Journal of medical microbiology最新文献

{"title":"Factors that contribute to the success of primary isolation of <i>Mycoplasma genitalium</i> from clinical samples.","authors":"Jose L Huaman, Catriona S Bradshaw, Teck-Phui Chua, Erica L Plummer, Jennifer A Danielewski, Lenka A Vodstrcil, Jorgen S Jensen, Suzanne M Garland, Natasha Wild, Gerald L Murray","doi":"10.1099/jmm.0.002040","DOIUrl":"10.1099/jmm.0.002040","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Mycoplasma genitalium</i>, a small and slow-growing bacterium, has gained notoriety due to rapidly increasing rates of antibiotic resistance.<b>Gap Statement.</b> <i>M. genitalium</i> is difficult to culture, limiting efforts to understand its biology and the mechanisms of antimicrobial resistance.<b>Aim.</b> To understand factors that influence success in primary isolation of <i>M. genitalium</i> from clinical samples.<b>Methodology.</b> Neat urine or swabs (high vaginal and anal, in universal transport medium) were collected from patients with confirmed or suspected <i>M. genitalium</i> infections attending the Melbourne Sexual Health Centre. The specimens were stored at -80 °C prior to laboratory analysis. Initial diagnosis was by transcription-mediated amplification (TMA) assay, and samples subsequently testing positive by quantitative PCR (qPCR) were washed twice and inoculated into Vero cell monolayers with a selective antibiotic mixture (cycloheximide and Thayer-Martin Medium I). Cultures were incubated at 37 °C with 5% CO₂ for 8 weeks and observed daily, with qPCR used to monitor growth.<b>Results.</b> In total, 127 TMA-positive samples were subjected to qPCR, and <i>M. genitalium</i> genomic DNA (gDNA) was detected in 53.5% (68/127) of these samples. An isolate was obtained from 26.5% (18/68) of the gDNA-positive samples following co-culture with Vero cells. The isolation rate varied between sample types, with growth detected in 12.5% (3/24) of the high vaginal swabs and 37.5% (15/40) of the urine samples. No isolates were obtained from anal swabs. The proportion with a successful culture was influenced by the initial <i>M. genitalium</i> load in the sample, which translated into the inoculum size for the Vero cell monolayer. Isolation was unsuccessful with low inoculum (<2,000 genome equivalents, geq), partially successful (13.3%) with a moderate inoculum (2,500-9,500 geq) and highly successful (100%) in samples with a high inoculum (>10,000 geq).<b>Conclusion.</b> The initial bacterial load emerged as a critical determinant of isolation success. This emphasizes the importance of optimizing sample collection and <i>M. genitalium</i> isolation procedures.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144562373","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}

{"title":"Distribution and prevalence of <i>Sarcina troglodytae</i> in chimpanzees and the environment throughout Africa.","authors":"Emily Dunay, Ismail Hirji, Leah A Owens, Konkofa Marah, Naomi Anderson, Maria Ruiz, Rebeca Atencia, Joshua Rukundo, Alexandra G Rosati, Megan F Cole, Melissa Emery Thompson, Jacob D Negrey, Samuel Angedakin, Johanna R Elfenbein, Tony L Goldberg","doi":"10.1099/jmm.0.002044","DOIUrl":"10.1099/jmm.0.002044","url":null,"abstract":"<p><p><b>Introduction.</b> Since 2005, the leading cause of death for western chimpanzees (<i>Pan troglodytes verus</i>) at Tacugama Chimpanzee Sanctuary (TCS) in Sierra Leone has been epizootic neurologic and gastroenteric syndrome (ENGS), associated with the bacterium <i>Sarcina troglodytae</i> (family <i>Clostridiaceae</i>).<b>Gap Statement.</b> The prevalence of <i>S. troglodytae</i> at TCS in clinically normal chimpanzees and the environment remains unknown, as does its distribution in other captive and wild chimpanzee populations and their environments across Africa.<b>Aim.</b> The aim of this study was to determine the distribution and prevalence of <i>Sarcina</i> bacteria in sanctuary and wild chimpanzee populations across Africa and to identify demographic and ecological risk factors for <i>S. troglodytae</i> in chimpanzees and the environment.<b>Methodology.</b> We conducted a prospective, multi-season epidemiological investigation of <i>S. troglodytae</i> in chimpanzees and the environment at TCS and a parallel study at a sanctuary in the Republic of Congo. We also describe the results of surveys of chimpanzees at a sanctuary in Uganda and wild chimpanzee populations in Sierra Leone and Uganda for <i>S. troglodytae</i>. In total, we tested 637 chimpanzee and environmental samples using a species-specific PCR for <i>S. troglodytae</i> and a pan-<i>Sarcina</i> PCR.<b>Results.</b> <i>S. troglodytae</i> was more prevalent in chimpanzees at TCS (<i>n</i>=60) during the dry season (96.7%) than during the rainy season (55.2%). Soil was the most common environmental source of the bacterium (54% dry season vs. 4.8% rainy season). Notably, we did not detect <i>S. troglodytae</i> in faecal samples from sanctuary chimpanzees in the Republic of Congo (<i>n</i>=79) or in wild chimpanzees in Sierra Leone (<i>n</i>=18). We did detect the bacterium in East African chimpanzees (<i>n</i>=84) but at low prevalence (2.6%-10.9%). In contrast, we found the genus <i>Sarcina</i> to be ubiquitous in all chimpanzee populations with a higher prevalence in sanctuary chimpanzees (93.1%-100%) than in wild chimpanzees (66.7%-68.4%).<b>Conclusion.</b> <i>S. troglodytae</i> is markedly more prevalent at TCS, the only location affected by ENGS, than at any other location tested, and soil is a likely reservoir of <i>S. troglodytae</i>. These findings strengthen the association between <i>S. troglodytae</i> and ENGS and have implications for sanctuary management and conservation of western chimpanzees.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144664135","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}

