Microbiology spectrum最新文献

{"title":"Clinical prediction model for bacterial co-infection in hospitalized COVID-19 patients during four waves of the pandemic.","authors":"Meital Elbaz, Itay Moshkovits, Tali Bar-On, Noam Goder, Yael Lichter, Ronen Ben-Ami","doi":"10.1128/spectrum.00251-24","DOIUrl":"10.1128/spectrum.00251-24","url":null,"abstract":"<p><p>The reported estimates of bacterial co-infection in COVID-19 patients are highly variable. We aimed to determine the rates and risk factors of bacterial co-infection and develop a clinical prediction model to support early decision-making on antibiotic use. This is a retrospective cohort study conducted in a tertiary-level academic hospital in Israel between March 2020 and May 2022. All adult patients with severe COVID-19 who had a blood or lower respiratory specimen sent for microbiological analyses within 48 h of admission were included. The primary study endpoint was the prevalence of bacterial co-infection at the time of hospital admission. We created a prediction model using the R XGBoost package. The study cohort included 1,050 patients admitted with severe or critical COVID-19. Sixty-two patients (5.9%) had a microbiologically proven bacterial infection on admission. The variables with the greatest impact on the prediction model were age, comorbidities, functional capacity, and laboratory parameters. The model achieved perfect prediction on the training set (area under the curve = 1.0). When applied to the test dataset, the model achieved 56% and 78% specificity with the area under the receiver operating curve of 0.784. The negative and positive predictive values were 0.975 and 0.105, respectively. Applying the prediction model would have resulted in a 2.5-fold increase in appropriate antibiotic use and an 18% reduction in inappropriate use in patients with severe and critical COVID-19. The use of a clinical prediction model can support decisions to withhold empiric antimicrobial treatment at the time of hospital admission without adversely affecting patient outcomes.</p><p><strong>Importance: </strong>Estimates of bacterial coinfection in COVID-19 patients are highly variable and depend on many factors. Patients with severe or critical COVID-19 requiring intensive care unit admission have the highest risk of infection-related complications and death. Thus, the study of the incidence and risk factors for bacterial coinfection in this population is of special interest and may help guide empiric antibiotic therapy and avoid unnecessary antimicrobial treatment. The prediction model based on clinical criteria and simple laboratory tests may be a useful tool to predict bacterial co-infection in patients hospitalized with severe COVID-19.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308142","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":"Coupling antitoxins and blue/white screening with <i>parAB</i>/resolvase mutation as a strategy for <i>Salmonella</i> spp. plasmid curing.","authors":"Dereje D Gudeta, Shaohua Zhao, Nesreen Aljahdali, Steven L Foley","doi":"10.1128/spectrum.01220-24","DOIUrl":"10.1128/spectrum.01220-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Despite the dissemination of multidrug resistance plasmids, including those carrying virulence genes in &lt;i&gt;Salmonella&lt;/i&gt; spp., efficient plasmid curing tools are lacking. Plasmid partitioning and multimer resolution systems are attractive targets for plasmid cure. However, plasmid curing strategies targeting these systems are often hindered by the host addiction system through a process known as post-segregation killing. Here, we developed vector tools that can mutate the above systems while replenishing short-lived antitoxins. Cloning was performed using Gibson assembly. &lt;i&gt;parAB&lt;/i&gt; or resolvase (&lt;i&gt;res&lt;/i&gt;) genes on Incompatibility Group (Inc)FIB, IncA/C, IncX4, and plasmids carried by &lt;i&gt;Salmonella&lt;/i&gt; species were deleted by first knocking in the N-terminal ß-galactosidase encoding gene (&lt;i&gt;bgaB&lt;/i&gt;), followed by in-frame insertion of its C-terminal region using pDG1 and pDG2 vectors, respectively. pDG1 was used as a backbone to develop a vector, designated as pDG-At, expressing 13 antitoxins driven by strong promoters. Plasmid curing was achieved by transforming pDG-At to &lt;i&gt;parAB&lt;/i&gt; or &lt;i&gt;res&lt;/i&gt; mutants followed by blue-white screening and PCR; however, &lt;i&gt;parAB&lt;/i&gt; mutant isolation with this method was low and often non-reproducible. To elucidate whether the prior presence of pDG-At in cells improves