scholarly journals A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Leonor Sánchez-Busó ◽  
Corin A. Yeats ◽  
Benjamin Taylor ◽  
Richard J. Goater ◽  
Anthony Underwood ◽  
...  
Keyword(s):  
Public Health ◽  
Neisseria Gonorrhoeae ◽  
Point Of Care ◽  
Epidemiological Data ◽  
Empiric Therapy ◽  
Health Concern ◽  
Easy Access ◽  
Advisory Group ◽  
Public Health Genetics ◽  
Genomic Epidemiology

Abstract Background Antimicrobial-resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last-line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones and transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community-driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance. Methods Here we present a public health-focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch (https://pathogen.watch/ngonorrhoeae). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization. Results AMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin-resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasising the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern. Conclusions The N. gonorrhoeae scheme in Pathogenwatch provides customised bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower-resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.

scholarly journals A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

2020 ◽  
Author(s):  
Leonor Sánchez-Busó ◽  
Corin A. Yeats ◽  
Benjamin Taylor ◽  
Richard J. Goater ◽  
Anthony Underwood ◽  
...  
Keyword(s):  
Public Health ◽  
Neisseria Gonorrhoeae ◽  
Point Of Care ◽  
Epidemiological Data ◽  
Empiric Therapy ◽  
Health Concern ◽  
Easy Access ◽  
Advisory Group ◽  
Public Health Genetics ◽  
Genomic Epidemiology

AbstractBackgroundAntimicrobial resistant (AMR) Neisseria gonorrhoeae is an urgent threat to public health, as strains resistant to at least one of the two last line antibiotics used in empiric therapy of gonorrhoea, ceftriaxone and azithromycin, have spread internationally. Whole genome sequencing (WGS) data can be used to identify new AMR clones, transmission networks and inform the development of point-of-care tests for antimicrobial susceptibility, novel antimicrobials and vaccines. Community driven tools that provide an easy access to and analysis of genomic and epidemiological data is the way forward for public health surveillance.MethodsHere we present a public health focussed scheme for genomic epidemiology of N. gonorrhoeae at Pathogenwatch (https://pathogen.watch/ngonorrhoeae). An international advisory group of experts in epidemiology, public health, genetics and genomics of N. gonorrhoeae was convened to inform on the utility of current and future analytics in the platform. We implement backwards compatibility with MLST, NG-MAST and NG-STAR typing schemes as well as an exhaustive library of genetic AMR determinants linked to a genotypic prediction of resistance to eight antibiotics. A collection of over 12,000 N. gonorrhoeae genome sequences from public archives has been quality-checked, assembled and made public together with available metadata for contextualization.ResultsAMR prediction from genome data revealed specificity values over 99% for azithromycin, ciprofloxacin and ceftriaxone and sensitivity values around 99% for benzylpenicillin and tetracycline. A case study using the Pathogenwatch collection of N. gonorrhoeae public genomes showed the global expansion of an azithromycin resistant lineage carrying a mosaic mtr over at least the last 10 years, emphasizing the power of Pathogenwatch to explore and evaluate genomic epidemiology questions of public health concern.ConclusionsThe N. gonorrhoeae scheme in Pathogenwatch provides customized bioinformatic pipelines guided by expert opinion that can be adapted to public health agencies and departments with little expertise in bioinformatics and lower resourced settings with internet connection but limited computational infrastructure. The advisory group will assess and identify ongoing public health needs in the field of gonorrhoea, particularly regarding gonococcal AMR, in order to further enhance utility with modified or new analytic methods.

scholarly journals First National Genomic Epidemiological Study of Neisseria gonorrhoeae Strains Spreading Across Sweden in 2016

2022 ◽  
Vol 12 ◽  
Author(s):  
Ronza Hadad ◽  
Daniel Golparian ◽  
Inga Velicko ◽  
Anna-Karin Ohlsson ◽  
Ylva Lindroth ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Health Agency ◽  
Epidemiological Data ◽  
Health Concern ◽  
Dynamic Evolution ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Public ◽  
Genomic Epidemiology ◽  
Sequence Types

