bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical implications of decision making in colorectal polypectomy: an international survey of Western endoscopists suggests priorities for change
Authors: Tate David J. , Desomer Lobke , Heitman Steven J. , Forbes Nauzer , Burgess Nicholas G. , Awadie Halim , Gralnek Ian M. , Geldof Jeroen , De Looze Danny , Rex Douglas , Anderson John , Bourke Michael J.
Published: April 2020

Introduction Colonoscopy prevents colorectal cancer via the detection and resection of premalignant polyps. This effect may be attenuated by variations in polypectomy, with multiple techniques available and a wide range of experience amongst endoscopists. We assessed current practice against the best available contemporary evidence.

Methods An online survey was distributed to members of the gastroenterological and surgical societies of seven countries during July 2017. Images of colorectal polyps were presented and respondents requested to provide the polypectomy technique they would employ in their daily practice. Responses were compared to the evidence-based techniques in the 2017 ESGE Colorectal Polypectomy Guideline.

Results In total, 707 endoscopists (627 physicians, 71 surgeons, 9 nurse endoscopists, median practice duration 18 years) completed the survey. Of these, 3.1 % selected hot biopsy forceps and 5.2 % hot snare polypectomy (without submucosal lifting) to remove a 3 mm ascending colon polyp. Only 43.3 % selected cold snare polypectomy (CSP) to remove an 8 mm ascending colon polyp. Surgical referral was selected by 16.7 % of respondents for a 45 mm transverse colon polyp without endoscopic evidence of submucosal invasive cancer (SMIC). Endoscopic resection was selected by 12.0 % for an 80 mm sigmoid polyp with imaging consistent with deep SMIC, and a further 26.4 % selected tertiary endoscopist referral, suggesting they had not appreciated that it was endoscopically unresectable.

Conclusion CSP is underutilized for small polyp resection despite its favorable safety and efficacy. Benign polyps are commonly referred for surgery and overt SMIC is underappreciated using endoscopic imaging. Addressing these issues may reduce diathermy-related adverse events, surgery, and unnecessary colonoscopic procedures for patients and reduce rates of post-colonoscopy colorectal cancer.
Impacto femoroacetabular e lesão do lábio acetabular - Parte 1: Fisiopatologia e biomecânic
Authors: Ejnisman Leandro , Ricioli Júnior Walter , Queiroz Marcelo Cavalheiro , Vicente Jose Ricardo Negreiros , Croci Alberto Tesconi , Polesello Giancarlo Cavalli
Published: April 2020

O impacto femoroacetabular (IFA) é uma importante causa de dor no quadril, e a principal etiologia da osteoartrose do quadril no jovem. O IFA é caracterizado por alterações sutis da anatomia do acetábulo e do fêmur proximal que podem causar lesões do complexo condrolabial. O lábio é uma estrutura fibrocartilaginosa essencial na estabilidade articular. Três tipos de IFA são descritos: came (onde há uma anesfericidade da cabeça femoral), pincer (onde há uma sobrecobertura acetabular) e misto (que apresenta características de ambos). A etiologia do IFA está relacionada com características genéticas e ambientais. O conhecimento desta doença e sua fisiopatologia é essencial para o tratamento de pacientes que apresentam dor no quadril.
A Nationwide Enumeration of Operations Performed for Pediatric Patients in Ghana
Authors: Gyedu Adam , Stewart Barclay , Gaskill Cameron , Salia Emmanuella , Wadie Raymond , Abantanga Francis , Donkor Peter , Mock Charles
Published: April 2020

Introduction Currently, there are no existing benchmarks for evaluating a nation's pediatric surgical capacity in terms of met and unmet needs.

Materials and Methods Data on pediatric operations performed from 2014 to 2015 were obtained from a representative sample of hospitals in Ghana, then scaled up for national estimates. Operations were categorized as “essential” (most cost-effective, highest population impact) as designated by the World Bank's Disease Control Priorities versus “other.” Estimates were then compared with pediatric operation rates in New Zealand to determine unmet pediatric surgery need in Ghana.

Results A total of 29,884 operations were performed for children <15 years, representing an annual operation rate of 284/100,000 (95% uncertainty interval: 205–364). Essential procedures constituted 66% of all pediatric operations; 12,397 (63%) were performed at district hospitals. General surgery (8,808; 29%) and trauma (6,302; 21%) operations were most common. Operations for congenital conditions were few (826; 2.8%). Tertiary hospitals performed majority (55%) of operations outside of the essential category. Compared with the New Zealand benchmark (3,806 operations/100,000 children <15 years), Ghana is meeting only 7% of its pediatric surgical needs.

Conclusion Ghana has a large unmet need for pediatric surgical care. Pediatric-specific benchmarking is needed to guide surgical capacity efforts in low- and middle-income country healthcare systems.
Resultados funcionais do tratamento artroscópico no impacto femoroacetabular em pacientes com mais de 60 anos em comparação com pacientes com 40 anos ou menos
Authors: Aguilera-Bohórquez Bernardo , Brugiatti Miguel , Coaquira Ruddy , Cardozo Orlando , Cantor Erika
Published: April 2020

Objetivo Avaliar os resultados funcionais de pacientes diagnosticados com impacto femoroacetabular (IFA) e com mais de 60 anos de idade em comparação aos resultados de pacientes com até 40 anos de idade.