viable mutant isolation, we re-constructed pDG-At, designated as pDG-Atπ, using a vector with the R6K&lt;sub&gt;ϒ&lt;/sub&gt; origin of replication with its π-factor required for replication under &lt;i&gt;araBAD&lt;/i&gt; promoter. Results showed that pDG-Atπ can replicate in the absence of arabinose but can be cured by growing cells in glucose-rich media. Next, we repeated IncFIB's &lt;i&gt;parAB&lt;/i&gt; deletion using pDG1 but in cells carrying pDG-Atπ. Many white colonies were detected on X-Gal-supplemented media but none of them carried the target &lt;i&gt;parA&lt;/i&gt; mutation; however, ~80% of the white colonies lost IncFIB plasmid, while the others retained the wild-type plasmid. Similar results were obtained for IncX4 plasmid curing but also found that this method was not reproducible as the white colonies obtained after allelic replacement did not always result in plasmid curing or mutant isolation. This is the first report describing a simple blue/white screening method for plasmid curing that can avoid laborious screening procedures.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Plasmids play an important role in bacterial physiology, adaptation, evolution, virulence, and antibiotic resistance. An in-depth study of these roles partly depends on the generation of plasmid-free cells. This study shows that vector tools that target genes required for plasmid stability in the presence of an antitoxin-expressing helper plasmid are a viable approach to cure specific plasmids. Expression of bgaB from target plasmids can greatly facilitate visual detection of plasmid cured colonies avoiding time-consuming screening procedures. This approach can be refined for the development of a univ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142308143","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":"Discovery of benzo[c]phenanthridine derivatives with potent activity against multidrug-resistant <i>Mycobacterium tuberculosis</i>.","authors":"Yi Chu Liang, Zhiqi Sun, Chen Lu, Andréanne Lupien, Zhongliang Xu, Stefania Berton, Peng Xu, Marcel A Behr, Weibo Yang, Jim Sun","doi":"10.1128/spectrum.01246-24","DOIUrl":"10.1128/spectrum.01246-24","url":null,"abstract":"<p><p><i>Mycobacterium tuberculosis</i> (Mtb), the pathogen responsible for tuberculosis (TB), is the leading cause of bacterial disease-related death worldwide. Current antibiotic regimens for the treatment of TB remain dated and suffer from long treatment times as well as the development of drug resistance. As such, the search for novel chemical modalities that have selective or potent anti-Mtb properties remains an urgent priority, particularly against multidrug-resistant (MDR) Mtb strains. Herein, we design and synthesize 35 novel <u>b</u>enzo[c]<u>p</u>henanthridine <u>d</u>erivatives (BPDs). The two most potent compounds, BPD-6 and BPD-9, accumulated within the bacterial cell and exhibited strong inhibitory activity (MIC₉₀ ~2 to 10 µM) against multiple <i>Mycobacterium</i> strains while remaining inactive against a range of other Gram-negative and Gram-positive bacteria. BPD-6 and BPD-9 were also effective in reducing Mtb survival within infected macrophages, and BPD-9 reduced the burden of <i>Mycobacterium bovis</i> BCG in the lungs of infected mice. The two BPD compounds displayed comparable efficacy to rifampicin (RIF) against non-replicating Mtb (NR-Mtb). Importantly, BPD-6 and BPD-9 inhibited the growth of multiple MDR Mtb clinical isolates. Generation of BPD-9-resistant mutants identified the involvement of the Mmr efflux pump as an indirect resistance mechanism. The unique specificity of BPDs to <i>Mycobacterium</i> spp. and their efficacy against MDR Mtb isolates suggest a potential novel mechanism of action. The discovery of BPDs provides novel chemical scaffolds for anti-TB drug discovery.IMPORTANCEThe emergence of drug-resistant tuberculosis (TB) is a serious global health threat. There remains an urgent need to discover new antibiotics with unique mechanisms of action that are effective against drug-resistant <i>Mycobacterium tuberculosis</i> (Mtb). This study shows that novel semi-synthetic compounds can be derived from natural compounds to produce potent activity against Mtb. Importantly, the identified compounds have narrow spectrum activity against <i>Mycobacterium</i> species, including clinical multidrug-resistant (MDR) strains, are effective in infected macrophages and against non-replicating Mtb (NR-Mtb), and show anti-mycobacterial activity in mice. These new compounds provide promising chemical scaffolds to develop potent anti-Mtb drugs of the future.