scholarly journals Identification of Microbes Associated with the Urethra during Health and Inflammation

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Jonathan Alessi ◽  
Rowan Farrell ◽  
Evelyn Toh ◽  
Xiaoli Zhang ◽  
David E. Nelson ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Sequence Data ◽  
The United States ◽  
Metagenomic Sequence ◽  
Sexually Transmitted ◽  
The Us ◽  
Novel Taxa ◽  
Complete Survey ◽  
Crucial Information ◽  
Metagenomic Sequence Data

The number of cases of urethritis, or inflammation of the male urethra, in the US has been estimated to be 2.8 million each year in the United States.1 It is the most common reason young men seek primary care and this syndrome is associated with acute proctitis, epididymitis, and orchitis.2 Approximately half of the cases are idiopathic, meaning that a causative agent cannot be identified. The goal of my project is to identify and characterize novel microorganisms that may be associated with male idiopathic urethritis. We used a variety of approaches to cultivate microorganisms from archived urethral swabs collected from men with idiopathic urethritis and healthy controls. We defined the phylogeny of the isolates using 16S rRNA sequencing to identify organisms that are not presently represented in microbial databases. Currently, we are scaling up a number of novel taxa we identified for genome sequencing. By adding these new genome sequencing to the existing databases we will be able to assign a higher proportion of reads from corresponding metagenomic sequence data and achieve a more complete survey of the male urethral microbiota in health and urethritis. This will provide crucial information which may permit us to identify urethritis associated organisms, develop new molecular diagnostics for these organisms, and discern if how these organisms are sexually transmitted References 1. Brill JR. Diagnosis and treatment of urethritis in men. Am Fam Physician 2010; 81:873–8. 2. Bachmann LH, Manhart LE, Martin DH, Sena AC, Dimitrakoff J, Jensen JS, et al. Advances in the Understanding and Treatment of Male Urethritis. Clin Infect Dis. 2015;61 Suppl 8:S763–S9.

scholarly journals 130. increase in Multidrug Resistance (2011–2018) and the Emergence of Extensive Drug Resistance (2020) in shigella Sonnei in the United States

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S195-S195
Author(s):  
Naeemah Z Logan ◽  
Beth E Karp ◽  
Kaitlin A Tagg ◽  
Claire Burns-Lynch ◽  
Jessica Chen ◽  
...  
Keyword(s):  
United States ◽  
Multidrug Resistance ◽  
Disease Surveillance ◽  
Sequence Data ◽  
The United States ◽  
Multidrug Resistant ◽  
Shigella Sonnei ◽  
Short Read ◽  
Men 2 ◽  
The Us

Abstract Background Multidrug-resistant (MDR) Shigella sonnei infections are a serious public health threat, and outbreaks are common among men who have sex with men (MSM). In February 2020, Australia’s Department of Health notified CDC of extensively drug-resistant (XDR) S. sonnei in 2 Australian residents linked to a cruise that departed from Florida. We describe an international outbreak of XDR S. sonnei and report on trends in MDR among S. sonnei in the United States. Methods Health departments (HDs) submit every 20th Shigella isolate to CDC’s National Antimicrobial Resistance Monitoring System (NARMS) laboratory for susceptibility testing. We defined MDR as decreased susceptibility to azithromycin (MIC ≥32 µg/mL) with resistance to ampicillin, ciprofloxacin, and cotrimoxazole, and XDR as MDR with additional resistance to ceftriaxone. We used PulseNet, the national subtyping network for enteric disease surveillance, to identify US isolates related to the Australian XDR isolates by short-read whole genome sequencing. We screened these isolates for resistance determinants (ResFinder v3.0) and plasmid replicons (PlasmidFinder) and obtained patient histories from HDs. We used long-read sequencing to generate closed plasmid sequences for 2 XDR isolates. Results NARMS tested 2,781 S. sonnei surveillance isolates during 2011–2018; 80 (2.9%) were MDR, including 1 (0.04%) that was XDR. MDR isolates were from men (87%), women (9%), and children (4%). MDR increased from 0% in 2011 to 15.3% in 2018 (Figure). In 2020, we identified XDR isolates from 3 US residents on the same cruise as the Australians. The US residents were 41–42 year-old men; 2 with available information were MSM. The US and Australian isolates were highly related (0–1 alleles). Short-read sequence data from all 3 US isolates mapped to the blaCTX-M-27 harboring IncFII plasmids from the 2 Australian isolates with >99% nucleotide identity. blaCTX-M-27 genes confer ceftriaxone resistance. Increase in Percentage of Shigella sonnei Isolates with Multidrug Resistance* in the United States, 2011–2018† Conclusion MDR S. sonnei is increasing and is most often identified among men. XDR S. sonnei infections are emerging and are resistant to all recommended antibiotics, making them difficult to treat without IV antibiotics. This outbreak illustrates the alarming capacity for XDR S. sonnei to disseminate globally among at-risk populations, such as MSM. Disclosures All Authors: No reported disclosures

