Access microbiology最新文献

Prevalence and characterization of β-lactamase-producing bacteria in gingivitis among diabetic and non-diabetic patients: a comparative microbiological study. 糖尿病和非糖尿病患者牙龈炎中β-内酰胺酶产生细菌的患病率和特征：一项比较微生物学研究。

Access microbiology Pub Date : 2025-10-03 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.001094.v3

Mohanned Mohamed Alwashsiah, Asma Abdellatif Abbas

{"title":"Prevalence and characterization of β-lactamase-producing bacteria in gingivitis among diabetic and non-diabetic patients: a comparative microbiological study.","authors":"Mohanned Mohamed Alwashsiah, Asma Abdellatif Abbas","doi":"10.1099/acmi.0.001094.v3","DOIUrl":"10.1099/acmi.0.001094.v3","url":null,"abstract":"Background. Gingivitis is a reversible gingival inflammation that may progress to periodontitis if untreated. Diabetes mellitus alters the oral microbiota and weakens host defenses, increasing susceptibility to infection. Objectives. To investigate the prevalence and characterization of β-lactamase-producing bacteria isolated from gingival swabs of diabetic and non-diabetic patients with clinically confirmed gingivitis. Methods. Thirty-seven patients were enrolled (17 diabetics and 20 non-diabetics). Gingival swabs were cultured and identified by conventional microbiological and analytical profile index (API). Antimicrobial susceptibility was tested according to the Clinical and Laboratory Standards Institute 2023 guidelines. β-Lactamase activity was assessed using an iodometric colourimetric assay. Results. A total of 65 bacterial isolates were obtained from 37 gingivitis patients. Polymicrobial infections predominated in diabetics (82.4%) vs. non-diabetics (45.0%). Non-diabetics were mainly colonized by Streptococcus mutans (45.9%) and Staphylococcus aureus (40.5%), while diabetics harboured more Gram-negative species, particularly Pseudomonas aeruginosa (21.4%) and Enterobacteriaceae (46.4 % vs. 2.7 %). Overall, 67.7 % of isolates were β-lactamase producers. Resistance was highest to ampicillin (92.3%) and amoxicillin-clavulanate (84.6%), whereas ciprofloxacin (89.2%) and piperacillin-tazobactam (78.5%) retained the greatest activity. Conclusions. Diabetes is associated with increased microbial diversity, Gram-negative colonization, and a frequency of β-lactamase-producing bacteria in gingivitis. These findings highlight diabetes as a risk factor for resistant oral infections and underscore the need for antimicrobial stewardship, resistance surveillance and future molecular studies to clarify resistance mechanisms in high-risk groups.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12494487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145234740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Articular flare-up of systemic scleroderma revealing a rare form of tuberculosis of the shoulder and extensor tendons: a case report and literature review. 关节突发的系统性硬皮病揭示一种罕见形式的结核肩和伸肌腱：一个病例报告和文献复习。

Access microbiology Pub Date : 2025-10-01 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.001023.v3

H Zouaki, H Laatiris, L Taoubane, A Mejjad, H Toufik, N Elouardi, A Bezza

引用次数: 0

SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data. SNiPgenie：从全基因组测序数据中检测微生物SNP位点的工具。

Access microbiology Pub Date : 2025-09-22 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.001021.v3

Damien Farrell, Viktor Perets, Stephen V Gordon

引用次数: 0

In vitro activity of cefiderocol against Pseudomonas aeruginosa isolated from adult patients with cystic fibrosis. 头孢地洛尔体外抗囊性纤维化成人铜绿假单胞菌活性的研究。

Access microbiology Pub Date : 2025-09-19 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.001001.v3

