Cost of whole genome sequencing for non-typhoidal Salmonella enterica.

BACKGROUND: While whole genome sequencing (WGS) may be more expensive than traditional testing and polymerase chain reaction (PCR), simple cost comparisons ignore the potential for WGS to reduce the societal costs of non-typhoidal Salmonella enterica through public health action to prevent illness. METHODS: We determined how many cases the use of WGS data would need to prevent to be cost-equal to serotyping and MLVA, or culture independent testing based on PCR in Australia. We then examined the costs and cost-savings of current typing methods compared with WGS in outbreak scenarios. RESULTS: A median of 275 (90% CrI -55-775) or 1.9% (90% CrI -0.4%-5.4%) of notified serotyped Salmonella cases would need to be prevented for WGS to be cost-equal to current typing methods and 1,550 (90% CrI 820-2,725) or 9.6% of all notified Salmonella cases would need to be prevented to be cost-equal to PCR. WGS is likely to result in cost savings in prolonged outbreaks, where data can support earlier public health action. CONCLUSIONS: Despite currently having a higher cost per isolate, routine WGS of Salmonella was no more expensive than existing typing methods or PCR where >2% of illness was averted.

Ocular Filariasis in Human Caused by Breinlia (Johnstonema) annulipapillata Nematode, Australia.

We report a human case of ocular filariasis, caused by a species of Breinlia nematode, from Queensland, Australia. Morphological and molecular evidence indicated that the nematode Breinlia (Johnstonema) annulipapillata, or a closely related taxon, likely transmitted from a macropodid marsupial host was involved, which might represent an accidental finding or an emerging zoonosis.

Pertussis Seasonality Evident in Polymerase Chain Reaction and Serological Testing Data, Queensland, Australia.

We investigated the seasonality of pertussis in Queensland, Australia, between 2008 and 2011 using notification and laboratory data. Polymerase chain reaction and serology testing data demonstrate that in the vaccine era, pertussis remains a seasonal illness, with annual peaks in summer months, and that the seasonality of notification data is masked by testing trends.

Advances in molecular diagnosis of parasitic enteropathogens.

Here, recent developments in the detection and identification of parasites causing enteric infection are reviewed including the utility and challenges of multi-target molecular assays. Difficulties in clinical interpretation arising from increased detection of parasites, of co-infection with other enteropathogens and of asymptomatic carriage are discussed. Published approaches for detection across a broad range of organisms are described, including commercial assays available to Australian laboratories. Using local data, the impact of introduction of modern molecular assays is assessed. In addition, recent advances in high density multi-target molecular platforms are discussed as potential platforms for increasing the scope of enteric pathogens to be detected whilst maintaining appropriate costs.

Acellular pertussis vaccine effectiveness for children during the 2009-2010 pertussis epidemic in Queensland.

UNLABELLED: OBJECTIVES To assess the effectiveness of three, four and five doses of acellular pertussis vaccine against pertussis notification for children aged 1 - < 4 years and 5 - < 12 years, and the effectiveness of three doses of acellular pertussis vaccine against pertussis hospitalisation for children aged 1 - < 4 years. DESIGN, SETTING AND PARTICIPANTS: A population-based retrospective study of children aged 1 - < 12 years residing in Queensland, Australia, during 2009 and 2010. Routinely collected notification, hospitalisation, testing and vaccination data were used to describe notification rates and testing patterns and to assess vaccine effectiveness (VE) by the screening method. MAIN OUTCOME MEASURES: VE against pertussis notification for children aged 1 - < 4 years and 5 - < 12 years, by birth year, and VE against pertussis hospitalisation for children aged 1 - < 4 years. RESULTS: 1961 notifications and 29 hospitalisations were included in the VE calculations. VE point estimates against pertussis notification and hospitalisation in children aged 1 - < 4 years were similar in 2009 and 2010, and ranged between 83.5% and 89.4%. VE point estimates against notification among children aged 5 - < 12 years were between 71.2% and 87.7% in 2009, and between 34.7% and 70.3% in 2010. The numbers of pertussis tests performed for children, particularly polymerase chain reaction (PCR) tests, increased between 2009 and 2010. CONCLUSIONS: Acellular pertussis vaccine provided good protection within the first years of priming, but this waned as age increased. Changes in pertussis testing behaviour, because of increases in PCR use and awareness, may have contributed to increased pertussis notification rates and lower estimates of VE against notification owing to identification of milder disease.

Histoplasmosis in Australia: report of 16 cases and literature review.

We describe 16 previously unreported patients with histoplasmosis from Queensland and northern New South Wales, Australia, and review all previous Australian reports, providing 63 cases in total to study (17 cases of acute pulmonary histoplasmosis, 2 cases of chronic pulmonary disease, and 44 cases of systemic disease, including 17 cases of single-organ infection and 27 instances of disseminated disease). All acute pulmonary disease was acquired in Australia, with 52% of systemic disease definitely autochthonous. Most cases of single-organ disease occurred in immunocompetent patients (76%), and were oropharyngeal (53%) in location. Forty-one percent of disseminated disease occurred in patients with human immunodeficiency virus (HIV). Patients with HIV had high rates of systemic symptoms, pancytopenia, fungemia, and hepatosplenomegaly. Oropharyngeal and adrenal involvement as well as systemic symptoms were prominent in immunocompetent patients with disseminated disease, with 6 of 7 cases of adrenal involvement leading to Addison disease. Most systemic disease was diagnosed by culture of Histoplasma capsulatum. Where serology was assessed in cases other than acute pulmonary disease, it was positive in only 32%.Prognosis for patients with single-organ disease was excellent. Disseminated disease was associated with recurrence in 30% and death in 37%. The results of this study confirm several previously known patterns of disease but also provide new insights into this rare but endemic condition in Australia.

9: Infections in the returned traveller.

The usual presentation of a returned traveller is with a particular syndrome - fever, respiratory infection, diarrhoea, eosinophilia, or skin or soft tissue infection - or for screening for asymptomatic infection. Fever in a returned traveller requires prompt investigation to prevent deaths from malaria; diagnosis of malaria may require up to three blood films over 36-48 hours. Diarrhoea is the most common health problem in travellers and is caused predominantly by bacteria; persistent diarrhoea is less likely to have an infectious cause, but its prognosis is usually good. While most travel-related infections present within six months of return, some important chronic infections may present months or years later (eg, strongyloidiasis, schistosomiasis). Travellers who have been bitten by an animal require evaluation for rabies prophylaxis.