Causes of severe pneumonia requiring hospital admission in children without HIV infection from Africa and Asia: the PERCH multi-country case-control study

Background Pneumonia is the leading cause of death among children younger than 5 years. In this study, we estimated causes of pneumonia in young African and Asian children, using novel analytical methods applied to clinical and microbiological findings. Methods We did a multi-site, international case-control study in nine study sites in seven countries: Bangladesh, The Gambia, Kenya, Mali, South Africa, Thailand, and Zambia. All sites enrolled in the study for 24 months. Cases were children aged 1–59 months admitted to hospital with severe pneumonia. Controls were age-group-matched children randomly selected from communities surrounding study sites. Nasopharyngeal and oropharyngeal (NP-OP), urine, blood, induced sputum, lung aspirate, pleural fluid, and gastric aspirates were tested with cultures, multiplex PCR, or both. Primary analyses were restricted to cases without HIV infection and with abnormal chest x-rays and to controls without HIV infection. We applied a Bayesian, partial latent class analysis to estimate probabilities of aetiological agents at the individual and population level, incorporating case and control data. Findings Between Aug 15, 2011, and Jan 30, 2014, we enrolled 4232 cases and 5119 community controls. The primary analysis group was comprised of 1769 (41·8% of 4232) cases without HIV infection and with positive chest x-rays and 5102 (99·7% of 5119) community controls without HIV infection. Wheezing was present in 555 (31·7%) of 1752 cases (range by site 10·6–97·3%). 30-day case-fatality ratio was 6·4% (114 of 1769 cases). Blood cultures were positive in 56 (3·2%) of 1749 cases, and Streptococcus pneumoniae was the most common bacteria isolated (19 [33·9%] of 56). Almost all cases (98·9%) and controls (98·0%) had at least one pathogen detected by PCR in the NP-OP specimen. The detection of respiratory syncytial virus (RSV), parainfluenza virus, human metapneumovirus, influenza virus, S pneumoniae, Haemophilus influenzae type b (Hib), H influenzae non-type b, and Pneumocystis jirovecii in NP-OP specimens was associated with case status. The aetiology analysis estimated that viruses accounted for 61·4% (95% credible interval [CrI] 57·3–65·6) of causes, whereas bacteria accounted for 27·3% (23·3–31·6) and Mycobacterium tuberculosis for 5·9% (3·9–8·3). Viruses were less common (54·5%, 95% CrI 47·4–61·5 vs 68·0%, 62·7–72·7) and bacteria more common (33·7%, 27·2–40·8 vs 22·8%, 18·3–27·6) in very severe pneumonia cases than in severe cases. RSV had the greatest aetiological fraction (31·1%, 95% CrI 28·4–34·2) of all pathogens. Human rhinovirus, human metapneumovirus A or B, human parainfluenza virus, S pneumoniae, M tuberculosis, and H influenzae each accounted for 5% or more of the aetiological distribution. We observed differences in aetiological fraction by age for Bordetella pertussis, parainfluenza types 1 and 3, parechovirus–enterovirus, P jirovecii, RSV, rhinovirus, Staphylococcus aureus, and S pneumoniae, and differences by severity for RSV, S aureus, S pneumoniae, and parainfluenza type 3. The leading ten pathogens of each site accounted for 79% or more of the site's aetiological fraction. Interpretation In our study, a small set of pathogens accounted for most cases of pneumonia requiring hospital admission. Preventing and treating a subset of pathogens could substantially affect childhood pneumonia outcomes

Experimental warming shows that decomposition temperature sensitivity increases with soil organic matter recalcitrance

