Journal of Clinical Microbiology最新文献

{"title":"Characterization of carbapenem-resistant Enterobacterales and <i>Pseudomonas aeruginosa</i> carrying multiple carbapenemase genes-Antimicrobial Resistance Laboratory Network, 2018-2022.","authors":"Sarah Sabour, Kristin R V Harrington, Ellen Martinson, Amelia S Bhatnagar, Jennifer Y Huang, Dustin Duffy, Katie Bantle, Joseph D Lutgring, Maria Karlsson, Allison C Brown","doi":"10.1128/jcm.01220-24","DOIUrl":"https://doi.org/10.1128/jcm.01220-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Carbapenem-resistant Enterobacterales (CRE) and carbapenem-resistant &lt;i&gt;Pseudomonas aeruginosa&lt;/i&gt; (CRPA) are significant public health threats, particularly when harboring carbapenemases. Literature describing the frequencies and phenotypic and genotypic characteristics of isolates harboring multiple carbapenemase genes is limited. Using data collected from the Antimicrobial Resistance Laboratory Network (AR Lab Network) in 2018-2022, we describe CRE and CRPA isolates that harbor multiple acquired carbapenemase genes. Clinical laboratories submitted CRE and CRPA isolates to AR Lab Network public health laboratories for additional characterization that included antimicrobial susceptibility testing and detection of five targeted carbapenemase genes. Isolates were classified as non-carbapenemase producing (non-CP) when negative for carbapenemase production and all targeted carbapenemase genes, or positive for a single-CP (SCP) or multiple-carbapenemase (MCP) targeted gene. Among 79,799 CREs tested, 27,599 (35%) were SCP and 611 (1%) were MCP. MCP-CRE most often carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC&lt;/sub&gt;/&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; (&lt;i&gt;n&lt;/i&gt; = 285, 47%). Both SCP-CRE and MCP-CRE were most commonly &lt;i&gt;Klebsiella&lt;/i&gt; spp. &lt;i&gt;Enterobacter&lt;/i&gt; spp. and &lt;i&gt;Escherichia coli&lt;/i&gt; isolates harboring MCP were detected at slightly higher frequencies (18% and 15%; &lt;i&gt;n&lt;/i&gt; = 109 and &lt;i&gt;n&lt;/i&gt; = 88, respectively) than &lt;i&gt;Enterobacter&lt;/i&gt; spp. and &lt;i&gt;Escherichia coli&lt;/i&gt; isolates harboring SCP (13% and 13%; &lt;i&gt;n&lt;/i&gt; = 3,653 and 3,471, respectively). The number of MCP-CRE detected increased from 54 of 5,105 (1%) in 2018 to 223 of 6,994 (3%) in 2022. Among 54,490 CRPA tested, 2% (&lt;i&gt;n&lt;/i&gt; = 1,249) were SCP and 31 were MCP. MCP-CRPA most often carried &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt;/&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt; (&lt;i&gt;n&lt;/i&gt; = 13, 42%). A higher proportion of MCP-CRE (97%, &lt;i&gt;n&lt;/i&gt; = 330) isolates were categorized as resistant to meropenem, compared to SCP-CRE (79%; &lt;i&gt;n&lt;/i&gt; = 11,227) and non-CP (13%; &lt;i&gt;n&lt;/i&gt; = 2,683). Although MCP organisms represent a small proportion of total CP detected in the AR Lab Network, there is a need for continued monitoring and additional research.IMPORTANCECarbapenemase-producing organisms are of significant clinical and public health concerns, and rapid detection and containment of such threats are vital to preventing their spread. In this article, we used a collection of over 130,000 contemporary isolates to evaluate frequencies and phenotypic and genotypic properties of CRE and CRPA isolates harboring multiple carbapenemase genes across the United States, from 2018 to 2022. Of note, 95% and 100% of CRE and CRPA isolates co-harbored at least one metallo-β-lactamase gene, respectively, indicating a high proportion of isolates originating from patients with difficult-to-treat infections. Both clinical and public health professionals across the nation can use these data and key findings to better understand the molecular landscape of these isolates. Timely d","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0122024"},"PeriodicalIF":6.1,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142675982","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}

