Urban Market Gardening and Rodent-Borne Pathogenic Leptospira in Arid Zones: A Case Study in Niamey,Niger

Leptospirosis essentially affects human following contact with rodent urine-contaminated water. As such, it was mainly found associated with rice culture, recreational activities and flooding. This is also the reason why it has mainly been investigated in temperate as well as warm and humid regions, while arid zones have been only very occasionally monitored for this disease. In particular, data for West African countries are extremely scarce. Here, we took advantage of an extensive survey of urban rodents in Niamey, Niger, in order to look for rodent-borne pathogenic Leptospira species presence and distribution across the city. To do so, we used high throughput bacterial 16S-based metabarcoding, lipL32 gene-targeting RT-PCR, rrs gene sequencing and VNTR typing as well as GIS-based multivariate spatial analysis. Our results show that leptospires seem absent from the core city where usual Leptospira reservoir rodent species (namely R. rattus and M. natalensis) are yet abundant. On the contrary, L. kirschneri was detected in Arvicanthis niloticus and Cricetomys gambianus, two rodent species that are restricted to irrigated cultures within the city. Moreover, the VNTR profiles showed that rodent-borne leptospires in Niamey belong to previously undescribed serovars. Altogether, our study points towards the importance of market gardening in maintain and circulation of leptospirosis within Sahelian cities. In Africa, irrigated urban agriculture constitutes a pivotal source of food supply, especially in the context of the ongoing extensive urbanization of the continent. With this in mind, we speculate that leptospirosis may represent a zoonotic disease of concern also in arid regions that would deserve to be more rigorously surveyed, especially in urban agricultural settings.     

Toxoplasmosis seroprevalence in urban rodents: a survey in Niamey,Niger

A serological survey of Toxoplasma gondii was conducted on 766 domestic and peridomestic rodents from 46 trapping sites throughout the city of Niamey, Niger. A low seroprevalence was found over the whole town with only 1.96% of the rodents found seropositive. However, differences between species were important, ranging from less than 2% in truly commensal Mastomys natalensis, Rattus rattus and Mus musculus, while garden-associated Arvicanthis niloticus displayed 9.1% of seropositive individuals. This is in line with previous studies on tropical rodents - that we reviewed here - which altogether show that Toxoplasma seroprevalence in rodent is highly variable, depending on many factors such as locality and/or species. Moreover, although we were not able to decipher statistically between habitat or species effect, such a contrast between Nile grass rats and the other rodent species points towards a potentially important role of environmental toxoplasmic infection. This would deserve to be further scrutinised since intra-city irrigated cultures are extending in Niamey, thus potentially increasing Toxoplasma circulation in this yet semi-arid region. As far as we are aware of, our study is one of the rare surveys of its kind performed in Sub-Saharan Africa and the first one ever conducted in the Sahel.     

Epidemiological, clinical and biological features of malaria among children in Niamey, Niger

Background

Malaria takes a heavy toll in Niger, one of the world's poorest countries. Previous evaluations conducted in the context of the strategy for the Integrated Management of Childhood Illness, showed that 84% of severe malaria cases and 64 % of ordinary cases are not correctly managed. The aim of this survey was to describe epidemiological, clinical and biological features of malaria among <5 year-old children in the paediatric department of the National Hospital of Niamey, Niger's main referral hospital.

Methods

The study was performed in 2003 during the rainy season from July 25^th to October 25^th. Microscopic diagnosis of malaria, complete blood cell counts and measurement of glycaemia were performed in compliance with the routine procedure of the laboratory. Epidemiological data was collected through interviews with mothers.

Results

256 children aged 3–60 months were included in the study. Anthropometrics and epidemiological data were typical of a very underprivileged population: 58% of the children were suffering from malnutrition and all were from poor families. Diagnosis of malaria was confirmed by microscopy in 52% of the cases. Clinical symptoms upon admission were non-specific, but there was a significant combination between a positive thick blood smear and neurological symptoms, and between a positive thick blood smear and splenomegaly. Thrombopaenia was also statistically more frequent among confirmed cases of malaria. The prevalence of severe malaria was 86%, including cases of severe anaemia among < 2 year-old children and neurological forms after 2 years of age. Overall mortality was 20% among confirmed cases and 21% among severe cases.

