The brown dog tick Rhipicephalus sanguineus sensu Roberts, 1965 across Australia: Morphological and molecular identification of R. sanguineus s.l. tropical lineage

The brown dog tick Rhipicephalus sanguineus (Latreille, 1806) is the most widely distributed tick species globally. Throughout the world there are at least two divergent lineages on dogs that are traditionally grouped into what was known as R. sanguineus. The species R. sanguineus was recently redescribed using a neotype reported from countries with a temperate climate. The second lineage distributed in countries with primarily tropical climates is currently designated R. sanguineus s.l. tropical lineage. Here, we present a comprehensive genetic evaluation of Australian brown dog ticks from across the continent that complements the morphological study of R. sanguineus sensu Roberts (1965). A total of 294 ticks were collected from dogs around Australia ― including New South Wales, Queensland, the Northern Territory and Western Australia ― for morphological identification. All ticks were morphologically identified as R. sanguineus sensu Roberts (1965). DNA was isolated from a single leg from morphologically characterised individuals from New South Wales (n = 14), Queensland (n = 18), Northern Territory (n = 7) and Western Australia (n = 13), together with ticks from Fiji (n = 1) and the Seychelles (n = 1) for comparison with Australian ticks. The study revealed three cox1 haplotypes clustered only with R. sanguineus s.l. tropical lineage’. An updated distribution of R. sanguineus sensu Roberts (1965) is compared to the 1965 distribution. In the Australian context, R. sanguineus s.l. has appeared in north-western New South Wales but remains absent from coastal New South Wales. Despite both temperate and tropical climates being present in Australia, only R. sanguineus s.l. tropical lineage was found. The evidence does not support the presence of the strictly defined brown dog tick, R. sanguineus by Nava et al. (2018) in Australia, because the examined ticks are genetically and morphologically distinct. We recommend using the term brown dog tick, R. sanguineus sensu Roberts (1965) for specimens from Australia.     

Genetic diversity and geographical distribution of the Siberian subtype of the tick-borne encephalitis virus

The tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is currently subdivided into three main subtypes—the European (TBEV-Eu), the Far-Eastern (TBEV-FE), and the Siberian (TBEV-Sib). The TBEV-Sib is the most common subtype and found in all regions where TBEV was detected, except for Central and Western Europe. Currently, four genetic lineages have been described within TBEV-Sib.In this study, detailed analysis of TBEV-Sib genetic diversity, geographic distribution, phylogeography and divergence time of different TBEV-Sib genetic lineages based on E gene fragments, complete genome sequences, and all currently available data in the GenBank database was performed. As a result, a novel Bosnia lineage within the TBEV-Sib was identified. It was demonstrated that the Zausaev lineage is the most widely distributed among the TBEV-Sib lineages, and was detected in all studied regions except the Far East. The Vasilchenko lineage was found from Western Siberia to the Far East. The Baltic lineage is presented from Europe to Western Siberia. The Obskaya lineage was found only in Western Siberia. TBEV strains from a newly described Bosnia lineage were detected in Bosnia, the Crimean peninsula, Kyrgyzstan and Kazakhstan. The greatest divergence of the TBEV-Sib genetic variants was observed in Western Siberia. Within the TBEV-Sib, the Obskaya lineage diverged from the common ancestor the earliest, after that the Bosnia lineage was separated, then the Baltic lineage, and the Zausaev and Vasilchenko lineages diverged most recently.     

Trace Element Concentrations in Feathers of Flesh-footed Shearwaters (Puffinus carneipes) from Across Their Breeding Range

Seabirds are convenient indicators of contamination of the marine environment because feathers can be sampled non-destructively, and a great deal is known about their ecology. Flesh-footed Shearwaters (Puffinus carneipes) are of conservation concern in Australia and New Zealand, partly because ingestion of marine debris may be reducing breeding success at their largest colony. Because marine plastics accumulate contaminants in the ocean environment, an assessment of metal and metalloid contaminants was initiated. We sampled feathers from Kauwahaia (n?=?18) and Lady Alice Island, New Zealand (n?=?30), Lord Howe Island (n?=?24) and Western Australia (n?=?33) during the 2008 austral summer, making this the most complete assessment of metal and metalloid contamination of any shearwater. We found colony differences in all elements except lead and thallium. Samples from Western Australia had higher silver, aluminium, cadmium, and copper concentrations, while shearwaters from Lord Howe Island (eastern Australia) had elevated concentrations of mercury (mean?±?S.D., 11221?±?5612?ppb). We conclude that mercury, and potentially arsenic and cadmium represent toxicological concerns for this declining species.     

