Microbiology spectrum最新文献

{"title":"<i>In vivo</i> evaluation of phage therapy against <i>Klebsiella pneumoniae</i> using the <i>Galleria mellonella</i> model and molecular characterization of a novel <i>Drulisvirus</i> phage species.","authors":"Gustavo Quispe-Villegas, Gabriela I Alcántara-Lozano, Diego Cuicapuza, Raúl Laureano, Brenda Ayzanoa, Pablo Tsukayama, Jesús Tamariz","doi":"10.1128/spectrum.01145-24","DOIUrl":"https://doi.org/10.1128/spectrum.01145-24","url":null,"abstract":"<p><p>Multidrug-resistant (MDR) <i>Klebsiella pneumoniae</i> is challenging to treat with conventional antibiotic regimens, posing a threat to healthcare systems. Phage therapy presents a promising alternative treatment strategy; however, characterization of its efficacy and safety is required. Here, we describe the microbiological and molecular characterization of a novel bacteriophage with activity against MDR <i>K. pneumoniae</i> using a greater wax moth (<i>Galleria mellonella</i>) model system. A bacteriophage was isolated from hospital wastewater. Viral kinetics and phage stability were evaluated under varied pH and temperature conditions. The therapeutic efficacy of the phage was evaluated using MDR <i>Klebsiella</i>-infected <i>G. mellonella</i> larvae as an <i>in vivo</i> model. Phage titers and larva survival were compared in phage-treated and control groups. Genomic sequencing (Nanopore and Illumina) was used to classify the bacteriophage and identify any resistance genes or virulence factors present in its genome. Functional characterization demonstrated effective lytic activity, favorable burst size (161 PFU/cell), and an optimal MOI of 0.1. The phage demonstrated stability across a wide range of temperatures (8°C-40°C) and pH levels (4-8). Experiments using the <i>G. mellonella</i> model showed improved larval survival with phage treatment. The novel bacteriophage was identified as a new species within the genus <i>Drulisvirus</i> with no lysogeny-associated, antimicrobial resistance, or virulence genes detected. The new <i>Drulisvirus</i> phage identified is a promising candidate for treatment of infections caused by MDR <i>K. pneumoniae</i>.IMPORTANCEThe study describes a bacteriophage with potential for use in phage therapy against <i>Klebsiella pneumoniae</i>, one of the most clinically significant bacterial pathogens today. Microbiological and genomic characterization of the phage revealed advantageous properties for therapeutic applications, while also identifying a novel species within the <i>Drulisvirus</i> genus. These findings significantly contribute to our understanding of bacteriophage diversity and their utility in combating antibiotic-resistant infections. Moreover, the authors developed an <i>in vivo</i> preclinical model of MDR infection using <i>Galleria mellonella</i> larvae and successfully applied it to study the bacteriophage's therapeutic efficacy. This model offers a robust and efficient platform for preclinical testing.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0114524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial communities on dry natural rocks are richer and less stressed than those on man-made playgrounds.","authors":"J Manninen, M Saarenpää, M Roslund, P Galitskaya, A Sinkkonen","doi":"10.1128/spectrum.01930-24","DOIUrl":"https://doi.org/10.1128/spectrum.01930-24","url":null,"abstract":"<p><p>In modern urbanized societies, the incidence of major immune-mediated diseases is several times higher than before World War II. A potential explanation is that these diseases are triggered by limited possibilities to be exposed to rich environmental microbiota. This requires that the urban environment hosts less and poorer microbiota than the natural environment. The current study was designed to test the assumption that urban man-made environments host less and poorer environmental microbiota, compared to natural habitats. We selected two types of dry environments, natural rocks and playground rubber mats, both of which were used daily and extensively by children. In quantitative PCR and next-generation sequencing, bacterial abundance and richness were higher on the natural rocks than the rubber mats. Altogether, 67 amplicon sequence variants (ASVs) belonging mostly to Actinobacteria