Publications by authors named "Deborah Holt"

70 Publications

First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans.

Microorganisms 2021 Apr 23;9(5). Epub 2021 Apr 23.

Scabies Laboratory, Infectious Diseases Program, Biology Department, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia.

Epidemiological studies link infection and impetigo. Scabies mites can promote (Group A ) and infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses. However, little is known about the composition and the function of the scabies-associated microbiota. Here, high-throughput whole-metagenome sequencing was used to explore the scabies-associated microbiome. Scabies mites including their immediate microenvironments were isolated from two patients with severe scabies in Northern Australia. Two ~45-50 million paired-end reads Illumina libraries were generated of which ~2 (5.1%) and 0.7 million (1.3%) microbial reads were filtered out by mapping to human (hg19) and mite draft genomes. Taxonomic profiling revealed a microbial community dominated by the phylum Firmicutes (A: 79% and B: 59%) and genera that comprise , , and . Assembly of the metagenome reads resulted in genome bins representing reference genomes of , (Group C/G), and . The contigs contained genes relevant to pathogenicity and antibiotics resistance. Confocal microscopy of a patient skin sample confirmed , Streptococci and in scabies mite gut and faeces and the surrounding skin. The study provides fundamental evidence for the association of opportunistic pathogens with scabies infection.
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http://dx.doi.org/10.3390/microorganisms9050907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8146700PMC
April 2021

Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome.

PLoS Negl Trop Dis 2021 02 24;15(2):e0009149. Epub 2021 Feb 24.

QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Background: The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings.

Methodology/principal Findings: High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings.

Conclusions/significance: This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.
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http://dx.doi.org/10.1371/journal.pntd.0009149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939366PMC
February 2021

Clinical and Molecular Epidemiology of an Emerging Panton-Valentine Leukocidin-Positive ST5 Methicillin-Resistant Staphylococcus aureus Clone in Northern Australia.

mSphere 2021 02 10;6(1). Epub 2021 Feb 10.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia

Recently, we identified a sequence type 5 (ST5) clone in northern Australia with discrepant trimethoprim-sulfamethoxazole (SXT) susceptibility results. We aimed to identify isolates of this clone using Vitek 2 SXT resistance as a proxy and to compare its epidemiology with those of other circulating strains. We collated Vitek 2 susceptibility data for isolates collected through our laboratory and conducted a prospective, case-control study comparing clinical, microbiological, epidemiological, and genomic data for subsets of isolates reported as SXT resistant (cases) and SXT susceptible (controls) by Vitek 2. While overall SXT resistance rates remained relatively stable from 2011 to 2018 among 27,721 isolates, non-multidrug-resistant methicillin-resistant (MRSA) strains almost completely replaced multidrug-resistant MRSA strains as the predominant SXT-resistant MRSA phenotype. Demographic and clinical features of 51 case-control pairs were similar, but genotyping revealed stark differences: clonal complex 5 (CC5) MRSA predominated among SXT-resistant cases (34/51 [67%]), while CC93 MRSA predominated among susceptible controls (26/51 [51%]). All CC5 isolates were an ST5 clonal lineage that possessed the trimethoprim resistance gene within SCC IVo; all were SXT susceptible by Etest. The replacement of Vitek 2 reported SXT-resistant multidrug-resistant MRSA by non-multidrug-resistant MRSA appears related to the emergence of an ST5-MRSA-SCC IVo clone that is SXT susceptible by Etest and causes clinical disease similar to that caused by ST93-MRSA-SCC IVa. Reliance on Vitek 2 SXT reporting may lead to unnecessary restriction of effective oral treatment options for infections. Whether the presence of within SCC IVo provides a selective advantage at the population level is currently unclear. is an important human pathogen that causes a wide range of clinical infections. In the past 2 decades, an epidemic of community-associated skin and soft tissue infections has been driven by strains with specific virulence factors and resistance to beta-lactam antibiotics. Recently, an strain with discrepant antimicrobial susceptibility testing results has emerged in northern Australia. This ST5-MRSA-SCC IVo clone is reported as resistant to trimethoprim-sulfamethoxazole by Vitek 2 but susceptible by phenotypic methods. ST5-MRSA-SCC IVo is now the second most common community-associated MRSA clone in parts of Australia and causes a spectrum of clinical disease similar to that caused by the virulent ST93-MRSA lineage. Whole-genome sequence analysis demonstrates that ST5-MRSA-SCCIVo is causing a clonal outbreak across a large geographical region. Although phenotypic testing suggests susceptibility to trimethoprim-sulfamethoxazole, it is unclear at this stage whether the presence of within SCC IVo provides a selective advantage at the population level.
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http://dx.doi.org/10.1128/mSphere.00651-20DOI Listing
February 2021

Longitudinal whole-genome based comparison of carriage and infection associated Staphylococcus aureus in northern Australian dialysis clinics.

PLoS One 2021 5;16(2):e0245790. Epub 2021 Feb 5.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.

Background: The study objective was to reveal reservoirs potentially leading to Staphylococcus aureus infections in haemodialysis clinic clients in the tropical north of the Australian Northern Territory (NT). This client population are primarily Aboriginal Australians who have a greater burden of ill health than other Australians. Reservoir identification will enhance infection control in this client group, including informing potential S. aureus decolonisation strategies.

Methods And Findings: The study participants were 83 clients of four haemodialysis clinics in the Darwin region of the NT, and 46 clinical staff and researchers who had contact with the clinic clients. The study design was longitudinal, encompassing swabbing of anatomical sites at two month intervals to yield carriage isolates, and also progressive collection of infection isolates. Swab sampling was performed for all participants, and infection isolates collected for dialysis clients only. Analysis was based on the comparison of 139 carriage isolates and 27 infection isolates using whole genome sequencing. Genome comparisons were based on of 20,651 genome-wide orthologous SNPs, presence/absence of the mecA and pvl genes, and inferred multilocus sequence type and clonal complex. Pairs of genomes meeting the definition of "not discriminated" were classed as defining potential transmission events. The primary outcome was instances of potential transmission between a carriage site other than a skin lesion and an infection site, in the same individual. Three such instances were identified. Two involved ST762 (CC1) PVL- MRSA, and one instance ST121 PVL+ MSSA. Three additional instances were identified where the carriage strains were derived from skin lesions. Also identified were six instances of potential transmission of a carriage strains between participants, including transmission of strains between dialysis clients and staff/researchers, and one potential transmission of a clinical strain between participants. There were frequent occurrences of longitudinal persistence of carriage strains in individual participants, and two examples of the same strain causing infection in the same participants at different times. Strains associated with infections and skin lesions were enriched for PVL and mecA in comparison to strains associated with long term carriage.

