Towards a genomics-informed, real-time, global pathogen surveillance system.

The recent Ebola and Zika epidemics demonstrate the need for the continuous surveillance, rapid diagnosis and real-time tracking of emerging infectious diseases. Fast, affordable sequencing of pathogen genomes - now a staple of the public health microbiology laboratory in well-resourced settings - can affect each of these areas. Coupling genomic diagnostics and epidemiology to innovative digital disease detection platforms raises the possibility of an open, global, digital pathogen surveillance system. When informed by a One Health approach, in which human, animal and environmental health are considered together, such a genomics-based system has profound potential to improve public health in settings lacking robust laboratory capacity.

Challenges in Having Vaccines Available to Control Transboundary Diseases of Livestock.

The global human population is growing at a rapid rate leading to the need for continued expansion of food animal production to meet the world's increasing nutritional requirements. As a consequence of this increased production demand, the use of high volume, animal dense systems have expanded providing high quality protein at reduced costs. Backyard animal production has also expanded. This increased food animal production has facilitated the rapid spread, mutation, and adaptation of pathogens to new hosts. This scenario continues to drive the emergence and reemergence of diseases in livestock species increasing the urgency for development and availability of vaccines for transboundary animal diseases (TADs). Even though vaccines are widely recognized as being an essential tool for control of TADs, there are many scientific, economic, political, and logistical challenges to having vaccine available to control an outbreak. This article will focus on examples of the challenges associated with having vaccines available for emergency response, as well as the characteristics of 'ideal' TAD vaccines, the need for complementary diagnostic assays, and hurdles involved in bringing efficacious veterinary TAD vaccines to market including regulatory constraints and considerations for stockpiling vaccines for emergency use in non-endemic countries. Examples will also highlight the complicated interplay between animal health and human health and demonstrate the lasting benefits that can be gained from an efficacious vaccine.

Climate change: how it impacts the emergence, transmission, resistance and consequences of viral infections in animals and plants.

The ongoing COVID-19 pandemic has made us wonder what led to its occurrence and what can be done to avoid such events in the future. As we document, one changing circumstance that is resulting in the emergence and changing the expression of viral diseases in both plants and animals is climate change. Of note, the rapidly changing environment and weather conditions such as excessive flooding, droughts, and forest fires have raised concerns about the global ecosystem's security, sustainability, and balance. In this review, we discuss the main consequences of climate change and link these to how they impact the appearance of new viral pathogens, how they may facilitate transmission between usual and novel hosts, and how they may also affect the host's ability to manage the infection. We emphasize how changes in temperature and humidity and other events associated with climate change influence the reservoirs of viral infections, their transmission by insects and other intermediates, their survival outside the host as well the success of infection in plants and animals. We conclude that climate change has mainly detrimental consequences for the emergence, transmission, and outcome of viral infections and plead the case for halting and hopefully reversing this dangerous event.

A case of SFTS coinfected with E. coli bacteremia.

BACKGROUND: Severe fever thrombocytopenia syndrome virus (SFTSV) is the causative agent of severe fever thrombocytopenia syndrome (SFTS). SFTS is an emerging infectious disease, characterized by high fever, gastrointestinal symptoms, leukopenia, thrombocytopenia, and a high mortality rate. Until now, little importance has been given to the association of SFTS with leukocytosis and bacterial co-infection. CASE PRESENTATION: A 51-year old man visited our hospital with fever and low blood pressure. He was a farmer by occupation and often worked outdoors. He had a Foley catheter inserted due to severe BPH. Laboratory tests revealed thrombocytopenia, elevated liver function, and elevated CRP levels. He had marked leukocytosis, proteinuria, hematuria, and conjunctival hemorrhage. Initially, we thought that the patient was suffering from hemorrhagic fever with renal syndrome (HFRS). However, we confirmed SFTS through PCR and increasing antibody titer. However, his blood culture also indicated E. coli infection. CONCLUSION: SFTS displays characteristics of fever, thrombocytopenia, elevated liver function, and leukocytopenia. We described a case of SFTS with leukocytosis due to coinfection with E. coli. Since patients with SFTS usually have leukocytopenia, SFTS patients with leukocytosis are necessarily evaluated for other causes of leukocytosis. Here, we report the first case of an SFTS with concurrent E. coli bacteremia.

