Infectious Disease Epidemiology Research Articles

Evaluating Seasonal Variations in Human Contact Patterns and Their Impact on the Transmission of Respiratory Infectious Diseases.

Human contact patterns are a key determinant driving the spread of respiratory infectious diseases. However, the relationship between contact patterns and seasonality as well as their possible association with the seasonality of respiratory diseases is yet to be clarified. We investigated the association between temperature and human contact patterns using data collected through a cross-sectional diary-based contact survey in Shanghai, China, between December 24, 2017, and May 30, 2018. We then developed a compartmental model of influenza transmission informed by the derived seasonal trends in the number of contacts and validated it against A(H1N1)pdm09 influenza data collected in Shanghai during the same period. We identified a significant inverse relationship between the number of contacts and the seasonal temperature trend defined as a spline interpolation of temperature data (p = 0.003). We estimated an average of 16.4 (95% PrI: 15.1-17.5) contacts per day in December 2017 that increased to an average of 17.6 contacts (95% PrI: 16.5-19.3) in January 2018 and then declined to an average of 10.3 (95% PrI: 9.4-10.8) in May 2018. Estimates of influenza incidence obtained by the compartmental model comply with the observed epidemiological data. The reproduction number was estimated to increase from 1.24 (95% CI: 1.21-1.27) in December to a peak of 1.34 (95% CI: 1.31-1.37) in January. The estimated median infection attack rate at the end of the season was 27.4% (95% CI: 23.7-30.5%). Our findings support a relationship between temperature and contact patterns, which can contribute to deepen the understanding of the relationship between social interactions and the epidemiology of respiratory infectious diseases.

Towards Machine-FAIR: Representing software and datasets to facilitate reuse and scientific discovery by machines

ObjectiveTo use software, datasets, and data formats in the domain of Infectious Disease Epidemiology as a test collection to evaluate a novel M1 use case, which we introduce in this paper. M1 is a machine that upon receipt of a new digital object of research exhaustively finds all valid compositions of it with existing objects. MethodWe implemented a data-format-matching-only M1 using exhaustive search, which we refer to as M1DFM. We then ran M1DFM on the test collection and used error analysis to identify needed semantic constraints. ResultsPrecision of M1DFM search was 61.7%. Error analysis identified needed semantic constraints and needed changes in handling of data services. Most semantic constraints were simple, but one data format was sufficiently complex to be practically impossible to represent semantic constraints over, from which we conclude limitatively that software developers will have to meet the machines halfway by engineering software whose inputs are sufficiently simple that their semantic constraints can be represented, akin to the simple APIs of services. We summarize these insights as M1-FAIR guiding principles for composability and suggest a roadmap for progressively capable devices in the service of reuse and accelerated scientific discovery. ConclusionAlgorithmic search of digital repositories for valid workflow compositions has potential to accelerate scientific discovery but requires a scalable solution to the problem of knowledge acquisition about semantic constraints on software inputs. Additionally, practical limitations on the logical complexity of semantic constraints must be respected, which has implications for the design of software.

The Results of Work of Infectious Disease Specialists and Epidemiologists of the Rospotrebnadzor during the Outbreak of Acute Intestinal Infections in the Republic of the Congo (Brazzaville) in 2023

This paper provides an analysis of the results of joint work of Russian and Congolese infectious disease specialists and epidemiologists to decipher the etiology and causes of the outbreak of intestinal infections in Dolisie (Republic of the Congo) in the summer of 2023. It has been found that the increase in the incidence of intestinal infections was caused mainly by the agents of typhoid fever and dysentery; tropical malaria was a combined pathology. No cases of cholera patient detection were registered. Failure of water supply system, domestic disrepair, and low public awareness about prevention of intestinal infections contributed to the active transmission of pathogens. The combination of epidemic process manifestations testified to the aquatic nature of the outbreak. Also, cases of pathogen transmission through contact household route were recorded, food transmission was not excluded. Patients with severe and complicated forms of typhoid fever and shigellosis accounted for 50 % of those hospitalized. There was delay in seeking medical care. The available regimens of antibacterial therapy were ineffective, since there was no possibility of laboratory confirmation of the diagnosis with determination of sensitivity to drugs. Uncontrolled treatment facilitated the emergence of antibiotic resistance in pathogens, prolonged bacterial release and subsequent spread of infection. Infectious disease specialists and epidemiologists of the Rospotrebnadzor provided consulting and practical assistance to Congolese colleagues, developed and presented recommendations for optimizing anti-epidemic and therapeutic measures, taking into account the results of assessment of the causes for onset and development of the outbreak.