Métodos Esta é uma revisão retrospectiva de pacientes com IFA submetidos à artroscopia do quadril entre 2010 e 2015. Os pacientes eram adultos com mais de 60 anos de idade e Tönnis ≤ 1, alocados na proporção de 1:1 com adultos de até 40 anos de idade, de acordo com o tipo de deformidade (came, pincer, ou misto), sexo e data de realização da cirurgia.

Resultados Trinta e quatro pacientes foram incluídos em cada grupo. A idade média foi de 30,6 ± 6,9 anos e 65,6 ± 4,6 anos nos grupos controle e de casos, respectivamente. Não houve diferenças significativas entre os grupos no acompanhamento de 1 ano (p > 0.05). No primeiro ano após a cirurgia, a pontuação Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) passou de 46,3 para 22,0 no grupo de pacientes mais velhos (casos) e de 38,1 para 7,2 no grupo controle em comparação ao estágio pré-operatório.

Conclusão O grupo de pacientes com até 40 anos de idade apresentou uma mudança considerável na pontuação WOMAC, mas sem significado estatístico em comparação ao grupo de pacientes acima de 60 anos. Essa observação sugere que a artroscopia do quadril é benéfica quando a seleção de pacientes com IFA é apropriada, independentemente da idade dos indivíduos.
Microfluidic methods for precision diagnostics in food allergy
Authors: Castaño Nicolas , Cordts Seth C. , Nadeau Kari C. , Tsai Mindy , Galli Stephen J. , Tang Sindy K. Y.
Published: April 2020

Food allergy has reached epidemic proportions and has become a significant source of healthcare burden. Oral food challenge, the gold standard for food allergy assessment, often is not performed because it places the patient at risk of developing anaphylaxis. However, conventional alternative food allergy tests lack a sufficient predictive value. Therefore, there is a critical need for better diagnostic tests that are both accurate and safe. Microfluidic methods have the potential of helping one to address such needs and to personalize the diagnostics. This article first reviews conventional diagnostic approaches used in food allergy. Second, it reviews recent efforts to develop novel biomarkers and in vitro diagnostics. Third, it summarizes the microfluidic methods developed thus far for food allergy diagnosis. The article concludes with a discussion of future opportunities for using microfluidic methods for achieving precision diagnostics in food allergy, including multiplexing the detection of multiple biomarkers, sampling of tissue-resident cytokines and immune cells, and multi-organ-on-a-chip technology.
Hypothesis driven drug discovery
Authors: Clarke Joanne , Gillings Michael , Beattie Andrew
Published: April 2020

Antibiotics were discovered over 50 years ago, providing a long sought after treatment for infectious diseases. These drugs effectively suppressed diseases such as tuberculosis and infections such as those caused by Staphylococcus aureus.
Old therapies, new science
Authors: V Riley Thomas
Published: April 2020

With the emergence of antibiotic resistance as a major public health problem and the apparent decline in pharmaceutical company drive to produce new antimicrobials, there has been an increase in interest in revisiting remedies and agents once popular before the advent of the antibiotic era.
Fast tracking drug development: balancing risks and rewards
Authors: Majewski Harry
Published: April 2020

The biotechnology revolution offers great hope for new therapies based on rational approaches to target discovery and drug design based on genomics, proteomics, advanced chemistry (3-D modelling, combinatorial chemistry) and high throughput screening.
Trials and tribulations of veterinary drugs
Authors: Hampson David
Published: April 2020

In general terms, the discovery and development of drugs for veterinary use follows the processes and procedures used for human drug discovery. Some interesting differences do arise, however. For example, when developing veterinary drugs it is necessary to be aware of the great diversity in physiology and disease profiles of the various species of animals, birds and fish for which new drugs may be sought. Hence, veterinary drugs may need to be targeted at specific species, rather than just for animals in general. Routes of delivery also can be very important ? for example it is desirable to treat fish through the water, or chickens either through the oral or respiratory routes, rather than having to handle large numbers of individuals.
Probiotics in aquaculture
Authors: J W Moriarty David
Published: April 2020

Aquaculture, especially prawn (shrimp) culture, is a major and rapidly increasing source of income in the agribusiness sector of tropical countries. Although probiotic bacteria are being used in aquaculture, there is scope, and indeed a need, for them to be used much more widely as replacements for antibiotics.
Probiotics: issues of credibility and safety
Authors: Donohue Diana
Published: April 2020

People have believed for more than a century that live microorganisms in foods may benefit human health. More recently, probiotics have appealed to consumers who want nutritional products with added health attributes. The demonstration of efficacy in probiotics thus offers vast opportunities for the development of human and veterinary products. However, the addition of novel bacterial strains to foods and therapeutic products presents a challenge in safety assessment for regulatory authorities. Probiotic products which claim specific nutritional, functional or therapeutic characteristics blur the boundaries of what is a food, a diet supplement or a medicine.
Adventures with mucus and Stubby: Life amongst the helicobacters
Authors: Lee Adrian
Published: April 2020

The following article is based on the Rubbo Oration that I was honoured to present at the 2002 Annual Scientific Meeting in Melbourne.
Vertical Transmission, May 2003
Authors: Ellis David
Published: April 2020

