Journal of medical microbiology最新文献

{"title":"The Apoprotein E4 isotype does not affect the severity of COVID-19 infection and other flu-like syndromes.","authors":"Marina Carvalho-Rassbach, Lucas Haniel Araujo Ventura, Larissa Oliveira Assis, Sabrina Fabrini, Manuelle Maria Pereira Natividade, Janayne Luihan Silva, Karina Braga Gomes, Ana Maria Caetano Faria, Jacqueline I Alvarez-Leite","doi":"10.1099/jmm.0.001951","DOIUrl":"10.1099/jmm.0.001951","url":null,"abstract":"<p><p><b>Introduction.</b> Apolipoprotein E (ApoE), especially the ApoE4 isotype, is suggested to influence the severity of respiratory viral infections; however, this association is still unclear.<b>Hypothesis.</b> The presence of allele ε4 impacts the development of flu-like syndromes.<b>Aim.</b> This study aimed to evaluate the impact of the Apo E4 isoform on the severity and duration of flu-like syndromes, including the coronavirus disease COVID-19.<b>Methodology.</b> This study comprised 280 individuals presenting flu-like symptoms, all genotyped for ApoE isoforms. Data were collected on clinical course, comorbidities, nutritional status, biochemical and inflammatory markers, SARS-CoV-2 reverse transcription PCR results and disease severity (mild, moderate or severe) according to the World Health Organization criteria. The individuals were analysed as a whole and within subgroups based on the SARS-CoV-2-positive (COVID-19 group) or SARS-CoV-2-negative (flu-like syndrome group) test.<b>Results.</b> The frequency of the ε4 allele was similar across the whole population and in both the COVID-19 and flu-like syndrome subgroups (17 and 18%, respectively). No differences were seen in sex, age range, self-reported skin colour, body mass index (BMI), number of comorbidities, vaccination status, biochemical, cytokine and lipid profiles (except for total cholesterol) in the flu-like group when ε4 allele carriers and non-carriers were compared. In the COVID-19 group, the ε4 allele did not correlate with disease severity or duration, number of comorbidities or inflammatory biomarkers. While gender distribution was equal in the overall COVID-19 population, male gender strongly correlated with COVID-19 severity. Multivariate analysis showed that older individuals, male gender, higher BMI and the presence of comorbidities were linked to increased chances of developing moderate and severe disease. IL-4 was the only factor found to reduce the risk of severe COVID-19.<b>Conclusion.</b> The presence of one ɛ4 allele showed no association with the duration and severity of flu-like syndromes, including COVID-19. Nonetheless, SARS-CoV-2-positive individuals tend to be older men with a higher BMI and a tendency to be overweight or with obesity. Regarding COVID-19 severity, BMI, male sex and the number of associated comorbidities were the factors that increased the chance of developing a more severe form of COVID-19.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143018994","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":"Hybrid strains of enterotoxigenic/Shiga toxin-producing <i>Escherichia coli</i>, United Kingdom, 2014-2023.","authors":"Ella V Rodwell, David R Greig, Suzanne Gokool, Israel Olonade, Craig Swift, Yung-Wai Chan, Claire Jenkins","doi":"10.1099/jmm.0.001946","DOIUrl":"10.1099/jmm.0.001946","url":null,"abstract":"<p><p><b>Introduction.</b> Diarrhoeagenic <i>Escherichia coli</i> (DEC) pathotypes are defined by genes located on mobile genetic elements, and more than one definitive pathogenicity gene may be present in the same strain. In August 2022, UK Health Security Agency (UKHSA) surveillance systems detected an outbreak of hybrid Shiga toxin-producing <i>E. coli</i>/enterotoxigenic <i>E. coli</i> (STEC-ETEC) serotype O101:H33 harbouring both Shiga toxin (<i>stx</i>) and heat-stable toxin (<i>st</i>).<b>Gap statement.</b> These hybrid strains of DEC are a public health concern, as they are often associated with enhanced pathogenicity. However, little is known about their epidemiology, clinical significance and associated public health burden.<b>Aim.</b> The aim of this study was to describe the microbiology, epidemiology and genomic analysis of this novel hybrid serotype in the context of the STEC-ETEC strains in the UKHSA archive.<b>Methodology.</b> From 2014 to 2023, STEC isolated from faecal specimens testing positive for STEC by PCR were sequenced on the NextSeq 1000 short read platform and a subset were selected for long read nanopore sequencing. Genomes were analysed to determine serotype, <i>stx</i> subtype, DEC pathogenicity genes and antimicrobial resistance determinants.