Vera Radisic, Didrik H. Grevskott, Nadja Junghardt, Lise Øvreås, Nachiket P. Marathe
This study aimed to understand the antibiotic resistance prevalence among Enterococcus spp. from raw and treated sewage in Bergen city, Norway. In total, 517 Enterococcus spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with Enterococcus faecium as the most prevalent (n = 492) species. E. faecium strains (n = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. E. faecium strains (n = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) E. faecium strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the Enterococcus spp. strains (n = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR Enterococcus spp. strains are entering the marine environment through treated sewage.
{"title":"Multidrug-resistant Enterococcus faecium strains enter the Norwegian marine environment through treated sewage","authors":"Vera Radisic, Didrik H. Grevskott, Nadja Junghardt, Lise Øvreås, Nachiket P. Marathe","doi":"10.1002/mbo3.1397","DOIUrl":"10.1002/mbo3.1397","url":null,"abstract":"<p>This study aimed to understand the antibiotic resistance prevalence among <i>Enterococcus</i> spp. from raw and treated sewage in Bergen city, Norway. In total, 517 <i>Enterococcus</i> spp. isolates were obtained from raw and treated sewage from five sewage treatment plants (STPs) over three sampling occasions, with <i>Enterococcus faecium</i> as the most prevalent (<i>n</i> = 492) species. <i>E. faecium</i> strains (<i>n</i> = 307) obtained from the influent samples, showed the highest resistance against quinupristin/dalfopristin (67.8%). We observed reduced susceptibility to erythromycin (30.6%) and tetracycline (6.2%) in these strains. <i>E. faecium</i> strains (<i>n</i> = 185) obtained from the effluent samples showed highest resistance against quinupristin/dalfopristin (68.1%) and reduced susceptibility to erythromycin (24.9%) and tetracycline (8.6%). We did not detect resistance against last-resort antibiotics, such as linezolid, vancomycin, and tigecycline in any of the strains. Multidrug-resistant (MDR) <i>E. faecium</i> strains were detected in both influent (2.3%) and effluent (2.2%) samples. Whole genome sequencing of the <i>Enterococcus</i> spp. strains (<i>n</i> = 25) showed the presence of several antibiotic resistance genes, conferring resistance against aminoglycosides, tetracyclines, and macrolides, as well as several virulence genes and plasmid replicons. Two sequenced MDR strains from the effluents belonged to the hospital-associated clonal complex 17 and carried multiple virulence genes. Our study demonstrates that clinically relevant MDR <i>Enterococcus</i> spp. strains are entering the marine environment through treated sewage.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1397","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140028420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass can also be estimated by applying quantitative sequencing with information on rRNA gene copy numbers in genomes; however, information on rRNA gene copy numbers is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this study, we report an alternative approach that is more appropriate than the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.
{"title":"The copy number of the eukaryotic rRNA gene can be counted comprehensively","authors":"Akinori Yabuki, Tatsuhiko Hoshino, Tamiko Nakamura, Keiko Mizuno","doi":"10.1002/mbo3.1399","DOIUrl":"10.1002/mbo3.1399","url":null,"abstract":"<p>Gene sequence has been widely used in molecular ecology. For instance, the ribosomal RNA (rRNA) gene has been widely used as a biological marker to understand microbial communities. The variety of the detected rRNA gene sequences reflects the diversity of the microorganisms existing in the analyzed sample. Their biomass can also be estimated by applying quantitative sequencing with information on rRNA gene copy numbers in genomes; however, information on rRNA gene copy numbers is still limited. Especially, the copy number in microbial eukaryotes is much less understood than that of prokaryotes, possibly because of the large and complex structure of eukaryotic genomes. In this study, we report an alternative approach that is more appropriate than the existing method of quantitative sequencing and demonstrate that the copy number of eukaryotic rRNA can be measured efficiently and comprehensively. By applying this approach widely, information on the eukaryotic rRNA copy number can be determined, and their community structures can be depicted and compared more efficiently.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1399","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xi Ye, Bindusmita Paul, Joyce Mo, Eric C. Reynolds, Debnath Ghosal, Paul D. Veith
