Clostridioides (Clostridium) difficile (C. difficile) infection (CDI), often severe when producing toxin A, toxin B, and CDT, can cause life-threatening fulminant infections, especially in vulnerable patients. This case report discusses a 39-year-old woman with no medical history who developed severe CDI after antibiotic treatment, leading to fatal hypovolemic shock. A rare C. difficile PCR-ribotype 153 strain which is positive for toxin A, toxin B, and CDT was identified. This case emphasizes the need for early CDI diagnosis, cautious antibiotic use, and prompt treatment to prevent severe outcomes like shock and multiorgan failure.
{"title":"Fulminant Clostridioides (Costridium) difficile infection caused by a rare strain of PCR-ribotype 153 in Japan: A case report.","authors":"Daichi Yomogida, Suguru Hasegawa, Shiori Mizuta, Shinjiro Horikawa, Yoshinao Koshida, Koichiro Matsuda, Masahiko Nakamura, Hiroyasu Kaya, Akio Uchiyama, Mitsutoshi Senoh","doi":"10.1016/j.anaerobe.2024.102936","DOIUrl":"https://doi.org/10.1016/j.anaerobe.2024.102936","url":null,"abstract":"<p><p>Clostridioides (Clostridium) difficile (C. difficile) infection (CDI), often severe when producing toxin A, toxin B, and CDT, can cause life-threatening fulminant infections, especially in vulnerable patients. This case report discusses a 39-year-old woman with no medical history who developed severe CDI after antibiotic treatment, leading to fatal hypovolemic shock. A rare C. difficile PCR-ribotype 153 strain which is positive for toxin A, toxin B, and CDT was identified. This case emphasizes the need for early CDI diagnosis, cautious antibiotic use, and prompt treatment to prevent severe outcomes like shock and multiorgan failure.</p>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":" ","pages":"102936"},"PeriodicalIF":2.5,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142881141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-22DOI: 10.1016/j.anaerobe.2024.102922
Yongmei Li , Jing Zhao , Qiong Ma , Junhong Xu , Youhua Yuan , Qi Zhang , Wenjuan Yan , Wenbo Xu , Zhiyu Yang , Gang Li , Lan Gao , Baoya Wang
Objectives
This study aimed to explore the epidemiology, clinical presentation, and risk factors for treatment failure in patients infected with various Bacteroides fragilis group (BFG) species.
Methods
We analyzed clinical and laboratory data from 178 patients infected with BFG who were admitted to our hospital between 2017 and 2024. We analyzed categorical data using Chi-square and Fisher exact tests, continuous variables using Student's t-tests or Mann–Whitney U-tests, and risk factors using multivariate logistic regression and Pearson's chi-squared tests.
Results
Bacteroides fragilis (69.7 %) and Bacteroides thetaiotaomicron (16.9 %) were the most prevalent species among 178 BFG isolates. Most patients had polymicrobial infections, with the following pathogens isolated from concurrent samples: Escherichia coli, Klebsiella spp., and Enterococcus spp. Intra-abdominal sites were most frequently infected with BFG. Patients aged >50 years and those who had intravascular catheters were infected with more other Bacteroides species than B. fragilis. Admission to an ICU, respiratory, renal and cardiovascular diseases, and chest drainage were associated more often with B. thetaiotaomicron than with B. fragilis. Gastrointestinal diseases, tracheal intubation, and ICU admission were associated more frequently with treatment failure in patients infected with B. fragilis whereas solid cancers, renal disease, multiple organ dysfunction syndrome, and tracheal intubation were more likely to be associated with treatment failure in patients infected with other Bacteroides spp.
Conclusions
The most prevalent BFG species in the patients were B. fragilis and B. thetaiotaomicron. The demographic characteristics of the patients, underlying diseases, and risk factors for poor clinical outcomes clearly differed among species.
