scholarly journals Towards next-generation diagnostics for tuberculosis: identification of novel molecular targets by large-scale comparative genomics

2019 ◽  
Author(s):  
Galo A Goig ◽  
Manuela Torres-Puente ◽  
Carla Mariner-Llicer ◽  
Luis M Villamayor ◽  
Álvaro Chiner-Oms ◽  
...  

Abstract Motivation Tuberculosis (TB) remains one of the main causes of death worldwide. The long and cumbersome process of culturing Mycobacterium tuberculosis complex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel TB diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study has been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. Results In this work, we used large-scale comparative genomics to identify 40 MTBC-specific loci. We assessed their genetic diversity and physiological features to select 30 that are good targets for diagnostic purposes. Some of these markers could be used to assess the physiological status of the bacilli. Remarkably, none of the most used MTBC markers is in our catalog. Illustrating the translational potential of our work, we develop a specific qPCR assay for quantification and identification of MTBC DNA. Our rational design of targeted molecular assays for TB could be used in many other fields of clinical and basic research. Availability and implementation The database of non-tuberculous mycobacteria assemblies can be accessed at: 10.5281/zenodo.3374377. Supplementary information Supplementary data are available at Bioinformatics online.

2019 ◽  
Author(s):  
Galo A. Goig ◽  
Manuela Torres-Puente ◽  
Carla Mariner-Llicer ◽  
Luis M. Villamayor ◽  
Álvaro Chiner-Oms ◽  
...  

AbstractTuberculosis remains one of the main causes of death worldwide. The long and cumbersome process of culturingMycobacterium tuberculosiscomplex (MTBC) bacteria has encouraged the development of specific molecular tools for detecting the pathogen. Most of these tools aim to become novel tuberculosis diagnostics, and big efforts and resources are invested in their development, looking for the endorsement of the main public health agencies. Surprisingly, no study had been conducted where the vast amount of genomic data available is used to identify the best MTBC diagnostic markers. In this work, we use large-scale comparative genomics to provide a catalog of 30 characterized loci that are unique to the MTBC. Some of these genes could be targeted to assess the physiological status of the bacilli. Remarkably, none of the conventional MTBC markers is in our catalog. In addition, we develop a qPCR assay to accurately quantify MTBC DNA in clinical samples.


Author(s):  
Imran Rafi ◽  
Judith Hayward ◽  
Peter English

The COVID-19 Genomics UK (COG-UK) Consortium was created to deliver large-scale and rapid whole-genome virus sequencing. Its data will help Public Health Agencies to manage the COVID-19 pandemic in the UK and inform vaccine research efforts. From a wider perspective, data sharing around the genomics of viruses (and bacteria, protozoa parasites and fungi) offers researchers contrasting perspectives and new biological insights into the evolution of microbes and the development of new tools in managing infectious disease, which on a global scale causes significant mortality. Genomics has an evolving role in pathogen diagnosis and surveillance.


Author(s):  
Allison Black ◽  
Duncan R. MacCannell ◽  
Thomas R. Sibley ◽  
Trevor Bedford

Public health agencies are increasingly using pathogen whole genome sequencing (WGS) to support surveillance and epidemiologic investigations. As access to WGS has grown, greater amounts of molecular data have helped improve our ability to detect outbreaks, investigate transmission chains, and explore large-scale population dynamics, such as the spread of antibiotic resistance. However, the wide adoption of WGS also poses challenges due to the amount of data generated and the need to transform raw data prior to analysis. This complexity means that public health agencies may need more advanced computational infrastructure, a broader technical workforce, and new approaches to data management and stewardship. As both a guide for how this development could occur, and a place to initiate discussion, we describe ten proposals for developing and supporting an informatics infrastructure for public health.


