scholarly journals ­­­Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

2020 ◽  
Author(s):  
Cody Glickman ◽  
Sara M. Kammlade ◽  
Nabeeh A. Hasan ◽  
L. Elaine Epperson ◽  
Rebecca M. Davidson ◽  
...  
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Gene Annotation ◽  
Virulence Gene ◽  
The United States ◽  
Clinical Samples ◽  
Diverse Species ◽  
Bacterial Fitness ◽  
Environmental Bacteria ◽  
Bacterial Genes

Abstract Background Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic diversity within mycobacteria is the integration of viruses called prophages. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhageDB, an environmental mycobacteriophage database.Methods Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhageDB lettered clusters using BLAST-p. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs.Results Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM.

scholarly journals ­­­Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

2020 ◽  
Author(s):  
Cody Glickman ◽  
Sara M. Kammlade ◽  
Nabeeh A. Hasan ◽  
L. Elaine Epperson ◽  
Rebecca M. Davidson ◽  
...  
Keyword(s):  
Growth Rate ◽  
Virulence Genes ◽  
Gene Annotation ◽  
Virulence Gene ◽  
Selective Advantage ◽  
The United States ◽  
Bacterial Virulence ◽  
Clinical Samples ◽  
Clinical Environment ◽  
Genetic Elements

Abstract Background Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differences in virulence among strains of the same species. A potential mechanism of genetic evolution and diversity within mycobacteria is the presence of integrated viruses called prophages in the host genome. Prophages may act as carriers of bacterial genes, with the potential of altering bacterial fitness through horizontal gene transfer. In this study, we quantify the frequency and composition of prophages within mycobacteria isolated from clinical samples and compare them against the composition of PhagesDB, an environmental mycobacteriophage database. Methods Prophages were predicted by agreement between two discovery tools, VirSorter and Phaster, and the frequencies of integrated prophages were compared by growth rate. Prophages were assigned to PhagesDB lettered clusters. Bacterial virulence gene frequency was calculated using a combination of the Virulence Factor Database (VFDB) and the Pathosystems Resource Integration Center virulence database (Patric-VF) within the gene annotation software Prokka. CRISPR elements were discovered using CRT. ARAGORN was used to quantify tRNAs. Results Rapidly growing mycobacteria (RGM) were more likely to contain prophage than slowly growing mycobacteria (SGM). CRISPR elements were not associated with prophage abundance in mycobacteria. The abundance of tRNAs was enriched in SGM compared to RGM. We compared the abundance of bacterial virulence genes within prophage genomes from clinical isolates to mycobacteriophages from PhagesDB. Our data suggests that prophages from clinical mycobacteria are enriched for bacterial virulence genes relative to environmental mycobacteriophage from PhagesDB. Conclusion Prophages are present in clinical NTM isolates. Prophages are more likely to be present in RGM compared to SGM genomes. The mechanism and selective advantage of this enrichment by growth rate remain unclear. In addition, the frequency of bacterial virulence genes in prophages from clinical NTM is enriched relative to the PhagesDB environmental proxy. This suggests prophages may act as a reservoir of genetic elements bacteria could use to thrive within a clinical environment.

scholarly journals Listeria monocytogenes Isolates from Foods and Humans Form Distinct but Overlapping Populations

2004 ◽  
Vol 70 (10) ◽  
pp. 5833-5841 ◽  
Author(s):  
Michael J. Gray ◽  
Ruth N. Zadoks ◽  
Esther D. Fortes ◽  
Belgin Dogan ◽  
Steven Cai ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Plaque Assay ◽  
Virulence Gene ◽  
The United States ◽  
Polymorphism Analysis ◽  
Genetic Lineages ◽  
The Public ◽  
Cell Spread ◽  
Specific Food

