Last data update: May 06, 2024. (Total: 46732 publications since 2009)
Records 1-30 (of 48 Records) |
Query Trace: Thomson A[original query] |
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Global phylogeography and evolutionary history of Shigella dysenteriae type 1.
Njamkepo E , Fawal N , Tran-Dien A , Hawkey J , Strockbine N , Jenkins C , Talukder KA , Bercion R , Kuleshov K , Kolínská R , Russell JE , Kaftyreva L , Accou-Demartin M , Karas A , Vandenberg O , Mather AE , Mason CJ , Page AJ , Ramamurthy T , Bizet C , Gamian A , Carle I , Sow AG , Bouchier C , Wester AL , Lejay-Collin M , Fonkoua MC , Le Hello S , Blaser MJ , Jernberg C , Ruckly C , Mérens A , Page AL , Aslett M , Roggentin P , Fruth A , Denamur E , Venkatesan M , Bercovier H , Bodhidatta L , Chiou CS , Clermont D , Colonna B , Egorova S , Pazhani GP , Ezernitchi AV , Guigon G , Harris SR , Izumiya H , Korzeniowska-Kowal A , Lutyńska A , Gouali M , Grimont F , Langendorf C , Marejková M , Peterson LA , Perez-Perez G , Ngandjio A , Podkolzin A , Souche E , Makarova M , Shipulin GA , Ye C , Žemličková H , Herpay M , Grimont PA , Parkhill J , Sansonetti P , Holt KE , Brisse S , Thomson NR , Weill FX . Nat Microbiol 2016 1 16027 Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease. |
Monitoring and reporting the US COVID-19 vaccination effort
Scharf LG , Adeniyi K , Augustini E , Boyd D , Corvin L , Kalach RE , Fast H , Fath J , Harris L , Henderson D , Hicks-Thomson J , Jones-Jack N , Kellerman A , Khan AN , McGarvey SS , McGehee JE , EMiner C , Moore LB , Murthy BP , Myerburg S , Neuhaus E , Nguyen K , Parker M , Pierce-Richards S , Samchok D , Shaw LK , Spoto S , Srinivasan A , Stearle C , Thomas J , Winarsky M , Zell E . Vaccine 2023 Immunizations are an important tool to reduce the burden of vaccine preventable diseases and improve population health.(1) High-quality immunization data is essential to inform clinical and public health interventions and respond to outbreaks of vaccine-preventable diseases. To track COVID-19 vaccines and vaccinations, CDC established an integrated network that included vaccination provider systems, health information exchange systems, immunization information systems, pharmacy and dialysis systems, vaccine ordering systems, electronic health records, and tools to support mass vaccination clinics. All these systems reported data to CDC's COVID-19 response system (either directly or indirectly) where it was processed, analyzed, and disseminated. This unprecedented vaccine tracking effort provided essential information for public health officials that was used to monitor the COVID-19 response and guide decisions. This paper will describe systems, processes, and policies that enabled monitoring and reporting of COVID-19 vaccination efforts and share challenges and lessons learned for future public health emergency responses. |
Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda
Monod M , Brizzi A , Galiwango RM , Ssekubugu R , Chen Y , Xi X , Kankaka EN , Ssempijja V , Abeler-Dörner L , Akullian A , Blenkinsop A , Bonsall D , Chang LW , Dan S , Fraser C , Golubchik T , Gray RH , Hall M , Jackson JC , Kigozi G , Laeyendecker O , Mills LA , Quinn TC , Reynolds SJ , Santelli J , Sewankambo NK , Spencer SEF , Ssekasanvu J , Thomson L , Wawer MJ , Serwadda D , Godfrey-Faussett P , Kagaayi J , Grabowski MK , Ratmann O . Nat Microbiol 2023 9 (1) 35-54 HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted: whereas HIV transmission to girls and women (aged 15-24 years) from older men declined by about one-third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programmes to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa. |
Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
Carey ME , Dyson ZA , Ingle DJ , Amir A , Aworh MK , Chattaway MA , Chew KL , Crump JA , Feasey NA , Howden BP , Keddy KH , Maes M , Parry CM , Van Puyvelde S , Webb HE , Afolayan AO , Alexander AP , Anandan S , Andrews JR , Ashton PM , Basnyat B , Bavdekar A , Bogoch II , Clemens JD , da Silva KE , De A , de Ligt J , Diaz Guevara PL , Dolecek C , Dutta S , Ehlers MM , Francois Watkins L , Garrett DO , Godbole G , Gordon MA , Greenhill AR , Griffin C , Gupta M , Hendriksen RS , Heyderman RS , Hooda Y , Hormazabal JC , Ikhimiukor OO , Iqbal J , Jacob JJ , Jenkins C , Jinka DR , John J , Kang G , Kanteh A , Kapil A , Karkey A , Kariuki S , Kingsley RA , Koshy RM , Lauer AC , Levine MM , Lingegowda RK , Luby SP , Mackenzie GA , Mashe T , Msefula C , Mutreja A , Nagaraj G , Nagaraj S , Nair S , Naseri TK , Nimarota-Brown S , Njamkepo E , Okeke IN , Perumal SPB , Pollard AJ , Pragasam AK , Qadri F , Qamar FN , Rahman SIA , Rambocus SD , Rasko DA , Ray P , Robins-Browne R , Rongsen-Chandola T , Rutanga JP , Saha SK , Saha S , Saigal K , Sajib MSI , Seidman JC , Shakya J , Shamanna V , Shastri J , Shrestha R , Sia S , Sikorski MJ , Singh A , Smith AM , Tagg KA , Tamrakar D , Tanmoy AM , Thomas M , Thomas MS , Thomsen R , Thomson NR , Tupua S , Vaidya K , Valcanis M , Veeraraghavan B , Weill FX , Wright J , Dougan G , Argimón S , Keane JA , Aanensen DM , Baker S , Holt KE . Elife 2023 12 BACKGROUND: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. RESULTS: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. CONCLUSIONS: The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. FUNDING: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]). | Salmonella Typhi (Typhi) is a type of bacteria that causes typhoid fever. More than 110,000 people die from this disease each year, predominantly in areas of sub-Saharan Africa and South Asia with limited access to safe water and sanitation. Clinicians use antibiotics to treat typhoid fever, but scientists worry that the spread of antimicrobial-resistant Typhi could render the drugs ineffective, leading to increased typhoid fever mortality. The World Health Organization has prequalified two vaccines that are highly effective in preventing typhoid fever and may also help limit the emergence and spread of resistant Typhi. In low resource settings, public health officials must make difficult trade-off decisions about which new vaccines to introduce into already crowded immunization