bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing biosecurity risks from imported materials
Authors: Nunn Mike
Published: April 2020

Biosecurity Australia is responsible for assessing and providing policy advice on the sanitary (animal health) and phytosanitary (plant health) risks arising from imports of people, animals and plants, and other goods and materials entering Australia. Biosecurity Australia meets this responsibility by undertaking import risk analyses (IRAs) to establish policy and by conducting reviews of existing policy as necessary. If Biosecurity Australia assesses the risk of a proposed import as acceptable (with or without risk management measures), it makes a recommendation to the Director of Animal and Plant Quarantine, who makes a determination. The Australian Quarantine and Inspection Service (AQIS) implements this policy determination, by issuing an import permit and ensuring that any recommended risk management measures are undertaken.
The initial laboratory diagnosis of equine influenza in Australia in 2007
Authors: Jeggo Martyn H , Hammond Jef M , Kirkland Peter D
Published: April 2020

Until August 2007, Australia had not recorded an outbreak of equine influenza; indeed, significant quarantine precautions exist to safeguard against such an event. This article outlines the lead up to virus confirmation and the procedures to first test, then contain it.
PC4 laboratory construction: a users’ point of view
Authors: James Greg
Published: April 2020

The Sydney 2000 Olympic Games was a tremendous event for Australia, bringing the world?s best athletes and thousands of visitors to Sydney. As it was a global event with comprehensive media coverage, it also bought to our shores the possibility of terrorist activity. During the period the games were held, the Centre for Infectious Diseases and Microbiology (CIDM) performed laboratory investigations of suspicious substances found at Olympic Games venues and Sydney airport and worked with the Defence Science and Technology Organisation (DSTO) testing air samples, taken at venues, for the presence of bioterrorism agents.
Two approaches to Staphylococcus aureus typing
Authors: O'Brien Frances , Giffard Phil
Published: April 2020

Typing of Staphylococcus aureus is carried out to detect outbreaks, monitor transmission and infer virulence and resistance properties. There are now many different extant typing methods. This article summarises the broad classes of typing approaches and describes two methods. One is based on micro-array technology while the other is based upon the interrogation of polymorphic sites using real-time PCR.
AGAR community and hospital Staphylococcus aureus surveillance
Authors: Pearson Julie
Published: April 2020

Point-prevalence antimicrobial surveillance programmes conducted by the Australian Group on Antimicrobial Resistance (AGAR) from 1986-1999 included consecutive clinical isolates of Staphylococcus aureus regardless of acquisition. Following a reported increase in community-acquired infections caused by methicillin-resistant S. aureus (MRSA) in the literature, AGAR performed the first survey of infections from outpatients, emergency department and general practitioner patients in 2000. Further community surveys were conducted in 2002, 2004 and 2006. In 2005 AGAR performed the first hospital-acquired infections survey (infections acquired more than 48 hours post admission) in part to track community MRSA clones emerging in the hospital setting. This article discusses the focus and main outcomes of the AGAR hospital and community surveys.
Staphylococcus aureus and food borne disease
Authors: Tan Agnes , Hogg Geoff
Published: April 2020

Staphylococcal food poisoning, which usually presents clinically at 2-6 hours post exposure, is attributed to the ingestion of food containing pre-formed staphylococcal enterotoxins (SEs) which are quite resistant to acid and proteolysis. Most cases of staphylococcal intoxication resolve within 24-48 hours, although they may be serious.
Vertical Transmission, November 2008
Authors: Stokes Hatch
Published: April 2020

Planning for the national meeting in Perth is now very much in full swing. As mentioned previously, we hope to make this meeting extra special as the Society will be turning 50 in 2009. We will have the usual impressive array of international speakers that will include Bonnie Bassler as the Rubbo Orator. In addition, the American Society for Microbiology has very generously agreed to sponsor an additional speaker to this meeting to help us celebrate our 50th anniversary. Following an approach from the Perth LOC, I am pleased to be able to announce that Rita Colwell has accepted an invitation to attend the conference and speak. As many of you know, Rita has a number of links to Australia and has attended past meetings.
Infection and preterm birth
Authors: McDonald Helen
Published: April 2020

Preterm birth (PTB) before 37 weeks? gestation remains an important cause of perinatal morbidity and mortality, despite modern advances in obstetric and neonatal care. The causes of spontaneous PTB are multi-factorial; however, infection has been implicated as a significant cause of both PTB and late miscarriage, often with no visible signs or symptoms.
Vertical Transmission, March 2009
Authors: Stokes Hatch
Published: April 2020

In recent years there has been a growing concern about the increasing shortfall in a trained workforce in pathology and related fields. This culminated last October with the release of the, so called, Legg report, entitled The Australian Pathology Workforce Crisis commissioned by the Department of Health and Aging. In the lead up to this report, and following its release, the Pathology Associations Committee (PAC), of which ASM is a member, has been working to revise and update the competency based standards for medical scientists.
Enteric bacteria build-up in effluent irrigated plantations
Authors: Sharma Ajay , Harrower Keith , Ashwath Nanjappa
Published: April 2020

