bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathogens and indicators in wastewater matrices
Authors: Keegan Alexandra , Tutuka Candani , Monis Paul
Published: April 2020

As climate change and increasing population sizes continue to place stress on water resources, communities are increasingly looking to recycled water as a supplementary water source, whether for drinking water, domestic irrigation, industrial or agricultural use. Protecting public health by ensuring the safety of water supplies is a key concern for the water industry and health authorities.
Quantitative microbial risk assessment (QMRA) for water re-use via aquifers
Authors: Page Declan , Toze Simon
Published: April 2020

Worldwide, there is an increasing interest in the recharge of aquifers as a method for augmenting urban water supplies. Managed aquifer recharge (MAR) can utilise a variety of non-traditional source waters including urban stormwater and reclaimed water from sewage effluent. However, these alternate water sources may contain a wide range of pathogenic hazards that pose risks to human health. Hence the safe use of recycling water via aquifers requires potential risks to be reduced to acceptable levels. This article outlines the approach recommended by the draft Australian Guidelines for Water Recycling (AGWR) (Phase 2C Managed Aquifer Recharge) to quantify the aquifer treatment using a quantitative microbial risk assessment (QMRA) approach.
Vertical Transmission, May 2009
Authors: Stokes Hatch
Published: April 2020

Our Golden Jubilee annual meeting is very near and I look forward to seeing as many of you as possible in Perth. As I mentioned in my last VT, we have a number of special events planned and a particularly stellar cast of international speakers. One event of note is that Australia Post will be releasing a Golden Jubilee ASM pre-stamped envelope on our behalf. The first day of release will be 1 July, timed to coincide with our annual meeting. I would like to thank the National Office and the Microbiology Australia Editorial Board for providing valuable input into the design. The final result is absolutely stunning, so be sure and look out for it.
The global climate is changing. It’s true! How do we know it’s happening? What has it got to do with microbes
Authors: Blackall Linda L
Published: April 2020

This issue of Microbiology Australia is mostly dedicated to global climate change (GCC), the effects of climate change on disease agents and ecosystems, and the role that microbes play and potentially can play in the production and mitigation of GCC.
A changing climate: evidence and consequences
Authors: Lough Janice M
Published: April 2020

Global climate is changing rapidly as a consequence of human activities increasing the concentration of ?greenhouse gases? in the atmosphere. The natural mix of these gases allows incoming solar radiation to warm the earth?s surface and prevents a proportion of the outgoing long-wave radiation from escaping to space. Without these radiative controls provided by our atmosphere, the earth would be about 30oC cooler and life as we know it would not have developed. Human activities, primarily burning of fossil fuels and land-use changes, have significantly increased the concentration of these atmospheric gases, with the consequence that more energy is trapped in the climate system, resulting in global warming. There are various lines of evidence to support the proposition that we are living in an era of rapid, human-induced changes in our global climate environment ? theory, instrumental observations, paleoclimatic reconstructions and modelling.
The effect of climate change on Australian arboviruses
Authors: Mackenzie John S
Published: April 2020

Since it was first raised more than 20 years ago, there has been increasing concern about the potential impacts of climate change on mosquito-borne viral diseases in Australia. This has generated a number of predictions and projections on the effect of global warming on the incidence and spread of Australian arboviruses. These have been discussed recently by Russell and Jacobs & colleagues and thus need not be repeated in detail here. In addition, it was also the topic of a previous ?In Focus? article. This paper will briefly focus on the complex interplay between climate-associated factors which may affect the incidence and spread of mosquito-borne viruses, and show how these factors may influence the ecologies of the major Australian arboviruses.
2009 human H1N1 influenza (swine flu)
Authors: Prowse Stephen J , MacKenzie John S
Published: April 2020

The 2009 H1N1 influenza, initially known as swine flu, originated in North America in early 2009. This new strain of influenza A virus (H1N1) came to the attention of the international public health community when several foci of influenza-like illness were identified in Mexico, which had more than 850 cases of pneumonia, of whom 59 had died. Mild cases of influenza-like illness were also reported from Texas and California. Virus isolates were obtained from the cases in California and from samples of cases sent from Mexico to the Canadian National Public Health Laboratory in Winnipeg. Molecular analysis of these virus isolates showed that they were virtually identical and indicated that they represented a completely new, rapidly spreading strain of H1N1 virus, which appeared to have originated in swine. This was the first reassorted influenza virus to emerge since the 1968-1969 pandemic caused by the Hong Kong influenza virus. Under the new International Health Regulations (2005), this rapidly spreading, novel virus was quickly recognised by the World Health Organization as constituting a Public Health Emergency of International Concern, the first such emergency since the new International Health Regulations were introduced in mid-2007.
Indigenous Health
Authors: Good Michael F , Fischer Katja
Published: April 2020