Saied Ali, Sinead McDermott

{"title":"In vitro activity of cefiderocol against Pseudomonas aeruginosa isolated from adult patients with cystic fibrosis.","authors":"Saied Ali, Sinead McDermott","doi":"10.1099/acmi.0.001001.v3","DOIUrl":"10.1099/acmi.0.001001.v3","url":null,"abstract":"Background. Pseudomonas aeruginosa is a key pathogen in cystic fibrosis (CF), driving pulmonary decline and exhibiting resistance through virulence factors and adaptive mutations. Cefiderocol (FDC) is a novel siderophore cephalosporin with activity against Gram-negative bacteria. We aimed to assess the in vitro efficacy of FDC against P. aeruginosa isolates in a CF population. Methods. The study was conducted in a tertiary hospital with a specialist adult CF service. All first isolates of significant respiratory pathogens among this cohort are cryopreserved at -80 °C. Antimicrobial susceptibility testing to FDC was performed as per European Committee on Antimicrobial Susceptibility Testing Disk-Diffusion (version 10) for all stored isolates of P. aeruginosa from 2017 to 2022 inclusive. Results. Eighty-five isolates from seventy-one patients were included. Resistance phenotypes comprised 19% (n=16) multidrug-resistant (MDR), 16% (n=14) extensively drug-resistant (XDR) and 24% (n=20) pandrug-resistant (PDR), with 24 % (n=20) exhibiting the mucoid phenotype. Overall, 85% of isolates were susceptible to FDC, with a mean inhibition zone of 25.2 mm. Antimicrobial activity was retained in 81% of MDR, 86% of XDR, 60% of PDR and 90% of mucoid isolates. Seventy-four per cent of meropenem-non-susceptible isolates remained susceptible to FDC, compared with lower susceptibility to ceftolozane-tazobactam (42%), tobramycin (36%) and ciprofloxacin (22%). Conclusion. FDC exhibited excellent in vitro activity against P. aeruginosa from adults with CF, including highly resistant and mucoid phenotypes. These findings highlight its potential as a salvage option in this high-risk population and provide the first Irish surveillance data to inform antimicrobial stewardship and future clinical use.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection of ERG11 gene mutation in coding and non-coding regions of clinical Candida glabrata (Nakaseomyces glabratus) isolates from Pakistan. 巴基斯坦临床脱落假丝酵母（Nakaseomyces glabratus）编码区和非编码区ERG11基因突变检测

Access microbiology Pub Date : 2025-09-19 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000952.v6

Saba Memon, Najia Karim Ghanchi, Urooj Zafar, Joveria Farooqi, Sadaf Zaka, Kauser Jabeen

{"title":"Detection of ERG11 gene mutation in coding and non-coding regions of clinical Candida glabrata (Nakaseomyces glabratus) isolates from Pakistan.","authors":"Saba Memon, Najia Karim Ghanchi, Urooj Zafar, Joveria Farooqi, Sadaf Zaka, Kauser Jabeen","doi":"10.1099/acmi.0.000952.v6","DOIUrl":"10.1099/acmi.0.000952.v6","url":null,"abstract":"Azoles inhibit the cytochrome P450-dependent enzyme lanosterol 14α-demethylase (CYP51) that is encoded by the ERG11 gene. Azole resistance in Candida species arises through different mechanisms, like mutations in the ERG11 gene, ERG11 overexpression, CDR1,2 (Candida drug resistance) overexpression that actively efflux azole drugs, reducing their intracellular concentration and therapeutic effectiveness, and biofilm formation. We sequenced the ERG11 gene to determine mutations in the coding and non-coding regions of ERG11 in clinical isolates of Candida glabrata (Nakaseomyces glabratus) from Pakistan. Eight C. glabrata (N. glabratus) strains from our fungal strain bank (five fluconazole-resistant and three susceptible dose-dependent) were revived and used. The ERG11 gene was amplified by PCR, sequenced using the Sanger methodology and analysed using bioinformatic tools. We identified a change in nucleotide at c. -66 T/G upstream of the start codon ATG in the promoter region of the ERG11 gene in fluconazole-resistant C. glabrata (N. glabratus). Within the downstream (coding region), where numbering begins at the ATG start codon as position +1, two novel synonymous mutations at positions T300C and T834C and previously reported synonymous mutations T768C, A1023G, T1557A and A1581G were also observed. This is the first study evaluating ERG11 mutations in C. glabrata (N. glabratus) from Pakistan. The clinical significance of such uncommon ERG11 gene mutations, such as c. -66 T/G, should be explored further through correlation with treatment outcome data.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451296/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel case of prosthetic joint infection due to Clostridioides difficile successfully suppressed with oral doxycycline. 口服强力霉素成功抑制难辨梭菌引起的假体关节感染一例。

Access microbiology Pub Date : 2025-09-19 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000943.v3

Holly Jordan, Rikki Graham, Sanmarie Schlebusch, Aileen Oon, Hemalatha Varadhan, Syeda Naqvi