Conclusions: This study indicated that strains differ with respect to propensity to stably colonise sites such as the nose, and cause skin infections. PVL+ strains were associated with infection and skin lesions and were almost absent from the carriage sites. PVL- MRSA (mainly CC1) strains were associated with infection and also with potential transmission events involving carriage sites, while PVL- MSSA were frequently observed to stably colonise individuals without causing infection, and to be rarely transmitted. Current clinical guidelines for dialysis patients suggest MRSA decolonisation. Implementation in this client group may impact infections by PVL- MRSA, but may have little effect on infection by PVL+ strains. In this study, the PVL+ strains were predominant causes of infection but rarely colonised typical carriage sites such as the nose, and in the case of ST121, were MSSA. The important reservoirs for infection by PVL+ strains appeared to be prior infections.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245790PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7864423PMC
February 2021

High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite.

PLoS Negl Trop Dis 2020 10 1;14(10):e0008720. Epub 2020 Oct 1.

Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. In humans, this mite causes a neglected tropical disease (NTD), called scabies. This disease results in major morbidity, disability, stigma and poverty globally and is often associated with secondary bacterial infections. Currently, anti-scabies treatments are not sufficiently effective, resistance to them is emerging and no vaccine is available. Here, we report the first high-quality genome and transcriptomic data for S. scabiei. The genome is 56.6 Mb in size, has a a repeat content of 10.6% and codes for 9,174 proteins. We explored key molecules involved in development, reproduction, host-parasite interactions, immunity and disease. The enhanced 'omic data sets for S. scabiei represent comprehensive and critical resources for genetic, functional genomic, metabolomic, phylogenetic, ecological and/or epidemiological investigations, and will underpin the design and development of new treatments, vaccines and/or diagnostic tests.
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http://dx.doi.org/10.1371/journal.pntd.0008720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591027PMC
October 2020

Correction to: Nevus of Ota - an intraoral presentation: a case report.

J Med Case Rep 2019 Aug 7;13(1):263. Epub 2019 Aug 7.

Oral Medicine Department, Liverpool University Dental Hospital, Liverpool, UK.

In the publication of this article [1], the figures were accidentally omitted due to an error. This has now been updated in the original article within the Case presentation section.
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http://dx.doi.org/10.1186/s13256-019-2194-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685178PMC
August 2019

Identification and Discrimination of Chlamydia trachomatis Ocular and Urogenital Strains and Major Phylogenetic Lineages by CtGEM Typing, A Double-Locus Genotyping Method.

Methods Mol Biol 2019 ;2042:87-122

Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.

CtGEM typing was developed to subdivide the bacterial species Chlamydia trachomatis on the basis of genome phylogeny and anatomical tropism. The rationale was facilitation of surveillance for ocular strains, although the method is applicable to essentially any C. trachomatis surveillance application that does not require high resolution. CtGEM is a double-locus genotyping method. The loci included in the assay were identified by computerized analysis of 65 complete genomes for resolution optimized sets of single nucleotide polymorphisms (SNPs). From this, two PCR amplifiable fragments were defined. One, rg1, is within a hypothetical gene annotated as Jali-1891 within the C. trachomatis B_Jali20 genome. The other, ofr, is within the ompA gene which encodes the major outer membrane protein. Variation in rg1 is conferred by two SNPs defining four haplotypes that exhibit concordance with genome phylogeny. Variation within ofr is more complex and allows for inference of ompA genotype, either to the level of single genotype, or group of closely related genotypes. Two CtGEM formats were developed. One is based on interrogation of the two loci by high resolution melting analysis (HRMA), and the other based on analysis of the loci by Sanger sequencing. The genotypes defined identify known ocular genotypes, discriminate known ocular genotypes from each other, discriminate the major phylogenetic lineages of the species, and discriminate all ompA genotypes with the exception of closely related variants within the genotypes H, I, J cluster. The Sanger sequencing format provides slightly more resolution that the HRMA format with respect to ompA genotype. An unusual aspect of this method is that all possible combinations of rg1 haplotype, and inferred ompA genotype(s) have been given CtGEM typing numbers. This includes types that at this time have not been shown to exist.
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http://dx.doi.org/10.1007/978-1-4939-9694-0_8DOI Listing
April 2020

Concerns for efficacy of a 30-valent M-protein-based Streptococcus pyogenes vaccine in regions with high rates of rheumatic heart disease.

PLoS Negl Trop Dis 2019 07 3;13(7):e0007511. Epub 2019 Jul 3.

Menzies School of Health Research, Division of Global and Tropical Health, Darwin, Australia.

The prevalence of rheumatic heart disease (RHD) in the Aboriginal population of the Australian Northern Territory is high, and Streptococcus pyogenes skin infections likely contribute to this. A promising candidate S. pyogenes "30mer" vaccine is composed of 30 pharyngitis associated type-specific antigens from the S. pyogenes M protein. Cross opsonisation experiments suggest that 30mer vaccine protection may extend to non-cognate emm types. A new "emm cluster" scheme for classifying M protein is based on the full-length coding sequence, and correlates with functional and immunological properties, and anatomical tropism. Twenty-seven years of research in the Northern Territory has yielded 1810 S. pyogenes isolates with clinical and emm type data. The primary aim was to analyse these data with reference to the emm cluster scheme and cross opsonisation information, to inform estimation of 30mer vaccine efficacy in the Northern Territory. The isolates encompass 101 emm types. Variants of cluster A-C were enriched in throat isolates, and variants of emm cluster D enriched in skin isolates. Throat isolates were enriched for 30mer vaccine cognate emm types in comparison with skin isolates of which only 25% were vaccine emm types. While cross opsonisation data indicates potential for enhancing 30mer vaccine coverage, more than one third of skin isolates were within 38 emm types untested for cross opsonisation. Emm cluster D variants, in particular emm cluster D4, were not only all non-cognate with the vaccine, but were abundant and diverse, and less likely to be cross-opsonisation positive than other emm clusters. Long term persistence of many emm types in the study area was revealed. It was concluded that the 30mer vaccine efficacy in the Northern Territory will likely require both cross protection, and additional measures to elicit immunity against variants of emm cluster D.
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http://dx.doi.org/10.1371/journal.pntd.0007511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6634427PMC
July 2019

Nevus of Ota - an intraoral presentation: a case report.