<b>Results.</b> There were 162 STEC-ETEC strains isolated between 2014 and 2023, of which 117/162 were human clinical isolates and 45 were of food or animal origin. An average of 16 STEC-ETEC strains were identified each year, exhibiting a range of different <i>stx</i> subtypes, the most common profiles being <i>stx2g,st</i> (<i>n</i>=65, 40%) and <i>stx2a,st</i> (<i>n</i>=48, 30%). The most common sequence types were ST329 and ST200 (<i>n</i>=24 each), and the most frequently detected serotype was O187:H28 (<i>n</i>=25). Nine cases of genetically linked STEC-ETEC O101:H33, <i>stx1a,st</i> were detected between 8 August and 21 September 2022. Although the temporal and geographical distribution of the cases was characteristic of a foodborne outbreak, the contaminated vehicle was not identified.<b>Conclusions.</b> Phylogenetic analysis and long-read sequencing of the outbreak strain provided insight into the stepwise acquisition of <i>st</i> and <i>stx</i> and the evolutionary history of STEC-ETEC pathotypes. The integration of epidemiological data and whole-genome sequencing for routine surveillance of gastrointestinal pathogens is key to understanding the emergence of zoonotic hybrid DEC pathotypes and monitoring foodborne threats to public health.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11753528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061854","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":"Inactivation of <i>Candida albicans</i>, <i>Staphylococcus aureus</i> and multidrug-resistant <i>Escherichia coli</i> with dielectric barrier discharged cold atmospheric plasma: a comparative study with antimicrobial drugs.","authors":"Punam Talukdar, Reetesh Borpatra Gohain, Pranami Bharadwaj, Debajit Thakur, Subir Biswas","doi":"10.1099/jmm.0.001965","DOIUrl":"10.1099/jmm.0.001965","url":null,"abstract":"<p><p><b>Introduction.</b> Cold atmospheric plasma (CAP) has emerged as a promising technology for neutralizing microbes, including multidrug-resistant strains. This study investigates CAP's potential as an alternative to traditional antimicrobial drugs for microbial inactivation.<b>Hypothesis/Gap Statement.</b> In the era of increasing antimicrobial resistance, there is a persistent need for alternative antimicrobial strategies. CAP exerts its effects by generating reactive oxygen and nitrogen species (RONS), but its comparative efficacy against antimicrobial drugs requires further exploration.<b>Aim.</b> To evaluate the antimicrobial efficacy of CAP in inactivating multidrug-resistant <i>Escherichia coli</i> (ATCC BAA-2469), <i>Staphylococcus aureus</i> (MTCC 96) and <i>Candida albicans</i> (MTCC 227) and to compare its effectiveness with standard antimicrobial drugs.<b>Methodology.</b> CAP, produced by an indigenously developed dielectric barrier discharge (DBD) setup comprising a quartz-glass-covered high-voltage electrode and a grounded stainless steel mesh electrode, was used to treat three pathogenic samples with varying treatment times (0-60 s). The zone of inhibition (ZoI; zone where microbes cannot grow) induced by CAP was compared with the ZoI of selected antimicrobial drugs (5-300 mcg). Scanning electron microscopy (SEM) analysed morphological changes, while optical emission spectroscopy (OES) detected RONS generated during treatment. Growth curve analysis assessed CAP's impact on microbial growth, and statistical analysis compared CAP-induced ZoI with drug-induced ZoI.<b>Results.</b> CAP treatment produced substantial ZoI against <i>E. coli</i>, <i>S. aureus</i> and <i>C. albicans,</i> with the largest ZoI (1194±35.35 mm²) in <i>C. albicans</i> after 60 s. DBD-CAP showed equivalent or superior efficacy compared with selected antimicrobial drugs based on ZoI comparisons. SEM revealed extensive cellular damage in all three pathogens, with visible morphological disruption within 60 s. Growth curve analysis showed a significant delay in microbial proliferation with increasing CAP exposure, effectively inhibiting growth over 24 h. OES confirmed the presence of RONS-related molecular bands [N₂(C-B), N₂ ⁺(B-X) and OH(A-X)] and atomic O lines in the CAP.<b>Conclusion.</b> CAP treatment exhibits equivalent or superior antimicrobial activity compared to selected antimicrobial drugs. CAP treatment exerts effects by inactivating pathogens, disintegrating cellular morphology and delaying microbial growth. These findings highlight CAP as a promising alternative to prolonged treatments, addressing antimicrobial resistance and advancing clinical strategies.