{"title":"A novel case of prosthetic joint infection due to Clostridioides difficile successfully suppressed with oral doxycycline.","authors":"Holly Jordan, Rikki Graham, Sanmarie Schlebusch, Aileen Oon, Hemalatha Varadhan, Syeda Naqvi","doi":"10.1099/acmi.0.000943.v3","DOIUrl":"10.1099/acmi.0.000943.v3","url":null,"abstract":"Extra-colonic infections caused by Clostridioides difficile are exceptionally rare, with prosthetic joint infections (PJIs) comprising only a small fraction of the reported cases. Moreover, there is limited guidance on the optimal management of such infections. We present the case of a 76-year-old man who developed a left hip PJI due to C. difficile 6 weeks after undergoing surgical revision for a periprosthetic fracture. Given the complexity of the case, curative surgical intervention was not considered feasible. The patient was treated with repeated debridement, intravenous vancomycin and oral (PO) metronidazole, followed by successful suppression with PO doxycycline - a novel therapeutic approach not previously documented. To date, only seven cases of C. difficile-associated PJI have been reported in the literature; this is the first known instance in which suppression of a C. difficile PJI has been achieved and the first to utilize whole-genome sequencing for further analysis of the isolate.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of the efficacy of chlorous acid water and sodium hypochlorite solution against SARS-CoV-2 in the presence of organic matter. 有机物存在下氯酸水和次氯酸钠溶液对SARS-CoV-2的防治效果评价

Access microbiology Pub Date : 2025-09-19 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000984.v3

Basirat Mojisola Lawal-Ayinde, Kosuke Oda, Abeer Mohamed Abdelfattah Elsayed, Tomoyuki Akita, Miuko Kurose, Hiroaki Sasaki, Toshihito Nomura, Akima Yamamoto, Akifumi Higashiura, Isanori Horiuchi, Hisataka Goda, Takemasa Sakaguchi

{"title":"Evaluation of the efficacy of chlorous acid water and sodium hypochlorite solution against SARS-CoV-2 in the presence of organic matter.","authors":"Basirat Mojisola Lawal-Ayinde, Kosuke Oda, Abeer Mohamed Abdelfattah Elsayed, Tomoyuki Akita, Miuko Kurose, Hiroaki Sasaki, Toshihito Nomura, Akima Yamamoto, Akifumi Higashiura, Isanori Horiuchi, Hisataka Goda, Takemasa Sakaguchi","doi":"10.1099/acmi.0.000984.v3","DOIUrl":"10.1099/acmi.0.000984.v3","url":null,"abstract":"Chlorous acid water and sodium hypochlorite solution are effective disinfectants against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that caused the pandemic. Recent studies have shown that both compounds have equivalent inactivation effects when tested on purified viruses. However, in practical applications, the presence of organic matter is common and can significantly affect disinfectant performance. We conducted several experiments comparing these two disinfectants under different conditions to better understand their practical efficacy. When an infected cell culture medium (serum-free) was used as the test virus, chlorous acid water and sodium hypochlorite solution showed reduced efficacy. This decrease was attributed to the presence of aa in the medium. Notably, sodium hypochlorite solution showed a more pronounced reduction in potency compared with chlorous acid water. In addition, we evaluated the SARS-CoV-2 inactivation effects of chlorous acid water and sodium hypochlorite solution under various organic loading conditions simulating real-world contamination scenarios such as blood, vomit and saliva. The organic materials used included BSA, SRBCs, polypeptone, FBS and artificial saliva. The results showed that chlorous acid water demonstrated superior resilience to organic matter interference compared with sodium hypochlorite solution. These results suggest that chlorous acid water may be more effective than sodium hypochlorite solution in inactivating viruses on contaminated surfaces, particularly in healthcare settings where organic contamination is common. In summary, our research suggests that chlorous acid water may be a more effective disinfectant in practical settings.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells. 直接RNA测序揭示了sars - cov -2感染的HEK细胞中m6A的修饰和异构体的变化。

Access microbiology Pub Date : 2025-09-17 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.001019.v3

Ilhan Cem Duru, Zlatka Plavec, Anne Ylinen, Pia Laine, Martyn James, Lotta Riihimäki, Sarah J Butcher, Maria Anastasina, Petri Auvinen

