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  1. Article ; Online: Long COVID in Australia: achieving equitable access to supportive health care.

    Sorrell, Tania C / Hensher, Martin / Sanci, Lena A

    The Medical journal of Australia

    2023  Volume 218, Issue 10, Page(s) 455–457

    MeSH term(s) Humans ; Post-Acute COVID-19 Syndrome ; COVID-19/epidemiology ; Health Services Accessibility ; Australia/epidemiology
    Language English
    Publishing date 2023-05-10
    Publishing country Australia
    Document type Editorial
    ZDB-ID 186082-3
    ISSN 1326-5377 ; 0025-729X
    ISSN (online) 1326-5377
    ISSN 0025-729X
    DOI 10.5694/mja2.51950
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  2. Article ; Online: Persistence of the Omicron variant of SARS-CoV-2 in Australia: The impact of fluctuating social distancing.

    Chang, Sheryl L / Nguyen, Quang Dang / Martiniuk, Alexandra / Sintchenko, Vitali / Sorrell, Tania C / Prokopenko, Mikhail

    PLOS global public health

    2023  Volume 3, Issue 4, Page(s) e0001427

    Abstract: We modelled emergence and spread of the Omicron variant of SARS-CoV-2 in Australia between December 2021 and June 2022. This pandemic stage exhibited a diverse epidemiological profile with emergence of co-circulating sub-lineages of Omicron, further ... ...

    Abstract We modelled emergence and spread of the Omicron variant of SARS-CoV-2 in Australia between December 2021 and June 2022. This pandemic stage exhibited a diverse epidemiological profile with emergence of co-circulating sub-lineages of Omicron, further complicated by differences in social distancing behaviour which varied over time. Our study delineated distinct phases of the Omicron-associated pandemic stage, and retrospectively quantified the adoption of social distancing measures, fluctuating over different time periods in response to the observable incidence dynamics. We also modelled the corresponding disease burden, in terms of hospitalisations, intensive care unit occupancy, and mortality. Supported by good agreement between simulated and actual health data, our study revealed that the nonlinear dynamics observed in the daily incidence and disease burden were determined not only by introduction of sub-lineages of Omicron, but also by the fluctuating adoption of social distancing measures. Our high-resolution model can be used in design and evaluation of public health interventions during future crises.
    Language English
    Publishing date 2023-04-17
    Publishing country United States
    Document type Journal Article
    ISSN 2767-3375
    ISSN (online) 2767-3375
    DOI 10.1371/journal.pgph.0001427
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  3. Article ; Online: Pathways to COVID-19 ‘community protection’

    Marais, Ben J / Sorrell, Tania C

    2020  

    Abstract: To date, no country has reached a natural COVID-19 epidemic peak and observed peaks essentially reflect the effectiveness of ‘lockdown’ measures. The major challenge is finding a responsible way out of ‘lockdown’, given that SARS- CoV-2 is now an ... ...

    Abstract To date, no country has reached a natural COVID-19 epidemic peak and observed peaks essentially reflect the effectiveness of ‘lockdown’ measures. The major challenge is finding a responsible way out of ‘lockdown’, given that SARS- CoV-2 is now an established global pathogen. Acknowledging limitations in our knowledge regarding the sufficiency and durability of immune responses following natural SARS Cov-2 infection, we discuss three pathways to ‘community protection’. Uncontrolled epidemic spread (route 1; R0 > 2) has been associated with overwhelmed health care systems and high death rates, especially in the vulnerable. Controlled epidemic spread (route 2; effective R0 1–2) can be achieved with limited or strict control of social mixing; strict control will be necessary to ensure that only low-risk individuals become infected, without spill-over to vulnerable groups during their period of infectiousness. It has been demonstrated that local epidemic elimination (route 3; effective R0 < 1) can be achieved through prolonged ‘lock down’, supplemented by early active case finding with quarantine of close contacts to ensure rapid termination of transmission chains within the community. Although universal availability of a safe and effective vaccine remains the preferred ‘exit strategy’, this may be hard to achieve and alternative options must be considered with careful consideration of all adverse outcomes – including health, social and economic consequences.
    Keywords COVID-19 ; Coronavirus ; covid19
    Subject code 360
    Language English
    Publishing date 2020-01-01
    Publishing country au
    Document type Article ; Online
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  4. Article ; Online: The use of taxon-specific reference databases compromises metagenomic classification.

    R Marcelino, Vanessa / Holmes, Edward C / Sorrell, Tania C

    BMC genomics

    2020  Volume 21, Issue 1, Page(s) 184

    Abstract: A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the ... ...