Conclusions

The study confirmed that malaria was a major burden for the National Hospital of Niamey. Children hospitalized for malaria had an underprivileged background. Two distinctive features were the prevalence of severe malaria and a high mortality rate. Medical and non-medical underlying factors which may explain such a situation are discussed.     

A qualitative study of the promotion of exclusive breastfeeding by health professionals in Niamey, Niger

Infant feeding by HIV-infected mothers has been a major global public health dilemma and a highly controversial matter. The controversy is reflected in the different sets of WHO infant feeding guidelines that have been issued over the last two decades. This thematic series, 'Infant feeding and HIV: lessons learnt and ways ahead' highlights the multiple challenges that HIV-infected women, infant feeding counsellors and health systems have encountered trying to translate and implement the shifting infant feeding recommendations in different local contexts in sub-Saharan Africa. As a background for the papers making up the series, this editorial reviews the changes in the guidelines in view of the roll out of prevention of mother to child transmission (PMTCT) programmes in sub-Saharan Africa between 2001 and 2010.     

Establishment and Control of Hay-scented Fern: A Native Invasive Species

Hay-scented fern (Dennstaedtia punctilobula (Michx.) Moore) is a native forest understory species that behaves as an invasive plant under certain conditions. Previous work has shown that both increased understory light intensity following overstory thinning and removal of competing plants by herbivores can lead to accelerated growth of hay-scented fern, allowing it to develop dense, nearly monospecific understories that inhibit tree seedling regeneration. To study the relationship between these two factors, we sampled 28 forest stands thinned at different times and subjected to different levels of browsing by white-tailed deer (Odocoileus virginianus), and concluded that more than 15 years of intensive browsing following thinning was necessary for ferns to form closed understory canopies with densities of >90 fronds/m² and canopy heights of 60–80 cm; thinning alone or intensive browsing alone was not sufficient to cause this level of fern invasion. We applied three treatments to dense fern understories to determine the relative importance of the fern canopy and the dense mat of roots, rhizomes, and dead fronds in the inhibition of tree seedling establishment. Results after two years were: (1) complete removal of the organic mat produced a large germination response of woody and herbaceous species; (2) mixing the organic mat into the mineral soil produced an initial germination response but poor seedling survivorship, as the fern canopy regrew to near pretreatment density; (3) repeatedly clipping the ferns for two years without disturbing the organic mat resulted in a lower germination response than the removal treatment, but rapid growth of seedlings.     

Sulfur Cycling in the Terrestrial Subsurface: Commensal Interactions, Spatial Scales, and Microbial Heterogeneity

Abstract Microbiological, geochemical, and isotopic analyses of sediment and water samples from the unconsolidated Yegua formation in east-central Texas were used to assess microbial processes in the terrestrial subsurface. Previous geochemical studies suggested that sulfide oxidation at shallow depths may provide sulfate for sulfate-reducing bacteria (SRB) in deeper aquifer formations. The present study further examines this possibility, and provides a more detailed evaluation of the relationship between microbial activity, lithology, and the geochemical environment on meter-to-millimeter scales. Sediment of varied lithology (sands, silts, clays, lignite) was collected from two boreholes, to depths of 30 m. Our findings suggest that pyrite oxidation strongly influences the geochemical environment in shallow sediments (∼5 m), and produces acidic waters (pH 3.8) that are rich in sulfate (28 mM) and ferrous iron (0.3 mM). Sulfur and iron-oxidizing bacteria are readily detected in shallow sediments; they likely play an indirect role in pyrite oxidation. In consistent fashion, there is a relative paucity of pyrite in shallow sediments and a low ³⁴S/³²S-sulfate ratio (0.2‰) (reflecting contributions from ³⁴S-depleted sulfides) in shallow regions. Pyrite oxidation likely provides a sulfate source for both oxic and anoxic aquifers in the region. A variety of assays and direct-imaging techniques of ³⁵S-sulfide production in sediment cores indicates that sulfate reduction occurs in both the oxidizing and reducing portions of the sediment profile, with a high degree of spatial variability. Narrow zones of activity were detected in sands that were juxtaposed to clay or lignite-rich sediments. The fermentation of organic matter in the lignite-rich laminae provides small molecular weight organic acids to support sulfate reduction in neighboring sands. Consequently, sulfur cycling in shallow sediments, and sulfate transport represent important mechanisms for commensal interaction among subsurface microorganisms by providing electron donors for chemoautotrophic bacteria and electron acceptors for SRB. The activity of SRB is linked to the availability of suitable electron donors from spatially distinct zones. Received: 10 November 1997; Accepted: 10 February 1998     