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070362","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":"Impact of dairy calf management practices on the intestinal tract microbiome pre-weaning.","authors":"Aisling Carroll, Matt J Bell, Emma C L Bleach, Dann Turner, Lisa K Williams","doi":"10.1099/jmm.0.001957","DOIUrl":"10.1099/jmm.0.001957","url":null,"abstract":"<p><p><b>Introduction.</b> Microbiota in the gastrointestinal tract (GIT) consisting of the rumen and hindgut (the small intestine, cecum and colon) in dairy calves play a vital role in their growth and development. This review discusses the development of dairy calf intestinal microbiomes with an emphasis on the impact that husbandry and rearing management have on microbiome development, health and growth of pre-weaned dairy calves.<b>Discussion.</b> The diversity and composition of the microbes that colonize the lower GIT (small and large intestine) can have a significant impact on the growth and development of the calf, through influence on nutrient metabolism, immune modulation, resistance or susceptibility to infection, production outputs and behaviour modification in adult life. The colonization of the calf intestinal microbiome dynamically changes from birth, increasing microbial richness and diversity until weaning, where further dynamic and drastic microbiome change occurs. In dairy calves, neonatal microbiome development prior to weaning is influenced by direct and indirect factors, some of which could be considered stressors, such as maternal interaction, environment, diet, husbandry and weaning practices. The specific impact of these can dictate intestinal microbial colonization, with potential lifelong consequences.<b>Conclusion.</b> Evidence suggests the potential detrimental effect that sudden changes and stress may have on calf health and growth due to management and husbandry practices, and the importance of establishing a stable yet diverse intestinal microbiome population at an early age is essential for calf success. The possibility of improving the health of calves through intestinal microbiome modulation and using alternative strategies including probiotic use, faecal microbiota transplantation and novel approaches of microbiome tracking should be considered to support animal health and sustainability of dairy production systems.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143061857","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":"Prevalence, aetiology and antimicrobial resistance profile of diabetic individuals suffering from community-acquired urinary tract infection.","authors":"Ankita Priyadarshini, Priyal Kalola, Hemantkumar Patadia, Janvi Shah, Ajit Gangawane","doi":"10.1099/jmm.0.001962","DOIUrl":"10.1099/jmm.0.001962","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; The rise in antimicrobial resistance poses a significant threat to global health, particularly among diabetic patients who are prone to urinary tract infections (UTIs).&lt;b&gt;Hypothesis.&lt;/b&gt; Pathogens that cause UTI among diabetic patients exhibit significant multidrug resistance (MDR) patterns, necessitating more precise empirical treatment strategies.&lt;b&gt;Aim&lt;/b&gt;. This study aimed to determine the prevalence of UTI among diabetic patients and study the antimicrobial susceptibility profiles of uropathogens, detected and identified the potential differences in age groups and between genders, focusing on MDR and gender-based variations, causing a global concern in deciding empirical treatment.&lt;b&gt;Methodology.&lt;/b&gt; A prospective study was conducted from August 2021 to December 2023 in Gujarat, India. During the period, 1023 diabetic patients with symptoms of UTI were diagnosed by urine culture and 280 individuals tested positive for UTIs. Antibiotic susceptibility testing was carried out on these 280 micro-organism isolates.&lt;b&gt;Results.&lt;/b&gt; Among the 280 UTI-positive patients, 166 (59.29%) were females and 114 (40.71%) were males, with the prevalence of UTI in diabetic females being 27.34% (166/607) and males being 27.40% (114/416). Among the isolated uropathogens, &lt;i&gt;Escherichia coli&lt;/i&gt; (56.78%) was the predominant organism followed by &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; (13.57%) and &lt;i&gt;Klebsiella&lt;/i&gt; (13.21%). High resistance was noted to various antibiotics in Gram-negative bacteria including both genders. In &lt;i&gt;E. coli&lt;/i&gt;, resistance was predominantly high against the penicillin sub-class of the beta-lactam group (70.23%, 69.58%), cephalosporins (66.23%, 76.52%) and least against nitrofurans (30.10%, 40%) in males and females, respectively. &lt;i&gt;Klebsiella&lt;/i&gt; has shown higher resistance to cephalosporins (66.23%, 76.52%) and aminoglycosides (60.92%, 62.66%) and least resistance to carbapenem (41.67%) and phosphonic (33.33%) in males and females, respectively. A high proportion of isolates, ~82.5%, exhibited MDR. Among these MDR isolates, those from female patients accounted for a higher percentage (58.44%) compared with males (41.55%). The highest prevalence of MDR was observed in the 41-60-year age group. This pattern highlights notable differences in MDR prevalence across gender and age groups.