Review of genetic diversity in malaria vectors (Culicidae: Anophelinae)

We review previous studies on the genetic diversity of malaria vectors to highlight the major trends in population structure and demographic history. In doing so, we outline key information about molecular markers, sampling strategies and approaches to investigate the causes of genetic structure in Anopheles mosquitoes. Restricted gene flow due to isolation by distance and physical barriers to dispersal may explain the spatial pattern of current genetic diversity in some Anopheles species. Nonetheless, there is noteworthy disagreement among studies, perhaps due to variation in sampling methodologies, choice of molecular markers, and/or analytical approaches. More refined genealogical methods of population analysis allowing for the inclusion of the temporal component of genetic diversity facilitated the evaluation of the contribution of historical demographic processes to genetic structure. A common pattern of past unstable demography (i.e., historical fluctuation in the effective population size) by several Anopheles species, regardless of methodology (DNA markers), mosquito ecology (anthropophilic vs zoophilic), vector status (primary vs secondary) and geographical distribution, suggests that Pleistocene environmental changes were major drivers of divergence at population and species levels worldwide.     

A Two‐Compartment Mixed‐Effects Gamma Regression Model for Quantifying Between‐Unit Variability in Length of Stay among Children Admitted to Intensive Care

Objective

To quantify between-unit variability in mean length of stay (LoS) between intensive care units (ICUs) after adjusting for differences in case mix using a method that does not require arbitrary trimming of data.

Setting

An analysis of registry data from pediatric ICUs (PICUs) in Australia and New Zealand.

Study Design

The relationships between patient LoS and associated patient factors were modeled as a log-linear function of the covariates using two gamma distributions. The predicted distribution is estimated as a weighted average of the two distributions where the relative weighting is conditional on the patient''s elective status.

Data Collection

Data for 12,763 admissions submitted to the Australian and New Zealand Paediatric Intensive Care Registry from the eight dedicated PICUs in Australia and New Zealand in 2007 and 2008.

Principal Findings

The two distributions of the mixture model accurately described the distribution of short- and long-stay patients in ICUs. After adjusting for patient case mix, several sites had a statistically significant effect on patient LoS.

Conclusion

The two-compartment model characterizes ICU LoS for short- and long-stay patients more effectively than a single-compartment model. There is significant site-level variation in the LoS among children admitted to ICUs in Australia and New Zealand. Differences in the site-level variation between short- and long-stay patients indicate differences in discharge practice.     

Genetic structure and phylogeography of Aedes aegypti, the dengue and yellow-fever mosquito vector in Bolivia

Between the 16th and 18th centuries, Aedes aegypti (Diptera: Culicidae), a mosquito native to Africa, invaded the Americas, where it was successively responsible for the emergence of yellow fever (YF) and dengue (DEN). The species was eradicated from numerous American countries in the mid-20th century, but re-invaded them in the 1970s and 1980s. Little is known about the precise identities of Ae. aegypti populations which successively thrived in South America, or their relation with the epidemiological changes in patterns of YF and DEN. We examined these questions in Bolivia, where Ae. aegypti, eradicated in 1943, re-appeared in the 1980s. We assessed the genetic variability and population genetics of Ae. aegypti samples in order to deduce their genetic structure and likely geographic origin. Using a 21-population set covering Bolivia, we analyzed the polymorphism at nine microsatellite loci and in two mitochondrial DNA regions (COI and ND4). Microsatellite markers revealed a significant genetic structure among geographic populations (F(ST)=0.0627, P<0.0001) in relation with the recent re-expansion of Ae. aegypti in Bolivia. Analysis of mtDNA sequences revealed the existence of two genetic lineages, one dominant lineage recovered throughout Bolivia, and the second restricted to rural localities in South Bolivia. Phylogenic analysis indicated that this minority lineage was related to West African Ae. aegypti specimens. In conclusion, our results suggested a temporal succession of Ae. aegypti populations in Bolivia, that potentially impacted the epidemiology of dengue and yellow fever.     