schedules. Understanding the local burden of antimicrobial-resistant Typhi and how it is spreading could help inform their actions. The Global Typhoid Genomics Consortium analyzed 13,000 Typhi genomes from 110 countries to provide a global overview of genetic diversity and antimicrobial-resistant patterns. The analysis showed great genetic diversity of the different strains between countries and regions. For example, the H58 Typhi variant, which is often drug-resistant, has spread rapidly through Asia and Eastern and Southern Africa, but is less common in other regions. However, distinct strains of other drug-resistant Typhi have emerged in other parts of the world. Resistance to the antibiotic ciprofloxacin was widespread and accounted for over 85% of cases in South Africa. Around 70% of Typhi from Pakistan were extensively drug-resistant in 2020, but these hard-to-treat variants have not yet become established elsewhere. Variants that are resistant to both ciprofloxacin and ceftriaxone have been identified, and azithromycin resistance has also appeared in several different variants across South Asia. The Consortium’s analyses provide valuable insights into the global distribution and transmission patterns of drug-resistant Typhi. Limited genetic data were available fromseveral regions, but data from travel-associated cases helped fill some regional gaps. These findings may help serve as a starting point for collective sharing and analyses of genetic data to inform local public health action. Funders need to provide ongoing supportto help fill global surveillance data gaps. | eng |
HDV RNA Assays: Performance characteristics, clinical utility and challenges
Wedemeyer H , Leus M , Battersby TR , Glenn J , Gordien E , Kamili S , Kapoor H , Kessler HH , Lenz O , Lütgehetmann M , Mixson-Hayden T , Simon CO , Thomson M , Westman G , Miller V , Terrault N , Lampertico P . Hepatology 2023 Co-infection with hepatitis B virus (HBV) and hepatitis D virus (HDV) results in hepatitis D, the most severe form of chronic viral hepatitis, frequently leading to liver decompensation and hepatocellular carcinoma. Pegylated interferon alpha, the only treatment option for chronic hepatitis D for many years, has limited efficacy. New treatments are in advanced clinical development, with one recent approval. Diagnosis and antiviral treatment response monitoring are based on detection and quantification of HDV RNA. However, the development of reliable HDV RNA assays is challenged by viral heterogeneity (at least 8 different genotypes and several subgenotypes), intra-host viral diversity, rapid viral evolution, and distinct secondary structure features of HDV RNA. Different RNA extraction methodologies, primer/probe design for Nucleic Acid Tests, lack of automation, and overall dearth of standardization across testing laboratories contribute to substantial variability in performance characteristics of research-based and commercial HDV RNA assays. A WHO standard for HDV RNA, available for about 10 years, has been used by many laboratories to determine the limit of detection of their assays and facilitates comparisons of RNA levels across study centers. Here we review challenges for robust pan genotype HDV RNA quantification, discuss particular clinical needs and the importance of reliable HDV RNA quantification in the context of drug development and patient monitoring. We summarize distinct technical features and performance characteristics of available HDV RNA assays. Finally, we provide considerations for the use of HDV RNA assays in the context of drug development and patient monitoring. |
Growing gender disparity in HIV infection in Africa: sources and policy implications (preprint)
Monod M , Brizzi A , Galiwango RM , Ssekubugu R , Chen Y , Xi X , Kankaka EN , Ssempijja V , Dorner LA , Akullian A , Blenkinsop A , Bonsall D , Chang LW , Dan S , Fraser C , Golubchik T , Gray RH , Hall M , Jackson JC , Kigozi G , Laeyendecker O , Mills LA , Quinn TC , Reynolds SJ , Santelli J , Sewankambo NK , Spencer SEF , Ssekasanvu J , Thomson L , Wawer MJ , Serwadda D , Godfrey-Faussett P , Kagaayi J , Grabowski MK , Ratmann O . medRxiv 2023 17 HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years, but as new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and the population groups driving transmission have evolved over a 15 year period from 2003 to 2018 in Uganda. HIV viral suppression increased more rapidly in women than men, resulting in 1.5-2 fold higher suppression rates in women with HIV by 2018 across age groups. Incidence declined more slowly in women than men, increasing pre-existing gender imbalance in HIV burden. Age-specific transmission flows shifted; the share of transmission to girls and women aged 15-24 years from older men declined by approximately one third, whereas the contribution of transmission to women aged 25-34 years from men aged 0-6 years older doubled from 2003 to 2018. We estimated closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018 and ended gender disparities in incidence. This study suggests that male-targeted HIV programs to increase HIV suppression are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. |
HIV recent infection and past HIV testing history among newly HIV-diagnosed 15-24-year-olds in Malawi: An analysis of 2019-2022 HIV recent infection surveillance data
Kabaghe AN , Stephens R , Payne D , Theu J , Luhanga M , Chalira D , Arons MM , O'Malley G , Thomson KA , Nyangulu M , Nyirenda R , Patel P , Wadonda-Kabondo N . AIDS Educ Prev 2023 35 4-19 Awareness of HIV status in Malawi is 88.3% and lowest among 15-24-year-olds (76.2%). There is a need to understand HIV testing history and transmission in this age group. We analyzed pooled HIV surveillance data to describe testing history and HIV recent infection among 8,389 HIV-positive 15-24-year-olds from 251 sites in Malawi between 2019 and 2022. Most HIV-positive 15-24-year-olds were female; aged 23-24 years; rural residents; and diagnosed at voluntary counseling and testing. No prior HIV testing was reported in 43.5% and 32.9% of 15-19-year-olds and males, respectively. Overall, 4.9% of HIV-positive diagnoses were classified as recent HIV infections, with the highest proportions among breastfeeding women (8.2%); persons tested at sexually transmitted infection clinics (9.0%); persons with a prior negative test within 6 months (13.0%); and 17-18-year-olds (7.3%). Tailored and innovative HIV prevention and testing strategies for young adolescents, young males, and pregnant and breastfeeding women are needed for HIV epidemic control. |