This issue of Microbiology Australia is devoted to Microbes that cause disease particularly in our Indigenous populations. We have for example the worldwide highest rates of Rheumatic Fever and Heart Disease in Aboriginal and Torres Strait Islander people. These follow streptococcal infections mostly as a result of skin damage through primary infections with pathogens such as parasitic scabies mites.
Epidemiology of group A streptococcus in Australia
Authors: Carpetis Johnathan R
Published: April 2020

The Australian population experiences the extremes of group A streptococcal (GAS) disease. The majority of our population lives an affluent, middle class existence and experiences the same types and rates of GAS disease as are found in most industrialised countries. By contrast, the Aboriginal and Torres Strait Islander populations, particularly those living in remote and rural settings, experience a developing-country profile of GAS disease, which is almost entirely attributable to poverty, particularly as it is manifest by overcrowded housing, poor environmental health and reduced access to health care.
Control of intestinal helminths in Indigenous communities
Authors: McCarthy James S
Published: April 2020

Parasite infections, like most other infectious diseases disproportionately affect people living in poverty. Thus, it is no surprise that the prevalence of intestinal helminth infections has remained higher in Indigenous communities in Australia, compared to that observed in more affluent groups in the population.
HPV-related disease in Indigenous health
Authors: Garland Suzanne M
Published: April 2020

Cervical cancer is the second most common cancer in women worldwide, with the majority of cases occurring in the developing world. With effective high-quality cervical cytology screening programs, with wide coverage of target populations, precursor lesions can be detected and treated, ultimately preventing progression to the development of cervix cancer.
Introduction - The beginnings of a society:
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

Every year Australian microbiologists gather. The locations alternate ? Perth, Melbourne, Sydney, Brisbane, Adelaide, and all over Australia. They gather to discuss the science of microbiology. The gatherings are world-renowned and attract high-profile speakers from Australia and around the world. Associated with the gatherings are highly anticipated traditions, the Rubbo Oration, the Frank Fenner Research Award, the ringing of the Nancy Atkinson Bell and the annual dinner to name just a few. These gatherings ? the first one dating back to 1959 ? are organised and coordinated by the Australian Society for Microbiology (ASM), which also came into being in 1959, and which in 2009 celebrates its 50th year of existence.
Frank Macfarlane Burnet
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

Sir Frank Macfarlane Burnet was born in Traralgon, Victoria, in 1899. He received his medical degree in 1924 from the University of Melbourne and performed research (1925-27) at the Lister Institute of Preventive Medicine, London. After receiving his PhD from the University of London (1928), Burnet ? usually known as Mac ? became Assistant Director of the Walter and Eliza Hall Institute of Medical Research at Royal Melbourne Hospital. From 1944-65 he was Director of the Institute and Professor of Experimental Medicine at the University of Melbourne.
Nancy Atkinson
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

Born in Melbourne in 1910, Nancy Atkinson was educated at the University of Melbourne, graduating BSc in 1931 and MSc in 1932. She worked as a research scholar and demonstrator in the Department of Bacteriology in Melbourne from 1932-37, before moving to South Australia where she was to play a major role in the development of bacteriology in Adelaide.
Chapter Two - Growth and professionalisation: towards a national, professional and scientific society
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

Immediately after its establishment, the Australian Society for Microbiology began to thrive. The founders of the ASM had been correct in their assessment of the need for the Society. By the second decade of its existence, membership numbers had swelled to over 1200. The services it provided for members had also diversified as the Society consolidated and became a strong voice of microbiology in Australia. Not only did the number of members grow, but the Scientific Meetings became more frequent and attracted international speakers, the committees on which the ASM was asked to be represented became more numerous, and the activities in which the Society was involved continued to grow. The needs of members also began to change. It soon became clear that the structure of the ASM needed be addressed so that the Society could adapt to the changing roles it was being called upon to play.
Chapter Three - Implementing change
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

The decision to incorporate, professionalise and nationalise the Australian Society for Microbiology heralded a transformation. After lengthy debate, spanning the best part of a decade, the steady evolution of the Society gave way to rapid change. Implementation commenced immediately. Membership categories changed and continued to evolve throughout the 1980s as the ASM adapted to the needs of its broadening membership base. Relationships with state branches and communication with members became increasingly important. Maintaining its unique character, closeness and sense of community despite its rapid growth became a major challenge for the ASM.
Bibliography & Appendix
Authors: Rood Sarah , Sheedy Katherine
Published: April 2020

Presidents; Honorary Life Members; Rubbo Orators; Annual Scientific Meetings; National Council
The challenges of teaching microbiology
Authors: Burke Chris , Power Cheryl
Published: April 2020