and Proteobacteria were indicative of rock microbiota, while three ASVs were indicative of rubber mats. Interestingly, bacteria formed more complex networks on rubber mats than natural rocks. Based on the literature, this indicates that the studied artificial dry environment is more challenging and stressful for bacterial communities than dry natural rocks. The results support the hypothesis that urban man-made environments host poor microbial communities, which is in accordance with the biodiversity hypothesis of immune-mediated diseases.IMPORTANCEThe current study provides new evidence that artificial urban play environments host poor microbial communities and provide a stressful environment for microbes, as compared to dry natural rocks. Through this, the current study underlines the need to enhance microbial diversity in urban areas, especially in outdoor play environments, which have a crucial role in providing essential microbial exposure for the development of children's immune system. This research can potentially offer guidance for urban planning and public health strategies that support planetary health.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0193024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CAMP-negative <i>Streptococcus agalactiae</i> strains exhibited complete or partial chromosomal deletions of the CAMP-factor encoding gene <i>cfb</i>.","authors":"Xixi Lai, Meihong Chen, Jianwei Wang, Junjun Wang, Hui Lv, Haihua Xie, Wenjuan He, Dongjie Chen, Yi Huang, Pengwei Cai, Lilan Zheng","doi":"10.1128/spectrum.03257-24","DOIUrl":"https://doi.org/10.1128/spectrum.03257-24","url":null,"abstract":"<p><p>Universal antepartum group B streptococcus (GBS) screening and intrapartum antibiotic prophylaxis (IAP) have effectively reduced early-onset GBS infections. However, GBS strains with chromosomal deletions affecting the <i>cfb</i> gene may produce false negatives in both the CAMP test and <i>cfb</i>-based molecular diagnostics, potentially increasing the risk of neonatal infections. Vaginal swabs were collected from pregnant women at 35-37 weeks of gestation in our hospital and cultured on agar. Suspected GBS strains were initially identified using the CAMP test and then confirmed with the VITEK-2 system. CAMP-negative GBS strains underwent additional testing by qPCR, 16S rDNA, serotyping, and multilocus sequence typing (MLST). PCR for the <i>cfb</i> gene and whole-genome sequencing were performed on CAMP-negative strains. From 5,794 samples, 526 (9.1%) GBS strains, including 19 (3.6%) CAMP-negative strains and 2 strains from the same patient, were isolated. All 19 CAMP-negative strains were serotypes III and ST862. Among these strains, only one strain was <i>cfb</i> positive by qPCR, whereas all tested positive with a multitarget qPCR kit for <i>cfb</i> and <i>cps</i>. PCR amplification upstream of the <i>cfb</i> gene produced a specific band in strain PP669713 only, suggesting N-terminal <i>cfb</i> gene retention in PP669713 and complete <i>cfb</i> loss in the other strains. Whole-genome sequencing confirmed a chromosomal deletion in PP669713. Antibiotic susceptibility testing revealed no resistance to penicillin. However, CAMP-positive strains presented a greater prevalence of resistance to ciprofloxacin, and levofloxacin than CAMP-negative strains did. Our study highlights the potential risk of missed GBS detection using CAMP tests and <i>cfb</i>-targeted molecular assays.</p><p><strong>Importance: </strong>Our work makes several novel contributions to the field. (i) We report the first documented case of a C-terminal deletion of the <i>cfb</i> gene in a CAMP-negative GBS strain, demonstrating that both N-terminal and C-terminal regions are essential for cohemolytic activity. (ii) Our findings reveal that CAMP-negative GBS strains (3.6% of isolates) are more prevalent than previously recognized, with most cases resulting from complete chromosomal deletions of the <i>cfb</i> gene. (iii) We provide evidence that single-target molecular assays targeting only the <i>cfb</i> gene may miss GBS detection, highlighting the necessity for multi-target approaches in clinical diagnostics. (iv) We demonstrate a unique antibiotic resistance pattern in CAMP-negative strains, showing significantly lower resistance to certain antibiotics compared to CAMP-positive strains.