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Unveiling the complexity of rifampicin drug susceptibility testing in Mycobacterium tuberculosis: comparative analysis with next-generation sequencing. 揭示结核分枝杆菌利福平药敏试验的复杂性:利用新一代测序技术进行比较分析。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001884
Mehmood Qadir, Muhammad Tahir Khan, Sajjad Ahmed Khan, Muhammad Akram, Julio Ortiz Canseco, Rani Faryal, Dong Qing Wei, Sabira Tahseen
{"title":"Unveiling the complexity of rifampicin drug susceptibility testing in <i>Mycobacterium tuberculosis</i>: comparative analysis with next-generation sequencing.","authors":"Mehmood Qadir, Muhammad Tahir Khan, Sajjad Ahmed Khan, Muhammad Akram, Julio Ortiz Canseco, Rani Faryal, Dong Qing Wei, Sabira Tahseen","doi":"10.1099/jmm.0.001884","DOIUrl":"https://doi.org/10.1099/jmm.0.001884","url":null,"abstract":"<p><p><b>Introduction.</b> The discordance between phenotypic and molecular methods of rifampicin (RIF) drug susceptibility testing (DST) in <i>Mycobacterium tuberculosis</i> poses a significant challenge, potentially resulting in misdiagnosis and inappropriate treatment.<b>Hypothesis/gap statement.</b> A comparison of RIF phenotypic and molecular methods for DST, including whole genome sequencing (WGS), may provide a better understanding of resistance mechanisms.<b>Aim.</b> This study aims to compare RIF DST in <i>M. tuberculosis</i> using two phenotypic and molecular methods including the GeneXpert RIF Assay (GX) and WGS for better understanding.<b>Methodology.</b> The study evaluated two phenotypic liquid medium methods [Lowenstein-Jensen (LJ) and Mycobacterium Growth Indicator Tube (MGIT)], one targeted molecular method (GX), and one WGS method. Moreover, mutational frequency in <i>ponA1</i> and <i>ponA2</i> was also screened in the current and previous RIF resistance <i>M. tuberculosis</i> genomic isolates to find their compensatory role.<b>Results.</b> A total of 25 RIF-resistant isolates, including nine from treatment failures and relapse cases with both discordant and concordant DST results on LJ, MGIT and GX, were subjected to WGS. The phenotypic DST results indicated that 11 isolates (44%) were susceptible on LJ and MGIT but resistant on GX. These isolates exhibited multiple mutations in <i>rpoB</i>, including Thr444>Ala, Leu430>Pro, Leu430>Arg, Asp435>Gly, His445>Asn and Asn438>Lys. Conversely, four isolates that were susceptible on GX and MGIT but resistant on LJ were wild type for <i>rpoB</i> in WGS. However, these isolates possessed several novel mutations in the PonA1 gene, including a 10 nt insertion and two nonsynonymous mutations (Ala394>Ser, Pro631>Ser), as well as one nonsynonymous mutation (Pro780>Arg) in PonA2. The discordance rate of RIF DST is higher on MGIT than on LJ and GX when compared to WGS. These discordances in the Delhi/CAS lineages were primarily associated with failure and relapse cases.<b>Conclusion.</b> The WGS of RIF resistance is relatively expensive, but it may be considered for isolates with discordant DST results on MGIT, LJ and GX to ensure accurate diagnosis and appropriate treatment options.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127766","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}
引用次数: 0
Relationship of Salmonella Typhimurium 14028 strain and its dam and seqA mutants with gut microbiota dysbiosis in rats. 鼠伤寒沙门氏菌 14028 株及其 dam 和 seqA 突变体与大鼠肠道微生物群失调的关系
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001893
Hafize Dilşad Yanık, Nefise Akçelik, Elif Gamze Has, Mustafa Akçelik
{"title":"Relationship of <i>Salmonella</i> Typhimurium 14028 strain and its <i>dam</i> and <i>seqA</i> mutants with gut microbiota dysbiosis in rats.","authors":"Hafize Dilşad Yanık, Nefise Akçelik, Elif Gamze Has, Mustafa Akçelik","doi":"10.1099/jmm.0.001893","DOIUrl":"https://doi.org/10.1099/jmm.0.001893","url":null,"abstract":"<p><p><b>Introduction.</b> Disruptions in gut microbiota, known as dysbiosis, have been increasingly linked to pathogenic infections, with <i>Salmonella</i> Typhimurium being a notable contributor to these disturbances.<b>Hypothesis.</b> We hypothesize that the <i>S</i>. Typhimurium 14028 WT strain induces significant dysbiosis in the rat gut microbiota and that the <i>dam</i> and <i>seqA</i> genes play crucial roles in this process.