Journal of Clinical Microbiology最新文献

{"title":"Comparative analysis of the detection of antibiotic genotypic resistance with gastric mucosa, gastric fluid, and fecal samples in patients with <i>Helicobacter pylori</i> infection.","authors":"Xinlu Ren, Baojun Suo, Cailing Li, Guangjie Ping, Lingling Ma, Yanyan Shi, Kai Zhou, Yuxin Wang, Xueli Tian, Liya Zhou, Zhiqiang Song","doi":"10.1128/jcm.01034-24","DOIUrl":"10.1128/jcm.01034-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Genotypic methods for detecting antibiotic resistance in &lt;i&gt;Helicobacter pylori&lt;/i&gt; infection offer a rapid, convenient, and accurate approach for tailored therapy. However, existing studies predominantly examine single sample types and lack comparative analyses across different samples. This study comprehensively detects and compares genotypic resistance to clarithromycin and levofloxacin in gastric mucosa, gastric fluid, and fecal samples from the same patients. The study enrolled 183 participants, comprising 124 &lt;i&gt;H&lt;/i&gt;. &lt;i&gt;pylori&lt;/i&gt;-positive and 59 &lt;i&gt;H&lt;/i&gt;. &lt;i&gt;pylori&lt;/i&gt;-negative patients. All participants provided fecal samples and underwent gastroscopy for the collection of gastric mucosa and gastric fluid. Real-time PCR was employed to detect genotypic resistance to clarithromycin and levofloxacin in conjunction with bacterial culture and antibiotic susceptibility testing. Genotypic resistance detection rates for clarithromycin were 100% in gastric mucosa, 99.2% in gastric fluid, and 79.8% in fecal samples. For levofloxacin, detection rates were 97.6%, 96.8%, and 72.6%, respectively. The results showed that PCR detection for clarithromycin exhibited high sensitivity (0.94-0.95) and specificity (0.88-0.89) across all sample types. However, PCR detection for levofloxacin demonstrated slightly lower sensitivity (0.79-0.89) and specificity (0.79-0.83). The comparison of genotypic resistance results by PCR among the three sample types showed that gastric mucosa and gastric juice exhibited higher consistency, while the consistency between feces and both gastric mucosa and gastric juice was lower. This study confirmed good consistency between genotypic and phenotypic resistance in clarithromycin and levofloxacin. While both gastric mucosa and gastric fluid samples demonstrated high detection performance, the efficiency of detecting fecal samples was constrained by challenges in DNA extraction.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;This study, with a large sample size, comprehensively tested both &lt;i&gt;Helicobacter&lt;/i&gt; pylori-negative and -positive patients, including rapid urease test, histopathological evaluation and staining, bacterial culture, susceptibility testing, and resistance gene mutation analysis. By simultaneously examining gastric mucosa, gastric juice, and fecal samples from the same individuals, we minimized confounding factors arising from different sample sources, ensuring the reliability of our results. This approach effectively delineated the differences and characteristics in detection performance among different sample types, offering crucial reference data for selecting appropriate detection samples and identifying areas for improvement. The findings revealed robust concordance between genotypic and phenotypic resistance, with both gastric mucosa and gastric juice samples demonstrating excellent detection performance. However, the efficiency of detecting resistance in fecal samples was hampered by challenges in DNA extrac","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0103424"},"PeriodicalIF":6.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784280/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828801","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid detection of carbapenemase production in <i>Aeromonas</i> using phenotypic tests based on colorimetric microtube assay.","authors":"Hui Liu, Lijun Zhang, Min Jiang, Yuhong Zhang, Bin Sun","doi":"10.1128/jcm.01104-24","DOIUrl":"10.1128/jcm.01104-24","url":null,"abstract":"<p><p>Antibiotic resistance, particularly carbapenem resistance, poses a significant global health threat due to the limited availability of effective antibiotics. Carbapenem-resistant <i>Aeromonas</i> are increasingly recognized for their role in various infections, necessitating rapid and accurate detection methods. This study aimed to evaluate several phenotypic tests, including the Carba NP test (CNPt), Carba NP-direct test (CNPd), and Blue-Carba test (BCT), for their effectiveness in rapidly detecting carbapenemase production in <i>Aeromonas</i>. These tests target both the chromosomally encoded CphA metallo-β-lactamase (MBL) and acquired carbapenemases. Additionally, a modified phenotypic test called the Colony-Carba NP test (c-CNPt) was introduced to enhance sensitivity and specificity. A retrospective analysis was conducted on 131 clinically