By its nature, education looks to the future ? in that the benefits are in the future with an educated populace. However, education functions in the present and faces problems that must be resolved now, in order to achieve the future benefit. The true measure of education, then, is the success of student learning, which is served by good teaching. Altering our perspective as teachers to seeing the goal as student learning outcomes rather than being ?good teachers? opens up many different challenges. Understanding too that if we have taught well, then student learning will continue lifelong. As the American philosopher, Eric Hoffer, said ?The central task of education is to implant a will and facility for learning; it should produce not learned but learning people?.
Peer review of teaching to promote learning outcomes
Authors: Burke Chris
Published: April 2020

In 1990, American educator Ernest Boyer asked us to reconsider scholarship. In doing this he recognised not only the importance of teaching, but also that it was undervalued. Boyer concluded that for teaching to become valued it needed to be evaluated as rigorously as research is and suggested, among other things, that peer evaluation was an effective means of assessing quality ? just as it is in research. Boyer noted that peer evaluation of teaching was not commonly practised in American higher education. The situation remains similar to this day in Australia with peer review of teaching (PRT) being uncommon.
Digital wet laboratories: blended learning to improve student learning
Authors: Grando Danilla
Published: April 2020

To create great learning environments we need to actively engage our learners. Microbiology laboratory work experience for students is a powerful motivator; students returning from placement back to university often buzz with stories and look forward to a future place in industry. Unfortunately, opportunities for working in industry are limited and thus the next best thing is to ensure that university laboratory practicals also actively engage students. Traditional laboratory practical classes can be supported by and better simulate the activities undertaken in the workplace through the blending of computer-aided instruction with wet practical exercises.
Collaborative practice re-energises bioscience teaching in schools
Authors: Stevenson Brian
Published: April 2020

This year marks the first decade of operations for the Gene Technology Access Centre (GTAC). The decade has seen a grassroots initiative by a small group of eminent research scientists and dedicated personnel from the University High School in Melbourne grow into a specialist education centre in cell and molecular biology that attracts over 6000 students and their teachers each year. GTAC has not only refocused student and teacher attention on the interdisciplinary nature of contemporary biology, but has also highlighted how a ?centre model for learning?, based upon collaboration and partnerships, can exist within ?the school system? and meet the needs of students and teachers from across Victoria and beyond.
Significance of laboratory experience in undergraduate microbiology
Authors: Agus Helen
Published: April 2020

The 2008 Review of Australian Higher Education highlighted current financial constraints on higher education in Australia that impact negatively on the quality of student experience and their learning outcomes. Practical laboratory experience is costly in providing venues, staffing, materials and equipment. However, the practical nature of microbiology necessitates acquisition of significant knowledge and experience of laboratory skills to effectively support the profession. This article provides evidence that inclusion of practical classes in undergraduate microbiology courses has multiple advantages: quality learning facilitated through experiential, engaging learning activity; undergraduates in theory plus practical courses achieve significantly higher results than those taking theory-only units; and student feedback that articulates that laboratory experience facilitates quality learning outcomes.
Engaging students in clinical Bacteriology: a fresh look
Authors: O'Brien Mark , Beames Stephanie
Published: April 2020

Frequently there is a disconnectedness, either perceived or actual, between theoretical principles and laboratory practice in science education and this holds true for clinical microbiology where traditionally knowledge is delivered in ?chunks? in a lecture format with the misguided belief that students have to know ?everything about everything?. This preoccupation with content delivery often leaves no time for active class discussion or reflection. Moreover, laboratory classes are treated as add-ons to the process, rather than an integrated part of the whole learning experience. In redesigning our units (subjects) we have bridged the gap between the theory and practice of clinical bacteriology. In doing so, we have seen a transformation in the learning experiences of our students and in the way we teach.
Vertical Transmission, May 2010
Authors: Stokes Hatch
Published: April 2020

Science Meets Parliament was held as usual in early March and ASM again sponsored two of our members to attend. This year it was Glen Ulett, The Queensland Branch Chair and Gabrielle Belz from Victoria. They will report in the next issue of Microbiology Australia on why they found the experience to be useful and positive.
Biodiscovery from microbial resources: Actinomycetes leading the way
Authors: Kurtboke Ipek
Published: April 2020

Biodiscovery from microbial resources can be defined as the exploration of microbial metabolic products to detect, identify and evaluate their potential for medicinal, agricultural and biotechnological operations. Microbial resource centres house microbial compounds produced under different physical and nutritional parameters to maximise the production of metabolites and are subsequently tested in different bioassays to define targeted activity.
Bacteriophages as tools in drug discovery programs
Authors: Kurtboke Ipek
Published: April 2020

Screening of microbial natural products continues to represent an important route to the discovery of novel bioactive compounds for the development of new therapeutic or other important industrial agents. However, a continuous supply of diverse compounds is needed to meet the needs of industry. Such a supply can only be derived through systematic screening of bioactive compound-producing microorganisms from natural sources.
Biodiscovery of chemo preventatives of Alzheimer’s disease using yeast
Authors: Mcreadie Ian , Bharadwaj Prashant , Martins Ralph
Published: April 2020