<b>Aim</b>. In this study, it was aimed at investigating the dysbiotic activity of the <i>S</i>. Typhimurium 14028 WT strain on the rat gut microbiota and the roles of <i>dam</i> and <i>seqA</i> genes on this activity.<b>Method.</b> Changes in the rat gut microbiota were determined by examining the anal swap samples taken from the experimental groups of these animals using 16S rRNA high-throughput sequencing technology.<b>Results.</b> In the experimental groups, the dominant phyla were determined to be <i>Firmicutes</i> and <i>Bacteroidetes</i> (<i>P</i><0.05). However, while the rate of <i>Bacteroidetes</i> was significantly reduced in those treated with the WT and <i>seqA</i> mutants, no significant difference was observed in the <i>dam</i> mutant compared to the control group (<i>P</i><0.05). In all experimental animals, the dominant species was determined to be <i>Prevotella copri</i>, regardless of the experiment time and application. The analysis results of the samples taken on the third day from the rat groups infected with the <i>S.</i> Typhimurium 14028 WT strain (W2) presented the most striking data of this study.<b>Conclusion.</b> Through distance analysis, we demonstrated that a successful <i>Salmonella</i> infection completely changes the composition of the microbiota, dramatically reduces species diversity and richness in the microbiota and encourages the growth of opportunistic pathogens.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335312","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}
引用次数: 0
Lessons learned: drive-through COVID-19 clinic testing during an adaptive epidemic response and a point-of-care test assessment of a computer-read rapid lateral flow immunoassay with fluorescence-based detection. 经验总结:在适应性流行病反应期间进行的驾车通过式 COVID-19 诊所检测,以及对基于荧光检测的计算机读取快速侧流免疫测定进行的护理点检测评估。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001875
Leah Rankine-Wilson, Teresa Oncken, Irshan Basrewan, Courtney Jeffery, Todd M Pryce, Rebecca Wake, Aus A L Molan, T F Paton, Tim J J Inglis
{"title":"Lessons learned: drive-through COVID-19 clinic testing during an adaptive epidemic response and a point-of-care test assessment of a computer-read rapid lateral flow immunoassay with fluorescence-based detection.","authors":"Leah Rankine-Wilson, Teresa Oncken, Irshan Basrewan, Courtney Jeffery, Todd M Pryce, Rebecca Wake, Aus A L Molan, T F Paton, Tim J J Inglis","doi":"10.1099/jmm.0.001875","DOIUrl":"10.1099/jmm.0.001875","url":null,"abstract":"<p><p><b>Background.</b> The COVID-19 pandemic demonstrated a need for robust SARS-CoV-2 test evaluation infrastructure to underpin biosecurity and protect the population during a pandemic health emergency.<b>Gap statement.</b> The first generation of rapid antigen tests was less accurate than molecular methods due to their inherent sensitivity and specificity shortfalls, compounded by the consequences of self-testing. This created a need for more accurate point-of-care SARS-CoV-2 detection methods.<b>Aim.</b> Here we present the lessons-learned during the COVID-19 emergency response in Western Australia including the detailed set-up, evaluation and operation of rapid antigen test in a state-run drive-through sample collection service during the COVID-19 pandemic after the strict border shutdown ended.<b>Methods.</b> We report a conformity assessment of a novel, second-generation rapid antigen test (Virulizer) comprising a technician-operated rapid lateral flow immunoassay with fluorescence-based detection.<b>Results.</b> The Virulizer rapid antigen test demonstrated up to 100% sensitivity (95% CI: 61.0-100%), 91.94% specificity (95% CI: 82.5-96.5%) and 92.65% accuracy when compared to a commercial PCR assay method. Wide confidence intervals in our series reflect the limits of small sample size. Nevertheless, the Virulizer assay performance was well-suited to point-of-care screening for SARS-CoV-2 in a drive-through clinic setting.<b>Conclusion.</b> The adaptive evaluation process necessary under changing pandemic conditions enabled assessment of a simple sample collection and point-of-care testing process, and showed how this system could be rapidly deployed for SARS-CoV-2 testing, including to regional and remote settings.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116600","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}
引用次数: 0