conserved <i>Aeromonas</i> strains harboring identified carbapenem resistance genes, using CNPt, CNPd, BCT, and the newly developed c-CNPt and EDTA-Colony-Carba NP test (ec-CNPt). The stability of c-CNPt reagents stored at -80°C was also assessed. Additionally, a prospective study conducted from July 2021 to November 2023 evaluated 152 <i>Aeromonas</i> isolates to determine the clinical applicability of these tests. Our results demonstrated that CNPd and BCT achieved 100% sensitivity and specificity, surpassing the traditional CNPt, which showed only 63.6% sensitivity for <i>Aeromonas</i> strains. The c-CNPt also showed 100% sensitivity and specificity, with the ec-CNPt effectively differentiating between MBL and serine carbapenemase types. Stability tests confirmed that c-CNPt reagents could be stored at -80℃ for up to 1 year without performance degradation. These findings highlight the practicality and reliability of these phenotypic tests for routine laboratory use, providing a rapid and cost-effective method for detecting carbapenemase production.The rapid detection of carbapenemase production in <i>Aeromonas</i> is of paramount importance due to the significant clinical and public health implications associated with antibiotic resistance. The development and validation of rapid phenotypic tests such as the Colony-Carba NP test (c-CNPt) and the EDTA-Colony-Carba NP test (ec-CNPt) are crucial advancements in the field. These tests offer a highly sensitive and specific method for detecting carbapenemase production in <i>Aeromonas</i>, including the differentiation between metallo-β-lactamase and serine carbapenemases. The c-CNPt and ec-CNPt are cost-effective, easy to perform, and provide rapid results, making them suitable for routine clinical use. Additionally, the stability of the reagents ensures their practicality for long-term application in various healthcare settings. Implementing these phenotypic tests in clinical laboratories can significantly enhance the early detection and appropriate treatment of carbapenem-resistant <i>Aeromonas</i> infections.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0110424"},"PeriodicalIF":6.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11784260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142785782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serum antigen tests for the diagnosis of invasive aspergillosis: a retrospective comparison of five <i>Aspergillus</i> antigen assays and one beta-D-glucan assay.","authors":"Thilo Schub, Isabel Klugherz, Johannes Wagener, Juergen Prattes, Martin Hoenigl, Sebastian Suerbaum, Jürgen Held, Karl Dichtl","doi":"10.1128/jcm.00950-24","DOIUrl":"10.1128/jcm.00950-24","url":null,"abstract":"<p><p>Invasive aspergillosis (IA) is a life-threatening infection. Early and specific diagnosis is pivotal to ensure adequate therapy. Antigen testing from blood is a widespread and convenient diagnostic approach. Various tests for the detection of <i>Aspergillus</i> antigen as well as for the panfungal antigen β-1,3-D-glucan (BDG) are available, for which comprehensive comparisons are still lacking. Blood samples of 82 proven/probable (11/71) IA patients and 52 controls were tested using two enzyme-linked immunosorbent assays (ELISAs) (Bio-Rad and Euroimmun), one chemiluminescent immunoassay (CLIA) (Vircell), one BDG assay (Fujifilm Wako), and two point of care (PoC) assays (Immy sōna and OLM). PoC assays were evaluated visually and used automated read out systems. Of the 82 IA patients, 37 had received solid organ transplantation (SOT) and 25 hematopoietic stem cell transplant (HSCT). Sensitivities and specificities for the eight test systems ranged from 27% to 71% and from 64% to 100%. Estimating a 10% prevalence of IA, test performance would have resulted in positive and negative predictive values of 14%-100% and 91%-95%. Areas under the curve (AUCs) for all tests except GM were below 0.7. When the cut-off values for quantitative tests were normalized to a specificity close to 95%, sensitivities ranged from 14% to 40%. The use of automated read out systems for the PoC assays had a significant impact. Combining different tests did not result in better test strategies. Sensitivity of <i>Aspergillus</i> antigen testing from single serum samples is low. Due to specificity issues, the majority of tests is not suited for screening purposes. The different assays can meet different needs in different diagnostic settings.