In this issue

Microbiology Australia Microbiology Australia
Issue 1

Steadying the ship
The last nine months have been an interesting and challenging time for the Executive of the ASM. I am taking this opportunity to describe the problems and what we are proposing to do about them, and have done so far. You may know that we have had a series of resignations from the office staff: our Conference Manager in May, our Office Manager in August and our Events Manager in November. At this time the ASM is no longer an employer. We have had to consider a number of things as these resignations have accumulated. You’d be aware already that we brought in a professional conference organiser (ICMS) to manage the annual meeting in July at short notice. Given the circumstances, ICMS did a great job, and the meeting went ahead smoothly and did not suffer financially.
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Influenza – our constant companion
On 11 June 2009, Dr Margaret Chan, the Director-General of the World Health Organization, announced to the world that following the emergence of a novel influenza A virus in late April 2009 and its extensive spread that, “I have therefore decided to raise the level of influenza pandemic alert from phase 5 to phase 6. The world is now at the start of the 2009 influenza pandemic.” Dr Chan also commented, “No previous pandemic has been detected so early or watched so closely, in real-time, right at the very beginning. The world can now reap the benefits of investments, over the last five years, in pandemic preparedness.” Also observed was that, “Globally, we have good reason to believe that this pandemic, at least in its early days, will be of moderate severity”.
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Swine flu – lessons we need to learn
Important lessons need to be learnt from the recent swine flu pandemic. Overall the population health effects of swine flu were less than a moderately severe seasonal influenza outbreak. A pandemic should not be declared unless we have both the spread of the virus but also when its virulence is above a predefined level. We need to ensure that we improve techniques to decrease the spread of infection both in the community and within our hospitals. This means improved infection control and hygiene with the use of masks, alcohol hand rubs and so on We also need to have a different approach to vaccines. Effective vaccines were produced only after the epidemic had passed and so had relatively little efficacy in preventing many infections. Mass population strategies involving vaccines and antivirals also misused large amounts of scarce medical resources.
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Laboratory diagnosis of influenza and the impact of the pandemic (H1N1) 2009 virus
Aetiological confirmation of respiratory tract infections in patients facilitates appropriate antimicrobial use and infection control procedures. From a public health perspective, the laboratory confirmation of influenza allows assessment of circulating viruses, community attack rates and the efficacy of vaccination programs, while assisting modelling as part of pandemic preparedness planning. Rapid antigen and immunofluorescent antigen tests are relatively insensitive in detecting pandemic (H1N1) 2009 influenza compared to seasonal subtypes, and influenza subtype-specific nucleic acid amplification tests should be used as the ‘gold-standard’ for diagnosis. Pathogen-specific serological testing aids the retrospective diagnosis of infection, and is used in seroprevalence studies. Influenza virus isolation is needed for vaccine assessment and formulation. Although some challenges surrounding diagnostic testing during pandemic (H1N1) 2009 have been resolved, others remain; this may test laboratories again in future pandemics.
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Development and testing of the Australian pandemic influenza vaccine – a timely response
In April 2009 a novel virus strain appeared which would cause the first influenza pandemic of the 21st century. This pandemic was the first to occur in an era where bioinformatic technologies contributed to the response to this virus; still, the creation of a vaccine relied largely on existing egg-based technology. The ongoing threat of a H5N1 pandemic spurred the development of strategies to rapidly produce a pandemic vaccine. These plans were implemented and allowed CSL and Australia to conduct the first clinical trials and produce one of the first 2009 pandemic vaccines. However, new candidate influenza vaccine viruses often present challenges to manufacturing a new vaccine. This pandemic virus was no exception. Being in the post-pandemic phase, it is important to review lessons learned to improve our response to future pandemics. In hindsight, the production of a pandemic vaccine is similar to that of seasonal influenza vaccines, yet the urgency of the pandemic response compresses timelines. This report explores those timelines and implications for producing a pandemic vaccine for Australia.
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How did the 2009 pandemic compare with previous pandemics?
