471 research outputs found
Micro-hotspots of Risk in Urban Cholera Epidemics
No full textThis contains the data and code to reproduce analyses from Micro-hotspots of Risk in Urban Cholera Epidemics (Azman et al, Journal of Infectious Diseases, 2018, https://doi.org/10.1093/infdis/jiy283). Please contact [email protected] with any questions or feedback
Preventing cholera outbreaks through early targeted interventions.
Get PDFIn a Perspective, Lorenz von Seidlein and Jacqueline L. Deen discuss the implications of Andrew Azman and colleagues' accompanying study for management of cholera outbreaks
Search engine for books / Amierul Izzuddin Azman
Get PDFSearch engine is web-based software that searches for and identifies things in a collection that match the user's keywords or characters, and is mostly used to locate specific websites on the Internet. The basic idea of information retrieval (IR), as is well-known in the computer industry, is to search a given amount of data and retrieve those records that fulfil a set of criteria. For this project, it will be more on developing a search system that focus on the domain of books. Although many search engines available for book searching, most of them still have room for improvement. The reality to find books using search engine are quite challenging because, the users need to know the title of the book in order to retrieved relevant result from the search engine. Therefore, this project aims to propose a search engine that might produce better result by manipulating the indexing structure of the search engine. Software Development Life Cycle also known as SDLC was used as the methodology in this project development. This project applies the vector space model for the matching process, because the chosen software library for this project which is Apache Lucene is using the vector space model as its foundation. In addition, the Bag-of-Words approach was used as the basis for the indexing module. The indexing process indexed the information of the books such as the book title, the author name, publisher, year published, pages count and synopsis of the book. The search engine's assessment criteria include recall and precision. In IR, recall and precision have long been used as standard evaluation criteria. Keenly, the results of this project prove that index files that contain more domain information can increase the relevancy of a search engin
HopkinsIDD/cholera-systems-serology: version 1.0
No full textFirst release of code and data to reproduce analyses for the manuscript "A systems serology analysis of correlates of protection against cholera" by Kirsten E. Wiens, Anita S. Iyer, Taufiqur R. Bhuiyan, Lenette L. Lu, Deniz Cizmeci, Matthew J. Gorman, Dansu Yuan, Rachel L. Becker, Edward T. Ryan, Stephen B. Calderwood, Regina C. LaRocque, Fahima Chowdhury, Ashraful I. Khan, Myron M. Levine, Wilbur H. Chen, Richelle C. Charles, Andrew S. Azman, Firdausi Qadri, Galit Alter, Jason B. Harris
sj-docx-1-sjp-10.1177_14034948211048050 – Supplemental material for Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study
No full textSupplemental material, sj-docx-1-sjp-10.1177_14034948211048050 for Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study by Aude Richard, Ania Wisniak, Javier Perez-Saez, Henri Garrison-Desany, Dusan Petrovic, Giovanni Piumatti, Hélène Baysson, Attilio Picazio, Francesco Pennacchio, David De Ridder, François Chappuis, Nicolas Vuilleumier, Nicola Low, Samia Hurst, Isabella Eckerle, Antoine Flahault, Laurent Kaiser, Andrew S. Azman, Idris Guessous and Silvia Stringhini in Scandinavian Journal of Public Health</p
Treatment responses to Azithromycin and Ciprofloxacin in uncomplicated <i>Salmonella</i> Typhi infection: A comparison of Clinical and Microbiological Data from a Controlled Human Infection Model
Get PDFBackgroundThe treatment of enteric fever is complicated by the emergence of antimicrobial resistant Salmonella Typhi. Azithromycin is commonly used for first-line treatment of uncomplicated enteric fever, but the response to treatment may be sub-optimal in some patient groups when compared with fluoroquinolones.MethodsWe performed an analysis of responses to treatment with azithromycin (500mg once-daily, 14 days) or ciprofloxacin (500mg twice-daily, 14 days) in healthy UK volunteers (18–60 years) enrolled into two Salmonella controlled human infection studies. Study A was a single-centre, open-label, randomised trial. Participants were randomised 1:1 to receive open-label oral ciprofloxacin or azithromycin, stratified by vaccine group (Vi-polysaccharide, Vi-conjugate or control Men-ACWY vaccine). Study B was an observational challenge/re-challenge study, where participants were randomised to challenge with Salmonella Typhi or Salmonella Paratyphi A. Outcome measures included fever clearance time, blood-culture clearance time and a composite measure of prolonged treatment response (persistent fever ≥38.0°C for ≥72 hours, persistently positive S. Typhi blood cultures for ≥72 hours, or change in antibiotic treatment). Both trials are registered with ClinicalTrials.gov (NCT02324751 and NCT02192008).FindingsIn 81 participants diagnosed with S. Typhi in two studies, treatment with