Australia uses more than 70% of re-used effluent as irrigation in playgrounds, parks, golf courses and race courses. This land irrigation is preferred over other methods (wetlands, tertiary treatment and aquifer storage) for being the economical, practical and vastly applicable option. Bacteria (Escherichia coli, and Salmonella spp.), protozoa (Giardia spp. and Cryptosporidium spp.), viruses (Poliovirus, Coxsackie virus and Norwalk virus) and helminths (tapeworms and hookworms) are the major pathogens present in municipal effluent. These enteric pathogens have the potential to enter the food chain and cause health risks. Although enteric pathogens start dying once in contact with aerobic environment, bacterial build-up as well as decay rate should be probed periodically.
Zooxanthellae (Symbiodinium, Dinophyceae) symbioses on coral reefs
Authors: van Oppen Madeleine JH , Burghardt Ingo
Published: April 2020

The large three-dimensional structures that make up coral reefs are primarily the product of calcium carbonate deposition by zooxanthellate scleractinian corals, i.e., stony corals living in symbiosis with dinoflagellate algae of the genus Symbiodinium (a.k.a. zooxanthellae). This photosymbiosis permits fast nutrient cycling in the generally oligotrophic tropical waters.
Mitigation of global climate change – control of greenhouse gas flux by microbes
Authors: Holmes Andrew
Published: April 2020

The role of microbes in ecosystems is generally underappreciated. In any ecosystem microbial biomass represents a large fraction of the macronutrients (C, N, P and S), microbial biochemical activity often dominates transformations of key compounds, and microbial behaviour and physiological activity influence translocation of chemical species. However, perhaps most importantly of all, their rapid growth rates give them a fast feedback response time. Microbes have a greater capacity to participate in ecological feedback mechanisms that contribute to homeostasis than other biological groups. All this means that microbes will be at the forefront of the global response to climate change. They will respond faster and at a larger scale than us. Our generation has the option of managing this global microbial response, either via strategies to adapt to climate change or via introduction of strategies to mitigate climate change.
From wastewater treatment to biorefining
Authors: Rabaey Korneel
Published: April 2020

Wastewater, whether it is domestic or industrial, represents a great opportunity to recover water, energy or chemicals, and nutrients. Today, wastewater treatment is energy-consuming, and does not recover the resources from the wastewater. Bioelectrochemical systems (BESs), which have recently been developed, allow for adequate harvesting of the energy or for the production of high quality chemicals. In this article, the basic principles and opportunities of BESs in the context of wastewater treatment are explained.
Identification of novel drug targets using model organisms
Authors: Brzoska Anthony , Withers Ryan , Turner Kylie , Robinson Andrew , Dizon Nick , Harry Liz , Lewis Peter
Published: April 2020

Antibiotic resistance is an endemic problem within hospitals worldwide, and is becoming an increasing problem within the general community. Traditionally, physicians and the public have relied on the belief that as bacteria acquired resistance to one antibiotic, new drugs would be made available that could be used to combat those infections. The appearance of vancomycin-resistant Enterococcus (VRE) infections in the 1990s, combined with the withdrawal of funding for antimicrobial drug discovery and development by big Pharma, has led to the realisation that we can no longer assume that all infections can be treated with a ?magic bullet?. Recent years have seen the emergence of infections that are resistant to all clinically available antibiotics, including newly released drugs such as tigecycline. The cupboard is bare. Or at least it is heading that way.
Mosquitoes and disease in Australia, what does the future hold?
Authors: Russell Richard C
Published: April 2020

Australia has a history of mosquito-borne disease, with historic accounts of endemic malaria, filariasis and dengue during the 19th and early 20th centuries. Bancroftian filariasis, once relatively prevalent in Queensland, has been eliminated and malaria was declared eradicated from Australia in 1981. However, the endemic flaviruses Murray Valley encephalitis and Kunjin and the alphaviruses Ross River and Barmah Forest, which cause encephalitic and polyarthritic syndromes, respectively, continue to be active. Dengue, although no longer considered endemic, is an ongoing issue for Queensland and exotics such as Japanese encephalitis, chikungunya, West Nile and Rift Valley Fever viruses provide some cause for concern with respect to their possible introduction. Further, climate change has been proposed as likely to bring increased distribution and abundance of vectors and diseases, although regional, rural and residential development may be as much or more important. The various pathogens and the diseases they cause have to be viewed in their particular ecological contexts for a proper understanding of what the future might hold and how we will need to deal with the potential public health issues.
A new arbovirus in northern Australia
Authors: Cowled Christopher
Published: April 2020

Routine arbovirus surveillance has unearthed a number of novel viruses circulating in domestic and wild animals in northern Australia. One of these is a new virus named Middle Point orbivirus (MPOV). While its disease potential remains unknown, evidence suggests that this virus emerged quite recently in Australia and it has now become the single most commonly isolated animal virus in the Northern Territory. The discovery of MPOV highlights the importance of obtaining prototype data on novel Australian viruses.
Horses, humans and Hendra virus
Authors: Field Hume
Published: April 2020