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0095024"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633112/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance evaluation of the Specific Reveal system for rapid antibiotic susceptibility testing from positive blood cultures containing Gram-negative pathogens.","authors":"Greta Ostermann, Barbara Körber-Irrgang, Alexander Krüger, Pragya Singh, Kenny Vo, Jörg Gielen, Ute Aurbach, Hilmar Wisplinghoff, Nathalie Jazmati","doi":"10.1128/jcm.00692-24","DOIUrl":"10.1128/jcm.00692-24","url":null,"abstract":"<p><p>Rapid antimicrobial drug administration is crucial for the efficient treatment of sepsis or septic shock, but empirical therapy is limited by the increasing prevalence of multidrug-resistant bacteria. Thus, rapid and reliable antimicrobial susceptibility testing (AST) is needed to start appropriate antimicrobial drug administration as quickly as possible. In the present study, we evaluated the performance of the Reveal rapid AST system. From February to April 2021, 102 positive blood culture bottles (BCBs) from hospitalized patients with bacteremia caused by Gram-negative bacteria were included in the study. All isolates were tested by the Reveal system directly from the positive BCBs in comparison to the DxM MicroScan WalkAway. Essential agreement (EA) and category agreement (CA) were high with 98.5% and 97.1%, respectively. We also determined the susceptibility of 10 highly resistant CDC & FDA AR strains in duplicate. Here, EA was 99.6% and CA 97.9%. The average time to result by Reveal was 5.4 h ± 1.2 h compared to an average of 16 h by DxM MicroScan WalkAway for clinical strains and 3.8 h ± 1.2 h for more resistant CDC & FDA AR strains. Susceptibility determination with the Reveal rapid AST system directly from positive BCBs is for the frequently represented bug-drug combinations a reliable and accurate approach, meeting the European ISO guideline for the performance of AST systems. Moreover, AST directly from blood cultures performed with the Reveal system saves time when compared to the conventional AST, as no subculturing is needed and time to result is very short.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0069224"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prospective evaluation of non-invasive saliva specimens for the diagnosis of syphilis and molecular surveillance of <i>Treponema pallidum</i>.","authors":"Kazuo Imai, Akihiro Sato, Masashi Tanaka, Yuki Ohama, Shu-Ichi Nakayama, Ryuha Omachi, Keita Takeuchi, Norihito Tarumoto, Mieko Tokano, Shigefumi Mesaki, Takuya Maeda, Yukihiro Akeda","doi":"10.1128/jcm.00809-24","DOIUrl":"10.1128/jcm.00809-24","url":null,"abstract":"<p><p>The promising diagnostic performance of molecular testing for syphilis using saliva and urine samples has been reported; however, further evaluation of its possible application for diagnosis and molecular surveillance is required. In addition, the development of a rapid and easy-to-perform molecular test for syphilis is important for its use in the clinical setting. We comprehensively evaluated the diagnostic and surveillance performance of two novel loop-mediated isothermal amplification (LAMP) assays using saliva and urine samples. Saliva, urine, and whole blood were collected from patients who underwent serological testing for syphilis at outpatient clinics. <i>Treponema pallidum</i> DNA in specimens was detected using quantitative PCR (qPCR), nested PCR, and novel LAMP assays. <i>T. pallidum</i> genotyping was conducted by multi-locus sequence typing (MLST). Of the 163 patients recruited, 98 were diagnosed with syphilis (primary: <i>n</i> = 35; secondary: <i>n</i> = 40; latent: <i>n</i> = 23). qPCR showed the highest sensitivity among the molecular tests performed with a sensitivity of 54.1% and 30.3% for all syphilis patients using saliva and urine samples, respectively. A novel method of LAMP combined with dry reagents and crude DNA extraction (Dry-LAMP) showed a probit detection limit of 37.4 copies/reaction within 45 min. The agreement rate between Dry-LAMP and qPCR for saliva was 95.7% (<i>κ</i> coefficient 0.90). The <i>T. pallidum</i> genotype was identified in 48 patients by MLST using saliva samples. Molecular analysis of saliva could be used as a supplementary diagnostic test for syphilis and molecular surveillance of the <i>T. pallidum</i> genotype. Dry-LAMP is expected to be helpful in the clinical diagnosis of syphilis.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0080924"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel LAMP-based assay for the identification of <i>Streptococcus pneumoniae</i> and <i>Streptococcus pseudopneumoniae</i> in clinical isolates.","authors":"Mariam Basheer, Katarina Sasic, Alice Carlsson, Nora Vestberg, Birgitta Henriques-Normark, Karin Blomqvist, Geneviève Garriss","doi":"10.1128/jcm.00912-24","DOIUrl":"10.1128/jcm.00912-24","url":null,"abstract":"<p><p>The Gram-positive bacteria <i>Streptococcus pneumoniae</i> is part of the <i>Streptococcus mitis</i> group (SMG) and causes life-threatening infections, such as pneumonia, sepsis, and meningitis. The closely related <i>Streptococcus pseudopneumoniae</i> has recently been shown to cause respiratory tract infections, as well as invasive infections, especially in patients with comorbidities. Due to the genetic and phenotypic similarities of species belonging to the SMG, the identification of <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> is difficult and unreliable using phenotypic tests, as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and 16S rRNA sequencing. In this study, a loop-mediated isothermal amplification (LAMP)-based assay was developed using molecular markers specific for <i>S. pneumoniae</i> (SPN0001) and <i>S. pseudopneumoniae</i> (SPPN_RS10375). The LAMP assay was evaluated using a collection of SMG clinical isolates, concluding that the method provides a correct, reliable, and fast identification of both <i>S. pneumoniae</i> and <i>S. pseudopneumoniae</i> clinical isolates.