Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12

We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.     

Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity

A recent emergence of Cryptococcus gattii in the Pacific Northwest involves strains that fall into three primarily clonal molecular subtypes: VGIIa, VGIIb and VGIIc. Multilocus sequence typing (MLST) and variable number tandem repeat analysis appear to identify little diversity within these molecular subtypes. Given the apparent expansion of these subtypes into new geographic areas and their ability to cause disease in immunocompetent individuals, differentiation of isolates belonging to these subtypes could be very important from a public health perspective. We used whole genome sequence typing (WGST) to perform fine-scale phylogenetic analysis on 20 C. gattii isolates, 18 of which are from the VGII molecular type largely responsible for the Pacific Northwest emergence. Analysis both including and excluding (289,586 SNPs and 56,845 SNPs, respectively) molecular types VGI and VGIII isolates resulted in phylogenetic reconstructions consistent, for the most part, with MLST analysis but with far greater resolution among isolates. The WGST analysis presented here resulted in identification of over 100 SNPs among eight VGIIc isolates as well as unique genotypes for each of the VGIIa, VGIIb and VGIIc isolates. Similar levels of genetic diversity were found within each of the molecular subtype isolates, despite the fact that the VGIIb clade is thought to have emerged much earlier. The analysis presented here is the first multi-genome WGST study to focus on the C. gattii molecular subtypes involved in the Pacific Northwest emergence and describes the tools that will further our understanding of this emerging pathogen.     

Allozyme analysis reveals six species within the Anopheles punctulatus complex of mosquitoes in Papua New Guinea

Abstract. Among samples collected from nineteen localities in Papua New Guinea, we have identified six species within the Anopheles punctulatus complex of mosquitoes, by means of cellulose acetate allozyme electrophoresis. An.punctulatus Dönitz sensu stricto was collected from seven villages in the Madang area and from Buksak, Sausi Mission and an area 18 km SW of Tari; An.koliensis Owen from eight villages in the Madang area, from Popondetta and Brown River near Karema; and An.farauti No. 1 from ten coastal areas including Madang, Lorengau, Popondetta, Port Moresby, Rabaul and Wewak. Three newly recognized species, reported here for the first time, are designated as An.farauti No. 4 from Gonoa and Hudini, Madang area; An.farauti No. 5 from Ketarabo near Goroka; and An.farauti No. 6 from Hiwanda near Tari. Three other known members of the complex, An.clowi Rozeboom & Knight, An.farauti No. 2 (Bryan, 1973) and An.farauti No. 3 (Mahon & Meithke, 1982) were not detected in Papua New Guinea. Problems arising with morphological characters for the identification of species in this group are discussed.     

Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea

Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of two Salmonella Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essential step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of these and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere.     

Diversity of genome structure in Salmonella enterica serovar Typhi populations

The genomes of most strains of Salmonella and Escherichia coli are highly conserved. In contrast, all 136 wild-type strains of Salmonella enterica serovar Typhi analyzed by partial digestion with I-CeuI (an endonuclease which cuts within the rrn operons) and pulsed-field gel electrophoresis and by PCR have rearrangements due to homologous recombination between the rrn operons leading to inversions and translocations. Recombination between rrn operons in culture is known to be equally frequent in S. enterica serovar Typhi and S. enterica serovar Typhimurium; thus, the recombinants in S. enterica serovar Typhi, but not those in S. enterica serovar Typhimurium, are able to survive in nature. However, even in S. enterica serovar Typhi the need for genome balance and the need for gene dosage impose limits on rearrangements. Of 100 strains of genome types 1 to 6, 72 were only 25.5 kb off genome balance (the relative lengths of the replichores during bidirectional replication from oriC to the termination of replication [Ter]), while 28 strains were less balanced (41 kb off balance), indicating that the survival of the best-balanced strains was greater. In addition, the need for appropriate gene dosage apparently selected against rearrangements which moved genes from their accustomed distance from oriC. Although rearrangements involving the seven rrn operons are very common in S. enterica serovar Typhi, other duplicated regions, such as the 25 IS200 elements, are very rarely involved in rearrangements. Large deletions and insertions in the genome are uncommon, except for deletions of Salmonella pathogenicity island 7 (usually 134 kb) from fragment I-CeuI-G and 40-kb insertions, possibly a prophage, in fragment I-CeuI-E. The phage types were determined, and the origins of the phage types appeared to be independent of the origins of the genome types.     