Hendra virus again demonstrated its zoonotic capacity with the infection of two veterinary clinic staff (one fatally) in an outbreak in a Brisbane equine referral veterinary practice in 2008. Bats are recognised as the natural host of the virus.
The research road less travelled
Authors: Gooda Mick
Published: April 2020

If there is one thing that should be clear by now to anyone working in the area of Aboriginal and Torres Strait Islander health, it is that biomedical research carried out in isolation from the Aboriginal and Torres Strait Islander community will not significantly improve health outcomes for Australia?s Indigenous peoples.
Otitis media: an ongoing microbial challenge
Authors: Smith-Vaughan Heidi , Marsh Robyn , Leach Amanda
Published: April 2020

Young Australian Indigenous children in remote Northern Territory communities suffer excessively high rates of otitis media (OM) and remain at high risk of suppurative complications with poor audiological and educational sequelae. Efforts to effectively treat this condition are confounded by the frequent failure of standard antibiotic treatment regimens, despite good therapeutic compliance and susceptibility of the major pathogens. OM has a complex, polymicrobial aetiology. Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are the recognised major pathogens; however, bacteria from at least 15 other genera have been identified in middle ear effusions. It is often unclear whether detection of many of these bacteria is circumstantial, or if they are contributing to the infection either directly, or through competitive or cooperative processes. While culture remains the gold standard for detecting the major pathogens, molecular methods are changing the ways we explore the complex polymicrobial dynamics of OM.
CA-MRSA: emerging remotely
Authors: Tong Steven YC , Giffard Philip M , Holt Deborah C
Published: April 2020

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) was first described in remote Indigenous populations in Australia over 20 years ago. The burden of staphylococcal disease, including S. aureus bacteraemia, disproportionately affects Indigenous populations and is likely related to socio-economic disadvantage. Factors such as domestic crowding, poor hygiene and high rates of scabies, skin sores and antibiotic use contribute to the transmission and emergence of CA-MRSA. Studies focusing on two clones, sequence type (ST) 93 and clonal complex (CC) 75, provide supportive evidence for the emergence of methicillin-resistance in Indigenous communities.
Chlamydial infections and Indigenous health
Authors: Debattista Joseph , Hutton Susan , Timms Peter
Published: April 2020

Chlamydia are obligate, intracellular, bacterial pathogens that cause three main diseases in humans worldwide: sexually transmitted disease (infertility and pelvic inflammatory disease), trachoma and respiratory infections. Rates of sexually transmitted infections (STIs) due to C. trachomatis are increasing (a 61% increase in notifications in Australia between 2003 and 2007) and the levels in Indigenous Australians continue to be unacceptably high: nearly five times higher than in non-Indigenous people. C. trachomatis also causes the ocular disease trachoma and, unfortunately, this condition continues to be common in Indigenous Australians, a situation that is unacceptable in a developed country. The other chlamydial species that infects humans is C. pneumoniae. While clinically less severe, the Australian Aboriginal population in the Top End have high rates of serologically diagnosed C. pneumoniae infection, which may contribute to the higher rates of respiratory disease observed in this group.
Challenging STIs in remote Central Australia
Authors: Huang Rae-Lin , Torzillo Paul J
Published: April 2020

Sexually transmitted infections (STIs) are endemic in remote Central Australia in Aboriginal communities, but usually don?t prompt individuals to seek testing or treatment. Untreated, a proportion of such infections result in ectopic pregnancies, miscarriages, infertility and enhanced transmission of HIV. The majority of STIs in Central Australia can be diagnosed with current nucleic acid amplification test (NAAT) technologies and treated with single-dose antibiotic treatment. Successful long-term STI control has been achieved in some areas of remote Central Australia by increasing access to testing and treatment for STIs as part of a comprehensive program. Successful control of gonorrhoea also depends on adequate antimicrobial surveillance, which is particularly difficult to achieve in remote areas of Australia.
Detecting the dual presence of AmpC and ESBL enzymes
Authors: Sfakinos John
Published: April 2020

Inducible-chromosomal AmpC cephalosporinase enzymes have been recognised for several years in the ESCAPPM (Enterobacter spp., Serratia spp., Citrobacter freundii, Acinetobacter spp., Proteus vulgaris, Providencia spp. and Morganella morganii) group of gram-negative organisms, which result in the potential resistance to third-generation cephalosporin drugs. More recently several non-ESCAPPM Enterobacteriaceae (particularly E coli, Klebsiella and Proteus mirabilis) have been found to harbour a non-inducible-plasmid form of AmpC. This is particularly important when found in bacteremic patients where third-generation cephalosporins are often the first line drugs of choice.
Practicum and work experience in microbiology and related disciplines
Authors: Schliephake Kirsten , Mosse Jennifer
Published: April 2020

