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Saberi P, Neilands TB, Lally MA, Hosek SG, Hightow-Weidman L. The Association between Use of Online Social Networks to Find Sex Partners and Sexually Transmitted Infection Diagnosis among Young Men Who Have Sex with Men and Transgender Women Living with HIV. J Int Assoc Provid AIDS Care 2019; 18:2325958219867324. [PMID: 31389285 PMCID: PMC6900576 DOI: 10.1177/2325958219867324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/23/2019] [Accepted: 07/02/2019] [Indexed: 11/17/2022] Open
Abstract
We conducted a cross-sectional analysis of baseline data from the Adolescent Trials Network for HIV/AIDS Interventions to examine the association between the use of social media sites to find sex partners and recent diagnosis of sexually transmitted infections (STIs) among 13- to 24-year-old men who have sex with men and transgender women living with HIV. We used linear regression to determine the relationship between the number of STIs and the number of social media sites used to find sex partners with each type of sex act included in the analysis. Secondary analyses substituted frequency of social media site use for number of social media sites. Among 741 participants, for every 1 social media account used to find sex partners, there was a 2.53% (95% confidence interval: 0.28-5.54) increase in STIs. This association was mediated through condomless receptive anal intercourse or condomless insertive anal intercourse but not barrierless oral intercourse. Similar but attenuated associations were found when frequency of social media site use was substituted for number of social media sites. Future research should examine innovative interventions on these social media sites with respect for its users.
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Affiliation(s)
- Parya Saberi
- Department of Medicine, University of California San Francisco, San
Francisco, CA, USA
| | - Torsten B. Neilands
- Department of Medicine, University of California San Francisco, San
Francisco, CA, USA
| | - Michelle A. Lally
- Department of Medicine, Alpert Medical School of Brown University and
Lifespan Hospital System, Providence, RI, USA
| | - Sybil G. Hosek
- Department of Psychiatry, Stroger Hospital of Cook County, Chicago, IL,
USA
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2
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Spencer-Smith R, Gould SW, Pulijala M, Snyder LAS. Investigating Potential Chromosomal Rearrangements during Laboratory Culture of Neisseria gonorrhoeae. Microorganisms 2018; 6:microorganisms6010010. [PMID: 29361673 PMCID: PMC5874624 DOI: 10.3390/microorganisms6010010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/19/2017] [Accepted: 01/19/2018] [Indexed: 01/02/2023] Open
Abstract
Comparisons of genome sequence data between different strains and isolates of Neisseria spp., such as Neisseria gonorrhoeae, reveal that over the evolutionary history of these organisms, large scale chromosomal rearrangements have occurred. Factors within the genomes, such as repetitive sequences and prophage, are believed to have contributed to these observations. However, the timescale in which rearrangements occur is not clear, nor whether it might be expected for them to happen in the laboratory. In this study, N. gonorrhoeae was repeatedly passaged in the laboratory and assessed for large scale chromosomal rearrangements. Using gonococcal strain NCCP11945, for which there is a complete genome sequence, cultures were passaged for eight weeks in the laboratory. The resulting genomic DNA was assessed using Pulsed Field Gel Electrophoresis, comparing the results to the predicted results from the genome sequence data. Three cultures generated Pulsed Field Gel Electrophoresis patterns that varied from the genomic data and were further investigated for potential chromosomal rearrangements.
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Affiliation(s)
- Russell Spencer-Smith
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
- National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
| | - Simon W Gould
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
| | - Madhuri Pulijala
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
| | - Lori A S Snyder
- School of Life Sciences, Pharmacy, and Chemistry, Kingston University, Penrhyn Road, Kingston upon Thames KT1 2EE, UK.
