Identifying and characterising sexual transmission of enteric pathogens in men who have sex with men using classical and molecular epidemiological methods

Enteric pathogens are transmitted via the faecal-oral route and commonly cause diarrhoea and/or vomiting. In recent years, there have been numerous outbreaks in men who have sex with men (MSM), primarily Shigella spp., often associated with antimicrobial resistance. My research aimed to investigate the characteristics, risk factors and burden of bacterial enteric pathogens (BEPs) in MSM that could inform control. I conducted a cross-sectional study at a London sexual health clinic (SHC) to estimate the prevalence of BEPs in MSM and associated risk factors. I linked whole genome sequencing (WGS) data with clinical and behavioural data on reported cases of Shigella flexneri to i) characterise transmission within sexual networks of MSM and ii) validate a public health tool for identifying MSM clusters in near real-time. One in 10 predominantly asymptomatic MSM attending the SHC had a BEP detected, which was associated with higher-risk sexual behaviours. Among MSM with a BEP, presence of a genotypic marker of azithromycin resistance was associated with a history of bacterial sexually transmitted infections (STIs). In the WGS study, S. flexneri isolates from MSM largely belonged to two clades associated with genotypic markers of azithromycin resistance, with evidence of sustained transmission through sex between men. Over one third of isolates within MSM clades were from people living with HIV. The public health tool distinguished MSM from non-sexual transmission clusters. My research provides strong evidence that BEPs are transmitted sexually in MSM and asymptomatic carriage may be sustaining transmission. The findings suggest that antimicrobial treatment for STIs selected for resistance in gut organisms, emphasising the need for better antimicrobial stewardship. Phylogenetic analyses provided novel insights about S. flexneri transmission in sexual networks of MSM that could inform clinical care and public health management. Real-time identification of MSM clusters might inform the delivery of rapid and appropriate responses

Improving empirical antibiotic treatment:The role of diagnostic accuracy and surveillance

Antimicrobial Resistance (AMR) is a global health and development threat quickly worsening, especially in low-middle and middle-income countries. Overuse of antibiotics and inappropriate antibiotic treatment are the main drivers of AMR. The thesis describes the use of the urinary dipstick and the adherence to clinical guidelines as ways to improve the diagnostic process of urinary tract infection (UTI) and sepsis, respectively. An improved diagnostic process steers the prescription of the right antibiotic at the right time. Empirical antibiotic treatment requires insight into the prevailing prevalence of AMR, which population-based surveillance provides, in general, more accurate data compared to laboratory-based surveillance. In Southeast Asian countries where the prevalence of AMR is high, there are limited surveillance activities precluding guidance to empirical antibiotic treatment. The thesis discusses findings from current AMR surveillance in Indonesia, showing an extremely high prevalence of AMR in bacterial isolates from urine samples of patients suspected of UTI, threatening rational choices for empirical treatment. The thesis introduces the technique of Lots Quality Assurance Sampling as a way to make AMR surveillance more efficient while obtaining relevant local data to facilitate the choice of an appropriate antibiotic treatment strategy and steer empirical treatment guidelines and antimicrobial stewardship efforts

Emerg Infect Dis

Emerging Infectious Diseases is providing access to these abstracts on behalf of the ICEID 2022 program committee (http://www.iceid.org), which performed peer review. ICEID is organized by the Centers for Disease Control and Prevention and Task Force for Global Health, Inc.Emerging Infectious Diseases has not edited or proofread these materials and is not responsible for inaccuracies or omissions. All information is subject to change. Comments and corrections should be brought to the attention of the authors.Suggested citation: Authors. Title [abstract]. International Conference on Emerging Infectious Diseases 2022 poster and oral presentation abstracts. Emerg Infect Dis. 2022 Sep [date cited]. http://www.cdc.gov/EID/pdfs/ICEID2022.pdf2022PMC94238981187

Syndromic molecular testing in adults hospitalized for suspected community-acquired pneumonia