scholarly journals Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton

2008 ◽  
Vol 74 (10) ◽  
pp. 2933-2939 ◽  
Author(s):  
Erin J. Biers ◽  
Kui Wang ◽  
Catherine Pennington ◽  
Robert Belas ◽  
Feng Chen ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Sequence Data ◽  
Genome Sequences ◽  
Metagenomic Sequence ◽  
Marine Bacterioplankton ◽  
Extracellular Release ◽  
Gene Transfer Agent ◽  
Metagenomic Sequence Data ◽  
Search For Homologs

ABSTRACT Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.

scholarly journals The composition and functional protein subsystems of the human nasal microbiome in granulomatosis with polyangiitis: a pilot study

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Josef Wagner ◽  
Ewan M. Harrison ◽  
Marcos Martinez Del Pero ◽  
Beth Blane ◽  
Gert Mayer ◽  
...  
Keyword(s):  
Granulomatosis With Polyangiitis ◽  
Sequence Data ◽  
Bacterial Species ◽  
Vitamin B ◽  
Diversity Analysis ◽  
Healthy Controls ◽  
Functional Protein ◽  
Metagenomic Sequence ◽  
Metagenomic Sequence Data ◽  
Nasal Microbiota

Abstract Background Ear, nose and throat involvement in granulomatosis with polyangiitis (GPA) is frequently the initial disease manifestation. Previous investigations have observed a higher prevalence of Staphylococcus aureus in patients with GPA, and chronic nasal carriage has been linked with an increased risk of disease relapse. In this cross-sectional study, we investigated changes in the nasal microbiota including a detailed analysis of Staphylococcus spp. by shotgun metagenomics in patients with active and inactive granulomatosis with polyangiitis (GPA). Shotgun metagenomic sequence data were also used to identify protein-encoding genes within the SEED database, and the abundance of proteins then correlated with the presence of bacterial species on an annotated heatmap. Results The presence of S. aureus in the nose as assessed by culture was more frequently detected in patients with active GPA (66.7%) compared with inactive GPA (34.1%). Beta diversity analysis of nasal microbiota by bacterial 16S rRNA profiling revealed a different composition between GPA patients and healthy controls (P = 0.039). Beta diversity analysis of shotgun metagenomic sequence data for Staphylococcus spp. revealed a different composition between active GPA patients and healthy controls and disease controls (P = 0.0007 and P = 0.0023, respectively), and between healthy controls and inactive GPA patients and household controls (P = 0.0168 and P = 0.0168, respectively). Patients with active GPA had a higher abundance of S. aureus, mirroring the culture data, while healthy controls had a higher abundance of S. epidermidis. Staphylococcus pseudintermedius, generally assumed to be a pathogen of cats and dogs, showed an abundance of 13% among the Staphylococcus spp. in our cohort. During long-term follow-up of patients with inactive GPA at baseline, a higher S. aureus abundance was not associated with an increased relapse risk. Functional analyses identified ten SEED protein subsystems that differed between the groups. Most significant associations were related to chorismate synthesis and involved in the vitamin B12 pathway. Conclusion Our data revealed a distinct dysbiosis of the nasal microbiota in GPA patients compared with disease and healthy controls. Metagenomic sequencing demonstrated that this dysbiosis in active GPA patients is manifested by increased abundance of S. aureus and a depletion of S. epidermidis, further demonstrating the antagonist relationships between these species. SEED functional protein subsystem analysis identified an association between the unique bacterial nasal microbiota clusters seen mainly in GPA patients and an elevated abundance of genes associated with chorismate synthesis and vitamin B12 pathways. Further studies are required to further elucidate the relationship between the biosynthesis genes and the associated bacterial species.

scholarly journals A Need for Improved Cellulase Identification from Metagenomic Sequence Data

2020 ◽  
Vol 87 (1) ◽  
Author(s):  
Rebecca Co ◽  
Laura A. Hug
Keyword(s):  
Sequence Data ◽  
Industrial Applications ◽  
Data Sets ◽  
Metagenomic Sequence ◽  
Environmental Sequence ◽  
Sequencing Technologies ◽  
Current Classification ◽  
Applied Microbiology ◽  
Environmental Surveys ◽  
Metagenomic Sequence Data

ABSTRACT Improved sequencing technologies and the maturation of metagenomic approaches allow the identification of gene variants with potential industrial applications, including cellulases. Cellulase identification from metagenomic environmental surveys is complicated by inconsistent nomenclature and multiple categorization systems. Here, we summarize the current classification and nomenclature systems, with recommendations for improvements to these systems. Addressing the issues described will strengthen the annotation of cellulose-active enzymes from environmental sequence data sets—a rapidly growing resource in environmental and applied microbiology.