研究目的本研究旨在探讨各种脆弱拟杆菌属（BFG）感染患者的流行病学、临床表现和治疗失败的风险因素：我们分析了2017年至2024年间本院收治的178名BFG感染者的临床和实验室数据。我们使用卡方检验（Chi-square）和费雪精确检验（Fisher exact）对分类数据进行分析，使用学生 t 检验或曼惠尼 U 检验对连续变量进行分析，使用多变量逻辑回归和皮尔逊卡方检验对风险因素进行分析：结果：在178个BFG分离株中，最常见的菌种是脆弱拟杆菌（69.7%）和泰奥米克隆拟杆菌（16.9%）。大多数患者有多微生物感染，同时从样本中分离出以下病原体：腹腔部位最常感染 BFG。年龄大于 50 岁的患者和使用血管内导管的患者感染的其他乳杆菌要多于脆弱拟杆菌。与脆弱拟杆菌相比，入住重症监护室、患有呼吸系统、肾脏和心血管疾病以及胸腔引流的患者更常感染泰氏菌。胃肠道疾病、气管插管和入住重症监护室与感染脆弱拟杆菌的患者治疗失败的相关性更高，而实体瘤、肾脏疾病、多器官功能障碍综合征和气管插管与感染其他乳杆菌属的患者治疗失败的相关性更高：结论：患者中最常见的乳糜泻菌为脆弱拟杆菌（B. fragilis）和大肠杆菌（B. thetaiotaomicron）。不同菌种的患者人口统计学特征、基础疾病和临床疗效不佳的风险因素明显不同。
{"title":"Comparison of clinical characteristics, risk factors, and outcomes of patients infected with Bacteroides fragilis group at a tertiary care hospital in central China between 2017 and March 2024","authors":"Yongmei Li , Jing Zhao , Qiong Ma , Junhong Xu , Youhua Yuan , Qi Zhang , Wenjuan Yan , Wenbo Xu , Zhiyu Yang , Gang Li , Lan Gao , Baoya Wang","doi":"10.1016/j.anaerobe.2024.102922","DOIUrl":"10.1016/j.anaerobe.2024.102922","url":null,"abstract":"<div><h3>Objectives</h3><div>This study aimed to explore the epidemiology, clinical presentation, and risk factors for treatment failure in patients infected with various <em>Bacteroides fragilis</em> group (BFG) species.</div></div><div><h3>Methods</h3><div>We analyzed clinical and laboratory data from 178 patients infected with BFG who were admitted to our hospital between 2017 and 2024. We analyzed categorical data using Chi-square and Fisher exact tests, continuous variables using Student's <em>t</em>-tests or Mann–Whitney <em>U</em>-tests, and risk factors using multivariate logistic regression and Pearson's chi-squared tests.</div></div><div><h3>Results</h3><div><em>Bacteroides fragilis</em> (69.7 %) and <em>Bacteroides thetaiotaomicron</em> (16.9 %) were the most prevalent species among 178 BFG isolates. Most patients had polymicrobial infections, with the following pathogens isolated from concurrent samples: <em>Escherichia coli</em>, <em>Klebsiella</em> spp., and <em>Enterococcus</em> spp. Intra-abdominal sites were most frequently infected with BFG. Patients aged >50 years and those who had intravascular catheters were infected with more other <em>Bacteroides</em> species than <em>B. fragilis</em>. Admission to an ICU, respiratory, renal and cardiovascular diseases, and chest drainage were associated more often with <em>B. thetaiotaomicron</em> than with <em>B. fragilis</em>. Gastrointestinal diseases, tracheal intubation, and ICU admission were associated more frequently with treatment failure in patients infected with <em>B. fragilis</em> whereas solid cancers, renal disease, multiple organ dysfunction syndrome, and tracheal intubation were more likely to be associated with treatment failure in patients infected with other <em>Bacteroides</em> spp.</div></div><div><h3>Conclusions</h3><div>The most prevalent BFG species in the patients were <em>B</em>. <em>fragilis</em> and <em>B</em>. <em>thetaiotaomicron</em>. The demographic characteristics of the patients, underlying diseases, and risk factors for poor clinical outcomes clearly differed among species.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"91 ","pages":"Article 102922"},"PeriodicalIF":2.5,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142708878","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}
Pub Date : 2024-10-10DOI: 10.1016/j.anaerobe.2024.102917
Júlia Meireles , Renata F.F. Moraes , Débora Lins , Thaís da Silveira Oliveira , Eduardo Butturini de Carvalho , Kelly Rainha , Eliane de O. Ferreira
Introduction
In the past decade, the incidence of community-acquired Clostridioides difficile infection (CA-CDI) has increased, suggesting a role for community reservoirs such as animals in its spread.
Objective
This study aimed to isolate and characterize C. difficile strains from domestic dogs at veterinary clinics to enhance our understanding of C. difficile epidemiology in Rio de Janeiro.
Material and methods
For this study 90 stool samples from dogs were collected and cultured in a selective medium (Clostridioides difficile Brucella agar – CDBA) for isolation. Species were identified by MALDI-TOF MS, with confirmation provided by PCR targeting the tpi gene. The antibiotic susceptibility test of the strains was performed using five antibiotics: vancomycin, metronidazole, moxifloxacin, rifampicin, and erythromycin. Strains resistant to metronidazole were further analyzed for the presence of the plasmid pCD-METRO using PCR. The presence of toxin genes (tcdA, tcdB, and cdtB) was investigated, alongside ribotyping and tcdC sequencing analyses. The strains were also tested for biofilm formation and motility.
Results
C. difficile was isolated in 15.5 % (14/90) of the samples. Among the strains analyzed, 87.71 % (12/14) tested positive for both toxin genes tcdA and tcdB and belonged to ribotypes 106 (10/14) and 014/020 (2/14). The remaining 14.3 % (2/14) were non-toxigenic and were identified as ribotype 010. Regarding the antibiotic profile, 42.85 % (6/14) of the strains exhibited resistance to at least one antibiotic, including vancomycin (1/14) and metronidazole (1/14). The metronidazole-resistant strain was also positive for the plasmid pCD-METRO. All strains exhibited both biofilm formation and motility. Among the 12 toxigenic strains sequenced for the tcdC gene, two exhibited a deletion in the same region as the epidemic strain, NAP1 (RT027).