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372331","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":"Diversity of culturable bacterial isolates and their potential as antimicrobial against human pathogens from Afar region, Ethiopia.","authors":"Sisay Demisie, Dong-Chan Oh, Dawit Wolday, Tobias F Rinke de Wit, Adugna Abera, Geremew Tasew, Abebe Mekuria Shenkutie, Sisay Girma, Ketema Tafess","doi":"10.1128/spectrum.01810-24","DOIUrl":"10.1128/spectrum.01810-24","url":null,"abstract":"<p><p>Antimicrobial resistance is a growing global concern exacerbated by the scarcity of new medications and resistance to current antibiotics. Microbes from unexplored habitats are promising sources of natural products to combat this challenge. This study aimed to isolate bacteria producing secondary metabolites and assess their antimicrobial efficacy against human pathogens. Soil and liquid samples were collected from Afar region, Ethiopia. Bacterial isolates were obtained using standard serial dilution techniques. Antimicrobial activity was evaluated using agar plug and well diffusion methods. matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS) were conducted for the isolate exhibiting the highest antimicrobial activity. Secondary metabolites were extracted and analyzed using gas chromatography-mass spectra (GC-MS). In this study, 301 bacteria isolates were identified, of which 68 (22.6%) demonstrated antagonistic activity against at least one reference pathogen. Whole-genome sequencing revealed that Sl00103 belongs to the genus Bacillus, designated as Bacillus sp. Sl00103. The extract of Sl00103 showed zones of inhibition ranging between 17.17 ± 0.43 and 26.2 ± 0.4 mm against bacterial pathogens and 19.5 ± 0.44 to 21.0 ± 1.01 mm against <i>Candida albicans</i>. GC-MS analysis of ethyl acetate and <i>n</i>-hexane extracts identified major compounds including (R,R)-butane-2,3-diol; 3-isobutylhexahydropyrrolo[1,2a] pyrazine-1,4-dione; cyclo(L-prolyl-L-valine); and tetradecanoic acid, 12-methyl-, methyl ester; hexadecanoic acid, methyl ester among other. In conclusion, this study isolated several promising bacterial strains from the Afar region in Ethiopia, with strain Sl00103 (Bacillus sp. Sl00103) demonstrating notable antimicrobial and antioxidant activities and warranting further studies.</p><p><strong>Importance: </strong>Antimicrobial resistance (AMR) is an escalating global health threat affecting humans, animals, and the environment, underscoring the urgent need for alternative pathogen control methods. Natural products, particularly secondary metabolites from bacteria, continue to be a vital source of antibiotics. However, microbial habitats and metabolites in Africa remain largely unexplored. In this study, we isolated and screened bacteria from Ethiopia's Afar region, characterized by extreme conditions like high temperatures, volcanic activity, high salinity, and hot springs to identify potential bioactive compounds. We discovered diverse bacterial isolates with antimicrobial activity against various pathogens, including strain Sl00103 (Bacillus sp. Sl00103), which demonstrated significant antimicrobial and antioxidant activities. GC-MS analysis identified several antimicrobial compounds, highlighting strain Sl00103 as a promising source of secondary metabolites with potential pharmaceutical applications and warranting further investigation.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142372332","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":"Association of the gut microbiome and different phenotypes of COPD and asthma: a bidirectional Mendelian randomization study.","authors":"Zihan Wang, Jingge Qu, Chun Chang, Yongchang Sun","doi":"10.1128/spectrum.01760-24","DOIUrl":"10.1128/spectrum.01760-24","url":null,"abstract":"<p><p>Mounting evidence has revealed the association between gut microbiota and both chronic obstructive pulmonary disease (COPD) and asthma; however, the causal association between gut microbiota and specific disease phenotypes remains to be determined. This study employed bidirectional two-sample Mendelian randomization (MR) analyses to investigate the potential causal relationship between gut microbiota and these conditions. The research utilized genome-wide association study (GWAS) data from the MiBioGen consortium for gut microbiota and the integrative epidemiology unit (IEU) Open GWAS for these conditions. Four MR analysis methods were employed: the inverse variance weighted (IVW) test, MR-Egger, weighted median, and weighted mode methods. The IVW method results are considered