Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.

The impact of endotracheal intubation on oxygen delivery, trachea pressure and wall deformation

This paper concerns improving endotracheal tube (ETT) insertion through advanced computational science modelling. The study aims to better understand endotracheal intubation (ETI) and reduce medical errors in intensive and critical care units since ETT insertion is unique for each patient, depending on age, gender, size, physiology, and underlying health conditions. We have employed computational fluid dynamics and biomechanics modelling to investigate the effect of ETT for three ventilation modes on (a) local oxygen delivery to the lungs, (b) air pressure and wall shear stress at the tracheal walls, and (c) oscillatory elastic deformation of the tracheal tissues and muscle. For the first time, we reveal how the ventilation mode and ETT insertion in the trachea may induce major complications, especially in long periods of ETT. We show that rotating the ETT or displacing it by 2 mm only can induce a significant rise in the tracheal pressure up to 177 cmH2O. This study, for the first time, shows the vital role of computers in biology and medicine to provide enhanced decision-making-support to clinicians and medical doctors dealing with ETI.

Fluconazole Resistance and Virulence in In Vitro Induced-Fluconazole Resistant Strains and in Clinical Fluconazole Resistant Strain of Cryptococcus deuterogattii

Neuromeningeal cryptococcosis is a life-threatening infection of the central nervous system, caused by encapsulated yeast belonging to the Cryptococcus neoformans and Cryptococcus gattii species complexes. Recent data showed that virulence and antifungal resistance are variable for yeasts belonging to the C. gattii species complex. There is an increase in resistance to fluconazole for yeasts of the C. gattii species complex and the virulence is variable according to the genotype. In the present study, (i) we explored and compared the mechanisms of resistance to fluconazole between C. deuterogattii clinically resistant strains and induced fluconazole-resistant strains by exposure to fluconazole in vitro, and (ii) we studied their virulence in the Galleria mellonella study model. We demonstrated that the fluconazole resistance mechanisms involved were different between clinically resistant strains and induced resistant strains. We also demonstrated that fluconazole-induced resistant strains are less virulent when compared to the original susceptible strains. On the contrary, the clinically resistant strain tested maintains its virulence compared to fluconazole-susceptible strains of the same sequence type.

Exposure of Cryptococcus neoformans to Seven Commonly Used Agricultural Azole Fungicides Induces Resistance to Fluconazole as Well as Cross-Resistance to Voriconazole, Posaconazole, Itraconazole and Isavuconazole

BACKGROUND

Cross-resistance to medical azoles by exposure to azole pesticides is well documented for Aspergillus family fungi but is poorly evaluated for other environmental pathogen fungi, particularly for yeasts belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes.

METHODS

One thousand C. neoformans yeast were exposed to various concentrations of seven different commonly used azole pesticides. Clones surviving exposure were picked randomly, and their minimal inhibitory concentrations (MICs) of fluconazole, voriconazole, posaconazole, itraconazole and isavuconazole were assessed.

RESULTS

Depending on the pesticide used for exposure, up to 13.3% of selected Cryptococcus colonies showed a phenotype of resistance to fluconazole, and among them, several showed cross-resistance to another or several other medical azoles. Molecular mechanisms involved in the resistance setups seem to be dependent on ERG11 and AFR1 gene overexpression.

CONCLUSION

Exposure to any of the seven azole pesticides tested is capable of increasing the MIC of fluconazole in C. neoformans, including up to the level of the fluconazole-resistant phenotype, as well as generating cross-resistance to other medical azoles in some cases.

Tablets in Capsule as Strategy to Improve Adherence in Patients Cardiovascular Disease

Aims: The main objective of this work has been the development of delayed-release hard capsule containing mini-tablets of two-platelet antiaggregant, acetylsalicylic acid and clopidogrel, for the treatment of patients suffering from acute coronary syndrome at risk of gastrointestinal bleeding, therefore jointly is administered an inhibitor of gastric acid secretion, the ranitidine. Study Design: Design of mini-tablets into a capsule for the treatment of acute coronary syndrome. Methodology: For the galenic preparation of the three mini-tablets, an in-depth study of the choice of excipients and the most appropriate manufacturing methodology was carried out. Once the suitability of the mixture for use in direct compression was determined, which is the selected technological method, as it is the most profitable and involves less time, the mini-tablets were prepared and their physical characterization. Tablet appearance and physical characteristics such as dimensions, thickness, mass, resistance to crushing, friability, disintegration time and content uniformity met the requirements established according to pharmacopoeia to ensure the quality of the tablets. Results: The final formulation consists of the grouping of mini-tablets of three drugs in a delayed-release hard capsule ("tablets-in-capsule") for the treatment of patients suffering from acute coronary syndrome at risk of gastrointestinal bleeding. All tablets show resistance to crushing, disintegration, and friability features that strictly meet pharmacopoeia requirements. Conclusion: Adherence to treatment is increased because the concomitant administration of three active ingredients is unified in a single pharmaceutical dosage form.