    Abstract A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.
    MeSH term(s) Amphibians/classification ; Amphibians/genetics ; Animals ; Bacteria/classification ; Bacteria/genetics ; Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Data Curation ; Diet ; Feces/chemistry ; Feces/microbiology ; Fungi/classification ; Fungi/genetics ; Humans ; Italy ; Metagenomics/methods ; Reptiles/classification ; Reptiles/genetics ; Tanzania
    Language English
    Publishing date 2020-02-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-020-6592-2
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  5. Article ; Online: Central Nervous System Cryptococcal Infections in Non-HIV Infected Patients.

    Beardsley, Justin / Sorrell, Tania C / Chen, Sharon C-A

    Journal of fungi (Basel, Switzerland)

    2019  Volume 5, Issue 3

    Abstract: Central nervous system (CNS) cryptococcosis in non-HIV infected patients affects solid organ transplant (SOT) recipients, patients with malignancy, rheumatic disorders, other immunosuppressive conditions and immunocompetent hosts. More recently described ...

    Abstract Central nervous system (CNS) cryptococcosis in non-HIV infected patients affects solid organ transplant (SOT) recipients, patients with malignancy, rheumatic disorders, other immunosuppressive conditions and immunocompetent hosts. More recently described risks include the use of newer biologicals and recreational intravenous drug use. Disease is caused by
    Language English
    Publishing date 2019-08-02
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2784229-0
    ISSN 2309-608X ; 2309-608X
    ISSN (online) 2309-608X
    ISSN 2309-608X
    DOI 10.3390/jof5030071
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  6. Article ; Online: What's New in

    Beardsley, Justin / Dao, Aiken / Keighley, Caitlin / Garnham, Katherine / Halliday, Catriona / Chen, Sharon C-A / Sorrell, Tania C

    Journal of fungi (Basel, Switzerland)

    2022  Volume 9, Issue 1

    Abstract: ... ...

    Abstract Cryptococcus
    Language English
    Publishing date 2022-12-27
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2784229-0
    ISSN 2309-608X ; 2309-608X
    ISSN (online) 2309-608X
    ISSN 2309-608X
    DOI 10.3390/jof9010041
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  7. Article ; Online: Antibiotic exposure within six months before systemic therapy was associated with lower cancer survival.

    Morrell, Stephen / Kohonen-Corish, Maija R J / Ward, Robyn L / Sorrell, Tania C / Roder, David / Currow, David C

    Journal of clinical epidemiology

    2022  Volume 147, Page(s) 122–131

    Abstract: Objectives: The objective of the study was to quantify associations between cancer survival and antibiotic exposure before systemic anticancer therapy.: Study design and setting: This population-based cohort study compares cause-specific survival ... ...

    Abstract Objectives: The objective of the study was to quantify associations between cancer survival and antibiotic exposure before systemic anticancer therapy.
    Study design and setting: This population-based cohort study compares cause-specific survival according to antibiotic exposure before non-immune checkpoint inhibitor (ICI) systemic therapy in patients diagnosed with single primary cancers in New South Wales between 2013 and 2016. Proportional hazards regression was used to control for confounding, with no antibiotic exposure in the six months before non-ICI systemic therapy serving as the comparator.
    Results: After adjusting for tumour spread, cancer site, age, sex and comorbidity, people having antibiotic exposure within 180 days before non-ICI systemic therapy had poorer cancer survival (hazard ratios ranging from 1.21 [95% confidence interval: 1.06-1.39] to 1.58 [1.34-1.87]) for shorter periods since antibiotic exposure (P < .0001). Similarly, poorer survival trends applied for localized and metastatic cancer. Of six prevalent cancers studied, lung and breast primaries showed the strongest associations of lower survival with prior antibiotic exposure.
    Conclusion: Antibiotic exposure within 180 days before non-ICI systemic cancer treatment is associated with poorer survival. If confirmed in other studies, it provides another reason for vigilant antibiotic stewardship.
    MeSH term(s) Anti-Bacterial Agents/therapeutic use ; Cohort Studies ; Humans ; Immunotherapy ; Lung Neoplasms/etiology ; Neoplasms/drug therapy ; New South Wales ; Retrospective Studies
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2022-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639306-8
    ISSN 1878-5921 ; 0895-4356
    ISSN (online) 1878-5921
    ISSN 0895-4356
    DOI 10.1016/j.jclinepi.2022.04.003
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    In stock of ZB MED Cologne/Königswinter

    Uh III Zs.206: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  8. Article ; Online: Consensus guidelines for the diagnosis and management of cryptococcosis and rare yeast infections in the haematology/oncology setting, 2021.