The pandemic spread of the novel H1N1 virus in 2009 was unusual in that the attack rates and mortality rates were often lower than in earlier pandemics. However, most affected populations reported that morbidity and mortality were greater in younger adults than in children or older persons, reproducing the age distribution of earlier pandemics. A small proportion of affected persons became so ill that they required intensive care or died. Aboriginality, pregnancy and obesity were risk factors for severe disease, but many patients requiring intensive care had no identifiable risk factors. The pandemic features in 2009 can be explained, at least in part, in immunological terms. As with earlier pandemics, older people were probably protected by specific antibodies resulting from exposure to a similar virus which last circulated when they were children. In 2009, as in earlier pandemics, children were relatively protected against their first exposure to the new virus by the strength of their innate immune response, while many people of all ages were protected in whole or in part by short-lived, strain-transcending immunity resulting from their most recent exposure to seasonal influenza. On this view, the individuals developing severe disease were those who were too young to be protected by specific high-avidity antibodies, too old to be well-protected by innate immunity, and unlucky enough to have missed out on recent exposures to seasonal influenza.
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What serosurveillance studies tell us about the 2009 influenza pandemic
Surveillance of the impact of pandemic (H1N1) 2009 influenza during its initial seasons in both hemispheres relied on routinely available indicators, including numbers and rates of laboratory-detected cases, hospitalisations, ICU admissions and deaths, along with monitoring of influenza-like illness (ILI) from primary care sentinel surveillance systems. Estimates of the clinical attack rate and the case fatality ratio were imperfect. Understanding of the pathogenicity of the pandemic virus and prediction of the impact in subsequent seasons was hindered by a lack of information on actual infection rates in the population. Results of a number of serosurveys conducted in Australia and overseas countries have now become available, revealing that the arrival of the pandemic virus in modern urbanised and non-immune populations resulted in relatively similar infection rates in both the southern and northern hemispheres. Around 30–50% of children and teenagers were infected during the first pandemic season, with lower rates, around 10–20%, in young and middle-aged adults, and very few infections in older adults. There were significant numbers of mild or asymptomatic infections, and case fatality and hospitalisation ratios were much lower than those contemplated in pandemic plans. Many populations, including Australia, achieved a significant level of herd immunity during the first wave, and community susceptibility was further reduced by vaccination programs, although coverage was lower than expected. In the absence of significant antigenic drift or changes in virulence, the impact of the pandemic H1N1 virus should continue to decline in future influenza seasons.
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T-cell immunity against the A(H1N1) 2009 pandemic virus
The sudden emergence of the novel reassortant A(H1N1) 2009 influenza virus led to rapid global spread, due to minimal pre-existing antibody levels in those born after 1950. Memory T cells specific for more conserved viral peptides elicit broad immunity and can promote more rapid recovery. However, mutations within T-cell immunogenic peptides occur, although less commonly than at antibody-binding sites. Comparison of human T-cell peptides between the pandemic H1N1 2009 and seasonal strains showed 50–70% conservation, depending on the particular virus protein and influenza strains. Experimental analysis demonstrated cross-recognition of some T-cell epitopes (for example, HLA-A2+M158-66), although there was also evidence of immune escape by other immunodominant peptides (for example, NP418-426 presented by the HLA-B7 family). Non-conserved T-cell regions of A(H1N1) 2009 highly resembled those derived from H1N1-1918 rather than recent seasonal viruses, reflecting protein conservation (in the parent swine virus) from influenza strains circulating early in the 20th century. As a consequence, individuals with HLA types presenting variable T-cell peptides had diminished pre-existing T-cell memory towards the A(H1N1) 2009 virus.
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Antiviral drug resistance in seasonal and pandemic influenza
Two classes of anti-influenza drugs are currently available for the treatment or prophylaxis of influenza. These are the adamantanes (amantadine and rimantadine), which block the activity of the M2 ion channel of influenza A viruses (but not influenza B viruses), and the neuraminidase inhibitors (NAIs), which act by binding to the enzymatic site of the influenza neuraminidase (NA) thereby preventing progeny virions from being released from the host cell during viral replication. Antiviral resistance can occur in influenza viruses and render the drug ineffective for the treatment of patients. Virtually all influenza A viruses currently circulating in the human population are resistant to the adamantanes, while in comparison these viruses remain susceptible to the NAIs. In particular, very low NAI resistance has been observed in pandemic A(H1N1) 2009 viruses, even though unprecedented amounts of these drugs were used.
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Clinical impact of influenza – lessons learnt from the pandemic influenza A (H1N1) 2009