azithromycin was associated with prolonged bacteraemia (median 90.8 hours [95% CI: 65.9–93.8] vs. 20.1 hours [95% CI: 7.8–24.3], pInterpretationAzithromycin at a dose of 500mg daily is an effective treatment for fully sensitive strains of S. Typhi but is associated with delayed treatment response and prolonged bacteraemia when compared with ciprofloxacin within the context of a human challenge model. Whilst the cellular accumulation of azithromycin is predicted to be sufficient to treat intracellular S. Typhi, systemic exposure may be sub-optimal for the elimination of extracellular circulating S. Typhi. In an era of increasing antimicrobial resistance, further studies are required to define appropriate azithromycin dosing regimens for enteric fever and to assess novel treatment strategies, including combination therapies.Trial registrationClinicalTrials.gov (NCT02324751 and NCT02192008).</div
Case-control investigation of invasive Salmonella disease in Malawi reveals no evidence of environmental or animal transmission of invasive strains, and supports human to human transmission
Get PDFBackground Invasive Salmonella infections cause significant morbidity and mortality in Sub-Saharan Africa. However, the routes of transmission are uncertain. We conducted a case-control study of index-case and geographically-matched control households in Blantyre, Malawi, sampling Salmonella isolates from index cases, healthy people, animals, and the household environment. Methodology Sixty index cases of human invasive Salmonella infection were recruited (March 2015-Oct 2016). Twenty-eight invasive Non-Typhoidal Salmonella (iNTS) disease and 32 typhoid patients consented to household sampling. Each index-case household was geographically matched to a control household. Extensive microbiological sampling included stool sampling from healthy household members, stool or rectal swabs from household-associated animals and boot-sock sampling of the household environment. Findings 1203 samples from 120 households, yielded 43 non-Typhoidal Salmonella (NTS) isolates from 25 households (overall sample positivity 3.6%). In the 28 iNTS patients, disease was caused by 3 STs of Salmonella Typhimurium, mainly ST313. In contrast, the isolates from households spanned 15 sequence types (STs). Two S . Typhimurium isolates from index cases closely matched isolates from their respective asymptomatic household members (2 and 3 SNP differences respectively). Despite the recovery of a diverse range of NTS, there was no overlap between the STs causing iNTS disease with any environmental or animal isolates. Conclusions The finding of NTS strains from index cases that matched household members, coupled with lack of related animal or environmental isolates, supports a hypothesis of human to human transmission of iNTS infections in the household. The breadth of NTS strains found in animals and the household environment demonstrated the robustness of NTS sampling and culture methodology, and suggests a diverse ecology of Salmonella in this setting. Healthy typhoid ( S . Typhi) carrier state was not detected. The lack of S . Typhi isolates from the household environment suggests that further methodological development is needed to culture S . Typhi from the environment. Author summary Invasive Salmonella infections cause the loss of millions of disability adjusted life years (DALYs) every year globally. The two main types of invasive Salmonella infections in Africa are i) typhoid fever, caused by Salmonella Typhi, and ii) invasive Non-Typhoidal Salmonella (iNTS) disease, primarily caused in our setting by Salmonella Typhimurium. Despite the high disease burden, and the observed differences between the epidemiology of typhoid and iNTS disease, we lack an understanding of the reservoirs and transmission routes of iNTS. Therefore, we carried out extensive microbiological sampling of the household members, domestic animals, and living environments of patients with invasive Salmonella infections, and of geographically-matched control households, and investigated the genetic relationships between household Salmonella and index-case blood-stream isolates by whole genome sequencing (WGS). We identified a wide range of NTS serovars / sequence types across all households and sample-types, but only identified Salmonella that matched iNTS that matched invasive cases strains in the stool of healthy people from the same households. Our findings support, but cannot prove, the hypothesis that iNTS-associated strains are transmitted from person-to-person. Boot-sock sampling of the household environment gave the highest yield of Salmonella of any of our sampling strategies. None of the 41 environmental Salmonella isolates from non-human sources, including 4 domestic animal-associated isolates, matched the disease-causing sequence types. Our findings are consistent with a hypothesis that the reservoir of Typhimurium iNTS infections is the human gastrointestinal tract, and transmission occurs within households. Longitudinal studies are required, however, to confirm this hypothesis
Homologous and heterologous re-challenge with Salmonella Typhi and Salmonella Paratyphi A in a randomised controlled human infection model.