Soil C decomposition is sensitive to changes in temperature, and even small increases in temperature may prompt large releases of C from soils. But much of what we know about soil C responses to global change is based on short-term incubation data and model output that implicitly assumes soil C pools are composed of organic matter fractions with uniform temperature sensitivities. In contrast, kinetic theory based on chemical reactions suggests that older, more-resistant C fractions may be more temperature sensitive. Recent research on the subject is inconclusive, indicating that the temperature sensitivity of labile soil organic matter (OM) decomposition could either be greater than, less than, or equivalent to that of resistant soil OM. We incubated soils at constant temperature to deplete them of labile soil OM and then successively assessed the CO2-C efflux in response to warming. We found that the decomposition response to experimental warming early during soil incubation (when more labile C remained) was less than that later when labile C was depleted. These results suggest that the temperature sensitivity of resistant soil OM pools is greater than that for labile soil OM and that global change-driven soil C losses may be greater than previously estimated

Appendix A. Mean cumulative respiration (µg CO2-C/g soil) over successive 60-d periods for control sites incubated at constant temperature and soils that underwent incubation experimental warming after 60, 150, 300, and 450 days.

Mean cumulative respiration (µg CO2-C/g soil) over successive 60-d periods for control sites incubated at constant temperature and soils that underwent incubation experimental warming after 60, 150, 300, and 450 days

Accumulation of aliphatic compounds in soil with increasing mean annual temperature

International audienceChemical recalcitrance of biomolecules, physical protection by soil minerals and spatial inaccessibility to decomposer organisms are hypothesized to be primary controls on soil organic matter (SOM) turnover. Previous studies have observed increased sequestration of plant derived aliphatic compounds in experimentally warmed soils but did not identify the mechanisms for this enhanced preservation. To further test the role of environmental conditions in the preservation of aliphatic carbon, we analyzed native soils along a bicontinental, longitudinal, mean annual temperature (MAT) gradient to examine relationships between SOM composition, soil physical properties and temperature. Using biomarker analysis by gas chromatography–mass spectrometry and solid state 13C nuclear magnetic resonance to characterize SOM, we observed that the concentration of aliphatic compounds derived from the waxes and cuticles of plant leaves increased with MAT. We did not observe any significant correlations between aliphatic SOM and clay mineral content which suggests that their inherent chemical recalcitrance is responsible for their persistence in soils. Other SOM components were not correlated with MAT, indicating that temperature alone does not control the overall preservation and biodegradation of soil carbon. As such, other environmental factors (e.g., microbial community structure and activity, litter quality and quantity, mineral surfaces, soil moisture content and antioxidant capacity) also play a role in the selective preservation or accumulation of various SOM components. However, our study shows that the accumulation of aliphatic SOM components is highly correlated to MAT

Litter Decomposition in Grasslands of Central North America (US Great Plains)

One of the major concerns about global warming is the potential for an increase in decomposition and soil respiration rates, increasing CO2 emissions and creating a positive feedback between global warming and soil respiration. This is particularly important in ecosystems with large belowground biomass, such as grasslands where over 90% of the carbon is allocated belowground. A better understanding of the relative influence of climate and litter quality on litter decomposition is needed to predict these changes accurately in grasslands. The Long-Term Intersite Decomposition Experiment Team (LIDET) dataset was used to evaluate the influence of climatic variables (temperature, precipitation, actual evapotranspiration, and climate decomposition index), and litter quality (lignin content, carbon : nitrogen, and lignin : nitrogen ratios) on leaf and root decomposition in the US Great Plains. Wooden dowels were used to provide a homogeneous litter quality to evaluate the relative importance of above and belowground environments on decomposition. Contrary to expectations, temperature did not explain variation in root and leaf decomposition, whereas precipitation partially explained variation in root decomposition. Percent lignin was the best predictor of leaf and root decomposition. It also explained most variation in root decomposition in models which combined litter quality and climatic variables. Despite the lack of relationship between temperature and root decomposition, temperature could indirectly affect root decomposition through decreased litter quality and increased water deficits. These results suggest that carbon flux from root decomposition in grasslands would increase, as result of increasing temperature, only if precipitation is not limiting. However, where precipitation is limiting, increased temperature would decrease root decomposition, thus likely increasing carbon storage in grasslands. Under homogeneous litter quality, belowground decomposition was faster than aboveground and was best predicted by mean annual precipitation, which also suggests that the high moisture in soil accelerates decomposition belowground