Yeasts have been used as models for just about everything, from basic studies in molecular biology and genetics to cancer and studies of drug resistance. Initially Alzheimer?s disease (AD) was seen as an extracellular disease, so it was hard to see how yeast might make a contribution to AD research. However, there is now recognition that the main player, A?, has intracellular and extracellular effects. Furthermore, it is now clear that yeast studies are relevant to AD.
Salmonella in food products – a vector for distribution of antibiotic resistance
Authors: Van Thi Thu Hao , Gan Emily Teck Fong , Smooker Peter M , Coloe Peter J
Published: April 2020

Non-typhoidal Salmonella spp. are common food-associated pathogens, and Salmonella infections are one of the most common causes of death associated with food-associated illness, especially in developing countries. As in many other developing countries, raw food hygiene and antimicrobial resistance epidemiology are in their infancy in Vietnam. In addition, the lack of stringent controls on antimicrobial usage in human health and particularly in animal production systems increases the risk of food-borne pathogens harbouring and disseminating antibiotic resistance genes. For countries such as Vietnam, Thailand and other Asian countries, Salmonella vaccination is a more cost-effective way of controlling Salmonella in food production animals than the use of antibiotic therapy.
Rapid microbial identifications by MALDI-TOF – Viva la revolution!
Authors: Neville Stephen A , Gosbell Iain B
Published: April 2020

Although the application of mass spectrometry to bacterial identification was proposed as far back as 1975 by John Anhalt, it was not until 1987 when Professor Franz Hillenkamp and Dr Michael Karas first pioneered Matrix Assisted Laser Desorption/Ionisation Time-of-Flight mass spectrometry (MALDI-TOF MS) for truly rapid microbial identification in diagnostic microbiology laboratories. Conventional phenotypic methods of identifying isolates of bacteria, yeasts and filamentous fungi require hours to several days to complete, depending on the type of organism involved, and may be prone to error due to bias or inexperience. Even the more recent molecular innovations have their limitations that place them outside the scope and budget of many routine laboratories. However, MALDI-TOF MS technology has changed the way we think about microbial identifications and strain differentiation by providing results from plate to name in approximately five minutes for one isolate and around 90 minutes for 60 isolates at under $2 an identification. It is likely to be particularly helpful clinically for identification of species in positive blood culture broths and for organisms that are hard to identify quickly.
Applications and integration of chromogenic culture media in clinical microbiology
Authors: Merlino John
Published: April 2020

The ability to rapidly detect and identify micro-organisms is of paramount importance for many microbiology laboratories. The application of new classes of enzymatic-based chromogenic compounds has revolutionised traditional culture media, leading to the developments of a new generation of chromogenic media. Many studies have shown that the chromogenic agar has become more than an isolation media when compared to conventional culture media. A newer, faster, more cost-effective means in the presumptive identification or screening of microorganisms which are either genus, or in some cases species-specific, and allows superior differentiation of mixed micro-organisms in cultures. When supplemented with antibiotics or other agents, chromogenic media allows the screening for multidrug resistance and virulence in many micro-organisms and can be easily integrated with other automated and/or molecular-based methods.
Rapid detection of bacteraemia
Authors: Nimmo Graeme R
Published: April 2020

Bacteraemic sepsis has a high mortality that can be reduced by early diagnosis and initiation of appropriate antimicrobial therapy 1. Rapid confirmation of the diagnosis and identification of the causal agent provide guidance on the adequacy and duration of antimicrobial therapy and on the need for source investigation. Clinical microbiology laboratories have rightly placed great emphasis on this aspect of their practice. As causal organisms are usually present in low titre, direct microscopy is impractical and laboratories have generally relied on culture of blood in broth, which is relatively insensitive and too slow to influence initial management. Phenotypic methods for the identification and antimicrobial susceptibility testing (AST) of isolates have progressively improved over the last two decades, but still require significant periods of incubation. Similarly, commercial blood culture systems have been refined with better systems for automated detection of growth in broth, but still require incubation for up to five days and subculture for the isolation of pathogens. Constantly monitored blood culture systems and automated identification/AST are now the norm in most clinical laboratories. Although there will undoubtedly be further development of phenotypic methods, with incremental improvements in sensitivity and time-to-detection, research and development now concentrated on molecular detection methods has the potential to result in a paradigm shift in our approach to the microbiological diagnosis of this condition.
‘Swabs’ then and now: cotton to flocked nylon
Authors: Faoagali Joan
Published: April 2020