The increasing transmission and antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global health concern with worrying trends of decreasing susceptibility to also the last-line extended-spectrum cephalosporin (ESC) ceftriaxone. A dramatic increase of reported gonorrhea cases has been observed in Sweden from 2016 and onward. The aim of the present study was to comprehensively investigate the genomic epidemiology of all cultured N. gonorrhoeae isolates in Sweden during 2016, in conjunction with phenotypic AMR and clinical and epidemiological data of patients. In total, 1279 isolates were examined. Etest and whole-genome sequencing (WGS) were performed, and epidemiological data obtained from the Public Health Agency of Sweden. Overall, 51.1%, 1.7%, and 1.3% resistance to ciprofloxacin, cefixime, and azithromycin, respectively, was found. No isolates were resistant to ceftriaxone, however, 9.3% of isolates showed a decreased susceptibility to ceftriaxone and 10.5% to cefixime. In total, 44 penA alleles were found of which six were mosaic (n = 92). Using the typing schemes of MLST, NG-MAST, and NG-STAR; 133, 422, and 280 sequence types, respectively, and 93 NG-STAR clonal complexes were found. The phylogenomic analysis revealed two main lineages (A and B) with lineage A divided into two main sublineages (A1 and A2). Resistance and decreased susceptibility to ESCs and azithromycin and associated AMR determinants, such as mosaic penA and mosaic mtrD, were predominantly found in sublineage A2. Resistance to cefixime and azithromycin was more prevalent among heterosexuals and MSM, respectively, and both were predominantly spread through domestic transmission. Continuous surveillance of the spread and evolution of N. gonorrhoeae, including phenotypic AMR testing and WGS, is essential for enhanced knowledge regarding the dynamic evolution of N. gonorrhoeae and gonorrhea epidemiology.

scholarly journals Aerosol Transmission of Coronavirus and Influenza Virus of Animal Origin

2021 ◽  
Vol 8 ◽  
Author(s):  
Jing Lv ◽  
Jing Gao ◽  
Bo Wu ◽  
Meiling Yao ◽  
Yudong Yang ◽  
...  
Keyword(s):  
Public Health ◽  
Influenza Virus ◽  
Epidemiological Data ◽  
Scientific Basis ◽  
Animal Origin ◽  
Easy Access ◽  
Global Public Health ◽  
Long Distance ◽  
Aerosol Generation ◽  
Viral Aerosol

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused great harm to global public health, resulting in a large number of infections among the population. However, the epidemiology of coronavirus has not been fully understood, especially the mechanism of aerosol transmission. Many respiratory viruses can spread via contact and droplet transmission, but increasing epidemiological data have shown that viral aerosol is an essential transmission route of coronavirus and influenza virus due to its ability to spread rapidly and high infectiousness. Aerosols have the characteristics of small particle size, long-time suspension and long-distance transmission, and easy access to the deep respiratory tract, leading to a high infection risk and posing a great threat to public health. In this review, the characteristics of viral aerosol generation, transmission, and infection as well as the current advances in the aerosol transmission of zoonotic coronavirus and influenza virus are summarized. The aim of the review is to strengthen the understanding of viral aerosol transmission and provide a scientific basis for the prevention and control of these diseases.

Costo-beneficio del trattamento con i farmaci antivirali ad azione diretta nei consumatori di sostanze con epatite C: una valutazione del percorso di point of care

MISSION ◽  
2021 ◽  
pp. 8-17
Author(s):  
Felice A. Nava ◽  
Lucia Trevisi ◽  
Alfio Lucchini
Keyword(s):  
Public Health ◽  
Cost Saving ◽  
Drug Users ◽  
Cost Benefit Analysis ◽  
Point Of Care ◽  
Cost Benefit ◽  
Health Concern ◽  
Hcv Treatment ◽  
The Public ◽  
The Cost

