Genomic analysis of the mesophilic Thermotogae genus Mesotoga reveals phylogeographic structure and genomic determinants of its distinct metabolism.

The genus Mesotoga, the only described mesophilic Thermotogae lineage, is common in mesothermic anaerobic hydrocarbon-rich environments. Besides mesophily, Mesotoga displays lineage-specific phenotypes, such as no or little H2 production and dependence on sulfur-compound reduction, which may influence its ecological role. We used comparative genomics of 18 Mesotoga strains (pairwise 16S rRNA identity >99%) and a transcriptome of M. prima to investigate how life at moderate temperatures affects phylogeography and to interrogate the genomic features of its lineage-specific metabolism. We propose that Mesotoga accomplish H2 oxidation and thiosulfate reduction using a sulfide dehydrogenase and a hydrogenase-complex and that a pyruvate:ferredoxin oxidoreductase acquired from Clostridia is responsible for oxidizing acetate. Phylogenetic analysis revealed three distinct Mesotoga lineages (89.6%-99.9% average nucleotide identity [ANI] within lineages, 79.3%-87.6% ANI between lineages) having different geographic distribution patterns and high levels of intra-lineage recombination but little geneflow between lineages. Including data from metagenomes, phylogeographic patterns suggest that geographical separation historically has been more important for Mesotoga than hyperthermophilic Thermotoga and we hypothesize that distribution of Mesotoga is constrained by their anaerobic lifestyle. Our data also suggest that recent anthropogenic activities and environments (e.g., wastewater treatment, oil exploration) have expanded Mesotoga habitats and dispersal capabilities.

Burden of malaria is higher among children in an internal displacement camp compared to a neighbouring village in the Democratic Republic of the Congo.

BACKGROUND: In the Democratic Republic of the Congo (DRC), violent conflict has caused the displacement of millions of people into camps where they are exposed to poor living conditions and high rates of infectious diseases. Malaria, in particular, is a major cause of mortality in children under five; however, the burden of disease in displacement camps has not previously been described. METHODS: Two cross-sectional surveys were performed. First, prevalence of Plasmodium falciparum antigenemia was measured in a random sample of 200 children living in a displacement camp and 200 children from a nearby village (control group). Second, the proportion of febrile illness attributable to malaria was measured in a study of 100 children from the displacement camp and 100 children from the control village presenting to the same health clinic with fever. All participants were tested for P. falciparum with a rapid diagnostic test and additional demographic data, clinical characteristics, and malaria risk factors were determined using a parental questionnaire. RESULTS: In the community survey, children living in the displacement camp had a higher prevalence of P. falciparum infection (17 %) than controls (7.5 %) (OR 2.6; 95 % CI 1.3-4.1; P = 0.0095). In the clinic-based survey, the proportion of febrile illness attributable to malaria was higher among children from the displacement camp (78 %) than controls (39 %) (OR 5.5; 95 % CI 3.0-10.3; P < 0.001). Household bed net ownership and use was significantly lower in the displacement camp than control village in both surveys. Statistically significant differences in household wealth, maternal education, and exposure to community violence were also found. CONCLUSIONS: Population displacement due to violent conflict appears to be a risk factor for malaria, a major cause of child mortality. Children living in displacement camps are a relatively understudied population, but have a high burden of malaria, despite control programmes focused on bed net distribution.

Draft Genome Sequences of Kosmotoga sp. Strain DU53 and Kosmotoga arenicorallina S304.

Here, we announce the draft genome sequences of two thermophilic Thermotogae bacteria: Kosmotoga sp. strain DU53, isolated from a continental oil reservoir, and Kosmotoga arenicorallina, isolated from hydrothermal sediments. The sequences will provide further insight into evolution of the Kosmotogales.

Lack of household clustering of malaria in a complex humanitarian emergency: implications for active case detection.