PCR-based study on viral pathogens circulation among cervids in the Moscow region

A molecular survey of selected viruses in free-ranging cervids was conducted in 15 different districts of Moscow region. Samples were collected from 178 game animals including 144 moose (Alces alces), 19 roe deer (Capreolus capreolus) and 15 deer without species information. Nasal swabs and tissue samples including parts of the nasal septum, upper tracheal rings, lung, heart, liver, kidneys and pooled organ samples were tested using polymerase chain reaction (PCR). Samples were studied for pestiviruses, herpesviruses, coronaviruses, group A rotaviruses, adenoviruses, hepatitis e and parainfluenza type 3 virus. None of the samples were positive for Bovine Coronavirus and SARS-COV-2, hepatitis E virus and parainfluenza type 3 virus. PCR results were positive for bovine herpesviruses (5.05%), pestiviruses (0.56%), rotaviruses (1.68%). DNA of a new adenovirus, presumably causing a mild course of animal respiratory disease, was detected in samples of 6 animals (3.37%). In conclusion, the conducted studies have shown that game animals of the Moscow region can be a natural reservoir of cattle viruses, and this must be taken into account when planning and organizing measures for the control and eradication of such notifiable diseases as bovine viral diarrhoea and infectious bovine rhinotracheitis. Monitoring studies and general disease surveillance of wild animal populations provide additional information on the epidemiology of infectious diseases in the region and allow timely measures to be taken to protect wild animals, domestic animals and the public.

The Enterics for Global Health (EFGH) Shigella Surveillance Study in Mali.

In 2002, the Centre pour le Développement des Vaccins du Mali (CVD-Mali) was established as a partnership between the Mali Ministry of Health and the University of Maryland, Baltimore. Since its creation, CVD-Mali has been dedicated to describing the epidemiology of infectious diseases, supporting the development of vaccines, and training a team of local researchers. CVD-Mali participated in the Global Enteric Multicenter Study from 2007 to 2010 and the Vaccine Impact on Diarrhea in Africa study from 2015 to 2018, where the importance of Shigella as an enteric pathogen was established. In the Enterics for Global Health (EFGH) Shigella surveillance study, CVD-Mali will conduct Shigella surveillance at 4 health centers serving the population currently participating in a demographic surveillance system and will measure the local incidence of Shigella diarrhea and related outcomes in 6- to 35-month-old children. Antibiotic sensitivity patterns and the costs related to these cases will also be measured. We anticipate reporting the number of diarrhea episodes that are positive by stool culture, the antibiotic susceptibility of these isolates, and the management and outcomes of these cases. In Mali, the EFGH study will contribute valuable information to understanding the burden of Shigella in this population. These data will inform the evaluation of vaccine candidates.

Growth of Public Health Care System in British India

The public healthcare system in India founded during colonial rule. At that time various researches and surveys were done, medical topography was prepared, legislations for public health were brought and various commissions were set up to monitor British troops by the colonial administration. Gradually this led to the foundation of public healthcare system in India. The period of 19th century and early 20th century India witnessed the development of new trends in medical systems and a transition from surveys to microscopic studies in medicine. The history of disease and their prevention in the colonial context traces back the epidemiology of infectious disease.

A retrospective and prospective study of biostatistics in Canada.