Altered intestinal Streptococcus anginosus and 5α-reductase gene levels in patients with hepatocellular carcinoma and elevated Bacteroides stercoris in atezolizumab/bevacizumab non-responders. 肝细胞癌患者肠道链球菌anginosus和5α-还原酶基因水平的改变,以及阿特珠单抗/贝伐珠单抗无应答者肠道链球菌Bacteroides stercoris的升高。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001878
Tadashi Fujii, Teiji Kuzuya, Nobuhiro Kondo, Kohei Funasaka, Eizaburo Ohno, Yoshiki Hirooka, Takumi Tochio
{"title":"Altered intestinal <i>Streptococcus anginosus</i> and 5α-reductase gene levels in patients with hepatocellular carcinoma and elevated <i>Bacteroides stercoris</i> in atezolizumab/bevacizumab non-responders.","authors":"Tadashi Fujii, Teiji Kuzuya, Nobuhiro Kondo, Kohei Funasaka, Eizaburo Ohno, Yoshiki Hirooka, Takumi Tochio","doi":"10.1099/jmm.0.001878","DOIUrl":"10.1099/jmm.0.001878","url":null,"abstract":"<p><p><b>Introduction.</b> Hepatocellular carcinoma (HCC) is one of the deadliest cancers worldwide.<b>Gap statement.</b> Monitoring of HCC and predicting its immunotherapy responses are challenging.<b>Aim.</b> This study explored the potential of the gut microbiome for HCC monitoring and predicting HCC immunotherapy responses.<b>Methods.</b> DNA samples were collected from the faeces of 22 patients with HCC treated with atezolizumab/bevacizumab (Atz/Bev) and 85 healthy controls. The gut microbiome was analysed using 16S rRNA next-generation sequencing and quantitative PCR (qPCR).<b>Results.</b> The microbiomes of patients with HCC demonstrated significant enrichment of <i>Lactobacillus</i>, particularly <i>Lactobacillus fermentum</i>, and <i>Streptococcus</i>, notably <i>Streptococcus anginosus</i>. Comparative analysis between Atz/Bev responders (R) and non-responders (NR) revealed a higher abundance of <i>Bacteroides stercoris</i> in the NR group and <i>Bacteroides coprocola</i> in the R group. Using qPCR analysis, we observed elevated levels of <i>S. anginosus</i> and reduced levels of 5α-reductase genes, essential for the synthesis of isoallolithocholic acid, in HCC patients compared to controls. Additionally, the analysis confirmed a significantly lower abundance of <i>B. stercoris</i> in the Atz/Bev R group relative to the NR group.<b>Conclusions.</b> The gut microbiome analysis and specific gene quantification via qPCR could provide a rapid, less invasive, and cost-effective approach for assessing the increased risk of HCC, monitoring patient status, and predicting immunotherapy responses.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142201","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}
引用次数: 0
Marginal notes, September 2024: in the antimicrobial resistance hot seat. 边注,2024 年 9 月:抗菌药耐药性的热点问题。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001906
Timothy J J Inglis
{"title":"Marginal notes, September 2024: in the antimicrobial resistance hot seat.","authors":"Timothy J J Inglis","doi":"10.1099/jmm.0.001906","DOIUrl":"https://doi.org/10.1099/jmm.0.001906","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335311","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
Current status of clinical trials for phage therapy. 噬菌体疗法临床试验现状。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001895
Chidiebere F Uchechukwu, Adedayo Shonekan
{"title":"Current status of clinical trials for phage therapy.","authors":"Chidiebere F Uchechukwu, Adedayo Shonekan","doi":"10.1099/jmm.0.001895","DOIUrl":"https://doi.org/10.1099/jmm.0.001895","url":null,"abstract":"<p><p>Recently, bacteriophages have been considered alternatives to antibacterial treatments. Infectious diseases continue to plague the world because bacteria can adapt and develop defence mechanisms against antibiotics. The growing incidence of antibiotic-resistant bacterial infections necessitated the development of new techniques for treating bacterial infections worldwide. Clinical trials have shown efficiency against antibiotic-resistant bacteria. However, scientists in future clinical trials should scrutinize phage resistance implications, assess combination strategies with antimicrobial agents and address challenges in phage therapy delivery for effective implementation.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423923/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335309","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
Evaluating the accuracy of the MBT Lipid Xtract Kit for assessing colistin resistance in comparison to broth microdilution. 与肉汤微量稀释法相比,评估 MBT 脂质提取试剂盒在评估秋水仙碱耐药性方面的准确性。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001881