Gaining hands-on experience throughout an under graduate degree is regarded as a competitive advantage by science students. At the Gippsland campus of Monash University, the Industry Placement Program (IPP) allows students to gain industry experience throughout their entire course. Science students enrolled in the IPP undertake a practicum learning experience, equivalent to a 12-point unit, whose emphasis is on identifying and building transferable skills while gaining technical competency. The combination of academic studies, relevant paid work experience and professional development training produces capable, work-ready graduates.
Catalysing interdisciplinary and integrative thinking through the scholarship of teaching and learning
Authors: Takayama Kathy
Published: April 2020

Science by its very nature is interdisciplinary and scientific research relies on the collaborative skills and expertise of researchers across the disciplines. Yet, science as taught in the university classroom is usually compartmentalised into separate subjects. Most undergraduate students are not exposed to the excitement and challenge of connecting the concepts, skills and processes learnt within these distinct disciplines until they enter the laboratory as an honours student. Indeed, opportunities for problem-solving, novel application of concepts, articulation of the broader impacts and societal benefits of scientific research and understanding are not usually explicitly designed and scaffolded as an integral part of the university syllabus, but these lifelong skills are essential for scientific thinking. Furthermore, one of the most crucial elements that nurtures scientists? engagement and creativity is seldom considered an essential component of the curriculum ? the interaction with local, national and international peer communities to share, to receive feedback and to foster new ideas and collaborations. Considered from a holistic perspective, many academics tend to focus on content, while the process of scientific inquiry is peripheral to the formal syllabus. The scholarship of teaching and learning brings the focus back to inquiry thinking and learning, by prompting academics to critically engage with the pedagogical process.
Finding the right balance in the delivery of undergraduate biology programs: a personal perspective
Authors: Young Paul
Published: April 2020

Universities, and indeed the wider community, are facing a huge challenge with what has been referred to as the ?flight from science? of recent generations of students. This trend began some 2 decades ago and has become an acute problem in recent years. It could be argued that it has come at a time when there has never been a greater need by society for graduates with the scientific expertise to address the big issues now confronting us. The potential impact of global warming, the continuing emergence of new disease threats, the advent of cutting-edge cloning and stem cell technologies are all challenging both practical and ethical boundaries requiring considered debate and engagement. Yet, we still aren?t attracting into science enough of our ?best? students, nor are we retaining enough of them once they choose to undertake an undergraduate science program.
Biodiscovery and industrial applications of microbial resources
Authors: Kurtboke Ipek , Mcreadie Ian
Published: April 2020

This issue of Microbiology Australia focuses on an aspect of microbiology increasingly becoming important to us microbiologists ? the applied and industrial microbiology. The majority of microbiologists in the global context are in the business of dealing with the challenges that microorganisms bring to society involving processes and products that are of major economic, environmental and social importance. These include production of valuable microbial products via fermentation processes such as fermented foods, beverages and dairy products as well as direct application of microorganisms or their products in environmental and biotechnological operations. In addition, over the past 20 years, many traditional and established industrial fermentation processes have advanced through the contribution of genetic engineering, which has facilitated the development of many novel processes and products.
Endophytes and the microbial genetics of traditional medicines
Authors: Miller Kristin I , Ingrey Shane D , Alvin Alfonsus , Sze Man Yuen Daniel , Roufogalis Basil D , Neilan Brett A
Published: April 2020

Traditional medicine continues to play an essential role in the healthcare systems of many cultures. In some Asian and African countries up to 80% of the population depend on these ancient and culturally based medicinal practices for their primary healthcare needs. Plants and their derived natural products are frequently employed as traditional medicine and such plants are viewed as attractive targets for the discovery of novel therapeutic agents in natural product investigations. A variety of useful drugs has been discovered following the investigation of traditional herbs, such as morphine (analgesic), digitoxin (cariotonic) and ephedrine (sympathomimetic). These ethnopharmacology approaches to drug discovery are based on the premise that plants used as traditional medicines have shown some form of bioactivity and have the increased likelihood of containing bioactive compounds in comparison to plants selected at random. Three systems of traditional medicine that are relevant to Australian drug discovery researchers include the Chinese, Australian Aboriginal and Indonesian systems.
Australian microbial biodiscovery: from bugs to drugs
Authors: Capon Robert J
Published: April 2020

To maintain and improve the quality of life offered by modern healthcare requires an ongoing commitment to the development of new drugs, to improve and replace those that have become less effective, and to bring to the community safer treatments for an ever-wider array of important diseases. Irrespective of the specific medical need, the drug discovery pipeline is critically dependent on access to diverse, high-quality molecular libraries capable of inspiring drug-led discovery, and ultimately new drugs. A poor choice of chemistry leads to wasted resources and no drugs. Historically the pharmaceutical industry has relied heavily on microbial natural products, which represent an extraordinarily diverse, preassembled pool of biologically active molecules, programmed to be potent and selective modulators of key biopolymers, cells, tissues, organs and animals. Knowledge of Nature?s intellectual property, gleaned from the evolutionary equivalent of a billion-year global drug discovery program, with an unlimited budget and a workforce of trillions, can disclose privileged bioactive structures that inform, guide and inspire modern drug discovery, re-purposing ecological advantage to pharmaceutical benefit.
A tribute to Professor Arnold L Demain – a lifetime in industrial microbiology
Authors: Britz Margaret
Published: April 2020