{"title":"Scanning electron microscopy and extended viability testing as a tool to evaluate the safety of MALDI-TOF extracts for risk group 3 spore-forming bacteria.","authors":"Kym S Antonation, Britni L Baron, Timothy F Booth, Daniel R Beniac, Cindi R Corbett","doi":"10.1099/jmm.0.001992","DOIUrl":"10.1099/jmm.0.001992","url":null,"abstract":"<p><p><b>Introduction.</b> Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS for rapid identification of risk group 3 (RG3) bacteria is impeded by the following two main limitations: (a) equipment and maintenance costs for instruments placed within containment and (b) lack of a validated inactivation protocol to move RG3 material to a lower containment level. A validated inactivation method would improve operations of public health laboratories by allowing safe triage of potential RG3 agents. Albeit a validated, zero-risk inactivation protocol is unlikely, scientific interrogation of methods to identify and mitigate procedural biosafety risks is vital for institutional risk assessment.<b>Gap.</b> To investigate the effect of a standard MALDI-TOF chemical extraction, hypothesized to alter cells, allowing passage through a filter and maintaining ability to replicate, this study paired visualization using a scanning electron microscope (SEM) with extended viability testing.<b>Aim.</b> This work is intended to support risk assessments for the removal of material from a containment laboratory for MALDI-TOF MS.<b>Methodology.</b> A standard set of <i>Bacillus cereus</i> and <i>Bacillus anthracis</i> vegetative and spore preparations was treated with a formic acid:acetonitrile extraction, with or without filtration, and plated on five types of media to monitor growth over 14 days. SEM images were taken of treated and untreated preparations, prior, during and after filtration across two filters. Reference beads provided accurate pore size measurements.<b>Results.</b> SEM demonstrated no difference in treated and untreated cells but did indicate the ineffectiveness of cellulose filters compared to PVDF filters. Growth was observed in preparations that did not include PVDF filtration, whereas all preparations (<i>n</i>=60) that included PVDF filtration were 100% non-viable. Although non-viability was observed, an important finding was the passage of 0.262 and 0.173 µm microspheres through the 0.1 µm PVDF filter. Growth of unfiltered preparations was detected between 1 and 7 days.<b>Conclusions.</b> This investigation demonstrates the value of interrogating materials used for bacterial inactivation, highlighting significant issues in the application of filters for exclusion purposes. Visual examination via SEM was key to providing evidence towards a low-risk inactivation method. These findings, with an understanding of limitations identified herein, can be used to inform risk assessments for the removal of RG3 bacteria from containment.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12263287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144644461","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}

