Constant monitoring of viruses, fungi and bacteria can prevent future pandemics, scientists insist

Experts who took part in the fourth FAPESP 60 Years Conference discussed the challenges of diagnosing and combating emerging pathogens and the need to integrate multidisciplinary teams and governments if outbreaks of infectious disease are to be prevented.

By André Julião  |  Agência FAPESP – The COVID-19 pandemic brought to the fore the need for what epidemiologists call sentinel systems, which keep a watch for pathological agents with the aim of preventing outbreaks or even predicting epidemics. Besides viruses like SARS-CoV-2, however, it is also vital to monitor fungi and bacteria for which no effective treatment exists and which could spread. This was the focus for the fourth in the series of FAPESP 60 Years Conferences, entitled “Global Health Challenges” and held on September 22.

The event was mediated by Helena Nader, a professor at the Federal University of São Paulo’s Medical School (EPM-UNIFESP) and a member of FAPESP’s Board of Trustees.

“It’s very important for us to have sentinel systems so that pandemics can be rapidly detected and combated early on, but this requires interaction and cooperation, which aren’t always natural,” said Luiz Eugênio Mello, FAPESP’s Scientific Director, in his welcoming remarks. 

Andrea Dessen, a researcher at France’s National Center for Scientific Research (CNRS), warned that pandemics are not caused only by viruses but also by bacteria. Since the 1960s, however, few new antibiotics have been discovered, and several “superbugs” are now able to resist existing treatments.

“The United Nations reckons 700,000 deaths are caused by resistance to antibiotics every year, but the number will be 10 million per year by 2050 if we do nothing,” said Dessen, who leads a project supported by FAPESP at Brazil’s National Center for Research on Energy and Materials (CNPEM) under the aegis of the São Paulo Excellence Chair (SPEC) program. 

Dessen added that six reasons for antibiotic resistance have been listed by the World Health Organization (WHO): overprescribing, unfinished treatment courses, overuse in cattle raising (which accounts for 80% of worldwide antibiotic consumption), insufficient control of hospital-acquired infections, lack of hygiene and basic sanitation, and a shortage of antibiotics on the market.

Virus monitoring

Ester Sabino, a professor at the University of São Paulo’s Medical School (FM-USP) and a researcher at its Institute of Tropical Medicine (IMT-USP), noted that the Brazil-UK Center for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE), supported by FAPESP and led by her, was set up to keep watch for novel viruses transmitted by arthropods (chiefly insects) but that the COVID-19 emergency widened the scope of the project.

CADDE’s work as a sentinel includes monitoring blood banks to detect the presence of viruses, and in the case of SARS-CoV-2 estimating antibody levels in the population and sequencing viral isolates from patients treated at health clinics, partly to measure the prevalence of variants such as Delta, which now accounts for 100% of cases in the city of São Paulo.

“We expected a dengue epidemic last year, but it didn’t happen. Dengue may be sensitive to mobility. We observed a fall in the number of cases when mobility was reduced [by the restrictions imposed to contain COVID-19]. This year the main concern is chikungunya, which could rebound when mobility rises again. There have already been cases in Santos [on the coast of São Paulo state] and elsewhere,” Sabino said.

“We need the SUS [Sistema Único de Saúde, Brazil’s national health system], universities and government to understand what’s being said so they can formulate policy better. This has to be done before epidemics happen. We must act in time to improve our response.”

Unknown fungi

Arnaldo Colombo, a professor at EPM-UNIFESP, said the impact of fungal diseases is a silent crisis for biodiversity, food security and human health.

These pathogens threaten amphibians and other wildlife, account for 30% of the diseases that affect plants, including grain crops, and could compromise some 20% of the world’s harvest.

Agricultural activity is a cause of disease for farmworkers, as the soil is a source of countless fungal species. Fungi are major agents of skin disease and lung infection but are very rarely diagnosed. Some 1.2 million people with fungal pneumonia are treated as if they had tuberculosis, for example. 

Advances in medicine such as intensive care units, chemotherapy and organ transplants have paradoxically advanced the emergence of novel disease-bearing fungi. Opportunistic mycoses, as they are known, account for 1.8 million cases per year worldwide, with mortality rates ranging from 20% to 70%.

Even so, fungal pathogens are little known and even ignored by physicians. An analysis covering 129 Latin American health centers showed that only 9% had the capability to diagnose fungal infections.

“It’s most important to discuss economic models that are more compatible with the planet’s health, such as sustainable development. We’re lagging in the effort to contain global warming, which has enabled pathogens to acclimatize to temperatures as high as 37 °C and infect us as a result,” Colombo said.

“Investment is urgently needed in global health centers that work with a holistic concept of health to understand the natural history of pathogens before they reach human beings.”

Colombo also argued that fungicides can be substituted by other pest control strategies so as to prevent the emergence of resistant fungi. Lastly, it is vital to invest in the development of diagnostic platforms and not just drug discovery.

“We need to learn to manipulate the human microbiome more effectively in order to contain the dysbiosis induced by the use of antibiotics, and unquestionably there’s scope for making more rational use of antimicrobials in hospitals and the community,” he said. Dysbiosis is an undesirable alteration of the gut microbiota resulting in an imbalance between protective and harmful bacteria.

A recording of the entire event can be watched at: youtu.be/-22tnw4Q_Qo. The first three FAPESP 60 Years Conferences are at: 60anos.fapesp.br/conferencias.