Professor Arnold (Arny) Lester Demain is one of the few scientists who have witnessed the progress of biotechnology in a career that has spanned almost 60 years. He is one of the world?s leading industrial microbiologists who has pioneered discovery in genetic and nutritional regulation of biosynthetic pathways leading to overproduction of a suite of primary and secondary metabolites, and their subsequent scale-up in manufacturing processes. These metabolites have huge economic value due to their application in the food, pharmaceutical and agricultural sectors. In this article, Arny?s story is summarised and put in context of the changing face of biotechnology in the various ?golden ages? of biotechnology. A former Rubbo Orator in 1979, Arny will be visiting Australia again in 2010 to present the closing plenary address at the Genetics of Industrial Microorganisms Symposium (GIMS) in Melbourne, a role he played before at the first GIMS in 1970.
Diagnostic microbiology in the 21st century – a quiet revolution
Authors: Kok Tuckweng , Gosbell Iain B
Published: April 2020

It is a very exciting time to be a microbiologist. In the early 21st century we are seeing a maturation of molecular biology methods and their translation into the clinical microbiology laboratory, in combination with improvements in existing methods and substantial increases in the power of information technology.
A pragmatic approach to screening for transmissible resistance in the Enterobacteriaceae
Authors: Ellem Justin , Iredell Jon
Published: April 2020

Determining the origin, spread and characteristics of important resistance genes and plasmids in Gram-negative bacteria may be more informative than determining the epidemiology of bacteria themselves. Infection control resistance surveillance and containment efforts should focus on the transmission characteristics of the resistance rather than those of the index organism at the point of recognition.
Detection and diagnosis of new pathogens
Authors: Sloots Theo P
Published: April 2020

Molecular laboratory techniques are widely used to detect new or previously unrecognised agents which are implicated in infectious disease. In many cases, the traditional microbiology techniques are inadequate and commonly fail to uncover the aetiologic agent, particularly new viruses that continue to challenge the human population. Metagenomics-based tools, such as microarrays and high-throughput deep sequencing are increasingly applied and are ideal for the identification of new human pathogens, particularly viruses.
Vertical Transmission, November 2010
Authors: Turnidge John
Published: April 2020

Many of you would have heard about the difficulties the Society has been experiencing in the National Office over recent months. We have had a number of resignations; first our executive officer, then our conference manager and most recently our office manager. As I outlined in the last Vertical Transmission, in order to cope with the resignation of our conference manager in May (two months before the Sydney meeting), we were required to call in an experienced professional conference organiser (ICMS) to ensure that the Sydney meeting did not suffer in terms of organisation over such a crucial period. Hopefully, you will agree that the meeting ran successfully given these circumstances.
Biocide use, integrons and novel genetic elements
Authors: Gillings Michael R
Published: April 2020

Resistance to antibiotics threatens our ability to control bacterial pathogens. It is clear that the persistence of cells containing resistance determinants is promoted by the strong selective pressure imposed by antibiotic use. This problem has been exacerbated by inappropriate and excessive use of antibiotics in both medicine and animal production. Concern has also been raised that inappropriate use of biocides contributes to the selection of resistant bacterial strains. This may occur because detoxification mechanisms for biocides and antibiotics are shared, or via selection for biocide resistance genes that are physically linked to antibiotic resistance genes and their mobile DNA vectors. In this brief review I will illustrate the latter phenomenon using the evolutionary history of the class 1 integron as an example, and then examine whether the increasing trend towards indiscriminate use of biocides in homes and consumer products might result in the selection of novel genetic elements that will have negative and unpredictable consequences for human health.
A universal influenza vaccine – are we almost there?
Authors: Hampson Alan W
Published: April 2020

Seasonal influenza has a significant health care and economic impact and pandemic influenza is believed to have the potential to result in a global catastrophe. Regardless of developments with antivirals, vaccination remains the most effective option for limiting the impact of both seasonal and pandemic influenza.
Herpes simplex virus vaccines
Authors: Cunningham Anthony L , Jones Cheryl A , Kim Min
Published: April 2020

Herpes simplex virus (HSV) types 1 and 2 cause herpes labialis and genital herpes respectively, although genital herpes caused by HSV-1 is increasing in adolescence. Adult HSV-1 seroprevalence in western countries is 55% to 80% (80% in Australia) and acquired in two peaks, in infancy and adolescence. HSV-2 seroprevalence is highly variable geographically, reaching 12% in Australian adults but up to 90% in African countries. After initial HSV-1 or 2 infection, asymptomatic shedding occurs in the mouth and genital tract respectively in nearly all infected subjects. Complications of HSV-1 include keratitis and blindness and life-threatening encephalitis. Severe complications of HSV-2 include acute urinary retention, meningitis and neonatal herpes (25% fatality). In addition, prior infection with HSV-2 consistently enhances HIV acquisition three- to fourfold. In immunosuppressed persons, HSV-1 and 2 may cause indolent ulcers, oesophagitis and pneumonia. Ultimately, a childhood vaccine effective against both HSV-1 and 2 disease is needed.
From omics to systems biology: Exploring the mystery box of microbial life
Authors: Ostrowski Martin , Tetu Sasha , Hassan Karl , Penesyan Anahit , Lim Kent , Elbourne Liam , Li Liping , Varkey Deepa , Paulsen Ian
Published: April 2020