Microbiological sample collections using cotton-tipped swabs (with or without serum), Dacron?, rayon and calcium alginate, with shafts of wood, plastic and various thicknesses and types of metal have all been used over the years. The swabs have been contained in glass or plastic tubes with and without various types of transport media. Swabs are an easy and popular method of sample collection, although microbiology laboratories traditionally prefer tissue, body fluids or aspirates ahead of swabs. As microbiology laboratories increasingly adopt near patient testing and molecular detection methods to reduce test turnaround times, new sample collection methods are required to maximise the sensitivity of these expensive tests and reduce the possibility of failed tests due to sample inhibitors or poor collection techniques. Flocked nylon swabs have been developed by Copan in the last decade and are produced using a technique of spraying nylon fibres onto a rigid core. This has the effect of increasing the surface area for sample collection and also provides easy elution of the collected material. These swabs are polymerase chain reaction (PCR) inhibitor-free, RNase-negative and DNase-free and there is in addition a range of flocked swabs, specifically intended for forensic DNA investigations that are certified human DNA-free. The advantages, disadvantages and appropriate use of swab collections for microbial detection in the 21st century will be presented.
Biocides in the health industry
Authors: Merlino John , Browning Melissa
Published: April 2020

Biocides, whether naturally extracted or chemically engineered, are invaluable compounds that provide the health industry with numerous benefits. They can be used as disinfectants or antiseptics playing an important role in the control of bacteria and viruses. Thus, they are a precious resource that must be managed so as to be protected from loss of activity over time; these compounds are often overlooked in the significance of bacterial persistence and resistance.
What serosurveillance studies tell us about the 2009 influenza pandemic
Authors: Dowse Gary K , Barr Ian
Published: April 2020

Surveillance of the impact of pandemic (H1N1) 2009 influenza during its initial seasons in both hemispheres relied on routinely available indicators, including numbers and rates of laboratory-detected cases, hospitalisations, ICU admissions and deaths, along with monitoring of influenza-like illness (ILI) from primary care sentinel surveillance systems. Estimates of the clinical attack rate and the case fatality ratio were imperfect. Understanding of the pathogenicity of the pandemic virus and prediction of the impact in subsequent seasons was hindered by a lack of information on actual infection rates in the population. Results of a number of serosurveys conducted in Australia and overseas countries have now become available, revealing that the arrival of the pandemic virus in modern urbanised and non-immune populations resulted in relatively similar infection rates in both the southern and northern hemispheres. Around 30?50% of children and teenagers were infected during the first pandemic season, with lower rates, around 10?20%, in young and middle-aged adults, and very few infections in older adults. There were significant numbers of mild or asymptomatic infections, and case fatality and hospitalisation ratios were much lower than those contemplated in pandemic plans. Many populations, including Australia, achieved a significant level of herd immunity during the first wave, and community susceptibility was further reduced by vaccination programs, although coverage was lower than expected. In the absence of significant antigenic drift or changes in virulence, the impact of the pandemic H1N1 virus should continue to decline in future influenza seasons.
Pandemic H1N1 2009 influenza in pigs in Australia
Authors: Wong Frank YK , Deng Yi-Mo
Published: April 2020

The novel H1N1 2009 virus that is the cause of the most recent human influenza pandemic is able to infect a number of animal hosts, most notably reported in domesticated swine. The first confirmed 2009 pandemic H1N1 (H1N1pdm) influenza infection of a commercial swine herd occurred in Alberta, Canada in late April 2009. The early incidences of H1N1pdm influenza in swine were of great concern to public and animal health agencies alike, and numerous subsequent cases were reported to the World Organization for Animal Health (OIE) by different countries following prevalence of the pandemic virus in the human population, including Australia. In almost all cases, outbreak investigations have indicated an epidemiological link with farm in-contact persons reporting recent influenza-like illness (ILI), some diagnostically confirmed as H1N1pdm infections. These have suggested interspecies transmissions from human to swine. This article describes the first reported cases and our investigations of swine influenza due to H1N1pdm virus in Australia.
Capturing and taming Earth’s wild microbes
Authors: Staley James T
Published: April 2020

Among the organisms of the biosphere, the diversity of the Bacteria and Archaea is the most poorly understood. Our lack of knowledge about microbial diversity is important because the majority of these organisms still remain undescribed and unclassified and the roles they perform in their environments, their geochemical activities and their biotechnological potential still need to be ascertained. For these reasons, this rich, unknown diversity comprises an enormous untapped resource for science and society. Only recently have microbiologists begun to more fully realise how great our ignorance of microbial diversity truly is. This paper discusses how technology, persistence and serendipity play important roles in unveiling the vast diversity of uncultivated microorganisms through their capture (isolation) and taming (cultivation, naming and description). Perhaps citizens can be recruited to become ?microbe hunters? to assist in efforts to characterise new microbial species. Their potential reward could be a trophy for the ?smallest game?: the capture and naming of a novel bacterial species.
Size does matter – distinguishing bacteriophages by genome length (and ‘breadth’)
Authors: Abedon Stephen T
Published: April 2020

