Journal of Clinical Microbiology最新文献

{"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}

{"title":"Evaluation of the QIAstat-Dx BCID GN and GPF kits for direct identification and antimicrobial resistance prediction from blood culture bottles.","authors":"Sally Ng, Chai Yuin Tan, Jing Yan Yah, Nur A'tikah Binte Osman, Ka Lip Chew","doi":"10.1128/jcm.01169-24","DOIUrl":"10.1128/jcm.01169-24","url":null,"abstract":"<p><p>Rapid multiplex PCR kits have been used for rapid identification of blood culture isolates and prediction of antimicrobial resistance. We performed an evaluation of the QIAstat-Dx BCID GN and GPF research use only (RUO) kits on positive blood culture bottles using routine laboratory testing as the reference standard. Positive blood culture bottles between November 2023 and January 2024 were tested with QIAstat-Dx BCID GN and GPF kits based on initial Gram stain results and compared against routine identification and phenotypic susceptibility testing. A total of 174 monomicrobial blood cultures were included in the final analysis. The 174 monomicrobial blood cultures composed of 129 BCID GN tests and 45 BCID GPF tests. The majority of on-target Gram-negative organisms in monomicrobial cultures were identified. One <i>Escherichia coli</i> isolate was not identified as such, although the pan-Enterobacterales target was positive. All on-target Gram-positive organisms in monomicrobial cultures were identified. Overall sensitivity and specificity of <i>tem/shv</i> for detection of aminopenicillin resistance in <i>E. coli</i> was 94.7% (18/19) and 95.8% (23/24). The presence/absence of <i>ctx-m</i> and <i>ampC</i> had 100% sensitivity and specificity for identification of third-generation cephalosporin resistance in <i>E. coli</i> and <i>Klebsiella pneumoniae</i>. The combination of <i>blaZ</i> and <i>mecA</i> gene detection was fully predictive of phenotypic susceptibility results to penicillin and cloxacillin for <i>Staphylococcus aureus</i>. Overall, the QIAstat-Dx BCID GN and GPF kits were able to identify on-target pathogens. Detected resistance mechanisms were highly predictive of β-lactam resistance. Prediction of resistance for non-β-lactam antimicrobial was more variable.</p><p><strong>Importance: </strong>This is one of the first evaluations of the QIAstat BCID kit and demonstrates high levels of correlation for both identification and antimicrobial resistance prediction.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0116924"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583229","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":"Nomenclature for human and animal fungal pathogens and diseases: a proposal for standardized terminology.","authors":"Sybren de Hoog, Thomas J Walsh, Sarah A Ahmed, Ana Alastruey-Izquierdo, Maiken Cavling Arendrup, Andrew Borman, Sharon Chen, Anuradha Chowdhary, Robert C Colgrove, Oliver A Cornely, David W Denning, Philippe J Dufresne, Laura Filkins, Jean-Pierre Gangneux, Josepa Gené, Andreas H Groll, Jaques Guillot, Gerhard Haase, Catriona Halliday, David L Hawksworth, Roderick Hay, Martin Hoenigl, Vit Hubka, Tomasz Jagielski, Hazal Kandemir, Sarah E Kidd, Julianne V Kus, June Kwon-Chung, Shawn R Lockhart, Jacques F Meis, Leonel Mendoza, Wieland Meyer, M Hong Nguyen, Yinggai Song, Tania C Sorrell, J Benjamin Stielow, Rachel Vilela, Roxana G Vitale, Nancy L Wengenack, P Lewis White, Luis Ostrosky-Zeichner, Sean X Zhang","doi":"10.1128/jcm.00937-24","DOIUrl":"10.1128/jcm.00937-24","url":null,"abstract":"<p><p>Medically important pathogenic fungi invade vertebrate tissue and are considered primary when part of their nature life cycle is associated with an animal host and are usually able to infect immunocompetent hosts. Opportunistic fungal pathogens complete their life cycle in environmental habitats or occur as commensals within or on the vertebrate body, but under certain conditions can thrive upon infecting humans. The extent of host damage in opportunistic infections largely depends on the portal and modality of entry as well as on the host's immune and metabolic status. Diseases caused by primary pathogens and common opportunists, causing the top approximately 80% of fungal diseases [D. W. Denning, Lancet Infect Dis, 24:e428-e438, 2024, https://doi.org/10.1016/S1473-3099(23)00692-8], tend to follow a predictive pattern, while those by occasional opportunists are more variable. For this reason, it is recommended that diseases caused by primary pathogens and the common opportunists are named after the etiologic agent, for example, histoplasmosis and aspergillosis, while this should not be done for occasional opportunists that should be named as [causative fungus] [clinical syndrome], for example, <i>Alternaria alternata</i> cutaneous infection. The addition of a descriptor that identifies the location or clinical type of infection is required, as the general name alone may cover widely different clinical syndromes, for example, \"rhinocerebral mucormycosis.\" A list of major recommended human and animal disease entities (nomenclature) is provided in alignment with their causative agents. Fungal disease names may encompass several genera of etiologic agents, consequently being less susceptible to taxonomic changes of the causative species, for example, mucormycosis covers numerous mucormycetous molds.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0093724"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11633119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621319","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":"Comparison of the molecular FluoroType Mycobacteria VER 1.0 and the Maldi BioTyper Mycobacteria assays for the identification of non-tuberculous mycobacteria.","authors":"Jennifer Guiraud, Caroline Piau, Cécilia Enault, Emilie Nkpa Charron, Danièle Ducos, Christine Lafuente, Armelle Ménard, Olivia Peuchant","doi":"10.1128/jcm.01206-24","DOIUrl":"https://doi.org/10.1128/jcm.01206-24","url":null,"abstract":"<p><p>Accurate identification of non-tuberculous mycobacterial (NTM) species is crucial for the diagnosis and appropriate management of NTM infections. This study aimed to evaluate the performance of two assays, FluoroType Mycobacteria VER 1.0 and Maldi BioTyper (MBT) Mycobacteria. The two assays were evaluated using 119 NTM, including 85 slow-growing mycobacteria and 34 rapid-growing mycobacteria, representing a total of 33 species isolated in three French clinical laboratories. We used the GenoType assays as reference method for species identification, followed by 16S rRNA gene sequencing if the GenoType kits returned <i>Mycobacterium</i> sp. Compared to the reference method, the FluoroType Mycobacteria assay provided correct species identification in 89.9% of cases (107/119). Among the most frequently encountered species in clinical settings, low concordance was obtained for <i>Mycobacterium intracellulare</i> (82.4%, 14/17), <i>Mycobacterium gordonae</i> (66.7%, 6/9), and <i>Mycobacterium xenopi</i> (75%, 6/8). Misidentification was obtained in two cases (<i>Mycobacterium smegmatis</i> instead of <i>Mycobacterium mageritense</i>, and <i>Mycobacterium mucogenicum</i> instead of <i>Mycobacterium phocaicum</i>). Using the MBT Mycobacteria assay, 78.1% (93/119) of NTM isolates were correctly identified at the species level. One <i>Mycobacterium europaeum</i> isolate was misidentified as <i>M. intracellulare</i>/<i>Mycobacterium chimaera</i>. In five cases, the assay provided more accurate NTM identification compared to GenoType assays, in which closely related species are identified as a group. The FluoroType Mycobacteria VER 1.0 and the MBT Mycobacteria assays are useful tools for NTM identification from positive cultures, reducing handling time compared to GenoType assays. Their routine use in laboratories must take into consideration their performance and limitations in clinical settings.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0120624"},"PeriodicalIF":6.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142807342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}