J Med Case Rep 2019 Jun 7;13(1):174. Epub 2019 Jun 7.

Oral Medicine Department, Liverpool University Dental Hospital, Liverpool, UK.

Background: Nevus of Ota or "oculodermal melanocytosis" is a rare congenital hamartoma of dermal melanocytes causing a blue-gray hyperpigmentation of the eye and surrounding structures. The condition, originally described by Ota and Tanino in 1939, mainly affects the ophthalmic and maxillary divisions of the trigeminal nerve. We describe the first reported case of unilateral oculodermal melanocytosis in a Caucasian woman with oral buccal mucosal involvement. Oral involvement of nevus of Ota is very rare.

Case Presentation: A 48-year-old Caucasian woman was referred by the dermatology division to the oral medicine department at the University of Liverpool School of Dentistry with new-onset oral pigmentation to the left buccal mucosa. The patient had a previous diagnosis of oculodermal nevus.

Conclusion: An incisional biopsy of the left buccal mucosa was completed. The report stated that histological and immunohistochemical features were in keeping with a blue nevus, but within the context of the preexisting occulodermal pigmentation, a diagnosis of oculodermal melanocytosis, also known as "nevus of Ota," was made. The patient will be kept under review in the oral medicine department because the progression of the lesion on the left buccal mucosa requires active monitoring owing to the potential for malignant change. The patient also requires regular review in the dermatology and ophthalmology divisions.
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http://dx.doi.org/10.1186/s13256-019-2101-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6554954PMC
June 2019

Potential for Molecular Testing for Group A Streptococcus to Improve Diagnosis and Management in a High-Risk Population: A Prospective Study.

Open Forum Infect Dis 2019 Apr 26;6(4):ofz097. Epub 2019 Feb 26.

Menzies School of Health Research, Charles Darwin University.

Background: In high-burden settings, guidelines recommend antibiotic treatment for all suspected group A (GAS) infections to prevent rheumatic fever and poststreptococcal glomerulonephritis. Highly sensitive rapid GAS tests could reduce unnecessary antibiotic use in these settings.

Methods: This was a prospective study of the Xpert Xpress Strep A (Cepheid) molecular test compared with culture of throat swab samples collected at a referral hospital in northern Australia. Demographic and clinical data and results of streptococcal serology and culture were collected.

Results: Of 164 throat swab samples, 145 (88%) were eligible for inclusion; 49 (34%) were molecular test positive and 24 (17%) were culture positive for GAS. The sensitivity, specificity, and positive and negative predictive values for the molecular test versus culture were 100.0%, 79.3%, 48.8%, and 100.0%, respectively. Among 25 samples testing positive with the molecular test and negative with culture, group C or G streptococci were cultured in 2, and a plausible clinical explanation, such as pharyngotonsillitis, or rheumatic fever with positive results of streptococcal serology, was apparent in 19 instances. In 25 patients with rheumatic fever or poststreptococcal glomerulonephritis diagnoses, molecular testing nearly trebled the detection of GAS in throat swab samples, from 3 (12%) detected with culture to 8 (32%) detected with molecular testing. Reasons for "false-positive" molecular test results could include the presence of GAS below the threshold of culture detection or persistence of nonviable organisms after infection.

Conclusion: Implementation of molecular testing could improve antibiotic use in this high-burden setting. The incremental yield in poststreptococcal syndromes, by which time cultures are negative, has high potential in the diagnostic workup of autoimmune poststreptococcal syndromes and warrants further investigation.
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http://dx.doi.org/10.1093/ofid/ofz097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469435PMC
April 2019

A cluster of acute rheumatic fever cases among Aboriginal Australians in a remote community with high baseline incidence.

Aust N Z J Public Health 2019 Jun 17;43(3):288-293. Epub 2019 Apr 17.

Northern Territory Centre for Disease Control, Northern Territory.

Objectives: We report a cluster of acute rheumatic fever (ARF) cases and the public health response in a high-burden Australian setting.

Methods: The public health unit was notified of an increase in ARF cases in a remote Australian Aboriginal community. A multi-disciplinary group coordinated the response. Household contacts were screened for ARF or group A Streptococcus (GAS) infection by questionnaire and swab collection, offered an echocardiogram if aged 5-20 years, and intramuscular benzathine benzylpenicillin if aged over one year or if less than one year with impetigo.

Results: Fifteen definite and seven probable ARF cases were diagnosed in the community in July-December 2014 (all-age incidence of definite ARF: 1,473/100,000). The public health response identified two additional cases of ARF. A total of 81 contacts were screened; GAS was detected in 3/76 (4%) throat swabs and 11/24 (46%) skin swabs. Molecular typing revealed high GAS strain diversity.

Conclusions: The incidence of ARF during this cluster was very high. Carriage and infection with GAS was observed, but no outbreak strain identified. Implications for public health: A national public health guideline has since been developed that includes advice on the investigation of an ARF outbreak/cluster. Sustained efforts with strong community engagement are required to tackle high ARF rates.
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http://dx.doi.org/10.1111/1753-6405.12893DOI Listing
June 2019

Soil-Transmitted Helminths in Children in a Remote Aboriginal Community in the Northern Territory: Hookworm is Rare but Strongyloides stercoralis and Trichuris trichiura Persist.

Trop Med Infect Dis 2017 Oct 4;2(4). Epub 2017 Oct 4.

Menzies School of Health Research, Charles Darwin University, Darwin NT 0811, Australia.

