Map of Australasia.

<p><b>a</b>) 21,500 years ago during the last glacial maximum. The shaded regions represent what was dry land during the period. Note that Australia and PNG comprised a single continent (Sahul) and that most of Southeast Asia (Sunda) was linked by land bridges <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018343#pone.0018343-OConnell1" target="_blank">[19]</a>. <b>b</b>) The Balimo region of the Western Province of Papua New Guinea on the Aramia River floodplain.</p

Neighbor joining tree constructed from <i>B. pseudomallei</i> MLVA data.

<p>The isolates in box A represent those with very short branch lengths and resistance to chloramphenicol, suggesting a high level of relatedness.</p

<i>B. pseudomallei</i> isolates used in this study.

<p>Multiple identifiers indicate isolates that were isolated concurrently from a single patient. Isolates C5 & C6 and C7 & C8 were recovered from siblings.</p

High <i>Leptospira</i> Diversity in Animals and Humans Complicates the Search for Common Reservoirs of Human Disease in Rural Ecuador

<div><p>Background</p><p>Leptospirosis is a zoonotic disease responsible for high morbidity around the world, especially in tropical and low income countries. Rats are thought to be the main vector of human leptospirosis in urban settings. However, differences between urban and low-income rural communities provide additional insights into the epidemiology of the disease.</p><p>Methodology/Principal findings</p><p>Our study was conducted in two low-income rural communities near the coast of Ecuador. We detected and characterized infectious leptospira DNA in a wide variety of samples using new real time quantitative PCR assays and amplicon sequencing. We detected infectious leptospira in a high percentage of febrile patients (14.7%). In contrast to previous studies on leptospirosis risk factors, higher positivity was not found in rats (3.0%) but rather in cows (35.8%) and pigs (21.1%). Six leptospira species were identified (<i>L</i>. <i>borgpetersenii</i>, <i>L kirschnerii</i>, <i>L santarosai</i>, <i>L</i>. <i>interrogans</i>, <i>L noguchii</i>, and an intermediate species within the <i>L</i>. <i>licerasiae</i> and <i>L</i>. <i>wolffii</i> clade) and no significant differences in the species of leptospira present in each animal species was detected (χ² = 9.89, adj.p-value = 0.27).</p><p>Conclusions/Significance</p><p>A large portion of the world’s human population lives in low-income, rural communities, however, there is limited information about leptospirosis transmission dynamics in these settings. In these areas, exposure to peridomestic livestock is particularly common and high prevalence of infectious leptospira in cows and pigs suggest that they may be the most important reservoir for human transmission. Genotyping clinical samples show that multiple species of leptospira are involved in human disease. As these genotypes were also detected in samples from a variety of animals, genotype data must be used in conjunction with epidemiological data to provide evidence of transmission and the importance of different potential leptospirosis reservoirs.</p></div

Association between rainfall and presence of <i>Leptospira</i> DNA in sera and urine febrile patients during the period of this study.

<p>Data were stratified into low precipitation (< 50 mm) and high precipitation months (>50 mm).</p

<i>Leptospira</i> DNA positivity in samples collected in 2014 and the first 6 months of 2015 from two rural communities in Manabi-Ecuador.

<p><i>Leptospira</i> DNA positivity in samples collected in 2014 and the first 6 months of 2015 from two rural communities in Manabi-Ecuador.</p

Leptospira genotyping results in febrile patients, cattle, pigs and rats sampled at our study sites.

<p>Concentric circles represent the sample size in Site 1 (colored with light gray) and Site 2 (dark gray). The order of these concentric circles is dependent on the sample size at each site. The proportion of each <i>Leptospira</i> genotype is marked with a different color, however white portions represent the percentage of samples for which genotyping was unsuccessful. Sample sizes for each group is detailed in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004990#pntd.0004990.t002" target="_blank">Table 2</a> and <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004990#pntd.0004990.s010" target="_blank">S6 Table</a>.</p

Details of assays for detecting pathogenic and intermediate leptospira species.

<p>These two assays amplify the same region but the probes anneal to different targets within the amplified region. See also <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0004990#pntd.0004990.s004" target="_blank">S3 Fig</a>.</p

Genotyping of <i>Burkholderia mallei</i> from an Outbreak of Glanders in Bahrain Suggests Multiple Introduction Events

<div><p>Background</p><p>Glanders, caused by the gram-negative bacterium <i>Burkholderia mallei</i>, is a highly infectious zoonotic disease of solipeds causing severe disease in animals and men. Although eradicated from many Western countries, it recently emerged in Asia, the Middle-East, Africa, and South America. Due to its rareness, little is known about outbreak dynamics of the disease and its epidemiology.</p><p>Methodology/Principal Findings</p><p>We investigated a recent outbreak of glanders in Bahrain by applying high resolution genotyping (multiple locus variable number of tandem repeats, MLVA) and comparative whole genome sequencing to <i>B. mallei</i> isolated from infected horses and a camel. These results were compared to samples obtained from an outbreak in the United Arab Emirates in 2004, and further placed into a broader phylogeographic context based on previously published <i>B. mallei</i> data. The samples from the outbreak in Bahrain separated into two distinct clusters, suggesting a complex epidemiological background and evidence for the involvement of multiple <i>B. mallei</i> strains. Additionally, the samples from Bahrain were more closely related to <i>B. mallei</i> isolated from horses in the United Arab Emirates in 2004 than other <i>B. mallei</i> which is suggestive of repeated importation to the region from similar geographic sources.</p><p>Conclusion/Significance</p><p>High-resolution genotyping and comparative whole genome analysis revealed the same phylogenetic patterns among our samples. The close relationship of the Dubai/UAE <i>B. mallei</i> populations to each other may be indicative of a similar geographic origin that has yet to be identified for the infecting strains. The recent emergence of glanders in combination with worldwide horse trading might pose a new risk for human infections.</p></div

Population genetics of Orientia tsutsugamushi

These are supplemental files associated with a manuscript about the genomic evolution of <i>Orientia tsutsugamushi.</i