ABSTRACT A total of 502 Listeria monocytogenes isolates from food and 492 from humans were subtyped by EcoRI ribotyping and PCR-restriction fragment length polymorphism analysis of the virulence gene hly. Isolates were further classified into genetic lineages based on subtyping results. Food isolates were obtained through a survey of selected ready-to-eat food products in Maryland and California in 2000 and 2001. Human isolates comprised 42 isolates from invasive listeriosis cases reported in Maryland and California during 2000 and 2001 as well as an additional 450 isolates from cases that had occurred throughout the United States, predominantly from 1997 to 2001. Assignment of isolates to lineages and to the majority of L. monocytogenes subtypes was significantly associated with the isolate source (food or human), although most subtypes and lineages included both human and food isolates. Some subtypes were also significantly associated with isolation from specific food types. Tissue culture plaque assay characterization of the 42 human isolates from Maryland and California and of 91 representative food isolates revealed significantly higher average infectivity and cell-to-cell spread for the human isolates, further supporting the hypothesis that food and human isolates form distinct populations. Combined analysis of subtype and cytopathogenicity data showed that strains classified into specific ribotypes previously linked to multiple human listeriosis outbreaks, as well as those classified into lineage I, are more common among human cases and generate larger plaques than other subtypes, suggesting that these subtypes may represent particularly virulent clonal groups. These data will provide a framework for prediction of the public health risk associated with specific L. monocytogenes subtypes.

scholarly journals 1392. Nontuberculous Mycobacteria Isolated from Wisconsin Residents, 2010-2018

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S781-S781
Author(s):  
Bryan J Vonasek ◽  
Daniele Y Gusland ◽  
Kevin P Hash ◽  
Julie L Tans-Kersten ◽  
Suzanne N Gibbons-Burgener ◽  
...  
Keyword(s):  
Soft Tissue ◽  
Bronchoalveolar Lavage ◽  
Nontuberculous Mycobacteria ◽  
Tracheal Aspirate ◽  
The United States ◽  
Demographic Characteristics ◽  
Clinical Samples ◽  
Annual Number ◽  
Rapidly Growing Mycobacteria ◽  
Respiratory Specimens

Abstract Background Wisconsin is one of a handful of states in which laboratory identification of nontuberculous mycobacteria (NTM) from clinical samples is reportable to public health. The aims of this study were to characterize the demographic features of Wisconsin adults with NTM, assess the relative abundance of NTM species recovered, and describe trends in NTM isolation over the study period. Methods We conducted a retrospective cohort study of Wisconsin residents 18 years of age and older from whom NTM isolates were recovered and reported to the Wisconsin Electronic Disease Surveillance System (WEDSS) between 2010 and 2018. Isolates of M. gordonae were excluded. For the analysis of NTM frequency, multiple reports from the same individual were enumerated as separate isolates when non-identical or collected from different sites. Because NTM were usually reported into WEDSS without clinical data, this study couldn’t discern the clinical significance of the isolates. Results A total of 9,032 NTM isolates from 7,722 adults were analyzed. The average annual number of reported NTM cases was 950 (21.7/100,000 adults) during 2011-2018. Table 1 shows the demographic characteristics of individuals with NTM isolates, stratified by specimen collection site and NTM species. M. avium complex (MAC) accounted for 75.7% of respiratory isolates. An important pathogenic NTM, M. xenopi, accounted for 8.9% of non-MAC respiratory isolates. As shown in Table 2, M. chelonae, a rapidly growing mycobacteria (RGM), was the most common species isolated from skin and soft tissue, head, ears, nose and throat, and eye specimens. MAC was the most common isolate from other tissue sites. Table 1. Demographic characteristics of individuals with NTM isolates. Categorization was based upon the initially recovered sample when multiple samples were obtained from a given individual. “Respiratory” samples included sputum, bronchoalveolar lavage, and tracheal aspirate specimens. IQR, interquartile range. RGM, rapidly growing mycobacteria (M. chelonae and the M. abscessus, M. chelonae-abscessus, and M. fortuitum groups). SST, skin and soft tissue. Table 2. Most common NTM species isolated from non-respiratory sites. *’Respiratory specimens’ was inclusive of sputum, bronchoalveolar lavage, and tracheal aspirate specimens. CNS, central nervous system. HENT, head, ears, nose, or throat. SST, skin and soft tissue. Conclusion Consistent with prior studies, MAC is the predominant NTM isolated from respiratory specimens in Wisconsin. RGM are important minority respiratory pathogens, and predominate as skin and soft tissue NTMs. We highlight M. xenopi as an important pathogen in Wisconsin compared to other parts of the United States. In contrast to recent reports of increasing incidence of NTM disease, we found a stable annual incidence of NTM isolation between 2010 and 2018. Disclosures All Authors: No reported disclosures