    Chang, Christina C / Hall, Victoria / Cooper, Celia / Grigoriadis, George / Beardsley, Justin / Sorrell, Tania C / Heath, Christopher H

    Internal medicine journal

    2022  Volume 51 Suppl 7, Page(s) 118–142

    Abstract: Cryptococcosis caused by the Cryptococcus neoformans-Cryptococcus gattii complex is an important opportunistic infection in people with immunodeficiency, including in the haematology/oncology setting. This may manifest clinically as cryptococcal ... ...

    Abstract Cryptococcosis caused by the Cryptococcus neoformans-Cryptococcus gattii complex is an important opportunistic infection in people with immunodeficiency, including in the haematology/oncology setting. This may manifest clinically as cryptococcal meningitis or pulmonary cryptococcosis, or be detected incidentally by cryptococcal antigenemia, a positive sputum culture or radiological imaging. Non-Candida, non-Cryptococcus spp. rare yeast fungaemia are increasingly common in this population. These consensus guidelines aim to provide clinicians working in the Australian and New Zealand haematology/oncology setting with clear guiding principles and practical recommendations for the management of cryptococcosis, while also highlighting important and emerging rare yeast infections and their recommended management.
    MeSH term(s) Australia/epidemiology ; Cryptococcosis/diagnosis ; Cryptococcosis/drug therapy ; Cryptococcus gattii ; Cryptococcus neoformans ; Hematology ; Humans ; Saccharomyces cerevisiae
    Language English
    Publishing date 2022-01-05
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 2045436-3
    ISSN 1445-5994 ; 1444-0903
    ISSN (online) 1445-5994
    ISSN 1444-0903
    DOI 10.1111/imj.15590
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    Zs.A 792: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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    Zs.MO 424: Show issues

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  9. Book ; Online: Persistence of the Omicron variant of SARS-CoV-2 in Australia

    Chang, Sheryl L. / Nguyen, Quang Dang / Martiniuk, Alexandra / Sintchenko, Vitali / Sorrell, Tania C. / Prokopenko, Mikhail

    The impact of fluctuating social distancing

    2022  

    Abstract: We modelled emergence and spread of the Omicron variant of SARS-CoV-2 in Australia between December 2021 and June 2022. This pandemic stage exhibited a diverse epidemiological profile with emergence of co-circulating sub-lineages of Omicron, further ... ...

    Abstract We modelled emergence and spread of the Omicron variant of SARS-CoV-2 in Australia between December 2021 and June 2022. This pandemic stage exhibited a diverse epidemiological profile with emergence of co-circulating sub-lineages of Omicron, further complicated by differences in social distancing behaviour which varied over time. Our study delineated distinct phases of the Omicron-associated pandemic stage, and retrospectively quantified the adoption of social distancing measures, fluctuating over different time periods in response to the observable incidence dynamics. We also modelled the corresponding disease burden, in terms of hospitalisations, intensive care unit occupancy, and mortality. Supported by good agreement between simulated and actual health data, our study revealed that the nonlinear dynamics observed in the daily incidence and disease burden were determined not only by introduction of sub-lineages of Omicron, but also by the fluctuating adoption of social distancing measures. Our high-resolution model can be used in design and evaluation of public health interventions during future crises.

    Comment: 30 pages, 12 figures, source code: https://doi.org/10.5281/zenodo.7325675
    Keywords Quantitative Biology - Populations and Evolution ; Computer Science - Multiagent Systems ; 92D30 ; 93A16 ; J.3 ; I.6
    Publishing date 2022-11-20
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Pangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene

    Svahn, Adam J / Suster, Carl J E / Chang, Sheryl L / Rockett, Rebecca J / Sim, Eby M / Cliff, Oliver M / Wang, Qinning / Arnott, Alicia / Ramsperger, Marc / Sorrell, Tania C / Sintchenko, Vitali / Prokopenko, Mikhail

    Microbiology spectrum

    2023  , Page(s) e0279122

    Abstract: A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome ... ...

    Abstract A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome analysis helped to quantify and isolate prophage content within the accessory partition of the pangenome. A prophage similar to Gifsy-1 (henceforth GF-1L) was found to occur in all isolates of the outbreak core SNP cluster, and in three other isolates. Further analysis revealed that the GF-1L prophage carried the
    Language English
    Publishing date 2023-03-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.02791-22
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