Biostatistics is foundational to public health research and Canada has a history of high impact contributions both in seminal methodological advances and in the rigorous application of methods for the design or analysis of public health studies. In this article, we provide a brief and personal review of selected contributions from Canadian biostatisticians to fields such as survival and life history analysis, sampling, clinical trial methodology, environmental risk assessment, infectious disease epidemiology, and early work on prediction. We also provide a brief look forward at the upcoming needs and future directions of biostatistical research.

Epidemiology of Reportable Bacterial Infectious Diseases in Saudi Arabia.

Bacterial infections have a significant impact on human health; they can cause severe morbidity and mortality, particularly in susceptible populations. Epidemiological surveillance is a critical tool for monitoring the population's health and facilitate the prevention and control of infectious disease outbreaks. Knowing the burden of bacterial communicable diseases is an initial core step toward public health goals. Saudi epidemiology surveillance data were utilized to depict the changing epidemiology of bacterial infectious diseases in Saudi Arabia from 2018 to 2021. The cumulative numbers of cases, demographics, and incidence rates were analyzed and visualized. Parametric tests were used to compare the difference in the mean values between categorical variables. Regression analysis was employed to estimate trends in disease rates over time. Statistical significance was set at pvalue ≤ 0.05. The results revealed that brucellosis, tuberculosis, and salmonellosis were the most frequently reported bacterial infectious diseases in Saudi Arabia. Males were more significantly affected by brucellosis and tuberculosis infections than females. Salmonellosis infections were more significant among Saudi citizens, while pulmonary tuberculosis was more significant in non-Saudis. Interestingly, there was a decline in the incidence rates of numerous bacterial infectious diseases during the Coronavirus Disease 2019 (COVID-19) pandemic and COVID-19 restrictions. Some bacterial infectious diseases were rarely reported in Saudi Arabia, including syphilis and diphtheria. The future perspective of this research is to enhance disease surveillance reporting by including different variables, such as the source of infection, travel history, hospitalization, and mortality rates. The aim is to improve the sensitivity and specificity of surveillance data and focus on the mortality associated with bacterial pathogens to identify the most significant threats and set a public health priority.

ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious Agents.

In response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like Chlamydia trachomatis and Legionella pneumophila. In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.

A case of septicemia with meningitis caused by Neisseria weaveri in a 7-year-old child

A case of septicemia with meningitis caused by Neisseria weaveri in a 7-year-old child

Behavioral game of quarantine during the monkeypox epidemic: Analysis of deterministic and fractional order approach

This work concerns the epidemiology of infectious diseases like monkeypox (mpox) in humans and animals. Our models examine transmission scenarios, including transmission dynamics between humans, animals, and both. We approach this using evolutionary game theory, specifically the intervention game-theoretical (IGT) framework, to study how human behavior can mitigate disease transmission without perfect vaccines and treatments. To do this, we use non-pharmaceutical intervention, namely the quarantine policy, which demonstrates the delayed effect of the epidemic. Additionally, we contemplate quarantine-based behavioral intervention policies in deterministic and fractional-order models to show behavioral impact in the context of the memory effect. Firstly, we extensively analyzed the model's positivity and boundness of the solution, reproduction number, disease-free and endemic equilibrium, possible stability, existence, concavity, and Ulam-Hyers stability for the fractional order. Subsequently, we proceeded to present a numerical analysis that effectively illustrates the repercussions of varying quarantine-related factors, information probability, and protection probability. We aimed to comprehensively examine the effects of non-pharmaceutical interventions on disease control, which we conveyed through line graphs and 2D heat maps. Our findings underscored the significant influence of strict quarantine measures and the protection of both humans and animals in mitigating disease outbreaks. These measures not only significantly curtailed the spread of the disease but also delayed the occurrence of the epidemic's peak. Conversely, when quarantine maintenance policies were implemented at lower rates and protection levels diminished, we observed contrasting outcomes that exacerbated the situation. Eventually, our analysis revealed the emergence of animal reservoirs in cases involving disease transmission between humans and animals.

The effect of infectious diseases on lung transplantation in Japan.