Search for Cryptococcus neoformans/gattii Complexes and Related Genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) spp. Biotope: Two Years Surveillance of Wild Avian Fauna in Southern France

Fungi belonging to the Cryptococcus genus and related genera (Filobasidium, Holtermanniella, Naganishia, Papiliotrema, Solicoccozyma, Vishniacozyma) are encapsulated yeasts found in either the environment or animal sources. However, the precise biotopes of most species remain poorly defined. To assess whether wild birds from southern France can carry or spread the most pathogenic species (i.e., species belonging to the C. neoformans and C. gattii complexes), as well as lesser-studied species (non-neoformans/gattii Cryptococcus and former Cryptococcus spp.), 669 birds belonging to 89 species received for care over a two-year period at the Centre de Protection de la Faune Sauvage of Villeveyrac (Bird Protection League nongovernmental organization (NGO) care center) were sampled. Samples were cultured, and Cryptococcus and former Cryptococcus yeasts were identified by PCR sequencing. The purpose was to evaluate whether there was any health risk to local populations or care personnel in aviaries and gather new data on the ecological niches of lesser-known species. One hundred and seven birds (16%) were found to be positive for at least one Cryptococcus or former Cryptococcus species. No yeasts belonging to the highly pathogenic C. neoformans or C. gattii complexes were isolated. However, diversity was notable, with 20 different Cryptococcus or former Cryptococcus species identified. Furthermore, most bird–yeast species associations found in this study have never been described before.

Multilocus sequence typing of strains from the Cryptococcus gattii species complex from different continents

BACKGROUND

Cryptococcus neoformans and Cryptococcus gattii species complexes are pathogens causing cryptococcal meningitis, a fungal infection that leads to death unless treated. Worldwide, it is estimated to kill over 180,000 individuals annually.

OBJECTIVES

We aim to investigate the molecular diversity of C. gattii isolates from strains isolated from 1995 to the present day from different continents.

METHOD

In this study, we analysed the molecular diversity by MLST and antifungal susceptibility by using the broth microdilution method according to the CLSI M27-A4 protocol of a total of 26 strains from Cryptococcus gattii species complex from both clinical and environmental sources.

RESULTS

Genotyping showed that most of the strains (17/26; 65.4%) belonged to serotype B and were distributed between three genotypes: VGI (13/17; 76.5%), VGII (3/17; 17.6%) and VGVI (1/17; 5.9%). The serotype C strains (9/26; 34.6%) were distributed between the VGIII (1/9; 11.1%) and VGIV (8/9; 88.9%) genotypes. The 26 strains belonged to 17 different MLST subtypes, and we highlight four new MLST genotypes (ST553, 554, 555 and 556). The two environmental strains were identified as serotype B and genotype VGI, but were of ST 51 and 154. All isolates have wild-type MIC of fluconazole and flucytosine. Regarding amphotericin B, five VGI strains showed MICs to AMB equal to 1 µg/ml, and according to the ECV for these genotypes, they were considered non-wild-type strains.

CONCLUSIONS

The current study reveals the genetic diversity and new sequence types among strains from the C. gattii complex species.

First report of cryptococcosis due to Cryptococcus gattii sensu stricto VGI in an Ivorian HIV negative patient

INTRODUCTION

Cryptococcus gattii species complex is endemic to tropical and subtropical regions and is described as a causative agent of cryptococcosis in immunocompetent individuals.

CASE PRESENTATION

We describe the first case of cryptococcosis in a HIV-negative patient from Ivory Coast infected by Cryptococcus gattii sensu stricto VGI. Isolates were recovered from cerebrospinal fluid (CSF) prior to systemic antifungal treatment up to 42 days after detection of the presence of yeasts in the CSF. Eighteen isolates were recovered, genetic diversity and antifungal susceptibility analyses were performed. All the isolates belonged to the Cryptococcus gattii sensu stricto (B;VGI) and were identified as a new sequence type (ST) 553 by Multilocus Sequence Typing (MLST) analyses. Susceptibility testing showed that all the strains had a wild-type phenotype for fluconazole, amphotericin B and flucytosine. Treatment with fluconazole (1200mg/day) was initiated with success.

CONCLUSION

This is the first case report of the presence of C. gattii sensu stricto VGI in a HIV-negative ivorian patient and the second report of the presence of species from the C. gattii complex species in this country.

Chaos theory applied to the outbreak of COVID-19: an ancillary approach to decision making in pandemic context

While predicting the course of an epidemic is difficult, predicting the course of a pandemic from an emerging virus is even more so. The validity of most predictive models relies on numerous parameters, involving biological and social characteristics often unknown or highly uncertain. Data of the COVID-19 epidemics in China, Japan, South Korea and Italy were used to build up deterministic models without strong assumptions. These models were then applied to other countries to identify the closest scenarios in order to foresee their coming behaviour. The models enabled to predict situations that were confirmed little by little, proving that these tools can be efficient and useful for decision making in a quickly evolving operational context.

Cryptococcus genetic diversity and mixed infections in Ivorian HIV patients: A follow up study