Predicting Summer Site Occupancy for an Invasive Species,the Common Brushtail Possum (Trichosurus vulpecula), in an Urban Environment

Invasive species are often favoured in fragmented, highly-modified, human-dominated landscapes such as urban areas. Because successful invasive urban adapters can occupy habitat that is quite different from that in their original range, effective management programmes for invasive species in urban areas require an understanding of distribution, habitat and resource requirements at a local scale that is tailored to the fine-scale heterogeneity typical of urban landscapes. The common brushtail possum (Trichosurus vulpecula) is one of New Zealand’s most destructive invasive pest species. As brushtail possums traditionally occupy forest habitat, control in New Zealand has focussed on rural and forest habitats, and forest fragments in cities. However, as successful urban adapters, possums may be occupying a wider range of habitats. Here we use site occupancy methods to determine the distribution of brushtail possums across five distinguishable urban habitat types during summer, which is when possums have the greatest impacts on breeding birds. We collected data on possum presence/absence and habitat characteristics, including possible sources of supplementary food (fruit trees, vegetable gardens, compost heaps), and the availability of forest fragments from 150 survey locations. Predictive distribution models constructed using the programme PRESENCE revealed that while occupancy rates were highest in forest fragments, possums were still present across a large proportion of residential habitat with occupancy decreasing as housing density increased and green cover decreased. The presence of supplementary food sources was important in predicting possum occupancy, which may reflect the high nutritional value of these food types. Additionally, occupancy decreased as the proportion of forest fragment decreased, indicating the importance of forest fragments in determining possum distribution. Control operations to protect native birds from possum predation in cities should include well-vegetated residential areas; these modified habitats not only support possums but provide a source for reinvasion of fragments.     

Minimum Incidence of Adult Invasive Pneumococcal Disease in Blantyre,Malawi an Urban African Setting: A Hospital Based Prospective Cohort Study

Invasive pneumococcal disease causes substantial morbidity and mortality in Africa. Evaluating population level indirect impact on adult disease of pneumococcal conjugate vaccine (PCV) programmes in infants requires baseline population incidence rates but these are often lacking in areas with limited disease surveillance. We used hospital based blood culture and cerebrospinal fluid surveillance to calculate minimal incidence of invasive pneumococcal disease in the adult (≥15 years old) population of Blantyre, a rapidly growing urban centre in southern Malawi, in the period preceding vaccine introduction. Invasive pneumococcal disease incidence in Blantyre district was high, mean 58.1 (95% confidence interval (CI): 53.7, 62.7) per 100,000 person years and peaking among 35 to 40 year olds at 108.8 (95%CI: 89.0, 131.7) mirroring the population age prevalence of HIV infection. For pneumococcal bacteraemia in urban Blantyre, mean incidence was 60.6 (95% CI: 55.2, 66.5) per 100,000 person years, peaking among 35 to 40 year olds at 114.8 (95%CI: 90.3, 143.9). We suspected that our surveillance may under-ascertain the true burden of disease, so we used location data from bacteraemic subjects and projected population estimates to calculate local sub-district incidence, then examined the impact of community level socio-demographic covariates as possible predictors of local sub-district incidence of pneumococcal and non-pneumococcal pathogenic bacteraemia. Geographic heterogeneity in incidence was marked with localised hotspots but ward level covariates apart from prison were not associated with pneumococcal bacteraemia incidence. Modelling suggests that the current sentinel surveillance system under-ascertains the true burden of disease. We outline a number of challenges to surveillance for pneumococcal disease in our low-resource setting. Subsequent surveillance in the vaccine era will have to account for geographic heterogeneity when evaluating population level indirect impact of PCV13 introduction to the childhood immunisation program.     