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3
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FtsK translocation permits discrimination between an endogenous and an imported Xer/dif recombination complex. Proc Natl Acad Sci U S A 2016; 113:7882-7. [PMID: 27317749 DOI: 10.1073/pnas.1523178113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In bacteria, the FtsK/Xer/dif (chromosome dimer resolution site) system is essential for faithful vertical genetic transmission, ensuring the resolution of chromosome dimers during their segregation to daughter cells. This system is also targeted by mobile genetic elements that integrate into chromosomal dif sites. A central question is thus how Xer/dif recombination is tuned to both act in chromosome segregation and stably maintain mobile elements. To explore this question, we focused on pathogenic Neisseria species harboring a genomic island in their dif sites. We show that the FtsK DNA translocase acts differentially at the recombination sites flanking the genomic island. It stops at one Xer/dif complex, activating recombination, but it does not stop on the other site, thus dismantling it. FtsK translocation thus permits cis discrimination between an endogenous and an imported Xer/dif recombination complex.
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4
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Merchant S, Wood DE, Salzberg SL. Unexpected cross-species contamination in genome sequencing projects. PeerJ 2014; 2:e675. [PMID: 25426337 PMCID: PMC4243333 DOI: 10.7717/peerj.675] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/01/2014] [Indexed: 11/29/2022] Open
Abstract
The raw data from a genome sequencing project sometimes contains DNA from contaminating organisms, which may be introduced during sample collection or sequence preparation. In some instances, these contaminants remain in the sequence even after assembly and deposition of the genome into public databases. As a result, searches of these databases may yield erroneous and confusing results. We used efficient microbiome analysis software to scan the draft assembly of domestic cow, Bos taurus, and identify 173 small contigs that appeared to derive from microbial contaminants. In the course of verifying these findings, we discovered that one genome, Neisseria gonorrhoeae TCDC-NG08107, although putatively a complete genome, contained multiple sequences that actually derived from the cow and sheep genomes. Our findings illustrate the need to carefully validate findings of anomalous DNA that rely on comparisons to either draft or finished genomes.
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Affiliation(s)
- Samier Merchant
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University , Baltimore, MD , USA ; Department of Computer Science, Brown University , Providence, RI , USA
| | - Derrick E Wood
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University , Baltimore, MD , USA ; Department of Computer Science, Johns Hopkins University , USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University , Baltimore, MD , USA ; Department of Computer Science, Johns Hopkins University , USA ; Department of Biomedical Engineering, Johns Hopkins University , USA
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5
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Ripp F, Krombholz CF, Liu Y, Weber M, Schäfer A, Schmidt B, Köppel R, Hankeln T. All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing. BMC Genomics 2014; 15:639. [PMID: 25081296 PMCID: PMC4131036 DOI: 10.1186/1471-2164-15-639] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 07/24/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND DNA-based methods like PCR efficiently identify and quantify the taxon composition of complex biological materials, but are limited to detecting species targeted by the choice of the primer assay. We show here how untargeted deep sequencing of foodstuff total genomic DNA, followed by bioinformatic analysis of sequence reads, facilitates highly accurate identification of species from all kingdoms of life, at the same time enabling quantitative measurement of the main ingredients and detection of unanticipated food components. RESULTS Sequence data simulation and real-case Illumina sequencing of DNA from reference sausages composed of mammalian (pig, cow, horse, sheep) and avian (chicken, turkey) species are able to quantify material correctly at the 1% discrimination level via a read counting approach. An additional metagenomic step facilitates identification of traces from animal, plant and microbial DNA including unexpected species, which is prospectively important for the detection of allergens and pathogens. CONCLUSIONS Our data suggest that deep sequencing of total genomic DNA from samples of heterogeneous taxon composition promises to be a valuable screening tool for reference species identification and quantification in biosurveillance applications like food testing, potentially alleviating some of the problems in taxon representation and quantification associated with targeted PCR-based approaches.