Crimean-Congo hemorrhagic fever virus in ticks collected from livestock in Albania

Albania is a Balkan country endemic for Crimean-Congo hemorrhagic fever (CCHF). It was shown previously that CCHF virus (CCHFV) sequences from Albanian patients cluster into Europe 1 clade. Aim of the present study was to test for CCHFV ticks collected in several regions of Albania, and to determine the genetic lineage(s) of the CCHFV strains in relation with their geographic distribution. A total of 726 ticks (366 Hyalomma marginatum, 349 Rhipicephalus bursa and 11 Rhipicephalus sanguineus) collected from livestock during 2007–2014 were included in the study. Thirty of 215 (13.9%) tick pools were positive for CCHFV. Lineage Europe 1 was detected in H. marginatum ticks collected in the endemic region of Albania, while lineage Europe 2 was detected mainly in R. bursa ticks in various regions of the country. Both genetic lineages were detected in the CCHF endemic area (northeastern Albania), while only Europe 2 lineage was detected in the south of the country. A higher genetic diversity was seen among Europe 2 than Europe 1 Albanian sequences (mean distance 3.7% versus 1%), suggesting a longer evolution of AP92-like strains (Europe 2) in their tick hosts. The present study shows that besides CCHFV lineage Europe 1, lineage Europe 2 is also present in Albania. Combined with results from recent studies, it is concluded that lineage Europe 2 is widely spread in the Balkans and Turkey, and is associated mainly with R. bursa ticks (at least in this region). Its pathogenicity and impact to the public health remain to be elucidated.     

Australia and New Zealand's contribution to Pacific Island health worker brain drain

Objective: The paper aims to quantify Australia and New Zealand's contribution to the brain drain of Pacific Island health workers and to contribute firm evidence to the ongoing, highly‐contested health professional migration issue. Methods: The study uses the Australian and New Zealand 2006 census data to examine the number of Pacific Island born health professionals living in Australia and New Zealand and uses World Health Organization data to compare it against the numbers of health workers in Pacific Island countries. Results: Six hundred and fifty‐two Pacific Island born doctors and 3,467 Pacific Island born nurses and midwives are working in Australia and New Zealand, more than half of whom are from Fiji with significant numbers from Papua New Guinea, Samoa and Tonga as well. There are almost as many Fiji‐born doctors in Australia and New Zealand as there are in Fiji. There are more Samoa, Tonga and Fiji‐born nurses and midwives in Australia and New Zealand than in the domestic workforce. Conclusions: Migration of Pacific Island health professionals to Australia and New Zealand is very high and contributes to the shortage of health workers in Pacific Island countries. Implications: Australia and New Zealand are encouraged to actively address the issue in collaboration with Pacific Island partners with a number of solutions proposed.     

Genetic structure and connectivity among Aedes aegypti populations within Madurai city in Southern India

We investigated the genetic variability and differentiation among 12 Ae. aegypti populations collected within the Madurai city in Tamil Nadu state of Southern India. Genotyping of 12 microsatellite markers in 353 individual samples showed moderate levels of genetic diversity among 12 populations. UPGMA tree, hierarchical clustering, Bayesian clustering and Discriminant Analysis on Principal Components roughly divided these populations into two genetic clusters: main city populations and the populations located at the border of the corporation limit. Significant positive correlation between genetic and geographic distance was observed among 12 populations, however, the correlation was non-significant within each genetic cluster. Population assignment and divMigrate graph depicted less migration between two groups. Overall, the findings of this study provided an overview of Ae. aegypti population structure within an urban setting in India that have implications in effective implementation of vector control in the city area.     