scholarly journals Characterization of integrated prophages within diverse species of clinical nontuberculous mycobacteria

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Cody Glickman ◽  
Sara M. Kammlade ◽  
Nabeeh A. Hasan ◽  
L. Elaine Epperson ◽  
Rebecca M. Davidson ◽  
...  
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Diverse Species

scholarly journals I’m Every Woman: Advancing the Intersectional Leadership of Black Women School Leaders as Anti-Racist Praxis

2021 ◽  
Vol 31 (1-2) ◽  
pp. 7-28
Author(s):  
April L. Peters ◽  
Angel Miles Nash
Keyword(s):  
Black Women ◽  
The United States ◽  
Women's Leadership ◽  
Three Dimensions ◽  
Race And Gender ◽  
Leadership Framework ◽  
And Gender ◽  
Resisting Oppression ◽  
Epistemological Basis

The rallying, clarion call to #SayHerName has prompted the United States to intentionally include the lives, voices, struggles, and contributions of Black women and countless others of her ilk who have suffered and strived in the midst of anti-Black racism. To advance a leadership framework that is rooted in the historicity of brilliance embodied in Black women’s educational leadership, and their proclivity for resisting oppression, we expand on intersectional leadership. We develop this expansion along three dimensions of research centering Black women’s leadership: the historical foundation of Black women’s leadership in schools and communities, the epistemological basis of Black women’s racialized and gendered experiences, and the ontological characterization of Black women’s expertise in resisting anti-Black racism in educational settings. We conclude with a four tenet articulation detailing how intersectional leadership: (a) is explicitly anti-racist; (b) is explicitly anti-sexist; (c) explicitly acknowledges the multiplicative influences of marginalization centering race and gender, and across planes of identity; and (d) explicitly leverages authority to serve and protect historically underserved communities.

scholarly journals Molecular characterization of clinical carbapenem-resistant Enterobacterales from Qatar

2021 ◽  
Author(s):  
Fatma Ben Abid ◽  
Clement K. M. Tsui ◽  
Yohei Doi ◽  
Anand Deshmukh ◽  
Christi L. McElheny ◽  
...  
Keyword(s):  
Common Species ◽  
Clinical Samples ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Genes Encoding ◽  
Encoding Genes ◽  
Sequence Types ◽  
Common Sequence

AbstractOne hundred forty-nine carbapenem-resistant Enterobacterales from clinical samples obtained between April 2014 and November 2017 were subjected to whole genome sequencing and multi-locus sequence typing. Klebsiella pneumoniae (81, 54.4%) and Escherichia coli (38, 25.5%) were the most common species. Genes encoding metallo-β-lactamases were detected in 68 (45.8%) isolates, and OXA-48-like enzymes in 60 (40.3%). blaNDM-1 (45; 30.2%) and blaOXA-48 (29; 19.5%) were the most frequent. KPC-encoding genes were identified in 5 (3.6%) isolates. Most common sequence types were E. coli ST410 (8; 21.1%) and ST38 (7; 18.4%), and K. pneumoniae ST147 (13; 16%) and ST231 (7; 8.6%).

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