Genome size and nucleic acid composition are basic characteristics of bacteriophages (phages). With larger genomes come increases in gene number, greater infection and virion sophistication, higher likelihood of gene acquisition via horizontal gene transfer (HGT), and additional genetic redundancy both within and between genomes (the latter referring to gene duplication and redundancy with host functions, respectively). Larger, that is, tailed phages in fact are among the most recombinogenic organisms on earth, often possessing numerous genes of mysterious function, many of which in at least some phages can be deleted without greatly impacting laboratory propagation. Larger phages, through the use of more sophisticated polymerases as well as proofreading and genome repair functions, also are less prone to replicative infidelities. As a consequence, their per-nucleotide mutation rates are substantially lower than those of smaller phages. Here, rather than macroevolutionary trends as typically considered from the perspective of comparative genomics, I emphasise instead microevolutionary processes, particularly the role of mutation as an immediate source of genetic variation within populations. Within this context I differentiate the viruses of domain Bacteria into four genome-size categories: very small (single-stranded RNA phages), small (single-stranded DNA phages), medium (lipid-containing, double-stranded DNA, tailless phages), and large, or at least larger (tailed phages).
Impact of DNA data on fungal and yeast taxonomy
Authors: Groenewald Johannes Z , Groenewald Marizeth , Crous Pedro W
Published: April 2020

The species richness and diversity existing in microorganisms are unparalleled on our planet. In recent years, the use of molecular techniques for the detection and identification of microorganisms, especially through DNA sequencing, has revolutionised the way taxonomists look at the systematics of a species, especially when applying multilocus sequence data and concepts such as the genealogical concordance phylogenetic species recognition (GCPSR) concept1. Particularly problematic topics arising in the fungi are, for example, naming pleomorphic fungi (that is, fungi for which a teleomorph, meaning sexual form, and one or more anamorphs, meaning asexual forms, are formed), polyphyletic genera (that is, the same genus being presented in several distinct phylogenetic lineages or clades), morphospecies (a species which is differentiated from other species based on its distinctive morphological characters) that in fact represent distinct phylogenetic lineages and how to deal with species that are only known by their DNA sequence(s). Here we provide a brief overview of the effects and implications that the applications of molecular techniques such as DNA sequencing are having on the taxonomy of fungi (part 1) and yeasts (part 2), with specific reference to those which can be cultured. Although fungi and yeasts both belong to the kingdom Fungi, sometimes different approaches to the taxonomy of these two ?groups? were followed in the past and, therefore, they are treated individually below. For the purpose of this overview, genera of Oomycetes are excluded.
Real-time PCR for laboratory diagnosis of Acanthamoeba keratitis
Authors: Cheng Joanna , Carter Ian , Wang Liping , Taylor Peter
Published: April 2020

Acanthamoeba keratitis is a painful vision-threatening disease of the human cornea. It is characterised by severe ocular pain or partial paracentral stromal ring infiltrate, which can be frequently misdiagnosed as herpes simplex virus keratitis. If the infection is not treated promptly, it may progress to ulceration of the cornea, loss of visual acuity, possibly blindness and even require enucleation. Acanthamoeba sp are found commonly in freshwater, tap water, seawater, hot springs and swimming pools. An epidemiologic case study revealed that major risk factors were the use of contact lenses, predominantly extended-wear soft lenses, the use of homemade rinsing saline and users who wear their lenses while swimming. The conventional method of detecting the formation of oocysts of Acanthamoeba by a culture technique takes an average three?five days. DNA amplification by PCR can improve turnaround time for the diagnosis. A study was carried out in this laboratory to compare the traditional culture method with a real-time PCR assay.
Adjuvants for the next generation of vaccines
Authors: Pearse Martin
Published: April 2020

The use of aluminium phosphate to enhance the immune response to vaccines was first described by Glenny and Pope in 19261, and for the ensuing 70 years aluminium-based adjuvants (alum) were the only adjuvants used in registered human vaccines. It is only in the last two decades that novel adjuvants have been utilised in the formulation of newly licensed human vaccines.
A vaccine to provide strain-transcending immunity to group A streptococci
Authors: Good Michael F , Batzloff Michael R
Published: April 2020

Organisms such a Streptococcus pyogenes (group A streptococcus), Plasmodium spp parasites and HIV present significant obstacles to vaccine development. They can subvert the immune system and present dominant antigens that can display a vast array of allelic types of variants. In spite of these obvious decoys, the main strategy to develop vaccines for these organisms has been to focus on dominant antigens or epitopes. The obvious reason for this approach is that such antigens and epitopes are easy to define. Early successes are often posted largely because homologous organisms are typically used to challenge animals post-vaccination. However, success in efficacy trials with heterologous challenge is yet to be seen.
Getting closer to a vaccine against malaria
Authors: Anders Robin F
Published: April 2020