Calvin Ka-Fung Lo, Gordon Ritchie, Jennifer Bilawka, Leah Gowland, Samuel D Chorlton, Willson Jang, Nancy Matic, Marc G Romney, Aleksandra Stefanovic, Christopher F Lowe
{"title":"Evaluating the accuracy of the MBT Lipid Xtract Kit for assessing colistin resistance in comparison to broth microdilution.","authors":"Calvin Ka-Fung Lo, Gordon Ritchie, Jennifer Bilawka, Leah Gowland, Samuel D Chorlton, Willson Jang, Nancy Matic, Marc G Romney, Aleksandra Stefanovic, Christopher F Lowe","doi":"10.1099/jmm.0.001881","DOIUrl":"10.1099/jmm.0.001881","url":null,"abstract":"<p><p>Colistin resistance testing methods such as broth microdilution (BMD) are time-consuming and labour intensive for clinical laboratories. MBT Lipid Xtract Kit on MALDI Biotyper Sirius System (Bruker, Billerica, MA, USA) utilizes lipidomic analysis to identify specific cell wall modifications associated with colistin resistance. We compared MBT to BMD (ComASP Colistin, Liofilchem) across 36 Gram-negative isolates (non-resistant MIC ≤2 µg ml<sup>-1</sup>, resistant MIC ≥4 µg ml<sup>-1</sup>). All samples were tested twice on MBT with discrepant results repeated before assessing categorical agreement between MBT and BMD. 44.4% (16/36) of isolates were colistin resistant via BMD. MBT Lipid Xtract had 80.6% agreement (29/36) with BMD, with 5/7 discrepancies corrected to match upon repeat testing. There was 100% agreement for <i>Escherichia coli</i> isolates (<i>n</i>=16). The whole-genome sequencing was completed on the two discrepant <i>Klebsiella pneumoniae</i> isolates, with variants within colistin resistance-associated loci identified (MIC 0.5 µg ml<sup>-1</sup>: <i>arnC</i> S30T, <i>pmrB</i> T246A, <i>lapB</i> N212T, <i>lpxM</i> S253G, <i>crrB</i> Q287K and MIC >16 µg ml<sup>-1</sup>: <i>arnC</i> S30T, <i>pmrB</i> R90insRN, <i>pmrB</i> T246A, <i>pmrA</i> E57G, <i>lpxM</i> S253G). Further evaluation, particularly for non-<i>E. coli</i>, of MBT is required prior to implementation in clinical laboratories.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142116599","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
Routine blood parameters as auxiliary diagnostic tools for Mycoplasma pneumoniae infection in children. 将常规血液参数作为儿童肺炎支原体感染的辅助诊断工具。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001885
Chu Qiu-Ju, Gao Ling-Yu, Zhou Ting-Dong, Tong Yang, Han Ning, Wang Ai-Hua, Hu Huai-Lou, Zhou Qiang, Chen Bing
{"title":"Routine blood parameters as auxiliary diagnostic tools for <i>Mycoplasma pneumoniae</i> infection in children.","authors":"Chu Qiu-Ju, Gao Ling-Yu, Zhou Ting-Dong, Tong Yang, Han Ning, Wang Ai-Hua, Hu Huai-Lou, Zhou Qiang, Chen Bing","doi":"10.1099/jmm.0.001885","DOIUrl":"https://doi.org/10.1099/jmm.0.001885","url":null,"abstract":"<p><p><b>Introduction.</b> Recently, the incidence of <i>Mycoplasma pneumoniae</i> (<i>M. pneumoniae</i>) infection in children has been increasing annually. Early differential diagnosis of <i>M. pneumoniae</i> infection can not only avoid the abuse of antibiotics, but also is essential for early treatment and reduction of transmission.<b>Gap statement.</b> The change of routine blood parameters may have important clinical significance for the diagnosis of <i>M. pneumoniae</i> infection, but it has not been reported so far.<b>Aim.</b> This study aims to establish a predictive model for <i>M. pneumoniae</i> infection and explore the changes and clinical value of routine blood parameters in children with <i>M. pneumoniae</i> infection, serving as auxiliary indicators for the diagnosis and differentiation of clinical <i>M. pneumoniae</i> infection.<b>Methodology.</b> A total of 770 paediatric patients with respiratory tract infections were enrolled in this study, including 360 in the <i>M. pneumoniae</i> group, 40 in the SARS-CoV-2 group, 200 in the influenza A virus group, and 170 in the control group. The differences of routine blood parameters among all groups were compared, and risk factors were analysed using multivariate logistics analysis, and the diagnostic efficacy of differential indicators using ROC curves.<b>Results.