Microbial molecular biology has traditionally used very reductionist approaches; for example, find a gene of interest, clone it or knock it out and see if you can detect a phenotype. The genomics era has opened up the possibility of analysing microbes and communities at a systems level by combining high-throughput experimental data from genomic, transcriptomic, proteomic and phenomic techniques. This parallels earlier reductionist approaches by going from DNA to RNA to protein to phenotype, albeit on a global rather than individual gene scale.
Yeast as a system for systems biology
Authors: Dawes Ian W , Lee Johhny C-Y , Tsoi Abraham M-C , Kornfield Geoffrey D , Ayer Anita
Published: April 2020

There are almost as many definitions of systems biology as there are workers in the field and we won?t attempt to add any further definition. In order to obtain an holistic view to the functioning of all of the processes in a cell, it is important to obtain sufficient data to understand the relationships between the many components that make up the cell.
Microbial proteomics: how far have we come?
Authors: Cordwell Stuart J
Published: April 2020

It is now over 15 years since the beginning of the microbial genome era. At that time, great interest was invested in the idea of understanding bacterial genome dynamics via the analysis of their protein components or 'proteomes'. As bacterial analysis had driven the early advances in genomic squencing, these organisms were amongst the first subjected to protein-based studies. it is fair to suggest in hindsight that the original hype did not match the outcomes. At that time the term proteome was coined, en masse protein analysis meant little more than two-dimensional electrophoresis gels and mainly Edman sequencing for protein identification. As such, only the most abundant cellular constituents could be analysed and interest soon turned for many researchers towards microarray-based transcriptomics where a much greater percentage of the genome could be surveyed. Despite this, substantial and continuing evidence has demonstrated that transcript and protein levels (and, of course, the associated substrates and products of the predicted protein functions) often do not correlate. Therefore, a truly ?systems biology? organism-wide approach is necessary, where genomics, transcriptomics, proteomics and metabolomics are integrated to understand how microbes respond to changes in their genetic or physiological environments, and thus generate new hypotheses for functional understanding. This article will examine how proteomics technology has evolved to the stage at which the total proteome can be elucidated, and provide a guide for ?best practice? for undertaking successful proteomics analyses.
First Words
Authors: Davison Elaine
Published: April 2020

With more than 7 million mouths to feed, world food security (insecurity would be a better description), is high on the international radar. In his article, Les Baxter points out that the term food security means that sufficient quantities of food must be available, that people must have sufficient resources to obtain nutritious food, that it is used appropriately, and that a consistent food supply is not subject to sporadic or periodic shocks. Plant pathogens adversely affect all of these factors. They reduce the quantity and quality of food, they reduce income through reduced marketable yield, and disease epidemics result in sporadic reductions in food supply.
Future planning for capacity in plant pathology
Authors: Hirsch Mikeal
Published: April 2020

We are all familiar with the three constants of life: death, taxes ? and strategic planning. As professionals, we are frequently getting involved in developing vision statements, strategies for change, action plans, performance indicators, impact metrics, review processes and so on. Strategic planning goes in cycles. At the national level we are now engaged in a new exercise, setting broad directions for the future of rural research and, in particular, biosecurity science. This is likely to impact on the future of professionals in microbiology and beyond. As always with these exercises, it is the ?journey? rather than the ?destination? that is important, as it enables us to take stock and reflect on where we are heading in terms of future capacity. This paper outlines some of these planning activities and earlier findings, with a focus on future capacity in plant pathology, but the lessons apply to all readers of this journal. It is important that members of the Australian Society for Microbiology (ASM) and other professional societies engage in these strategic planning efforts to shape our own future.
Microbial threat– a growing challenge for plant biosecurity
Authors: McKirdy Simon , Rodoni Brendan , Moran Jane , Sharma Shashi
Published: April 2020

Australia is relatively free from many of the plant pathogens that seriously impact on agricultural production and natural environment in other countries. This provides a valuable competitive advantage for Australia?s plant industries in terms of securing market access and maintaining lower production costs. The increasing growth in global trade, travel and tourism is exposing Australia?s plant industries and environment to ever-increasing risk of exotic microbial pathogens. At risk are approximately $14 billion per annum in crop exports, the environment and its associated tourism, the sustainability of regional communities with plant industries contributing approximately $25 billion annually, and indirectly animal and human health and safety. In addition, biosecurity threats are recognised as a serious risk to global food security.
Death by toxin net blotch disease of barley
Authors: Wong Darren CJ , Ismail Ismail A , Godfrey Dale , Abe Amanda J
Published: April 2020