Scrub typhus as a rare cause of acute pyelonephritis: case report.

BACKGROUND: Scrub typhus can present with atypical signs and symptoms such as those of acute kidney injury, gastroenteritis, pneumonitis, and acute respiratory distress syndrome. Meningitis, encephalitis, and hepatic dysfunction have also been reported, particularly in severe cases with multisystem involvement. Scrub typhus has never been reported in the literature to cause urinary tract infections (UTIs) which includes cystitis and pyelonephritis. CASE PRESENTATION: A 45-year old male presenting to the outpatient unit with fever, right flank pain, and burning micturition for three days was initially treated for UTI. However, he returned to the hospital on the fourth day of illness with persistent symptoms. He was hospitalized, with intravenous (IV) ceftriaxone. Computerized tomography scan of his abdomen-pelvis showed features of acute pyelonephritis, so his antibiotics were upgraded to meropenem and teicoplanin. Despite this, the patient's condition deteriorated. Laboratory investigations showed multisystem involvement: decreasing platelets, raised creatinine, and deranged liver panel. As Kathmandu was hit by dengue epidemic during the patient's hospitalization, on the seventh day of his illness, blood samples were sent for tropical fever investigation. All tests came out negative except for scrub typhus-IgM antibodies positive on rapid diagnostic test. The patient's symptoms subsided after 48 h of starting doxycycline and he became fully asymptomatic four days later. Fever did not recur even after discontinuing other IV antibiotics, favoring scrub typhus disease rather than systemic bacterial sepsis. CONCLUSIONS: Scrub typhus is an emerging infectious disease of Nepal. Therefore, every unexplained fever cases (irrespective of clinical presentation) should be evaluated for potential Rickettsiosis. Moreover, for cases with acute pyelonephritis, atypical causative agents should be investigated, for example scrub typhus in this case.

Risk factors for bat contact and consumption behaviors in Thailand; a quantitative study.

BACKGROUND: Bats serve as an important reservoir for emerging infectious diseases. Bat contact and consumption, which persists in Asia, poses risks for the transmission of bat-borne infections. METHODS: An analytical cross-sectional survey for risk factors associated with bat contact and consumption behaviors was conducted in ten provinces of Thailand from May 2016 to December 2017. A standardized questionnaire administered through face-to-face interviews was used to collect information from 626 villagers who lived in or nearby areas of high bat density. The questionnaire contained 23 independent variables related to sociodemographic, knowledge, attitudes, practices, and perceptions. RESULTS: The respondents (n = 626) were 285 females and 341 males, mean age of respondents was 47.58 years-old and lived in rural setting. Our results showed that 36.42% of respondents (n1 = 228) in 10 provinces reported bat contact during the past 6 months. Furthermore, 15.34% of respondents (n2 = 96) in 9 out of 10 provinces reported of having consumed bat meat in the past 6 months. Risk factors for bat contact included sex (male) (OR = 1.56, 95% CI 1.09-2.28), educational attainment (lower than secondary school) (OR = 1.45, 95% CI 1.02-2.18), and the consideration of bats as being economically beneficial to the community (OR = 3.18, 95% CI 2.03-4.97), while agriculture-related occupation (OR = 0.54, 95% CI 0.37-0.79), knowledge that it is safe to eat bats (OR = 0.58, 95% CI 0.37-0.93), practice of allowing children to play with bats (OR = 0.65, 95% CI 0.44-0.96), and attitude of feeling safe in areas where bats live (OR = 0.56, 95% CI 0.38-0.86) were statistically significant protective factors against bat contact. Risk factors for bat consumption included sex (male) (OR = 2.48, 95% CI 1.49-4.11) and educational attainment (lower than secondary school) (OR = 2.21, 95% CI 1.27-3.85), while knowledge of whether bats are safe to eat (OR = 0.04, 95% CI 0.01-0.25), knowledge of whether there are laws pertaining to hunting bats for consumption (OR = 0.35, 95% CI 0.18-0.71), and the practice of allowing children to play with bats (OR = 0.51, 95% CI 0.31-0.81) were statistically significant protective factors against bat consumption. CONCLUSIONS: This study provides a better understanding of the sociodemographic factors, knowledge, attitudes, perceptions and practices that might influence bat contact and bat consumption behaviors. Information on risk factors can be used for the development of appropriate education and communication interventions to promote proper knowledge, attitudes and practices regarding bats and bat-borne zoonotic diseases in Thailand and other areas in the Southeast Asia region with similar environmental and cultural characteristics.