Den mikrobielle etiologien hos pasienter med samfunnservervet lungebetennelse (CAP) blir ofte ikke avklart på grunn av utilstrekkelige mikrobiologiske metoder og vanskeligheter med å skaffe prøver fra nedre luftveier. Rask påvisning av luftveismikrober kan potensielt redusere unødvendig bruk av empirisk antimikrobiell behandling og øke andelen pasienter som får mikrobiologistyrt behandling. Moderne syndrombaserte PCR-paneler muliggjør rask deteksjon av både virale- og bakterielle luftveismikrober. CAPNOR Feasibility studien undersøkte gjennomførbarheten av flere viktige ledd fra vår planlagte CAPNOR RCT (Paper I). Studien viste at det var mulig å skaffe nedre luftveisprøver fra CAP pasienter allerede i akuttmottaket. Ved bruk av et syndrombasert PCR-panel, fant vi betydelig flere luftveismikrober på kortere tid, sammenliknet med bruk av standard metoder, noe som indikerer at det er mulig å oppnå mikrobiologiske resultater allerede i akuttmottaket. Vår CAPNOR RCT fokuserer på andelen som mottar mikrobiologistyrt behandling og tiden det tar. Prøver fra nedre luftveier ble randomisert til testing med kun standardmetoder eller med tillegg av et syndrombasert PCR-panel (Paper II). COVID-19 pandemien traff Norge da vi skulle starte vår RCT, noe som resulterte i forsinket start av studien og behov for justeringer av protokollen. I denne unike situasjonen valgte vi å undersøke pandemiens potensielle implikasjoner på både antall sykehusinnleggelser og detekterte mikrober hos pasienter med mistenkt CAP, ved å sammenlikne pasienter inkludert før og etter utbruddet av COVID-19 (Paper III). Smitteverntiltak relatert til COVID-19 forverret utfordringene med prøvetakning fra nedre luftveier ytterligere. Dette bidro til en studie som viste at testing av halsprøver med et syndrombasert PCR-panel oppdaget de vanligste bakterielle luftveismikrober med høy positiv og negativ prosentvis overensstemmelse sammenlignet med testing av nedre luftveisprøver (Paper IV). Dette antyder at halsprøver analysert av et syndrombasert PCR-panel kan representere en alternativ metode for rask mikrobiologisk testing i akuttmottaket. Oppsummert har våre studier demonstrert at det er mulig å oppnå omfattende mikrobiologiske resultater hos en stor andel CAP pasienter få timer etter innleggelse. Fremtidige studier av syndrombaserte PCR-paneler bør fokusere videre på kliniske endepunkter, kostnadseffektivitet og utvikling av implementeringsstrategier for innføring i klinisk praksis.The microbial etiology of patients with community-acquired pneumonia (CAP) is often not established due to insufficient methods for microbial detection and difficulties in obtaining lower respiratory tract (LRT) samples. Early microbial detections could potentially reduce unnecessary empirical antimicrobial treatment and improve the proportion of patients receiving pathogen-directed treatment. Recently introduced syndromic PCR-based panels enable rapid detection of both viral- and bacterial pathogens. The CAPNOR Feasibility study (Paper I) was initiated with a view to informing the design of a planned RCT and demonstrated that obtaining LRT samples from CAP patients in the emergency department (ED) was feasible. The microbial yield and time to results improved significantly by using a syndromic PCR-based panel compared to standard methods, indicating that it is possible to obtain microbiological results already in the ED. In the CAPNOR RCT, LRT samples were randomized to testing by either standard methods alone or with the addition of syndromic PCR-based testing, focusing on the time to, and provision of pathogen-directed treatment in CAP patients (Paper II). When we were about to initiate the CAPNOR RCT, Norway faced the COVID-19 pandemic, resulting in a delayed start, with mandatory adjustments needed in the protocol. Faced with this unprecedented situation, we evaluated the pandemic’s potential implications on both hospital admissions and microbial detections in patients with suspected CAP, i.e., before and after the outbreak of COVID-19 and the subsequent strict infection control measures (Paper III). Moreover, the COVID-19-related infection control measures further hampered the difficulties of LRT sampling. This fostered a study where we demonstrated that syndromic PCR-based testing of oropharyngeal (OP) swabs could detect the most common bacterial CAP pathogens with high positive and negative percent agreement compared with testing of LRT samples (Paper IV). These findings suggest that OP swabs analyzed by a syndromic panel could represent an alternative approach for rapid microbiological testing in the ED. In conclusion, our studies have demonstrated an ability to provide close to real-time microbiological results for CAP patients. Future studies should focus on the impact of rapid syndromic testing in terms of clinical outcomes, cost-effectiveness, and the development of implementation strategies to facilitate integration into clinical practice.Doktorgradsavhandlin