Despite recent progress in the control of malaria in several countries, this disease still kills nearly one million young children in sub-Saharan Africa each year and it contributes significantly to poverty in many of the poorest countries in the world. The effective use of existing control tools (insecticide-impregnated bed nets, residual insecticide spraying and early case detection with effective treatment) should eliminate malaria from additional regions but global eradication of malaria is not feasible without the development of a highly effective vaccine. The most advanced malaria vaccine, known as RTS,S, is likely to be licensed for use in the next few years. The protective efficacy of RTS,S is unlikely to exceed 50% but numerous other approaches to vaccinating against malaria are showing some promise and, consequently, there are good prospects that a second-generation malaria vaccine will be much more effective.
Dengue vaccines
Authors: Whitehorn Jamie , Simmons Cameron P
Published: April 2020

Dengue is globally the most important arboviral infection of humans with an estimated 100 million infections per annum and 2.5 billion people at risk in >100 countries. The burden of dengue is substantial in economic terms and in the strain it places on already fragile health systems. There are currently no licensed vaccines or therapeutics and disease control relies, mostly unsuccessfully, on suppressing the mosquito vector.
Microbial communities in Antarctic lakes: Entirely new perspectives from metagenomics and metaproteomics
Authors: Yau Sheree , Cavicchioli Ricardo
Published: April 2020

Driven by advances in DNA sequencing technologies, an astounding amount of data is being generated from genetic material sourced directly from the environment, and this exponential growth of data is set to continue. By surmounting the challenges of working with such vast datasets, a whole new level of understanding is being gained about microbial diversity, microbial evolution and whole ecosystem function. For precious, pristine and logistically difficult to obtain Antarctic samples, metagenomic and metaproteomic approaches are providing the basis for fundamental new discoveries about how Antarctic systems function.
Comparative genomics in the wine bacterium Oenococcus oeni
Authors: Borneman Anthony R , Bartowsky Eveline J
Published: April 2020

The production of wine from grape juice relies on the combined actions of both yeast and bacteria which shape the aroma and flavour of wine through the production of secondary metabolites and the biochemical transformation of many grape-derived constituents. Whereas the principal wine yeast, Saccharomyces cerevisiae, is primarily involved in the alcoholic fermentation in which glucose and fructose are converted into alcohol, the wine bacterium, Oenococcus oeni, is primarily involved in a secondary fermentation reaction where malic acid is decarboxlyated into lactic acid. This conversion, known as malolactic fermentation (MLF), results in an increase in wine pH and reduction in the sourness of the wine, while also providing microbial stability through the reduction of potential carbon sources for wine spoilage bacteria such as Lactobacilli and Pediococci1. In addition to its primary role in performing MLF, the metabolic by-products produced during the growth of O. oeni in wine have been shown to positively contribute to the flavour and mouth feel of wines which have undergone MLF.
Molecular epidemiology of noroviruses and sapoviruses and their role in Australian outbreaks of acute gastroenteritis
Authors: White Peter , Eden John-Sebastian , Hansman Grant
Published: April 2020

Every winter since 2004, (except 2005) there have been outbreaks of acute gastroenteritis across Australia, caused by norovirus (NoV). These outbreaks are frequently seen in aged-care facilities, hospitals and cruise ships. Why has this become the norm and what has happened in virological terms to cause this? A single genetic lineage of NoV has emerged as the major cause of pandemic and epidemic viral gastroenteritis. The first reported pandemic of acute gastroenteritis occurred in 1996, discovered through the advent of molecular detection assays. Following a second pandemic in 2002, NoV-associated pandemics of gastroenteritis have occurred with increasing frequency. Here we describe the current molecular epidemiological trends of human NoV, and its milder cousin, sapovirus (SaV), and explain why, in particular, NoV has become the biggest player in the field of viral gastroenteritis. With encouraging results from the first vaccine trial recently reported and continuing research towards the development of vaccines and antiviral agents, we ask whether better weapons to fight and deter gastroenteritis viruses will be available in the future?
From Actinomycin onwards: Actinomycete success stories
Authors: Kurtböke Ipek
Published: April 2020

The discovery, development and exploitation of antibiotics was one of the most significant advances in medicine in the 20th century. In a golden era lasting from the 1940s to the late 1960s, antibiotic research provided mankind with a wide range of structurally diverse and effective agents for the treatment of microbial infections. Since then, the members of the order Actinomycetales, most notably the genus Streptomyces have proved to be a particularly rich source of antibiotics (Table 1) with extensive therapeutic applications, possibly because of the extra-large DNA complement of these bacteria.
The millennium bugs
Authors: Fisher Paul R
Published: April 2020