Resurgence of Vaccine-Preventable Diseases in Venezuela as a Regional Public Health Threat in the Americas.

Venezuela's tumbling economy and authoritarian rule have precipitated an unprecedented humanitarian crisis. Hyperinflation rates now exceed 45,000%, and Venezuela's health system is in free fall. The country is experiencing a massive exodus of biomedical scientists and qualified healthcare professionals. Reemergence of arthropod-borne and vaccine-preventable diseases has sparked serious epidemics that also affect neighboring countries. In this article, we discuss the ongoing epidemics of measles and diphtheria in Venezuela and their disproportionate impact on indigenous populations. We also discuss the potential for reemergence of poliomyelitis and conclude that action to halt the spread of vaccine-preventable diseases within Venezuela is a matter of urgency for the country and the region. We further provide specific recommendations for addressing this crisis.

Emerging arboviruses and implications for pediatric transplantation: A review.

Recent years have brought a rise in newly emergent viral infections, primarily in the form of previously known arthropod-transmitted viruses that have increased significantly in both incidence and geographical range. Of particular note are DENV, CHIKV, and ZIKV, which are transmitted mostly by Aedes species of mosquitoes that exhibit a wide and increasing global distribution. Being important pathogens for the general population, these viruses have the potential to be devastating in the international transplant community, with graft rejection and death as possible outcomes of infection. In this review, we discuss the current state of knowledge for these viruses as well as repercussions of infection in the solid organ and HSCT population, with a focus, when possible, on pediatric patients.

Reemergence of Intravenous Drug Use as Risk Factor for Candidemia, Massachusetts, USA.

The epidemic of illicit intravenous drug use (IVDU) in the United States has been accompanied by a surge in drug overdose deaths and infectious sequelae. Candida albicans infections were associated with injection of contaminated impure brown heroin in the 1970s-1990s; however, candidiasis accompanying IVDU became considerably rarer as the purity of the heroin supply increased. We reviewed cases of candidemia occurring over a recent 7-year period in persons >14 years of age at a tertiary care hospital in central Massachusetts. Of the 198 patients with candidemia, 24 cases occurred in patients with a history of IVDU. Compared with non-IVDU patients, those with a history of IVDU were more likely to have non-albicans Candida, be co-infected with hepatitis C, and have end-organ involvement, including endocarditis and osteomyelitis. Thus, IVDU appears to be reemerging as a risk factor for invasive candidiasis.

Haematology patients and the risk of transfusion transmitted infection.

A 2014 study by NHS Blood and Transplant indicated that over one quarter of red cells were transfused to patients with haematological conditions. For platelet components, the figure is higher. Certain diagnostic groups, such as haemoglobinopathies, myelodysplastic syndromes and some haemato-oncology patients, receive multiple transfusion episodes, either over long periods, or more intensively over shorter periods. Haematology patients account for the majority of the multi-transfused population. The risk of transfusion-transmitted infection (TTI) increases with number of donor exposures, and the consequences of TTI are often more significant in immunosuppressed individuals. Historically, use of pooled plasma products in patients with clotting disorders resulted in widespread transmission of hepatitis B virus, hepatitis C virus and human immunodeficiency virus before effective screening and viral inactivation methods were introduced.

The Threat and Response to Infectious Diseases (Revised).

The threat from microorganisms is complex, and the approaches for reducing the challenges the world is facing are also multifaceted, but a combination approach including several simple steps can make a difference and reduce morbidity and mortality and the economic cost of fighting infectious diseases. This paper discusses the continually evolving infectious disease landscape, contributing factors in the rise of the threat, reasons for optimism, and the policies, technologies, actions, and institutions that might be harnessed to further reduce the dangers introduced by pathogens. It builds upon and updates the work of other authors that have recognized the dangers of emerging and re-emerging pathogens and have explored and documented potential solutions.

Public health issues in the 21st century: National challenges and shared challenges for the Maghreb countries.