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0091224"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pleural space infection microbiology as assessed using a clinical sequencing-based assay: <i>Fusobacterium nucleatum</i> group, <i>Streptococcus intermedius,</i> and other oral normal microbiota are the most common bacteria identified in community-acquired pleural space infections.","authors":"Judith Alvarez Otero, Jay Mandrekar, Matt J Wolf, Jordan C Starkey, Eva M Carmona, Ruben Dyrhovden, Øyvind Kommedal, Robin Patel","doi":"10.1128/jcm.00694-24","DOIUrl":"10.1128/jcm.00694-24","url":null,"abstract":"<p><p>The definition of the microbiology of pleural space infection has been challenging due to the poor yield of conventional culture. Here, the results of a 16S ribosomal RNA gene PCR/sequencing assay performed on pleural fluid in routine clinical practice between August 2020 and January 2023 were evaluated. Amplified 16S rRNA gene DNA was submitted to Sanger sequencing and/or next-generation sequencing or results were reported as negative, depending on PCR crossing threshold value. In all, 496 pleural fluids were tested at Mayo Clinic Laboratories, with 227 positive results, including 57 from Mayo Clinic patients. Among the 57 Mayo Clinic patients, pleural space infection was community acquired in 48 (84%); <i>Fusobacterium nucleatum</i> group and/or <i>Streptococcus intermedius</i> were detected in 31/57 (54%) cases [including 28/48 (58%) community-acquired cases], with additional facultative and/or anaerobic species also found in various combinations in 17/31 (55%). Results of this study suggest that the most frequent microorganism profile involved in community-acquired pleural space infection may be a combination of <i>F. nucleatum</i> group and/or <i>S. intermedius</i>, with or without other normal microbiota.</p><p><strong>Importance: </strong>We describe here the most frequent microorganisms detected in community-acquired pleural space infection using a clinically performed sequencing-based assay. We found that the most common detection was the <i>Fusobacterium nucleatum</i> group and/or <i>Streptococcus intermedius</i>, with or without other normal microbiota. We propose the term e-FuSion (effusion with <i>Fusobacterium nucleatum</i> group, <i>Streptococcus intermedius</i>, and other oral normal microbiota) for this entity.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0069424"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of the LifeScale automated rapid phenotypic antimicrobial susceptibility testing on Gram-negative rods directly from positive blood cultures.","authors":"James W Snyder, Nadia Chaudhry, Wesley Hoffmann","doi":"10.1128/jcm.00922-24","DOIUrl":"10.1128/jcm.00922-24","url":null,"abstract":"<p><p>Rapid antimicrobial susceptibility testing (rAST) performed directly from blood cultures is essential to influencing the selection of appropriate antibiotics, preferably targeted therapy, for the treatment of bloodstream infections. Affinity Biosensors has developed the LifeScale, a phenotypic rAST system based on microfluidic sensors with a mechanical resonator that measures the mass of individual microbes. The combination of replication, biomass, and population profiling of individual microbes is analyzed to produce rAST results. The performance of the LifeScale was evaluated and compared to our current standard of care (SOC) antimicrobial susceptibility testing (AST) system under clinical conditions. The results indicated that the LifeScale is easy to use and provides rapid, reliable, and accurate AST results in less than 5 h directly from from positive blood cultures containing Gram-negative organisms listed in the current database. For all organism-antibiotic combinations involving polymicrobial cultures, LifeScale showed a resistant result when either mixed isolate was resistant. If these results prove to be robust on further testing, this may justify the reporting of rapid LifeScale results without the need for additional confirmatory testing.</p><p><strong>Importance: </strong>This is the first clinical-based study of a unique technology using microfluidic sensors to generate rapid antimicrobial susceptibility test results directly from blood cultures containing Gram-negative rods. The issue of polymicrobial cultures was also addressed in this study, which, to our knowledge, has not been addressed in publications of other rapid phenotypic AST systems. Overall, LifeScale results compared favorably with the SOC in terms of overall agreement, especially categorical agreement.