</b> This study revealed that Mono% (OR: 3.411; 95% CI: 1.638-7.102; <i>P</i>=0.001) was independent risk factor associated with <i>M. pneumoniae</i> infection, and Mono% (AUC=0.786, the optimal cutoff at 7.8%) had a good discriminative ability between patients with <i>M. pneumoniae</i> infection and healthy individuals. Additionally, Mono% (OR: 0.424; 95% CI: 0.231-0.781; <i>P</i>=0.006) and Lymp% (OR: 0.430; 95% CI: 0.246-0.753; <i>P</i>=0.003) were independent risk factors for distinguishing <i>M. pneumoniae</i> infection from influenza A virus infection, and the Lymp% (AUC=0.786, the optimal cutoff at 22.1%) and Net% (AUC=0.761, the optimal cutoff at 65.2%) had good discriminative abilities between <i>M. pneumoniae</i> infection and influenza A infection. Furthermore, platelet distribution width (OR: 0.680; 95% CI: 0.538-0.858; <i>P</i>=0.001) was independent risk factor for distinguishing <i>M. pneumoniae</i> infection from SARS-CoV-2 infection. Meanwhile, the ROC curve demonstrated that PDW (AUC=0.786, the optimal cutoff at 15%) has a good ability to differentiate between <i>M. pneumoniae</i> infection and SARS-CoV-2 infection.<b>Conclusion.</b> This study demonstrates that routine blood parameters can be used as auxiliary diagnostic indicators for <i>M. pneumoniae</i> infection and provide reference for the diagnosis and differentiation of clinical <i>M. pneumoniae</i> infection.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142127765","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}
引用次数: 0
Development of novel broad-range pan-genus PCR assays for the detection of Tropheryma species. 开发新型广谱泛属 PCR 检测方法,用于检测 Tropheryma 物种。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001889
Florian Tagini, Mhedi Belkoniene, Katia Jaton, Onya Opota, Gilbert Greub
{"title":"Development of novel broad-range pan-genus PCR assays for the detection of <i>Tropheryma</i> species.","authors":"Florian Tagini, Mhedi Belkoniene, Katia Jaton, Onya Opota, Gilbert Greub","doi":"10.1099/jmm.0.001889","DOIUrl":"https://doi.org/10.1099/jmm.0.001889","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Tropheryma whipplei</i> is responsible for the classical Whipple's disease. Recently, a new <i>Tropheryma</i> species was described in a Belgian immunocompromised patient with pleuritis.<b>Gap Statement.</b> There is currently no specific molecular diagnostic test detecting other <i>Tropheryma</i> species than <i>Tropheryma whipplei</i>.<b>Aim.</b> To develop and validate two broad-range pan-<i>Tropheryma</i> genus PCRs detecting both <i>T. whipplei</i> and new <i>Tropheryma</i> species.<b>Methodology.</b> From shotgun sequencing data of the lung tissue biopsy of the Belgian subject, we designed two PCRs targeting the 23S rRNA and <i>rnpB</i> genes. Prospectively, requests for <i>T. whipplei</i> PCR were tested with <i>T. whipplei</i>-specific PCRs and the two <i>Tropheryma</i> broad-range PCRs from January 2019 to November 2022.<b>Results.</b> In total, 2605 samples were tested using both the pan-<i>Tropheryma</i> 23S rRNA PCR and the <i>T. whipplei</i>-specific PCR. In addition, 833 of the 2605 samples were also tested using the pan-<i>Tropheryma rnpB</i> PCRs. Sensitivity was 78.8% and 79.7% for 23S rRNA and <i>rnpB</i> PCRs, as compared with the species-specific <i>T. whipplei</i> PCR. Specificity was 99.9% and 99.7% for the 23S rRNA and the <i>rnpB</i> PCRs, respectively. We identified a patient whose bronchoalveolar lavage tested positive with the two broad-range PCRs with >10<sup>5</sup> copies ml<sup>-1</sup>. Specific <i>T. whipplei</i> PCRs were negative. Known for panuveitis, this 49-year-old male presented with an eye inflammation recurrence, and a CT scan showed multiple mediastino-hilar necrotic adenopathies. Doxycyclin (1 year), hydroxychloroquin (1 year) and co-trimoxazol (1 month) treatments led to a favourable outcome.<b>Conclusion.</b> Specific <i>T. whipplei</i> PCR exhibited better sensitivity than the pan-<i>Tropheryma</i> PCRs. However, both broad-range pan-<i>Tropheryma</i> PCRs demonstrated excellent specificity and were pivotal to identifying a new probable case of <i>Tropheryma</i> infection due to another species-level lineage.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"73 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335310","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}
引用次数: 0
Knocking Out AMR project review. 淘汰 AMR 项目审查。
Journal of medical microbiology Pub Date : 2024-09-01 DOI: 10.1099/jmm.0.001900
Lovleen Tina Joshi, Catrin E Moore
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