Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-8 (of 8 Records) |
Query Trace: de Man TJ[original query] |
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Multicenter performance assessment of the Carba NP Test
Cunningham SA , Limbago B , Traczewski M , Anderson K , Hackel M , Hindler J , Sahm D , Alyanak E , Lawsin A , Gulvik CA , de Man TJ , Mandrekar JN , Schuetz AN , Jenkins S , Humphries R , Palavecino E , Vasoo S , Patel R . J Clin Microbiol 2017 55 (6) 1954-1960 Eighty Gram-negative bacilli (54 Enterobacteriaceae and 26 non-fermenting Gram-negative bacilli), obtained from multiple institutions in the United States were distributed in a blinded manner to seven testing laboratories to compare the performance of a test for detection of carbapenemase production, the Carba NP test. The Carba NP test was performed by all laboratories, following the Clinical and Laboratory Standards Institute (CLSI) procedure. Site-versus-site comparisons demonstrated a high level of consistency for the Carba NP assay with just 3/21 site comparisons yielding a difference in sensitivity (p<0.05). Previously described limitations with blaOXA-48-like carbapenemases and blaOXA carbapenemases associated with Acinetobacter baumannii were noted. Based on these data, we demonstrate that the Carba NP test, when implemented with the standardized CLSI methodology, provides reproducible results across multiple sites for detection of carbapenemases. |
The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention.
Kelley CF , Kraft CS , de Man TJ , Duphare C , Lee HW , Yang J , Easley KA , Tharp GK , Mulligan MJ , Sullivan PS , Bosinger SE , Amara RR . Mucosal Immunol 2016 10 (4) 996-1007 Most HIV transmissions among men who have sex with men (MSM), the group that accounted for 67% of new US infections in 2014, occur via exposure to the rectal mucosa. However, it is unclear how the act of condomless receptive anal intercourse (CRAI) may alter the mucosal immune environment in HIV-negative MSM. Here, we performed a comprehensive characterization of the rectal mucosal immune environment for the phenotype and production of pro-inflammatory cytokines by CD4 and CD8 T cells, global transcriptomic analyses, and the composition of microbiota in HIV-negative MSM. Our results show that compared with men who had never engaged in anal intercourse, the rectal mucosa of MSM engaging in CRAI has a distinct phenotype characterized by higher levels of Th17 cells, greater CD8+ T cell proliferation and production of pro-inflammatory cytokines, molecular signatures associated with mucosal injury and repair likely mediated by innate immune cells, and a microbiota enriched for the Prevotellaceae family. These data provide a high-resolution model of the immunological, molecular, and microbiological perturbations induced by CRAI, will have direct utility in understanding rectal HIV transmission among MSM, and will enhance the design of future biomedical prevention interventions, including candidate HIV vaccines. |
A Novel Rapidly Growing Mycobacterium Species Causing an Abdominal Cerebrospinal Fluid Pseudocyst Infection.
Hussain CK , de Man TJ , Toney NC , Kamboj K , Balada-Llasat JM , Wang SH . Open Forum Infect Dis 2016 3 (3) ofw146 Nontuberculous mycobacteria (NTM) are a rare cause of ventriculoperitoneal shunt infections. We describe the isolation and identification of a novel, rapidly growing, nonpigmented NTM from an abdominal cerebrospinal fluid pseudocyst. The patient presented with fevers, nausea, and abdominal pain and clinically improved after shunt removal. NTM identification was performed by amplicon and whole-genome sequencing. |
SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor.
de Man TJ , Limbago BM . mSphere 2016 1 (1) We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included. Unique about this tool is the ability to easily detect putative new alleles and truncated versions of existing AR genes. Variants and potential new alleles are brought to the attention of the user for further investigation. For instance, SSTAR is able to identify modified or truncated versions of porins, which may be of great importance in carbapenemase-negative carbapenem-resistant Enterobacteriaceae. SSTAR is written in Java and is therefore platform independent and compatible with both Windows and Unix operating systems. SSTAR and its manual, which includes a simple installation guide, are freely available from https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance -SSTAR-. IMPORTANCE Whole-genome sequencing (WGS) is quickly becoming a routine method for identifying genes associated with antimicrobial resistance (AR). However, for many microbiologists, the use and analysis of WGS data present a substantial challenge. We developed SSTAR, software with a graphical user interface that enables the identification of known AR genes from WGS and has the unique capacity to easily detect new variants of known AR genes, including truncated protein variants. Current software solutions do not notify the user when genes are truncated and, therefore, likely nonfunctional, which makes phenotype predictions less accurate. SSTAR users can apply any AR database of interest as a reference comparator and can manually add genes that impact resistance, even if such genes are not resistance determinants per se (e.g., porins and efflux pumps). |
Draft Genome Sequence of Mycobacterium wolinskyi, a Rapid-Growing Species of Nontuberculous Mycobacteria.