BACKGROUND: Malaria contributes to elevated morbidity and mortality in populations displaced by conflict in tropical zones. In an attempt to reduce malaria transmission in an internally displaced persons (IDP) camp in eastern Democratic Republic of Congo (DRC), we tested a strategy of active case detection of household contacts of malaria cases. METHODS: Prospective community-based survey. RESULTS: From a convenience sample of 100 febrile patients under 5 years of age from the IDP camp presenting to a nearby clinic for management of a fever episode, 19 cases of uncomplicated malaria and 81 controls with non-malarial febrile illness (NFMI) were diagnosed. We engaged community health workers in the IDP camp to screen their household contacts for malaria using rapid diagnostic tests. We detected 29 cases of malaria through this active case-finding procedure. Household contacts of children with uncomplicated malaria were no more likely to have positive Plasmodium falciparum antigenemia than controls with NFMI (OR 0.89, 95% CI 0.33 to 2.4, p = 1.0), suggesting that malaria cases did not cluster at the household level. However, household contacts reporting mild symptoms at the time of community survey (headache, myalgia) had a higher odds of malaria than asymptomatic individuals (OR 14 (95% CI 4.2-48), p ≤ 0.001 and 18 (95% CI 5.9-54), p ≤ 0.001, respectively). CONCLUSION: Screening household contacts of malaria cases was not an efficient case-finding strategy in a Congolese IDP camp. Symptom-based screening may be a simpler and cost-effective method to identify individuals at increased risk of malaria for targeted screening and treatment in an IDP camp.

Elevated prevalence of malnutrition and malaria among school-aged children and adolescents in war-ravaged South Sudan.

Emerging as a sovereign state from decades of civil war, the Republic of South Sudan now faces poverty, a lack of health care infrastructure, a high burden of infectious diseases and a widespread food insecurity. School-aged children and youth, in particular, represent a high-risk demographic for malnutrition and infectious diseases. We screened 109 school-aged children and youth for nutritional status and malaria antigenaemia in Akuak Rak, South Sudan, and found a large proportion of underweight (77/109 = 73%) and prevalent malaria (44/109 = 40%). There was no significant association between malnutrition and malaria. This study represents one of the few published reports on child and youth nutritional status and malaria prevalence in South Sudan since its independence. The implementation of nutrition and malaria screening combined with evidence-based interventions in schools could help target this high burden vulnerable group.

Draft Genome Sequence of Uncultivated Firmicutes (Peptococcaceae SCADC) Single Cells Sorted from Methanogenic Alkane-Degrading Cultures.

The draft genome of an uncultivated bacterium affiliated with the Peptococcaceae was reconstructed by co-assembling Illumina MiSeq sequences from three single cells sorted by microfluidics from two methanogenic alkane-degrading cultures. Peptococcaceae SCADC (short-chain alkane-degrading culture) may be genetically capable of anaerobic alkane activation by fumarate addition in the absence of sulfate.

Distinct bacterial assemblages reside at different depths in Arctic multiyear sea ice.

Bacterial communities in Arctic sea ice play an important role in the regulation of nutrient and energy dynamics in the Arctic Ocean. Sea ice has vertical gradients in temperature, brine salinity and volume, and light and UV levels. Multiyear ice (MYI) has at least two distinct ice layers: old fresh ice with limited permeability, and new saline ice, and may also include a surface melt pond layer. Here, we determine whether bacterial communities (1) differ with ice depth due to strong physical and chemical gradients, (2) are relatively homogenous within a layer, but differ between layers, or (3) do not vary with ice depth. Cores of MYI off northern Ellesmere Island, NU, Canada, were subsectioned in 30-cm intervals, and the bacterial assemblage structure was characterized using 16S rRNA gene pyrotag sequencing. Assemblages clustered into three distinct groups: top (0-30 cm); middle (30-150 cm); and bottom (150-236 cm). These layers correspond to the occurrence of refrozen melt pond ice, at least 2-year-old ice, and newly grown first-year ice at the bottom of the ice sheet, respectively. Thus, MYI houses multiple distinct bacterial assemblages, and in situ conditions appear to play a less important role in structuring microbial assemblages than the age or conditions of the ice at the time of formation.