&lt;b&gt;Conclusion.&lt;/b&gt; The high prevalence of UTI caused by MDR organisms based on gender and age group highlights the need for clinicians to choose antibiotics more judiciously for empirical treatment, thereby reducing misuse and overuse in the community. For diabetic UTI patients in this region, nitrofurantoin may be recommended for uncomplicated cases due to low resistance in &lt;i&gt;E. coli&lt;/i&gt;, while fosfomycin could be a viable alternative for &lt;i&gt;Klebsiella&lt;/i&gt;-related infections. Carbapenems may be reserved for severe cases with MDR pathogens, and combination therapy could be considered for complicated infections, particularly in high-risk ag","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143054693","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":"Prospective evaluation of different faecal preservation media for travellers' diarrhoea diagnostic application with multiplex PCR BioFire FilmArray in resource-limited settings.","authors":"R Toriro, S D Woolley, I Hale, C J Bennett, C J Phelps, W D Nevin, D S Burns, T Edwards, N J Beeching, M K O'Shea, T E Fletcher","doi":"10.1099/jmm.0.001954","DOIUrl":"10.1099/jmm.0.001954","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; Immediate identification of travellers' diarrhoea-causing pathogens may not be possible in remote settings, but samples can be stored for epidemiological and related research. We collected pilot data to evaluate the utility of three different preservation media for testing stored faecal samples compared to immediate testing of fresh samples using the BioFire&lt;sup&gt;®&lt;/sup&gt; FilmArray&lt;sup&gt;®&lt;/sup&gt; multiplex PCR gastrointestinal panel (bioMérieux).&lt;b&gt;Gap statement.&lt;/b&gt; No previous studies have demonstrated the utility of testing faecal samples directly by PCR BioFire&lt;sup&gt;®&lt;/sup&gt; FilmArray&lt;sup&gt;®&lt;/sup&gt; following prolonged storage and transportation in OMNIgene&lt;sup&gt;®&lt;/sup&gt;, DNA&lt;sup&gt;™&lt;/sup&gt; shield and FTA&lt;sup&gt;™&lt;/sup&gt; cards.&lt;b&gt;Aims.&lt;/b&gt; To evaluate the reliability of OMNIgene&lt;sup&gt;®&lt;/sup&gt;, DNA shield&lt;sup&gt;™&lt;/sup&gt; and FTA&lt;sup&gt;™&lt;/sup&gt; card faecal storage and transport media in parallel, compared to initial testing of fresh faeces obtained from the same individuals at the time of presentation with diarrhoea in the field compare the results of faecal samples stored and transported at ambient temperature in OMNIgene&lt;sup&gt;®&lt;/sup&gt;, DNA shield&lt;sup&gt;™&lt;/sup&gt; and FTA&lt;sup&gt;™&lt;/sup&gt; cards then tested using PCR BioFire&lt;sup&gt;®&lt;/sup&gt; FilmArray&lt;sup&gt;®&lt;/sup&gt; 6-18 months later with those obtained from fresh faecal samples during a diarrhoea outbreak.&lt;b&gt;Methodology.&lt;/b&gt; Fresh faecal samples were obtained from British military personnel who developed diarrhoea during deployment to Kenya between February-April 2022. Unpreserved fresh samples were tested onsite using PCR BioFire&lt;sup&gt;®&lt;/sup&gt; FilmArray&lt;sup&gt;®&lt;/sup&gt; and corresponding samples were stored at ambient temperature in OMNIgene&lt;sup&gt;®&lt;/sup&gt;200 (DNAgenotek&lt;sup&gt;®&lt;/sup&gt;), DNA/RNA shield DX&lt;sup&gt;™&lt;/sup&gt; (Zymo Research) and Whatman FTA™ Elute cards (GE Healthcare) then repatriated to the UK for direct testing by PCR BioFire&lt;sup&gt;®&lt;/sup&gt; FilmArray&lt;sup&gt;®&lt;/sup&gt;, 6-18 months later. The most common enteropathogens evaluated were: &lt;i&gt;Cryptosporidium&lt;/i&gt; spp., Enteroaggregative &lt;i&gt;Escherichia coli&lt;/i&gt; (&lt;i&gt;E. coli&lt;/i&gt;; EAEC), Enteropathogenic &lt;i&gt;E. coli&lt;/i&gt; (EPEC), Shiga toxin-producing &lt;i&gt;E. coli&lt;/i&gt; (STEC) and &lt;i&gt;Campylobacter&lt;/i&gt; spp. Test results for the three storage modalities were compared to the fresh sample tests as a reference standard.&lt;b&gt;Results.