A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia
Cuypers WL , Meysman P , Weill FX , Hendriksen RS , Beyene G , Wain J , Nair S , Chattaway MA , Perez-Sepulveda BM , Ceyssens PJ , de Block T , Lee WWY , Pardos de la Gandara M , Kornschober C , Moran-Gilad J , Veldman KT , Cormican M , Torpdahl M , Fields PI , Černý T , Hardy L , Tack B , Mellor KC , Thomson N , Dougan G , Deborggraeve S , Jacobs J , Laukens K , Van Puyvelde S . Nat Commun 2023 14 (1) 3517 Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance. |
Implementation of BPaL in the United States: Experience using a novel all-oral treatment regimen for treatment of rifampin-resistant or rifampin-intolerant TB disease
Haley CA , Schechter MC , Ashkin D , Peloquin CA , Cegielski JP , Andrino BB , Burgos M , Caloia LA , Chen L , Colon-Semidey A , DeSilva MB , Dhanireddy S , Dorman SE , Dworkin FF , Hammond-Epstein H , Easton AV , Gaensbauer JT , Ghassemieh B , Gomez ME , Horne D , Jasuja S , Jones BA , Kaplan LJ , Khan AE , Kracen E , Labuda S , Landers KM , Lardizabal AA , Lasley MT , Letzer DM , Lopes VK , Lubelchek RJ , Macias CP , Mihalyov A , Misch EA , Murray JA , Narita M , Nilsen DM , Ninneman MJ , Ogawa L , Oladele A , Overman M , Ray SM , Ritger KA , Rowlinson MC , Sabuwala N , Schiller TM , Schwartz LE , Spitters C , Thomson DB , Tresgallo RR , Valois P , Goswami ND . Clin Infect Dis 2023 77 (7) 1053-1062 BACKGROUND: Rifampin-resistant tuberculosis is a leading cause of morbidity worldwide; only one-third of persons initiate treatment and outcomes are often inadequate. Several trials demonstrate 90% efficacy using an all-oral, six-month regimen of bedaquiline, pretomanid, and linezolid (BPaL), but significant toxicity occurred using 1200 mg linezolid. After U.S. FDA approval in 2019, some U.S. clinicians rapidly implemented BPaL using an initial linezolid 600 mg dose adjusted by serum drug concentrations and clinical monitoring. METHODS: Data from U.S. patients treated with BPaL between 10/14/2019 and 4/30/2022 were compiled and analyzed by the BPaL Implementation Group (BIG), including baseline examination and laboratory, electrocardiographic, and clinical monitoring throughout treatment and follow-up. Linezolid dosing and clinical management was provider-driven, and most had linezolid adjusted by therapeutic drug monitoring (TDM). RESULTS: Of 70 patients starting BPaL, two changed to rifampin-based therapy, 68 (97.1%) completed BPaL, and two of these 68 (2.9%) patients relapsed after completion. Using an initial 600 mg linezolid dose daily adjusted by TDM and careful clinical and laboratory monitoring for side effects, supportive care, and expert consultation throughout BPaL treatment, three (4.4%) patients with hematologic toxicity and four (5.9%) with neurotoxicity required a change in linezolid dose or frequency. The median BPaL duration was 6 months. CONCLUSIONS: BPaL has transformed treatment for rifampin-resistant or intolerant tuberculosis. In this cohort, effective treatment required less than half the duration recommended in ATS/CDC/ERS/IDSA 2019 guidelines for drug-resistant tuberculosis. Use of individualized linezolid dosing and monitoring likely enhanced safety and treatment completion. The BIG cohort demonstrates that early implementation of new tuberculosis treatments in the U.S. is feasible. |
Rapid analysis of drugs: A pilot surveillance system to detect changes in the illicit drug supply to guide timely harm reduction responses - eight syringe services programs, Maryland, November 2021-August 2022
Russell E , Sisco E , Thomson A , Lopes J , Rybak M , Burnett M , Heilman D , Appley MG , Gladden RM . MMWR Morb Mortal Wkly Rep 2023 72 (17) 458-462 A record number of 2,912 drug overdose deaths occurred in Maryland during the 12-month period July 1, 2020-June 30, 2021. Illicitly manufactured fentanyl, fentanyl analogs, or both* were involved in 84% of these deaths.(†) Timely identification of illicit drug market changes (e.g., fentanyl rapidly replacing heroin) could improve the public health response, specifically communications about risks for novel psychoactive substances. During November 19, 2021-August 31, 2022, the National Institute of Standards and Technology (NIST)(§) tested 496 deidentified drug paraphernalia samples that staff members collected at eight Maryland syringe services programs (SSPs), also known as needle exchange programs,(¶) in partnership with the Maryland Department of Health Center for Harm Reduction Services (CHRS).** All test results were available within 48 hours. Among the 496 paraphernalia samples collected, 367 (74.0%) tested positive for an opioid, and 364 (99.2%) of these samples contained fentanyl or fentanyl analogs. Approximately four fifths of fentanyl-positive samples also tested positive for the veterinary medicine xylazine, a sedative that when combined with opioids might increase the potential for fatal respiratory depression and soft tissue infections when injected (1). For 248 of the 496 samples, SSP participants also completed a questionnaire about the drugs they had intended to purchase. Among the 212 participants who had intended to buy an opioid, 87.7% were exposed to fentanyl, fentanyl analogs, or both, and 85.8% were unknowingly exposed to xylazine. Results improved awareness of fentanyl and xylazine among SSP staff members and galvanized efforts to enhance SSPs' wound care services for participants experiencing soft tissue injuries possibly associated with injecting xylazine. Rapid analysis of drug paraphernalia can provide timely data on changing illicit drug markets that can be used to mitigate the harms of drug use more effectively. |
WHO competency framework for health authorities and institutions to manage infodemics: its development and features.