Prevotella intermedia, a Gram-negative bacterium from the Bacteroidota phylum, is associated with periodontitis. Other species within this phylum are known to possess the general O-glycosylation system. The O-glycoproteome has been characterized in several species, including Tannerella forsythia, Porphyromonas gingivalis, and Flavobacterium johnsoniae. In our study, we used electron cryotomography (cryoET) and glycoproteomics to reveal the ultrastructure of P. intermedia and characterize its O-glycoproteome. Our cryoET analysis unveiled the ultrastructural details of the cell envelope and outer membrane vesicles (OMVs) of P. intermedia. We observed an electron-dense surface layer surrounding both cells and OMVs. The OMVs were often large (>200 nm) and presented two types, with lumens being either electron-dense or translucent. LC-MS/MS analyses of P. intermedia fractions led to the identification of 1655 proteins, which included 62 predicted T9SS cargo proteins. Within the glycoproteome, we identified 443 unique O-glycosylation sites within 224 glycoproteins. Interestingly, the O-glycosylation motif exhibited a broader range than reported in other species, with O-glycosylation found at D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P). We identified a single O-glycan with a delta mass of 1531.48 Da. Its sequence was determined by MS2 and MS3 analyses using both collision-induced dissociation and high-energy collisional dissociation fragmentation modes. After partial deglycosylation with trifluoromethanesulfonic acid, the O-glycan sequence was confirmed to be dHex-dHex-HexNAc (HPO3-C6H12O5)-dHex-Hex-HexA-Hex(dHex). Bioinformatic analyses predicted the localization of O-glycoproteins, with 73 periplasmic proteins, 53 inner membrane proteins, 52 lipoproteins, 26 outer membrane proteins, and 14 proteins secreted by the T9SS.
{"title":"Ultrastructural and glycoproteomic characterization of Prevotella intermedia: Insights into O-glycosylation and outer membrane vesicles","authors":"Xi Ye, Bindusmita Paul, Joyce Mo, Eric C. Reynolds, Debnath Ghosal, Paul D. Veith","doi":"10.1002/mbo3.1401","DOIUrl":"10.1002/mbo3.1401","url":null,"abstract":"<p><i>Prevotella intermedia</i>, a Gram-negative bacterium from the Bacteroidota phylum, is associated with periodontitis. Other species within this phylum are known to possess the general <i>O</i>-glycosylation system. The <i>O</i>-glycoproteome has been characterized in several species, including <i>Tannerella forsythia</i>, <i>Porphyromonas gingivalis</i>, and <i>Flavobacterium johnsoniae</i>. In our study, we used electron cryotomography (cryoET) and glycoproteomics to reveal the ultrastructure of <i>P. intermedia</i> and characterize its <i>O</i>-glycoproteome. Our cryoET analysis unveiled the ultrastructural details of the cell envelope and outer membrane vesicles (OMVs) of <i>P. intermedia</i>. We observed an electron-dense surface layer surrounding both cells and OMVs. The OMVs were often large (>200 nm) and presented two types, with lumens being either electron-dense or translucent. LC-MS/MS analyses of <i>P. intermedia</i> fractions led to the identification of 1655 proteins, which included 62 predicted T9SS cargo proteins. Within the glycoproteome, we identified 443 unique <i>O</i>-glycosylation sites within 224 glycoproteins. Interestingly, the <i>O</i>-glycosylation motif exhibited a broader range than reported in other species, with <i>O</i>-glycosylation found at D(S/T)(A/I/L/M/T/V/S/C/G/F/N/E/Q/D/P). We identified a single <i>O</i>-glycan with a delta mass of 1531.48 Da. Its sequence was determined by MS2 and MS3 analyses using both collision-induced dissociation and high-energy collisional dissociation fragmentation modes. After partial deglycosylation with trifluoromethanesulfonic acid, the <i>O</i>-glycan sequence was confirmed to be dHex-dHex-HexNAc (HPO<sub>3</sub>-C<sub>6</sub>H<sub>12</sub>O<sub>5</sub>)-dHex-Hex-HexA-Hex(dHex). Bioinformatic analyses predicted the localization of <i>O</i>-glycoproteins, with 73 periplasmic proteins, 53 inner membrane proteins, 52 lipoproteins, 26 outer membrane proteins, and 14 proteins secreted by the T9SS.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1401","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139972635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Matthew Myles, Heba Barnawi, Mahmoud Mahmoudpour, Sargon Shlimon, Adrienne Chang, Daniel Zimmermann, Chiwon Choi, Najwa Zebian, Carole Creuzenet
Campylobacter jejuni is a commensal in many animals but causes diarrhea in humans. Its polysaccharide capsule contributes to host colonization and virulence in a strain- and model-specific manner. We investigated if the capsule and its heptose are important for interactions of strain NCTC 11168 with various hosts and their innate immune defenses. We determined that they support bacterial survival in Drosophila melanogaster and enhance virulence in Galleria mellonella. We showed that the capsule had limited antiphagocytic activity in human and chicken macrophages, decreased adherence to chicken macrophages, and decreased intracellular survival in both macrophages. In contrast, the heptose increased uptake by chicken macrophages and supported adherence to human macrophages and survival within them. While the capsule triggered nitric oxide production in chicken macrophages, the heptose mitigated this and protected against nitrosative assault. Finally, the C. jejuni strain NCTC 11168 elicited strong cytokine production in both macrophages but quenched ROS production independently from capsule and heptose, and while the capsule and heptose did not protect against oxidative assault, they favored growth in biofilms under oxidative stress. This study shows that the wild-type capsule with its heptose is optimized to resist innate defenses in strain NCTC 11168 often via antagonistic effects of the capsule and its heptose.