Odonata Diversity and Synanthropy in Urban Areas: A Case Study in Avellaneda City,Buenos Aires,Argentina

The increase of human population, especially in urban areas, correlates with an alarming destruction of green spaces. Therefore, understanding the mechanisms by which urbanization processes affect biodiversity is crucial in integrating the environment in a proper urban planning. The main urban center of Argentina is known as the Greater Buenos Aires (GBA), and it includes the autonomous city of Buenos Aires and 24 surrounding districts. Avellaneda, one of the districts of the GBA, is an important urban and industrial center with green areas and low level of urbanization on the coastal area of the Río de la Plata. This paper provides the first Odonata inventory for Avellaneda, determines the species’ level of synanthropy with the Nuorteva index, and assess the Odonata species replacement along a latitudinal gradient on the occidental margin of the Río de la Plata.     

Sharing the Space: Distribution,Habitat Segregation and Delimitation of a New Sympatric Area of Subterranean Rodents

Subterranean rodents of the genus Ctenomys usually present an allopatric or parapatric distribution. Currently, two cases of sympatry have been recognized for the genus in the coastal dunes of southern Argentina and southern Brazil. In this context, they are ideal models to test hypotheses about the factors that delimit the patterns of space use and to understand interspecific interactions in small mammals. We investigated the vegetation structure, plant biomass and soil hardness selected by two species of subterranean rodents (Ctenomys flamarioni and C. minutus) when distributed in sympatry and allopatry from nine different areas along the line of coastal dunes in southern Brazil. In addition, our work presents a new record of a third area of sympatry for the genus Ctenomys. Ctenomys flamarioni and C. minutus show habitat segregation in the area where they occur in sympatry. These species show segregation in their selection of microhabitats, differing in relation to soil hardness, plant biomass, and plant cover. Ctenomys flamarioni showed a distinction in habitat selection when occurring in allopatry and sympatry, whereas C. minutus selected the same habitat characteristics under both conditions. A possible explanation to the observed pattern is that these species have acquired different adaptations over time which allows them the ability to exploit different resources and thus avoid competitive interactions all together.     

Competition between Invasive and Indigenous Species: Impact of Spatial Pattern and Developmental Stage

Elodea canadensis (indigenous) and Elodea nuttallii (invasive) were grown in experimental tanks in monocultures and mixtures in two spatial patterns (aggregated or mixed) and two developmental stages (small or large plants of E. canadensis, and small plants of E. nuttallii). Competitive interactions between the two species were assessed by monitoring the area colonised by each species, the number of rootings and biomass after 10 weeks. In monocultures the growth of E. canadensis was significantly lower than that of E. nuttallii. In mixtures the number of rootings and biomass of E. canadensis were always significantly less than those of E. nuttallii. The tank surface area colonised by E. canadensis was always significantly less than that occupied by E. nuttallii, but it was higher in the aggregated treatment, where the colonisation of E. nuttallii was lower. Therefore both spatial pattern and developmental stage of an indigenous species (E. canadensis) may influence the outcome of competition with potential invaders (E. nuttallii).     