Genetic diversity analyses were performed by sero-genotyping and multi-locus sequence typing on 252 cryptococcal isolates from 13 HIV-positive Ivorian patients followed-up for cryptococcal meningitis. Antifungal susceptibility analyses were performed according to the CLSI M27A3 method. The majority (67.8%) of the isolates belonged to the Cryptococcus neoformans (serotype A) species complex, with 93% being VNI and 7% being VNII. Cryptococcus deuterogattii VGII (serotype B) represented 16.7% of the strains, while C. neoformans/C. deneoformans VNIII (serotype AD) hybrids accounted for 15.1% of the strains. One strain (0.4%) was not identifiable. Nine different sequence types (STs 5, 6, 23, 40, 93, 207, 311, and a new ST; 555) were identified in the C. neoformans population, while the C. deuterogattii population comprised the single ST 173. The distribution of the strains showed that, while the majority of patients (9/13) harboured a single sequence type, 4 patients showed mixed infections. These patients experienced up to 4 shifts in strain content either at the species and/or ST level during their follow-up. This evolution of diversity over time led to the co-existence of up to 3 different Cryptococcus species and 4 different ST within the same individual during the course of infection. Susceptibility testing showed that all strains were susceptible to amphotericin B while 3.6% of them had a none-wild type phenotype to 5-flucytosine. Concerning fluconazole, 2.9% of C.neoformans serotype A strains and 2.4% of C. deuterogattii had also respectively a none-wild type phenotype to this molecule. All C. neoformans x C. deneoformans serotype AD hybrids had however a wild type phenotype to fluconazole. The present study showed that mixed infections exist and could be of particular importance for care outcomes. Indeed, (i) the different Cryptococcus species are known to exhibit different virulence and different susceptibility patterns to antifungal drugs and (ii) the strains genetic diversity within the samples may influence the susceptibility to antifungal treatment.

Comparative typing analyses of clinical and environmental strains of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast

PURPOSE

The aim of this study was to assess the biotope of the Cryptococcus neoformans/Cryptococcus gattii species complex from Ivory Coast, and clarify the possible epidemiological relationship between environmental and clinical strains.

METHODOLOGY

Samples from Eucalyptus camaldulensis (n=136), Mangifera indica (n=13) and pigeon droppings (n=518) were collected from different sites close to the living environment of Ivorian HIV patients with cryptococcosis (n=10, 50 clinical strains). Clinical and environmental strains were characterized by molecular serotyping and genotyping [RFLP analysis of the URA5 gene, (GACA)4, (GTG)5 and M13 PCR fingerprinting] and compared.Results/Key findings. Environmental strains were recovered only from the pigeon droppings. In vitro susceptibility profiles showed that all strains were susceptible to fluconazole, flucytosine and amphotericin B. All environmental strains consisted of C. neoformans (A, AFLP1/VNI), whereas clinical strains included C. neoformans (A, AFLP1/VNI), C. neoformans x Cryptococcus deneoformans hybrids (AD, AFLP3/VNIII) and Cryptococcus deuterogattii (B, AFLP6/VGII). Two patients were co-infected with both C. neoformans and C. neoformans x C. deneoformans hybrids. We noticed a low genetic diversity among the environmental samples compared to the high diversity of the clinical samples. Some clinical strains were genetically more similar to environmental strains than to other clinical strains, including those from the same patient.

CONCLUSION

These results provide new information on the ecology and epidemiology of the C. neoformans/C. gattii species complex in Ivory Coast.

Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)

Aeromonas spp. are ubiquitous bacteria primarily recovered from aquatic ecosystems. They are found in fresh water as well as estuarine and marine waters, and in association with numerous autochthonous aquatic organisms in these environments. However, aeromonads are also etiologic agents of fish diseases and are now recognized as emerging pathogens in humans. The estuary is therefore a key environment, harboring autochthonous aeromonads, and aeromonads originating from humans and animals, mainly released by treated WWTP effluent or watershed run-off via tributaries. The present study compares the abundance and the diversity of Aeromonas populations. Over 2 years of monitoring (eight campaigns from February 2013 to November 2015), the occurrence of Aeromonas was investigated within the water column (water and fluid mud) and in association with copepods. Moreover, the diversity of Aeromonas populations was ascertained by analyzing gyrB and radA sequences, and the antibiotic-resistance phenotypes were determined using the disk diffusion method. This study shows, for the first time, the presence of Aeromonas spp. in water (1.1 × 10² to 1.2 ± 0.3 × 10³ CFU.100 mL^-1), fluid mud (2.6 ± 2.6 × 10² to 9.8 ± 0.9 × 10³ CFU.g^-1) and in association with living copepods (1.9 ± 0.7 × 10² to >1.1 × 10⁴ CFU.g^-1) in the Seine estuary. Moreover, the diversity study, conducted on 36 strains isolated from the water column and 47 strains isolated from copepods, indicates distinct populations within these two compartments. Strains distributed in five clusters corresponding to A. bestiarum (n = 6; 5.45%), A. encheleia (n = 1; 0.91%), A. media (n = 22; 20.0%), A. rivipollensis (n = 34; 30.91%) and A. salmonicida (n = 47; 42.73%). A. salmonicida is the most abundant species associated with Eurytemora affinis (n = 35; 74.47%). In contrast, A. salmonicida accounts for only 30.56% (n = 11) of isolates in the water column. This study shows the coexistence of distinct populations of Aeromonas in the oligohaline area of an anthropized estuary. Moreover, A. media, a putative human pathogen, present in the water column and abundant in the WWTP samples, was not detected in association with living copepods.

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.