Recently I have attended two ASM branch functions; one a student happy hour in South Australia designed to introduce students to ASM, the other was a visit to Perth where I gave a presentation to the WA branch. Both were enjoyable evenings but the take home message for me was that all state branches have progressive and innovative committees. This is without doubt one of the real strengths of ASM. If any member has an idea for the advancement of microbiology or for what ASM can do for its members, then please contact your branch, I can guarantee you will get a positive response.
Bioterrorism: an historical perspective
Authors: J Della-Porta Antony
Published: April 2020

During the Middle Ages it was recognised that victims of infections could become weapons themselves. Victims of plague were catapulted into the city of Caffa (Feodosiya, Ukraine) and the epidemic of plague that followed forced the retreat of the Genoese forces from the city. Pizarro is said to have given smallpox-contaminated clothing to South American native people in the 15th century. In 1763 it is reportedthat Captain Ecuyer of the Royal Americans deliberately distributed variola-contaminated blankets and a handkerchief to enemy American Indian tribes. This was followed several months later by a large smallpox outbreak amongst various Indian tribes in the Ohio area.
The role of the forensic science laboratory
Authors: Raymond Tony
Published: April 2020

Every incident attended by police in Australia is always initially considered to be a potential crime scene until evidence dictates otherwise. Consequently, forensic science organisational responsibilities typically include: ? The provision of a coordinated multidisciplined scientific field and laboratory response in support of both criminal and non-criminal investigations. ? The effective management of a disaster victim identification (DVI) response to a multi-casualty incident on behalf of the Coroner. In other words, the forensic science mission includes both the crisis (including threat assessment) and consequence of any incident or potential incident.
The role of DSTO in bioterrorism response
Authors: Borrett Veronica , Paul Brent
Published: April 2020

The role of Defence Science and Technology Organisation (DSTO) in national bioterrorism incident response had its inception in the capability developed to provide for chemical/biological security at the Sydney 2000 Olympic Games. DSTO is now an integral component in the broader planning and operational support framework to counter chemical, biological and radiological (CBR) terrorism
Fungal friends and foes
Authors: Hocking Ailsa
Published: April 2020

The Australian Society for Microbiology does not have a strong representation of non-medical mycologists within its membership, although mycology has always been well represented in the clinical arena. Mycologists interested in plant pathology are more likely to be active in the Australasian Plant Pathology Society, those whose interests lie in natural ecosystems are members of the Australasian Mycological Society, and those interested in the compounds produced by fungi may belong to the Royal Australian Chemical Institute. There is, perhaps, scope for greater interaction between ASM and some of these other organisations.
Fluorophores from fungi
Authors: Veal Duncan , Bell Philip , Brown Hayley , Choi Hung-Yoon , Karuso Peter
Published: April 2020

Fluorescence has many advantages over traditional colour and radioactive labels, and is playing an increasingly important role in the most powerful analytical techniques. For example, fluorescence is at the heart of many nucleic acid based diagnostics (e.g. DNA microarray, real time-PCR, fluorescence in situ hybridisation, etc), immunofluorescence assays, defined substrate technologies and differential display proteomics and is gradually replacing or complementing other techniques based on colour or radiolabels.
Powdery mildew and wine quality
Authors: E Stummer Belinda , Leigh Francis I , J Markides Andrew , S Scott Eileen
Published: April 2020

Powdery mildew, caused by the fungus Uncinula necator, is a widespread and economically important disease of grapevines. The fungus grows superficially on green tissues of grapevines and other members of the Vitaceae. Powdery mildew costs the Australian grape and wine industry approximately A$30 million per year in terms of lost yield, reduced quality and disease management.
Restoration of Australia?s native fungi: For improved commercial environmental forestry, farm revegetation and sustainability in the Australian wheatbelt region
Authors: L Bougher Neale , C Tommerup Inez
Published: April 2020

There is currently much effort being put into methods of harnessing Australia?s plant biodiversity for profitable farming systems with multiple environmental benefits. However, less attention has been given to significant components of natural ecosystems other than plants. One such component is Australia?s diverse and unique native fungi, and the range of largely ignored, out of sight, ecosystem functions provided by fungi. Though poorly recognised to date, management and restoration of Australia?s native fungi and other soil organisms in tandem with animals and plants are likely to be key parts of an overall strategy to achieve environmentally sustainable and economically profitable agricultural landscapes for the long term.
From the Editors, November 2003
Authors: Bishop Penny
Published: April 2020

The guest editor for this issue is Cheryl Power who is the convenor of the ASM Education SIG. Cheryl has many years of experience in education and is a recipient of the ASM David White Award for Excellence in Teaching. She has invited a number of other educators to contribute to this issue, many of whom are recipients of teaching awards from this society or their own teaching institutions.
Focus on a changing World
Authors: Salyers Abigail , Mary Kirov Sylvia , J Power Cheryl , Sheorey Harsha
Published: April 2020

The excitement of microbiology; Teaching and research: impossible or essential link?; Serving two masters: the student work dilemma; Medical microbiology education: what?s missing?
Vertical Transmission. March 2004
Authors: Ellis David
Published: April 2020