Rubinelli S , Purnat TD , Wihelm E , Traicoff D , Namageyo-Funa A , Thomson A , Wardle C , Lamichhane J , Briand S , Nguyen T . Hum Resour Health 2022 20 (1) 35 BACKGROUND: In April 2020, the World Health Organization (WHO) Information Network for Epidemics produced an agenda for managing the COVID-19 infodemic. "Infodemic" refers to the overabundance of information-including mis- and disinformation. In this agenda it was pointed out the need to create a competency framework for infodemic management (IM). This framework was released by WHO on 20th September 2021. This paper presents the WHO framework for IM by highlighting the different investigative steps behind its development. METHODS: The framework was built through three steps. Step 1 included the preparatory work following the guidelines in the Guide to writing Competency Framework for WHO Academy courses. Step 2 was based on a qualitative study with participants (N = 25), identified worldwide on the basis of their academic background in relevant fields of IM or of their professional experience in IM activities at the institutional level. The interviews were conducted online between December 2020 and January 2021, they were video-recorded and analyzed using thematic analysis. In Step 3, two stakeholder panels were conducted to revise the framework. RESULTS: The competency framework contains four primary domains, each of which comprised main activities, related tasks, and knowledge and skills. It identifies competencies to manage and monitor infodemics, to design, conduct and evaluate appropriate interventions, as well as to strengthen health systems. Its main purpose is to assist institutions in reinforcing their IM capacities and implementing effective IM processes and actions according to their individual contexts and resources. CONCLUSION: The competency framework is not intended to be a regulatory document nor a training curriculum. As a WHO initiative, it serves as a reference tool to be applied according to local priorities and needs within the different countries. This framework can assist institutions in strengthening IM capacity by hiring, staff development, and human resources planning. |
Integration of prevention and control measures for female genital schistosomiasis, HIV and cervical cancer
Engels D , Hotez PJ , Ducker C , Gyapong M , Bustinduy AL , Secor WE , Harrison W , Theobald S , Thomson R , Gamba V , Masong MC , Lammie P , Govender K , Mbabazi PS , Malecela MN . Bull World Health Organ 2020 98 (9) 615-624 Female genital schistosomiasis as a result of chronic infection with Schistosoma haematobium (commonly known as bilharzia) continues to be largely ignored by national and global health policy-makers. International attention for large-scale action against the disease focuses on whether it is a risk factor for the transmission of human immunodeficiency virus (HIV). Yet female genital schistosomiasis itself is linked to pain, bleeding and sub-or infertility, leading to social stigma, and is a common issue for women in schistosomiasis-endemic areas in sub-Saharan Africa. The disease should therefore be recognized as another component of a comprehensive health and human rights agenda for women and girls in Africa, alongside HIV and cervical cancer. Each of these three diseases has a targeted and proven preventive intervention: antiretroviral therapy and pre-exposure prophylaxis for HIV; human papilloma virus vaccine for cervical cancer; and praziquantel treatment for female genital schistosomiasis. We discuss how female genital schistosomiasis control can be integrated with HIV and cervical cancer care. Such a programme will be part of a broader framework of sexual and reproductive health and rights, women’s empowerment and social justice in Africa. Integrated approaches that join up multiple public health programmes have the potential to expand or create opportunities to reach more girls and women throughout their life course. We outline a pragmatic operational research agenda that has the potential to optimize joint implementation of a package of measures responding to the specific needs of girls and women. |
STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
Bharucha T , Oeser C , Balloux F , Brown JR , Carbo EC , Charlett A , Chiu CY , Claas ECJ , de Goffau MC , de Vries JJC , Eloit M , Hopkins S , Huggett JF , MacCannell D , Morfopoulou S , Nath A , O'Sullivan DM , Reoma LB , Shaw LP , Sidorov I , Simner PJ , Van Tan L , Thomson EC , van Dorp L , Wilson MR , Breuer J , Field N . Lancet Infect Dis 2020 20 (10) e251-e260 The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving. |
Expert opinion on verification of antimicrobial susceptibility tests
Patel JB , Thomson RB , Alby K , Babady E , Culbreath K , Galas MF , Lockhart SR , Lubbers BV , Morgan M , Richter SS , Sharp S , Shawar RM , Cardenas AM , Esparza G , Hubbard N , Papich MG , Schuetz AN . J Clin Microbiol 2020 58 (11) On behalf of the Clinical and Laboratory Standards Institute (CLSI), the Expert Panel on Microbiology would like to respond to the recent commentary by Kirby and colleagues voicing concerns related to verification of commercial antimicrobial susceptibility testing (AST) for new drugs that are introduced into the clinical laboratory (1)..... |
WHO malaria nucleic acid amplification test external quality assessment scheme: results of distribution programmes one to three.