{"title":"Effect of the polysaccharide capsule and its heptose on the resistance of Campylobacter jejuni to innate immune defenses","authors":"Matthew Myles, Heba Barnawi, Mahmoud Mahmoudpour, Sargon Shlimon, Adrienne Chang, Daniel Zimmermann, Chiwon Choi, Najwa Zebian, Carole Creuzenet","doi":"10.1002/mbo3.1400","DOIUrl":"10.1002/mbo3.1400","url":null,"abstract":"<p><i>Campylobacter jejuni</i> is a commensal in many animals but causes diarrhea in humans. Its polysaccharide capsule contributes to host colonization and virulence in a strain- and model-specific manner. We investigated if the capsule and its heptose are important for interactions of strain NCTC 11168 with various hosts and their innate immune defenses. We determined that they support bacterial survival in <i>Drosophila melanogaster</i> and enhance virulence in <i>Galleria mellonella</i>. We showed that the capsule had limited antiphagocytic activity in human and chicken macrophages, decreased adherence to chicken macrophages, and decreased intracellular survival in both macrophages. In contrast, the heptose increased uptake by chicken macrophages and supported adherence to human macrophages and survival within them. While the capsule triggered nitric oxide production in chicken macrophages, the heptose mitigated this and protected against nitrosative assault. Finally, the <i>C. jejuni</i> strain NCTC 11168 elicited strong cytokine production in both macrophages but quenched ROS production independently from capsule and heptose, and while the capsule and heptose did not protect against oxidative assault, they favored growth in biofilms under oxidative stress. This study shows that the wild-type capsule with its heptose is optimized to resist innate defenses in strain NCTC 11168 often via antagonistic effects of the capsule and its heptose.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1400","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139906018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chava L. Weitzman, Dana M. Hawley, Bahman Rostama, Meghan May, Lisa K. Belden
DNA-based methods to measure the abundance and relative abundance of bacterial taxa can be skewed by the presence of dead or transient bacteria. Consequently, the active, functional members of the community may be a small subset of the detected bacterial community. This mismatch can make inferences about the roles of communities in host health difficult and can be particularly problematic for low-abundance microbiomes, such as those on conjunctival surfaces. In this study, we manipulated bacterial communities on bird conjunctiva with a bacteriostatic antibiotic, reducing bacterial activity while preserving viability, to identify the living and active conjunctival communities using comparisons of 16S ribosomal DNA and RNA in paired samples. DNA amplicons included many more sequence variants than RNA amplicons from the same communities, with consequent differences in diversity. While we found that changes in communities in DNA samples broadly represent shifts in the living (RNA-amplicon) communities, assessments of community function may be better described by RNA samples, reducing background noise from dead cells. We further used these data to test RNA:DNA ratios, used in other microbiological contexts, to detect shifts in bacterial activity after antibiotic disruption but were unable to detect changes in bacterial activity with this method.