Potential Role of Deer Tick Virus in Powassan Encephalitis Cases in Lyme Disease–endemic Areas of New York,USA

Powassan virus, a member of the tick-borne encephalitis group of flaviviruses, encompasses 2 lineages with separate enzootic cycles. The prototype lineage of Powassan virus (POWV) is principally maintained between Ixodes cookei ticks and the groundhog (Marmota momax) or striped skunk (Mephitis mephitis), whereas the deer tick virus (DTV) lineage is believed to be maintained between Ixodes scapularis ticks and the white-footed mouse (Peromyscus leucopus). We report 14 cases of Powassan encephalitis from New York during 2004–2012. Ten (72%) of the patients were residents of the Lower Hudson Valley, a Lyme disease–endemic area in which I. scapularis ticks account for most human tick bites. This finding suggests that many of these cases were caused by DTV rather than POWV. In 2 patients, DTV infection was confirmed by genetic sequencing. As molecular testing becomes increasingly available, more cases of Powassan encephalitis may be determined to be attributable to the DTV lineage.     

The epidemiology of acute haematogenous osteomyelitis of childhood

Hospital morbidity data from New Zealand, Western Australia, England and Wales and Scotland are reviewed. The incidence of osteomyelitis in childhood is greater in males than females, greater in European children in Australia and New Zealand than in Great Britain, and much greater in Aboriginal and New Zealand Maori children than in European children. A seasonal peak is present in late summer and autumn in both hemispheres. The reported incidence is generally declining, except in Western Australia. Local variations in incidence within New Zealand correlate with mean annual vapour pressure. The male/female sex ratio increases with age. Discussion centres on possible inferences from the data.     

Circulation and antigenic drift in human influenza B viruses in SE Asia and Oceania since 2000

During annual influenza epidemics, influenza B viruses frequently co-circulate with influenza A viruses and in some years, such as 2005, large outbreaks have occurred while in other years, the virus virtually disappears. Since 1987 there have been two lineages of influenza B viruses co-circulating in various countries and causing disease in humans. The proportions of these two lineages vary from year to year and country to country. For example, in 2005, the B/Victoria/2/87 lineage was predominant in New Zealand while in Australia the B/Yamagata/16/88 lineage was more common. Antigenic and genetic analysis has revealed gradual movement in the both lineages. Careful monitoring of the two virus lineages is important, as they are antigenically distinct. This is an important consideration for influenza vaccine formulation decisions, as only one influenza B component is traditionally included in the annual trivalent influenza vaccine.     

Molecular characterization of species of Cloacina (Strongyloidea: Cloacininae) from the common wallaroo,Macropus robustus (Marsupialia: Macropodidae) in Australia

This study examined genetic variation within and among species of Cloacina found in the common wallaroo (Macropus robustus) collected at different localities from mainland Australia, and evaluated geographical distance as a potential driver for genetic variation. The first and second internal transcribed spacers (ITS-1 and ITS-2 = ITS) of nuclear ribosomal DNA were used to characterize individuals of 17 morphospecies of Cloacina that parasitize Macropus robustus and its sub-species. Results revealed intraspecific variation in ITS within some morphospecies of Cloacina. Phylogenetic analyses showed little correlation between host speciation patterns and geographical location for the majority of the nematode species, although it did suggest geographical distance was a driver for speciation within Cloacina communis, C. phaethon and C. parva. Our results suggest that nucleotide variation within Cloacina species is complex, and is likely to be propagated by factors such as geographical distance and host sub-species. Further studies determining factors involved in speciation, such as host-parasite relationships, are needed to improve our understanding of the diversity of populations of species of Cloacina.     

The genetic architecture of a complex trait: Resistance to multiple toxins produced by Bacillus thuringiensis israelensis in the dengue and yellow fever vector,the mosquito Aedes aegypti

The bacterial insecticide Bacillus thuringiensis subsp. israelensis (Bti) is an increasingly popular alternative to chemical insecticides for controlling mosquito populations. Because Bti toxicity relies on the action of four main toxins, resistance to Bti is very likely a complex phenotype involving several genes simultaneously. Dissecting the underlying genetic basis thus requires associating a quantitative measure of resistance to genetic variation at many loci in a segregating population. Here, we undertake this task using the dengue and yellow fever vector, the mosquito Aedes aegypti, as a study model. We conducted QTL (Quantitative Trait Locus) and admixture mapping analyses on two controlled crosses and on an artificial admixed population, respectively, all obtained from resistant and susceptible lab strains. We detected 16 QTL regions, among which four QTLs were revealed by different analysis methods. These four robust QTLs explained altogether 29.2% and 62.2% of the total phenotypic variance in the two QTL crosses, respectively. They also all showed a dominant mode of action. In addition, we found six loci showing statistical association with Bti resistance in the admixed population. Five of the supercontigs highlighted in this study contained candidate genes as suggested by their function, or by prior evidence from expression and/or outlier analyses. These genomic regions are thus good starting points for fine mapping of resistance to Bti or functional analyses aiming at identifying the underlying genes and mutations. Moreover, for the purpose of this work, we built the first Ae. aegypti genetic map based on markers associated with genes expressed in larvae. This genetic map harbors 229 SNP markers mapped across the three chromosomes for a total length of 311.9 cM. It brought to light several assembly discrepancies with the reference genome, suggesting a high level of genome plasticity in Ae. aegypti.     