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0325724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Salmonella enterica</i> serotypes causing infection in Kuwait during 2018-2021, determined by multi-locus sequence typing or whole genome sequencing.","authors":"Amani H Al Fadhli, Wafaa Y Jamal, Fatema Bibi Khodakhast, Glen P Carter, Dieter Bulach, M John Albert","doi":"10.1128/spectrum.02248-24","DOIUrl":"https://doi.org/10.1128/spectrum.02248-24","url":null,"abstract":"<p><p>Salmonellosis due to non-typhoidal <i>Salmonellae</i> (NTS) is a zoonotic infection that has epidemiological uniqueness in different settings. The current study aimed to determine the serotypes and the genetic diversity of human <i>Salmonella enterica</i> isolates causing infection in Kuwait. Isolates were obtained from feces of healthy adults and diarrheal patients between 2018 and 2021. Multi-locus sequence typing (MLST) was used to study sequence types (STs) and infer serotypes. Whole genome sequencing (WGS) was used to investigate six selected isolates, which included two isolates from a foodborne outbreak and two isolates whose serotypes could not be determined. Antibiotic susceptibility was studied by E-test and interpreted according to the Clinical and Laboratory Standards Institute guidelines. During the study period, 112/8,019 stool samples, 39/129,130 blood samples, 4/1,835 tissue samples, 3/1,209 pleural fluids, 3/9,388 pus samples, 4/80,799 urine samples, 1/7,053 endotracheal secretions, and 1/18 liver abscess samples were culture positive for <i>Salmonella</i>, yielding a total of 167 isolates with 30 different serotypes. <i>S</i>. Enteritidis (36.5%, <i>n</i> = 61), <i>S</i>. Typhimurium (14.97%, <i>n</i> = 25), <i>S</i>. Kentucky (5.9%, <i>n</i> = 10), and <i>S</i>. Newport (5.9%, <i>n</i> = 10) were the predominant serotypes. A new sequence type, ST 10217 corresponding to <i>S</i>. Schwarzengrund, was found by WGS. Two <i>S</i>. Enteritidis isolates from the foodborne outbreak showed a unique phylogenetic profile. In the phylogenetic analysis of serotypes, the number of clades was equal to the number of STs. No resistance to carbapenems was found among the isolates. This study provided data on the epidemiology of <i>Salmonella</i> serotypes causing infection in Kuwait.IMPORTANCEHuman salmonellosis due to nontyphoid <i>Salmonellae</i> is a major foodborne disease throughout the world. We determined the serotypes of isolates causing salmonellosis in Kuwait during the study period. We inferred the serotypes of isolates based on their sequence types as determined by multi-locus sequence typing, which is more amenable to laboratories than the traditional serotyping. By whole genome sequencing, we determined that the strain causing a foodborne outbreak was unique, and a new sequence type not in the serotyping scheme represented a rare serotype. We learnt the resistance pattern of isolates and lack of resistance to carbapenems that will be useful for treating multi-drug-resistant infection. Our data will contribute to planning strategies for treatment and control of salmonellosis and the epidemiology of salmonellosis in the Middle East.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0224824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mitomycin C eliminates cyanobacterial transcription without detectable prophage induction in a <i>Microcystis</i>-dominated harmful algal bloom in Lake Erie.","authors":"Robbie M Martin, Elizabeth R Denison, Helena L Pound, Ellen A Barnes, Justin D Chaffin, Steven W Wilhelm","doi":"10.1128/spectrum.02872-24","DOIUrl":"https://doi.org/10.1128/spectrum.02872-24","url":null,"abstract":"<p><p>Although evidence indicates that viruses are important in the ecology of <i>Microcystis</i> spp., many questions remain. For example, how does <i>Microcystis</i> exist at high, bloom-associated cell concentrations in the presence of viruses that infect it? The phenomenon of lysogeny and associated homoimmunity offer possible explanations for this question. Virtually nothing is known about lysogeny in <i>Microcystis</i>, but a metatranscriptomic study suggests that widespread, transient lysogeny is active during blooms. These observations