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Affiliation(s)
- Fabian Ripp
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | | | - Yongchao Liu
- />Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Mathias Weber
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Anne Schäfer
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Bertil Schmidt
- />Institute of Computer Science, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
| | - Rene Köppel
- />Official Food Control Authority of the Canton Zürich, Zürich, Switzerland
| | - Thomas Hankeln
- />Institute of Molecular Genetics, Johannes Gutenberg University Mainz, D55099 Mainz, Germany
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Antibodies with higher bactericidal activity induced by a Neisseria gonorrhoeae Rmp deletion mutant strain. PLoS One 2014; 9:e90525. [PMID: 24594737 PMCID: PMC3942440 DOI: 10.1371/journal.pone.0090525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 02/03/2014] [Indexed: 11/22/2022] Open
Abstract
Neisseria gonorrhoeae (N. gonorrhoeae) outer membrane protein reduction modifiable protein (Rmp) has strong immunogenicity. However, anti-Rmp antibodies block rather than preserve the antibacterial effects of protective antibodies, which hampers the development of vaccines for gonococcal infections. We herein constructed an Rmp deletion mutant strain of N. gonorrhoeae by gene homologous recombination. The 261–460 nucleotide residues of Rmp gene amplified from N. gonorrhoeae WHO-A strain were replaced with a kanamycin-resistant Kan gene amplified from pET-28a. The resultant hybridized DNA was transformed into N. gonorrhoeae WHO-A strain. PCR was used to screen the colonies in which wild-type Rmp gene was replaced with a mutant gene fragment. Western blotting revealed that the Rmp deletion mutant strain did not express Rmp protein. Rmp deletion did not alter the morphological and Gram staining properties of the mutant strain that grew slightly more slowly than the wild-type one. Rmp gene mutated stably throughout 25 generations of passage. Antibody-mediated complement-dependent cytotoxicity assay indicated that the antibodies induced by the mutant strain had evidently higher bactericidal activities than those induced by the wild-type strain. Further modification of the Rmp deletion mutant strain is still required in the development of novel live attenuated vaccines for gonorrhea by Opa genes deletion or screening of phenotypic variant strains that do not express Opa proteins.
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Grad YH, Kirkcaldy RD, Trees D, Dordel J, Harris SR, Goldstein E, Weinstock H, Parkhill J, Hanage WP, Bentley S, Lipsitch M. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. THE LANCET. INFECTIOUS DISEASES 2014; 14:220-6. [PMID: 24462211 PMCID: PMC4030102 DOI: 10.1016/s1473-3099(13)70693-5] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The emergence of Neisseria gonorrhoeae with decreased susceptibility to extended spectrum cephalosporins raises the prospect of untreatable gonorrhoea. In the absence of new treatments, efforts to slow the increasing incidence of resistant gonococcus require insight into the factors that contribute to its emergence and spread. We assessed the relatedness between isolates in the USA and reconstructed likely spread of lineages through different sexual networks. METHODS We sequenced the genomes of 236 isolates of N gonorrhoeae collected by the Centers for Disease Control and Prevention's Gonococcal Isolate Surveillance Project (GISP) from sentinel public sexually transmitted disease clinics in the USA, including 118 (97%) of the isolates from 2009-10 in GISP with reduced susceptibility to cefixime (cef(RS)) and 118 cefixime-susceptible isolates from GISP matched as closely as possible by location, collection date, and sexual orientation. We assessed the association between antimicrobial resistance genotype and phenotype and correlated phylogenetic clustering with location and sexual orientation. FINDINGS Mosaic penA XXXIV had a high positive predictive value for cef(RS). We found that two of the 118 cef(RS) isolates lacked a mosaic penA allele, and rechecking showed that these two were susceptible to cefixime. Of the 116 remaining cef(RS) isolates, 114 (98%) fell into two distinct lineages that have independently acquired mosaic penA allele XXXIV. A major lineage of cef(RS) strains spread eastward, predominantly through a sexual network of men who have sex with men. Eight of nine inferred transitions between sexual networks were introductions from men who have sex with men into the heterosexual population. INTERPRETATION Genomic methods might aid efforts to slow the spread of antibiotic-resistant N gonorrhoeae through augmentation of gonococcal outbreak surveillance and identification of populations that could benefit from increased screening for asymptomatic infections.