Barley net blotch is a destructive disease which results in loss of yield (as high as 40%) and quality in barley grain, the world?s fourth largest crop. In Australia, the economic losses caused by net blotch disease have been predicted to be greater than $62 million per year.
First Words
Authors: Bishop Ruth , Kirkwood Carl
Published: April 2020

Acute gastroenteritis is a common illness occurring in the neonatal period and throughout life in humans and animals. Infections with viral, bacterial or protozoal pathogens can precipitate the rapid onset of life-threatening symptoms, including diarrhoea, vomiting, fever and dehydration due to fluid and electrolyte loss.
Rotavirus infection in Northern Territory before and after vaccination
Authors: Snelling Thomas , Markey Peter , Carapetis Jonathan , Andrews Ross
Published: April 2020

Globally, rotavirus vaccines have been found to have reduced effectiveness in resource-poor and high disease burden settings. Prior to vaccination, the burden of rotavirus gastroenteritis was substantially higher among Indigenous children in the Northern Territory (NT) than among other Australian children, giving rise to concern about the likely impact of vaccination in this population. Post-licensure studies in the NT indicate that vaccination protects infants against hospitalisation in this setting, but vaccine effectiveness (VE) among older children and against heterotypic serotypes needs to be more clearly determined.
Use of bacterial vaccines in the livestock industries
Authors: EL-Osta Youssef Abs , Youil Rima
Published: April 2020

The prophylactic use of antibiotics in animal feed has been a long-held practice in intensive livestock production for maintaining animal health by controlling disease and promoting growth enhancement. However, the continuous use of antibiotics has evoked strong concerns over emergence of antibiotic-resistant bacteria. There has been a concerted effort over the years by US, EU and Australian legislative authorities to reduce or eliminate prophylactic use of antibiotics in animal feed. In principle, these efforts are commendable; however, an alternative and effective method to managing disease must be available to ensure the health and welfare of livestock. There will likely be a greater reliance on vaccination programs to protect livestock from various infectious diseases. With respect to bacterial diseases, bacteria themselves form the core of vaccine development. In this article, an overview of bacterial vaccine technologies available to the livestock industries will be presented.
The role of One Health in understanding and controlling zoonotic diseases in Australia
Authors: Coghill Adrian , Black Peter , Schipp Mark
Published: April 2020

One Health recognises that the health of humans, animals and ecosystems is intimately connected. One Health involves a coordinated, collaborative, multidisciplinary and cross-sectoral approach to addressing a wide range of potential or existing risks at the animal–human–ecosystem interface. Globally, a surge in emerging infectious diseases and their associated costs to society over the last 15 years has reignited interest in the idea that human health is linked to animals and our shared environment. In 2004 at the meeting Building Interdisciplinary Bridges to Health in a Globalized World held in New York, the 12 Manhattan Principles were defined to guide scientists and policy makers to "devise adaptive, forward-looking and multidisciplinary solutions to the challenges that undoubtedly lie ahead". These principles remain fundamental in defining the role of One Health.
infection: the next big thing!
Authors: Squire Michele M. , Riley Thomas V.
Published: April 2020

Clostridium difficile causes infectious diarrhoea in humans and animals. It has been found in pigs, horses, and cattle, suggesting a potential reservoir for human infection, and in 20-40% of meat products in Canada and the USA, suggesting the possibility of food-borne transmission. It is likely that excessive antimicrobial exposure is driving the establishment of C. difficile in animals, in a manner analogous to human infection, rather than the organism just being normal flora of the animal gastrointestinal tract. Outside Australia, PCR ribotype 078 is the most common ribotype of C. difficile found in pigs (83% in one study in the USA) and cattle (up to 100%) and this ribotype is now the third most common ribotype of C. difficile found in humans in Europe. Human and pig strains of C. difficile are genetically identical in Europe confirming that a zoonosis exists. Rates of community-acquired C. difficile infection (CDI) are increasing world-wide, and a new community strain of unidentified origin has recently emerged in Australia. Environmental contamination may also play a role. C. difficile spores survive in treated piggery effluent, the by-products of which are used to irrigate crops and pasture and manufacture compost. There is abundant evidence that food products intended for human consumption contain toxigenic strains of C. difficile but food-borne transmission remains unproven. Thus there are four problems that require resolution: a human health issue, an animal health issue and the factors common to both these problems, environmental contamination and antimicrobial misuse.
Cat scratch disease in Australia
Authors: Flexman James
Published: April 2020