lead us to posit that lysogeny is important in modulating <i>Microcystis</i> blooms. Using a classic mitomycin C-based induction study, we tested for lysogeny in a <i>Microcystis</i>-dominated community in Lake Erie in 2019. Treated communities were incubated with 1 mg L^-1 mitomycin C for 48 h alongside unamended controls. We compared direct counts of virus-like particles (VLPs) and examined community transcription for active infection by cyanophage. Mitomycin C treatment did not increase VLP count. Mitomycin C effectively eliminated transcription in the cyanobacterial community, while we detected no evidence of induction. Metatranscriptomic analysis demonstrated that the standard protocol of 1 mg L^-1 was highly toxic to the cyanobacterial population, which likely inhibited induction of any prophage present. Follow-up lab studies indicated that 0.1 mg L^-1 may be more appropriate for use in freshwater cyanobacterial studies. These findings will guide future efforts to detect lysogeny in <i>Microcystis</i> blooms.IMPORTANCEHarmful algal blooms dominated by <i>Microcystis</i> spp. occur throughout the world's freshwater ecosystems, leading to detrimental effects on ecosystem services that are well documented. After decades of research, the scientific community continues to struggle to understand the ecology of <i>Microcystis</i> blooms. The phenomenon of lysogeny offers an attractive potential explanation for several ecological questions surrounding blooms. However, almost nothing is known about lysogeny in <i>Microcystis</i>. We attempted to investigate lysogeny in a <i>Microcystis</i> bloom in Lake Erie and found that the standard protocols used to study lysogeny in aquatic communities are inappropriate for use in <i>Microcystis</i> studies, and perhaps freshwater cyanobacterial studies more broadly. This work can be used to design better methods to study the viral ecology of <i>Microcystis</i> blooms.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0287224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multiplex PCR assay to identify clinically important <i>Aeromonas</i> species.","authors":"Aki Sakurai, Naoto Hosokawa, Daisuke Ohkushi, Sohei Harada, Yasufumi Matsumura, Naoya Itoh, Kazuhiro Ishikawa, Sho Saito, Takayuki Sakurai, Ryota Hase, Takehiro Hashimoto, Yohei Doi, Masahiro Suzuki","doi":"10.1128/spectrum.03331-24","DOIUrl":"https://doi.org/10.1128/spectrum.03331-24","url":null,"abstract":"<p><p>The genus <i>Aeromonas</i> is increasingly implicated in human infections. However, accurate species-level identification remains challenging, particularly in clinical microbiology laboratories. This study aimed to develop a multiplex polymerase chain reaction (PCR) assay to identify four <i>Aeromonas</i> species-<i>Aeromonas hydrophila</i>, <i>Aeromonas caviae</i>, <i>Aeromonas veronii</i>, and <i>Aeromonas dhakensis-</i>most frequently associated with human infectious diseases. A total of 788 whole genome sequencing (WGS) data sets from 31 <i>Aeromonas</i> species were analyzed to identify open reading frames (ORFs) specifically present in <i>A. hydrophila</i>, <i>A. caviae</i>, <i>A. veronii</i>, and <i>A. dhakensis</i>. Primer sets were designed based on sequences of ORFs specific to each species to develop a multiplex PCR assay. To validate the efficacy of the assay, 256 clinical <i>Aeromonas</i> isolates were tested, and the results were compared with taxonomic affiliation inferred by WGS data, along with 19 type strains. The multiplex PCR successfully identified all strains of the four target species and produced no amplification in non-target species strains except the band for internal control. The multiplex PCR enables rapid and reliable identification of four <i>Aeromonas</i> spp. commonly involved in human infectious diseases.IMPORTANCEThe multiplex PCR assay facilitates accurate identification of clinically important <i>Aeromonas</i> spp. in clinical microbiology laboratories, providing crucial information to guide appropriate antimicrobial therapy and advance understanding of the epidemiology of <i>Aeromonas</i> spp.