Systematics of Mepraia (Hemiptera-Reduviidae): Cytogenetic and molecular variation

The haematophagous insects of the subfamily Triatominae (Hemiptera-Reduviidae) have great epidemiological importance as vectors of Trypanosoma cruzi, the causative agent of Chagas disease. Mepraia was originally described as a monotypic genus comprised of Mepraia spinolai, distributed along coastal areas of northern Chile (from Region I to the Metropolitan Region). Recently, some M. spinolai populations have been ranked as a new species named Mepraia gajardoi. Several populations along the distribution range of the genus were sampled, and genetic differentiation was studied based upon the analysis of three molecular markers: cytogenetics (karyotype and chromosome behaviour during meiosis using the C-banding technique), mitochondrial DNA (a cytochrome oxidase I gene fragment), and nuclear ribosomal DNA (intergenic region including the two internal transcribed spacers ITS-1 and ITS-2 and the 5.8S rRNA gene). The data here presented indicate that populations within the Mepraia genus (excluding Region II specimens) can be divided into two separate lineages. One lineage is comprised of specimens from the northernmost Region I and represents M. gajardoi. The other includes samples from the southern III, IV and the Metropolitan Regions, and represents M. spinolai. Region II individuals deserve particular attention as their relationship to the two identified lineages is not clear-cut. While they appear to belong to M. spinolai based on cytogenetics and rDNA markers, COI results indicate a closer relationship to M. gajardoi. This disagreement can be due to mitochondrial DNA introgression or the retention of ancestral polymorphisms.     

Community-acquired methicillin-resistant Staphylococcus aureus carrying Panton-Valentine leukocidin genes: worldwide emergence

Infections caused by community-acquired (CA)-methicillin--resistant Staphylococcus aureus (MRSA) have been reported worldwide. We assessed whether any common genetic markers existed among 117 CA-MRSA isolates from the United States, France, Switzerland, Australia, New Zealand, and Western Samoa by performing polymerase chain reaction for 24 virulence factors and the methicillin-resistance determinant. The genetic background of the strain was analyzed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). The CA-MRSA strains shared a type IV SCCmec cassette and the Panton-Valentine leukocidin locus, whereas the distribution of the other toxin genes was quite specific to the strains from each continent. PFGE and MLST analysis indicated distinct genetic backgrounds associated with each geographic origin, although predominantly restricted to the agr3 background. Within each continent, the genetic background of CA-MRSA strains did not correspond to that of the hospital-acquired MRSA.     

Crosses prior to parthenogenesis explain the current genetic diversity of tropical plant-parasitic Meloidogyne species (Nematoda: Tylenchida)

The tropical and subtropical parthenogenetic plant-parasitic nematodes Meloidogyne are polyphagous major agricultural pests. Implementing proper pest management approaches requires a good understanding of mechanisms, population structure, evolutionary patterns and species identification. A comparative analysis of the mitochondrial vs nuclear diversity was conducted on a selected set of Meloidogyne lines from various geographic origins. Mitochondrial co2-16S sequences and AFLP markers of total DNA were applied because of their ability to evidence discrete genetic variation between closely related isolates. Several distinct maternal lineages were present, now associated with different genetic backgrounds. Relative discordances were found when comparing mitochondrial and nuclear diversity patterns. These patterns are most likely related to crosses within one ancestral genetic pool, followed by the establishment of parthenogenesis. In this case, they mirror the genetic backgrounds of the original individuals. Another aspect could be that species emergence was recent or on process from this original genetic pool and that the relatively short time elapsed since then and before parthenogenesis settlement did not allow for lineage sorting. This could also be compatible with the hypothesis of hybrids between closely related species. This genetic pool would correspond to a species as defined by the species interbreeding concept, but also including the grey area of species boundaries. This complex process has implications on the way genotypic and phenotypic diversity should be addressed. The phenotype of parthenogenetic lines is at least for part determined by the ancestral amphimictic genetic background. A direct consequence is, therefore, in terms of risk management, the limited confidence one can have on the direct association of an agronomic threat to a simple typing or species delineation. Risk management strategies and tools must thus consider this complexity when designing quarantine implementation, resistance breeding programmes or molecular diagnostic.     