This issue contains important information about the next ASM Scientific Meeting and Exhibition to be held at the Superdome, Olympic Park, Homebush Bay in Sydney, 26 September to 1 October 2004. Some 30 overseas speakers have been invited and, with 50 symposia and workshops planned, this meeting promises to one of the best yet. The abstract deadline will be 14 May 2004. Registrations, including online registrations, are open, with the close of early bird registration being 30 June 2004.
A radon-resistant microbial community
Authors: P Anitori Roberto , M Henneberger Ruth
Published: April 2020

Over the past few decades, microbes have been discovered in a positively bewildering array of extreme environments. Bacterial and archaeal extremophiles exist, and often thrive, in conditions that would quickly kill eukaryotes, such as extremes of temperature, pH, pressure, salinity and radiation.
Biogenicity inferred from microbialite geochemistry
Authors: E Webb Gregory , S Kamber Balz
Published: April 2020

Microbes utilise and/or concentrate diverse metal cations, whose detection may become a potent tool for reconstructing microbial processes and, in particular, for establishing the genesis of ancient carbonate rocks that were produced by microbes. Such rocks, termed microbialites, consist of trapped and bound sediment and, importantly, carbonate minerals precipitated as accidental byproducts of metabolic or decay processes within biofilms. Where trace metals are predictably incorporated into microbialites, they may reflect biofilm processes and allow interpretation of preserved carbonates. Holocene (about 5-6,000 years old) microbialites that formed in reef cavities in the Great Barrier Reef (GBR) faithfully incorporated high concentrations of rare earth elements and yttrium proportional to their abundance in shallow seawater. Ancient microbialites display similar behaviour.
A nexus of complexity
Authors: Szabo Lisa , Desmarchelier Patricia
Published: April 2020

Many microbiology texts will state that food microbiology covers the interaction between microorganisms and food. An accurate enough description, albeit one that disguises the complexity of an interaction that can require considerations as seemingly diverse as pathogenicity and physical chemistry, and one that disguises operation in a nexus of profit, trade, regulation, public health, litigation, fads and consumerism.
Food biosecurity in the United States
Authors: J Knabel Stephen
Published: April 2020

The events of 11 September 2001 highlighted the vulnerability of US citizens and the US society in general to terrorist attacks. Since then, numerous governmental agencies and scientific bodies have emphasised the need to enhance the biosecurity of the US food supply. Food biosecurity is the prevention of intentional contamination of food with hazardous biological agents through tampering or other malicious, criminal or terrorist actions or threats. As part of the nation?s response to this issue, Congress passed the Public Health Security and Bioterrorism Response Act of 2002. Title III of the Bioterrorism Act includes a number of provisions designed to improve the food safety efforts of the Food and Drug Administration (FDA), including new authority to protect the food supply against terrorist acts and other threats.
Qualitative vs quantitative microbiology
Authors: Fegan Narelle
Published: April 2020

Escherichia coli O157 and Salmonella are food-borne pathogens of importance to the Australian beef and dairy industries. Cattle are a significant reservoir for both of these pathogens and beef has been the source of food-borne outbreaks of both E. coli O157 and Salmonella. The presence of pathogens in cattle can lead to contamination of carcasses during slaughter and products produced from these contaminated carcasses pose a risk to consumers. However, the magnitude of the risk is not clear. Until recently, almost all of the information published on E. coli O157 and Salmonella in cattle has consisted of only qualitative information i.e. the prevalence of these organisms in cattle. In order to estimate risk, it is important to understand not only how many cattle shed E. coli O157 and Salmonella but also the number of pathogens shed.
OzFoodNet: a network for enhancing food-borne disease surveillance and investigation across Australia
Authors: D Kirk Martyn
Published: April 2020

The Australian Government established OzFoodNet in 2000 to enhance surveillance and determine the burden of infection from food-borne illness across Australia. The OzFoodNet network collaborates nationally to investigate food-borne disease. OzFoodNet has three main areas of work, which are to: ? Determine the burden of food-borne illness in Australia. ? Identify the causes of food-borne disease. ? Coordinate investigations into outbreaks of food-borne illness.
pH-elevating Bacillus spp. in acid pasteurised foods
Authors: Olivier Sandra , Chapman Belinda
Published: April 2020

Trends in consumer and industry processing are influencing packaging formats for acid foods, which in turn impact upon in-pack oxygen availability. For example, microwave cooking is influencing the growing popularity of (oxygen permeable) polymer containers over traditional (oxygen impermeable) glass jars and cans. Single-serve packages that boast a higher surface-area-to-volume ratio than larger (e.g. family-serve) packs are similarly growing in popularity.
TB and not TB: Mycobacteriology in Australia in the 21st century
Authors: Bastian Ivan
Published: April 2020

In the past, non-mycobacteriologists may well have viewed the specialty as a backwater where the science and scientists moved slowly, and the organisms grew even more slowly! Little changed over nearly a century as mycobacteriologists employed the classic microscopy and culture techniques that had been developed and refined over the 2 decades following Koch?s description of the tubercle bacillus in 1884. However, mycobacteriology has undergone a renaissance in the last decade following a resurgence of tuberculosis (TB) in the United States, the increased recognition of the clinical significance of non-tuberculous mycobacteria (NTM), and the introduction of new molecular technologies such as nucleic acid amplification tests (NAAT). This brief review and other articles in this edition will highlight some of the exciting changes and challenges in the field of mycobacteriology in Australia.
Mycobacterium paratuberculosis: pain in the gut and challenge for science
Authors: Whittington Richard , Tizard Mark , Reddacliff Leslie
Published: April 2020