{"title":"Retrospective analysis of antimicrobial susceptibility profiles of non-<i>diphtheriae Corynebacterium</i> species from a tertiary hospital and reference laboratory, 2012-2023.","authors":"Ryan B Khodadadi, Said El Zein, Christina G Rivera O'Connor, Ryan W Stevens, Audrey N Schuetz, Omar M Abu Saleh, Madiha Fida","doi":"10.1128/jcm.01199-24","DOIUrl":"https://doi.org/10.1128/jcm.01199-24","url":null,"abstract":"<p><p>A total of 1,925 <i>Corynebacterium</i> isolates were tested for antimicrobial susceptibility at the Mayo Clinic Microbiology laboratory (Rochester, Minnesota) from January 2012 to March 2023, with <i>C. striatum</i> (35.6%) and <i>C. amycolatum</i> (24.4%) identified as the predominant species. Species known to potentially carry diphtheria toxin were excluded. Common sources of isolation included skin and soft tissue (56.8%), bone and/or native joint synovial fluid (14.2%), urine (13.1%), sputum (6.1%), and blood (5.9%). For penicillin, susceptibility decreased from 47.5% (58 of 122) in 2012 to 20.6% (14 of 68) in 2023. Isolates also showed a decrease in susceptibility to erythromycin from 22.4% (26 of 116) in 2012 to 13.2% (9 of 68) in 2023. Susceptibility to trimethoprim-sulfamethoxazole averaged around 50% throughout the period. Notably, linezolid and vancomycin were universally effective <i>in vitro</i> against all species. The highest susceptibility rates among tested oral agents were to linezolid and doxycycline for non-<i>C</i>. <i>striatum</i> species. Daptomycin minimal inhibitory concentrations (MICs) of >256 µg/mL were observed for one <i>C. amycolatum</i> isolate, one <i>C. tuberculostearicum</i> isolate, and for seven <i>C. striatum</i> isolates, all from patients with prior daptomycin exposure. Daptomycin MICs of 2 µg/mL (nonsusceptible) were observed in one <i>C. striatum</i> isolate recovered from a daptomycin-naïve patient and in six <i>C. jeikeium</i> isolates, from both daptomycin-exposed and non-exposed patients. Significant variation in susceptibility profiles across different <i>Corynebacterium</i> species underscores the importance of performing antimicrobial susceptibility testing to guide effective treatment. Moreover, multidrug resistance observed in <i>C. striatum</i> poses substantial therapeutic challenges especially in patients requiring prolonged or chronic antibiotic suppression.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0119924"},"PeriodicalIF":6.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647979","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}

{"title":"A simplified pyrazinamidase test for <i>Mycobacterium tuberculosis</i> pyrazinamide antimicrobial susceptibility testing.","authors":"Hsin-Hua Chan, Yu-Chen Wang, Ruwen Jou","doi":"10.1128/jcm.01227-24","DOIUrl":"10.1128/jcm.01227-24","url":null,"abstract":"<p><p>Pyrazinamide (PZA) is an important first-line drug for tuberculosis (TB) treatment by eradicating the persisting <i>Mycobacterium tuberculosis</i> complex (MTBC). Due to cost and technical challenges, end TB strategies are hampered by the lack of a simple and reliable culture-based PZA antimicrobial susceptibility testing (AST) for routine use. We initially developed a simplified chromogenic pyrazinamidase (PZase) test in the TB reference laboratory using a training set MTBC isolates with various drug-resistant profiles, and validated its performance using consecutive BACTEC MGIT 960 (MGIT)-culture-positive culture in 10 clinical laboratories. The <i>pncA</i> gene Sanger sequencing results were used as the reference, and compared to the MGIT-PZA AST. Differential diagnosis of <i>Mycobacterium bovis</i> was conducted using patented in-house real-time PCR. Of the 106 training isolates, the PZase test and MGIT-PZA AST showed 100.0% and 99.1% concordance as compared to Sanger sequencing, respectively. We found 32.1% (34/106) isolates harbored <i>pncA</i> mutations, including one isolate with silent mutation S65S. For validation, 1,793 clinical isolates were tested including 150 duplicate isolates from specimens of the same cases and 16 isolates with uncharacterized drug resistance (UDR)-associated mutations. Excluding duplicated and UDR isolates, we identified 2.6% (43/1,627) PZA-resistant isolates, including 1.3% (21/1,627) <i>M</i>. <i>bovis</i> isolates. The kappa values were 0.851-1.000. In addition, the accuracy of the PZase test conducted by 10 laboratories was 98.5%-100.0%. Our simplified PZase test demonstrated high concordance with Sanger sequencing and MGIT-PZA AST. Integrating the PZase test into routine first-line AST is effortless and represents an improvement in laboratory services for ending TB.</p><p><strong>Importance: </strong>We developed and validated a simple pyrazinamidase (PZase) test for pyrazinamide (PZA) antimicrobial susceptibility testing (AST). Our results demonstrated that the PZase test had high agreement with the <i>pncA</i> gene sequencing and MGIT-PZA AST. Integrating PZase test into routine AST is effortless and represents an improvement in laboratory services for ending TB.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0122724"},"PeriodicalIF":6.1,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647977","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}