以 DNA 为基础的细菌分类群丰度和相对丰度测量方法可能会因死亡细菌或瞬时细菌的存在而产生偏差。因此,群落中活跃的功能性成员可能只是检测到的细菌群落的一小部分。这种不匹配会使推断群落在宿主健康中的作用变得困难,对于低丰度微生物群落(如结膜表面的微生物群落)尤其如此。在这项研究中,我们用一种抑菌抗生素处理鸟类结膜上的细菌群落,在保持活力的同时降低细菌活性,从而通过比较配对样本中的 16S 核糖体 DNA 和 RNA 来确定活的和活跃的结膜群落。与来自相同群落的 RNA 扩增片段相比,DNA 扩增片段包含更多的序列变异,因此多样性也存在差异。我们发现,DNA 样本中群落的变化大致代表了活体(RNA 扩增子)群落的变化,而 RNA 样本可以更好地描述群落功能,减少死亡细胞带来的背景噪音。我们进一步利用这些数据测试了 RNA 与 DNA 的比率,这种比率在其他微生物学环境中被用来检测抗生素破坏后细菌活性的变化,但这种方法无法检测到细菌活性的变化。
{"title":"Characterizing living ocular bacterial communities and the effects of antibiotic perturbation in house finches","authors":"Chava L. Weitzman, Dana M. Hawley, Bahman Rostama, Meghan May, Lisa K. Belden","doi":"10.1002/mbo3.1398","DOIUrl":"https://doi.org/10.1002/mbo3.1398","url":null,"abstract":"<p>DNA-based methods to measure the abundance and relative abundance of bacterial taxa can be skewed by the presence of dead or transient bacteria. Consequently, the active, functional members of the community may be a small subset of the detected bacterial community. This mismatch can make inferences about the roles of communities in host health difficult and can be particularly problematic for low-abundance microbiomes, such as those on conjunctival surfaces. In this study, we manipulated bacterial communities on bird conjunctiva with a bacteriostatic antibiotic, reducing bacterial activity while preserving viability, to identify the living and active conjunctival communities using comparisons of 16S ribosomal DNA and RNA in paired samples. DNA amplicons included many more sequence variants than RNA amplicons from the same communities, with consequent differences in diversity. While we found that changes in communities in DNA samples broadly represent shifts in the living (RNA-amplicon) communities, assessments of community function may be better described by RNA samples, reducing background noise from dead cells. We further used these data to test RNA:DNA ratios, used in other microbiological contexts, to detect shifts in bacterial activity after antibiotic disruption but were unable to detect changes in bacterial activity with this method.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1398","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139682875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Stephen Mark Edward Fordham, Magdalena Barrow, Anna Mantzouratou, Elizabeth Sheridan
Escherichia coli and Klebsiella pneumoniae isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long-standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long-read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance-encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239-bp FIB(K) pKBM1, from the K. pneumoniae strain, additionally encoded the five AMR genes: sul2, strA, strB, blaTEM-1B, and blaCTX-M-15. A multimeric array of AMR genes and IS26 insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3-307_typeA, commonly identified in K. pneumoniae ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.
从同一导尿管尿液样本(CSU)中分离出的大肠埃希菌和肺炎克雷伯菌具有相同的抗菌药敏感性。这两种菌株都是从一名长期留置导尿管的患者体内分离出来的。每个分离株在培养后都提取了 DNA。利用纳米孔长读数测序技术构建了每株菌株的质粒和染色体,以确定抗性编码质粒的潜在水平传播以及抗性基因与插入序列之间的关系。从泌尿微生物群中的抗性菌株中提取的质粒仍然特征不清。在每个菌株的质粒中都发现了相同的 11 个抗菌素耐药性(AMR)基因。来自肺炎克氏菌菌株的 185,239-bp FIB(K) pKBM1 还编码了五个 AMR 基因:Sul2、strA、strB、blaTEM-1B 和 blaCTX-M-15。在两个分离株的质粒中都发现了多聚 AMR 基因阵列和 IS26 插入序列。每个分离物的两个质粒都很相似。质粒的水平转移和随后的质粒重排很可能发生在感染过程中。此外,质粒中的抗性区域与国际流行的质粒 pKPN3-307_typeA(通常在肺炎双球菌 ST307 中发现)具有相似性。导管病人体内生物膜的形成可能使菌株之间的细胞密切接触。耐药基因可能会发生水平传播,导致多微生物感染。
{"title":"Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co-infection using long-read nanopore sequencing","authors":"Stephen Mark Edward Fordham, Magdalena Barrow, Anna Mantzouratou, Elizabeth Sheridan","doi":"10.1002/mbo3.1396","DOIUrl":"https://doi.org/10.1002/mbo3.1396","url":null,"abstract":"<p><i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> isolates presenting with the same antimicrobial susceptibility profile were recovered from the same catheter sample of urine (CSU). Both strains were recovered from a patient with a long-standing indwelling urinary catheter. Each isolate had its DNA extracted following culture. Nanopore long-read sequencing was used to build the plasmids and chromosomes from each strain to closure to discern the potential horizontal propagation of resistance-encoding plasmids and the relationship between resistance genes and insertion sequences. Plasmids derived from resistance strains in the urinary microbiota remain poorly characterized. The same 11 antimicrobial resistance (AMR) genes were found in plasmids from each strain. The 185,239-bp FIB(K) pKBM1, from the <i>K. pneumoniae</i> strain, additionally encoded the five AMR genes: <i>sul2, strA, strB, bla</i><sub>TEM-1B</sub>, and <i>bla</i><sub>CTX-M-15</sub>. A multimeric array of AMR genes and IS<i>26</i> insertion sequences were found in the plasmids from both isolates. Both plasmids from each isolate were similar. Horizontal transfer of plasmids, followed by subsequent plasmid rearrangement, is likely to have occurred during infection. Furthermore, the resistance region in the plasmids shared similarity against the internationally prevalent plasmid, pKPN3-307_typeA, commonly identified in <i>K. pneumoniae</i> ST307. Biofilm formation in catheterized patients may allow close cell contact between strains. Horizontal propagation of resistance genes may occur, leading to polymicrobial infections.