Conclusion
Our study found some overlap between C. difficile ribotypes isolated from dogs and from cases of CDI in humans, and the C. difficile prevalence was higher in dogs with diarrhea (p = 0.034).
{"title":"Dogs in Rio de Janeiro as reservoirs of Clostridioides difficile ribotypes causing CDI in humans","authors":"Júlia Meireles , Renata F.F. Moraes , Débora Lins , Thaís da Silveira Oliveira , Eduardo Butturini de Carvalho , Kelly Rainha , Eliane de O. Ferreira","doi":"10.1016/j.anaerobe.2024.102917","DOIUrl":"10.1016/j.anaerobe.2024.102917","url":null,"abstract":"<div><h3>Introduction</h3><div>In the past decade, the incidence of community-acquired <em>Clostridioides difficile</em> infection (CA-CDI) has increased, suggesting a role for community reservoirs such as animals in its spread.</div></div><div><h3>Objective</h3><div>This study aimed to isolate and characterize <em>C. difficile</em> strains from domestic dogs at veterinary clinics to enhance our understanding of <em>C. difficile</em> epidemiology in Rio de Janeiro.</div></div><div><h3>Material and methods</h3><div>For this study 90 stool samples from dogs were collected and cultured in a selective medium (<em>Clostridioides difficile</em> Brucella agar – CDBA) for isolation. Species were identified by MALDI-TOF MS, with confirmation provided by PCR targeting the <em>tpi</em> gene. The antibiotic susceptibility test of the strains was performed using five antibiotics: vancomycin, metronidazole, moxifloxacin, rifampicin, and erythromycin. Strains resistant to metronidazole were further analyzed for the presence of the plasmid pCD-METRO using PCR. The presence of toxin genes (<em>tcdA</em>, <em>tcdB</em>, and <em>cdtB</em>) was investigated, alongside ribotyping and <em>tcdC</em> sequencing analyses. The strains were also tested for biofilm formation and motility.</div></div><div><h3>Results</h3><div><em>C. difficile</em> was isolated in 15.5 % (14/90) of the samples. Among the strains analyzed, 87.71 % (12/14) tested positive for both toxin genes <em>tcd</em>A and <em>tcd</em>B and belonged to ribotypes 106 (10/14) and 014/020 (2/14). The remaining 14.3 % (2/14) were non-toxigenic and were identified as ribotype 010. Regarding the antibiotic profile, 42.85 % (6/14) of the strains exhibited resistance to at least one antibiotic, including vancomycin (1/14) and metronidazole (1/14). The metronidazole-resistant strain was also positive for the plasmid pCD-METRO. All strains exhibited both biofilm formation and motility. Among the 12 toxigenic strains sequenced for the <em>tcdC</em> gene, two exhibited a deletion in the same region as the epidemic strain, NAP1 (RT027).</div></div><div><h3>Conclusion</h3><div>Our study found some overlap between <em>C. difficile</em> ribotypes isolated from dogs and from cases of CDI in humans, and the <em>C. difficile</em> prevalence was higher in dogs with diarrhea (<em>p</em> = 0.034).</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102917"},"PeriodicalIF":2.5,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1016/j.anaerobe.2024.102919
Yanan Zhang , Chunlong Mu , Kaifan Yu , Yong Su , Erwin G. Zoetendal , Weiyun Zhu
Objectives
Fructo-oligosaccharide (FOS) and citrus pectin (CP) are soluble fibers with different chemical composition. However, their fermentation pattern in large intestine remains unclear.
Methods
An in vitro batch fermentation using colonic digesta from pigs as inoculum was employed to investigate the fermentation dynamics of FOS and CP. The monosaccharides and SCFAs contents were assayed by high-performance liquid chromatography and gas chromatography, respectively. And the microbiota community was assessed by 16S rRNA gene high-throughput sequencing.
Results
Both FOS and CP were degarded after 6 h, especially to a neglected level in FOS. FOS group showed higher abundances of butyrate-producing bacteria such as Eubacterium rectale, Roseburia faecis and Coprococcus comes and butyrate compared to CP. CP stimulated the growth of pectinolytic microbes Lachnospira pectinoschiza, succinate-producing bacteria Succinivibrio dextrinosolvens, succinate-utilizing bacteria Phascolarctobacterium succinatutens and the production of acetate and propionate compared to FOS. Moreover, the relative abundances of key enzymes (e.g. butyrate kinase) involving in butyrate formation via the butyrate kinase route were upregulated in the FOS group. And the key enzymes (e.g. acetyl-CoA synthetase) associated with propionate production through the succinate pathway were upregulated in the CP group.