Cunningham JA , Thomson RM , Murphy SC , de la Paz Ade M , Ding XC , Incardona S , Legrand E , Lucchi NW , Menard D , Nsobya SL , Saez AC , Chiodini PL , Shrivastava J . Malar J 2020 19 (1) 129 BACKGROUND: The World Health Organization (WHO) recommends parasite-based diagnosis of malaria. In recent years, there has been surge in the use of various kinds of nucleic-acid amplification based tests (NAATs) for detection and identification of Plasmodium spp. to support clinical care in high-resource settings and clinical and epidemiological research worldwide. However, these tests are not without challenges, including lack (or limited use) of standards and lack of reproducibility, due in part to variation in protocols amongst laboratories. Therefore, there is a need for rigorous quality control, including a robust external quality assessment (EQA) scheme targeted towards malaria NAATs. To this effect, the WHO Global Malaria Programme worked with the UK National External Quality Assessment Scheme (UK NEQAS) Parasitology and with technical experts to launch a global NAAT EQA scheme in January 2017. METHODS: Panels of NAAT EQA specimens containing five major species of human-infecting Plasmodium at various parasite concentrations and negative samples were created in lyophilized blood (LB) and dried blood spot (DBS) formats. Two distributions per year were sent, containing five LB and five DBS specimens. Samples were tested and validated by six expert referee laboratories prior to distribution. Between 37 and 45 laboratories participated in each distribution and submitted results using the online submission portal of UK NEQAS. Participants were scored based on their laboratory's stated capacity to identify Plasmodium species, and individual laboratory reports were sent which included performance comparison with anonymized peers. RESULTS: Analysis of the first three distributions revealed that the factors that most significantly affected performance were sample format (DBS vs LB), species and parasite density, while laboratory location and the reported methodology used (type of nucleic acid extraction, amplification, or DNA vs RNA target) did not significantly affect performance. Referee laboratories performed better than non-referee laboratories. CONCLUSIONS: Globally, malaria NAAT assays now inform a range of clinical, epidemiological and research investigations. EQA schemes offer a way for laboratories to assess and improve their performance, which is critical to safeguarding the reliability of data and diagnoses especially in situations where various NAAT methodologies and protocols are in use. |
Development of a World Health Organization International Reference Panel for different genotypes of hepatitis E virus for nucleic acid amplification testing.
Baylis SA , Hanschmann KO , Matsubayashi K , Sakata H , Roque-Afonso AM , Kaiser M , Corman VM , Kamili S , Aggarwal R , Trehanpati N , Gartner T , Thomson EC , Davis CA , da Silva Filipe A , Abdelrahman TT , Blumel J , Terao E . J Clin Virol 2019 119 60-67 BACKGROUND: Globally, hepatitis E virus (HEV) is a major cause of acute viral hepatitis. Epidemiology and clinical presentation of hepatitis E vary greatly by location and are affected by the HEV genotype. Nucleic acid amplification technique (NAT)-based assays are important for the detection of acute HEV infection as well for monitoring chronic cases of hepatitis E. OBJECTIVES: The aim of the study was to evaluate a panel of samples containing different genotypes of HEV for use in nucleic NAT-based assays. STUDY DESIGN: The panel of samples comprises eleven different members including HEV genotype 1a (2 strains), 1e, 2a, 3b, 3c, 3e, 3f, 4c, 4g as well as a human isolate related to rabbit HEV. Each laboratory assayed the panel members directly against the 1(st) World Health Organization (WHO) International Standard (IS) for HEV RNA (6329/10) which is based upon a genotype 3 a strain. RESULTS: The samples for evaluation were distributed to 24 laboratories from 14 different countries and assayed on three separate days. Of these, 23 participating laboratories returned a total of 32 sets of data; 17 from quantitative assays and 15 from qualitative assays. The assays used consisted of a mixture of in-house developed and commercially available assays. The results showed that all samples were detected consistently by the majority of participants, although in some cases, some samples were detected less efficiently. CONCLUSIONS: Based on the results of the collaborative study the panel (code number 8578/13) was established as the "1st International Reference Panel (IRP) for all HEV genotypes for NAT-based assays" by the WHO Expert Committee on Biological Standardization. This IRP will be important for assay validation and ensuring adequate detection of different genotypes and clinically important sub-genotypes of HEV. |
Judicial opinions arising from emergency preparedness, response, and recovery activities
McCourt AD , Sunshine G , Rutkow L . Health Secur 2019 17 (3) 240-247 Legal Perspectives is aimed at informing healthcare providers, emergency planners, public health practitioners, and other decision makers about important legal issues related to public health and healthcare preparedness and response. The articles describe these potentially challenging topics and conclude with the authors' suggestions for further action. The articles do not provide legal advice. Therefore, those affected by the issues discussed in this column should seek further guidance from legal counsel. Readers may submit topics of interest to the column's editor, Lainie Rutkow, JD, PhD, MPH, at lrutkow@jhu.edu. This article describes and analyzes the body of emergency preparedness, response, and recovery litigation that has arisen since the September 11, 2001, terrorist attacks. Search terms were developed to identify judicial opinions related to emergency preparedness, response, and recovery activities. Using the Thomson Reuters Westlaw legal database, searches were conducted to collect judicial opinions related to disasters that occurred in the United States between September 11, 2001, and December 31, 2015. An electronic form was used for data abstraction. Cases that did not directly involve emergency response, preparedness, or recovery activities were excluded. Data were summarized with descriptive statistics. We identified 215 cases for data abstraction. Many of the cases stemmed from preparedness, response, and recovery activities related to hurricanes (57.7%) and terrorist attacks (16.7%). The most prevalent emergency response activities at issue were disaster mitigation (29.3%), disaster clean-up (21.9%), a defendant's duty to plan (14.4%), evacuation (12.6%), and conditions of incarceration (12.1%). Although it can be anticipated that litigation will arise out of all phases of disaster preparedness, response, and recovery, policymakers can anticipate that the most litigation will result from pre-event mitigation and post-event recovery activities, and allocate resources accordingly. |
Militaries and global health: peace, conflict, and disaster response