Get PDFEnteric fever is a systemic infection caused by Salmonella Typhi or Paratyphi A. In many endemic areas, these serovars co-circulate and can cause multiple infection-episodes in childhood. Prior exposure is thought to confer partial, but incomplete, protection against subsequent attacks of enteric fever. Empirical data to support this hypothesis are limited, and there are few studies describing the occurrence of heterologous-protection between these closely related serovars. We performed a challenge-re-challenge study using a controlled human infection model (CHIM) to investigate the extent of infection-derived immunity to Salmonella Typhi or Paratyphi A infection. We recruited healthy volunteers into two groups: naïve volunteers with no prior exposure to Salmonella Typhi/Paratyphi A and volunteers previously-exposed to Salmonella Typhi or Paratyphi A in earlier CHIM studies. Within each group, participants were randomised 1:1 to oral challenge with either Salmonella Typhi (104 CFU) or Paratyphi A (103 CFU). The primary objective was to compare the attack rate between naïve and previously challenged individuals, defined as the proportion of participants per group meeting the diagnostic criteria of temperature of ≥38°C persisting for ≥12 hours and/or S. Typhi/Paratyphi bacteraemia up to day 14 post challenge. The attack-rate in participants who underwent homologous re-challenge with Salmonella Typhi was reduced compared with challenged naïve controls, although this reduction was not statistically significant (12/27[44%] vs. 12/19[63%]; Relative risk 0.70; 95% CI 0.41-1.21; p = 0.24). Homologous re-challenge with Salmonella Paratyphi A also resulted in a lower attack-rate than was seen in challenged naïve controls (3/12[25%] vs. 10/18[56%]; RR0.45; 95% CI 0.16-1.30; p = 0.14). Evidence of protection was supported by a post hoc analysis in which previous exposure was associated with an approximately 36% and 57% reduced risk of typhoid or paratyphoid disease respectively on re-challenge. Individuals who did not develop enteric fever on primary exposure were significantly more likely to be protected on re-challenge, compared with individuals who developed disease on primary exposure. Heterologous re-challenge with Salmonella Typhi or Salmonella Paratyphi A was not associated with a reduced attack rate following challenge. Within the context of the model, prior exposure was not associated with reduced disease severity, altered microbiological profile or boosting of humoral immune responses. We conclude that prior Salmonella Typhi and Paratyphi A exposure may confer partial but incomplete protection against subsequent infection, but with a comparable clinical and microbiological phenotype. There is no demonstrable cross-protection between these serovars, consistent with the co-circulation of Salmonella Typhi and Paratyphi A. Collectively, these data are consistent with surveillance and modelling studies that indicate multiple infections can occur in high transmission settings, supporting the need for vaccines to reduce the burden of disease in childhood and achieve disease control. Trial registration NCT02192008; clinicaltrials.gov
Acute Watery Diarrhea Related Healthcare Seeking Behavior in Chittagong Bangladesh
No full textCholera surveillance in Bangladesh relies on a passive, clinical system that fails to cover most of the country’s population. By only counting those that present for care at designated surveillance facilities the system may miss various demographic and spatial groups of people. While these data are vital to estimating the burden of disease in Bangladesh, current modeling approaches do not account for care seeking trends that otherwise could be used to increase the accuracy of burden estimates. This analysis used hypothetical, report, and clinical care seeking data collected from Sitakunda Upazila, Bangladesh in 2021 and 2022 to explore care seeking trends in the study population with the goal of informing future burden of disease calculations. Generalized estimating equations and generalized linear models were used by the analysis to assess the strength of association of various independent variables. Analysis of these data found that as severity of hypothetical acute watery diarrhea (AWD, used as a proxy measurement for suspected cholera) increased, respondents were more willing to indicate that they would seek care. Where individuals would seek care was also impacted by the level of AWD severity, having implications on how researchers should control for variations in healthcare seeking trends when dealing with clinical data. Comparing hypothetical to reported care seeking, a notable qualitative shift across the null in the association of SES, household income, household distance to port, and household distance to the nearest health center was observed. We call for further studies to be conducted that are better powered to observe care seeking associations among individuals that reported experiencing AWD. These efforts could improve disease burden modeling practices in the future
Rainfall and other meteorological factors as drivers of urban transmission of leptospirosis
No full textBackground: Leptospirosis is an important public health problem affecting vulnerable urban slum populations in developing country settings. However, the complex interaction of meteorological factors driving the temporal trends of leptospirosis remain incompletely understood. Methods and findings: From March 1996—March 2010, we investigated the association between the weekly incidence of leptospirosis and meteorological anomalies in the city of Salvador, Brazil by using a dynamic generalized linear model that accounted for time lags, overall trend, and seasonal variation. Our model showed an increase of leptospirosis cases associated with higher than expected rainfall, lower than expected temperature and higher than expected humidity. There was a lag of one-to-two weeks between weekly values for significant meteorological variables and leptospirosis incidence. Independent of the season, a weekly cumulative rainfall anomaly of 20 mm increased the risk of leptospirosis by 12% compared to a week following the expected seasonal pattern. Finally, over the 14-year study period, the annual incidence of leptospirosis decreased significantly by a factor of 2.7 (8.3 versus 3.0 per 100,000 people), independently of variations in climate. Conclusions: Strategies to control leptospirosis should focus on avoiding contact with contaminated sources of Leptospira as well as on increasing awareness in the population and health professionals within the short time window after low-level or extreme high-level rainfall events. Increased leptospirosis incidence was restricted to one-to-two weeks after those events suggesting that infectious Leptospira survival may be limited to short time intervals
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