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1396","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139488617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Laura Marquardt, Federica Andreoni, Mathilde Boumasmoud, Tiziano A. Schweizer, Dorothea M. Heuberger, Elena Parietti, Sanne Hertegonne, Jana Epprecht, Dario Mattle, Anna K. Raez, Ewerton Marques-Maggio, Reto A. Schuepbach, Barbara Hasse, Srikanth Mairpady-Shambat, Silvio D. Brugger, Annelies S. Zinkernagel
Group A streptococcal (GAS; aka Streptococcus pyogenes) meningitis is a fulminant disease associated with high morbidity and mortality. To elucidate the mechanisms underlying the invasiveness of GAS in meningitis, we compared GAS isolates derived from five cases of meningitis to otitis and colonizing isolates. We did not observe differences in adherence to and invasion of human brain microvascular endothelial cells, virulence factors activity, or barrier disruption. Whole genome sequencing did not reveal particular invasiveness traits. Most patients previously suffered from otitis media suggesting that meningitis likely resulted from a continuous spread of the infection rather than being attributable to changes in the pathogen's virulence.
A 组链球菌(GAS)脑膜炎导致很高的发病率和死亡率。为了阐明 GAS 在脑膜炎中的侵袭性,我们将 5 株 GAS 脑膜炎分离株与耳炎和定植分离株进行了比较。所有菌株的基因和毒力特征都相当,这表明脑膜炎很可能是由感染的持续传播引起的。
{"title":"Group A Streptococcus strains causing meningitis without distinct invasive phenotype","authors":"Laura Marquardt, Federica Andreoni, Mathilde Boumasmoud, Tiziano A. Schweizer, Dorothea M. Heuberger, Elena Parietti, Sanne Hertegonne, Jana Epprecht, Dario Mattle, Anna K. Raez, Ewerton Marques-Maggio, Reto A. Schuepbach, Barbara Hasse, Srikanth Mairpady-Shambat, Silvio D. Brugger, Annelies S. Zinkernagel","doi":"10.1002/mbo3.1394","DOIUrl":"10.1002/mbo3.1394","url":null,"abstract":"<p>Group A streptococcal (GAS; aka <i>Streptococcus pyogenes</i>) meningitis is a fulminant disease associated with high morbidity and mortality. To elucidate the mechanisms underlying the invasiveness of GAS in meningitis, we compared GAS isolates derived from five cases of meningitis to otitis and colonizing isolates. We did not observe differences in adherence to and invasion of human brain microvascular endothelial cells, virulence factors activity, or barrier disruption. Whole genome sequencing did not reveal particular invasiveness traits. Most patients previously suffered from otitis media suggesting that meningitis likely resulted from a continuous spread of the infection rather than being attributable to changes in the pathogen's virulence.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139094480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lesley Sitter, Marion Schoof, Travis R. Glare, Murray P. Cox, Peter C. Fineran, Paul P. Gardner, Mark R. H. Hurst
A soil bacterium in the Serratia genus, carrying a 153 kb conjugative amber disease-associated plasmid (pADAP), is commercially exploited for population control of the New Zealand endemic pest beetle Costelytra giveni (Coleoptera: Scarabaeidae). The main insecticidal elements are an anti-feeding prophage and the Sep ABC toxin complex (Tc). Homologs of pADAP, encoding variant Tcs, convey different beetle disease phenotypes. To investigate the correlation between variable bioactivity and the Tc variant, 76 Serratia plasmids were sequenced, resulting in the identification of four additional tc variants. All Serratia tc variants were found to be colocated with a conserved type 1 sef fimbrial-like operon, indicating a conserved sef-tc genetic island not observed outside of the Serratia genus. The conserved co-location of the fimbrial and tc genes suggests the fimbriae somehow contribute to the lifestyle of Tc-producing cells. Expression of the sef operon in a fim-null Escherichia coli strain revealed fimbriae presence while a constructed sef-deficient mutant showed no reduction of virulence or host colonization. Although no detectable contribution of Sef to amber disease in C. giveni was observed, the Sef adhesin sequences clustered similarly to the Serratia species encoding it, suggesting Sef has a species-specific function.
