A pilot study to show that asymptomatic sexually transmitted infections alter the foreskin epithelial proteome

Chigorimbo-Murefu, Nyaradzo T. L.; Potgieter, Matthys; Dzanibe, Sonwabile; Gabazana, Zikhona; Buri, Gershom; Chawla, Aditya; Nleya, Bokani; Olivier, Abraham J.; Harryparsad, Rushil; Calder, Bridget; Garnett, Shaun; Maziya, Lungile; Lewis, David A.; Jaspan, Heather B.; Wilson, D. C.; Passmore, Jo‐Ann S.; Mulder, Nicola; Blackburn, Jonathan M.; Bekker, Linda‐Gail; Gray, Clive M.

doi:10.3389/fmicb.2022.928317

Cited by 5 publications

(2 citation statements)

References 75 publications

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“…STI is a disease that can be transmitted through sexual intercourse, whether vaginal or anal intercourse. STI is the entry point for HIV in both heterosexual groups and homosexual groups, namely MSM and gays (Australian Government et al, 2017;Chigorimbo-Murefu et al, 2022;Ditjen P3 Kemenkes, 2022). STI itself, once present in the human body, is usually characterized by pus coming out of the genitals, lumps on the genitals, and wounds around the genitals (Australian Government et al, 2017;KPA et al, 2012).…”

Section: Discussionmentioning

confidence: 99%

Prevention of STI Transmission among Men Who Have Sex with Men in Indonesia through Circumcision Behavior

Fatiah,

Purba

2023

JBC

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Introduction: The proportion of Sexually Transmitted Infections (STIs) among MSM has increased by around 0,2% from the first quarter and second quarter of 2023, for this reason, prevention efforts are needed in the form of implementing circumcision behavior among men. Objective: to understand the relationship between circumcision and transmission of STIs through MSM in Indonesia. Method: This research has a cross-sectional design with the population being men who have sex with men (MSM) across 24 provinces in Indonesia totaling 6,000 people, while the research sample is mostly MSM totaling 4,290 people with inclusion criteria being: men who are at least 15 years old, have ever had sex with men at least once in the past year, and have lived in the survey city for around one month. Samples were taken using the Respondent Driven Sampling (RDS) technique. The data used is secondary data in the form of 2018-2019 Biological Behavior Survey (STBP) data. Data in the study were analyzed using logistic regression analysis of risk factor models using STATA 14 software. Results: MSM who were circumcised had a 3.0 times greater chance of not having STI symptoms compared to MSM who were not circumcised (95% CI: 2.5- 3.7) after controlling for sex-buying and selling behavior. Conclusion: circumcision behavior is one of the efforts to prevent the spread of STI among MSM, recommending the need to create regulations regarding the importance of circumcision behavior in Indonesia.

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Section: Discussionmentioning

confidence: 99%

Prevention of STI Transmission among Men Who Have Sex with Men in Indonesia through Circumcision Behavior

Fatiah,

Purba

2023

JBC

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“…The MetaNovo software has already been used to obtain new insights into vaginal [ 19 , 20 ] and foreskin [ 21 ] microbiome dynamics and has been made publicly available on Galaxy [ 22 ] ( https://toolshed.g2.bx.psu.edu/repository?repository_id=f90d438ce91f95f1 , https://usegalaxy.eu/root?tool_id=metanovo ,). The tool is also available as a standalone package in Anaconda ( https://anaconda.org/bioconda/metanovo ).…”

Section: Introductionmentioning

confidence: 99%

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets

Nel

Fortuin

et al. 2023

PLoS Comput Biol

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Background Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines. Results We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database—but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation. Conclusions By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.

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Current Treatment Strategies Against Multidrug-Resistant Bacteria: A Review

et al. 2022

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There are several bacteria called superbugs that are resistant to multiple antibiotics which can be life threatening specially for critically ill and hospitalized patients. This article provides up-to-date treatment strategies employed against some major superbugs, like methicillin-resistant Staphylococcus aureus, carbapenem-resistant Enterobacteriaceae, vancomycin-resistant Enterococcus, multidrug-resistant Pseudomonas aeruginosa, and multidrug-resistant Escherichia coli. The pathogen-directed therapeutics decrease the toxicity of bacteria by altering their virulence factors by specific processes. On the other hand, the host-directed therapeutics limits these superbugs by modulating immune cells, enhancing host cell functions, and modifying disease pathology. Several new antibiotics against the global priority superbugs are coming to the market or are in the clinical development phase. Medicinal plants possessing potent secondary metabolites can play a key role in the treatment against these superbugs. Nanotechnology has also emerged as a promising option for combatting them. There is urgent need to continuously figure out the best possible treatment strategy against these superbugs as resistance can also be developed against the new and upcoming antibiotics in future. Rational use of antibiotics and maintenance of proper hygiene must be practiced among patients.

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A pilot study to show that asymptomatic sexually transmitted infections alter the foreskin epithelial proteome

Cited by 5 publications

References 75 publications

Prevention of STI Transmission among Men Who Have Sex with Men in Indonesia through Circumcision Behavior

Prevention of STI Transmission among Men Who Have Sex with Men in Indonesia through Circumcision Behavior

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets

Current Treatment Strategies Against Multidrug-Resistant Bacteria: A Review

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