Michaud J , Moss K , Licina D , Waldman R , Kamradt-Scott A , Bartee M , Lim M , Williamson J , Burkle F , Polyak CS , Thomson N , Heymann DL , Lillywhite L . Lancet 2019 393 (10168) 276-286 Many countries show a growing willingness to use militaries in support of global health efforts. This Series paper summarises the varied roles, responsibilities, and approaches of militaries in global health, drawing on examples and case studies across peacetime, conflict, and disaster response environments. Militaries have many capabilities applicable to global health, ranging from research, surveillance, and medical expertise to rapidly deployable, large-scale assets for logistics, transportation, and security. Despite this large range of capabilities, militaries also have limitations when engaging in global health activities. Militaries focus on strategic, operational, and tactical objectives that support their security and defence missions, which can conflict with humanitarian and global health equity objectives. Guidelines-both within and outside militaries-for military engagement in global health are often lacking, as are structured opportunities for military and civilian organisations to engage one another. We summarise policies that can help close the gap between military and civilian actors to catalyse the contributions of all participants to enhance global health. |
What contribution did economic evidence make to the adoption of universal newborn hearing screening policies in the United States
Grosse SD , Mason CA , Gaffney M , Thomson V , White KR . Int J Neonatal Screen 2018 4 (3) 25 Universal newborn hearing screening (UNHS), when accompanied by timely access to intervention services, can improve language outcomes for children born deaf or hard of hearing (D/HH) and result in economic benefits to society. Early Hearing Detection and Intervention (EHDI) programs promote UNHS and using information systems support access to follow-up diagnostic and early intervention services so that infants can be screened no later than 1 month of age, with those who do not pass their screen receiving diagnostic evaluation no later than 3 months of age, and those with diagnosed hearing loss receiving intervention services no later than 6 months of age. In this paper, we first document the rapid roll-out of UNHS/EHDI policies and programs at the national and state/territorial levels in the United States between 1997 and 2005. We then review cost analyses and economic arguments that were made in advancing those policies in the United States. Finally, we examine evidence on language and educational outcomes that pertain to the economic benefits of UNHS/EHDI. In conclusion, although formal cost-effectiveness analyses do not appear to have played a decisive role, informal economic assessments of costs and benefits appear to have contributed to the adoption of UNHS policies in the United States. |
Evaluation of an OV-16 IgG4 enzyme-linked immunosorbent assay in humans and its application to determine the dynamics of antibody responses in a non-human primate model of Onchocerca volvulus infection
Cama VA , McDonald C , Arcury-Quandt A , Eberhard M , Jenks MH , Smith J , Feleke SM , Abanyie F , Thomson L , Wiegand RE , Cantey PT . Am J Trop Med Hyg 2018 99 (4) 1041-1048 Onchocerciasis is a neglected parasitic disease targeted for elimination. Current World Health Organization guidelines for elimination include monitoring antibody responses to the recombinant Onchocerca volvulus antigen OV-16 in children to demonstrate the absence of transmission. We report the performance characteristics of a modified OV-16 enzyme-linked immunosorbent assay (ELISA) and describe anti-OV-16 responses in serum samples from laboratory-inoculated nonhuman primates (NHPs) in relation to microfilariae (mf) in skin snip biopsies. This OV-16 IgG4 ELISA had sensitivity and specificity of 88.2% and 99.7%, respectively, as determined by receiver operator characteristic analysis using a serum panel of 110 positive and 287 negative samples from people infected with other filariae or other parasitic infections. Anti-OV-16 responses in inoculated NHP (N = 9) were evaluated at quarterly intervals for IgM and the four IgG subclasses. Enzyme-linked immunosorbent assay results showed a well-defined IgG4 reactivity pattern and moderate IgG1 antibody responses. Meanwhile, the reactivity by IgG2, IgG3, or IgM did not show a clear pattern. Temporal evolution of IgG4 reactivity was evaluated through monthly testing, showing that NHPs developed anti-OV-16 IgG4 on average at 15 months postinoculation (range: 10-18 months). The average time to detectable mf was also 15 months (range: 11-25). The OV-16 ELISA used in this study was robust and allowed the detection of IgG4 responses, which were observed only among animals with detectable mf (N = 5), four of which showed declines in antibody responses once mf cleared. These findings also confirmed that the most informative antibody subclass responses to OV-16 are IgG4. |
Weight management and physical activity throughout the cancer care continuum
Demark-Wahnefried W , Schmitz KH , Alfano CM , Bail JR , Goodwin PJ , Thomson CA , Bradley DW , Courneya KS , Befort CA , Denlinger CS , Ligibel JA , Dietz WH , Stolley MR , Irwin ML , Bamman MM , Apovian CM , Pinto BM , Wolin KY , Ballard RM , Dannenberg AJ , Eakin EG , Longjohn MM , Raffa SD , Adams-Campbell LL , Buzaglo JS , Nass SJ , Massetti GM , Balogh EP , Kraft ES , Parekh AK , Sanghavi DM , Morris GS , Basen-Engquist K . CA Cancer J Clin 2017 68 (1) 64-89 Mounting evidence suggests that weight management and physical activity (PA) improve overall health and well being, and reduce the risk of morbidity and mortality among cancer survivors. Although many opportunities exist to include weight management and PA in routine cancer care, several barriers remain. This review summarizes key topics addressed in a recent National Academies of Science, Engineering, and Medicine workshop entitled, "Incorporating Weight Management and Physical Activity Throughout the Cancer Care Continuum." Discussions related to body weight and PA among cancer survivors included: 1) current knowledge and gaps related to health outcomes; 2) effective intervention approaches; 3) addressing the needs of diverse populations of cancer survivors; 4) opportunities and challenges of workforce, care coordination, and technologies for program implementation; 5) models of care; and 6) program coverage. While more discoveries are still needed for the provision of optimal weight-management and PA programs for cancer survivors, obesity and inactivity currently jeopardize their overall health and quality of life. Actionable future directions are presented for research; practice and policy changes required to assure the availability of effective, affordable, and feasible weight management; and PA services for all cancer survivors as a part of their routine cancer care. CA Cancer J Clin 2017. (c) 2017 American Cancer Society. |
Integrated view of Vibrio cholerae in the Americas.
Domman D , Quilici ML , Dorman MJ , Njamkepo E , Mutreja A , Mather AE , Delgado G , Morales-Espinosa R , Grimont PAD , Lizarraga-Partida ML , Bouchier C , Aanensen DM , Kuri-Morales P , Tarr CL , Dougan G , Parkhill J , Campos J , Cravioto A , Weill FX , Thomson NR . Science 2017 358 (6364) 789-793 Latin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies. |
Genomic history of the seventh pandemic of cholera in Africa.