Background Hepatitis C is a disease correlated with severe systemic consequences having elevated social and health costs. The HCV elimination is a public health concern that may be solved reaching DAAs treatment for drug users. The principal aim of this work is to evaluate the cost-benefit of a point of care for HCV treatment of drug users inside Drug abuse services (Ser.D.). Methods The study consists in a cost-benefit analysis able to evaluate the "return of health" induced by a point of care for a HCV treatment. Results The work shows that the point of care is cost-benefit in comparison with the "traditional" treatment being cost saving for the public health system. The data suggest that the cost of the point of care is corresponding to euros 593,40 while the cost of not treatment of euros 8.679,60 (due to the direct and indirect costs of the disease). Conclusions The study demonstrate the point of care is an effective model of care able to reduce the barriers of treatment and to induce a "health return" in term of cost saving for the public health systems. Indeed, the work shows how the point of care may make the elimination HCV plans sustainable for the public health agencies.

Antimicrobial susceptibility in Neisseria gonorrhoeae isolates from five sentinel surveillance sites in Zimbabwe, 2015–2016

2017 ◽  
Vol 94 (1) ◽  
pp. 62-66 ◽  
Author(s):  
Ahmed S Latif ◽  
Lovemore Gwanzura ◽  
Anna Machiha ◽  
Francis Ndowa ◽  
Andrew Tarupiwa ◽  
...  
Keyword(s):  
Public Health ◽  
Neisseria Gonorrhoeae ◽  
Inhibitory Concentration ◽  
Treatment Guidelines ◽  
Multidrug Resistant ◽  
Health Concern ◽  
National Treatment ◽  
African Region ◽  
Urethral Discharge ◽  
Ciprofloxacin Resistance

ObjectivesGonorrhoea and antimicrobial resistance (AMR) in Neisseria gonorrhoeae are major public health concerns worldwide. Enhanced AMR surveillance for gonococci is essential globally. In Zimbabwe, very limited gonococcal AMR data were reported. Our aims were to (i) implement quality-assured gonococcal AMR surveillance in Zimbabwe and (ii) investigate gonococcal AMR at five health centres in 2015–2016.MethodsGonococcal isolates from 104 men with urethral discharge were tested for susceptibility to kanamycin, ceftriaxone, cefixime, ciprofloxacin and azithromycin using Etest.ResultsAll isolates (102 possible to test) were susceptible to ceftriaxone and cefixime. The level of resistance (intermediate resistance) to kanamycin and ciprofloxacin was 2.0% (2.0%) and 18.6% (27.5%), respectively. The two kanamycin-resistant isolates (R≥128 mg/L) had a kanamycin minimum inhibitory concentration (MIC) of >256 mg/L. The ciprofloxacin resistance ranged from 9.5% to 30.8% in the five sentinel sites. Only 10 (9.6%) of the isolates were tested for susceptibility to azithromycin and 1 (10.0%) was resistant (MIC=4 mg/L).ConclusionsThe emergence of multidrug-resistant gonorrhoea internationally is a major public health concern and gonococcal AMR surveillance is crucial globally. In Zimbabwe, gonococcal AMR surveillance has now been implemented and quality assured according to WHO standards. The results of this first surveillance will be used to directly inform revisions of the national treatment guidelines. It is imperative to further strengthen the surveillance of gonococcal AMR, and ideally also treatment failures, in Zimbabwe and most countries in the WHO African region, which requires continuous national and international support, including technical support, and political and financial commitment.

scholarly journals Integration of Mobile Devices and Point-Of-Care Diagnostic Devices—The Case of C-Reactive Protein Diagnosis

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 181 ◽  
Author(s):  
Xin-Fang Wu ◽  
Ching-Fen Shen ◽  
Chao-Min Cheng
Keyword(s):  
Public Health ◽  
Antibiotic Resistance ◽  
Mobile Devices ◽  
Point Of Care ◽  
Health Concern ◽  
Global Public Health ◽  
C Reactive Protein ◽  
Public Health Concern ◽  
Reactive Protein

In recent years, the misuse and overuse of antibiotics has promoted antibiotic resistance, which has now become a global public health concern [...]

scholarly journals Scabies epidemiology in health care centers for refugees and asylum seekers in Greece