Mycobacterium paratuberculosis causes Johne?s disease in sheep, cattle, goats and other ruminants worldwide. It is a fatal, untreatable, chronic, granulomatous infection of the intestine. According to some researchers, the organism may be responsible for Crohn?s disease in man and, although not proven, this has led to a higher public profile for the disease. For this reason and because of animal welfare concerns and economic loss, animal health authorities in most developed countries aim to reduce the prevalence of infection.
Emerging threats to the blood supply: West Nile virus and beyond
Authors: R Young Paul
Published: April 2020

It is now more than 40 years since Sir Macfarlane-Burnet announced to the world that ?one can think of the mid-20th century as marking the virtual elimination of infectious disease as a significant factor in life? (1962). Along similar lines, Jesse Steinfeld, at the beginning of his reign as US Surgeon General, famously said that it was ?time to close the book? on the problem of infectious diseases (1969).
Blood supply protection: how much is enough?
Authors: Wood Robyn , Pembrey Richard
Published: April 2020

The delivery and maintenance of a safe blood supply are imperative for Australia?s security and medical advancement. Practices such as the use of voluntary nonremunerated donors (1927), and early coordination to identify optimal testing regimes, e.g. for Hepatitis B virus (HBV) 1975, Human Immunodeficiency virus (HIV) 1985 and Hepatitis C virus (HCV) 1990, have ensured the Australian public are at minimal risk of exposure to unsafe blood. However, the AIDS epidemic did reveal significant flaws and weaknesses in our delivery of a safe blood supply, unfortunately with some devastating ramifications. Since that time, public tolerance of adverse events following receipt of infectious donations is very low. Does Australia now have a safe blood supply, and is safety assured against future potential catastrophes?
Wildlife health in Australia
Authors: Humphreys Kaye
Published: April 2020

The intention of this issue is to improve awareness of the role of wildlife health in human health, biodiversity, tourism and agro-economy in Australia. The papers have been selected to highlight the importance of wildlife diseases with an emphasis on diseases with zoonotic potential, those that have threatened native fauna through causing population declines, or those that may threaten Australia?s trading status.
Emerging wildlife diseases ? impact on trade, human health and the environment
Authors: Bunn Christopher , Woods Rupert
Published: April 2020

Emerging wildlife diseases can occur anywhere in the world and the consequences can be severe. The recent epidemics of SARS, West Nile virus and avian influenza demonstrate the global importance of emerging pathogens and the important role of wildlife in initiating or maintaining such diseases. These recent epidemics and many other diseases have also highlighted the importance of creating new and more effective partnerships between government departments, animal industries and the community. It is important that a country has a system that is able to detect and identify emerging pathogens or diseases, rapidly analyse the situation, and, if necessary, disseminate the information and prompt a control response.
Volant viruses: a concern to bats, humans and other animals
Authors: Breed Andrew , Field Hume , Plowright Raina
Published: April 2020

Bats have a long and intimate association with viral diseases. There may be much to be learned from examining the disease ecology in this group of animals which would be to the benefit of humans, domestic animals and other wildlife species.
Molecular taxonomy of polymicrobial diseases ? finding novel bacteria not previously considered to be associated with oral diseases
Authors: Nadkarni Mangala , Byun Roy , Chhour Kim-Ly
Published: April 2020

Recombinant DNA technology and molecular biology have brought a revolution to the limitations imposed by traditional taxonomic methods of bacterial identification based solely on cultivation. Following on from the novel research of Carl Woese, molecular taxonomy is generally based on variations in the sequence of the 16S rRNA gene and has brought a new perspective to our understanding of the diversity of uncultured bacteria in a multitude of microbial habitats. Analysis of the polymicrobial oral diseases is no exception.
Vertical Transmission, November 2005
Authors: Rood Julian
Published: April 2020

An ASM member wins the Nobel Prize in physiology or medicine for microbiology research done in Australia; it doesn?t come any better than that! Congratulations to Professor Barry Marshall (University of Western Australia) and his colleague Dr Robin Warren for their seminal contribution in showing that a previously unknown bacterium, Helicobacter pylori, was the major cause of peptic ulcer disease.
2004 Boxing Day Tsunami
Authors: Hogg Geoff
Published: April 2020

This issue of Microbiology Australia focuses on the 2004 Boxing Day tsunami and the experiences of those directly involved in the initial response and in the assessment, clinical care, laboratory support and public health responses. The contributions reflect the experiences of professionals from different disciplines who describe their role in this event. The varied perspectives provide a context for the laboratory contribution.
The Asian Tsunami: Initial medical response to Banda Aceh
Authors: M Griggs William
Published: April 2020

Following a disaster, it is necessary to facilitate an appropriate response. However before any appropriate response can be made, it is essential to get an accurate assessment.
Establishment of L3 (field reference laboratory)
Authors: R Lederman Edith , Suwandono Agus
Published: April 2020