&lt;/b&gt; Samples from 60 individuals [80% male; median (interquartile range) age 24 (22-28) years] were analysed. Test sensitivity for &lt;i&gt;Campylobacter&lt;/i&gt; spp. and EAEC was high across all three storage modalities (86.4-100%). OMNIgene&lt;sup&gt;®&lt;/sup&gt;200 and DNA/RNA shield&lt;sup&gt;™&lt;/sup&gt; showed significant concordance with the reference standard test for other pathogens, but FTA&lt;sup&gt;™&lt;/sup&gt; Elute card tests had low sensitivity for STEC and poor specificity for &lt;i&gt;Campylobacter&lt;/i&gt; spp. Agreement between FTA&lt;sup&gt;™&lt;/sup&gt; Elute cards and the reference standard test was low-moderate (kappa coefficient ≤0-0.49) for all enteropathogens.&lt;b&gt;Conclusions.&lt;/b&gt; This study demonstrates succes","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"74 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070386","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":"Performance of metagenomic next-generation sequencing for microbiological diagnosis of infectious uveitis.","authors":"Zhen Cai, Xian Zhang, Yaqin Song, Yan Jiang, Ling Jiang, Tao Li, Xufang Sun","doi":"10.1099/jmm.0.001879","DOIUrl":"10.1099/jmm.0.001879","url":null,"abstract":"<p><p><b>Introduction.</b> Diagnosis of uveitis is challenging due to the multitude of possible pathogenies. Identifying infectious and non-infectious uveitis is of great clinical significance. Recently, metagenomic next-generation sequencing (mNGS) was used to detect infectious and non-infectious uveitis, but its efficacy has not been widely evaluated.<b>Hypothesis.</b> Compared with routine diagnostic tests (RDTs), mNGS is more effective in identifying infectious and non-infectious uveitis.<b>Aim.</b> To describe the microbiological diagnostic performance of mNGS in detecting infectious and non-infectious uveitis.<b>Methodology.</b> Patients with suspected infectious uveitis of uncertain pathogenesis were tested by mNGS and RDTs. Infectious and non-infectious uveitis were grouped according to the final diagnosis based on comprehensive analysis of the test results and the effect of therapy. The test results were used to assess the performance of mNGS in actual clinical practice.<b>Results.</b> Fifty-eight cases were enrolled in this project, including 32 cases of infectious uveitis and 26 cases of non-infectious uveitis. The sensitivity of mNGS was 96.88%, which was much higher than that of RDTs. The detected pathogenic micro-organisms included bacteria, fungi, viruses, <i>Toxoplasma gondii</i> and <i>Bartonella</i>. Consequently, mNGS showed a high negative predictive value (NPV) of 94.74%, indicating that an mNGS negative should be a true negative result most of the time, but a low positive predictive value (PPV) of 79.49%.<b>Conclusions.</b> mNGS showed extremely high sensitivity but low specificity, which increased the detection rate of infectious uveitis pathogens but might result in false positives. The excellent NPV suggested that the identification of non-infectious uveitis is of considerable clinical importance.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808914","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":"Concordance analysis between Human Papillomavirus genotyping assay and PCR-reverse spot hybridization for the detection of Human Papillomavirus infection.","authors":"Yanlin Chen, Ye Li, Lifang Xue, Mu Xu, Liying Wang, Binhua Dong, Liangzhi Cai","doi":"10.1099/jmm.0.001938","DOIUrl":"https://doi.org/10.1099/jmm.0.001938","url":null,"abstract":"<p><p><b>Introduction.</b> Human papillomavirus (HPV), the predominant viral infection affecting the anogenital tract, is closely linked to the development of intraepithelial neoplasia and malignancies in the cervix and other anal regions. Currently, 15 high-risk HPVs (HR-HPVs) and 3 potential HR-HPV types have been recognized as contributors to cervical cancer. Consequently, it is imperative to conduct HR-HPV screening using suitable tests in order to identify precancerous lesions and prevent the development of cancer.<b>Hypothesis.</b> The Human papillomavirus genotyping (type 23) detection kit (PCR-reverse point hybridization method) is reliable for clinical testing.<b>Aims.</b> The objective of this research was to assess the concordance between the Human papillomavirus genotyping (type 23) detection kit (PCR-reverse point hybridization method) and the approved HPV test.<b>Methodology.