In the first decade of the new millennium, microorganisms continued to have a disproportionately large impact on biomedical science, not so much because they cause disease but because they provide tractable models in which to study fundamental cellular processes. They have featured in Nobel Prizes every year this century except 2004 and 2010. Of the nine non-mammalian model organisms recognised in the first years of the millennium by the NIH for their value in biomedical research, four were microbes. Collectively, a nation?s effort in studying these model organisms correlates more strongly with its worldwide scientific impact than research in other fields. Compared to other fields, research on model organisms generates three to four times more publications per funding dollar and is three to four times more likely to be sufficiently significant for publication in Nature or Science. Given the scientific impact and value for money of model organism research, Australia in the third millennium should invest significantly more funds in this type of research.
Vertical Transmission
Authors: Young Paul
Published: April 2020

In this issue of Microbiology Australia, the guest editors Martyn Jeggo and John Mackenzie have assembled an excellent series of contributions around the important concept of "One Health". This is a relatively new label for what is essentially a more holistic view of health that has been around for a very long time.
The Concept of One Health – a holistic approach
Authors: Landford Julia
Published: April 2020

‘One Health’ is a global movement of practitioners and policy-makers to support a better understanding of the ecology of diseases at the animal–human–ecosystem interface. Globally, diseases such as Severe Acute Respiratory Syndrome (SARS), Bovine Spongiform Encephalopathy (BSE) and Highly Pathogenic Avian Influenza (H5N1 HPAI) have resulted in significant human fatalities, animal deaths and multi-billion dollar impacts. Several recent disease events in Australia also highlight the complexity of these issues including outbreaks of Hendra virus in Queensland and northern New South Wales resulting in four human fatalities and dozens of horse deaths. At a broader level, Australia faces ongoing challenges with infectious diseases such as air-borne influenza, antibiotic resistant diseases and food-borne disease outbreaks which have regular impacts on public health. The complexity surrounding transmission of diseases at the animal–human–ecosystem interface highlights the need for multidisciplinary approaches – known as One Health approaches. While there has been some progress with advocacy of One Health in Australia, stronger political will is needed to break down sectoral and disciplinary silos and to enable more effective measures at the operational level.
Bats as a source of emerging zoonotic diseases - the interface with wildlife
Authors: Wang Lin-Fa
Published: April 2020

Emerging infectious diseases (EIDs) are defined as infections that have newly appeared in a population or have undergone a rapid change in incidence or geographic location1. Since 1940s, more than 300 EIDs have been recorded2, most of which are viruses. Approximately 75% of human EIDs originated from animals. Of all the EIDs, zoonoses from wildlife represent the most significant threat to human health. Zoonotic EIDs have been identified in a variety of wildlife animals, including ungulates, carnivores, rodents, primates, bats and other mammal and non-mammal species. AIDS, the most significant EID of modern times, originated from non-human primates. Rodents have long been recognised as an important source of EIDs including hantavirus, plaque and lyme disease3. In the last few decades, bats (Order Chiroptera) have received growing attention as reservoirs for EIDs. Particularly, a number of high profile zoonotic viruses with significant human and animal morbidity and mortality have been linked to bat reservoirs4,5.
Eliminating bovine tuberculosis from Australia
Authors: Cousins Debby
Published: April 2020

Mycobacterium bovis, the causative organism of bovine tuberculosis (TB), has a worldwide distribution. Australia, like most developed countries, recognised the zoonotic risk of bovine TB, and embarked on state control programs to minimise the incidence of disease in cattle in the 1960’s and a national campaign to eradicate the disease in 1970. Veterinarians, physicians and many other different disciplines worked cooperatively in Australia to understand and solve the problem; perhaps a very early example of the One Health concept in action.
Avian influenza and the implication for human infection
Authors: Speers David J
Published: April 2020

Highly pathogenic avian influenza due to H5N1 virus has decimated poultry flocks throughout the eastern hemisphere and resulted in over 600 human infections. Despite the H5N1 virus being endemic in several Asian countries, with ongoing human exposure and infection, efficient human-to-human transmission has not been reported. There is much concern over the pandemic potential of this virus should this transmissibility develop due to its widespread circulation, continued evolution and recent research showing relatively few mutations are needed for airborne mammalian transmission. It is unknown whether the emergence of such a mutated H5N1 virus would cause a pandemic owing to uncertainties of how the virus would behave in humans.
Applied Microbiology and Biotechnology teaching tailored towards regional needs and graduate employment
Authors: Kurtböke Dİ
Published: April 2020

The University of the Sunshine Coast (USC) opened in 1996 and since 1999 held the full university status as well as being the first ‘Greenfield’ university to open in Australia since 1971 (https://my.usc.edu.au/). This status was in line with its mission to become an institution with strong emphasis on sustainability and environmentally friendly regional development while transforming a former cane farm into today’s multi award-winning modern and distinctive sub-tropical architectural structure. Over the past 20 years the university has played a role as an ‘urban catalyst’ in one of the rapidly growing and transforming regions of Australia with a foundational mission statement: ‘To be the major catalyst for the academic cultural and economic advancement of the region: by leadership; by pursuit of international standards in teaching and research; and by responsiveness to the needs of students, staff, community and the environment’.