Emerg Infect Dis

PMC4550154611

Influenza Division international activities

In 2010, the Division provided funding support and technical assistance for influenza activities to 48 countries in the form of direct cooperative agreements or indirectly through our partners. Under these agreements, partner countries have made significant progress in the development of their influenza surveillance capacity and pandemic preparedness. Their collective progress is evident in the positive movement of scores captured in 2010 using the Division's National Inventory of Core Capacities for Pandemic Preparedness and Response monitoring and evaluation tool (see page 258). There is no doubt the hard work countries have put in to developing both their laboratory and epidemiologic surveillance systems and strengthening their pandemic preparedness not only enhanced their response to the 2009 influenza pandemic but has also helped to build general capacity for all emerging infectious diseases. In other achievements for 2010, China's National Influenza Center in Beijing was designated a WHO Collaborating Center for Reference and Research on Influenza. The Division has worked closely with the National Influenza Center in Beijing for over two decades and congratulates China on becoming just one of five such Centers globally. Likewise, the Division wishes to congratulate its partner countries who achieved WHO National Influenza Center status in 2010 in the following locations: Guatemala City, Guatemala; Kathmandu, Nepal; Accra, Ghana; Ho Chi Minh City, Vietnam and Vientiane, Lao People's Democratic Republic.Influenza Division international overview -- WHO African Region (AFR) -- WHO Eastern Mediterranean Region (EMR) -- WHO European Region (EUR)...-- WHO Region of the Americas (AMR) -- WHO South-East Asia Region (SEAR) -- WHO Western Pacific Region (WPR) -- influenza research -- Meetings and training -- Influenza Division organization -- ReferencesSpecial thanks to Ann Moen, Emily Cramer, Sarah O'Brien, Howard Hall, Lucinda Johnson and Meg McCarron for editing and producing this 2010 International Influenza Report."Publication date: August 2011."System requirements: Adobe Acrobat Reader.Mode of access: World Wide Web.Includes bibliographical references (p. 292-296).Centers for Disease Control and Prevention. International Influenza Report FY 2010. Atlanta: U.S. Department of Health and Human Services; 2010.Electronic monograph in PDF format (24.29 MB, 304 p.)

The application of long‑read sequencing in clinical settings

Long-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, thereby providing a valuable tool for precision medicine. In the third-generation sequencing duopoly, Oxford Nanopore Technologies and Pacific Biosciences work towards increasing the accuracy, throughput, and portability of long-read sequencing methods while trying to keep costs low. These trades have made long-read sequencing an attractive tool for use in research and clinical settings. This article provides an overview of current clinical applications and limitations of long-read sequencing and explores its potential for point-of-care testing and health care in remote settings

Assessment of a Program for SARS-CoV-2 Screening and Environmental Monitoring in an Urban Public School District