(1) Background: soil-transmitted helminths are a problem worldwide, largely affecting disadvantaged populations. The little data available indicates high rates of infection in some remote Aboriginal communities in Australia. Studies of helminths were carried out in the same remote community in the Northern Territory in 1994⁻1996 and 2010⁻2011; (2) Methods: fecal samples were collected from children aged <10 years and examined for helminths by direct smear microscopy. In the 2010⁻2011 study, some fecal samples were also analyzed by agar plate culture and PCR for Strongyloides stercoralis DNA. Serological analysis of fingerprick dried blood spots using a S. stercoralis NIE antigen was also conducted; (3) Results and Conclusions: a reduction in fecal samples positive for S. stercoralis, hookworm and Trichuris trichiura was seen between the studies in 1994⁻1996 and 2010⁻2011, likely reflecting public health measures undertaken in the region to reduce intestinal helminths. Comparison of methods to detect S. stercoralis showed that PCR of fecal samples and serological testing of dried blood spots was at least as sensitive as direct smear microscopy and agar plate culture. These methods have advantages for use in remote field studies.
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http://dx.doi.org/10.3390/tropicalmed2040051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082063PMC
October 2017

Global Scale Dissemination of ST93: A Divergent Epidemic Lineage That Has Recently Emerged From Remote Northern Australia.

Front Microbiol 2018 9;9:1453. Epub 2018 Jul 9.

Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, Australia.

In Australia, community-associated methicillin-resistant (MRSA) lineage sequence type (ST) 93 has rapidly risen to dominance since being described in the early 1990s. We examined 459 ST93 genome sequences from Australia, New Zealand, Samoa, and Europe to investigate the evolutionary history of ST93, its emergence in Australia and subsequent spread overseas. Comparisons with other genomes indicate that ST93 is an early diverging and recombinant lineage, comprising of segments from the ST59/ST121 lineage and from a divergent but currently unsampled Staphylococcal population. However, within extant ST93 strains limited genetic diversity was apparent with the most recent common ancestor dated to 1977 (95% highest posterior density 1973-1981). An epidemic ST93 population arose from a methicillin-susceptible progenitor in remote Northern Australia, which has a proportionally large Indigenous population, with documented overcrowded housing and a high burden of skin infection. Methicillin-resistance was acquired three times in these regions, with a clade harboring a staphylococcal cassette chromosome (SCC) IVa expanding and spreading to Australia's east coast by 2000. We observed sporadic and non-sustained introductions of ST93-MRSA-IVa to the United Kingdom. In contrast, in New Zealand, ST93-MRSA-IVa was sustainably transmitted with clonal expansion within the Pacific Islander population, who experience similar disadvantages as Australian Indigenous populations. ST93 has a highly recombinant genome including portions derived from an early diverging population. Our findings highlight the need to understand host population factors in the emergence and spread of antimicrobial resistant community pathogens.
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http://dx.doi.org/10.3389/fmicb.2018.01453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6047344PMC
July 2018

Phylogenetic relationships, stage-specific expression and localisation of a unique family of inactive cysteine proteases in Sarcoptes scabiei.

Parasit Vectors 2018 05 16;11(1):301. Epub 2018 May 16.

QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.

Background: Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites. We postulated that the SMIPP-Cs have evolved as an adaptation to the parasitic lifestyle of the scabies mite. To formulate testable hypotheses for their functions and to propose possible strategies for translational research we investigated whether the SMIPP-Cs are common to all scabies mite varieties and where within the mite body as well as when throughout the parasitic life-cycle they are expressed.

Results: SMIPP-C sequences from human, pig and dog mites were analysed bioinformatically and the phylogenetic relationships between the SMIPP-C multi-copy gene families of human, pig and dog mites were established. Results suggest that amplification of the SMIPP-C genes occurred in a common ancestor and individual genes evolved independently in the different mite varieties. Recombinant human mite SMIPP-C proteins were produced and used for murine polyclonal antibody production. Immunohistology on skin sections from human patients localised the SMIPP-Cs in the mite gut and in mite faeces within in the epidermal skin burrows. SMIPP-C transcription into mRNA in different life stages was assessed in human and pig mites by reverse transcription followed by droplet digital PCR (ddPCR). High transcription levels of SMIPP-C genes were detected in the adult female life stage in comparison to all other life stages.

Conclusions: The fact that the SMIPP-Cs are unique to three Sarcoptes varieties, present in all burrowing life stages and highly expressed in the digestive system of the infective adult female life stage may highlight an essential role in parasitism. As they are excreted from the gut in scybala they presumably are able to interact or interfere with host proteins present in the epidermis.
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http://dx.doi.org/10.1186/s13071-018-2862-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5956821PMC
May 2018

CtGEM typing: Discrimination of Chlamydia trachomatis ocular and urogenital strains and major evolutionary lineages by high resolution melting analysis of two amplified DNA fragments.

PLoS One 2018 10;13(4):e0195454. Epub 2018 Apr 10.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Chlamydia trachomatis infects the urogenital tract (UGT) and eyes. Anatomical tropism is correlated with variation in the major outer membrane protein encoded by ompA. Strains possessing the ocular ompA variants A, B, Ba and C are typically found within the phylogenetically coherent "classical ocular lineage". However, variants B, Ba and C have also been found within three distinct strains in Australia, all associated with ocular disease in children and outside the classical ocular lineage. CtGEM genotyping is a method for detecting and discriminating ocular strains and also the major phylogenetic lineages. The rationale was facilitation of surveillance to inform responses to C. trachomatis detection in UGT specimens from young children. CtGEM typing is based on high resolution melting analysis (HRMA) of two PCR amplified fragments with high combinatorial resolving power, as defined by computerised comparison of 65 whole genomes. One fragment is from the hypothetical gene defined by Jali-1891 in the C. trachomatis B_Jali20 genome, while the other is from ompA. Twenty combinatorial CtGEM types have been shown to exist, and these encompass unique genotypes for all known ocular strains, and also delineate the TI and T2 major phylogenetic lineages, identify LGV strains and provide additional resolution beyond this. CtGEM typing and Sanger sequencing were compared with 42 C. trachomatis positive clinical specimens, and there were no disjunctions. CtGEM typing is a highly efficient method designed and tested using large scale comparative genomics. It divides C. trachomatis into clinically and biologically meaningful groups, and may have broad application in surveillance.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0195454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5892870PMC
July 2018

Staphylococcus aureus Prostatic abscess: a clinical case report and a review of the literature.