{"title":"A simple silicone elastomer colonization model highlights complexities of <i>Candida albicans</i> and <i>Staphylococcus aureus</i> interactions in biofilm formation.","authors":"Gail McConnell, Liam M Rooney, Mairi E Sandison, Paul A Hoskisson, Katherine J Baxter","doi":"10.1099/jmm.0.002047","DOIUrl":"10.1099/jmm.0.002047","url":null,"abstract":"<p><p><b>Introduction.</b> Healthcare-associated infections (HAIs) significantly contribute to the burden of antimicrobial resistance. A major factor in HAIs is the colonization of indwelling medical devices by biofilm-forming opportunistic pathogens such as <i>Candida albicans</i> and <i>Staphylococcus aureus</i>. These organisms frequently co-infect, resulting in synergistic interactions with enhanced virulence and resistance to treatment.<b>Hypothesis/Gap statement.</b> <i>C. albicans</i> and <i>S. aureus</i> readily form dual-species biofilms on silicone elastomers, a commonly used medical device material, yet the colonization phenotypes of these organisms on such surfaces remain poorly understood.<b>Aim.</b> We aimed to develop a simple, optically tractable model to mimic the colonization of indwelling medical devices to investigate <i>C. albicans</i> and <i>S. aureus</i> biofilm formation.<b>Methodology.</b> The system utilizes discs of a silicone elastomer embedded in agar, reflecting device-associated conditions and enabling high-resolution imaging of biofilms formed by <i>C. albicans</i> and <i>S. aureus</i> co-cultures.<b>Results.</b> Initial results using the silicone elastomer colonization model reveal robust biofilm formation. These biofilms exhibited morphological differences between dual-species biofilms formed by <i>S. aureus</i> co-cultures with either yeast- or hyphal-form <i>C. albicans,</i> indicating the impact of differing <i>C. albicans</i> cell morphotypes in biofilm-associated medical device colonization on silicone elastomers. Quantification of biofilm formation by crystal violet staining provided further validation of the system.<b>Conclusion.</b> These findings underscore the importance of developing tools for biofilm study which more closely resemble the infectious microenvironment, with our work detailing such a system which can be employed in further study to improve strategies against device-related HAIs.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12282317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144628358","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}

{"title":"Fosfomycin resistance in extended-spectrum beta-lactamase producing <i>Escherichia coli</i> isolated from urinary tract-infected patients in a tertiary care hospital.","authors":"Priksha Thakur, Narinder Kaur, Shubham Chauhan, Reham Abdelmonem, Richard Donkor Amponsah","doi":"10.1099/jmm.0.002039","DOIUrl":"10.1099/jmm.0.002039","url":null,"abstract":"<p><p><b>Introduction.</b> Urinary tract infections (UTIs) are a significant global health concern, with <i>Escherichia coli</i> being the predominant pathogen responsible for uncomplicated and complicated cases. Fosfomycin has emerged as a promising oral treatment option for multidrug-resistant UTIs, particularly those caused by extended-spectrum <i>β</i>-lactamase (ESBL)-producing <i>E. coli</i>. However, fosfomycin resistance has been paralleled by its irrational use and the emergence of enzymes that modify fosfomycin in ESBL-producing <i>Enterobacteriaceae</i>, especially in Asia.<b>Hypothesis/Gap Statement.</b> There is limited data on the prevalence of fosfomycin resistance among UTI patients in Northern Haryana, India. We hypothesize that demographic factors such as age, gender and patient type (inpatient vs. outpatient) may influence the prevalence of fosfomycin resistance and also provide insights into the effectiveness of fosfomycin in combating ESBL-producing <i>E. coli</i> infections in a tertiary care setting.<b>Aim.</b> This study aimed to investigate the prevalence of fosfomycin resistance among ESBL-producing <i>E. coli</i> among UTI patients in a tertiary care hospital.<b>Methodology.</b> Between March 2023 and February 2024, 7,348 urine samples were received from patients suspected of UTIs. The samples were subjected to screening using wet film examination and standard microbiological methods. Antibiotic susceptibility testing was done by VITEK-2 Compact (using an N-235 card), and ESBL production was confirmed using the combination disc diffusion test.<b>Results.</b> Out of 7,348 urine samples, 1,176 (16%) were culture-positive, with <i>E. coli</i> accounting for 57% of the isolates. Among the 385 <i>E. coli</i> isolates, 224 (58%) were ESBL producers. Fosfomycin demonstrated high efficacy, with 95% susceptibility among ESBL-producing <i>E. coli</i> and 96% among non-ESBL producers. However, 5% of ESBL-producing <i>E. coli</i> isolates were resistant to fosfomycin. Resistance to other antibiotics, such as nalidixic acid (98%) and ampicillin (93%), was notably high. No significant associations were found between ESBL production and demographic factors such as age, gender or patient type (outpatient vs. inpatient).<b>Conclusion.</b> Fosfomycin remains a highly effective treatment option for ESBL-producing <i>E. coli</i> UTIs in Northern Haryana, India, with low resistance rates observed. However, the emergence of fosfomycin resistance, albeit minimal, highlights the need for continuous surveillance and rational use of antibiotics to combat the growing threat of antimicrobial resistance.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic value of nanopore-based metagenomic third-generation sequencing in the diagnosis of <i>Pneumocystis jirovecii</i> infection in patients with lung cancer.","authors":"Yuyan Luo, Wei Cheng, Lei Ma, Tiantian Wang, Weirong Shi","doi":"10.1099/jmm.0.002031","DOIUrl":"10.1099/jmm.0.002031","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Pneumocystis jirovecii</i> pneumonia (PJP, formerly known as <i>Pneumocystis carinii</i> pneumonia), an opportunistic fungal infection caused by the fungus <i>P. jirovecii</i>, is a severe pulmonary infection that primarily affects immunocompromised patients, including those with lung cancer. Traditional diagnostic methods for PJP, such as Grocott-Gomori's methenamine silver staining and real-time PCR, have limitations, including low positivity and high missed diagnosis rates.<b>Gap Statement.</b> Despite the critical need for accurate and sensitive diagnostic tools for PJP, especially in immunocompromised populations, existing methods fall short in providing the necessary reliability and efficiency.<b>Aim.</b> This study aims to evaluate the efficacy of nanopore-based metagenomic third-generation sequencing in diagnosing <i>P. jirovecii</i> infection in lung cancer patients, hypothesizing that this approach may offer superior sensitivity and specificity.<b>Methodology.</b> A prospective observational study was conducted on 118 lung cancer patients with suspected pulmonary <i>P. jirovecii</i> infection at the Sixth Hospital of Nantong City, China, from January 2021 to December 2023. The identification of pathogens in bronchoalveolar lavage fluid samples was performed using both metagenomics and traditional tests.<b>Results.</b> Metagenomics showed a significantly higher detection rate of <i>P. jirovecii</i> (33.0%) compared to methenamine silver staining (4.2%) and real-time PCR (30.5%). The sensitivity, specificity and accuracy of metagenomics detection were all 100%, which is markedly superior to traditional methods. Furthermore, metagenomics also identified mixed infections with other pathogens, such as <i>Cytomegalovirus</i> and Epstein-Barr virus.<b>Conclusion.</b> Metagenomics technology demonstrates high sensitivity and specificity in diagnosing <i>P. jirovecii</i> infection, including mixed infections with other pathogens, in lung cancer patients. It provides a clear direction for clinical treatment and is a powerful tool for diagnosing PJP, contributing to improved diagnostic efficiency and accuracy, reducing misdiagnosis and missed diagnosis rates and improving clinical outcomes in these patients.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224071/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556287","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}