这篇文章描述了在感染甲虫幼虫 Costelytra giveni 的致病性沙雷氏菌中发现的与 ABC 毒素复合物(Tc)始终位于一起的 Sef 拟缘体的特征。在任何已知的 Tc 系统中,都没有记录过缘膜与 Tc 之间的这种独特联系,这就提出了一个问题:只有在编码 Tc 的细菌中才能维持这些缘膜的高选择压力。我们的研究还试图利用生物信息学、克隆和实验方法来描述 Sef 纤膜的结构和功能。
{"title":"Serratia-based toxin cluster elements are associated with a type I fimbria","authors":"Lesley Sitter, Marion Schoof, Travis R. Glare, Murray P. Cox, Peter C. Fineran, Paul P. Gardner, Mark R. H. Hurst","doi":"10.1002/mbo3.1395","DOIUrl":"10.1002/mbo3.1395","url":null,"abstract":"<p>A soil bacterium in the <i>Serratia</i> genus, carrying a 153 kb conjugative amber disease-associated plasmid (pADAP), is commercially exploited for population control of the New Zealand endemic pest beetle <i>Costelytra giveni</i> (Coleoptera: Scarabaeidae). The main insecticidal elements are an anti-feeding prophage and the Sep ABC toxin complex (Tc). Homologs of pADAP, encoding variant Tcs, convey different beetle disease phenotypes. To investigate the correlation between variable bioactivity and the Tc variant, 76 <i>Serratia</i> plasmids were sequenced, resulting in the identification of four additional <i>tc</i> variants. All <i>Serratia tc</i> variants were found to be colocated with a conserved type 1 <i>sef</i> fimbrial-like operon, indicating a conserved <i>sef-tc</i> genetic island not observed outside of the <i>Serratia</i> genus. The conserved co-location of the fimbrial and <i>tc</i> genes suggests the fimbriae somehow contribute to the lifestyle of Tc-producing cells. Expression of the <i>sef</i> operon in a fim-null <i>Escherichia coli</i> strain revealed fimbriae presence while a constructed <i>sef</i>-deficient mutant showed no reduction of virulence or host colonization. Although no detectable contribution of Sef to amber disease in <i>C. giveni</i> was observed, the Sef adhesin sequences clustered similarly to the <i>Serratia</i> species encoding it, suggesting Sef has a species-specific function.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1395","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139094476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isini Buthgamuwa, Jane C. Fenelon, Alice Roser, Haley Meer, Stephen D. Johnston, Ashley M. Dungan
Indigenous gut microbial communities (microbiota) play critical roles in health and may be especially important for the mother and fetus during pregnancy. Monotremes, such as the short-beaked echidna, have evolved to lay and incubate an egg, which hatches in their pouch where the young feeds. Since both feces and eggs pass through the cloaca, the fecal microbiota of female echidnas provides an opportunity for vertical transmission of microbes to their offspring. Here, we characterize the gut/fecal microbiome of female short-beaked echidnas and gain a better understanding of the changes that may occur in their microbiome as they go through pregnancy. Fecal samples from four female and five male echidnas were obtained from the Currumbin Wildlife Sanctuary in Queensland and sequenced to evaluate bacterial community structure. We identified 25 core bacteria, most of which were present in male and female samples. Genera such as Fusobacterium, Bacteroides, Escherichia-Shigella, and Lactobacillus were consistently abundant, regardless of sex or gestation stage, accounting for 58.00% and 56.14% of reads in male and female samples, respectively. The echidna microbiome remained stable across the different gestation stages, though there was a significant difference in microbiota composition between male and female echidnas. This study is the first to describe the microbiome composition of short-beaked echidnas across reproductive phases and allows the opportunity for this novel information to be used as a metric of health to aid in the detection of diseases triggered by microbiota dysbiosis.
