Mobile genetic elements in Neisseria gonorrhoeae: movement for change

Cehovin, Ana; Lewis, Steven B

doi:10.1093/femspd/ftx071

Cited by 25 publications

(24 citation statements)

References 118 publications

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“…: https://doi.org/10.5281/zenodo.2618836). The following three prevalent types of plasmids 48 were downloaded from GenBank, localized in the GISP database using BLAST 49 and removed from the dataset: the cryptic plasmid pJD1 (GenBank accession no. : NC_001377.1), the beta-lactamase plasmid pJD4 (GenBank accession no.…”

Section: Methodsmentioning

confidence: 99%

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

et al. 2020

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Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called 'genomic neighbour typing' for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both Streptococcus pneumoniae and Neisseria gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. This resulted in the determination of resistance within 10 min (91% sensitivity and 100% specificity for S. pneumoniae and 81% sensitivity and 100% specificity for N. gonorrhoeae from isolates with a representative database) of starting sequencing, and within 4 h of sample collection (75% sensitivity and 100% specificity for S. pneumoniae) for clinical metagenomic sputum samples. This flexible approach has wide application for pathogen surveillance and may be used to greatly accelerate appropriate empirical antibiotic treatment.

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Section: Methodsmentioning

confidence: 99%

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

et al. 2020

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“…However, the bacterium has developed resistance against all available classes of antimicrobials [ 2 ] and recently was added to the World Health Organization (WHO) list of highly antibiotic-resistant, priority pathogens [ 4 ]. While most AMR determinants exist on the chromosome, penicillin and tetracycline resistance can be conferred by plasmids (p bla TEM and pTetM), which can rapidly spread through gonococcal populations [ 5 ]; p bla TEM can be mobilized between gonococci by the conjugative plasmid pTetM [ 6 ]. Understanding the molecular epidemiology of gonococcal infection, including the development and acquisition of AMR, is therefore essential for effective management of gonococcal infection [ 2 ].…”

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confidence: 99%

Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya

Cehovin

Harrison

Lewis

et al. 2018

The Journal of Infectious Diseases

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BackgroundAfrica has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR).MethodsWhole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya. We annotated loci, defined the core genome, defined mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhea, we determined whether infections occurred with related strains.ResultsWe identified 3 clusters of isolates that are phylogenetically distinct from isolates found elsewhere. Plasmids were virtually ubiquitous: pTetM and pblaTEM were found in 97%, and 55% of isolates, respectively. This was associated with high doxycycline use for undiagnosed sexually transmitted infections. Twenty-three percent of multiple episodes of gonorrhea in the same individual were caused by a related strain, suggesting inadequate treatment or reinfection.ConclusionsThe prevalence of plasmid-mediated AMR in Kenyan gonococci contrasts with that in wealthy countries, where AMR is largely chromosomally mediated. Antimicrobials have a profound effect on the maintenance of lineages harboring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid cooperation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies.

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“…Additionally, there are reports that DNA-related defects have a much greater association with bacterial pathogen from symptomatic patients than samples of the same bacterial species isolated from environmental sources. [87][88][89] Pneumococcus Streptococcus pneumoniae, Gram-positive cocci bacteria that cause otitis media, bacteremia and pneumonia, are a public health concern, causing morbidity and mortality in adults and children. 90 Two forms of vaccines (polysaccharide and conjugate vaccines) are currently marketed for the prevention of pneumococcal infections.…”

Section: Neisseriamentioning

confidence: 99%

<p>Immunoinformatics and Vaccine Development: An Overview</p>

Oli

Obialor

Ifeanyichukwu

et al. 2020

ITT

141

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The use of vaccines have resulted in a remarkable improvement in global health. It has saved several lives, reduced treatment costs and raised the quality of animal and human lives. Current traditional vaccines came empirically with either vague or completely no knowledge of how they modulate our immune system. Even at the face of potential vaccine design advance, immune-related concerns (as seen with specific vulnerable populations, cases of emerging/reemerging infectious disease, pathogens with complex lifecycle and antigenic variability, need for personalized vaccinations, and concerns for vaccines' immunological safety -specifically vaccine likelihood to trigger non-antigen-specific responses that may cause autoimmunity and vaccine allergy) are being raised. And these concerns have driven immunologists toward research for a better approach to vaccine design that will consider these challenges. Currently, immunoinformatics has paved the way for a better understanding of some infectious disease pathogenesis, diagnosis, immune system response and computational vaccinology. The importance of this immunoinformatics in the study of infectious diseases is diverse in terms of computational approaches used, but is united by common qualities related to host-pathogen relationship. Bioinformatics methods are also used to assign functions to uncharacterized genes which can be targeted as a candidate in vaccine design and can be a better approach toward the inclusion of women that are pregnant into vaccine trials and programs. The essence of this review is to give insight into the need to focus on novel computational, experimental and computation-driven experimental approaches for studying of host-pathogen interactions and thus making a case for its use in vaccine development.

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Mobile genetic elements in Neisseria gonorrhoeae: movement for change

Cited by 25 publications

References 118 publications

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing

Identification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya

<p>Immunoinformatics and Vaccine Development: An Overview</p>

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