Emerging and re-emerging viral, fungal and bacterial diseases

Throughout history mankind has been facing emerging and re-emerging diseases. The most recent one has been COVID-19 where an unprepared situation emerged with millions of deaths. In this issue of Microbiology Australia, we deal with the emerging and re-emerging viral, fungal and bacterial diseases. On the positive side, diagnostics and rapid vaccine and drug development have been significantly advanced with record breaking results.

The emergence and re-emergence of viral, fungal and bacterial pathogens followed by opportunistic pathogens is also of concern especially for immunocompromised patients. In addition, changing climate conditions alter vector populations which also facilitate the dispersal of disease-causing agents. Permafrost is defrosting and as consequence pathogens are emerging, causing disease and death, like seal finger and anthrax in polar regions. UN SDGs #3 is about ‘Good health and Well-Being’. To be able to meet the envisioned deadline for the achievement of the SDGs surveillance, timely intervention and preventative measures are imperative and advanced level microbiological understanding will play a key role.

The emergence and re-emergence of viruses are of major concern to human health. The examples of SARS-CoV-2, mpox, measles, avian and swine influenza and Japanese encephalitis virus are familiar to most of us. The threat of these viruses is increased by vaccine hesitancy, climate change and flood events as well as the expansion of human habitation. Our great success with agriculture in Australia is enhanced by our relative isolation; however, with tourism and agricultural trade high vigilance needs to be maintained to protect our agriculture from viruses such as African swine fever and foot and mouth disease virus as well as plant viruses.

Medical Mycology is ‘the new kid on the block’, with fungal diseases emerging as a major health problem only in the late 20th century, in association with advances in modern medicine and increasing numbers of immunocompromised individuals. The current annual fungal disease burden exceeds several million cases worldwide, and is rising. In contrast to most bacterial infections, invasive fungal diseases are typically subacute or chronic and inexorably progressive, with high mortality. Invasive fungal diseases cause 1.6 million deaths/year globally and account for 10% of all hospital-acquired infections. Protracted therapy has increased the development of antifungal drug resistance, a problem that will only increase in the future, as currently non-pathogenic fungi adapt to higher temperatures as result of climate change, making them far more effective human pathogens. Newly multidrug resistant fungi emerge unexpectedly, as illustrated most recently by Candida auris, causing significant outbreaks in hospitals globally. Virtually unknown 2 years ago, the COVID-19 pandemic is now affecting millions worldwide, with a high case fatality rate in ICU-admitted patients drawing new attention to invasive fungal diseases, as COVID-19 associated pulmonary aspergillosis and mucormycosis have re-emerged as a serious comorbidity. All those factors make an effective screening for fungal infections, prompt and accurate diagnosis and rapid initiation of appropriate treatment crucial to achieve good outcomes.

Antigenic shifts resulting in remerging viral infections are not common in bacteria. Perhaps changing urban living patterns encourages encounters between human beings and pathogenic bacteria. With advances in molecular microbiology causative agents are now more easily identified than the past cases. An example is Ehrlichia canis, an emerging tick-borne zoonotic pathogen and the agent of human ehrlichiosis. Again, before the 1980s, only a few species of Rickettsia were identified; however, today molecular advances reveal greater number of species. Enterohemorrhagic Escherichia coli (O104:H4), which caused a large outbreak of hemolytic uremic syndrome, was due to contaminated sprout consumption. Improved diagnostic media and techniques such as the use of Kelly media allowed the recovery of Borrelia spp. Cell culture techniques also allowed recovery of unculturable bacterial pathogens such as the isolation of Bartonella quintana using endothelial cell lines. Metagenomics allowed establishment of the link between gut flora of preterm babies with necrotizing enterocolitis and the presence of Clostridium butyricum.¹ Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF) allowed the easier identification of emerging urinary pathogens such as Aerococcus spp. or Actinobaculum spp.¹ Sociodemographic changes also contribute to emergence and reemergence of bacterial diseases such as the reemergence of cholera (Vibrio cholerae O1) in South America in 1991, which is thought to be linked to the bilge water dumped by an Asian merchant ship off the Peruvian coast, with subsequent infection of over 1.4 million people over 6 years. Changes in the environment and the climate also contribute such as V. cholerae O139 emergence after heavy monsoon in 1993.¹ Emergence of more virulent bacterial pathogens and opportunistic infections can also happen. Examples include Corynebacterium amycolatum, multidrug-resistant strain-infected patients can be at risk of infection by Capnocytophaga canimorsus, which has now emerged as a cause of septicaemia in splenectomised or cirrhotic patients bitten by dogs.¹

In this issue, John Mackenzie and David Williams communicate the emerging and reemerging Japanese encephalitis virus in Australia, Cherrihan Adra, Harrchun Panchalingam and D. İpek Kurtböke investigate the rapidly expanding pathogen Pyrrhoderma noxium in Queensland infecting fig trees. Peter Irwin and John Beadle provide an overview on canine ehrlichiosis in Australia. Philip Taylor communicates the threat of the plant pathogen, Xylella fastidiosa. The emergence of amphibian chytridiomycosis in Australia is discussed by Rebecca Jane Webb and Anthony Wayne Waddle. Candida auris and its threat in hospitals is reviewed by Laszlo Irinyi, Richard Malik and Wieland Meyer and disease spread from water cycling is discussed by Erica Donner and Michael Short. Meg Allom, Harrchun Panchalingam, M. Katouli and D. İpek Kurtböke discuss the control of human pathogenic bacteria on fresh produce using bacteriophage treatment. African swine fever is communicated by Michael Ward, and lumpy skin disease by Kim Bowden and Kelly Stanger. One of the two overseas contributions are from CABI with David Smith, Jonathan Casey, Matthew J. Ryan, Lisa Offord, Alexis Rendell-Dunn and Rob Reeder provides information on CABI’s 100 years in identifying and combating emerging fungal diseases in response to climate change.

The authors declare they have no conflict of interest.