</b> A sample of 781 women who received HPV genotype testing during cervical cancer screening consultations at the Department of Gynecology, Fujian Maternity and Child Health Hospital, was examined. Thirty-two cases were excluded for lacking histological results or showing signs of vulvar intraepithelial rheology, leaving 749 valid histological samples. Only 181 valid pathological specimens were available after excluding those without cervical biopsy or total hysterectomy. The consistency of the test results was assessed using the kappa (<i>K</i>) statistic, with CIN2+ serving as the benchmark for determining sensitivity and specificity. Statistical significance was defined as differences with <i>P</i> values <0.05 (two-tailed).<b>Results.</b> The human papillomavirus genotyping (type 23) detection kit (PCR-reverse point hybridization method) and the approved HPV test demonstrated a high level of concordance with a total kappa value of 0.969 (<i>P</i><0.05). The overall concordance rate was found to be 98.720%. Using cervical intraepithelial neoplasia grade 2+ (CIN2+) as the reference standard, the human papillomavirus genotyping (type 23) detection kit (PCR-reverse point hybridization method) and the approved HPV test both showed 89.655% sensitivity (<i>P</i>>0.05), while the specificity values were 40.590 and 40.309%, respectively (<i>P</i>>0.05).<b>Conclusion.</b> The evaluated HPV test demonstrates comparable performance to other assays available during the same time frame and exhibits strong concordance in detecting the majority of HPV genotypes.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820520","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":"Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of <i>Staphylococcus aureus</i>.","authors":"Samuel González-García, Aida Hamdan-Partida, Julia Pérez-Ramos, José Félix Aguirre-Garrido, Anaíd Bustos-Hamdan, Jaime Bustos-Martínez","doi":"10.1099/jmm.0.001940","DOIUrl":"10.1099/jmm.0.001940","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Staphylococcus aureus</i> is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that <i>S. aureus</i> can colonize more the pharynx than the nose. In addition, <i>S. aureus</i> can persist in these sites for prolonged periods of time.<b>Hypothesis.</b> The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of <i>S. aureus</i>.<b>Aim.</b> Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of <i>S. aureus</i>.<b>Methodology.</b> <i>S. aureus</i> carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.<b>Results.</b> A greater colonization of <i>S. aureus</i> was found in the pharynx than in the nose. The microbiomes of <i>S. aureus</i> carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus <i>Staphylococcus</i> in pharyngeal and nasal <i>S. aureus</i> carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of <i>Staphylococcus</i>-associated pathways in the nose than in the pharynx.<b>Conclusion.</b> <i>S. aureus</i> can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of <i>S. aureus</i>, but the pharyngeal and nasal microbiomes are different independent of the type of <i>S. aureus</i> carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of <i>S. aureus</i>.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11616445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775422","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":"Diagnosis of <i>Clostridioides difficile</i> infection and impact of testing.","authors":"Virginie F Viprey, Emma Clark, Kerrie A Davies","doi":"10.1099/jmm.0.001939","DOIUrl":"10.1099/jmm.0.001939","url":null,"abstract":"<p><p>Diagnosis of <i>Clostridioides difficile</i> infection (CDI) remains challenging as it involves in the first instance recognition (clinical awareness) of the patients' symptoms for clinical suspicion of CDI to warrant testing, and secondly, different laboratory tests have been described for CDI. Due to the overwhelming amount of information in the literature on CDI tests and their performance, with separately published guidelines, this review aims to provide a comprehensive but concise summary of the current state of CDI diagnostic testing. Current knowledge and the impact of using different laboratory diagnostic procedures for CDI, including the most recommended approach as a two-step algorithm and the concept of diagnostic stewardship, are being discussed. This review provides an updated overview and valuable take-home messages in the field of CDI laboratory testing and highlights that timely diagnosis is important for the clinical management of CDI and that the recommended testing procedures are increasingly becoming more widely accepted.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11614105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142775680","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}