the primary findings. Sensitivity analyses, including heterogeneity tests, horizontal pleiotropy analysis, and leave-one-out analysis, were used to enhance robustness. Our MR study identified eight gut microbiota taxa potentially associated with the risk of different types of COPD and asthma. These include two taxa for early-onset COPD: <i>Streptococcaceae</i> [odds ratio (OR) = 1.315, 95% confidence interval (CI) = 1.071-1.616, <i>P</i> = 0.009] and <i>Holdemanella</i> (OR = 1.199, 95% CI = 1.063-1.352, <i>P</i> = 0.003); three for later-onset COPD: <i>Acidaminococcaceae</i> (OR = 1.312, 95% CI = 1.098-1.567, <i>P</i> = 0.003), <i>Holdemania</i> (OR = 1.165, 95% CI = 1.039-1.305, <i>P</i> = 0.009), and <i>Marvinbryantia</i> (OR = 0.814, 95% CI = 0.697-0.951, <i>P</i> = 0.009); one for allergic asthma: <i>Butyricimonas</i> (OR = 0.794, 95% CI = 0.693-0.908, <i>P</i> = 0.001); and two for non-allergic asthma: <i>Clostridia</i> (OR = 1.255, 95% CI = 1.043-1.511, <i>P</i> = 0.016) and <i>Clostridiales</i> (OR = 1.256, 95% CI = 1.048-1.506, <i>P</i> = 0.014).IMPORTANCEIndividuals with diverse phenotypes of chronic obstructive pulmonary disease (COPD) and asthma exhibit different responses to the conventional \"one treatment fits all\" approach. Recent research has revealed the significant role of the gut-lung axis in both COPD and asthma. However, the specific impact of gut microbiota on different subtypes of these conditions remains poorly understood. Our study has identified eight gut microbiota that may be associated with the risk of different types of COPD and asthma. These findings provide evidence suggesting a potential causal relationship between gut microbiota and various phenotypes of COPD and asthma. This offers a new perspective on the origins of different disease phenotypes and points toward future exploration of phenotype-specific and personalized therapies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381170","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":"Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis.","authors":"Yuan Fang, Xiaohong Liu, Jie Ren, Xing Wang, Feihan Zhou, Shi Huang, Lei You, Yupei Zhao","doi":"10.1128/spectrum.00962-24","DOIUrl":"10.1128/spectrum.00962-24","url":null,"abstract":"<p><p>Pancreatic cancer, predominantly pancreatic ductal adenocarcinoma (PDAC), is one of the most malignant tumors of the digestive system. Emerging evidence suggests the involvement of the microbiome and metabolic substances in the development of PDAC, yet the results remain contradictory. This study aims to identify the alterations and relationships in intratumoral microbiome and metabolites in PDAC. We collected matched tumor and normal adjacent tissue (NAT) samples from 105 PDAC patients and performed a 6-year follow-up. 2bRAD-M sequencing, untargeted liquid chromatography-tandem mass spectrometry, and untargeted gas chromatography-mass spectrometry were performed. Compared with NATs, microbial α-diversity decreased in PDAC tumors. The relative abundance of <i>Staphylococcus aureus</i>, <i>Cutibacterium acnes,</i> and <i>Cutibacterium granulosum</i> was higher in PDAC tumor after adjusting for confounding factors body mass index and M stage, and the presence of <i>Ralstonia pickettii_B</i> was found associated with a worse overall survival. Metabolomic analysis revealed distinctive differences in composition between PDAC and NAT, with 553 discriminative metabolites identified. Differential metabolites were revealed to originate from the microbiota and showed significant interactions with shifted bacterial species through KO (KEGG Orthology) genes. These findings suggest that the PDAC microenvironment harbors unique microbial-derived enzymatic reactions, potentially influencing the occurrence and development of PDAC by modulating the levels of glycerol-3-phosphate, succinate, carbonate, and beta-alanine.</p><p><strong>Importance: </strong>We conducted a large sample-size pancreatic adenocarcinoma microbiome study using a novel microbiome sequencing method and two metabolomic assays. Two significant outcomes of our analysis are: (i) commensal opportunistic pathogens <i>Staphylococcus aureus</i>, <i>Cutibacterium acnes</i>, and <i>Cutibacterium granulosum</i> were enriched in pancreatic ductal adenocarcinoma (PDAC) tumors compared with normal adjacent tissues, and (ii) worse overall survival was found related to the presence of <i>Ralstonia pickettii_B</i>. Microbial species affect the tumorigenesis, metastasis, and prognosis of PDAC via unique microbe-enzyme-metabolite interaction. Thus, our study highlights the need for further investigation of the potential associations between pancreatic microbiota-derived omics signatures, which may drive the clinical transformation of microbiome-derived strategies toward therapy-targeted bacteria.