100% in common aquaculture species. They are primarily responsible for seafood-related illnesses in humans, causing gastroenteritis. Except for <i>V. parahaemolyticus</i>, the ecological behaviour of these pathogens is poorly understood. We investigated the spatial and temporal distribution of <i>V. parahaemolyticus</i>, <i>V. alginolyticus</i>, <i>V. harveyi</i>/<i>V. campbellii,</i> and <i>V. splendidus</i> in three Georgia (USA) grounds for <i>Crassostrea virginica</i> and <i>Mercenaria mercenaria</i>. DNA from oysters, clams, water, and sediment was collected over a year-long study and analyzed using quantitative PCR (qPCR) to assess the prevalence and concentrations of the above <i>Vibrio</i> species. The study targeted the <i>tlh</i>, <i>VA1198230</i>, <i>rpoA</i>, and <i>recA</i> genes using species-specific primers. Species abundance was estimated based on the concentrations of the corresponding genes. The species abundance was profiled for water parameters and concentrations of the clade-specific virulence genes <i>toxR</i>, <i>luxR</i>, <i>srp</i>, <i>vhhA</i>, <i>vhh</i>, and <i>vhp</i> that were previously detected in the study area. <i>V. parahaemolyticus</i> was the most common species, detected year-round in 61% and 44% of the water and sediment samples, respectively, followed by <i>V. splendidus</i> (67% and 17%) and <i>V. harveyi</i>/<i>V. campbellii</i> (19% and 33%). <i>V. alginolyticus</i> was rarely detected in water and never in sediment. In bivalves, the highest frequency was observed for <i>V. parahaemolyticus</i>. This species was detected in 89% of clam and 100% of oyster samples, followed by <i>V. alginolyticus</i> (22% and 17%) and <i>V. splendidus</i> at 17% in both species. No <i>V. harveyi</i>/<i>V. campbellii</i> has been detected in clams and oysters. Seasonal dynamics and concentrations varied between the species. Water temperature (r = 0.58-0.63, <i>p</i> ≤ 0.05), pH (r = -0.46), and dissolved oxygen (r = -0.42 to -0.56, <i>p</i> ≤ 0.05) were reliable predictors for the abundance of the Harveyi and Splendidus clade pathogens in bivalves and the water column, but not in sediments. In water and sediments, the abundances of <i>V. harveyi</i>/<i>V. campbellii</i> and <i>V. parahaemolyticus</i> were highly correlated (r = 0.80-0.99, <i>p</i> ≤ 0.001) to concentrations of most of the virulence genes, with some heterogeneities between the sites. The study revealed the species-specific dynamic of the Harveyi and Splendidus clade pathogens, provided the first evidence for the presence of <i>V. harveyi</i>/<i>V. campbellii</i> in the Atlantic USA waters, and identified environmental predictors for monitoring the Harveyi and Splendidus clade pathogens in mollusks and the water column.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comparative Study of Extended Gentamicin and Tobramycin Release and Antibacterial Efficacy from Palacos and Simplex Acrylic Cements.","authors":"Débora Coraça-Huber, Martina Humez, Klaus-Dieter Kühn","doi":"10.3390/microorganisms13092174","DOIUrl":"10.3390/microorganisms13092174","url":null,"abstract":"<p><p>Antibiotic-loaded bone cements (ALBCs) are used to prevent and treat periprosthetic joint infections (PJI). This study compares the in vitro release and antibacterial effectiveness of gentamicin from Palacos^® R+G and tobramycin from Simplex^® T. Standardized cylindrical specimens of Palacos^® R+G and Simplex^® T were incubated in phosphate-buffered saline. Antibiotic release was quantified using high-performance liquid chromatography (HPLC) over 14 and 42 days. Antibacterial efficacy was assessed using inhibition zone tests (IZT) against <i>Staphylococcus aureus</i>, <i>Staphylococcus epidermidis</i>, and <i>Escherichia coli</i> over 42 days. Palacos^® R+G exhibited a significantly higher and more sustained antibiotic release of gentamicin compared to tobramycin from Simplex^® T. The cumulative release of gentamicin from Palacos^® R+G was 1.148 µg/cm², while Simplex^® T released 198.87 µg/cm² tobramycin over 14 days. Inhibition zone tests showed that Palacos^® R+G maintained antibacterial activity for 42 days, while Simplex^® T's activity diminished after 14 days. Statistical analysis confirmed significant differences in antibacterial efficacy between the two cements. Palacos^® R+G demonstrated superior gentamicin release and sustained antibacterial activity compared to tobramycin from Simplex^® T. These findings suggest that Palacos^® R+G may offer better clinical outcomes in preventing and treating PJIs.