{"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":"https://doi.org/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":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the KPC/IMP/NDM/VIM/OXA-48 Combo Test Kit and Carbapenem-Resistant K.N.I.V.O. Detection K-Set in detecting KPC variants.","authors":"Aline Valério de Lima, Keila de Oliveira Lima, Paola Cappellano, Sebastian Cifuentes, Nilton Lincopan, Suely Carlos Ferreira Sampaio, Jorge Luiz Mello Sampaio","doi":"10.1128/jcm.01123-24","DOIUrl":"https://doi.org/10.1128/jcm.01123-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0112324"},"PeriodicalIF":6.1,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621317","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}

{"title":"Clinical pilot of bacterial transcriptional profiling as a combined genotypic and phenotypic antimicrobial susceptibility test.","authors":"E L Young, D J Roach, M A Martinsen, G E G McGrath, N R Holbrook, H E Cho, E Y Seyoum, V M Pierce, R P Bhattacharyya","doi":"10.1128/jcm.00997-24","DOIUrl":"10.1128/jcm.00997-24","url":null,"abstract":"<p><p>Antimicrobial resistance is a growing health threat, but standard methods for determining antibiotic susceptibility are slow and can delay optimal treatment, which is especially consequential in severe infections such as bacteremia. Novel approaches for rapid susceptibility profiling have emerged that characterize either bacterial response to antibiotics (phenotype) or detect specific resistance genes (genotype). <u>G</u>en<u>o</u>typic and <u>Ph</u>enotypic <u>AST</u> through <u>R</u>NA detection (GoPhAST-R) is a novel assay, performed directly on positive blood cultures, that integrates rapid transcriptional response profiling with the detection of key resistance gene transcripts, thereby providing simultaneous data on both phenotype and genotype. Here, we performed the first clinical pilot of GoPhAST-R on 42 positive blood cultures: 26 growing <i>Escherichia coli</i>, 15 growing <i>Klebsiella pneumoniae</i>, and 1 with both. An aliquot of each positive blood culture was exposed to nine different antibiotics, lysed, and underwent rapid transcriptional profiling on the NanoString platform; results were analyzed using an in-house susceptibility classification algorithm. GoPhAST-R achieved 95% overall agreement with standard antimicrobial susceptibility testing methods, with the highest agreement for beta-lactams (98%) and the lowest for fluoroquinolones (88%). Epidemic resistance genes including the extended spectrum beta-lactamase <i>bla</i>_CTX-M-15 and the carbapenemase <i>bla</i>_KPC were also detected within the population. This study demonstrates the clinical feasibility of using transcriptional response profiling for rapid resistance determination, although further validation with larger and more diverse bacterial populations will be essential in future work. GoPhAST-R represents a promising new approach for rapid and comprehensive antibiotic susceptibility testing in clinical settings.IMPORTANCEExposure to antibiotics causes differential transcriptional signatures in susceptible vs resistant bacteria. These differences can be leveraged to rapidly predict resistance profiles of <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> in clinically positive blood cultures.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0099724"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142466715","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":"Reverse-transcriptase real-time PCR in the diagnostic strategy for invasive infections caused by <i>Aspergillus fumigatus</i>.","authors":"Charles Gibert, Pauline Tirard-Collet, Charline Miossec, Damien Dupont, Florence Persat, Martine Wallon, Florence Ader, Gilles Devouassoux, Sophie Ducastelle, Hélène Labussière-Wallet, Sylvie Paulus, Céline Guichon, Anne-Claire Lukaszewicz, Jean-Christophe Richard, Florent Wallet, Alexandre Alanio, Meja Rabodonirina, Jean Menotti","doi":"10.1128/jcm.00791-24","DOIUrl":"10.1128/jcm.00791-24","url":null,"abstract":"<p><p>The aim was to develop an RT-qPCR targeting <i>Aspergillus fumigatus</i> and compare its performance to that of <i>Aspergillus fumigatus</i> qPCR for the diagnosis of invasive aspergillosis (IA). Samples from patients of the Lyon University hospitals for whom a suspicion of IA led to the realization of an <i>Aspergillus fumigatus</i> qPCR molecular diagnostic test over a 2-year period were included. The patients were classified according to the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC-MSGERC) criteria for suspected IA; RT-qPCR