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11540152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470086","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 <i>Streptococcus agalactiae</i> LytSR two-component regulatory system promotes vaginal colonization and virulence <i>in vivo</i>.","authors":"Hajar AlQadeeb, Murielle Baltazar, Adrian Cazares, Tiraput Poonpanichakul, Morten Kjos, Neil French, Aras Kadioglu, Marie O'Brien","doi":"10.1128/spectrum.01970-24","DOIUrl":"10.1128/spectrum.01970-24","url":null,"abstract":"<p><p><i>Streptococcus agalactiae</i> (or group B <i>Streptococcus</i>, GBS) is a leading cause of neonatal sepsis and meningitis globally. To sense and respond to variations in its environment, GBS possesses multiple two-component regulatory systems (TCSs), such as LytSR. Here, we aimed to investigate the role of LytSR in GBS pathogenicity. We generated an isogenic <i>lytS</i> knockout mutant in a clinical GBS isolate and used a combination of phenotypic <i>in vitro</i> assays and <i>in vivo</i> murine models to investigate the contribution of <i>lytS</i> to the colonization and invasive properties of GBS. Deletion of the <i>lytS</i> gene in the GBS chromosome resulted in significantly higher survival rates in mice during sepsis, accompanied by reduced bacterial loads in blood, lung, spleen, kidney, and brain tissues compared to infection with the wild-type strain. In a mouse model of GBS vaginal colonization, we also observed that the <i>lytS</i> knockout mutant was cleared more readily from the vaginal tract compared to its wild-type counterpart. Interestingly, lower levels of proinflammatory cytokines were found in the serum of mice infected with the <i>lytS</i> mutant. Our results demonstrate that the LytSR TCS plays a key role in GBS tissue invasion and pathogenesis, and persistence of mucosal colonization.IMPORTANCE<i>Streptococcus agalactiae (</i>group B <i>Streptococcus,</i> or GBS) is a common commensal of the female urogenital tract and one of WHO's priority pathogens. The bacterium has evolved mechanisms to adapt and survive in its host, many of which are regulated via two-component signal transduction systems (TCSs); however, the exact contributions of TCSs toward GBS pathogenicity remain largely obscure. We have constructed a TCS <i>lytS-</i>deficient mutant in a CC-17 hypervirulent GBS clinical isolate. Using murine models, we showed that LytSR regulatory system is essential for vaginal colonization via promoting biofilm production. We also observed that <i>lytS</i> deficiency led to significantly attenuated virulence properties and lower levels of proinflammatory cytokines in blood. Our findings are of significant importance in that they unveil a previously unreported role for LytSR in GBS and pave the way toward a better understanding of its ability to transition from an innocuous commensal to a deadly pathogen.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537067/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470105","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":"Cell wall nanoparticles from hyphae of <i>Alternaria infectoria</i> grown with caspofungin, nikkomycin, or pyroquilon trigger different activation profiles in macrophages.","authors":"Daniela Antunes, Rita Domingues, Mariana Cruz-Almeida, Lisa Rodrigues, Olga Borges, Agostinho Carvalho, Arturo Casadevall, Chantal Fernandes, Teresa Gonçalves","doi":"10.1128/spectrum.00645-24","DOIUrl":"10.1128/spectrum.00645-24","url":null,"abstract":"<p><p><i>Alternaria infectoria</i> causes opportunistic human infections and is a source of allergens leading to respiratory allergies. In this work, we prepared cell wall nanoparticles (CWNPs) as a novel approach to study macrophage immunomodulation by fungal hyphal cell walls. <i>A. infectoria</i> was grown in the presence of caspofungin, an inhibitor of β(1,3)-glucan synthesis; nikkomycin Z, an inhibitor of chitin synthases; and pyroquilon, an inhibitor of dihydroxynaphthalene (DHN)-melanin synthesis. Distinct CWNPs were obtained from these cultures, referred to as casCWNPs, nkCWNPs, and pyrCWNPs, respectively. CWNPs are round-shaped particles with a diameter of 70-200 nm diameter particles that when added to macrophages are taken up by membrane ruffling. CWNPs with no DHN-melanin and more glucan (pyrCWNPs) caused early macrophage activation and lowest