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0333124"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prognostic implications of the interaction between intratumoral microbiome and immune response in gastric cancer.","authors":"Sifan Liu, Lingyu Qi, Lu Dong, Wenjing Sun, Siying Liu, Peng Li, Nan Zhang","doi":"10.1128/spectrum.02830-24","DOIUrl":"https://doi.org/10.1128/spectrum.02830-24","url":null,"abstract":"<p><p>Gastric cancer (GC) prognosis is significantly influenced by intratumoral microbiomes, which modulate host-immune interactions. This study analyzed data from the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to identify immune genes associated with GC prognosis and conducted prognostic immune subtypes. GC patients were classified into two distinct prognostic immune phenotypes C1 and C2 based on the non-negative matrix factorization consensus clusters. Phenotype C2 exhibited a better prognosis and distinct immune characteristics, including enhanced presence of Th2 and Th17 cells and improved response to chemotherapy. In contrast, phenotype C1 showed higher expression levels of PDCD1LG2 and TLR9, which were critical immune factors involved in immune regulation. Both phenotypes were linked to immune genes influencing intratumoral microbiomes and GC immunotherapy responses. A prediction risk model was constructed using the LASSO regression analysis and showed great prognostic value for GC patients. The key genes were correlated with immune cells and suppressed the function of the host immune system. The intratumoral microbiomes were strongly associated with the hosts' immune infiltration and significantly interacted with host immune genes to influence GC outcomes. <i>Candidatus Nitrosotenuis</i> plays a significant role in predicting the prognosis of GC patients. This research underscores the pivotal role of intratumoral microbiomes in GC prognosis and supports the development of future personalized therapeutic approaches.IMPORTANCEIncreasing evidence confirms the presence of intratumoral microbiomes. However, the role of the intratumoral microbiomes in the progression of gastric cancer and their relationship with the immune microenvironment remain unclear. Our study classified gastric cancer patients into two immune prognostic subtypes, C1 and C2, using non-negative matrix factorization consensus clusters. The C2 subtype exhibited a better prognosis and more pronounced immune characteristics. Microbiome analyses revealed associations between both subtypes and immune genes that affect intratumoral microbiomes and their responses to immunotherapy. The intratumoral microbiomes were closely linked with host immune infiltration and significantly interacted with immune genes, which influence the prognosis of gastric cancer. Notably, <i>Candidatus Nitrosotenuis</i> showed a significant prognostic value in gastric cancer patients. Our findings highlight the critical role of the intratumoral microbiomes in affecting gastric cancer prognosis and its interaction with the immune microenvironment, supporting future personalized therapeutic approaches.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0283024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The <i>Klebsiella pneumoniae</i> tellurium resistance gene <i>terC</i> contributes to both tellurite and zinc resistance.","authors":"Ruixiang Yang, Shuang Han, Yanshuang Yu, Hongru Li, John D Helmann, Katharina Schaufler, Michael D L Johnson, Qiu E Yang, Christopher Rensing","doi":"10.1128/spectrum.02634-24","DOIUrl":"https://doi.org/10.1128/spectrum.02634-24","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is widely recognized as a pathogen responsible for hospital-acquired infections and community-acquired invasive infections. It has rapidly become a significant global public health threat due to the emergence of hypervirulent and multidrug-resistant strains, which have increased the challenges associated with treating life-threatening infections. Tellurium resistance genes are widespread on virulence plasmids in <i>K. pneumoniae</i> isolates. However, the core function of the <i>ter</i> operon (<i>terZABCDEF</i>) in <i>K. pneumoniae</i> remains unclear. In this study, the multidrug-resistant <i>K. pneumoniae</i> P1927 strain was isolated from the sputum of a hospitalized pneumonia patient. The <i>ter</i> operon, along with antimicrobial resistance and virulence genes, was identified on a large hybrid plasmid in <i>K. pneumoniae</i> P1927. We generated a <i>terC</i> deletion mutant and demonstrated that this mutant exhibited reduced virulence in a <i>Galleria mellonella</i> larva infection model. Further physiological functional analysis revealed that <i>terC</i> is not only important for Te(IV) resistance but also for resistance to Zn(II), Mn(II), and phage infection. All genes of the <i>ter</i> operon were highly inducible by Zn(II), which is a stronger inducer than Te(IV), and the <i>terBCDE</i> genes were also induced by Mn(II). Collectively, our study demonstrates novel physiological functions of TerC in Zn(II) resistance and virulence in <i>K. pneumoniae</i>.IMPORTANCE<i>Klebsiella pneumoniae</i> has rapidly become a global threat to public health. Although the <i>ter</i> operon is widely identified in clinical isolates, its physiological function remains unclear. It has been proposed that proteins encoded by the <i>ter</i> operon form a multi-site metal-binding complex, but its exact function is still unknown. TerC, a central component of the tellurium resistance determinant, was previously shown to interact with outer membrane proteins OmpA and KpsD in <i>Escherichia coli</i>, suggesting potential changes in outer membrane structure and properties. Here, we report that TerC confers resistance to Zn(II), Mn(II), and phage infection, and Zn(II) was shown to be a strong inducer of the <i>ter</i> operon. Furthermore, TerC was identified as a novel virulence factor. Taken together, our results expand our understanding of the physiological functions encoded by the <i>ter</i> operon and its role in the virulence of <i>K. pneumoniae</i>, providing deeper insights into the link between heavy metal(loid) resistance determinants and virulence in pathogenic bacteria.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0263424"},"PeriodicalIF":3.7,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Improved isolation and PCR detection of <i>Phytophthora agathidicida</i> oospores from soils.","authors":"Jade T T Palmer, Jochem N A Vink, Leticia M Castro, Oliver J S Craig, Emily E Davison, Monica L Gerth","doi":"10.1128/spectrum.00135-25","DOIUrl":"https://doi.org/10.1128/spectrum.00135-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Phytophthora&lt;/i&gt; species are eukaryotic microorganisms responsible for severe dieback and root rot in plants worldwide, impacting crops, forests, and other important ecosystems. In New Zealand, &lt;i&gt;P. agathidicida&lt;/i&gt; leads to fatal dieback in kauri (&lt;i&gt;Agathis australis&lt;/i&gt;), long-lived endemic trees of significant cultural and ecological importance. A critical aspect of the &lt;i&gt;P. agathidicida&lt;/i&gt; lifecycle is the production of oospores-thick-walled spores essential for long-term survival in soil, dispersal, and disease inoculation. However, their heterogeneous distribution in soils, robust structure, and dormant state make them challenging to detect using soil baiting or DNA-based methods. Soil baiting is the basis of most current testing for &lt;i&gt;P. agathidicida&lt;/i&gt;, but baiting-based methods have low sensitivity, are slow, and require specialised facilities. To address these challenges, we developed and validated a PCR-based method for detecting &lt;i&gt;P. agathidicida&lt;/i&gt; oospores directly from soil. Our approach includes a technique for separating oospores from soil, improved oospore lysis and DNA extraction, and a primer pair that targets a repeat region of the &lt;i&gt;P. agathidicida&lt;/i&gt; genome with high sensitivity and specificity. The primers amplified the target product in all tested &lt;i&gt;P. agathidicida&lt;/i&gt; isolates without cross-reactivity against eight non-target &lt;i&gt;Phytophthora&lt;/i&gt; species. The detection limit was 1 femtogram of &lt;i&gt;P. agathidicida&lt;/i&gt; DNA via endpoint PCR. Performance assessment against 65 soil samples from kauri forests revealed &lt;i&gt;P. agathidicida&lt;/i&gt; in 69% of samples compared to only 11% detected by existing methods. By eliminating the need for baiting, our assay enhances the speed, accuracy, and accessibility of testing, thereby facilitating more comprehensive monitoring and improved disease management.