A Systematic Scoping Study of the Socio-Economic Impact of Rift Valley Fever: Research Gaps and Needs

Rift Valley fever (RVF) is a severe mosquito-borne disease affecting humans and domestic ruminants. RVF virus has been reported in most African countries, as well as in the Arabic Peninsula. This paper reviews the different types of socio-economic impact induced by RVF disease and the attempts to evaluate them. Of the 52 papers selected for this review, 13 types of socio-economic impact were identified according to the sector impacted, the level and temporal scale of the impact. RVF has a dramatic impact on producers and livestock industries, affecting public and animal health, food security and the livelihood of the pastoralist communities. RVF also has an impact on international trade and other agro-industries. The risk of introducing RVF into disease-free countries via the importation of an infected animal or mosquito is real, and the consequent restriction of access to export markets may induce dramatic economic consequences for national and local economies. Despite the important threat of RVF, few studies have been conducted to assess the socio-economic impact of the disease. The 17 studies identified for quantitative analysis in this review relied only on partial cost analysis, with limited reference to mid- and long-term impact, public health or risk mitigation measures. However, the estimated impacts were high (ranging from $5 to $470 million USD losses). To reduce the impact of RVF, early detection and rapid response should be implemented. Comprehensive disease impact studies are required to provide decision-makers with science-based information on the best intervention measure to implement ensuring efficient resource allocation. Through the analysis of RVF socio-economic impact, this scoping study proposes insights into the mechanisms underpinning its often-underestimated importance. This study highlights the need for comparative socio-economic studies to help decision-makers with their choices related to RVF disease management.

A meta-analysis of observational epidemiological studies of Newcastle disease in African agro-systems, 1980-2009

Newcastle disease (ND) is one of the most important and widespread avian pests. In Africa, backyard poultry production systems are an important source of protein and cash for poor rural livelihoods. ND mortality in these production systems is important and seriously disrupts benefits derived from it. This study undertook an African continental approach of ND epidemiology in backyard poultry. After a systematic literature review of studies published from 1980 to 2009, a meta-analysis of spatio-temporal patterns of serological prevalence and outbreak occurrence was performed. Average ND serological prevalence was estimated at 0·67 [95% confidence interval (CI) 0·58-0·75] in regions characterized by humid ecosystems, high human and poultry densities and low altitudes; 0·36 (95% CI 0·30-0·41) in dry ecosystems at intermediate altitude where human and poultry densities are low and 0·27 (95% CI 0·19-0·38) in mountain ecosystems where human and poultry densities are intermediate. In terms of seasonality, ND outbreaks occur mostly during the dry seasons in Africa, when environmental conditions are likely to be harshest for backyard poultry. In addition, a phylogeographical analysis revealed the regionalization of ND virus strains, their potential to evolve towards a higher pathogenicity from the local viral pool and suggests a risk for vaccine strains to provide new wild strains. These results present for the first time a continent-wide approach to ND epidemiology in Africa. More emphasis is needed for ND management and control in rural African poultry production systems.

Review of the sylvatic cycle of African swine fever in sub-Saharan Africa and the Indian ocean

African swine fever (ASF) is a major limiting factor for pig production in most of the countries in Sub-Saharan Africa and the Indian Ocean. In the absence of vaccine, a good understanding of the ecology and epidemiology of the disease is fundamental to implement effective control measures. In selected countries of Southern and East Africa, the association between Ornithodoros moubata ticks and warthogs has been described in detail in the literature. However, for many other countries in the region, information related to the sylvatic cycle is lacking or incomplete. In West African countries, for instance, the role of wild pigs in the epidemiology of ASF has never been demonstrated and the existence and potential impact of a sylvatic cycle involving an association between soft ticks and warthogs is questionable. In other countries, other wild pig species such as the bushpigs (Potamochoerus spp.) can also be asymptomatically infected by the virus but their role in the epidemiology of the disease is unclear and might differ according to geographic regions. In addition, the methods and techniques required to study the role of wild hosts in ASF virus (ASFV) epidemiology and ecology are very specific and differ from the more traditional methods to study domestic pigs or other tick species. The aim of this review is (i) to provide a descriptive list of the methodologies implemented to study the role of wild hosts in African swine fever, (ii) to compile the available knowledge about the sylvatic cycle of ASFV in different regions of Sub-Saharan Africa and the Indian Ocean in addition to the one that has been described for East and Southern Africa, and (iii) to discuss current methodologies and available knowledge in order to identify new orientations for further field and experimental surveys.

Ribosomal multi-operon diversity: an original perspective on the genus Aeromonas

16S rRNA gene (rrs) is considered of low taxonomic interest in the genus Aeromonas. Here, 195 Aeromonas strains belonging to populations structured by multilocus phylogeny were studied using an original approach that considered Ribosomal Multi-Operon Diversity. This approach associated pulsed-field gel electrophoresis (PFGE) to assess rrn operon number and distribution across the chromosome and PCR-temporal temperature gel electrophoresis (TTGE) to assess rrs V3 region heterogeneity. Aeromonads harbored 8 to 11 rrn operons, 10 operons being observed in more than 92% of the strains. Intraspecific variability was low or nul except for A. salmonicida and A. aquariorum suggesting that large chromosomic rearrangements might occur in these two species while being extremely rarely encountered in the evolution of other taxa. rrn operon number at 8 as well as PFGE patterns were shown valuable for taxonomic purpose allowing resolution of species complexes. PCR-TTGE revealed a high rate of strains (41.5%) displaying intragenomic rrs heterogeneity. Strains isolated from human samples more frequently displayed intragenomic heterogeneity than strains recovered from non-human and environmental specimens. Intraspecific variability ranged from 0 to 76.5% of the strains. The observation of species-specific TTGE bands, the recovery of identical V3 regions in different species and the variability of intragenomic heterogeneity (1-13 divergent nucleotides) supported the occurrence of mutations and horizontal transfer in aeromonad rrs evolution. Altogether, the presence of a high number of rrn operon, the high proportion of strains harboring divergent rrs V3 region and the previously demonstrated high level of genetic diversity argued in favor of highly adaptative capabilities of aeromonads. Outstanding features observed for A. caviae supported the ongoing process of adaptation to a specialized niche represented by the gut, previously hypothesized. 16S rRNA gene is an informative marker in the genus Aeromonas for both evolutionary and polyphasic taxonomic studies provided that multi-operon fingerprinting approaches are used.