de Man TJ , Perry KA , Lawsin A , Coulliette AD , Jensen B , Toney NC , Limbago BM , Noble-Wang J . Genome Announc 2016 4 (2) Mycobacterium wolinskyi is a nonpigmented, rapidly growing nontuberculous mycobacterium species that is associated with bacteremia, peritonitis, infections associated with implants/prostheses, and skin and soft tissue infections often following surgical procedures in humans. Here, we report the first functionally annotated draft genome sequence of M. wolinskyi CDC_01. |
Intestinal microbiome disruption in patients in a long-term acute care hospital: A case for development of microbiome disruption indices to improve infection prevention.
Halpin AL , de Man TJ , Kraft CS , Perry KA , Chan AW , Lieu S , Mikell J , Limbago BM , McDonald LC . Am J Infect Control 2016 44 (7) 830-6 BACKGROUND: Composition and diversity of intestinal microbial communities (microbiota) are generally accepted as a risk factor for poor outcomes; however, we cannot yet use this information to prevent adverse outcomes. METHODS: Stool was collected from 8 long-term acute care hospital patients experiencing diarrhea and 2 fecal microbiota transplant donors; 16S rDNA V1-V2 hypervariable regions were sequenced. Composition and diversity of each sample were described. Stool was also tested for Clostridium difficile, vancomycin-resistant enterococci (VRE), and carbapenem-resistant Enterobacteriaceae. Associations between microbiota diversity and demographic and clinical characteristics, including antibiotic use, were analyzed. RESULTS: Antibiotic exposure and Charlson Comorbidity Index were inversely correlated with diversity (Spearman = -0.7). Two patients were positive for VRE; both had microbiomes dominated by Enterococcus faecium, accounting for 67%-84% of their microbiome. CONCLUSIONS: Antibiotic exposure correlated with diversity; however, other environmental and host factors not easily obtainable in a clinical setting are also known to impact the microbiota. Therefore, direct measurement of microbiome disruption by sequencing, rather than reliance on surrogate markers, might be most predictive of adverse outcomes. If and when microbiome characterization becomes a standard diagnostic test, improving our understanding of microbiome dynamics will allow for interpretation of results to improve patient outcomes. |
Draft Genome Sequence of a New Delhi Metallo-ß-Lactamase-5 (NDM-5)-Producing Multidrug-Resistant Escherichia coli Isolate.
de Man TJ , Perry KA , Avillan JJ , Rasheed JK , Limbago BM . Genome Announc 2015 3 (2) A multidrug-resistant Escherichia coli isolate from an abdominal lesion displayed resistance to all beta-lactams tested, including carbapenems, in addition to macrolides, fluoroquinolones, and tetracycline. Sequence analyses demonstrated the presence of blaNDM-5 in addition to at least 13 genes and 6 efflux pumps associated with antibiotic resistance. |
Tenosynovitis caused by a novel nontuberculous Mycobacterium species initially misidentified as Mycobacterium tuberculosis complex
Simner PJ , Hyle EP , Buckwalter SP , Branda JA , Brown-Elliott BA , Franklin J , Toney NC , de Man TJ , Wallace RJ Jr , Vasireddy R , Gandhi RT , Wengenack NL . J Clin Microbiol 2014 52 (12) 4414-8 We present a case of tenosynovitis caused by a novel, slowly-growing, non-chromogenic, nontuberculous mycobacterium (NTM). Originally misidentified as Mycobacterium tuberculosis complex, the NTM cross-reacts with the M. tuberculosis complex nucleic acid hybridization probe, a M. tuberculosis gamma-interferon release assay, and is closely related to M. tuberculosis by 16S rRNA gene sequencing. |
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