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0092224"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Update on novel validly published and included bacterial taxa derived from human clinical specimens and taxonomic revisions published in 2023.","authors":"Arianna Carella, Karen C Carroll, Erik Munson","doi":"10.1128/jcm.01004-24","DOIUrl":"10.1128/jcm.01004-24","url":null,"abstract":"<p><p>Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the <i>International Journal of Systematic and Evolutionary Microbiology</i> during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to <i>Aerococcus</i> spp., several <i>Corynebacterium</i> spp., <i>Exercitatus varius</i> gen. nov., sp. nov., and <i>Mycoplasma phocimorsus</i> sp. nov. With respect to nomenclature revision, the <i>Bacillus</i> and <i>Clostridium</i> genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera <i>Hallella</i>, <i>Hoylesella</i>, <i>Leyella</i>, <i>Segatella</i>, and <i>Xylanibacter</i> impacted several <i>Bacteroides</i> spp. and <i>Prevotella</i> spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0100424"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering <i>Bordetella pertussis</i> epidemiology through culture-independent multiplex amplicon and metagenomic sequencing.","authors":"Laurence Don Wai Luu, Raisa Rafique, Michael Payne, Sophie Octavia, Jennifer Robson, Vitali Sintchenko, Ruiting Lan","doi":"10.1128/jcm.01178-24","DOIUrl":"10.1128/jcm.01178-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Whooping cough (pertussis) has re-emerged despite high vaccine coverage in Australia and many other countries worldwide, partly attributable to genetic adaptation of the causative organism, &lt;i&gt;Bordetella pertussis,&lt;/i&gt; to vaccines. Therefore, genomic surveillance has become essential to monitor circulating strains for these genetic changes. However, increasing uptake of PCR for the diagnosis of pertussis has affected the availability of cultured isolates for typing. In this study, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of &lt;i&gt;B. pertussis&lt;/i&gt; directly from respiratory swabs. We developed a nine-target mPCR amplicon assay that could accurately type major lineages [&lt;i&gt;ptxP3/&lt;/i&gt;non-&lt;i&gt;ptxpP3&lt;/i&gt;, &lt;i&gt;fim3A/B&lt;/i&gt;, &lt;i&gt;fhaB3/&lt;/i&gt;non-&lt;i&gt;fhaB3,&lt;/i&gt; and epidemic lineages (ELs) 1-5] circulating in Australia. Validation using DNA from isolates and 178 residual specimens collected in 2010-2012 (&lt;i&gt;n&lt;/i&gt; = 87) and 2019 (&lt;i&gt;n&lt;/i&gt; = 91) showed that mPCR amplicon sequencing was highly sensitive with a limit of detection of 4.6 copies [IS&lt;i&gt;481&lt;/i&gt; cycle threshold (Ct) 27.3]. Shotgun metagenomic sequencing was successful in genotyping &lt;i&gt;B. pertussis&lt;/i&gt; in 84% of clinical specimens with PCR Ct &lt; 24 and was concordant with mPCR typing results. The results revealed an expansion of EL4 strains from 2010 to 2012 to 2019 in Australia and identified unrecognized co-circulating cases of &lt;i&gt;Bordetella holmesii&lt;/i&gt;. This study provides valuable insight into the circulating lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussis cases to an all-time low, and paves the way for the genomic surveillance of &lt;i&gt;B. pertussis&lt;/i&gt; in the era of culture-independent PCR-based diagnosis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;In this paper, we evaluated the use of targeted multiplex PCR (mPCR) amplicon sequencing and shotgun metagenomic sequencing for culture-independent typing of &lt;i&gt;Bordetella pertussis&lt;/i&gt; directly in respiratory swabs. We first developed a novel targeted mPCR amplicon sequencing assay that can type major circulating lineages and validated its accuracy and sensitivity on 178 DNA extracts from clinical swabs. We also demonstrate the feasibility of using deep metagenomic sequencing for determining strain lineage and markers of virulence, vaccine adaptation, macrolide resistance, and co-infections. Our culture-independent typing methods applied to clinical specimens revealed the expansion of a major global epidemic lineage in Australia (termed EL4) just prior to the COVID-19 pandemic. It also detected cases of previously hidden co-infections from another &lt;i&gt;Bordetella&lt;/i&gt; species called &lt;i&gt;Bordetella holmesii&lt;/i&gt;. These findings offer valuable insight into the circulating pertussis lineages in Australia prior to the COVID-19 pandemic during which border closure and other interventions reduced pertussi","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0117824"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}