Lung transplantation in Japan is an increasingly accessible treatment option for end-stage lung disease; however, the lack of donor organs is a persisting challenge. Five- and 10-year survival rates of lung transplant recipients in Japan are comparable, if not superior, to international standards. The outcomes of lung transplantation in Japan are likely affected by multiple factors. Infectious disease complications are a significant burden to transplant recipients and account for approximately 30% of recipient mortality in Japan, presenting a major challenge in peri-transplant management. Herein, we explore the current status of infectious disease epidemiology, available evidence surrounding infectious diseases in lung transplantation, and potentially influential factors pertinent to lung transplantation outcomes in Japan. Although infection remains the major cause of morbidity and mortality associated with lung transplantation in Japan, there is limited data and evidence. Despite some uncertainties, publicly available data suggests a low rate of antimicrobial resistance in Gram-negative bacteria and a distinct set of endemic pathogens that recipients may encounter. As a countermeasure against the burden of infectious diseases, 8 out of 10 transplant centers in Japan have a dedicated infectious diseases department. Despite these efforts, specific surveillance, prevention, and management are indispensable to improving post-transplantation infectious disease management. We accordingly lay out potential areas for improving infectious disease-related outcomes among lung transplant recipients in Japan.

A comparative analysis of vaccine lists, prices, and candidates, and the national immunization program between China and the United States

Vaccines have an essential role in preventing infectious diseases and reducing the burden of disease. The differences in vaccine lists and prices, and the National Immunization Program (NIP) and vaccine development between China and the United States (US) in conjunction with epidemiologic data on infectious diseases were systematically compared. The epidemiologic data of infectious diseases in 2019 were extracted from the China National Health Commission and the US Centers for Disease Control and Prevention (CDC). The vaccine list was identified from the China National Medical Products Administration and US Food and Drug Administration databases. Vaccine prices were obtained via the China government procurement platform and the US CDC. The NIP vaccines for China and the US were obtained from the China and US CDCs. Vaccine candidates investigated in 2015-2022 were identified from the China Clinical Trial Registry Platform and the US clinicaltrials.gov database. Differences in the incidence of infectious diseases between China and the US were detected with both countries facing a lack of available vaccines for prevention of many diseases. The number of listed vaccines and preventable diseases in China was 59 and 36, respectively, which was higher than the US (45 and 31, respectively). The median price of NIP vaccines in China was significantly lower than the price in the US (median: $3.8 vs. $20; P<0.001); however, there was no significant difference in the price of non-NIP vaccines (median: $68 vs. $86; P=0.498). Vaccines developed by local manufacturers were less expensive than imported products despite the absence of significant differences (median: $16 vs. $31; P=0.180). The number and types of NIP vaccines used to prevent infectious diseases in China were lower than the US. The majority of vaccine candidates in China were not novel compared to the US. Vaccines marketed in China for infectious diseases were comparable to the US. Our findings suggest that China should further expand NIP vaccines and incentive research and development on novel vaccines to improve accessibility based on infectious disease epidemiology.

Implementing the WHO AWaRe antibiotic book guidance in lower-resource settings: the case of the Lao PDR.

In 2022, WHO released the WHO AWaRe (Access, Watch, Reserve) antibiotic book to promote the rational use of antibiotics. Here, we review the AWaRe antibiotic book from the perspective of implementation in low-resource settings, using the Lao PDR (Laos) as a case study. Not all recommendations in the AWaRe antibiotic book match the epidemiology of infectious diseases and antimicrobial susceptibility patterns in Laos and other low- and middle-income countries (LMICs), e.g. melioidosis, rickettsial disease and leptospirosis are common causes of sepsis and febrile illness in Laos but do not feature in the AWaRe book. Conversely, some infectious diseases like Clostridioides difficile-associated diarrhoea are in the AWaRe antibiotic book but rarely considered in Laos with no diagnostic tests available. Only 29/39 antibiotics in the AWaRe book are available in Laos, with no Reserve group antimicrobials available. The AWaRe book stimulates countries such as Laos to consider alternative diagnoses and include additional antimicrobials in the national essential medicines list (NEML). However, it should be updated to include regional important pathogens that are not included. Comprehensive antibiotic use guidelines alone might not assure appropriate use or control overuse of antibiotics. Access to antibiotics is challenging in low-resource settings in terms of unavailability in the country (low demand or small market size), patchy access, especially for those living in remote areas, and unaffordability. All these systemic factors can contribute to inappropriate use of antibiotics. Improved access to antibiotics, strengthening diagnostic capacity and promoting antibiotic stewardship should be combined.