Conclusions
FOS was preferred to ferment by butyrate-producing bacteria to yield a higher level of butyrate via the butyrate kinase pathway, while CP enhanced the cross-feeding of succinate-producing and succinate-utilizing bacteria to form propionate through the succinate pathway. These findings deepen our understanding on the fermentation characteristics of the soluble fibers, and also provide guidelines for fiber choice in precisely modulating the microbial composition and metabolism in large intestine.
{"title":"Fructo-oligosaccharides promote butyrate production over citrus pectin during in vitro fermentation by colonic inoculum from pig","authors":"Yanan Zhang , Chunlong Mu , Kaifan Yu , Yong Su , Erwin G. Zoetendal , Weiyun Zhu","doi":"10.1016/j.anaerobe.2024.102919","DOIUrl":"10.1016/j.anaerobe.2024.102919","url":null,"abstract":"<div><h3>Objectives</h3><div>Fructo-oligosaccharide (FOS) and citrus pectin (CP) are soluble fibers with different chemical composition. However, their fermentation pattern in large intestine remains unclear.</div></div><div><h3>Methods</h3><div>An <em>in vitro</em> batch fermentation using colonic digesta from pigs as inoculum was employed to investigate the fermentation dynamics of FOS and CP. The monosaccharides and SCFAs contents were assayed by high-performance liquid chromatography and gas chromatography, respectively. And the microbiota community was assessed by 16S rRNA gene high-throughput sequencing.</div></div><div><h3>Results</h3><div>Both FOS and CP were degarded after 6 h, especially to a neglected level in FOS. FOS group showed higher abundances of butyrate-producing bacteria such as <em>Eubacterium rectale</em>, <em>Roseburia faecis</em> and <em>Coprococcus comes</em> and butyrate compared to CP. CP stimulated the growth of pectinolytic microbes <em>Lachnospira pectinoschiza</em>, succinate-producing bacteria <em>Succinivibrio dextrinosolvens</em>, succinate-utilizing bacteria <em>Phascolarctobacterium succinatutens</em> and the production of acetate and propionate compared to FOS. Moreover, the relative abundances of key enzymes (e.g. butyrate kinase) involving in butyrate formation via the butyrate kinase route were upregulated in the FOS group. And the key enzymes (e.g. acetyl-CoA synthetase) associated with propionate production through the succinate pathway were upregulated in the CP group.</div></div><div><h3>Conclusions</h3><div>FOS was preferred to ferment by butyrate-producing bacteria to yield a higher level of butyrate via the butyrate kinase pathway, while CP enhanced the cross-feeding of succinate-producing and succinate-utilizing bacteria to form propionate through the succinate pathway. These findings deepen our understanding on the fermentation characteristics of the soluble fibers, and also provide guidelines for fiber choice in precisely modulating the microbial composition and metabolism in large intestine.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102919"},"PeriodicalIF":2.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142405948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-09DOI: 10.1016/j.anaerobe.2024.102915
Svetlana Boycheva , Anthony M. Roberton , Alessandro Pisaniello , Bikiran Pardesi , William Lindsey White , Kendall D. Clements
Objectives
The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air.
Methods
To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish.
Results
Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions.
Conclusion
Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.
目标：第三代测序的核心挑战在于满足对 DNA 质量（完整性和纯度）和数量的要求。因此，需要对 DNA 提取方法进行新的改进，以满足这些要求。我们推断，在厌氧微生物群落中，某些严格厌氧菌含有氧激活的 DNase 活性，如果暴露在空气中，可能会大大降低提取的元基因组 DNA（或某些纯培养物的基因组 DNA）的完整性：为了验证这一假设，我们开发了一种增强型基因组和元基因组 DNA 分离技术，并将其应用于一组特选的严格厌氧菌和耐气厌氧菌，以及一种食草海鱼的后肠微生物群：结果：考虑到在厌氧条件下和有氧条件下提取的DNA的质量（或降解），我们发现从一些严格厌氧菌细胞中有氧提取的DNA比在厌氧条件下提取的DNA降解得更多。与此相反，在所选的耐气厌氧菌中，有氧和无氧条件下提取的 DNA 分子大小没有明显差异。与有氧条件相比，厌氧条件下从鱼类后肠微生物群中提取的元基因组DNA产量更高、质量更好：我们的研究有效证明了我们改进的提取方案在厌氧条件下的优势。结论：我们的研究有效地证明了我们改进的提取方案在厌氧条件下的优势，提取的 DNA 质量明显提高。这些发现可能对研究，尤其是元基因组研究很有价值，因为DNA的质量和数量对下游分析至关重要。
{"title":"Oxygen exposure decreases the yield of high-molecular-weight DNA from some anaerobic bacteria and bacterial communities during DNA extraction","authors":"Svetlana Boycheva , Anthony M. Roberton , Alessandro Pisaniello , Bikiran Pardesi , William Lindsey White , Kendall D. Clements","doi":"10.1016/j.anaerobe.2024.102915","DOIUrl":"10.1016/j.anaerobe.2024.102915","url":null,"abstract":"<div><h3>Objectives</h3><div>The central challenge in third-generation sequencing lies in meeting the requirements for DNA quality (integrity and purity) and quantity. Therefore, novel improvements in DNA extraction methods are needed to satisfy these requirements. We reasoned that in anaerobic microbial communities, the presence of certain strict anaerobes containing oxygen-activated DNase activity might contribute substantially to the poor integrity of extracted metagenomic DNA (or genomic DNA from some pure cultures) if exposed to air.