Lumpy skin disease in Ethiopia: seroprevalence study across different agro-climate zones

A cross-sectional study was conducted to estimate the seroprevalence of lumpy skin disease (LSD) in the different agro-climatic zones prevailing in Ethiopia. A total of 2368 serum samples were collected from 42 kebeles located in 15 districts and tested using indirect fluorescent antibody test (IFAT) and virus neutralization test (VNT). The herd and animal true LSD serological prevalence were estimated in each agro-climate zone using a Bayesian model. The intra-cluster correlation coefficient (ICC) was evaluated using a random-effect model. According to the serological prevalence estimations, LSD affected differently the three agro-climatic zones considered. Herd level seroprevalence was higher in the midland agro-climate zone 64% (95% CI: 53-74) as compared to the highland 26% (95% CI: 17-36) and the lowland 50% (95% CI: 40-60) agro-climates. Animal level seroprevalence in infected herds was also higher in the midland agro-climate zone 31% (95% CI: 24-40) than in the highland and lowland zones (24% (95% CI: 18-31) and 23% (95% CI: 18-29), respectively). Higher ICC value in the highland agro-climate zone implies that increased sample sizes should be particularly required for this zone in future studies to estimate LSD prevalence or incidence with a desired precision level. This seroprevalence study also suggests that the prevalence of LSD infection in Ethiopia is higher than what has been previously reported. In the light of these updated estimations, we discuss options to trigger appropriate control measures in the future.

Evaluating the efficiency of participatory epidemiology to estimate the incidence and impacts of foot-and-mouth disease among livestock owners in Cambodia

The economic and social impacts of foot-and-mouth disease (FMD) for livestock owners of developed countries have been extensively documented over the past few years. In developing countries such as Cambodia, this evaluation is often lacking due to the scarcity of accurate data. In the present study, we used a range of participatory tools to infer farmers' knowledge and perception, and the relative incidence of FMD from January 2009 to June 2010 in fifty-one villages of Svay Rieng province, Cambodia. In addition, the detection of non-structural protein at village level was used to cross-validate the results from the participatory epidemiology (PE) study. A quantitative assessment using Bayesian modeling was carried out to assess the ability of PE to retrospectively determine the FMD-infected status of a village in Cambodia. Our study shows that even if FMD is ranked second in the list of priority diseases, livestock owners did not see any benefit in reporting it since the disease entailed low direct losses. The average clinical incidence rates at individual level for cattle-buffaloes and pigs in infected villages were assessed by proportional piling at 18% and 11%, respectively for the year 2009. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of PE study were estimated at 87%, 30%, 51% and 74%, respectively. This approach seems to largely overestimate the presence of the disease but proves useful in evaluating the impact of FMD at household level and in understanding the reasons for not reporting it. This information may be important in establishing well-adapted disease prevention and control strategies in Cambodia.

Multilocus genetics to reconstruct aeromonad evolution

BACKGROUND

Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA) based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes.

RESULTS

The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA) revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas.

CONCLUSIONS

Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or "disease specialized" while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been described as a genetically uniform pathogen that has adapted to fish through evolution from a variable ancestral population, we hypothesize that the population structure of aeromonads described herein suggested an ongoing process of adaptation to specialized niches associated with different degrees of advancement according to clades and clusters.

From environment to man: genome evolution and adaptation of human opportunistic bacterial pathogens

Environment is recognized as a huge reservoir for bacterial species and a source of human pathogens. Some environmental bacteria have an extraordinary range of activities that include promotion of plant growth or disease, breakdown of pollutants, production of original biomolecules, but also multidrug resistance and human pathogenicity. The versatility of bacterial life-style involves adaptation to various niches. Adaptation to both open environment and human specific niches is a major challenge that involves intermediate organisms allowing pre-adaptation to humans. The aim of this review is to analyze genomic features of environmental bacteria in order to explain their adaptation to human beings. The genera Pseudomonas, Aeromonas and Ochrobactrum provide valuable examples of opportunistic behavior associated to particular genomic structure and evolution. Particularly, we performed original genomic comparisons among aeromonads and between the strictly intracellular pathogens Brucella spp. and the mild opportunistic pathogens Ochrobactrum spp. We conclude that the adaptation to human could coincide with a speciation in action revealed by modifications in both genomic and population structures. This adaptation-driven speciation could be a major mechanism for the emergence of true pathogens besides the acquisition of specialized virulence factors.

Estimating spatial and temporal variations of the reproduction number for highly pathogenic avian influenza H5N1 epidemic in Thailand

Since 2003, highly pathogenic avian influenza (HPAI) H5N1 virus has spread, causing a pandemic with serious economic consequences and public health implications. Quantitative estimates of the spread of HPAI H5N1 are needed to adapt control measures. This study aimed to estimate the variations of the reproduction number R in space and time for the HPAI H5N1 epidemic in Thailand. Transmission between sub-districts was analyzed using three different and complementary methods. Transmission of HPAI H5N1 was intense (R(t)>1) before October 2004, at which point the epidemic started to progressively fade out (R(t)<1). The spread was mainly local, with 75% of the putative distances of transmission less than 32km. The map of the mean standardized ratio of transmitting the infection (sr) showed sub-districts with a high risk of transmitting infection. Findings from this study can contribute to discussions regarding the efficacy of control measures and help target surveillance programs.