Whole genome sequence analysis of Salmonella Typhi provides evidence of phylogenetic linkage between cases of typhoid fever in Santiago,Chile in the 1980s and 2010–2016

Typhoid fever epidemiology was investigated rigorously in Santiago, Chile during the 1980s, when Salmonella enterica serovar Typhi (S. Typhi) caused seasonal, hyperendemic disease. Targeted interventions reduced the annual typhoid incidence rates from 128–220 cases/10⁵ population occurring between 1977–1984 to <8 cases/10⁵ from 1992 onwards. As such, Santiago represents a contemporary example of the epidemiologic transition of an industrialized city from amplified hyperendemic typhoid fever to a period when typhoid is no longer endemic. We used whole genome sequencing (WGS) and phylogenetic analysis to compare the genotypes of S. Typhi cultured from acute cases of typhoid fever occurring in Santiago during the hyperendemic period of the 1980s (n = 74) versus the nonendemic 2010s (n = 80) when typhoid fever was rare. The genotype distribution between “historical” (1980s) isolates and “modern” (2011–2016) isolates was similar, with genotypes 3.5 and 2 comprising the majority of isolations, and 73/80 (91.3%) of modern isolates matching a genotype detected in the 1980s. Additionally, phylogenomically ‘ancient’ genotypes 1.1 and 1.2.1, uncommon in the global collections, were also detected in both eras, with a notable rise amongst the modern isolates. Thus, genotypes of S. Typhi causing acute illness in the modern nonendemic era match the genotypes circulating during the hyperendemic 1980s. The persistence of historical genotypes may be explained by chronic typhoid carriers originally infected during or before the 1980s.     

Whole‐genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea

Anopheles mosquitoes are the vectors of several human diseases including malaria. In many malaria endemic areas, several species of Anopheles coexist, sometimes in the form of related sibling species that are morphologically indistinguishable. Determining the size and organization of Anopheles populations, and possible ongoing gene flow among them is important for malaria control and, in particular, for monitoring the spread of insecticide resistance alleles. However, these parameters have been difficult to evaluate in most Anopheles species due to the paucity of genetic data available. Here, we assess the extent of contemporary gene flow and historical variations in population size by sequencing and de novo assembling the genomes of wild‐caught mosquitoes from four species of the Anopheles punctulatus group of Papua New Guinea. Our analysis of more than 50 Mb of orthologous DNA sequences revealed no evidence of contemporary gene flow among these mosquitoes. In addition, investigation of the demography of two of the An. punctulatus species revealed distinct population histories. Overall, our analyses suggest that, despite their similarities in morphology, behaviour and ecology, contemporary sympatric populations of An. punctulatus are evolving independently.     

Restricted polymorphisms of the mannose-binding lectin gene in a population of Papua New Guinea

The human mannose-binding lectin (MBL) is an important protein of the innate immune system. MBL is able to eliminate potential pathogens by activating the complement cascade or by opsonisation. We investigated the gene and promoter region of MBL in a population from Papua New Guinea infected with Plasmodium falciparum parasites and measured the appropriate serum concentrations of these individuals. Their serum levels of MBL, detected by ELISA, showed a wide range with concentrations between 632 and 7325 microg/l MBL. A known polymorphism in exon 1 at codon 54 causing an amino acid exchange from Gly to Asp occurred with a low frequency of 3%. Additional to the previously reported polymorphisms in the gene and promoter region of MBL, two novel polymorphic sites were found in the promoter region. One site was in the untranslated region of the MBL gene at position +1 (G-->A, termed R/S), and the second was located upstream of the gene at position -4 (G-->A, termed T/U).     