In the 21st century, public health is not only about fighting infectious diseases, but also contributing to a "multidimensional" well-being of people (health promotion, non-communicable diseases, the role of citizens and people in the health system etc.). Six themes of public health, issues of the 21st century will be addressed. Climate change is already aggravating already existing health risks, heat waves, natural disasters, recrudescence of infectious diseases. Big data is the collection and management of databases characterized by a large volume, a wide variety of data types from various sources and a high speed of generation. Big data permits a better prevention and management of disease in patients, the development of diagnostic support systems and the personalization of treatments. Big data raises important ethical questions. Health literacy includes the abilities of people to assess and critique and appropriate health information. Implementing actions to achieve higher levels of health literacy in populations remains a crucial issue. Since the 2000s, migration flows of health professionals have increased mainly in the "south-north" direction. India is the country with the most doctors outside its borders. The USA and the UK receive 80% of foreign doctors worldwide. Ways have been identified to try to regulate the migratory phenomena of health professionals around the world. The mobilization of citizen, health system users and patient associations is a strong societal characteristic over the last 30 years. In a near future, phenomena will combine to increase the need for accompaniment of patient or citizen to protect health, such increase of the prevalence of chronic diseases, reinforcement of care trajectories, medico-social care pathways, and importance of health determinants. Interventional research in public health is very recent. It is based on experimentation and on the capitalization of field innovations and uses a wide range of scientific disciplines, methods and tools. It is an interesting tool in the arsenal of public health research. It is essential today to be able to identify the multiple challenges that health systems will face in the coming years, to anticipate changes, and to explore possible futures.

Assessment of National Public Health and Reference Laboratory, Accra, Ghana, within Framework of Global Health Security.

The Second Year of Life project of the Global Health Security Agenda aims to improve immunization systems and strengthen measles and rubella surveillance, including building laboratory capacity. A new laboratory assessment tool was developed by the Centers for Disease Control and Prevention to assess the national laboratory in Ghana to improve molecular surveillance for measles and rubella. Results for the tool showed that the laboratory is well organized, has a good capacity for handling specimens, has a good biosafety system, and is proficient for diagnosis of measles and rubella by serologic analysis. However, there was little knowledge about molecular biology and virology activities (i.e., virus isolation on tissue culture was not available). Recommendations included training of technical personnel for molecular techniques and advocacy for funding for laboratory equipment, reagents, and supplies.

Potential impact of climate change on emerging vector-borne and other infections in the UK.

Climate is one of several causes of disease emergence. Although half or more of infectious diseases are affected by climate it appears to be a relatively infrequent cause of human disease emergence. Climate mostly affects diseases caused by pathogens that spend part of their lifecycle outside of the host, exposed to the environment. The most important routes of transmission of climate sensitive diseases are by arthropod (insect and tick) vectors, in water and in food. Given the sensitivity of many diseases to climate, it is very likely that at least some will respond to future climate change. In the case of vector-borne diseases this response will include spread to new areas. Several vector-borne diseases have emerged in Europe in recent years; these include vivax malaria, West Nile fever, dengue fever, Chikungunya fever, leishmaniasis, Lyme disease and tick-borne encephalitis. The vectors of these diseases are mosquitoes, sand flies and ticks. The UK has endemic mosquito species capable of transmitting malaria and probably other pathogens, and ticks that transmit Lyme disease. The UK is also threatened by invasive mosquito species known to be able to transmit West Nile, dengue, chikungunya and Zika, and sand flies that spread leishmaniasis. Warmer temperatures in the future will increase the suitability of the UK's climate for these invasive species, and increase the risk that they may spread disease. While much attention is on invasive species, it is important to recognize the threat presented by native species too. Proposed actions to reduce the future impact of emerging vector-borne diseases in the UK include insect control activity at points of entry of vehicles and certain goods, wider surveillance for mosquitoes and sand flies, research into the threat posed by native species, increased awareness of the medical profession of the threat posed by specific diseases, regular risk assessments, and increased preparedness for the occurrence of a disease emergency.

Is there a link between pollutant exposure and emerging infectious disease?

A scoping literature review found evidence supporting the hypothesis that a population's pollution status could help refine classification of emerging infectious disease (EID) hotspots. Systematic literature reviews and studies designed to specifically test the predictive value of pollutant status on EID risk are recommended.