Weill FX , Domman D , Njamkepo E , Tarr C , Rauzier J , Fawal N , Keddy KH , Salje H , Moore S , Mukhopadhyay AK , Bercion R , Luquero FJ , Ngandjio A , Dosso M , Monakhova E , Garin B , Bouchier C , Pazzani C , Mutreja A , Grunow R , Sidikou F , Bonte L , Breurec S , Damian M , Njanpop-Lafourcade BM , Sapriel G , Page AL , Hamze M , Henkens M , Chowdhury G , Mengel M , Koeck JL , Fournier JM , Dougan G , Grimont PAD , Parkhill J , Holt KE , Piarroux R , Ramamurthy T , Quilici ML , Thomson NR . Science 2017 358 (6364) 785-789 The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa. |
Engaging students in physical education: Key challenges and opportunities for physical educators in urban settings
Sliwa S , Nihiser A , Lee S , McCaughtry N , Culp B , Michael S . J Phys Educ Recreat Dance 2017 88 (8) 43-48 A well-designed physical education (PE) program is inclusive, active, enjoyable and supportive (SHAPE America – Society of Health and Physical Educators, 2015). Irrespective of location, programs are affected by a host of issues in the midst of various school and community climates. Trends toward urbanization in the United States (U.S. Census Bureau, 2012) and worldwide (World Health Organization, 2016) suggest that more and more PE teachers will be working in urban settings. | In October 2009, JOPERD published a special symposium about “Engaging Urban Youths in Physical Education and Physical Activity” (Murgia & McCullick, 2009). Seven years later, many of those considerations remain relevant, such as large class sizes (Dyson, Coviello, DiCesare, & Dyson, 2009; Schmidlein, Vickers, & Chepyator-Thomson, 2014) and limited access to equipment (Schmidlein et al., 2014), a dedicated gymnasium (Fernandes & Sturm, 2010), or outdoor space (Dyson et al., 2009; Hobin et al., 2013). These structural challenges matter. For example, some data suggest that larger class sizes and indoor lessons are associated with students spending significantly less time in moderate-to-vigorous physical activity and with teachers spending more time on classroom management (Skala et al., 2012). In addition, high rates of teacher turnover (Ingersoll, Merrill, & Stuckey, 2014), difficulties communicating with English language learners (ELLs; Kena et al., 2016), and low self-efficacy (Fletcher, Mandigo, & Kosnik, 2013) affect teachers’ ability to engage students in PE in urban settings. |
Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemase Production among Enterobacteriaceae
Pierce VM , Simner PJ , Lonsway DR , Roe-Carpenter DE , Johnson JK , Brasso WB , Bobenchik AM , Lockett ZC , Charnot-Katsikas A , Ferraro MJ , Thomson RB Jr , Jenkins SG , Limbago BM , Das S . J Clin Microbiol 2017 55 (8) 2321-2333 The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. Existing methods each have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended. A validation study was performed in a single clinical laboratory to determine the accuracy of the mCIM, followed by a nine-laboratory study to verify the reproducibility of these results and define the zone size cut-off that best discriminated between CP-CRE and Enterobacteriaceae that do not produce carbapenemases. Bacterial isolates previously characterized through whole genome sequencing or targeted PCR as to the presence or absence of carbapenemase genes were tested for carbapenemase production using the mCIM; isolates with Ambler class A, B, and D carbapenemases, non-CP-CRE isolates, and carbapenem-susceptible isolates were included. The sensitivity of the mCIM observed in the validation study was 99% (95% confidence interval [CI], 93 to 100) and the specificity was 100% (95% CI, 82 to 100). In the second stage of the study, the range of sensitivities observed across nine laboratories was 93% to 100%, with a mean of 97%; the range of specificities was 97% to 100%, with a mean of 99%. The mCIM was easy to perform and interpret for Enterobacteriaceae, with results in less than 24 hours and excellent reproducibility across laboratories. |
Fertility and HIV following universal access to ART in Rwanda: a cross-sectional analysis of demographic and health survey data
Remera E , Boer K , Umuhoza SM , Hedt-Gauthier BL , Thomson DR , Ndimubanzi P , Kayirangwa E , Mutsinzi S , Bayingana A , Mugwaneza P , Koama JB . Reprod Health 2017 14 (1) 40 BACKGROUND: HIV infection is linked to decreased fertility and fertility desires in sub-Saharan Africa due to biological and social factors. We investigate the relationship between HIV infection and fertility or fertility desires in the context of universal access to antiretroviral therapy introduced in 2004 in Rwanda. METHODS: We used data from 3532 and 4527 women aged 20-49 from the 2005 and 2010 Rwandan Demographic and Health Surveys (RDHS), respectively. The RDHSs included blood-tests for HIV, as well as detailed interviews about fertility, demographic and behavioral outcomes. In both years, multiple logistic regression was used to assess the association between HIV and fertility outcomes within three age categories (20-29, 30-39 and 40-49 years), controlling for confounders and compensating for the complex survey design. RESULTS: In 2010, we did not find a difference in the odds of pregnancy in the last 5 years between HIV-seropositive and HIV-seronegative women after controlling for potential biological and social confounders. Controlling for the same confounders, we found that HIV-seropositive women under age 40 were less likely to desire more children compared to HIV-seronegative women (20-29 years adjusted odds ratio (AOR) = 0.31, 95% CI: 0.17, 0.58; 30-39 years AOR = 0.24, 95% CI: 0.14, 0.43), but no difference was found among women aged 40 or older. No associations between HIV and fertility or fertility desire were found in 2005. CONCLUSIONS: These findings suggest no difference in births or current pregnancy among HIV-seropositive and HIV-seronegative women. That in 2010 HIV-seropositive women in their earlier childbearing years desired fewer children than HIV-seronegative women could suggest more women with HIV survived; and stigma, fear of transmitting HIV, or realism about living with HIV and prematurely dying from HIV may affect their desire to have children. These findings emphasize the importance of delivering appropriate information about pregnancy and childbearing to HIV-infected women, enabling women living with HIV to make informed decisions about their reproductive life. |