BMC Infect Dis 2017 07 21;17(1):509. Epub 2017 Jul 21.

Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia.

Background: Prostatic abscess is a rare complication of acute bacterial prostatitis and is most commonly caused by Enterobacteriaceae. We report on a case of prostatic abscess caused by Staphylococcus aureus and conduct a review of the literature.

Case Presentative: We present a case of S. aureus prostatic abscess that was successfully treated with a combination of antibiotic and surgical therapy. The isolate was non–multidrug-resistant, methicillin-resistant Staphylococcus aureus and was genotyped as clonal complex 5, an emerging regional clone that is trimethoprim resistant and Panton-Valentine leukocidin positive. This current case report is the first to describe the use of clindamycin step-down therapy. A literature review identified a further 39 cases of S. aureus prostatic abscesses, of which 26 were methicillin resistant.

Conclusion: S. aureus is an uncommon cause of prostatic abscess. Optimal management includes both antibiotic therapy and surgical drainage. Our use of clindamycin as step-down therapy was guided by its excellent prostatic penetration.
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http://dx.doi.org/10.1186/s12879-017-2605-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5521102PMC
July 2017

Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections.

PeerJ 2017 22;5:e3487. Epub 2017 Jun 22.

Division of Global and Tropical Health, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Background: The microbiome of built environment surfaces is impacted by the presence of humans. In this study, we tested the hypothesis that analysis of surface swabs from clinic toilet/bathroom yields results correlated with sexually transmitted infection (STI) notifications from corresponding human populations. We extended a previously reported study in which surfaces in toilet/bathroom facilities in primary health clinics in the Australian Northern Territory (NT) were swabbed then tested for nucleic acid from the STI agents and . This was in the context of assessing the potential for such nucleic acid to contaminate specimens collected in such facilities. STIs are notifiable in the NT, thus allowing comparison of swab and notification data.

Methods: An assumption in the design was that while absolute built environment loads of STI nucleic acids will be a function of patient traffic density and facility cleaning protocols, the relative loads of STI nucleic acids from different species will be largely unaffected by these processes. Another assumption was that the proportion of swabs testing positive for STIs provides a measure of surface contamination. Accordingly, "STI profiles" were calculated. These were the proportions that each of the three STIs of interest contributed to the summed STI positive swabs or notifications. Three comparisons were performed, using swab data from clinics in remote Indigenous communities, clinics in small-medium towns, and a single urban sexual health clinic. These data were compared with time and place-matched STI notifications.

Results: There were significant correlations between swab and notifications data for the both the remote Indigenous and regional data. For the remote Indigenous clinics the values ranged from 0.041 to 0.0089, depending on data transformation and value inference method. Further, the swab data appeared to strongly indicate known higher relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded values from 0.0088-0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated.

Discussion: Strong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for , although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs.
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http://dx.doi.org/10.7717/peerj.3487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483037PMC
June 2017

Management of proliferative verrucous leukoplakia: Justification for a conservative approach.

Head Neck 2017 10 22;39(10):1997-2003. Epub 2017 Jun 22.

Mersey Head and Neck Oncology Research Group (MHNORG), Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.

Background: Proliferative verrucous leukoplakia (PVL) is a progressive, multifocal, exophytic form of leukoplakia with high rates of malignant transformation. The purpose of this study was to evaluate a cohort of patients with PVL in a single tertiary referral clinic.

Method: Cases meeting accepted diagnostic criteria were reviewed with regard to their pathology, demographic characteristics, management, and outcomes. Human papillomavirus (HPV) testing was undertaken on a subset.

Results: Almost half of the 48 patients with PVL (48%; n = 23) underwent malignant transformation after a median 23.4 months. The characteristics of this cohort were similar to those previously described, but management was notably more conservative. Conservative management of PVL was used in 92% of our patients, but the clinical outcomes seem comparable with previously described cohorts in which PVL was predominantly treated by surgical excision. All HPV testing was negative.

Conclusion: Aggressive surgical intervention in the premalignant phase of PVL may not influence the rate of malignant transformation.
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http://dx.doi.org/10.1002/hed.24845DOI Listing
October 2017

Contaminated fingers: a potential cause of positive urine specimens.

Sex Transm Infect 2018 02 9;94(1):32-36. Epub 2017 Jun 9.

Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Objectives: The detection of an STI agent in a urogenital tract (UGT) specimen from a young child is regarded as being indicative of sexual abuse. However, the probabilities of contamination events that could conceivably lead to STI positive specimens in the absence of sexual contact are unclear. The objective was to estimate the potential for fingers that have come in contact with positive urine to detectably contaminate negative urine.

Methods: The study design was based on self-experimentation. Dilutions of elementary bodies (EBs) were prepared. A participant contacted an EB dilution then a urine surrogate specimen. The experiment was performed by three participants using three isolates, of genotype E, F and B. Two surrogate urine contact methods were used to mimic contamination of a carer assisting with a child's urine collection. All EB dilutions and urine surrogate specimens were subjected to assay and quantification in a real-time PCR-based diagnostic system.

Results: The amplimer crossing point (Cq) for EB dilutions was 10.0±1.6 less than for corresponding finger contacted urine specimens, which corresponds to ~10 µL of EB suspension transferred. This was largely independent of participant identity, strain or EB dilution. Hand decontamination led to large reductions in EBs transferred, but transfer remained consistently detectable. Recent Cq data from positive clinical urine specimens were collated, and 20% clearly contained sufficient to detectably contaminate another specimen by finger-mediated transfer, as in this experiment.