{"title":"Direct RNA sequencing reveals m6A modifications and isoform changes in SARS-CoV-2-infected HEK cells.","authors":"Ilhan Cem Duru, Zlatka Plavec, Anne Ylinen, Pia Laine, Martyn James, Lotta Riihimäki, Sarah J Butcher, Maria Anastasina, Petri Auvinen","doi":"10.1099/acmi.0.001019.v3","DOIUrl":"10.1099/acmi.0.001019.v3","url":null,"abstract":"The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection triggers complex host responses, including alterations in RNA transcription and modification. Understanding these changes is crucial for elucidating viral pathogenesis and identifying potential therapeutic targets. We used direct RNA sequencing to comprehensively profile the transcriptomic and epitranscriptomic landscapes of human HEK-AT cells infected with SARS-CoV-2 at 8 h post-infection, compared to mock controls. We analysed viral and host transcriptomes, focusing on gene and transcript expression, isoform usage and RNA m6A modifications. Viral RNA sequencing reads showed 3' end-biassed coverage indicative of subgenomic RNA synthesis, with high expression of N gene subgenomic RNA reads. Sixteen m6A modification sites were consistently identified in the viral genome, primarily within the ORF1ab and S genes. In the human transcriptome, we found 254 positions with significantly altered m6A modification rates, with 119 showing decreased modification and 135 showing increased modification in infected cells. Genes with decreased m6A modifications were enriched in the neurotrophin signalling pathway. Transcript-level analysis identified 19 upregulated and 12 downregulated transcripts. Notably, transcript discovery and quantification revealed a novel isoform of the HIST1H2BK gene, which was significantly more expressed in infected cells compared to mock controls. Isoform switching analysis revealed 24 significant switches involving 21 genes, implicating mitochondrial reprogramming and immune-related pathways. In conclusion, this study provides a detailed, direct RNA sequencing-based characterization of host-virus RNA interactions, revealing key insights into SARS-CoV-2 infection mechanisms and potential therapeutic targets.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A hydrocele revealing epididymal tuberculosis. 鞘膜积液显示附睾结核。

Access microbiology Pub Date : 2025-09-10 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000781.v4

Yassine Ben Lahlou, Zakaria Laanibi, Zakaria Malihy, Elmostapha Benaissa, Adil Maleb, Abderrahim Elktaibi, Mariama Chadli, Mostafa Elouennass

引用次数: 0

Allele-linked divergence in SlpA and TcdB drives distinct immune and cytotoxic responses that distinguish ST01 from non-ST01 strains in Clade 2 Clostridioides difficile. SlpA和TcdB等位基因连锁差异驱动不同的免疫和细胞毒性反应，区分ST01和非ST01菌株。

Access microbiology Pub Date : 2025-09-10 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000994.v3

Adriana Badilla-Lobo, Carlos Quesada-Gómez, Esteban Chaves-Olarte, César Rodríguez

{"title":"Allele-linked divergence in SlpA and TcdB drives distinct immune and cytotoxic responses that distinguish ST01 from non-ST01 strains in Clade 2 Clostridioides difficile.","authors":"Adriana Badilla-Lobo, Carlos Quesada-Gómez, Esteban Chaves-Olarte, César Rodríguez","doi":"10.1099/acmi.0.000994.v3","DOIUrl":"10.1099/acmi.0.000994.v3","url":null,"abstract":"Among the five MLST clades that define the global population structure of the bacterial pathogen Clostridioides difficile, Clade 2 has received special attention due to the global spread, clinical severity and hospital prevalence of ST01 strains. To identify features potentially contributing to the historically attributed higher virulence and epidemic potential of ST01 strains, we compared a range of phenotypic traits across the infection cycle between clinical Clade 2 ST01 and non-ST01 strains from ST41, ST47, ST67, ST154 and ST638. We found no significant differences in canonical virulence-associated characteristics such as spore adherence, motility, biofilm formation and resistance to a disinfectant. However, ST01 strains exhibited distinct profiles in surface layer protein A (SlpA)-mediated immune activation and toxin B (TcdB)-induced cytotoxicity that were consistent with allelic divergence. These findings highlight the need to reconsider current paradigms of Clade 2 hypervirulence and underscore the importance of allele-specific phenotypic variation in developing targeted public health strategies.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12451308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0