viability, with the cells exhibiting ultrastructural modifications such as higher vacuolization and formation of autophagy-like structures. CasCWNPs promoted the highest tumor necrosis factor alpha (TNF-α) and interleukin 1 beta (IL-1β) increase, also resulting in the release of partially degraded chitin, an aspect never observed in macrophage-like cells and fungi. After 6 h of interaction with CWNPs, only half were viable, except with control CWNPs. Overall, this work indicates that compounds that modify the fungal cell wall led to CWNPs with new properties that may have implications for the effects of drugs during antifungal therapy. CWNPs provide a new tool to study the interaction of hyphal fungal cell wall components with phagocytic cells and enable to show how the modification of cell wall components in <i>A. infectoria</i> can modulate the response by macrophages.IMPORTANCE<i>Alternaria</i> species are ubiquitous environmental fungi to which the human host can continuously be exposed, through the inhalation of fungal spores but also of fragments of hyphae, from desegregated mycelia. These fungi are involved in hypersensitization and severe respiratory allergies, such as asthma, and can cause opportunistic infections in immunodepressed human host leading to severe disease. The first fungal structures to interact with the host cells are the cell wall components, and their modulation leads to differential immune responses. Here, we show that fungal cells grown with cell wall inhibitors led to cell wall nanoparticles with new properties in their interaction with macrophages. With this strategy, we overcame the limitation of <i>in vitro</i> assays interacting with filamentous fungi and showed that the absence of DNH-melanin leads to higher virulence, while caspofungin leads to cells walls that trigger higher hydrolysis of chitin and higher production of cytokines.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537108/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350115","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":"Extensive genomic study characterizing three <i>Paracoccaceae</i> populations and revealing <i>Pseudogemmobacter lacusdianii</i> sp. nov. and <i>Paracoccus broussonetiae</i> sp. nov.","authors":"Yang Deng, Cong-Jian Li, Jing Zhang, Wei-Hong Liu, Li-Yan Yu, Yu-Qin Zhang","doi":"10.1128/spectrum.01088-24","DOIUrl":"10.1128/spectrum.01088-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Bacteria within the family &lt;i&gt;Paracoccaceae&lt;/i&gt; show promising potential for applications in various fields, garnering significant research attention. Three Gram stain-negative bacteria, strains CPCC 101601&lt;sup&gt;T&lt;/sup&gt;, CPCC 101403&lt;sup&gt;T&lt;/sup&gt;, and CPCC 100767, were isolated from diverse environments: freshwater, rhizosphere soil of &lt;i&gt;Broussonetia papyrifera&lt;/i&gt;, and the phycosphere, respectively. Analysis of their 16S rRNA gene sequences, compared with those in the GenBank database, indicated that they belong to the family &lt;i&gt;Paracoccaceae&lt;/i&gt;, with nucleotide similarities of 92.5%-99.9% to all of the &lt;i&gt;Paracoccaceae&lt;/i&gt; members with valid taxonomic names. Phylogenetic studies based on 16S rRNA gene and whole-genome sequences identified CPCC 101601&lt;sup&gt;T&lt;/sup&gt; as a member of the genus &lt;i&gt;Pseudogemmobacter&lt;/i&gt;, CPCC 101403&lt;sup&gt;T&lt;/sup&gt; belonging to the genus &lt;i&gt;Paracoccus&lt;/i&gt;, and CPCC 100767 as part of the genus &lt;i&gt;Gemmobacter&lt;/i&gt;. Notably, genomic analysis using average nucleotide identity (ANI; &lt;95%) and digital DNA-DNA hybridization (dDDH; &lt;70%) with their closely related strains suggested that CPCC 101601&lt;sup&gt;T&lt;/sup&gt; and CPCC 101403&lt;sup&gt;T&lt;/sup&gt; represent new species within their respective genera. Conversely, CPCC 100767 exhibited high ANI (98.5%) and dDDH (87.4%) values with &lt;i&gt;Gemmobacter fulvus&lt;/i&gt; con5&lt;sup&gt;T&lt;/sup&gt;, indicating it belongs to this already recognized species. The in-depth genomic analysis revealed that strains CPCC 101601&lt;sup&gt;T&lt;/sup&gt;, CPCC 101403&lt;sup&gt;T&lt;/sup&gt;, and CPCC 100767 harbor key genes related to the pathways for denitrifying, MA utilization, and polyhydroxyalkanoate biosynthesis. Moreover, genotyping and phenotyping analysis confirmed that strain CPCC 100767 has the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid, whereas CPCC 101601&lt;sup&gt;T&lt;/sup&gt; can only perform the former bioprocess.IMPORTANCEBased on polyphasic taxonomic study, two new species, &lt;i&gt;Pseudogemmobacter