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Phytophthora&lt;/i&gt; species are notorious plant pathogens responsible for severe dieback and root rot diseases, significantly impacting crops, forests, and irreplaceable natural ecosystems. Rapid and accurate detection of these pathogens is essential for effective disease management. In New Zealand, &lt;i&gt;P. agathidicida&lt;/i&gt; threatens the country's endemic kauri forests. In this study, we developed and validated a PCR-based method for detecting &lt;i&gt;P. agathidicida&lt;/i&gt; oospores in soil. Oospores are long-lived, thick-walled spores that serve as key propagules for survival in soil and the spread of disease. Their robust structure and dormant state make them particularly challenging to detect using traditional soil baiting techniques or DNA-based methods. Our method is fast, accurate, and requires minimal equipment, enabling local testing and thereby empowering communities and enhancing surveillance efforts. Although developed for &lt;i&gt;P. agathidicida&lt;/i&gt;, this method could be adapted for other plant pathogens, potentially improving disease management across various agricultural and ecologica","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0013525"},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial diversity in active and abandoned desert kangaroo rat burrows and from proximal surface sand.","authors":"Duygu Aydin, Janice M Parks, Sera Tirkes, Clint E Collins, Idil Deniz Akin, Maren L Friesen, Douglas R Call, Haluk Beyenal","doi":"10.1128/spectrum.01388-24","DOIUrl":"https://doi.org/10.1128/spectrum.01388-24","url":null,"abstract":"<p><p>Desert kangaroo rats (<i>Dipodomys deserti</i>) construct burrows that can create micro-niches favorable to increased microbial activity. The aim of this study was to characterize the bacterial communities found in kangaroo rat burrows, in proximal desert surface sand, and in samples from kangaroo rats. We collected samples from burrow ceilings of actively inhabited burrows, from burrows that were no longer in use, and from the proximal surface sand in the Sonoran Desert, Yuma, AZ. Following DNA extraction from samples, 16S rRNA gene sequencing was performed, and functional predictions were made and assessed for each characterized bacterial community. Active burrow samples exhibited greater alpha diversity but similar beta diversity when compared to surface sand (<i>P</i> < 0.05), with no significant differences observed between abandoned and active burrows. Bacterial genera and genes related to nitrogen fixation, nitrification, and urea hydrolysis were found in significantly higher abundance in active burrows compared to the surface sand (<i>P</i> < 0.05). The core microbiome of active burrow samples was different from surface sand, including higher abundances of <i>Acidimicrobiales</i> and <i>Acidobacteria</i> subdivision Gp7. Active burrow samples included 30 unique genera. Kangaroo rat anal swabs shared 12, cheek pouches shared 6 unique genera with burrows. These findings suggest that kangaroo rats can shape the microbial composition of their burrow environment through the introduction of food material and waste, facilitating increased species richness and bacterial diversity.IMPORTANCEAnimals can alter soil parameters, including microbial composition through burrowing activities, excretion, and dietary composition. Desert kangaroo rats (<i>Dipodomys deserti</i>) construct burrows within loose desert sand that have microclimatic conditions different from the surrounding desert climate. In this study, we explored the effect of disturbance from kangaroo rat activities on the bacterial composition of sand. We compared the bacterial community compositions of kangaroo rat (<i>D. deserti</i>) samples, their burrows, and the proximal surface sand. The results showed that burrow sand shows higher richness and diversity of bacterial community with higher abundances of bacterial genera and genes associated with nitrogen fixation, nitrification, and urea hydrolysis compared to the surface sand. These findings suggest that kangaroo rats affect the microbial composition of their burrow environment through the introduction of food material and waste.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0138824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}