Pre-capitalist modes of production in Papua New Guinea

Conclusion In the articulation-of-modes-of-production literature there is a tendency to treat conceptual structures as if they had lives of their own. Thus modes of production are sometimes portrayed as meeting, intertwining, and reproducing like giant organisms animated by ineluctable laws of motion. But these structures and categories are primarily the products of thought. As such, they cannotdo anything, and they possess no motivational capacity whatsoever. They are simply analytical tools, more-or-less useful in explaining how and why history unfolded in the way it did.The categories and relationships suggested in this paper represent a preliminary attempt to make some sense of pre-contact change in Papua New Guinea. Their adequacy or otherwise will be determined ultimately through more rigorous engagements with the empirical evidence than is possible here.Terence Wesley-Smith is Assistant Professor, University of Hawaii at Monoa, Center for Pacific Islands Studies.     

Molecular parasitology of malaria in Papua New Guinea

Research into the molecular biology of infectious diseases is mostly associated with well-developed countries. But in the midst of tropical Papua New Guinea, highly sophisticated molecular research has being conducted over years to understand and fight malaria and other tropical diseases. Here, we review such research carried out at the Papua New Guinea Institute of Medical Research. This Institute has considerably shaped research on molecular epidemiology through its analysis of the diversity and structure of the Plasmodium falciparum population. In addition, research has been conducted on human host factors and, more recently, the molecular analysis of drug resistance and the underlying molecular mechanisms of host-parasite interactions have been investigated.     

The epidemiology of malaria in Papua New Guinea

Papua New Guinea (PNG) is a patchwork of different ecological zones, inhabited by human populations of exceptional cultural and linguistic diversity. This results in complex variations in vector ecology and malaria epidemiology. Malaria is the main cause of morbidity in many health facilities in lowland areas, but it is absent in much of the highlands. All four human malaria species occur, but endemicity varies widely, with Plasmodium falciparum locally reaching holo-endemic levels that are rarely found outside sub-Saharan Africa. The high frequency of Plasmodium vivax is an important difference to most African situations. PNG is therefore a prime location for studies of interactions between different parasite species, and of the biology of local human genetic adaptation and its implications for malaria morbidity and mortality.     

Number concepts without number lines in an indigenous group of Papua New Guinea

Background

The generic concept of number line, which maps numbers to unidimensional space, is a fundamental concept in mathematics, but its cognitive origins are uncertain. Two defining criteria of the number line are that (i) there is a mapping of each individual number (or numerosity) under consideration onto a specific location on the line, and (ii) that the mapping defines a unidimensional space representing numbers with a metric — a distance function. It has been proposed that the number line is based on a spontaneous universal human intuition, rooted directly in brain evolution, that maps number magnitude to linear space with a metric. To date, no culture lacking this intuition has been documented.

Methodology/Principal Findings

By means of a number line task, we investigated the universality proposal with the Yupno of Papua New Guinea. Unschooled adults did exhibit a number-to-space mapping (criterion i) but, strikingly, despite having precise cardinal number concepts, they located numbers only on the endpoints, thus failing to use the extent of the line. The produced mapping was bi-categorical and metric-free, in violation of criterion ii. In contrast, Yupnos with scholastic experience used the extent of the segment according to known standards, but they did so not as evenly as western controls, exhibiting a bias towards the endpoints.

Conclusions/Significance

Results suggest that cardinal number concepts can exist independently from number line representations. They also suggest that the number line mapping, although ubiquitous in the modern world, is not universally spontaneous, but rather seems to be learned through — and continually reinforced by — specific cultural practices.     