lacusdianii&lt;/i&gt; and &lt;i&gt;Paracoccus broussonetiae,&lt;/i&gt; affiliated with the family &lt;i&gt;Paracoccaceae&lt;/i&gt; were identified. This expands our understanding of the family &lt;i&gt;Paracoccaceae&lt;/i&gt; and provides new microbial materials for further studies. Modern genomic techniques such as average nucleotide identity and digital DNA-DNA hybridization were utilized to determine species affiliations. These methods offer more precise results than traditional classification mainly based on 16S rRNA gene analysis. Beyond classification of these strains, the research delved into their genomes and discovered key genes related to denitrification, MA utilization, and polyhydroxyalkanoate biosynthesis. The identification of these genes provides a molecular basis for understanding the environmental roles of these strains. Particularly, strain CPCC 100767 demonstrated the ability to convert atmospheric nitrogen into ammonia and produce 5-aminolevulinic acid. These bioprocess capabilities are of significant practical value, such as in ag","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537045/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350132","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":"Comparison of the mechanism of antimicrobial action of the gold(I) compound auranofin in Gram-positive and Gram-negative bacteria.","authors":"Laísa Quadros Barsé, Agnes Ulfig, Marharyta Varatnitskaya, Melissa Vázquez-Hernández, Jihyun Yoo, Astrid M Imann, Natalie Lupilov, Marina Fischer, Katja Becker, Julia E Bandow, Lars I Leichert","doi":"10.1128/spectrum.00138-24","DOIUrl":"10.1128/spectrum.00138-24","url":null,"abstract":"<p><p>While highly effective at killing Gram-positive bacteria, auranofin lacks significant activity against Gram-negative species for reasons that largely remain unclear. Here, we aimed to elucidate the molecular mechanisms underlying the low susceptibility of the Gram-negative model organism <i>Escherichia coli</i> to auranofin when compared to the Gram-positive model organism <i>Bacillus subtilis</i>. The proteome response of <i>E. coli</i> exposed to auranofin suggests a combination of inactivation of thiol-containing enzymes and the induction of systemic oxidative stress. Susceptibility tests in <i>E. coli</i> mutants lacking proteins upregulated upon auranofin treatment suggested that none of them are directly involved in <i>E. coli</i>'s high tolerance to auranofin. <i>E. coli</i> cells lacking the efflux pump component TolC were more sensitive to auranofin treatment, but not to an extent that would fully explain the observed difference in susceptibility of Gram-positive and Gram-negative organisms. We thus tested whether <i>E. coli</i>'s thioredoxin reductase (TrxB) is inherently less sensitive to auranofin than TrxB from <i>B. subtilis</i>, which was not the case. However, <i>E. coli</i> strains lacking the low-molecular-weight thiol glutathione, but not glutathione reductase, showed a high susceptibility to auranofin. Bacterial cells expressing the genetically encoded redox probe roGFP2 allowed us to observe the oxidation of cellular protein thiols <i>in situ</i>. Based on our findings, we hypothesize that auranofin leads to a global disturbance in the cellular thiol redox homeostasis in bacteria, but Gram-negative bacteria are inherently more resistant due to the presence of drug export systems and high cellular concentrations of glutathione.IMPORTANCEAuranofin is an FDA-approved drug for the treatment of rheumatoid arthritis. However, it has also high antibacterial activity, in particular against Gram-positive organisms. In the current antibiotics crisis, this would make it an ideal candidate for drug repurposing. However, its much lower activity against Gram-negative organisms prevents its broad-spectrum application. Here we show that, on the level of the presumed target, there is no difference in susceptibility between Gram-negative and Gram-positive species: thioredoxin reductases from both <i>Escherichia coli</i> and <i>Bacillus subtilis</i> are equally inhibited by auranofin. In both species, auranofin treatment leads to oxidative protein modification on a systemic level, as monitored by proteomics and the genetically encoded redox probe roGFP2. The single largest contributor to <i>E. coli</i>'s relative resistance to auranofin seems to be the low-molecular-weight thiol glutathione, which is absent in <i>B. subtilis</i> and other Gram-positive species.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391739","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}