Companion animals such as cats are important for their health benefits. However, one of the risks of bringing cats into the household is cat scratch disease (CSD), with kittens or stray cats posing the highest risk. CSD is a clinical syndrome caused mainly by Bartonella henselae and is characterised by regional lymphadenopathy in patients with a history of close cat contact within three months of onset of symptoms. In most cases, CSD is a benign, self-limited infection, with more severe infections occurring only rarely in immunocompetent people. However, in immunocompromised patients, including those post-organ transplantation or with advanced HIV infection, the disease can be more severe and avoiding exposure needs to be considered. Improving flea control is also important, as transmission among cats occurs via the cat flea Ctenocephalides felis. To add to the data on B. henselae in Australia, I will report on some previously unpublished data on the seroprevalence and percentage of culture positives in WA domestic cats.
How rapidly do pathogens decay in sewage sludge treatment?
Authors: Rouch Duncan , Thurbon Nerida , Fleming Vennessa , Mondal Tania , Chellappan Sriharini , Khallaf Basma , Kong Fred , Zeng Shengxi , Deighton Margaret , Smith Stephen
Published: April 2020

Can sewage sludge be treated for shorter times than those currently required by national regulations? Key plant nutrients are lost by long-term storage of biosolids. Shorter treatment times are desirable, provided microbiological safety is assured. We have, therefore, investigated decay times of key pathogens present in raw sewage.
Culture Media SIG
Authors: Traynor Peter
Published: April 2020

The Culture Media Special Interest Group of the Australian Society for Microbiology was formed in 1991 by a group of interested individuals after an upsurge in interest in the issue of media quality and the appearance that no common standards or consensus existed in this area in Australia. Increased interest, especially amongst medical microbiologists, in what was being done, or should be done, by way of assuring the quality of microbiological media made the issue contentious.
Vertical Transmission
Authors: Iredell Jonathan
Published: April 2020

Increasing diversity in the general area of Microbiology is welcome and inevitable. The modern microbiologist is a mathematician or an experimentalist, an ecologist or a cell biologist, a geneticist or a population biologist. Rather than concern ourselves with a narrowing definition, we must aim for inclusiveness and opportunity. Maree Overall in the National Office and Cheryl Power, our Vice President (Corporate affairs), have undertaken an analysis of the declared interests of the members of the Society (many Society members listing more than one interest, of course), and there are obvious groupings of several hundred each.
Parasitic infections: overlooked, under-diagnosed and under-researched
Authors: Sheorey Harsha , Bradbury Richard S
Published: April 2020

Professor George Nelson (1924–2009) once stated that, ‘Parasitology is the preserve of the diagnostically destitute’. Little has changed to this day, with potentially relevant parasitic causes of illnesses often not being considered early in the differential diagnoses of clinical presentations. Parasitic infections are sometimes overlooked as causes of morbidity and (in some cases) mortality in both the medical and veterinary fields. In Australia there remain significant problems associated with giardiasis, cryptosporidiosis, strongyloidiasis and other parasitic diseases, particularly in remote, underserved and tropical regions of the country and also in the immuno-compromised individuals (HIV, immunosuppressive drugs etc.). The burden of many parasitic diseases is greater in tropical and sub-tropical areas of non-industrialised countries. With increasingly adventurous travel and dining, increasing numbers of Australians returning from travel overseas with added souvenirs of common or exotic parasitoses every year and refugees and migrants arriving in Australia, these infections are becoming increasingly important.
Vertical Transmission
Authors: Iredell Jonathan
Published: April 2020

The Australian Society for Microbiology has remained broad based for the many decades of its existence. In the absence of a publishing house to underwrite it, we continue to hold regular meetings and maintain a strong membership.
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

As this is my first communication for 2017, I will begin by wishing you a happy and prosperous New Year.
Bat-associated diseases
Authors: Marsh Glenn A
Published: April 2020

Emerging infectious diseases pose a significant threat to human and animal health. Increasingly, emerging and re-emerging infectious diseases are of zoonotic origin and are derived from wildlife. Bats have been identified as an important reservoir of zoonotic viruses belonging to a range of different virus families including SARSCoronavirus, Rabies virus, Hendra virus, Nipah virus, Marburg virus and Ebola virus.
Vale Sue Dixon
Authors: Davey George
Published: April 2020

Friends and colleagues of Sue Dixon were saddened to hear of her passing in August 2016 after a short illness. Sue was born on 10 January 1928 in Malvern, Adelaide. After graduating from Unley High School she commenced her career in microbiology as a laboratory assistant cleaning test tubes at the then recently established Institute of Medical and Veterinary Science (IMVS). Sue was awarded a cadetship by the IMVS to study at Adelaide University where she graduated with a BSc in 1949. From 1949 to 1952 Sue worked as a bacteriologist at the IMVS and then resigned to start a family. After rejoining the IMVS in 1960 Sue assumed responsibility for the National Salmonella Reference Centre established by her mentor and good friend the eminent Dr Nancy Atkinson. From 1967 until her retirement in 1983 Sue was the head of the Salmonella Reference Laboratory (SRL) and Food
Hygiene Laboratory at the IMVS.
Public Health
Authors: Smith Helen V
Published: April 2020

This issue of Microbiology Australia looks at some evolving aspects of microbiology as it relates to Public Health in Australia.
Vertical Transmission
Authors: Robins-Browne Roy
Published: April 2020

Dear fellow microbiologists, I suspect that this is my last contribution to Microbiology Australia
in my present role.