Urban Studies ◽  
1965 ◽  
Vol 2 (2) ◽  
pp. 195-196
Author(s):  
Andrew Semple

Author(s):  
Jonathan H. Marks

Collaboration with industry has become the paradigm in public health. Governments commonly develop close relationships with companies that are creating or exacerbating the very problems public health agencies are trying to solve. Nowhere is this more evident than in partnerships with food and soda companies to address obesity and diet-related noncommunicable diseases. The author argues that public-private partnerships and multistakeholder initiatives create webs of influence that undermine the integrity of public health agencies; distort public health research and policy; and reinforce the framing of public health problems and their solutions in ways that are least threatening to the commercial interests of corporate “partners.” We should expect multinational corporations to develop strategies of influence. But public bodies need to develop counter-strategies to insulate themselves from corporate influence in all its forms. The author reviews the ways in which we regulate public-public interactions (separation of powers) and private-private interactions (antitrust and competition laws), and argues for an analogous set of norms to govern public-private interactions. The book also offers a novel framework that is designed to help public bodies identify the systemic ethical implications of their existing or proposed relationships with industry actors. The book makes a compelling case that, in public health, the paradigm public-private interaction should be at arm’s length: separation, not collaboration. The author calls for a new paradigm to protect and promote public health while avoiding the ethical perils of partnership with industry.


2021 ◽  
pp. 000276422199283
Author(s):  
Serena Tagliacozzo ◽  
Frederike Albrecht ◽  
N. Emel Ganapati

Communicating during a crisis can be challenging for public agencies as their communication ecology becomes increasingly complex while the need for fast and reliable public communication remains high. Using the lens of communication ecology, this study examines the online communication of national public health agencies during the COVID-19 pandemic in Italy, Sweden, and the United States. Based on content analysis of Twitter data ( n = 856) and agency press releases ( n = 95), this article investigates two main questions: (1) How, and to what extent, did national public health agencies coordinate their online communication with other agencies and organizations? (2) How was online communication from the agencies diversified in terms of targeting specific organizations and social groups? Our findings indicate that public health agencies relied heavily on internal scientific expertise and predominately coordinated their communication efforts with national government agencies. Furthermore, our analysis reveals that agencies in each country differed in how they diversify information; however, all agencies provided tailored information to at least some organizations and social groups. Across the three countries, information tailored for several vulnerable groups (e.g., pregnant women, people with disabilities, immigrants, and homeless populations) was largely absent, which may contribute to negative consequences for these groups.


Author(s):  
Leigh Crilley ◽  
Brian Malile ◽  
Andrea Angelucci ◽  
Cora Young ◽  
Trevor C. VandenBoer ◽  
...  

Current guidance by leading public health agencies recommends wearing a 3-layer cloth-based face mask with a middle non-woven material insert to reduce the transmission of infectious respiratory viruses like SARS-CoV-2....


Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Michelle Seiler ◽  
Georg Staubli ◽  
Julia Hoeffe ◽  
Gianluca Gualco ◽  
Sergio Manzano ◽  
...  

Abstract Background We aimed to document the impact of the coronavirus disease 2019 (COVID-19) pandemic on regions within a European country. Methods Parents arriving at two pediatric emergency departments (EDs) in North of Switzerland and two in South of Switzerland completed an online survey during the first peak of the pandemic (April–June 2020). They were asked to rate their concern about their children or themselves having COVID-19. Results A total of 662 respondents completed the survey. Parents in the South were significantly more exposed to someone tested positive for COVID-19 than in the North (13.9 and 4.7%, respectively; P <  0.001). Parents in the South were much more concerned than in the North that they (mean 4.61 and 3.32, respectively; P <  0.001) or their child (mean 4.79 and 3.17, respectively; P <  0.001) had COVID-19. Parents reported their children wore facemasks significantly more often in the South than in the North (71.5 and 23.5%, respectively; P <  0.001). Conclusion The COVID-19 pandemic resulted in significant regional differences among families arriving at EDs in Switzerland. Public health agencies should consider regional strategies, rather than country-wide guidelines, in future pandemics and for vaccination against COVID-19 for children.


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