Looking for avian influenza in remote areas. A case study in Northern Vietnam

Epidemiological surveys of avian influenza infections rarely focus on backyard poultry systems in remote locations because areas with low levels of poultry production are considered to have little influence on the emergence, re-emergence, persistence or spread of avian influenza viruses. In addition, routine disease investigations in remote areas often are neglected due to the lower availability and relatively high cost of veterinary services there. A bank of avian sera collected in 2005 from ethnic minority households in Ha Giang province (Northern Vietnam), located on the Chinese border, was analysed to estimate the seroprevalence of avian influenza virus (AIV) during a H5N1 epidemic and to identify potential risk factors for infection. The results suggest that the chicken population had been exposed to AIV with a seroprevalence rate of 7.2% [1.45; 10.5]. The H5 and H9 subtypes were identified with a seroprevalence of 3.25% [2.39; 4.11] and 1.12% [0.61; 1.63], respectively. The number of inhabitants in a village and the distance to the main national road were the most influential risk factors of AIV infection, and high-risk clusters were located along the road leading to China. These two results suggest a virus spread through commercial poultry exchanges and a possible introduction of AIV from southern China. Remote areas and small-scale farms may play an under-estimated role in the spread and persistence of AIV.

Accuracy of 6 commercial systems for identifying clinical Aeromonas isolates

We compared the accuracy of 6 commercial systems for Aeromonas identification by testing 87 clinical isolates in routine conditions, using partial rpoB gene sequencing as the reference standard. The systems were API-20E, API-32GN, the ID-GN card with the Vitek2 system (bioMérieux, Marcy l'Etoile, France), the identification portion of the NFC47 panel (MicroScan Walk/Away system; Siemens Healthcare, Sacramento, CA), ID69 (Phoenix system; BD Diagnostic Systems, Sparks, MD), and GN2 microplates (Omnilog system; Biolog, Hayward, CA), for which 67 (77.1%), 80 (91.9%), 72 (82.7%), 70 (80.5%), 64 (73.5%), and 59 (67.8%) isolates, respectively, were correctly identified at the genus and species level. Confusion with Vibrio affected 6.9% and 16.1% of results obtained with NFC47 and API-20E, respectively. Overall, the accuracy of identification for aeromonads was hampered by outdated databases and taxonomy, weak algorithms, and impractical additional tests. Commercial identification systems should be redesigned to make Aeromonas identification algorithms more robust and to cover infrequent clinical species of this genus.

Zoonotic tuberculosis and brucellosis in Africa: neglected zoonoses or minor public-health issues? The outcomes of a multi-disciplinary workshop

Late in 2007, veterinary, medical and anthropological professionals from Europe and Africa met in a 2-day workshop in Pretoria, South Africa, to evaluate the burden, surveillance and control of zoonotic tuberculosis and brucellosis in sub-Saharan Africa. Keynote presentations reviewed the burden of these diseases on human and livestock health, the existing diagnostic tools, and the available control methods. These presentations were followed by group discussions and the formulation of recommendations. The presence of Mycobacterium bovis and Brucella spp. in livestock was considered to be a serious threat to public health, since livestock and animal products are the only source of such infections in human beings. The impact of these pathogens on human health appears to be relatively marginal, however, when compared with Mycobacterium tuberculosis infections and drug resistance, HIV and malaria. Appropriate diagnostic tools are needed to improve the detection of M. bovis and Brucella spp. in humans. In livestock, the 'test-and-slaughter' approach and the pasteurization of milk, which have been used successfully in industrialized countries, might not be the optimal control tools in Africa. Control strategies should fit the needs and perceptions of local communities. Improved intersectoral and international collaboration in surveillance, diagnosis and control, and in the education of medical and veterinary personnel, are advocated.

Multivariate analysis of management and biosecurity practices in smallholder pig farms in Madagascar

A cross-sectional study was carried out in 2005 and 2006 in three geographical areas of Madagascar to investigate and differentiate swine farm management and biosecurity practices in smallholder farming communities. Questionnaire data from a total of 709 pig farms were analysed using multiple factor analysis (MFA) and hierarchical cluster analysis (HCA). Variables describing management and biosecurity practices were organised into five groups: structure of the farm, animal-contacts, person- and vehicle-contacts, feeding, and sanitary aspects. In general, few biosecurity measures were implemented in the pig farms included in the study. Regional differences in management and biosecurity practices emerged from the MFA and were mainly due to, in order of decreasing importance: structure of the farm, sanitary aspects, feeding and animal-contacts and, to a lesser extent, person- and vehicle-contacts. HCA resulted in the differentiation of four distinct types of farms in each of two study areas, Arivonimamo and Marovoay, while no grouping could be identified amongst farms in Ambatondrazaka area. The characterisation of the different types of smallholder pig farms will allow adapting recommendations on husbandry practices and control measures in pig farms of these regions of Madagascar. The development of tailored recommendations is essential for Malagasy smallholders who have limited resources and need to make evidence-based management changes to reduce the risk of contagious diseases in their herds.

Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388(T) (=AIP 149.07(T)=CIP 109806(T)=DSM 21255(T)=CCUG 56017(T)) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes 'Bacilli', 'Clostridia', Thermolithobacteria and 'Erysipelotrichi' in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

Long-term storage at tropical temperature of dried-blood filter papers for detection and genotyping of RNA and DNA viruses by direct PCR

In tropical countries the diagnosis of viral infections of humans or animals is often hampered by the lack of suitable clinical material and the necessity to maintain a cold chain for sample preservation up to the laboratory. This study describes the use of filter papers for rapid sample collection, and the molecular detection and genotyping of viruses when stored over long periods at elevated temperatures. Infected blood was collected on filter papers, dried and stored at different temperatures (22, 32 and 37 degrees C) for various periods (up to 9 months). Two animal viruses, African swine fever, a large double-stranded DNA virus and Peste des Petits Ruminants, a negative single-stranded RNA virus, were used to validate the method. Filter papers with dried blood containing virus or control plasmid DNA were cut in small 5mm(2) pieces and added directly to the PCR tube for conventional PCR. Nucleic acid from both viruses could still be detected after 3 months at 32 degrees C. Moreover, the DNA virus could be detected at least 9 months after conservation at 37 degrees C. PCR products obtained from the filter papers were sequenced and phylogenetic analysis carried out. The results were consistent with published sequences, demonstrating that this method can be used for virus genotyping.

Conceptual framework for avian influenza risk assessment in Africa: the case of Ethiopia

The avian influenza (AI) epidemic is threatening Africa mainly because the flyways of migratory birds link the endemic and newly infected countries with disease-free areas in this continent and because of the risk of introduction through trade. Risk analysis provides a set of tools for supporting decision making by the veterinary services and other stakeholders, resulting in more effective surveillance and emergency preparedness. The risk assessment process could be split into three different steps: 1) risk release through the migratory birds and the official and unofficial poultry-product marketing chains; 2) risk exposure by means of studying interfaces among imported and exposed poultry and among wild and domestic birds; and 3) risk consequences for establishing the probability of AI spreading within the poultry population and the probability of it escaping detection. A conceptual framework is presented based on preliminary data and field missions carried out in Ethiopia. Field surveys and expert opinion will be necessary for the parameterization of the risk model. Spatial analysis will be used to identify high risk of exposure among wild and domestic birds. Risk communication and risk management will be based on the findings from the risk assessment model.

Descriptive and spatial epidemiology of Rift valley fever outbreak in Yemen 2000-2001

Rift valley fever (RVF) is an arboviral disease produced by a bunyavirus belonging to the genus Phlebovirus. Several species of Aedes and Culex are the vectors of this virus that affects sheep, goats, buffalos, cattle, camels and human beings. The human disease is well known, especially during periods of intense epizootic activity. The initial description of the disease dates back to 1930, when animals and human outbreaks appeared on a farm in Lake Naivasha, in the Great Rift Valley of Kenya. Until 2000, this disease was only described in Africa, and then outbreaks were also declared in the Kingdom of Saudi Arabia (2000-2001 and 2004) and in Yemen (2000-2001). Animal and human cases were recorded. This work presents a retrospective summary of the data collected on animal RVF cases during this epidemic in Yemen. Results from several RVF surveys were gathered from the Yemeni vet services and FAO experts. Geographical data (topographic maps and data freely available on internet) were used for the location of outbreaks. After cleaning and standardization of location names, all the data were introduced into a GIS database. The spatial distribution of outbreaks was then studied at two scales: at the national level and at a local scale in the particular area of Wadi Mawr in the Tihama plain, Western coast of Yemen.

Regional and international approaches on prevention and control of animal transboundary and emerging diseases

Transboundary animal diseases pose a serious risk to the world animal agriculture and food security and jeopardize international trade. The world has been facing devastating economic losses from major outbreaks of transboundary animal diseases (TADs) such as foot-and-mouth disease, classical swine fever, rinderpest, peste des petits ruminants (PPR), and Rift Valley fever. Lately the highly pathogenic avian influenza (HPAI) due to H5N1 virus, has become an international crisis as all regions around the world can be considered at risk. In the past decades, public health authorities within industrialized countries have been faced with an increasing number of food safety issues. The situation is equally serious in developing countries. The globalization of food (and feed) trade, facilitated by the liberalization of world trade, while offering many benefits and opportunities, also represents new risks. The GF-TADs Global Secretariat has carried out several regional consultations for the identification of priority diseases and best ways for their administration, prevention and control. In the questionnaires carried out and through the consultative process, it was noted that globally, FMD was ranked as the first and foremost priority. Rift Valley fever, and today highly pathogenic avian influenza, are defined as major animal diseases which also affect human health. PPR and CBPP, a disease which is particularly serious in Africa and finally, African swine fever (ASF) and classical swine fever (CSF) are also regionally recognised as top priorities on which the Framework is determined to work. The FAO philosophy--shared by the OIE--embraces the need to prevent and control TADs and emerging diseases at their source, which is most of the time in developing countries. Regional and international approaches have to be followed, and the FAO and OIE GF-TADs initiative provides the appropriate concepts and objectives as well as an organizational framework to link international and regional organizations at the service of their countries to better prevent and control the risks on animal and human health and the economic impact of TADs and emerging animal diseases.