and qPCR assays were performed on all included samples. The sensitivities and specificities of RT-qPCR and qPCR were calculated and compared using the results of the EORTC-MSGERC classification as reference. The cycle threshold (Ct) results were compared according to IA classification and sample type. Among the 193 samples analyzed, 91 were classified as IA excluded, 46 as possible IA, 53 as probable IA, and 3 as proven IA. For all sample types, RT-qPCR was significantly more sensitive than qPCR for all IA classifications with an additional 17/102 samples detected (<i>P</i>-value < 0.01). For plasma samples, sensitivity was significantly higher and specificity significantly lower using RT-qPCR for all IA classifications (<i>P</i>-value < 0.001). The mean Ct obtained with RT-qPCR were significantly lower than those obtained with qPCR for all IA classifications and all sample types (<i>P</i>-value < 0.001 and <i>P</i>-value < 0.0001, respectively). RT-qPCR presents a higher sensitivity than qPCR for the diagnosis of IA due to <i>Aspergillus fumigatus</i>, particularly in samples with an intrinsically low fungal load.IMPORTANCE<i>Aspergillus fumigatus</i> belongs to the critical priority group of the World Health Organization fungal priority pathogens list. Invasive aspergillosis (IA) is a life-threatening infection with poor prognosis and challenging diagnosis. PCR has been integrated into the 2020 European Organization for Research and Treatment of Cancer/Mycoses Study Group consensus definitions for IA diagnosis. However, due to frequent low fungal burdens, its sensitivity needs to be improved. This work presents an innovative method for detecting total nucleic acids, corresponding to both ribosomal RNA and DNA, that enables IA diagnosis with greater sensitivity than conventional techniques, especially in non-invasive samples such as blood, enhancing the monitoring of this infection in high-risk patients.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0079124"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501306","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":"Characterization of neurologic disease-associated <i>Streptococcus suis</i> strains within the United States swine herd and use of diagnostic tools.","authors":"Jessica Santos Streauslin, Daniel W Nielsen, Kent J Schwartz, Rachel J Derscheid, Drew R Magstadt, Eric R Burrough, Phillip C Gauger, Loni L Schumacher, Michael C Rahe, Alyona Michael, Panchan Sitthicharoenchai, Christopher L Siepker, Franco Matias Ferreyra, Marcelo Nunes de Almeida, Rodger Main, Laura K Bradner, Xiao Hu, Ganwu Li, Ana Paula S Poeta Silva, Orhan Sahin, Bailey L Arruda","doi":"10.1128/jcm.00374-24","DOIUrl":"10.1128/jcm.00374-24","url":null,"abstract":"<p><p><i>Streptococcus suis</i> negatively impacts swine health, posing diagnostic and preventative challenges. <i>S. suis</i> can induce disease and also quietly reside on mucosal surfaces. The limited use of diagnostic tools to identify disease-associated strains and rule out differential diagnoses, alongside the complex ecology of <i>S. suis</i>, poses significant challenges in comprehending this important pathogen and defining pathotypes. This study evaluated 2,379 <i>S</i>. <i>suis</i> central nervous system (CNS) isolates from diagnostic submissions between 2015 and 2019. Isolates originating from submissions with histologic evidence of CNS infection (<i>n</i> = 1,032) were further characterized by standard and advanced diagnostic techniques. We identified 29 <i>S</i>. <i>suis</i> serotypes and 4 reclassified serotypes as putative causes of CNS disease. Among these, serotypes 1 and 7 emerged as the predominant putative causes of CNS infection (32% of submissions). Furthermore, 51 sequence types (STs), of which 15 were novel, were detected with ST1 predominating. Through whole-genome sequencing of 145 isolates, we observed that five commonly used virulence-associated genes (VAGs; <i>epf</i>, <i>mrp</i>, <i>sly</i>, <i>ofs</i>, and <i>srtF</i>) were not present in most disease-associated isolates, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) yielded false-positive results in 7% of isolates. These data indicate that (i) clinical signs and site of isolation alone are insufficient for defining a pathotype, (ii) <i>S. suis</i> serotypes and STs associated with CNS infection are more diverse than previously reported, (iii) MALDI-TOF MS may need to be supplemented with additional diagnostic tools for precise <i>S. suis</i> identification, and (iv) VAGs remain an unreliable means for identifying isolates associated with CNS disease.IMPORTANCE<i>Streptococcus suis</i> is