An Official American Thoracic Society Workshop Report. A Framework for Addressing Multimorbidity in Clinical Practice Guidelines for Pulmonary Disease, Critical Illness, and Sleep Disorders
Wilson KC , Gould MK , Krishnan JA , Boyd CM , Brozek JL , Cooke CR , Douglas IS , Goodman RA , Joo MJ , Lareau S , Mularski RA , Patel MR , Rosenfeld RM , Shanawani H , Slatore C , Sockrider M , Sufian B , Thomson CC , Wiener RS . Ann Am Thorac Soc 2016 13 (3) S12-21 Coexistence of multiple chronic conditions (i.e., multimorbidity) is the most common chronic health problem in adults. However, clinical practice guidelines have primarily focused on patients with a single disease, resulting in uncertainty about the care of patients with multimorbidity. The American Thoracic Society convened a workshop with the goal of establishing a strategy to address multimorbidity within clinical practice guidelines. In this Workshop Report, we describe a framework that addresses multimorbidity in each of the key steps of guideline development: topic selection, panel composition, identifying clinical questions, searching for and synthesizing evidence, rating the quality of that evidence, summarizing benefits and harms, formulating recommendations, and rating the strength of the recommendations. For the consideration of multimorbidity in guidelines to be successful and sustainable, the process must be both feasible and pragmatic. It is likely that this will be achieved best by the step-wise addition and refinement of the various components of the framework. |
Travel- and community-based transmission of multidrug-resistant Shigella sonnei lineage among international Orthodox Jewish communities
Baker KS , Dallman TJ , Behar A , Weill FX , Gouali M , Sobel J , Fookes M , Valinsky L , Gal-Mor O , Connor TR , Nissan I , Bertrand S , Parkhill J , Jenkins C , Cohen D , Thomson NR . Emerg Infect Dis 2016 22 (9) 1545-53 Shigellae are sensitive indicator species for studying trends in the international transmission of antimicrobial-resistant Enterobacteriaceae. Orthodox Jewish communities (OJCs) are a known risk group for shigellosis; Shigella sonnei is cyclically epidemic in OJCs in Israel, and sporadic outbreaks occur in OJCs elsewhere. We generated whole-genome sequences for 437 isolates of S. sonnei from OJCs and non-OJCs collected over 22 years in Europe (the United Kingdom, France, and Belgium), the United States, Canada, and Israel and analyzed these within a known global genomic context. Through phylogenetic and genomic analysis, we showed that strains from outbreaks in OJCs outside of Israel are distinct from strains in the general population and relate to a single multidrug-resistant sublineage of S. sonnei that prevails in Israel. Further Bayesian phylogenetic analysis showed that this strain emerged approximately 30 years ago, demonstrating the speed at which antimicrobial drug-resistant pathogens can spread widely through geographically dispersed, but internationally connected, communities. |
Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings.
Feasey NA , Hadfield J , Keddy KH , Dallman TJ , Jacobs J , Deng X , Wigley P , Barquist Barquist L , Langridge GC , Feltwell T , Harris SR , Mather AE , Fookes M , Aslett M , Msefula C , Kariuki S , Maclennan CA , Onsare RS , Weill FX , Le Hello S , Smith AM , McClelland M , Desai P , Parry CM , Cheesbrough J , French N , Campos J , Chabalgoity JA , Betancor L , Hopkins KL , Nair S , Humphrey TJ , Lunguya O , Cogan TA , Tapia MD , Sow SO , Tennant SM , Bornstein K , Levine MM , Lacharme-Lora L , Everett DB , Kingsley RA , Parkhill J , Heyderman RS , Dougan G , Gordon MA , Thomson NR . Nat Genet 2016 48 (10) 1211-1217 An epidemiological paradox surrounds Salmonella enterica serovar Enteritidis. In high-income settings, it has been responsible for an epidemic of poultry-associated, self-limiting enterocolitis, whereas in sub-Saharan Africa it is a major cause of invasive nontyphoidal Salmonella disease, associated with high case fatality. By whole-genome sequence analysis of 675 isolates of S. Enteritidis from 45 countries, we show the existence of a global epidemic clade and two new clades of S. Enteritidis that are geographically restricted to distinct regions of Africa. The African isolates display genomic degradation, a novel prophage repertoire, and an expanded multidrug resistance plasmid. S. Enteritidis is a further example of a Salmonella serotype that displays niche plasticity, with distinct clades that enable it to become a prominent cause of gastroenteritis in association with the industrial production of eggs and of multidrug-resistant, bloodstream-invasive infection in Africa. |
Detection of Onchocerca volvulus in Skin Snips by Microscopy and Real-Time Polymerase Chain Reaction: Implications for Monitoring and Evaluation Activities.
Thiele EA , Cama VA , Lakwo T , Mekasha S , Abanyie F , Sleshi M , Kebede A , Cantey PT . Am J Trop Med Hyg 2016 94 (4) 906-11 Microscopic evaluation of skin biopsies is the monitoring and evaluation (M and E) method currently used by multiple onchocerciasis elimination programs in Africa. However, as repeated mass drug administration suppresses microfilarial loads, the sensitivity and programmatic utility of skin snip microscopy is expected to decrease. Using a pan-filarial real-time polymerase chain reaction with melt curve analysis (qPCR-MCA), we evaluated 1) the use of a single-step molecular assay for detecting and identifying Onchocerca volvulus microfilariae in residual skin snips and 2) the sensitivity of skin snip microscopy relative to qPCR-MCA. Skin snips were collected and examined with routine microscopy in hyperendemic regions of Uganda and Ethiopia (N = 500 each) and "residual" skin snips (tissue remaining after induced microfilarial emergence) were tested with qPCR-MCA. qPCR-MCA detected Onchocerca DNA in 223 residual snips: 139 of 147 microscopy(+) and 84 among microscopy(-) snips, suggesting overall sensitivity of microscopy was 62.3% (139/223) relative to qPCR-MCA (75.6% in Uganda and 28.6% in Ethiopia). These findings demonstrate the insufficient sensitivity of skin snip microscopy for reliable programmatic monitoring. Molecular tools such as qPCR-MCA can augment sensitivity and provide diagnostic confirmation of skin biopsies and will be useful for evaluation or validation of new onchocerciasis M and E tools. |
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