</div></div><div><h3>Methods</h3><div>To test this hypothesis, we developed an enhanced genomic and metagenomic DNA isolation technique that we applied to a specifically chosen set of both strict and aerotolerant anaerobes, as well as to the hindgut microbiota of a herbivorous marine fish.</div></div><div><h3>Results</h3><div>Considering the quality (or degradation) of extracted DNA obtained under anaerobic versus aerobic conditions, we found that DNA extracted aerobically from cells of some strict anaerobes showed more degradation of high molecular weight DNA than analogous preparations under anaerobic conditions. In contrast, with the selected aerotolerant anaerobes, no discernible difference was found between the molecular sizes of DNA extracted aerobically and anaerobically. Metagenomic DNA extracted from the fish hindgut microbiota showed higher yields and better quality under anaerobic conditions compared to aerobic conditions.</div></div><div><h3>Conclusion</h3><div>Our study effectively demonstrates the advantages of our improved extraction protocol in anaerobic conditions. This is evident through the improved quality of extracted DNA. Such findings may be valuable for studies, especially metagenomic studies, where the quality and quantity of DNA are crucial for downstream analysis.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102915"},"PeriodicalIF":2.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142399196","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}
Pub Date : 2024-10-05DOI: 10.1016/j.anaerobe.2024.102918
Gregory Whitehill , Ran Zhuo , Shangxin Yang
We present the first described case of bacteremia due to Butyricimonas paravirosa, a commensal gram-negative anaerobic bacterium identified by whole-genome sequencing in an elderly patient with acute terminal ileitis, who was successfully treated with ceftriaxone and metronidazole. We reviewed eleven previous cases of infection due to other Butyricimonas spp, which can cause a range of diseases but may be treated conservatively with a short antimicrobial course in the appropriate clinical setting. Additionally, while most Butyricimonas spp are susceptible to empiric anaerobic therapy, drug resistance has been reported in some cases.
{"title":"Butyricimonas paravirosa bacteremia associated with acute terminal ileitis: Case report and literature review","authors":"Gregory Whitehill , Ran Zhuo , Shangxin Yang","doi":"10.1016/j.anaerobe.2024.102918","DOIUrl":"10.1016/j.anaerobe.2024.102918","url":null,"abstract":"<div><div>We present the first described case of bacteremia due to <em>Butyricimonas paravirosa</em>, a commensal gram-negative anaerobic bacterium identified by whole-genome sequencing in an elderly patient with acute terminal ileitis, who was successfully treated with ceftriaxone and metronidazole. We reviewed eleven previous cases of infection due to other <em>Butyricimonas</em> spp, which can cause a range of diseases but may be treated conservatively with a short antimicrobial course in the appropriate clinical setting. Additionally, while most <em>Butyricimonas</em> spp are susceptible to empiric anaerobic therapy, drug resistance has been reported in some cases.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102918"},"PeriodicalIF":2.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379900","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}
We investigated the effects of Clostridioides difficile toxin B (TcdB), a major virulence factor in C. difficile infection (CDI), on human neutrophils. TcdB inhibits neutrophil migration via loss of polarity of F-actin polymerization in response to interleukin-8. TcdB facilitates CDI by allowing C. difficile to avert the host immune system.
{"title":"Clostridioides difficile toxin B suppresses human neutrophil migration","authors":"Yoshitaka Kimura, Nami Hatayama, Yoshinori Sato, Yusuke Yoshino","doi":"10.1016/j.anaerobe.2024.102916","DOIUrl":"10.1016/j.anaerobe.2024.102916","url":null,"abstract":"<div><div>We investigated the effects of <em>Clostridioides difficile</em> toxin B (TcdB), a major virulence factor in <em>C. difficile</em> infection (CDI), on human neutrophils. TcdB inhibits neutrophil migration via loss of polarity of F-actin polymerization in response to interleukin-8. TcdB facilitates CDI by allowing <em>C. difficile</em> to avert the host immune system.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102916"},"PeriodicalIF":2.5,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379901","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}
Although Clostridium perfringens sporulation is a key event in the pathogenesis of food-borne illness, the molecules and underlying mechanisms responsible for regulating sporulation are incompletely understood. The present study sought to identify amino acids that affect sporulation in C. perfringens strain SM101.
Methods
A C. perfringens strain was cultured in the chemically defined medium deficient in an amino acid. The bacterial growth was determined by spectrophotometrically measuring culture turbidity and by calculating colony-forming unit. Morphological characteristics were assessed by phase-contrast microscopy with fluorescent staining and by electron microscopy.