{"title":"Clinical evaluation of two commercial PCR kits for the detection of nonviral sexually transmitted infections.","authors":"Alexandre Gaudin, Nadège Hénin, Marie Gardette, Cécile Bébéar, Sabine Pereyre","doi":"10.1099/jmm.0.002037","DOIUrl":"10.1099/jmm.0.002037","url":null,"abstract":"<p><p><b>Introduction.</b> Sexually transmitted infections (STIs) are a worldwide health issue with a high number of asymptomatic cases and the possibility of multiple infections.<b>Gap statement.</b> New multiplex real-time PCR kits targeting pathogens involved in nonviral STIs are regularly launched, but only some of them have been evaluated in comparative studies.<b>Aim.</b> This study evaluated the clinical performance of two multiplex real-time PCR commercial kits for the detection of <i>Chlamydia trachomatis</i>, <i>Neisseria gonorrhoeae</i>, <i>Mycoplasma genitalium</i> and <i>Trichomonas vaginalis</i>: the Bosphore STD Urethritis Mini Bundle Kit (BK; Anatolia Geneworks) and the Viasure Sexually Transmitted Disease Real-Time PCR Detection Kit (VK; CerTest BIOTEC).<b>Methodology.</b> A total of 240 clinical specimens were evaluated. The results were compared with those of the Cobas CT/NG and TV/MG kits (Roche Diagnostics), used as reference methods.<b>Results.</b> Positive agreement ranged between 83.3% and 87.8% for the detection of <i>C. trachomatis</i>, <i>N. gonorrhoeae</i> and <i>T. vaginalis</i> using validated specimen types. For <i>M. genitalium</i> detection, positive agreement was 83.0% for the BK and 68.1% for the VK, which missed 31.9% of <i>M. genitalium</i>-positive specimens. Negative agreement ranged between 98.4% and 100% across the targeted micro-organisms. Both kits were easy to use and compatible with several DNA extraction and PCR thermal cyclers. The VK also detected the genital commensal bacteria <i>Ureaplasma</i> spp. and <i>Mycoplasma hominis</i>, which should not be targeted in STI detection kits.<b>Conclusion.</b> Both kits are convenient methods and showed good performance for the detection of nonviral STIs, but users should be aware of a lower sensitivity of the VK for the detection of <i>M. genitalium</i>.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12231094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556286","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}