Influenza is generally an acute, self-limiting, febrile illness without further complications in the majority of people. However, it can be associated with severe morbidity and mortality and the burden of the disease on society is likely to be underestimated. In 2009 an outbreak of H1N1 influenza A virus infection was detected in Mexico with further cases soon observed worldwide. Subsequently, in June 2009, the first influenza pandemic of the 21st century due to influenza A (H1N1) was declared by the World Health Organization (WHO). There were many uncertainties regarding the virulence, clinical symptoms and epidemiological features of this newly evolved influenza A strain. Over time, many similarities, but also some differences between the pandemic H1N1 influenza A and seasonal influenza were identified. We recently performed a systematic review of the literature, looking at articles published between 1 April 2009 and 31 January 2010, to identify the epidemiological and clinical features of the pandemic H1N1 influenza. In this current article we compare our findings with others from the international literature. There was more severe impact on young and healthy adults, children, pregnant women and the obese. Clinical features in general were similar between seasonal and pandemic influenza; however, there were more gastrointestinal symptoms associated with pandemic H1N1 influenza. Shortness of breath was characteristic of more severe pH1N1 2009 infection with a higher possibility of being admitted to an intensive care unit (ICU).
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A universal influenza vaccine – are we almost there?
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.
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H1N1 2009 pandemic influenza in Indigenous Australians
Given the known prevalence of chronic disease in the Australian Indigenous population, and the known risk factors for severe disease from influenza infection, it is not surprising that Indigenous Australians carried a higher burden of disease during the influenza pandemic of 2009. However, other determinants apart from comorbidities might also have affected influenza morbidity in Indigenous Australia. Factors such as overcrowding, sanitation infrastructure, remoteness, access to health care and availability of the specific hardware of the pandemic (such as personal protective equipment – PPE– and antivirals) may also have been risk factors for poor outcomes at the population level. This article summarises the impact of the 2009 influenza pandemic on Australia’s Indigenous population, with particular emphasis on those living remotely in the Northern Territory (NT).
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Pandemic H1N1 2009 influenza in pigs in Australia
The novel H1N1 2009 virus that is the cause of the most recent human influenza pandemic is able to infect a number of animal hosts, most notably reported in domesticated swine. The first confirmed 2009 pandemic H1N1 (H1N1pdm) influenza infection of a commercial swine herd occurred in Alberta, Canada in late April 2009. The early incidences of H1N1pdm influenza in swine were of great concern to public and animal health agencies alike, and numerous subsequent cases were reported to the World Organization for Animal Health (OIE) by different countries following prevalence of the pandemic virus in the human population, including Australia. In almost all cases, outbreak investigations have indicated an epidemiological link with farm in-contact persons reporting recent influenza-like illness (ILI), some diagnostically confirmed as H1N1pdm infections. These have suggested interspecies transmissions from human to swine. This article describes the first reported cases and our investigations of swine influenza due to H1N1pdm virus in Australia.
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An update of H5N1 viruses: Are they still a threat to Australia?
Highly pathogenic avian influenza (HPAI) H5N1 viruses are now endemic in poultry over much of Asia and in areas of Africa. The continued presence of the virus has led to repeated outbreaks in poultry, with associated economic losses, and also to increased cases of human infection. In this article we summarise the continuing evolution and activity of these H5N1 viruses.
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Reflections on the 2007 equine influenza outbreak
In late August 2007, Australia experienced its largest animal disease emergency with an outbreak of equine influenza (EI). This followed the importation of one or more infected horses and the entry of the virus into the Australian horse population. There are a number of aspects of this event that are not only applicable to the diagnosis and control of other high-consequence animal diseases but there are also many elements of interest and relevance to public health. In particular, there were interesting insights into the speed and manner of virus dissemination in a naive population. The benefits and capacity of real-time PCR and associated technology to support an emergency disease investigation and response were demonstrated, while the value of using a combination of a ‘marker’ vaccine and serological test that would differentiate between infected and vaccinated animals was clearly proven. Ultimately, the virus was eradicated following an outbreak on a scale and in a time frame not previously achieved in any other country.
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Influenza surveillance in wild birds in Australia
Wild aquatic birds are the natural reservoir for avian influenza viruses (AIVs)1. Increased surveillance has revealed that Australia has its own lineages of these AIVs.
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Past Issues


Volume 38

Issue 3 (September 2017)
Issue 2 (May 2017)
Issue 1 (March 2017)

Volume 37

Issue 4 (November 2016)
Issue 3 (September 2016)
Issue 2 (April 2016)
Issue 1 (March 2016)

Past Years

2010 to 2015
2002 to 2009

Feature Product

Guide to Mosquitoes of Australia

Guide to Mosquitoes of Australia

Provides a comprehensive, user-friendly guide to the mosquitoes of Australia and key strategies for managing them.

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