Association between number of sexual partners and utilization of family planning and sexually transmitted infection services by men aged 15–44 in the United States

2019 ◽  
Vol 52 (1) ◽  
pp. 14-26
Author(s):  
Mian B. Hossain ◽  
Yvonne Bronner ◽  
Ifeyinwa Udo ◽  
Sabriya Dennis
Keyword(s):  
United States ◽  
Family Planning ◽  
Health Services ◽  
Black Men ◽  
The United States ◽  
Sexual Partners ◽  
Family Planning Services ◽  
Sexually Transmitted ◽  
The Us ◽  
Number Of Sexual Partners

AbstractUnintended pregnancy and sexually transmitted infections (STIs) pose a huge public health problem in the United States. Efforts towards reducing unintended pregnancies have previously focused on women, but the role of men in family planning and preventing unwanted pregnancy is becoming clearer. The primary objective of the study was to fully examine the utilization of family planning services by men in the US, and to determine whether factors such as race, health insurance type and number of sexual partners influenced their utilization and receipt of family planning services and STI-related health services. Data were from the 2006–2010 National Survey on Family Growth (NSFG) study conducted in the US. The study sample comprised 7686 men aged 14–44 who ever had sex with women, and who had had at least one sexual partner in the 12 months before the survey. The receipt of family planning and STI-related health services by this group of men was estimated. The results showed that non-Hispanic Black men were more likely to receive family planning and STI-related services than Hispanic and non-Hispanic White males. Given that non-Hispanic Black men are disproportionately affected by STIs and are a high-risk group, the finding that this group received more family planning and STI services is a positive step towards reducing the disproportionately high prevalence of STIs in men in this under-privileged population.

scholarly journals Correction: TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data

PLoS ONE ◽  
2015 ◽  
Vol 10 (6) ◽  
pp. e0131379
Author(s):  
Bastiaan B. Wintermans ◽  
Bernd W. Brandt ◽  
Christina M. J. E. Vandenbroucke-Grauls ◽  
Andries E. Budding
Keyword(s):  
Sequence Data ◽  
Whole Genome ◽  
Metagenomic Sequence ◽  
Metagenomic Sequence Data

scholarly journals Acceptability of Couples’ Voluntary HIV Testing Among HIV-infected Patients in Care and Their HIV-negative Partners in the United States

2016 ◽  
Vol 10 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Kristin M. Wall ◽  
Lauren Canary ◽  
Kimberly Workowski ◽  
Annie Lockard ◽  
Jeb Jones ◽  
...  
Keyword(s):  
The United States ◽  
Consistent Condom ◽  
Willingness To Participate ◽  
Hiv Counseling ◽  
Sexually Transmitted ◽  
Counseling And Testing ◽  
Infected Partner ◽  
The Us ◽  
Exposure Prophylaxis ◽  
Hiv Negative

Introduction: Couples’ voluntary HIV counseling and testing (CHTC) is an HIV risk reduction strategy not widely available in the US. Methods: We assessed willingness to participate in CHTC among US HIV-infected clinic patients via tablet-based survey and among HIV-negative persons with HIV-infected partners in care via mixed-method phone interviews. Results: Most of the N=64 HIV-infected partners surveyed were men (89%), on antiretroviral treatment (ART) (92%), and many self-identified homosexual (62%). We observed high levels of willingness to participate in CHTC (64%) among HIV-infected partners. Reasons for not wanting to participate included perceived lack of need (26%), desire to self-disclose their status (26%), and fear of being asked sensitive questions with their partner present (17%). HIV-infected partners were interested in discussing ART (48%), other sexually transmitted infections (STIs) (44%), and relationship agreements like monogamy (31%) during CHTC sessions. All N=15 HIV-negative partners interviewed were men, most identified as homosexual (73%), and about half (54%) reported consistent condom use with HIV-infected partners. We observed high levels of willingness to participate in CHTC (87%) among HIV-negative partners, who were also interested in discussing ART (47%), other STIs (47%), mental health services (40%), and relationship agreements (33%). Most negative partners (93%) indicated that they believed their HIV-infected partner was virally suppressed, but in the event that they were not, many (73%) were willing to take pre-exposure prophylaxis (PrEP). Conclusion: These results indicate that CHTC for serodiscordant couples is acceptable and should emphasize aspects most pertinent to these couples, such as discussion of ART/PrEP, STIs, and relationship agreements.

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