Characteristics of health impact assessments reported in Australia and New Zealand 2005–2009

Objective : To describe the use and reporting of Health Impact Assessment (HIA) in Australia and New Zealand between 2005 and 2009. Methods : We identified 115 HIAs undertaken in Australia and New Zealand between 2005 and 2009. We reviewed 55 HIAs meeting the study's inclusion criteria to identify characteristics and appraise the quality of the reports. Results : Of the 55 HIAs, 31 were undertaken in Australia and 24 in New Zealand. The HIAs were undertaken on plans (31), projects (12), programs (6) and policies (6). Compared to Australia, a higher proportion of New Zealand HIAs were on policies and plans and were rapid assessments done voluntarily to support decision‐making. In both countries, most HIAs were on land use planning proposals. Overall, 65% of HIA reports were judged to be adequate. Conclusion : This study is the first attempt to empirically investigate the nature of the broad range of HIAs done in Australia and New Zealand and has highlighted the emergence of HIA as a growing area of public health practice. It identifies areas where current practice could be improved and provides a baseline against which future HIA developments can be assessed. Implications: There is evidence that HIA is becoming a part of public health practice in Australia and New Zealand across a wide range of policies, plans and projects. The assessment of quality of reports allows the development of practical suggestions on ways current practice may be improved. The growth of HIA will depend on ongoing organisation and workforce development in both countries.     

Reconsidering the classification of tick-borne encephalitis virus within the Siberian subtype gives new insights into its evolutionary history

Tick-borne encephalitis is widespread in Eurasia and transmitted by Ixodes ticks. Classification of its causative agent, tick-borne encephalitis virus (TBEV), includes three subtypes, namely Far-Eastern, European, and Siberian (TBEV-Sib), as well as a group of 886-84-like strains with uncertain taxonomic status. TBEV-Sib is subdivided into three phylogenetic lineages: Baltic, Asian, and South-Siberian. A reason to reconsider TBEV-Sib classification was the analysis of 186 nucleotide sequences of an E gene fragment submitted to GenBank during the last two years. Within the South-Siberian lineage, we have identified a distinct group with prototype strains Aina and Vasilchenko as an individual lineage named East-Siberian. The analysis of reclassified lineages has promoted a new model of the evolutionary history of TBEV-Sib lineages and TBEV-Sib as a whole. Moreover, we present arguments supporting separation of 886-84-like strains into an individual TBEV subtype, which we propose to name Baikalian (TBEV-Bkl).     

Geographical segregation of Cryptosporidium parvum multilocus genotypes in Europe

Cryptosporidium parvum is a common enteric protozoan pathogen of humans and livestock. Multilocus genotyping based on simple sequence repeat polymorphisms has been used extensively to identify transmission cycles and to investigate the structure of C. parvum populations and of the related pathogen Cryptosporidium hominis. Using such methods, the zoonotic transmission of C. parvum has been shown to be epidemiologically important. Because different genetic markers have been used in different surveys, the comparison of Cryptosporidium genotypes across different laboratories is often not feasible. Therefore, few comparisons of Cryptosporidium populations across wide geographical areas have been published and our understanding of the epidemiology of cryptosporidiosis is fragmented. Here we report on the genotypic analysis of a large collection of 692 C. parvum isolates originating primarily from cattle and other ruminants from Italy, Ireland and Scotland. Because the same genotypic markers were used in these surveys, it was possible to merge the data. We found significant geographical segregation and a correlation between genetic and geographic distance, consistent with a model of isolation by distance. The presence of strong LD and positive I_A^S values in the combined MLG dataset suggest departure from panmixia, with different population structures of the parasite prevailing in each country.