Due to structural damage, decimation of skilled laboratory staff, and loss of critical supplies, laboratory capabilities after 26 December were essentially nil in Banda Aceh, the city centre of Aceh Province. On 15 January 2005, staff from NIHRD and NAMRU-2 were jointly given the task of establishing a reference laboratory on the grounds of the Aceh provincial health laboratory unit (Labkesda Aceh) in response to the direct need for laboratory resources. This reference laboratory, known as L3, was funded by USAID.
Information infrastructure for global biological networks
Authors: A Lane Meredith
Published: April 2020

Any sort of global network of research facilities, in order to maintain a truly ?network? status, requires a mechanism for sharing information among the participating centres. The more immediate, transparent and effective the mechanism is, the more useful the research network is, not only to its participants but to the community at large.
Crime scene investigation: can we detect anthrax?
Authors: Hoile Rebecca
Published: April 2020

An act of bioterrorism refers to both the threat to conduct as well as an actual incident involving the use of a biological agent against the civilian population. The detection of potential biological pathogens and toxins can now be conducted at the scene of a biological threat or release of a suspicious substance. Improvements in science and technology have enabled manufacturers of traditional laboratory based equipment to produce smaller, more basic models, enabling microbial testing to be conducted in the field.
Transcriptional repressors
Authors: Kahler Charlene
Published: April 2020

Prokaryotes regulate cellular functions in response to environmental cues via signal transduction pathways. In principal, there are two thematic organisations of signal transduction proteins: ? One-component proteins, in which the input and output domains are physically linked. These are commonly called activators (see article by Schubert & Shearwin) and repressors (reviewed in this article). ? Two-component systems consisting of histidine kinases and response regulators (see article by Cheung & Rood). A recent survey of 145 prokaryotic genomes has revealed the predominance of one-component systems in this domain of life and has provided the first indication of the diversity inherent in these signal transduction pathways.
Influenza diagnosis and management
Authors: W Smith David
Published: April 2020

Influenza is already an important cause of illness and death each year in Australia and the impact of future pandemics will be many times greater. Compared with other respiratory viral illnesses, influenza is more severe in itself as well as being more likely to result in complications. These range from milder conditions such as otitis media and sinusitis to acute bronchitis, viral pneumonia and bacterial pneumonia. There are also a number of less common non-respiratory complications, including myocarditis, encephalitis, rhabdomyolysis and nephritis. In addition, a substantial component of severe disease and death from influenza is due to exacerbations of pre-existing cardiac conditions, respiratory disease or diabetes. Accurate diagnosis is the basis of the proper management of patients, understanding of the epidemiology of this virus, and detecting the entry and spread of new influenza strains.
The origins of pandemic influenza ? a perspective
Authors: Laver Graeme
Published: April 2020

Following the isolation of the first human influenza virus in 1933, there have been two Type A influenza pandemics. One was the Asian influenza pandemic in 1957, when an H2N2 virus replaced the H1N1 viruses then circulating, and the other was in 1968 when the Hong Kong H3N2 virus replaced the H2N2 viruses. The H1N1 virus that re-emerged in 1977 did cause a worldwide epidemic (or pandemic) but this virus is not considered by many people to be a true ?pandemic? virus.
New vaccines and therapeutic antibodies from yeast
Authors: Macreadie Ian
Published: April 2020

This year has seen another leap in the power of yeast to meet major pharmaceutical needs. One was the topic of the closing address by Prof Ian Frazer at the ASM?s Annual Scientific Meeting at the Gold Coast. That address discussed the major worldwide problem of human papilloma virus (HPV) infection, especially in young women. More importantly, he described the cure ? prevention by vaccination with the major capsid protein (L1) of HPV types 6, 11, 16 and 18.
Laboratory issues in STD diagnosis and their application to disease control in an Australian context
Authors: Tapsall John
Published: April 2020

This issue of Microbiology Australia features a selection of articles on novel and pragmatic contributions from Australian clinical laboratories to the diagnosis, management and control of sexually transmitted diseases (STDs).
Problems in diagnosing sexually transmitted infections in remote Australia
Authors: David Lum Gary
Published: April 2020

Times are changing. The National Aboriginal and Torres Strait Islander Sexual Health and Blood Borne Virus Strategy 2005-2008 provides current commentary on the problems facing Australia?s Indigenous population. While the rates of sexually transmitted infections have always been higher in Indigenous Australians, there is some evidence of increasing rates of HIV infection. The rate of Chlamydia infection in non-Indigenous Australians has doubled between 1999 and 2003, while the rate of infection in some populations of Indigenous Australians has moved from 658 per 100 000 to 1140 per 100 000 population. Indigenous Australians are forty-times more likely to be infected with the gonococcus than non-Indigenous Australian men and women. It should not be surprising that Indigenous Australian rates of syphilis are unacceptably high at ~250 per 100 000 population and almost non-existent in the non-Indigenous population.
Functional genomics in yeast
Authors: W Dawes Ian , D Kornfeld Geoffrey , G Perrone Gabriel
Published: April 2020