Results
The amino acids Arg, Cys, Gly, His, Ile, Leu, Met, Phe, Thr, Trp, Tyr, and Val were important for sporulation, and furthermore, Ser reduced sporulation. The mechanism underlying Ser-induced prevention of sporulation was assessed morphologically. The numbers of bacterial cells in sporulation stage II were significantly higher in the presence than in the absence of Ser. In the presence of Ser, almost all cells were in stage II−III, characterized by polar septation−early engulfment, and did not proceed to late engulfment.
Conclusions
These results suggest that Ser accelerated the early stage of sporulation of C. perfringens strain SM101, but disturbed the engulfment process, resulting in reduction of sporulation. To the best of our knowledge, this is the first study reporting that an amino acid affects engulfment during the C. perfringens sporulation process.
目的：尽管产气荚膜梭菌孢子化是食源性疾病致病机理中的一个关键事件，但人们对调控孢子化的分子和潜在机制却知之甚少。本研究试图找出影响产气荚膜杆菌菌株 SM101 孢子发生的氨基酸：方法：在缺乏一种氨基酸的化学定义培养基中培养细菌菌株。细菌生长情况通过分光光度法测量培养物浊度和计算菌落形成单位来确定。荧光染色相衬显微镜和电子显微镜评估了形态特征：结果：Arg、Cys、Gly、His、Ile、Leu、Met、Phe、Thr、Trp、Tyr 和 Val 等氨基酸对孢子的形成非常重要，而且 Ser 会降低孢子的形成。对 Ser 诱导的孢子生成抑制机制进行了形态学评估。在有 Ser 的情况下，几乎所有细胞都处于以极性隔膜-早期吞噬为特征的 II-III 期，没有进入后期吞噬：这些结果表明，Ser 加快了 C. perfringens 菌株 SM101 的早期孢子化，但干扰了吞噬过程，导致孢子化减少。据我们所知，这是首次有研究报道一种氨基酸会影响产气荚膜杆菌孢子形成过程中的吞噬作用。
{"title":"Serine affects engulfment during the sporulation process in Clostridium perfringens strain SM101","authors":"Mayo Yasugi , Akinobu Ohta , Keiko Takano , Kanako Yakubo , Michiko Irie , Masami Miyake","doi":"10.1016/j.anaerobe.2024.102914","DOIUrl":"10.1016/j.anaerobe.2024.102914","url":null,"abstract":"<div><h3>Objectives</h3><div>Although <em>Clostridium perfringens</em> sporulation is a key event in the pathogenesis of food-borne illness, the molecules and underlying mechanisms responsible for regulating sporulation are incompletely understood. The present study sought to identify amino acids that affect sporulation in <em>C. perfringens</em> strain SM101.</div></div><div><h3>Methods</h3><div>A <em>C. perfringens</em> strain was cultured in the chemically defined medium deficient in an amino acid. The bacterial growth was determined by spectrophotometrically measuring culture turbidity and by calculating colony-forming unit. Morphological characteristics were assessed by phase-contrast microscopy with fluorescent staining and by electron microscopy.</div></div><div><h3>Results</h3><div>The amino acids Arg, Cys, Gly, His, Ile, Leu, Met, Phe, Thr, Trp, Tyr, and Val were important for sporulation, and furthermore, Ser reduced sporulation. The mechanism underlying Ser-induced prevention of sporulation was assessed morphologically. The numbers of bacterial cells in sporulation stage II were significantly higher in the presence than in the absence of Ser. In the presence of Ser, almost all cells were in stage II−III, characterized by polar septation−early engulfment, and did not proceed to late engulfment.</div></div><div><h3>Conclusions</h3><div>These results suggest that Ser accelerated the early stage of sporulation of <em>C. perfringens</em> strain SM101, but disturbed the engulfment process, resulting in reduction of sporulation. To the best of our knowledge, this is the first study reporting that an amino acid affects engulfment during the <em>C. perfringens</em> sporulation process.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102914"},"PeriodicalIF":2.5,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379033","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}
Pub Date : 2024-09-27DOI: 10.1016/j.anaerobe.2024.102913
Yan Li , Yan Wang , Di Xiao , Jing Wang , Dong Jin
Objectives
To comprehensively characterize a new species, named Finegoldia dalianensis sp. nov., isolated from the pus of a skin abscess from a patient and genomic analysis of the strains belonging to Finegoldia genus.
Methods
Strain LY240594T was definitively characterized through phylogenetic, genomic, and biochemical approach. Extensive genomic comparisons, involving the genome of LY240594T and those of 82 Finegoldia strains from GenBank, were instrumental in revealing genetic relationships within the Finegoldia genus.
Results
Strain LY240594 was initially identified as F. magna based on MALDI-TOF MS analysis, showing 99.7 % 16S rRNA gene sequences similarity with the type strain of F. magna CCUG 17636T. However, there were 68.5 % similarity with dDDH method and 90.9 % similarity by ANI analysis respectively, between LY240594T and the selected type strain, F. magna DSM 20470T. Biochemical differences were also found between two strains. The ANI and genomic analysis of 82 Finegoldia sp. Strains and Strain LY240594 revealed that those strains could be categorized into at least three groups using a 95 % ANI threshold.