The World Was Their Laboratory: How Two Pioneer Scientist-Administrators,James Watt and Zdenek Fejfar, Advanced Methods and International Collaboration in Cardiovascular Disease Epidemiology During the Cold War.

In 1952, James Watt, a young U.S. Public Health Service (USPHS) infectious disease epidemiologist, was appointed--amid wide surprise--director of the U.S. National Heart Institute (NHI) where he served until 1961. He skillfully advanced epidemiological research methods and study conduct nationally while also establishing epidemiology in the administrative heirarchy of the institute. Watt soon turned to development of an effective program in international cardiovascular disease (CVD) epidemiology under auspices of the World Health Organization (WHO) at the United Nations (UN) in Geneva. That effort resulted in the 1959 appointment of Zdenek Fejfar, a young Czech clinical investigator, as director of the WHO CVD Unit. The coming together of Watt and Fejfar, with a joint focus on improved methods and population comparisons, helped establish a vigorous international community of CVD epidemiology. Their collaboration and friendship remained active and close throughout their career assignments and thereafter, as documented in this story.

Why It (Also) Matters What Infectious Disease Epidemiologists Call “Disease”

Infectious diseases figure prominently as (counter)examples in debates on how to conceptualize “disease.” But crucial epidemiological distinctions are often not heeded in the debate, and pathological and clinical perspectives focusing on individual patients are favored at the expense of perspectives from epidemiology focusing on populations. In clarifying epidemiological concepts, this paper highlights the distinct contributions infectious disease epidemiology can make to the conception of “disease,” and the fact that this is at least tacitly recognized by medical personnel and philosophers. Crucially, infectious disease epidemiology can help elucidate how carrying and transmitting infectious, communicable entities is a disease, even if the carriers themselves are not directly affected by symptoms detrimental to them.

Serological and molecular survey of brucellosis and chlamydiosis in dromedary camels from Tunisia

The present sero-epidemiological survey was designed and conducted to scrutinize the current status of camel-related brucellosis and chlamydiosis in Tunisia. Whole blood and serum samples were collected from 470 dromedaries (Camelus dromedarius) from eight different Tunisian governorates. Serum samples were subjected to indirect enzyme-linked immunosorbent assay (iELISA). The detection of Brucella and Chlamydia DNA was performed using conventional PCR targeting the bcsp-31 and 16S rRNA gene, respectively. Overall, 10/470(2.12%) and 27/470 (5.75%) camels were revealed seropositive to Brucella and Chlamydia, respectively. Multivariate logistic regression analysis showed different risk factors associated with these infections. Meaningful high rates of seropositivity of brucellosis (9.5%; p=0.000; OR=64.193) and chlamydiosis (22.6%; p=0.000; OR=42.860) were noted among camels showing previous abortions in particular for aged females. Besides, Chlamydia seropositivity is significantly important during winter (12.5%; p= 0.009; OR= 27.533), and in camels raised in small farms (11.4%, p= 0.000, OR=86.052). Molecular analysis revealed no positivity from all analyzed blood samples. These findings indicate the involvement of camels in the epidemiology of these abortive infectious diseases. This raises awareness and serious public health concern for infectious camel diseases in order to develop further diagnostic improvements and effective control strategies.