Conclusions: This study directly demonstrated the potential for urine contaminated fingers to convert a negative urine specimen to positive as a result of contact. Accordingly, procedures for urine specimen collection, particularly from children, need to be designed to prevent contamination.
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http://dx.doi.org/10.1136/sextrans-2016-053081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800334PMC
February 2018

High burden of complicated skin and soft tissue infections in the Indigenous population of Central Australia due to dominant Panton Valentine leucocidin clones ST93-MRSA and CC121-MSSA.

BMC Infect Dis 2017 06 7;17(1):405. Epub 2017 Jun 7.

Alice Springs Hospital, Alice Springs, Northern Territory, Australia.

Background: Superficial skin and soft tissue infections (SSTIs) are common among the Indigenous population of the desert regions of Central Australia. However, the overall burden of disease and molecular epidemiology of Staphylococcus aureus complicated SSTIs has yet to be described in this unique population.

Methods: Alice Springs Hospital (ASH) admission data was interrogated to establish the population incidence of SSTIs. A prospective observational study was conducted on a subset of S. aureus complicated SSTIs (carbuncles and furuncles requiring surgical intervention) presenting during a one month period to further characterize the clinical and molecular epidemiology. High resolution melting analysis was used for clonal complex discrimination. Real-time polymerase chain reaction identifying the lukF component of the Panton Valentine leucocidin (pvl) gene determined pvl status. Clinical and outcome data was obtained from the ASH medical and Northern Territory shared electronic health records.

Results: SSTIs represented 2.1% of ASH admissions during 2014. 82.6% occurred in Indigenous patients (n = 382) with an estimated incidence of 18.9 per 1, 000 people years compared to the non-Indigenous population of 2.9 per 1000, with an incident rate ratio of 6.6 (95% confidence interval 5.1-8.5). Clinical and molecular analysis was performed on 50 isolates from 47 patients. Community-associated methicillin-resistant S. aureus (CA-MRSA) predominated (57% of isolates). The high burden of SSTIs is partly explained by the prevalence of pvl positive strains of S. aureus (90% isolates) for both CA-MRSA and methicillin-susceptible S. aureus (MSSA). ST93-MRSA and CC121-MSSA were the most prevalent clones. SSTIs due to ST93-MRSA were more likely to require further debridement (p = 0.039), however they also more frequently received inactive antimicrobial therapy (p < 0.001).

Conclusions: ST93-MRSA and CC121-MSSA are the dominant causes of carbuncles and furuncles in Central Australia. Both of these virulent clones harbor pvl but the impact on clinical outcomes remains uncertain. The high prevalence of CA-MRSA supports empiric vancomycin use in this population when antimicrobial therapy is indicated. Prompt surgical intervention remains the cornerstone of treatment.
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http://dx.doi.org/10.1186/s12879-017-2460-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5463332PMC
June 2017

Strongyloides seroprevalence before and after an ivermectin mass drug administration in a remote Australian Aboriginal community.

PLoS Negl Trop Dis 2017 May 15;11(5):e0005607. Epub 2017 May 15.

Menzies School of Health Research, Charles Darwin University, Darwin, Australia.

Background: Strongyloides seroprevalence is hyper-endemic in many Australian Aboriginal and Torres Strait Islander communities, ranging from 35-60%. We report the impact on Strongyloides seroprevalence after two oral ivermectin mass drug administrations (MDAs) delivered 12 months apart in a remote Australian Aboriginal community.

Methods: Utilizing a before and after study design, we measured Strongyloides seroprevalence through population census with sequential MDAs at baseline and month 12. Surveys at months 6 and 18 determined changes in serostatus. Serodiagnosis was undertaken by ELISA that used sonicated Strongyloides ratti antigen to detect anti-Strongyloides IgG. Non-pregnant participants weighing ≥15 kg were administered a single 200 μg/kg ivermectin dose, repeated after 10-42 days if Strongyloides and/or scabies was diagnosed; others followed a standard alternative algorithm. A questionnaire on clinical symptoms was administered to identify adverse events from treatment and self-reported symptoms associated with serostatus.

Findings: We surveyed 1013 participants at the baseline population census and 1060 (n = 700 from baseline cohort and 360 new entrants) at month 12. Strongyloides seroprevalence fell from 21% (175/818) at baseline to 5% at month 6. For participants from the baseline cohort this reduction was sustained at month 12 (34/618, 6%), falling to 2% at month 18 after the second MDA. For new entrants to the cohort at month 12, seroprevalence reduced from 25% (75/297) to 7% at month 18. Strongyloides positive seroconversions for the baseline cohort six months after each MDA were 2.5% (4/157) at month 6 and 1% at month 18, whilst failure to serorevert remained unchanged at 18%. At 12 months, eosinophilia was identified in 59% of baseline seropositive participants and 89% of seropositive new entrants, compared with 47%baseline seronegative participants and 51% seronegative new entrants. Seropositivity was not correlated with haemoglobin or any self-reported clinical symptoms. Clinical symptoms ascertained on the day of treatment and 24-72 hrs after, did not identify any adverse events.

Significance: Two community ivermectin MDAs delivered 12 months apart by trained Aboriginal researchers in collaboration with non-Indigenous researchers resulted in a sustained and significant reduction in Strongyloides seroprevalence over 18 months. Similar reductions were seen in the baseline cohort and new entrants.
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http://dx.doi.org/10.1371/journal.pntd.0005607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444847PMC
May 2017

Whole genome sequencing to investigate a putative outbreak of the virulent community-associated methicillin-resistant ST93 clone in a remote Indigenous community.

Microb Genom 2016 12 12;2(12):e000098. Epub 2016 Dec 12.

1​Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

We report two cases of severe pneumonia due to clone ST93 methicillin-resistant (MRSA) presenting from a remote Australian Indigenous community within a 2-week period, and the utilization of whole genome sequences to determine whether these were part of an outbreak. was isolated from 12 of 92 nasal swabs collected from 25 community households (including the two index households); one isolate was ST93. Three of five skin lesion isolates obtained at the community were ST93. Whole genome sequencing of the ST93 isolates from this study and a further 20 ST93 isolates from the same region suggested that recent transmission and progression to disease had not taken place. The proximity in time and space of the two severe pneumonia cases is probably a reflection of the high burden of disease due to ST93 MRSA in this population where skin infections and household crowding are common.
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http://dx.doi.org/10.1099/mgen.0.000098DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5359412PMC
December 2016

Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis.