{"title":"Gut microbiota in the short-beaked echidna (Tachyglossus Aculeatus) shows stability across gestation","authors":"Isini Buthgamuwa, Jane C. Fenelon, Alice Roser, Haley Meer, Stephen D. Johnston, Ashley M. Dungan","doi":"10.1002/mbo3.1392","DOIUrl":"https://doi.org/10.1002/mbo3.1392","url":null,"abstract":"<p>Indigenous gut microbial communities (microbiota) play critical roles in health and may be especially important for the mother and fetus during pregnancy. Monotremes, such as the short-beaked echidna, have evolved to lay and incubate an egg, which hatches in their pouch where the young feeds. Since both feces and eggs pass through the cloaca, the fecal microbiota of female echidnas provides an opportunity for vertical transmission of microbes to their offspring. Here, we characterize the gut/fecal microbiome of female short-beaked echidnas and gain a better understanding of the changes that may occur in their microbiome as they go through pregnancy. Fecal samples from four female and five male echidnas were obtained from the Currumbin Wildlife Sanctuary in Queensland and sequenced to evaluate bacterial community structure. We identified 25 core bacteria, most of which were present in male and female samples. Genera such as <i>Fusobacterium</i>, <i>Bacteroides</i>, <i>Escherichia</i>-<i>Shigella</i>, and <i>Lactobacillus</i> were consistently abundant, regardless of sex or gestation stage, accounting for 58.00% and 56.14% of reads in male and female samples, respectively. The echidna microbiome remained stable across the different gestation stages, though there was a significant difference in microbiota composition between male and female echidnas. This study is the first to describe the microbiome composition of short-beaked echidnas across reproductive phases and allows the opportunity for this novel information to be used as a metric of health to aid in the detection of diseases triggered by microbiota dysbiosis.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1392","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138634348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The human gut microbiome contains thousands of small, novel peptides that could play a role in microbe–microbe and host–microbe interactions, contributing to human health and disease. Although these peptides have not yet been systematically characterized, computational tools can be used to elucidate the bioactivities they may have. This article proposes probing the functional space of gut microbiome-derived peptides (MDPs) using in silico approaches for three bioactivities: antimicrobial, anticancer, and nucleomodulins. Machine learning programs that support peptide and protein queries are provided for each bioactivity. Considering the biases of an activity-centric approach, activity-agnostic tools using structural and chemical similarity and target prediction are also described. Gut MDPs represent a vast functional space that can not only contribute to our understanding of microbiome interactions but potentially even serve as a source of life-changing therapeutics.
{"title":"Examining the functional space of gut microbiome-derived peptides","authors":"Ying-Chiang J. Lee","doi":"10.1002/mbo3.1393","DOIUrl":"https://doi.org/10.1002/mbo3.1393","url":null,"abstract":"<p>The human gut microbiome contains thousands of small, novel peptides that could play a role in microbe–microbe and host–microbe interactions, contributing to human health and disease. Although these peptides have not yet been systematically characterized, computational tools can be used to elucidate the bioactivities they may have. This article proposes probing the functional space of gut microbiome-derived peptides (MDPs) using in silico approaches for three bioactivities: antimicrobial, anticancer, and nucleomodulins. Machine learning programs that support peptide and protein queries are provided for each bioactivity. Considering the biases of an activity-centric approach, activity-agnostic tools using structural and chemical similarity and target prediction are also described. Gut MDPs represent a vast functional space that can not only contribute to our understanding of microbiome interactions but potentially even serve as a source of life-changing therapeutics.</p>","PeriodicalId":18573,"journal":{"name":"MicrobiologyOpen","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mbo3.1393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138570903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}