Completion of the Saccharomyces cerevisiae genome sequencing project in 1996 led to an incredible explosion of research on basic cellular processes and has provided the opportunity to determine how genes and their products are regulated and function on a genome-wide scale. The technologies that were developed from this provided an incredible array of tools to study cellular processes in great detail and were a paradigm for developments from subsequent sequencing projects.
Host factors in virus budding ? Insights from yeast
Authors: R Vajjhala Parimala , L Munn Alan
Published: April 2020

The budding yeast, Saccharomyces cerevisiae, is an excellentmodel organism for the study of eukaryotic cellular processes such as endocytosis 1. Like other eukaryotic cells, yeast take up extracellular material by invagination of the plasma membraneto form a vesicle. The internalised material is transported to a membrane-bound compartment, the early endosome. As the early endosome matures, internal vesicles form within the lumen giving it the appearance of a multivesicular body (vesicles enclosed by a membrane). The machinery required for endosome maturation is highly conserved between yeast and mammalian cells. In mammalian cells this machinery is also required for the budding of enveloped viruses. Here we discuss how studies of endosome maturation in S. cerevisiae have given valuable insights into the mechanism by which clinically important enveloped viruses, including human immunodeficiency virus (HIV) and hepatitis B virus, are released from mammalian cells.
The living soil ? an agricultural perspective
Authors: M Roper Margaret , V S R Gupta Vadakattu
Published: April 2020

Soils are much more than a porous medium for supporting plant growth. Soils are living, because they contain a wide range of microorganisms including bacteria, fungi, algae, protozoa, nematodes and other fauna including microarthropods, macroarthropods, termites and earthworms. All play a crucial role in the biological function of soils including decomposition of organic matter, nutrient transformations, biological control, development of soil structure to mention a few. Until recently the complexity of life in the soil has been difficult to unravel, but new DNA and biochemical tools are providing insights into its phenotypic and functional diversity and capability, and should drive the development of managements that nurture biodiversity and ecosystem function.
How viruses control microbial ecosystems
Authors: Pollard Peter
Published: April 2020

Viruses are the most abundant nucleic acid containing biological parcel on earth, being ten times more than bacteria and archaea. Most are phage (infect bacteria), have a genome of DNA or RNA, and are encapsulated in a protein coat at concentrations of 1010/L in aquatic environments. The planet holds 1031 viruses inthe oceans alone and their biomass equals 200 Mt of carbon or 75 million blue whales. Stretched end-to-end they would span 10 million light years. They are obligate parasites and without doubt a pervasive influence on microbial ecosystems.
Recent World Health Organization initiatives for antimicrobial resistance control
Authors: Tapsall John
Published: April 2020

The World Health Organization (WHO) overseeing of antimicrobial resistance (AMR) containment issues in the last decade has varied in intensity. From 1999 onwards, concerted focus from the WHO led to the development of a multi-disciplinary framework for AMR containment at a country level. However, implementation of the WHO Global Strategy for the Containment of Antimicrobial Resistance (the Global Strategy) was overtaken first by events in the USA in 2001 and later by related and other bio-security issues. By 2003, loss of funding and a restructured WHO saw AMR initiatives curtailed. Interest in AMR at the WHO has been recently rekindled and it is hoped that renewed attention will again be focused on this issue by the WHO and its member states.
Antimicrobial resistance in veterinary medicine ? issues and controversies from an Australian perspective
Authors: D Barton Mary
Published: April 2020

Antimicrobial resistance in veterinary isolates came to renewed prominence in the late 1990s in response to the recognition of an association between the use of avoparcin as a growth promotant in livestock feeds and vanA vancomycin resistance in enterococcal pathogens in humans 1. Since then there have been many regulatory changes in many countries that have resulted in a reduction in use of antimicrobial growth promoters (AGPs) in livestock feeds. The EU has banned the use of most growth promoters and in Australia post-JETACAR avoparcin (a glycopeptide) has been voluntarily withdrawn from the market by the manufacturer (in 2000), recommendations have been made to restrict the use of virginiamycin (a streptogrammin) to a prescription-only medicine for treatment and prevention of some specific conditions, and a review of macrolide AGPs is in the wings. In addition, many of the industries have voluntarily reduced or ceased their use of some of these products. For example, the pig industry stopped use of avoparcin in 1997 and the use of virginiamycin has been curtailed in the meat chicken industry.
A resistant culture - ?superbugs? in Australian hospitals
Authors: L Gilbert G
Published: April 2020

Antimicrobial resistance is not new in Australian hospitals. In 1946, shortly after penicillin became available for treatment of civilians, a penicillin resistant Staphylococcus aureus strain caused ~50% of staphylococcal surgical wound infections at the Royal Prince Alfred Hospital (RPAH), in Sydney. During the 1950s, another virulent penicillin resistant S. aureus strain (phage type 80/81) emerged in neonatal units in Sydney and spread to other hospitals in Australia and overseas, to the families of affected infants and to the general community, causing serious soft tissue infections, osteomyelitis, pneumonia and septicaemia.
Microbial diversity in petroleum reservoirs
Authors: Li Dongmei , Hendry Philip
Published: April 2020