Whole genome sequence of an unusual Borrelia burgdorferi sensu lato isolate

Human Lyme disease is caused by a number of related Borrelia burgdorferi sensu lato species. We report here the complete genome sequence of Borrelia sp. isolate SV1 from Finland. This isolate is to date the closest known relative of B. burgdorferi sensu stricto, but it is sufficiently genetically distinct from that species that it and its close relatives warrant its candidacy for new-species status. We suggest that this isolate should be named "Borrelia finlandensis."     

Multivariate analysis of periphytic and benthic diatom assemblages from Papua New Guinea

The benthic and periphytic diatom flora is studied in 136 fresh waters in Papua New Guinea. DCA ordination and TWINSPAN are used to describe 20 diatom assemblages. Conductivity, water temperature and altitude are the main sources for the variation in the data. Laing Island Biological Station publication n° 214 Laing Island Biological Station publication n° 214     

Water level and temperature and zooplankton population abundances in Lake Surinumu,Papua New Guinea

Lake Surinumu, an oligotrophic hydroelectric impoundment on the Laloki River in Central Province, Papua New Guinea, was sampled throughout 1982 for its zooplankton community composition, water level and surface temperature. The zooplankton community was observed to be normally dominated byEodiaptomus lumholtzi, Ceriodaphnia cornuta and theDiaphanosoma speciesD. sarsi andD. excisum, though the rotiferT. equatorialis became dominant toward the end of the sampling period. Nutrient levels, especially with regard to ionic nitrogen, were observed to decrease following the monsoonal influx. Close correlations were found between water level and surface temperature, and between water level and the relative abundances ofE. lumholtzi, diaphanosomids andT. equatorialis. The zooplankton community was observed to undergo the most significant changes during periods of monsoonal influx and lowest water level/highest water temperature. In the absence of significant interspecific abundance correlations, it is suggested that climatic factors are primarily responsible for the dynamics of the zooplankton community composition.     

RFLP-based phylogeny of Musa species in Papua New Guinea

Summary Random genomic probes were used to detect restriction fragment length polymorphisms (RFLPs) in 26 accessions of Musa representing eight species from Papua New Guinea (PNG), M. textilis, M. jackeyi and one accession of Ensete. Ninety-eight phylogenetically informative characters were scored and analyzed cladistically and phenetically. Results generally agreed with previous morphology-based phylogenetic analyses. However, the closest wild relative of the edible M. fehi (fe'i banana) appears to be M. lolodensis. Musa angustigemma is sister species with M. boman and M. jackeyi and is distinct from M. peekelii, with which it is often united. Musa boman is unambiguously placed in section Australimusa. The diploid parthenocarpic landraces of section Musa unique to PNG are closely related to, but apparently distinct from, M. acuminata ssp. banksii. The evolution of the fe'i bananas and the M. acuminata-derived diploid landraces of PNG are discussed.     

The effect of permethrin-impregnated bednets on a population of Anopheles farauti in coastal Papua New Guinea

The effect of introducing bednets impregnated with 0.4 g/m2 permethrin on local populations of the malaria vector mosquitoes Anopheles farauti Laveran and An. koliensis Owen was monitored in a coastal village of Papua New Guinea. Whole-night landing collections were undertaken for 25 consecutive nights before and 21 nights after the introduction of the nets. Capture-recapture experiments and resting collections were also performed before and after the introduction of the nets. Following the introduction of treated nets, the biting population of An. farauti, the predominant vector, dropped from an average of 689 to 483 per man-night and the oviposition cycle became irregular, although survival rates (determined by time series analysis of the landing catches and log regression of recapture rates) were not significantly affected. The densities of An. farauti resting in and around houses and the human blood index of the engorged females also decreased significantly after introduction of the treated bednets. The population of An. koliensis dropped prior to the introduction of the nets. However, the number of nulliparous females in the landing catches remained more or less constant which implies that, in this species, survival rates were affected by the nets but that recruitment to the population was not.