an important and complex systemic bacterial pathogen of swine. Characterization of <i>S. suis</i> strains originating from pigs with histologic confirmation of neurologic disease is limited. Review of swine diagnostic submissions revealed that fewer than half of cases from which <i>S. suis</i> was isolated from the brain had histologic evidence of neurologic disease. This finding demonstrates that clinical signs and site of isolation alone are not sufficient for identifying a neurologic disease-associated strain. Characterization of strains originating from cases with evidence of disease using classic and advanced diagnostic techniques revealed that neurologic disease-associated strains are diverse and commonly lack genes previously associated with virulence.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0037424"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11562895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142390929","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":"Whole-genome sequencing resolves biochemical misidentification of <i>Neisseria</i> species from urogenital specimens.","authors":"Amanda C Smith, Apurva Shrivastava, John C Cartee, Myriam Bélanger, Samera Sharpe, Jorden Lewis, Suzanna Budionno, Raquel Gomez, Manjeet K Khubbar, Cau D Pham, Kim M Gernert, Matthew W Schmerer, Brian H Raphael, Emily R Learner, Ellen N Kersh, Sandeep J Joseph","doi":"10.1128/jcm.00704-24","DOIUrl":"10.1128/jcm.00704-24","url":null,"abstract":"<p><p><i>Neisseria meningitidis</i> (Nm) and <i>Neisseria gonorrhoeae</i> (Ng) are human pathogens that sometimes occupy the same anatomical niche. Ng, the causative agent of gonorrhea, infects 87 million individuals annually worldwide and is an urgent threat due to increasing drug resistance. Ng is a pathogen of the urogenital tract and may infect the oropharyngeal or rectal site, often asymptomatically. Conversely, Nm is an opportunistic pathogen. While often a commensal in the oropharyngeal tract, it is also the leading cause of bacterial meningitis with 1.2 million cases globally, causing significant morbidity and mortality. Horizontal gene transfer (HGT) is likely to occur between Ng and Nm due to their shared anatomical niches and genetic similarity, which poses challenges for accurate detection and treatment. Routine surveillance through the Gonococcal Isolate Surveillance Project and Strengthening the U.S. Response to Resistant Gonorrhea detected six concerning urogenital <i>Neisseria</i> isolates with contradicting species identification in Milwaukee (MIL). While all six isolates were positive for Ng using nucleic acid amplification testing (NAAT) and matrix-assisted laser desorption/ionization time of flight identified the isolates as Ng, two biochemical tests, Gonochek-II and API NH, classified them as Nm. To address this discrepancy, we performed whole-genome sequencing (WGS) using Illumina MiSeq on all isolates and employed various bioinformatics tools. Species detection analysis using BMScan, which uses WGS data, identified all isolates as Ng. Furthermore, Kraken revealed over 98% of WGS reads mapped to the Ng genome and <1% to Nm. Recombination analysis identified putative HGT in all MIL isolates within the γ-glutamyl transpeptidase (<i>ggt</i>) gene, a key component in the biochemical tests used to differentiate between Nm and Ng. Further analysis identified Nm as the source of HGT event. Specifically, the active Nm <i>ggt</i> gene replaced the Ng pseudogenes, <i>ggt1</i> and <i>ggt2</i>. Together, this study demonstrates that closely related <i>Neisseria</i> species sharing a niche underwent HGT, which led to the misidentification of species following biochemical testing. Importantly, NAAT accurately detected Ng. The misidentification highlights the importance of using WGS to continually evaluate diagnostic or bacterial identification tests.</p>","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":" ","pages":"e0070424"},"PeriodicalIF":5.3,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365429","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":"The Brief Case: A fatal case of <i>Legionella pneumophila</i> in an elderly patient.","authors":"Andrew Sulaiman, Emily Gisriel, Karen C Carroll","doi":"10.1128/jcm.00863-24","DOIUrl":"10.1128/jcm.00863-24","url":null,"abstract":"","PeriodicalId":15511,"journal":{"name":"Journal of Clinical Microbiology","volume":"62 11","pages":"e0086324"},"PeriodicalIF":6.1,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11558997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621325","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}