Buried hydrocarbon deposits, such as liquid petroleum, represent an abundant source of reduced carbon for microbes. It is not surprising therefore that many organisms have adapted to an oily, anaerobic life deep underground, often at high temperatures and pressures, and that those organisms have had, and in some cases continue to have, an effect on the quality and recovery of the earth?s diminishing petroleum resources. There are three key microbial processes of interest to petroleum producers: reservoir souring, hydrocarbon degradation and microbially enhanced oil recovery (MEOR).
A green solution for ethanol production
Authors: Stevenson Trevor , McKenzie Belinda
Published: April 2020

The use of ethanol as an automotive fuel dates back to the early 20th century, with a memorable example being Henry Ford?s famous T model that was able to run on pure ethanol. With increased interest in renewable resources, the use of bioethanol as an automotive fuel on a global scale has been increasing; however, the long-term viability of ethanol as a renewable fuel is challenged by the availability of suitable feedstocks that can be used for the fermentation process.
Against the one hundredth locust: the commercial use of insect pathogens
Authors: Hauxwell Caroline
Published: April 2020

Insect pathology has a long history dating back to the earliest studies in microbiology. A select few of the many known insect pathogens can be produced and used on an industrial scale as biopesticides and are championed for their low environmental impact. The commercial application of microbial insecticides has been limited competition with chemical insecticides. However, the advent of gene technology led to a multibillion dollar industry incorporating bacterial toxins into insect resistant transgenic crops, and in the development of expression vectors. Recent use of insect pathogens in Australia has demonstrated that these biopesticides can play a significant role in mainstream commercial agriculture for the management of multiple-insecticide resistant pests and maintenance and in integrated pest management.
A need for an integrated management process for biorisks
Authors: Della-Porta Tony
Published: April 2020

Biosafety has been a long-term issue in microbiology laboratories and has arisen out of the need to properly handle and prevent laboratory acquired infections. Yet, despite the adoption of a Standard for biosafety in Australia over 3 decades ago, such infections still occur.
Why laboratories fail
Authors: Walls Neil
Published: April 2020

Recent inspections by the author of approximately 200 biocontainment laboratories have revealed substantial shortcomings. This paper presents a summary of these findings. Failures that may directly affect microbiological containment are explained in general terms to promote an improved understanding of the problems.
Health: how do we maintain the borders in the face of disease emergencies?
Authors: Flaherty Greg , Roberts Stewart
Published: April 2020

The Department of Health and Ageing (DoHA) aims to protect and improve the health of all Australians. One of the ways DoHA works to achieve this is through preventing the entry of communicable diseases into Australia. This is achieved in partnership with Australia?s border control agencies and with States and Territories.
Community MRSA and Panton-Valentine leukocidin (PVL): the perfect storm, or a storm in a tea-cup?
Authors: Murray Ronan
Published: April 2020

Staphylococcus aureus is well known for its propensity to encode and express a formidable range of virulence determinants that can cause considerable morbidity and mortality in its host. Amongst these determinants is Panton-Valentine leukocidin (PVL), a cytolytic exotoxin first described in the late 19th century. This toxin is found in many S. aureus clones; however, of particular concern is the fact that community-acquired methicillin-resistant S. aureus (CA-MRSA) clones that contain the PVL determinant have been associated with severe necrotising cutaneous and pulmonary infections in previously well individuals. These reports raise the spectre of a true ?superbug? ? one that is readily transmissible, resistant to front-line antimicrobial agents, and potentially more virulent that other S. aureus strains. Specific therapeutic approaches directed towards the expression and/or activity of PVL, or the elimination of carriage and transmission of S. aureus that contains PVL determinants, are being considered; however, the effectiveness of such approaches has yet to be determined.
Staphylococcus aureus bacteraemia: The Australia New Zealand Cooperative on Outcomes in Staphylococcal Sepsis (ANZCOSS)
Authors: Turnidge John , Kotsanas Despina
Published: April 2020

Staphylococcus aureus is such a common organism, both as a coloniser and cause of infection in humans, that it is easy to take it for granted. Microbiologists, infectious diseases specialists and infection control practitioners deal with the organism on a regular basis, from screening for methicillin-resistant strains (MRSA) in asymptomatic carriers to treating patients with life-threatening sepsis syndrome in intensive care units.
Improved methods in the identification and screening for antimicrobial resistance: chromogenic screening for Staphylococcus aureus and methicillin resistance
Authors: Merlino John
Published: April 2020

New enzyme specific synthetic chromogenic substrates offer an advance in the laboratory screening and detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA), with increased efficiency, reduced labour costs and decreased turn around times, especially when incorporated into existing laboratory workflows, to support current methods of microbial identification and the detection of resistance.
Toxoplasmosis in pregnancy: often suspected, rarely convicted
Authors: Gilbert Lyn
Published: April 2020

Toxoplasmosis during pregnancy is uncommon and usually asymptomatic but can cause catastrophic fetal disease. It is often suspected because of non-specific symptoms or positive serological tests. However, false-positive toxoplasma IgM tests are common and confirmatory tests not always reliable. The risk of fetal infection increases as pregnancy progresses; it should be diagnosed or excluded by amniotic fluid PCR, especially early in pregnancy when the risk of severe damage is high. Prompt antibiotic therapy of maternal infection probably reduces fetal infection and disease, but its efficacy has not been confirmed by randomised controlled trials.