Spatial Analysis of Childhood Cancer: A Case/Control Study

BackgroundChildhood cancer was the leading cause of death among children aged 1-14 years for 2012 in Spain. Leukemia has the highest incidence, followed by tumors of the central nervous system (CNS) and lymphomas (Hodgkin lymphoma, HL, and Non-Hodgkin’s lymphoma, NHL). Spatial distribution of childhood cancer cases has been under concern with the aim of identifying potential risk factors.ObjectiveThe two objectives are to study overall spatial clustering and cluster detection of cases of the three main childhood cancer causes, looking to increase etiological knowledge.MethodsWe ran a case-control study. The cases were children aged 0 to 14 diagnosed with leukemia, lymphomas (HL and NHL) or CNS neoplasm in five Spanish regions for the period 1996-2011. As a control group, we used a sample from the Birth Registry matching every case by year of birth, autonomous region of residence and sex with six controls. We geocoded and validated the address of the cases and controls. For our two objectives we used two different methodologies. For the first, for overall spatial clustering detection, we used the differences of K functions from the spatial point patterns perspective proposed by Diggle and Chetwynd and the second, for cluster detection, we used the spatial scan statistic proposed by Kulldorff with a level for statistical significance of 0.05.ResultsWe had 1062 cases of leukemia, 714 cases of CNS, 92 of HL and 246 of NHL. Accordingly we had 6 times the number of controls, 6372 controls for leukemia, 4284 controls for CNS, 552 controls for HL and 1476 controls for NHL. We found variations in the estimated empirical D(s) for the different regions and cancers, including some overall spatial clustering for specific regions and distances. We did not find statistically significant clusters.ConclusionsThe variations in the estimated empirical D(s) for the different regions and cancers could be partially explained by the differences in the spatial distribution of the population; however, according to the literature, we cannot discard environmental hazards or infections agents in the etiology of these cancers.     

Invasive Geotrichum clavatum Fungal Infection in an Acute Myeloid Leukaemia Patient: A Case Report and Review

Invasive Geotrichum clavatum fungal infections are extremely rare and unusual, occurring nearly exclusively in patients experiencing prolonged neutropenia during the treatment for acute myeloid leukaemia. Several groups of cases of fatal G. clavatum infection were reported in France between 2011 and 2012, but the ecological niche has not yet been identified. We report a case of a 32-year-old patient with acute myeloid leukaemia who developed G. clavatum sepsis with primary peritonitis, hepatic nodular lesions, and multivisceral failure during aplasia after induction followed by salvage chemotherapy. He was treated with voriconazole and is still alive 1 year after with controlled disease. We then discuss the epidemiological, clinical, and therapeutic features of these serious fungal infections compared to the published data.     

Antibiotic Resistance of Commensal Staphylococcus aureus and Coagulase-Negative Staphylococci in an International Cohort of Surgeons: A Prospective Point-Prevalence Study

Nasal colonization with antibiotic resistant bacteria represents both a risk factor for the colonized individual and their immediate contacts. Despite the fact that healthcare workers such as orthopedic surgeons are at a critical interface between the healthcare environment and an at-risk patient population, the prevalence of antibiotic resistant bacteria within the surgical profession remains unclear. This study offers a snapshot of the rate of nasal colonization of orthopedic surgeons with multi-resistant staphylococci including methicillin-resistant S. aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MRCoNS). We performed a prospective, observational study obtained at a single time point in late 2013. The participants were active orthopedic, spine and head & neck surgeons from 75 countries. The prevalence of nasal carriage of the different bacteria and the corresponding 95% confidence interval were calculated. From a cohort of 1,166 surgeons, we found an average S. aureus nasal colonization rate of 28.0% (CI 25.4;30.6) and MRSA rate of 2.0% (CI 1.3;2.9), although significant regional variations were observed. The highest rates of MRSA colonization were found in Asia (6.1%), Africa (5.1%) and Central America (4.8%). There was no MRSA carriage detected within our population of 79 surgeons working in North America, and a low (0.6%) MRSA rate in 657 surgeons working in Europe. High rates of MRCoNS nasal carriage were also observed (21.4% overall), with a similar geographic distribution. Recent use of systemic antibiotics was associated with higher rates of carriage of resistant staphylococci. In conclusion, orthopedic surgeons are colonized by S. aureus and MRSA at broadly equivalent rates to the general population. Crucially, geographic differences were observed, which may be partially accounted for by varying antimicrobial stewardship practices between the regions. The elevated rates of resistance within the coagulase-negative staphylococci are of concern, due to the increasing awareness of their importance in hospital acquired and device-associated infection.