Qualité de vision des patients porteurs d’un implant asphérique prolate après chirurgie de la cataracte

PURPOSE

To assess the quality of vision in pseudophakic patients with a prolate aspherical intraocular lens (IOL) compared to patients with a spherical IOL.

PATIENTS AND METHODS

Twenty patients undergoing cataract surgery were divided into two groups according to the type of IOL: ten prolate aspherical IOLs (TECNIS Z9000, AMO, USA) and ten spherical IOLs (911 CeeOn Edge, AMO, USA). The integrity of ocular functions was assessed with clinical examination and multifocal electroretinogram. Contrast sensitivities were tested preoperatively in photopic, mesopic, and glared conditions. Postoperative examinations included refractive evaluation before and after mydriasis, pupil diameter, contrast sensitivities, and wavefront aberration analysis.

RESULTS

Postoperative best-corrected visual acuity was 0.95 +/- 0.13 for the TECNIS group vs 0.98 +/- 0.11 for the 911 group (p=0.32). Refractive evaluation revealed mydriasis myopic shift in patients with the 911 IOL (- 0.10+/-0.30 D for the TECNIS group vs - 0.68+/-0.21 D for the 911 group, p=0.002). Mesopic contrast sensitivity was improved in the TECNIS group regarding medium and high spatial frequencies (p=0.003 and p=0.002, respectively), whereas photopic and glared contrast sensitivities were equal in both groups. RMS for high-order aberrations was 0.36 +/- 0.07 microm in the TECNIS group vs 0.33 +/- 0.19 microm in the 911 group (p=0.21), and spherical aberration was lower in patients with TECNIS IOL (Z40=0.03+/-0.06 microm vs 0.20+/-0.14 microm, for the TECNIS group and the 911 group, respectively, p=0.029).

CONCLUSION

Combining contrast sensitivities and wavefront aberration analysis provided an objective assessment of the quality of vision in pseudophakic patients. Using prolate aspherical IOL could reduce spherical aberration and improve visual acuity, especially in mesopic conditions.

HPAI surveillance programme in Cambodia: results and perspectives

Cambodia has faced 15 confirmed highly pathogenic avian influenza (H5N1) outbreaks in different sectors of the poultry industry since January 2004. The country has very limited human and financial resources and, when the outbreak first began, the veterinary services were not equipped with the basic tools to collect accurate epidemiological information or to fight the disease. Therefore, different agencies, under the umbrella of the Food and Agriculture Organisation, are providing support to the Government to strengthen its capacity to diagnose, survey and control the avian influenza (AI) virus. Different surveillance tools are being tested, such as market monitoring and a sentinel villages' network, to offset the weakness of the national passive surveillance network. Several constraints were identified during the implementation of this programme, such as a lack of motivation among provincial staff, the limited capacity of the central team to compile and analyse the data generated, the reluctance of farmers to have their animals sampled, and weak diagnostic capacities. The sustainability of such a surveillance system once international support ends remains to be seen. Participatory epidemiology (PE) may be an appropriate complementary tool to track diseases. PE works on the principle that livestock keepers often possess detailed knowledge of animal diseases and can provide valuable diagnostics that could help in identifying AI outbreaks, particularly in remote areas.

Antibody seroprevalences against peste des petits ruminants (PPR) virus in camels, cattle, goats and sheep in Ethiopia

A questionnaire-survey data indicated that 26% of 276 farmers reported the presence of respiratory disease in their herds in 2001. The incidence was perceived as "high" in small ruminants and camels, but as "low" in cattle. Simultaneously, 2815 serum samples from camels (n=628), cattle (n=910), goats (n=442) and sheep (n=835) were tested. The peste des petits ruminants (PPR) antibody seroprevalence was 3% in camels, 9% in cattle, 9% in goats and 13% in sheep. The highest locality-specific seroprevalences were: camels 10%, cattle 16%, goats 22% and sheep 23%. The animals had not been vaccinated against rinderpest or PPR. Antibody seroprevalences detected in camels, cattle, goats and sheep confirmed natural transmission of PPR virus under field conditions.

A Serological Investigation into Contagious Caprine Pleuropneumonia (CCPP) in Ethiopia

For a comparison of serological tests for CCPP, sera from 767 goats were examined. They were subjected to three tests: complement fixation test (CFT) with Mycoplasma capricolum subspecies capripneumoniae antigen; blocking ELISA (B-ELISA) with Mycoplasma capricolum subspecies capripneumoniae antigen; and CFT with Mycoplasma mycoides subspecies mycoides small colony type antigen. Antibodies were detected by these three tests in 23%, 2% and 12%, respectively, of sera from districts in which CCPP had not been reported, and in 60%, 83% and 87%, respectively, in sera from areas in which CCPP had been reported. The specificity of the tests is discussed. The use of the B-ELISA test for the diagnosis and for epidemiological studies of CCPP is strongly recommended.

Bluetongue control using vaccines: experience of the Mediterranean islands

Following the emergence of bluetongue (BT) virus serotype 2 on the island of Corsica in 2000, annual monovalent vaccination campaigns of the ovine population were conducted between 2001 and 2003. Despite vaccination, outbreaks were reported from several areas in 2001, but since November 2001, the absence of clinical cases in Corsica proves that vaccination is effective. This experience in Corsica is examined and, using available data, compared to the situation and the vaccination strategies on other Mediterranean islands. In light of the expansion of a new serotype of BTV onto these islands, a Mediterranean information network for BT and other emerging diseases is proposed.