2022 ◽  
Author(s):  
Christina Louka ◽  
Emmanouil Logothetis ◽  
Daniel Engelman ◽  
Eirini Samiotaki-Logotheti ◽  
Spyros Pournaras ◽  
...  
Keyword(s):  
Public Health ◽  
Health Care ◽  
Infectious Diseases ◽  
Surveillance System ◽  
Asylum Seekers ◽  
Respiratory Infections ◽  
Early Stage ◽  
Epidemiological Data ◽  
Health Concern ◽  
Refugees And Asylum Seekers

Background Scabies is a global health concern disproportionally affecting vulnerable population such as refugees and asylum seekers. Greece is a main geographical point of entry in Europe for refugees, but epidemiological data on scabies in this population is scarce. We aimed to evaluate the epidemiology of scabies, including trends over the study period. Methodology/Principal findings Data were collected from June, 2016 to July, 2020, using the surveillance system of the Greek National Public Health Organization. Staff at health centers for refugees/asylum seekers compiled daily reports on scabies and other infectious diseases. Observed proportional morbidity for scabies was calculated using consultations for scabies as a proportion of total consultations. There were a total of 13118 scabies cases over the study period. Scabies was the third most frequently observed infectious disease in refugees/asylum seekers population after respiratory infections and gastroenteritis without blood in the stool. The scabies monthly observed proportional morbidity varied between 0.3% (August 2017) to 5.6% (January 2020). Several outbreaks were documented during the study period. An increasing number of cases was observed from October 2019 until the end of the study period, with a peak of 1663 cases in January 2020, related to an outbreak at one center. Spearman correlation test between the number of reported scabies cases and time confirmed an increasing trend (ρ=0.67). Conclusions/Significance Scabies is one of the most frequently reported infectious diseases by health care workers in refugee/asylum seekers centers in Greece. Consultations for scabies increased over time and there were several outbreaks. The current surveillance system effectively detects new cases in an early stage. Public health interventions, including mass drug administration, should be considered to reduce the burden of scabies in refugee/migrant populations.

Dementia Around the World and the Latin America and Mexican Scenarios

2021 ◽  
Author(s):  
Rafael Brito-Aguilar
Keyword(s):  
Public Health ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Adult Population ◽  
Fine Particulate Matter ◽  
Public Health Problem ◽  
Epidemiological Data ◽  
Health Concern ◽  
Middle Income ◽  
The World

Dementia has become a major public health concern around the world. Dementia risk factors are significantly different among countries. The number of new cases of dementia anticipated each year worldwide is almost 7.7 million, one new case every four seconds. There are 3.6 million (46%) new cases per year in Asia, 2.3 million (31%) in Europe, 1.2 million (16%) in the Americas, and 0.5 million (7%) in Africa. Latin American and Caribbean low and middle-income countries are at high risk. Air pollution is an important risk modifiable factor for dementia across the world, and the recent report of the Alzheimer’s disease continuum in children and young adults residing in Metropolitan Mexico City along with the presence of cognitive impairment in 55% of the young adult population residing in Mexican cities with fine particulate matter concentrations above the current USEPA annual standard of 12 μg/m3 makes this a severe public health problem in progress. It is imperative to keep generating epidemiological data on dementia worldwide and their relationship with air pollutants to improve the strategies to face all the challenges associated with dementia and Alzheimer’s disease in particular. Alzheimer’s disease is a fatal disease, we have no cure, and we ought to invest in protecting our citizens by intervening in modifiable environmental factors.

Drassanes Exprés: a public and confidential testing service for asymptomatic STIs with same-day result notification

2021 ◽  
pp. sextrans-2020-054779
Author(s):  
Yannick Hoyos-Mallecot ◽  
Jorge Nestor Garcia ◽  
Elena Sulleiro ◽  
Juliana Esperalba ◽  
Paula Salmeron ◽  
...  
Keyword(s):  
Point Of Care ◽  
Health Concern ◽  
Easy Access ◽  
Electronic Patient Records ◽  
Population Coverage ◽  
Sample Collection ◽  
Time To Treatment ◽  
Testing Service ◽  
Message Service ◽  
Risk Practices