Y a-t-il un lien entre l'exposition aux polluants et les maladies infectieuses émergentes? Une recension extensive de la littérature a permis de trouver des données probantes appuyant l'hypothèse que l'état de pollution de la population pourrait aider à raffiner la classification des points chauds des maladies infectieuses émergentes (MIE). Des examens systématiques de la littérature et des études conçues spécifiquement pour tester la valeur prédictive de l'état des polluants sur le risque des MIE sont recommandés.(Traduit par Isabelle Vallières).

Incidence of Clinician-Diagnosed Lyme Disease, United States, 2005-2010.

National surveillance provides important information about Lyme disease (LD) but is subject to underreporting and variations in practice. Information is limited about the national epidemiology of LD from other sources. Retrospective analysis of a nationwide health insurance claims database identified patients from 2005-2010 with clinician-diagnosed LD using International Classification of Diseases, Ninth Revision, Clinical Modification, codes and antimicrobial drug prescriptions. Of 103,647,966 person-years, 985 inpatient admissions and 44,445 outpatient LD diagnoses were identified. Epidemiologic patterns were similar to US surveillance data overall. Outpatient incidence was highest among boys 5-9 years of age and persons of both sexes 60-64 years of age. On the basis of extrapolation to the US population and application of correction factors for coding, we estimate that annual incidence is 106.6 cases/100,000 persons and that ≈329,000 (95% credible interval 296,000-376,000) LD cases occur annually. LD is a major US public health problem that causes substantial use of health care resources.

Socioeconomic Status and Foodborne Pathogens in Connecticut, USA, 2000-2011(1).

Foodborne pathogens cause >9 million illnesses annually. Food safety efforts address the entire food chain, but an essential strategy for preventing foodborne disease is educating consumers and food preparers. To better understand the epidemiology of foodborne disease and to direct prevention efforts, we examined incidence of Salmonella infection, Shiga toxin-producing Escherichia coli infection, and hemolytic uremic syndrome by census tract-level socioeconomic status (SES) in the Connecticut Foodborne Diseases Active Surveillance Network site for 2000-2011. Addresses of case-patients were geocoded to census tracts and linked to census tract-level SES data. Higher census tract-level SES was associated with Shiga toxin-producing Escherichia coli, regardless of serotype; hemolytic uremic syndrome; salmonellosis in persons ≥5 years of age; and some Salmonella serotypes. A reverse association was found for salmonellosis in children <5 years of age and for 1 Salmonella serotype. These findings will inform education and prevention efforts as well as further research.

[Infectious diseases]. / Maladies infectieuses.

The recommendations for the treatment of gonorrhea have been changed: ceftriaxone 500 mg IM plus azithromycin 1 g PO is recommended. Prophylaxis of recurrent cellulitis with penicillin 250 mg 2 x/d PO may be considered. E. coli ESBL does not require contact isolation anymore. Fecal transplantation seems so far to be the most effective treatment of recurrent C. dificile. Two new respiratory viruses, Middle East Coronavirus (MERS-CoV) and avian-origin Influenza A (H7N9) have been reported. Oral valganciclovir treatment reduces the risk of hearing loss in congenital CMV infection. An outbreak of mould infections of the central nervous system has been described in the United States following injection of contaminated steroids.

Rare and emerging viral infections in transplant recipients.

Emerging viral pathogens include newly discovered viruses as well as previously known viruses that are either increasing, or threatening to increase in incidence. While often first identified in the general population, they may affect transplant recipients, in whom their manifestations may be atypical or more severe. Enhanced molecular methods have increased the rate of viral discovery but have not overcome the problem of demonstrating pathogenicity. At the same time, improved clinical diagnostic methods have increased the detection of reemerging viruses in immunocompromised patients. In this review, we first discuss viral diagnostics and the developing field of viral discovery and then focus on rare and emerging viruses in the transplant population: human T-cell leukemia virus type 1; hepatitis E virus; bocavirus; KI and WU polyomaviruses; coronaviruses HKU1 and NL63; influenza, H1N1; measles; dengue; rabies; and lymphocytic choriomeningitis virus. Detection and reporting of such rare pathogens in transplant recipients is critical to patient care and improving our understanding of posttransplant infections.