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12473054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering DENV, CHIKV, and ZIKV in Urban Wastewater in Brazil Through Genomic and Molecular Screening.","authors":"Juliana Calabria de Araujo, Ana Paula A Carvalho, Talita Adelino, Felipe Campos M Iani, Natalia Rocha Guimaraes, Sara Candida F Santos, Cintia D Leal, Manuelle Natividade, Mauricio Lima, Mariana Almada, Ana Carolina Bertuce, Augusto Guerra, Maria Cristina M Costa, Flavia Saia, Vagner Fonseca, Marta Giovanetti, Livia V Frutuoso, Luiz Carlos Junior Alcantara","doi":"10.3390/microorganisms13092164","DOIUrl":"10.3390/microorganisms13092164","url":null,"abstract":"<p><p>This study evaluated and compared molecular methods (Whole Genome Sequencing-WGS, MinION, and RT-qPCR) for the detection of arboviruses Dengue (DENV), Chikungunya (CHIKV), and Zika (ZIKV) in 63 hospital and municipal wastewater samples collected from July 2022 to May 2023 in the region of Belo Horizonte, Brazil. Detection rates varied substantially across the methods (WGS, MinION, and RT-qPCR). DENV was identified in 24% (15/63) of samples using a hybrid capture method of WGS and MinION sequencing and in 66.6% (20/30) using only WGS but was not detected using the CDC Trioplex RT-PCR Assay Kit or ZDC (IBMP). CHIKV was detected in 19.0% (12/63) of the samples by WGS and MinION and in 85.7% (12/14) using only MinION sequencing. Using the RT-qPCR kit to detect CHIKV yielded a rate of 4.7% (3/63) in false positives. ZIKV was found in only one sample (1/63) by WGS, while RT-qPCR yielded a high false positive rate (65.1%, 41/63). These findings highlight the operational advantage of these methods (WGS and MinION) for enhancing early-warning surveillance where standard RT-qPCR might underperform in low-prevalence settings. This is the first study that has compared these methods to detect and genetically characterize DENV, CHICK, and ZIKV in wastewater in Brazil and has indicated that hospital wastewater can be used as a sentinel system for arbovirus surveillance. The relative effectiveness of genomic wastewater surveillance for arboviruses was demonstrated, and it was found that diagnostic RT-qPCR kits used for clinical samples were not directly suitable for environmental surveillance. The feasibility of arbovirus wastewater surveillance as an epidemiological tool was demonstrated, although absolute quantifications were not performed.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strain-Dependent Thermoadaptation in the Fish Pathogen <i>Aeromonas salmonicida</i> subsp. <i>salmonicida</i>.","authors":"Kim C Fournier, Pierre-Étienne Marcoux, Antony T Vincent, Steve J Charette","doi":"10.3390/microorganisms13092171","DOIUrl":"10.3390/microorganisms13092171","url":null,"abstract":"<p><p>Strains of <i>Aeromonas salmonicida</i> subsp. <i>salmonicida</i>, a major pathogen of salmonids, typically do not grow at temperatures above 30 °C. The effects of thermal stress on this bacterium have been extensively studied. Recently, we demonstrated that repeated exposure to cyclical thermal stress, reaching up to 37 °C, can induce permanent thermoadaptation in certain strains of this bacterium. Many aspects of this adaptation process remain poorly understood. We generated 88 thermoadapted strains of <i>A. salmonicida</i> subsp. <i>salmonicida</i> capable of sustained growth at 33 °C or higher demonstrating that prolonged heat exposure can shift a substantial proportion of psychrophilic strains toward a more mesophilic-like behavior. Although growth at 35 °C was still weaker than in naturally mesophilic <i>A. salmonicida</i> strains, some thermoadapted strains were able to grow up to 37 °C. North American strains harboring the genomic island <i>AsaGEI1a</i>, a known biomarker, exhibited a significantly reduced capacity for thermoadaptation, suggesting a possible genetic constraint, although genomic analyses indicate that <i>AsaGEI1a</i> itself is not directly responsible for this limitation. Genotyping and phenotypic analyses revealed that thermoadaptation is frequently associated with the loss of Type III secretion system and the A-layer, two key virulence factors. Only 7% of the thermoadapted strains retained both features. Overall, our findings suggest that thermoadaptation may represent a potential mechanism influencing the persistence of some psychrophilic <i>A. salmonicida</i> subsp. <i>salmonicida</i> strains in warming aquatic environments under climate change.</p>","PeriodicalId":18667,"journal":{"name":"Microorganisms","volume":"13 9","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12472413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145176705","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}