BackgroundSTIs are a major public health concern. Screening programmes for asymptomatic users are key components of STI control. Traditional limitations of screening programmes include low population coverage and delays in treatments, thus reducing the expected impact on STI control. In our centre, the normal time from test to results was 4 days, and 7 days until treatment was established.To reduce time to treatment and to increase population coverage, we developed ‘Drassanes Exprés’, a testing service for asymptomatic STIs. The objectives of this study were to provide a guide for the implementation of a service with these characteristics and to evaluate the results of this intervention.MethodsThe Drassanes Exprés programme was launched in Spain on 07 November 2016 as a public, confidential and free-of-charge testing service for asymptomatic STIs, with same-day result notification. For this walk-in service, confidentiality was obtained by registering all information into the Laboratory Internal Software instead of the Electronic Patient Records. Samples were processed in a point-of-care laboratory and result notification was provided via mail or short message service.Information about workflow, screening protocols and result interpretation is detailed. Additionally, demographic characteristics, STI prevalence, and time from patients’ sample collection to notification and treatment are analysed.ResultsBetween 07 November 2016 and 07 November 2019, 13 993 users attended the Drassanes Exprés screening programme. Of these, 0.5% were transgender people, 29.3% women, 45.2% men who have sex with men and 25.1% men who have sex with women. The median age was 31 years (range: 26–39 years). Overall, 14.6% of users tested positive for at least one STI. The most prevalent infection was Chlamydia trachomatis (8.3%), followed by Neisseria gonorrhoeae (5.7%), syphilis (1.8%), HIV (0.4%) and hepatitis C virus (0.2%). The median time from test to results was 2.4 hours (range: 2–3.1 hours). Of 2049 users diagnosed with an STI, treatment was achieved in 97.0% of cases; the average time to treatment was 2.0 days.ConclusionsDrassanes Exprés is the first public programme for rapid, asymptomatic, STI screening and treatment in Spain. Assessing high-risk practices and providing confidentiality, easy access and rapid results/treatments are key elements in the development of STI screening programmes.

scholarly journals Prolonged Outbreak of Multidrug-Resistant Shigella sonnei Harboring blaCTX-M-27 in Victoria, Australia

2020 ◽  
Vol 64 (12) ◽  
Author(s):  
Danielle J. Ingle ◽  
Patiyan Andersson ◽  
Mary Valcanis ◽  
Jessica Barnden ◽  
Anders Gonçalves da Silva ◽  
...  
Keyword(s):  
Public Health ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Shigella Sonnei ◽  
Health Concern ◽  
Content Type ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum ◽  
Significant Public Health ◽  
Sex With Men

ABSTRACT In Australia, cases of shigellosis usually occur in returned travelers from regions of shigellosis endemicity or in men who have sex with men. Resistance to multiple antibiotics has significantly increased in Shigella sonnei isolates and represents a significant public health concern. We investigate an outbreak of multidrug-resistant S. sonnei in Victoria, Australia. We undertook whole-genome sequencing of 54 extended-spectrum-beta-lactamase (ESBL)-producing S. sonnei isolates received at the Microbiological Diagnostic Unit Public Health Laboratory between January 2019 and March 2020. The population structure and antimicrobial resistance profiles were identified by genomic analyses, with 73 previously characterized Australian S. sonnei isolates providing context. Epidemiological data, including age and sex of the shigellosis cases, were also collected. There was a significant increase in cases of ESBL S. sonnei from July 2019. Most of the ESBL S. sonnei isolates (65%) fell within a single cluster that was predominantly comprised of male cases that were characterized by the presence of the blaCTX-M-27 gene conferring resistance to extended-spectrum cephalosporins. These isolates were also multidrug resistant, including resistance to azithromycin and co-trimoxazole and reduced susceptibility to ciprofloxacin. Our data uncovered a prolonged clonal outbreak of ESBL S. sonnei infection that was likely first introduced by returned travelers and has subsequently been circulating locally in Australia. The emergence of a local outbreak of ESBL S. sonnei with a multidrug-resistant profile, including reduced susceptibility to ciprofloxacin, represents a significant public health threat.

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