{"title":"The Ebola virus - going beyond the bleeding edge.","authors":"Saadiya K Umar, Mathew A Diggle","doi":"10.1099/jmm.0.001998","DOIUrl":"10.1099/jmm.0.001998","url":null,"abstract":"<p><p>The Ebola virus (EBV) genus is responsible for severe viral haemorrhagic illness caused by a group of viruses belonging to the Filoviridae family. Five species have been identified as causative agents for Ebola virus disease (EVD). The EBV (Zaire) strain is the most predominant organism involved in recorded EVD outbreaks and has been reported as the most virulent. EVD was first identified in the Democratic Republic of Congo in 1976 and has occurred in sporadic outbreaks over the last few decades with the most recent episode in Uganda over the period September 2022-January 2023. EVD is zoonotic in nature with bats as reservoir host and humans become infected via a spillover event from contact with infected animals. EVD is transmitted through contact with infected bodily fluids. It is considered fatal with a high mortality and high infectivity rate. Treatment is generally supportive with the availability of intravenous fluids and medicines. Research into vaccine development is ongoing. EVD is a particular public health concern given the potential for global spread during an outbreak.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12224072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556288","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}

{"title":"Patients in hospital with confirmed bacterial airway infection are significantly more likely to have a respiratory virus co-infection.","authors":"Yunas Panikkaveettil Hamza, Mohamed Ali Ben Hadj Kacem, Naema Hassan Al Molawi, Hadi Mohamad Yassine, Hebah Atef Mohammad AlKhatib, Fatiha Benslimane, Hanan Ibrahim Kh B Al-Remaihi, Reham Awni El Kahlout, Basema Ibrahim Ahmed El Kahlout, Hajar Al Khalili, Makiyeh Ahmed Al Khalili, Sanjay H Doiphode, Emad Bashier Ibrahim Elmagboul, Javed Akhter, Einas A/Aziz Eid Al Kuwari, Peter V Coyle","doi":"10.1099/jmm.0.001996","DOIUrl":"10.1099/jmm.0.001996","url":null,"abstract":"<p><p><b>Introduction.</b> Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed.<b>Gap Statement.</b> The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies.<b>Aim.</b> The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture.<b>Methodology.</b> A total of 83 lower airway samples - 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates - were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined.<b>Results.</b> Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ²: <i>P</i>=0.04; <i>P</i>=0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50-0.82); diagnostic accuracy 83.13% (73.32-90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ² (χ²: 2.4 <i>P</i>=0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection.<b>Conclusion.</b> Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12251083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144612769","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}

{"title":"The bibliometric analysis of documents concerning the relationship between the microbiota and urological malignancies.","authors":"Uygar Bağcı, Özlem Ulusan Bağcı","doi":"10.1099/jmm.0.002041","DOIUrl":"10.1099/jmm.0.002041","url":null,"abstract":"<p><p><b>Introduction.</b> The microbiota, which has a major impact on both health and illness, has recently become one of the most popular research topics.<b>Hypothesis/Gap statement.</b> To the best of our knowledge, no research has undertaken a bibliometric analysis of publications examining the connection between microbiome and urological cancer to date. In this respect, it is thought that our study will contribute to the literature.<b>Aim.</b> The purpose of this study is to raise awareness of the topic by performing a bibliometric analysis of the publications examining the connection between the microbiota and the most common urological cancers, including bladder, prostate, and kidney cancers.<b>Methodology.</b> All publications about prostate, renal and bladder cancers and microbiota indexed in Web of Science between 2000 and 2024 were included in the study.<b>Results.</b> A total of 310 publications were obtained. Before 2018, there were only three or fewer publications annually; however, following 2018, the number of publications increased rapidly, reaching a peak of 77 in 2024. The USA led with 98 (31.61%) documents, followed by China (60, 19.35%) and Italy (31, 10%). With 19 publications, Hirotsugu Uemura is the most contributing author, followed by Norio Nonomura with 17. Prostate cancer accounted for 45.48% of the publications, bladder cancer for 36.77% and kidney malignancies for 17.64%.<b>Conclusion.</b> Despite the fact that microbiota has been known for 80 years, research on the connection between microbiota and cancer accelerated after the completion of the Human Microbiome Project. The number of studies examining the connection between urological cancer and microbiota peaked in 2024 and is probably going to rise. More research is required on this topic, since the correlation between microbiota and especially prostate and bladder malignancies raises the possibility that variations in microbiota may be utilized in diagnosis, treatment and prognosis.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12222730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546669","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}