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Affiliation(s)
- Yonatan H Grad
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | | | - David Trees
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Edward Goldstein
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | | | | | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Stephen Bentley
- Wellcome Trust Sanger Institute, Hinxton, UK; Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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8
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Putonti C, Nowicki B, Shaffer M, Fofanov Y, Nowicki S. Where does Neisseria acquire foreign DNA from: an examination of the source of genomic and pathogenic islands and the evolution of the Neisseria genus. BMC Evol Biol 2013; 13:184. [PMID: 24007216 PMCID: PMC3848584 DOI: 10.1186/1471-2148-13-184] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 08/28/2013] [Indexed: 02/03/2023] Open
Abstract
Background Pathogenicity islands (PAIs) or genomic islands (GEIs) are considered to be the result of a recent horizontal transfer. Detecting PAIs/GEIs as well as their putative source can provide insight into the organism’s pathogenicity within its host. Previously we introduced a tool called S-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. Utilizing S-plot and new functionality developed here, we examined 18 publicly available Neisseria genomes, including strains of both pathogenic and non-pathogenic species, in order to identify regions of unusual compositional properties (RUCPs) using both a sliding window as well as a gene-by-gene approach. Results Numerous GEIs and PAIs were identified including virulence genes previously found within the pathogenic Neisseria species. While some genes were conserved amongst all species, only pathogenic species, or an individual species, a number of genes were detected that are unique to an individual strain. While the majority of such genes have an origin unknown, a number of putative sources including pathogenic and capsule-containing bacteria were determined, indicative of gene exchange between Neisseria spp. and other bacteria within their microhabitat. Furthermore, we uncovered evidence that both N. meningitidis and N. gonorrhoeae have separately acquired DNA from their human host. Data suggests that all three Neisseria species have received horizontally transferred elements post-speciation. Conclusions Using this approach, we were able to not only find previously identified regions of virulence but also new regions which may be contributing to the virulence of the species. This comparative analysis provides a means for tracing the evolutionary history of the acquisition of foreign DNA within this genus. Looking specifically at the RUCPs present within the 18 genomes considered, a stronger similarity between N. meningitidis and N. lactamica is observed, suggesting that N. meningitidis arose before N. gonorrhoeae.
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Affiliation(s)
- Catherine Putonti
- Department of Biology, Loyola University Chicago, 1032 W, Sheridan Rd, Chicago, IL 60660, USA.
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Whole-genome sequencing of bacterial sexually transmitted infections: implications for clinicians. Curr Opin Infect Dis 2013; 26:90-8. [PMID: 23221768 DOI: 10.1097/qco.0b013e32835c2159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PURPOSE OF REVIEW Increasingly, genomics is being used to answer detailed clinical questions. Although genome analysis of bacterial sexually transmitted infections (STIs) lags far behind that of many other bacterial pathogens, genomics can reveal previously inaccessible aspects of pathogen biology. RECENT FINDINGS Comparative genomic studies on the most common bacterial STI, chlamydia, have revolutionized our understanding of this intracellular bacterium, demonstrating that it undergoes extensive recombination and that the traditional typing schemes can be misleading. Genome projects can also help us to understand the recently observed phenomenon of 'diagnostic escape' seen in both Chlamydia trachomatis and Neisseria gonorrhoeae. SUMMARY The routine use of genomics in clinical settings is becoming a reality. For STIs, a primary requirement is an understanding of the diversity of circulating strains and how they change over time. This can help to inform future studies and allow us to address real clinical issues such as outbreak identification, global spread of successful clones and antimicrobial resistance monitoring.
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Evaluation of Neisseria gonorrhoeae multiple-locus variable-number tandem-repeat analysis, N. gonorrhoeae Multiantigen sequence typing, and full-length porB gene sequence analysis for molecular epidemiological typing. J Clin Microbiol 2011; 50:180-3. [PMID: 22075591 DOI: 10.1128/jcm.05386-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance characteristics of Neisseria gonorrhoeae multilocus variable-number tandem-repeat analysis were evaluated, by comparison with N. gonorrhoeae multiantigen sequence typing and full-length porB sequence typing. Assessment of the relatedness of intra- and interpatient isolates showed that all three genotyping techniques display a high resolution and typeability.
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11
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Nelson OW, Garrity GM. Genome sequences published outside of Standards in Genomic Sciences, January – June 2011. Stand Genomic Sci 2011. [DOI: 10.4056/sigs.2044675] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Oranmiyan W. Nelson
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
| | - George M. Garrity
- 1Editorial Office, Standards in Genomic Sciences and Department of Microbiology, Michigan State University, East Lansing, MI, USA
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