Conclusion
Comprehensive characterization supported the proposal of a new species within the genus Finegoldia, named Finegoldia dalianensis sp. nov. The type strain, LY240594T (=GDMCC 1.4375T = KCTC 25838T), features 1938 genes and a G + C content of 31.8 mol%. Genomic comparisons and ANI studies elucidated substantial heterogeneity within the Finegoldia genus.
目的：从一名患者的皮肤脓肿脓液中分离出一个新物种，命名为Finegoldia dalianensis sp.nov.，并对属于Finegoldia属的菌株进行基因组分析：方法：通过系统发育、基因组和生化方法确定了菌株 LY240594T 的特征。通过对 LY240594T 基因组和 GenBank 中 82 株细金花属菌株的基因组进行广泛的基因组比较，有助于揭示细金花属内部的遗传关系：结果：根据 MALDI-TOF MS 分析，菌株 LY240594 与 F. magna 的模式菌株 CCUG 17636T 的 16S rRNA 基因序列相似度为 99.7%，被初步鉴定为 F. magna。然而，LY240594T 与所选模式菌株 F. magna DSM 20470T 的 dDDH 方法相似度为 68.5%，ANI 分析相似度为 90.9%。对 82 株 Finegoldia sp.菌株和菌株 LY240594 的 ANI 和基因组分析表明，以 95% 的 ANI 临界值为标准，这些菌株至少可分为三组：结论：综合分析结果表明，Finegoldia 属中有一个新种，命名为 Finegoldia dalianensis sp.模式菌株 LY240594T（=GDMCC 1.4375T =KCTC 25838T）有 1,938 个基因，G+C 含量为 31.8 摩尔%。基因组比较和 ANI 研究阐明了 Finegoldia 属内部的实质性异质性。
{"title":"The identification of Finegoldia dalianensis sp. nov., isolated from the pus of the patient with skin abscess and genomic analysis of the strains belonging to Finegoldia genus","authors":"Yan Li , Yan Wang , Di Xiao , Jing Wang , Dong Jin","doi":"10.1016/j.anaerobe.2024.102913","DOIUrl":"10.1016/j.anaerobe.2024.102913","url":null,"abstract":"<div><h3>Objectives</h3><div>To comprehensively characterize a new species, named <em>Finegoldia dalianensis</em> sp. nov., isolated from the pus of a skin abscess from a patient and genomic analysis of the strains belonging to <em>Finegoldia</em> genus.</div></div><div><h3>Methods</h3><div>Strain LY240594<sup>T</sup> was definitively characterized through phylogenetic, genomic, and biochemical approach. Extensive genomic comparisons, involving the genome of LY240594<sup>T</sup> and those of 82 <em>Finegoldia</em> strains from GenBank, were instrumental in revealing genetic relationships within the <em>Finegoldia</em> genus.</div></div><div><h3>Results</h3><div>Strain LY240594 was initially identified as <em>F. magna</em> based on MALDI-TOF MS analysis, showing 99.7 % 16S rRNA gene sequences similarity with the type strain of <em>F. magna</em> CCUG 17636<sup>T</sup>. However, there were 68.5 % similarity with dDDH method and 90.9 % similarity by ANI analysis respectively, between LY240594<sup>T</sup> and the selected type strain, <em>F. magna</em> DSM 20470<sup>T</sup>. Biochemical differences were also found between two strains. The ANI and genomic analysis of 82 <em>Finegoldia</em> sp. Strains and Strain LY240594 revealed that those strains could be categorized into at least three groups using a 95 % ANI threshold.</div></div><div><h3>Conclusion</h3><div>Comprehensive characterization supported the proposal of a new species within the genus <em>Finegoldia</em>, named <em>Finegoldia dalianensis</em> sp. nov. The type strain, LY240594<sup>T</sup> (=GDMCC 1.4375<sup>T</sup> = KCTC 25838<sup>T</sup>), features 1938 genes and a G + C content of 31.8 mol%. Genomic comparisons and ANI studies elucidated substantial heterogeneity within the <em>Finegoldia</em> genus.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102913"},"PeriodicalIF":2.5,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-24DOI: 10.1016/j.anaerobe.2024.102912
Mervenur Demir , Jozsef Soki , Elif Seren Tanrıverdi , Ceren Özkul , Bakhtiyar Mahmood , Barış Otlu , Gülşen Hazırolan , ESCMID Study Group for Anaerobic Infections (ESGAI)
Objectives
This study was conducted to measure the prevalence of antibiotic resistance, and corresponding resistance genes among Bacteroides and related genera in a tertiary hospital.
Methods
We examined 138 clinical strains of Bacteroides, Phocaeicola and Parabacteroides species isolated between July 2018 and June 2022. Antibiotic susceptibility tests were conducted using agar dilution. The bft gene and antibiotic resistance genes were targeted by real-time PCR.
