Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid.

The population of Salmonella enterica serovar Typhi (S. Typhi), the causative agent of typhoid fever, exhibits limited DNA sequence variation, which complicates efforts to rationally discriminate individual isolates. Here we utilize data from whole-genome sequences (WGS) of nearly 2,000 isolates sourced from over 60 countries to generate a robust genotyping scheme that is phylogenetically informative and compatible with a range of assays. These data show that, with the exception of the rapidly disseminating H58 subclade (now designated genotype 4.3.1), the global S. Typhi population is highly structured and includes dozens of subclades that display geographical restriction. The genotyping approach presented here can be used to interrogate local S. Typhi populations and help identify recent introductions of S. Typhi into new or previously endemic locations, providing information on their likely geographical source. This approach can be used to classify clinical isolates and provides a universal framework for further experimental investigations

What makes a swamp swampy? Water regime and the botany of endangered wetlands in western Victoria

Freshwater temporary wetlands are a little-studied ecosystem worldwide. They have been recognised as critically endangered in south-eastern Australia under Australian biodiversity conservation legislation. However, little has been recorded about their hydrology, functioning or biodiversity values; i.e. the factors that make them intrinsically ‘swampy’. In this paper, we developed a simple threshold model of wetland hydrology based on historical rainfall records and calculated evaporation records matched to records and recollections of the owners of swamps, and documented water-plant and microalgal species richness. The model indicated that swamps were inundated to at least 10-cm depth in an average of 6.3 years per decade for most of the 20th century. The average dry time between inundations was 1.27 years (maximum of 4.5 years). Since 1998, the frequency of inundation appears to have decreased, and the average dry times have increased. Despite, or because of, their temporary nature, these swamps have high biodiversity values among the vegetation and the microalgae, more than has been recorded for near-by permanent wetlands. There is no evidence that a drier and warmer climate will have a negative impact on biodiversity values; however, land management is likely to be important for maintaining these systems as the climate changes

Zooplankton diversity and assemblages in arid zone rivers of the Lake Eyre Basin, Australia

The responses of zooplankton assemblages in arid zone rivers to seasonal changes, flow events, drying and water quality changes are fundamental to our understanding of these unregulated rivers. For three years the zooplankton and littoral microfauna in three rivers in the Lake Eyre Basin were studied. A diverse assemblage was discovered with a total of 398 identifiable taxa being recorded, consisting of 72 protist, 227 rotifer and 93 microcrustacean taxa. Zooplankton diversity was highest in a boom phase during, or in the summer following, a large flood. The rotifer assemblage dominated during, or soon after, periods of flow. However, during the winter and early summer, there was a decline in rotifer taxon richness and abundance accompanied by an increase in microcrustacean taxon richness and abundance. The winter samples occurred during the recession of a large flood and the early summer samples during periods of no flow. These changes suggested the involvement of a strong annual cycle of ecosystem structure evident within the longer term patterns of boom and bust driven by the timing and size of flood events. Multivariate and regression analyses found that salinity was a significant and independent driver of assemblage composition

Twenty-six years of enteric fever in Australia: an epidemiological analysis of antibiotic resistance

Objectives: To determine incidence and trends in antibiotic resistance in Australian Salmonella enterica subspecies enterica serovars Typhi (S. Typhi) and Paratyphi (S. Paratyphi) isolates over the past 26 years.\ud \ud Design: A retrospective analysis of consecutive microbiologically confirmed enteric fever isolates.\ud \ud Participants and setting: All S. Typhi and S. Paratyphi isolates from patients diagnosed with enteric fever in Australia between 1985 and 2010.\ud \ud Main outcome measures: Incidence and variation in antibiotic resistance over time and according to country of origin.\ud \ud Results: We analysed 2551 isolates, which originated from 74 countries or regions, mainly India (33%) and Indonesia (22%). The incidence among Australian residents increased from four to five before 2003 to seven cases per million person-years after 2003. Multidrug resistance (chloramphenicol, ampicillin, trimethoprim) and nalidixic acid resistance emerged rapidly from the early 1990s, with nalidixic acid resistance increasing to 70% in 2009–2010, while multidrug resistance was relatively stable at between 4% and 11%. Nalidixic acid and multidrug resistance rates are highest in isolates from the Indian subcontinent. Some countries in South-East Asia, such as Indonesia, had very low rates of resistance; however, this varied across the region.\ud \ud Conclusions: Nalidixic acid resistance has become widespread in enteric fever isolates from the Indian subcontinent and some parts of South-East Asia, justifying the use of ceftriaxone or azithromycin rather than ciprofloxacin as first-line treatment. However, resistance in some countries remains rare, potentially allowing treatment to be adjusted according to country of origin.\u