Importance: Scalable programs for school-based SARS-CoV-2 testing and surveillance are needed to guide in-person learning practices and inform risk assessments in kindergarten through 12th grade settings. Objectives: To characterize SARS-CoV-2 infections in staff and students in an urban public school setting and evaluate test-based strategies to support ongoing risk assessment and mitigation for kindergarten through 12th grade in-person learning. Design, Setting, and Participants: This pilot quality improvement program engaged 3 schools in Omaha, Nebraska, for weekly saliva polymerase chain reaction testing of staff and students participating in in-person learning over a 5-week period from November 9 to December 11, 2020. Wastewater, air, and surface samples were collected weekly and tested for SARS-CoV-2 RNA to evaluate surrogacy for case detection and interrogate transmission risk of in-building activities. Main Outcomes and Measures: SARS-CoV-2 detection in saliva and environmental samples and risk factors for SARS-CoV-2 infection. Results: A total of 2885 supervised, self-collected saliva samples were tested from 458 asymptomatic staff members (mean [SD] age, 42.9 [12.4] years; 303 women [66.2%]; 25 Black or African American [5.5%], 83 Hispanic [18.1%], 312 White [68.1%], and 35 other or not provided [7.6%]) and 315 students (mean age, 14.2 [0.7] years; 151 female students [48%]; 20 Black or African American [6.3%], 201 Hispanic [63.8%], 75 White [23.8%], and 19 other race or not provided [6.0%]). A total of 46 cases of SARS-CoV-2 (22 students and 24 staff members) were detected, representing an increase in cumulative case detection rates from 1.2% (12 of 1000) to 7.0% (70 of 1000) among students and from 2.1% (21 of 1000) to 5.3% (53 of 1000) among staff compared with conventional reporting mechanisms during the pilot period. SARS-CoV-2 RNA was detected in wastewater samples from all pilot schools as well as in air samples collected from 2 choir rooms. Sequencing of 21 viral genomes in saliva specimens demonstrated minimal clustering associated with 1 school. Geographical analysis of SARS-CoV-2 cases reported district-wide demonstrated higher community risk in zip codes proximal to the pilot schools. Conclusions and Relevance: In this study of staff and students in 3 urban public schools in Omaha, Nebraska, weekly screening of asymptomatic staff and students by saliva polymerase chain reaction testing was associated with increased SARS-CoV-2 case detection, exceeding infection rates reported at the county level. Experiences differed among schools, and virus sequencing and geographical analyses suggested a dynamic interplay of school-based and community-derived transmission risk. Collectively, these findings provide insight into the performance and community value of test-based SARS-CoV-2 screening and surveillance strategies in the kindergarten through 12th grade educational setting

The Community Burden of Influenza

Background: Influenza causes substantial morbidity and mortality. Novel strains from animals can infect humans, but such transmission is poorly understood. Serosurveillance estimates levels of influenza population immunity and infection but obtaining representative sera is challenging. Health-related quality of life (HRQoL) and absenteeism inform cost-effectiveness models of influenza interventions but these parameters are poorly understood. The National Pandemic Flu Service (NPFS) aimed to treat community cases. Little is known about the scheme’s coverage or effectiveness. / Objectives: 1) Investigate whether occupational exposure to pigs increases risk of seasonal, pandemic and zoonotic influenza infection. 2) Describe population-level patterns of influenza infection and immunity in England during 2012/13. 3) Quantify work and school absences and HRQoL from community influenza illnesses. 4) Evaluate the success of the NPFS and propose algorithm changes to improve antiviral targeting. / Methods: Flu Watch is a prospective community cohort of influenza and included recruitment of pig workers during the 2009 pandemic. The Pandemic Immunity and Population Spread study (PIPS) is a novel, population-level, cross-sectional, pandemic serosurveillance system utilizing the Health Survey for England. / Results: Pig workers had increased odds of seropositivity to seasonal, pandemic, and zoonotic influenza compared to the general population. A(H1N1)pdm09 and A(H3N2) infected 40% and 25% of the population in 2012/13. HRQoL loss and absenteeism is low for individual community-level influenza cases. NPFS consultation was low and the case definition specificity was 51%. / Conclusions: Influenza spreads readily from pigs to pig workers, posing risks for novel virus emergence and pandemics. Representative, population-level serology show that, before COVID-19, a large proportion of the population was infected each winter. Most community influenza cases take little time off work and school and this has implications for transmission. The coverage and impact of NPFS was low. Community-based surveys are needed to inform the control of seasonal and pandemic respiratory infections

2019 EIS conference

Publication date from document properties.eis-conference-2019-508.pdf2019618