Gigascience 2016 06 2;5(1):23. Epub 2016 Jun 2.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.

Background: The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans and mange in other animal species. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where secondary group A streptococcal and Staphylococcus aureus infections of scabies sores are thought to drive the high rate of rheumatic heart disease and chronic kidney disease.

Results: We sequenced the genome of two samples of Sarcoptes scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of Sarcoptes scabiei var. suis from a pig model. Because of the small size of the scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins.

Conclusions: We have developed extensive genomic resources for the scabies mite, including reference genomes and a preliminary annotation.
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http://dx.doi.org/10.1186/s13742-016-0129-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4890329PMC
June 2016

Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections.

PLoS Negl Trop Dis 2016 Feb 12;10(2):e0004384. Epub 2016 Feb 12.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.

The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis) and two human patients (S. scabiei var. hominis) living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs) and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1-3 distinct haplotypes per infestation.
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http://dx.doi.org/10.1371/journal.pntd.0004384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4752359PMC
February 2016

Chlamydia trachomatis genotypes in a cross-sectional study of urogenital samples from remote Northern and Central Australia.

BMJ Open 2016 Jan 6;6(1):e009624. Epub 2016 Jan 6.

Sexual Assault Referral Centre (Darwin), Northern Territory Government, Darwin, Northern Territory, Australia Northern Territory Medical Program, Flinders University, Darwin, Northern Territory, Australia Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.

Objectives: The objective was to determine the frequency of trachoma genotypes of Chlamydia trachomatis-positive urogenital tract (UGT) specimens from remote areas of the Australian Northern Territory (NT).

Setting: The setting was analysis of remnants of C. trachomatis positive primarily UGT specimens obtained in the course of clinical practice. The specimens were obtained from two pathology service providers.

Participants: From 3356 C. trachomatis specimens collected during May 2012-April 2013, 439 were selected for genotyping, with a focus on specimens from postpubescent patients, in remote Aboriginal communities where ocular trachoma is potentially present.

Primary And Secondary Outcome Measures: The primary outcome measure was the proportion of successfully genotyped UGT specimens that were trachoma genotypes. The secondary outcome measures were the distribution of genotypes, and the frequencies of different classes of specimens able to be genotyped.

Results: Zero of 217 successfully genotyped UGT specimens yielded trachoma genotypes (95% CI for frequency=0-0.017). For UGT specimens, the genotypes were E (41%), F (22%), D (21%) and K (7%), with J, H and G and mixed genotypes each at 1-4%. Four of the five genotyped eye swabs yielded trachoma genotype Ba, and the other genotype J. Two hundred twenty-two specimens (50.6%) were successfully genotyped. Urine specimens were less likely to be typable than vaginal swabs (p<0.0001).

Conclusions: Unlike in some other studies, in the remote NT, trachoma genotypes of C. trachomatis were not found circulating in UGT specimens from 2012 to 2013. Therefore, C. trachomatis genotypes in UGT specimens from young children can be informative as to whether the organism has been acquired through sexual contact. We suggest inclusion of C. trachomatis genotyping in guidelines examining the source of sexually transmitted infections in young children in areas where trachoma genotypes may continue to circulate, and continued surveillance of UGT C. trachomatis genotypes.
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http://dx.doi.org/10.1136/bmjopen-2015-009624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4716167PMC
January 2016

Invasive Staphylococcus aureus Infections in Children in Tropical Northern Australia.

J Pediatric Infect Dis Soc 2014 Dec 26;3(4):304-11. Epub 2014 Mar 26.

Royal Darwin Hospital, Darwin, Australia; Menzies School of Health Research, Darwin, Australia;

Background: Despite a high burden of staphylococcal skin disease in children and high incidence of Staphylococcus aureus bacteremia in adult Indigenous populations in northern Australia, there are few studies describing incidence or clinical information of invasive S aureus (ISA) infections in children.

Methods: We conducted a retrospective review for all cases of S aureus bacteremia and sterile site infections, for children under 15 years, in northern Australia over a 4-year period (2007-2010). Cases were categorized as neonatal (<28 days) and pediatric (≥28 days).

Results: Forty-four cases (9 neonatal, 35 pediatric) were identified. The annual incidence of ISA was 27.9 cases per 100 000 population. Among pediatric cases, the annual incidence was significantly higher in the Indigenous (46.6) compared with the non-Indigenous (4.4) population (IRR: 10.6 [95% confidence interval, 3.8-41.4]). Pediatric infections were predominantly community-associated (86%). Clinical infection sites included osteoarticular (66%), pleuropulmonary (29%), and endocarditis (9%), and multifocal disease was common (20%). Eighty-three percent of pediatric cases presented with sepsis; 34% resulted in intensive care admission. Neonatal cases were all born prematurely; 89% were late-onset infections. Overall, 27% of infections were due to methicillin-resistant S aureus (MRSA). Compared with methicillin-sensitive S aureus (MSSA), there was no difference in severity or presentation in pediatric MRSA cases, but a higher proportion of MRSA cases were readmitted.

Conclusions: The annual incidence of ISA infection in this study is among the highest described, largely due to a disproportionate burden in Indigenous children. Infections are frequently severe and infection with MRSA is common. Children presenting with suspected ISA in this region should be treated empirically for MRSA.
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http://dx.doi.org/10.1093/jpids/piu013DOI Listing
December 2014

The Importance of Scabies Coinfection in the Treatment Considerations for Impetigo.

Pediatr Infect Dis J 2016 Apr;35(4):374-8

From the *Royal Children's Hospital Melbourne, Melbourne, Australia; †Royal Darwin Hospital, Darwin, Australia; ‡Menzies School of Health Research, Charles Darwin University, Darwin, Australia; §Telethon Kids Institute, University of Western Australia, Perth, Australia; and ¶Princess Margaret Hospital for Children, Perth, Australia.

Background: Skin infections account for a high disease burden in indigenous children living in northern Australia. Although the relationship between impetigo and scabies is recognized, the prevalence of scabies in children with impetigo is not well reported. We report the prevalence, demographics and treatment success outcomes of impetigo and scabies coinfection in indigenous children who were participants in a randomized controlled trial of impetigo treatment conducted in remote communities of the Northern Territory, Australia.