Specificity of Teaching in the Section «General Epidemiology of Infectious Diseases» for Foreign Students

Teaching the discipline «Epidemiology» to foreign students is associated with certain difficulties due to both the lack of equivalents in the English language of terms and concepts used in Russia and the historically established difference in approaches to studying the occurrence and spread of diseases in human society. Schematically, in English-language literature and textbooks on epidemiology, the process of the occurrence of diseases is described on the model of the epidemiological triangle, in Russian literature – historically on the model of the epidemic process, the founder of the doctrine of which is L.V. Gromashevsky. The epidemiological triad is represented by the interaction of a human host, agent and environment – the basis of the epidemic process are 3 elements: the source of infection, the transmission mechanism and the susceptible organism. At first glance, the model of the epidemic process and the epidemiological triangle are somewhat similar. However, the model of the epidemic process according to L.V. Gromashevsky more clearly indicates the population level of the phenomenon, and the epidemiological triangle pays more attention /emphasis on the properties of the pathogen and its interaction with the human body (the level of organism) in the external environment. Teaching in the section «General epidemiology of infectious diseases» teaching about the epidemic process for foreign students is advisable to build from universal models such as the epidemiological triad, harmoniously combining the epidemiology of infectious and non-communicable diseases, followed by the separation of these concepts and the introduction of specific terminology adopted in Russia (source of infection, epidemic focus, transmission mechanism, transmission pathways). At the same time, along with non- communicable diseases, the processes of the spread of infections associated with the provision of medical care, sapronoses are most significantly illustrated with the help of an epidemiological triangle.

Impact of voluntary testing on infectious disease epidemiology: A game theoretic approach.

The World Health Organization recommends test-and-treat interventions to curb and even eliminate epidemics of HIV, viral hepatitis, and sexually transmitted infections (e.g., chlamydia, gonorrhea, syphilis and trichomoniasis). Epidemic models show these goals are achievable, provided the participation of individuals in test-and-treat interventions is sufficiently high. We combine epidemic models and game theoretic models to describe individual's decisions to get tested for infectious diseases within certain epidemiological contexts, and, implicitly, their voluntary participation to test-and-treat interventions. We develop three hybrid models, to discuss interventions against HIV, HCV, and sexually transmitted infections, and the potential behavioral response from the target population. Our findings are similar across diseases. Particularly, individuals use three distinct behavioral patterns relative to testing, based on their perceived costs for testing, besides the payoff for discovering their disease status. Firstly, if the cost of testing is too high, then individuals refrain from voluntary testing and get tested only if they are symptomatic. Secondly, if the cost is moderate, some individuals will test voluntarily, starting treatment if needed. Hence, the spread of the disease declines and the disease epidemiology is mitigated. Thirdly, the most beneficial testing behavior takes place as individuals perceive a per-test payoff that surpasses a certain threshold, every time they get tested. Consequently, individuals achieve high voluntary testing rates, which may result in the elimination of the epidemic, albeit on temporary basis. Trials and studies have attained different levels of participation and testing rates. To increase testing rates, they should provide each eligible individual with a payoff, above a given threshold, each time the individual tests voluntarily.

A standardised differential privacy framework for epidemiological modeling with mobile phone data.

During the COVID-19 pandemic, the use of mobile phone data for monitoring human mobility patterns has become increasingly common, both to study the impact of travel restrictions on population movement and epidemiological modeling. Despite the importance of these data, the use of location information to guide public policy can raise issues of privacy and ethical use. Studies have shown that simple aggregation does not protect the privacy of an individual, and there are no universal standards for aggregation that guarantee anonymity. Newer methods, such as differential privacy, can provide statistically verifiable protection against identifiability but have been largely untested as inputs for compartment models used in infectious disease epidemiology. Our study examines the application of differential privacy as an anonymisation tool in epidemiological models, studying the impact of adding quantifiable statistical noise to mobile phone-based location data on the bias of ten common epidemiological metrics. We find that many epidemiological metrics are preserved and remain close to their non-private values when the true noise state is less than 20, in a count transition matrix, which corresponds to a privacy-less parameter ϵ = 0.05 per release. We show that differential privacy offers a robust approach to preserving individual privacy in mobility data while providing useful population-level insights for public health. Importantly, we have built a modular software pipeline to facilitate the replication and expansion of our framework.