Results
Resistance rates of all strains against ampicillin, cefoxitin, piperacillin-tazobactam, meropenem, imipenem, clindamycin, metronidazole, and tigecycline were 97.8 %, 28.3 %, 11.6 %, 7.9 %, 5.1 %, 47.8 %, 0 % and 4.3 %, respectively. Non-fragilis Bacteroidales spp. (NFB) exhibited lower susceptibility rates compared to B. fragilis for cefoxitin, clindamycin, and piperacillin-tazobactam. The prevalence of meropenem resistance was higher in B. fragilis (15.5 %) than in NFB (0 %). Among all strains, the rates of cepA, cfxA, cfiA, ermF, ermG, ermB, nim, linA, mefA, msrSA, tetQ, tetX, tetX1 and bft genes were 42.8 %, 44.9 %, 8.7 %, 44.2 %, 10.9 %, 2.2 %, 0.7 %, 29.0 %, 17.4 %, 7.2 %, 76.1 %, 8.0 %, 37.7 % and 16.7 %, respectively. In five B. fragilis strains, insertion sequences [IS1187(n = 3), ISBf6(n = 1), IS612B(n = 1)] were detected in the upstream region of cfiA. NimE with ISBf6 on plasmid pBFM29b was detected in one B. fragilis strain, intermediate to metronidazole (MIC = 16 μg/mL). ErmF was the most abundant gene responsible for clindamycin resistance. TetQ and tetX1 genes exhibited a higher frequency in strains that were not susceptible to tigecycline (MIC ≥8 μg/ml).
Conclusions
Monitoring the resistance trends of Bacteroides and related genera is crucial given the observed resistance to all classes of antibiotics and the presence of various resistance mechanisms.
{"title":"Molecular characterization and antibiotic resistance of clinical Bacteroides and related genera from a tertiary care center in Türkiye","authors":"Mervenur Demir , Jozsef Soki , Elif Seren Tanrıverdi , Ceren Özkul , Bakhtiyar Mahmood , Barış Otlu , Gülşen Hazırolan , ESCMID Study Group for Anaerobic Infections (ESGAI)","doi":"10.1016/j.anaerobe.2024.102912","DOIUrl":"10.1016/j.anaerobe.2024.102912","url":null,"abstract":"<div><h3>Objectives</h3><div>This study was conducted to measure the prevalence of antibiotic resistance, and corresponding resistance genes among <em>Bacteroides</em> and related genera in a tertiary hospital.</div></div><div><h3>Methods</h3><div>We examined 138 clinical strains of <em>Bacteroides, Phocaeicola</em> and <em>Parabacteroides</em> species isolated between July 2018 and June 2022. Antibiotic susceptibility tests were conducted using agar dilution. The <em>b</em><em>ft</em> gene and antibiotic resistance genes were targeted by real-time PCR.</div></div><div><h3>Results</h3><div>Resistance rates of all strains against ampicillin, cefoxitin, piperacillin-tazobactam, meropenem, imipenem, clindamycin, metronidazole, and tigecycline were 97.8 %, 28.3 %, 11.6 %, 7.9 %, 5.1 %, 47.8 %, 0 % and 4.3 %, respectively. Non-fragilis <em>Bacteroidales</em> spp. (NFB) exhibited lower susceptibility rates compared to <em>B. fragilis</em> for cefoxitin, clindamycin, and piperacillin-tazobactam. The prevalence of meropenem resistance was higher in <em>B. fragilis</em> (15.5 %) than in NFB (0 %). Among all strains, the rates of <em>cepA, cfxA, cfiA, ermF, ermG, ermB, nim, linA, mefA, msrSA, tetQ, tetX, tetX1</em> and <em>bft</em> genes were 42.8 %, 44.9 %, 8.7 %, 44.2 %, 10.9 %, 2.2 %, 0.7 %, 29.0 %, 17.4 %, 7.2 %, 76.1 %, 8.0 %, 37.7 % and 16.7 %, respectively. In five <em>B. fragilis</em> strains, insertion sequences [<em>IS1187</em>(n = 3), <em>ISBf6</em>(n = 1), <em>IS612B</em>(n = 1)] were detected in the upstream region of <em>cfiA</em>. <em>NimE</em> with <em>ISBf6</em> on plasmid pBFM29b was detected in one <em>B. fragilis</em> strain, intermediate to metronidazole (MIC = 16 μg/mL). <em>ErmF</em> was the most abundant gene responsible for clindamycin resistance. <em>TetQ</em> and <em>tetX1</em> genes exhibited a higher frequency in strains that were not susceptible to tigecycline (MIC ≥8 μg/ml).</div></div><div><h3>Conclusions</h3><div>Monitoring the resistance trends of <em>Bacteroides</em> and related genera is crucial given the observed resistance to all classes of antibiotics and the presence of various resistance mechanisms.</div></div>","PeriodicalId":8050,"journal":{"name":"Anaerobe","volume":"90 ","pages":"Article 102912"},"PeriodicalIF":2.5,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号