Methods: Of 1715 screening episodes for impetigo, 508 children were randomized to receive intramuscular benzathine benzylpenicillin (BPG), twice daily co-trimoxazole (SXT) for 3 days (4 mg/kg trimethoprim plus 20 mg/kg sulfamethoxazole per dose) or once daily SXT for 5 days (8 mg/kg trimethoprim plus 40 mg/kg sulfamethoxazole per dose). A clinical diagnosis of scabies; tinea of the skin, scalp or nail; and head lice was made on all children. Scabies presence was not confirmed using diagnostic scrapings. In a post-hoc analysis, we determined whether coinfection with scabies had an impact on treatment success for impetigo.

Results: Of children randomized to receive treatment for impetigo, 84 of 508 (16.5%) had scabies. The presence of scabies ranged from 14.3% to 20.0% in the 3 treatment groups. Treatment success for impetigo with and without scabies coinfection, independent of the treatment groups, was 75.9% and 86.6%, respectively, absolute difference 10.7% [95% confidence interval (CI): +1% to +21%]. Treatment success for impetigo with and without scabies coinfection in the BPG group was 69.6% and 88.0%, respectively, absolute difference 18.4% (95% CI: -1% to +38%). In the pooled SXT groups, the treatment success for impetigo with and without scabies coinfection was 78.6% and 86.0%, respectively, with absolute difference 7.4% (95% CI: -4% to +18%). Treatment success in the pooled SXT group with scabies (78.6%) was higher than in the BPG group (69.6%) with scabies, absolute difference 9.0% (95% CI: +0.1% to +18%). Prediction of treatment success for impetigo is dependent on the presence or absence of scabies and for scabies coinfected impetigo it was higher in the group treated with SXT.

Conclusions: The burden of scabies in an impetigo trial for Indigenous children was high. Treatment success for scabies coinfection was lower than for impetigo overall, with a higher success seen in the SXT group than the BPG group.
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http://dx.doi.org/10.1097/INF.0000000000001013DOI Listing
April 2016

Impact of an Ivermectin Mass Drug Administration on Scabies Prevalence in a Remote Australian Aboriginal Community.

PLoS Negl Trop Dis 2015 Oct 30;9(10):e0004151. Epub 2015 Oct 30.

Menzies School of Health Research, Charles Darwin University, Darwin, Australia.

Background: Scabies is endemic in many Aboriginal and Torres Strait Islander communities, with 69% of infants infected in the first year of life. We report the outcomes against scabies of two oral ivermectin mass drug administrations (MDAs) delivered 12 months apart in a remote Australian Aboriginal community.

Methods: Utilizing a before and after study design, we measured scabies prevalence through population census with sequential MDAs at baseline and month 12. Surveys at months 6 and 18 determined disease acquisition and treatment failures. Scabies infestations were diagnosed clinically with additional laboratory investigations for crusted scabies. Non-pregnant participants weighing ≥15 kg were administered a single 200 μg/kg ivermectin dose, repeated after 2-3 weeks if scabies was diagnosed, others followed a standard alternative algorithm.

Principal Findings: We saw >1000 participants at each population census. Scabies prevalence fell from 4% at baseline to 1% at month 6. Prevalence rose to 9% at month 12 amongst the baseline cohort in association with an identified exposure to a presumptive crusted scabies case with a higher prevalence of 14% amongst new entries to the cohort. At month 18, scabies prevalence fell to 2%. Scabies acquisitions six months after each MDA were 1% and 2% whilst treatment failures were 6% and 5% respectively.

Conclusion: Scabies prevalence reduced in the six months after each MDA with a low risk of acquisition (1-2%). However, in a setting where living conditions are conducive to high scabies transmissibility, exposure to presumptive crusted scabies and population mobility, a sustained reduction in prevalence was not achieved.

Clinical Trial Registration: Australian New Zealand Clinical Trial Register (ACTRN-12609000654257).
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http://dx.doi.org/10.1371/journal.pntd.0004151DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627839PMC
October 2015

Intestinal parasites of children and adults in a remote Aboriginal community of the Northern Territory, Australia, 1994-1996.

Western Pac Surveill Response J 2015 Jan-Mar;6(1):44-51. Epub 2015 Mar 6.

University of Queensland, Brisbane, Queensland, Australia .

Introduction: Parasitic infections can adversely impact health, nutritional status and educational attainment. This study investigated hookworm and other intestinal parasites in an Aboriginal community in Australia from 1994 to 1996.

Methods: Seven surveys for intestinal parasites were conducted by a quantitative formol-ether method on faecal samples. Serological testing was conducted for Strongyloides stercoralis and Toxocara canis IgG by enzyme-linked immunosorbent assays.

Results: Of the 314 participants, infections were as follows: Trichuris trichiura (86%); hookworm, predominantly Ancylostoma duodenale (36%); Entamoeba spp. (E. histolytica complex [E. histolytica, E. dispar and E. moskovski], E. coli and E. hartmanni) (25%); S. stercoralis (19%); Rodentolepis nana (16%); and Giardia duodenalis (10%). Serological diagnosis for 29 individuals showed that 28% were positive for S. stercoralis and 21% for T. canis. There was a decrease in the proportion positive for hookworm over the two-year period but not for the other parasite species. The presence of hookworm, T. trichiura and Entamoeba spp. was significantly greater in 5-14 year olds (n = 87) than in 0-4 year olds (n = 41), while the presence of S. stercoralis, R. nana, G. duodenalis and Entamoeba spp. in 5-14 year olds was significantly greater than 15-69 year olds (n = 91).

Discussion: Faecal testing indicated a very high prevalence of intestinal parasites, especially in schoolchildren. The decrease in percentage positive for hookworm over the two years was likely due to the albendazole deworming programme, and recent evidence indicates that the prevalence of hookworm is now low. However there was no sustained decrease in percentage positive for the other parasite species.
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http://dx.doi.org/10.2471/WPSAR.2015.6.1.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410104PMC
January 2016