BackgroundDiarrhea is the most frequent health problem among children in developing countries. This study investigated the bacterial and viral etiology and related clinical and epidemiological factors in children with acute diarrhea in Ouagadougou, Burkina Faso.MethodsStool specimens were collected from 283 children under 5 years of age visiting hospital due to acute diarrhea and from 60 healthy controls of similar age. Pathogens were investigated by using conventional culture techniques, PCR and immunochromatographic testing. Salmonella and Shigella strains were serotyped and their susceptibility to 23 antimicrobial agents was determined by the agar dilution method.ResultsAt least one pathogen was detected in 64% of the 283 patients and in 8% of the 60 controls (p < 0.001). Rotavirus was found in 30% of the patients, followed by diarrheagenic Escherichia coli (24%), Salmonella enterica ssp. enterica (9%), Shigella spp. (6%), adenovirus (5%) and Campylobacter spp. (2%). Multiple pathogens were found in 11% of the patients and in 2% of the controls (p = 0.028). Viruses were found mainly in children of ≤ 2 years of age, whereas bacteria were equally prevalent among all the age groups. Viral infections occurred mostly during the cool dry season and the bacterial infections during the rainy season. Fever (64%) and vomiting (61%) were the most common symptoms associated with diarrhea. Only one Salmonella strain was resistant to nalidixic acid and ciprofloxacin. Of the Shigella strains, one was resistant to nalidixic acid but 81% to trimethoprim- sulfamethoxazole, 63% to streptomycin and 50% to ampicillin. Most of all the other Salmonella and Shigella strains were sensitive to all antimicrobials tested.ConclusionRotaviruses and diarrheal E. coli were the most predominant pathogens associated with acute diarrhea in Burkinabe children. Constant antimicrobial surveillance is warranted to observe for the emergence of enteric bacteria resistant to antimicrobials that are important in treatment also of severe infections.

BackgroundProduction and wild animals are major sources of human salmonellosis and animals raised for food also play an important role in transmission of antimicrobial resistant Salmonella strains to humans. Furthermore, in sub-Saharan Africa non-typhoidal Salmonella serotypes are common bloodstream isolates in febrile patients. Yet, little is known about the environmental reservoirs and predominant modes of transmission of these pathogens. The purpose of this study was to discover potential sources and distribution vehicles of Salmonella by isolating strains from apparently healthy slaughtered food animals and wild hedgehogs and by determining the genetic relatedness between the strains and human isolates. For this purpose, 729 feces samples from apparently healthy slaughtered cattle (n = 304), poultry (n = 350), swine (n = 50) and hedgehogs (n = 25) were examined for the presence of Salmonella enterica in Burkina Faso. The isolates were characterized by serotyping, antimicrobial-susceptibility testing, phage typing, and pulsed-field gel electrophoresis (PFGE) with XbaI and BlnI restriction enzymes.ResultsOf the 729 feces samples, 383 (53%) contained Salmonella, representing a total of 81 different serotypes. Salmonella was present in 52% of the cattle, 55% of the poultry, 16% of the swine and 96% of the hedgehog feces samples. Antimicrobial resistance was detected in 14% of the isolates. S. Typhimurium isolates from poultry and humans (obtained from a previous study) were multiresistant to the same antimicrobials (ampicillin, chloramphenicol, streptomycin, sulfonamides and trimethoprim), had the same phage type DT 56 and were closely related in PFGE. S. Muenster isolates from hedgehogs had similar PFGE patterns as the domestic animals.ConclusionsBased on our results it seems that production and wild animals can share the same Salmonella serotypes and potentially transmit some of them to humans. As the humans and animals often live in close vicinity in Africa and the hygiene control of the meat retail chain is defective, high Salmonella carriage rates of the animals can pose a major public health risk in Burkina Faso. This underlines the necessity for a joint and coordinated surveillance and monitoring programs for salmonellosis in Africa.

Changes in bacterioplankton community composition were followed in mesocosms set up in the littoral of Lake Vesijärvi, southern Finland, over two summers. Increasing nitrogen and phosphorus concentrations in the mesocosms represented different trophic states, from mesotrophic to hypertrophic. In 1998, the mesocosms were in a turbid state with a high biomass of phytoplankton, whereas in 1999, macrophytes proliferated and a clear-water state prevailed. The bacterial communities in the mesocosms also developed differently, as shown by denaturing gradient gel electrophoresis profiling of partial 16S rRNA gene fragments and by nonmetric multidimensional scaling analysis. In 1998, nutrient treatments affected the diversity and clustering of bacterial communities strongly, but in 1999, the bacterial communities were less diversified and not clearly affected by treatments. Canonical correspondence analysis indicated that bacterioplankton communities in the mesocosms were influenced by environmental physicochemical variables linked to the increasing level of eutrophication. Nitrogen concentration correlated directly with the bacterioplankton composition. In addition, the high nutrient levels had indirect effects through changes in the biomass and composition of phyto- and zooplankton. Sequencing analysis showed that the dominant bacterial divisions remained the same, but the dominant phylotypes changed during the 2-year period. The occurrence of Verrucomicrobia correlated with more eutrophic conditions, whereas the occurrence of Actinobacteria correlated with less eutrophic conditions.

BackgroundYersinia enterocolitica (YE) is the causative agent of yersiniosis. YE encompass strains of diverse pathogenicity: YE biotypes 1B and 2-5 are considered pathogenic, whereas biotype 1A is in general considered nonvirulent. Also YE-like species, which can sometimes be misidentified as YE, are considered nonvirulent.MethodsIn order to study differences in clinical picture caused by different YE types and their possible sources a case-control study was conducted in 2006. In this case-control study, 295 case-patients with YE or YE-like finding and their 758 controls responded to the questionnaire about symptoms and possible sources of infection.ResultsStrains of pathogenic YE bio/serotypes 3-4/O:3 or 2/O:9 were found in 18%, YE biotype 1A in 65% and YE -like strains of 17% of the patients. Patients infected with the strains of pathogenic YE bio/serotypes were younger and had fever more often than those with BT 1A who suffered more from vomiting. Symptoms of reactive arthritis were reported by 10% of pathogenic YE infections, 3% of YE BT 1A, and 0.3% of the controls. Eating or tasting raw or medium done pork was a significant risk factor for pathogenic YE bio/serotype infection (OR 6.6; 95% CI 1.7-24.9) as well as eating in a canteen (OR 3.5; 95% CI 1.6-7.9). Imported fruits and berries were associated with increased risk of YE BT 1A finding.ConclusionsThe symptoms of the patients with YE BT 1A differed from yersiniosis caused by the classic pathogenic YE bio/serotypes. In addition, the patients with YE BT 1A had more protracted gastrointestinal disorders and unspecific complaints. Small children were overrepresented in classic pathogenic bio/serotypes while in BT 1A or YE-like species were not found among children younger than two years. This suggests the lacking virulence of the BT 1A strains. We can not, however, rule out the possibility that some strains of genetically heterogeneous group of BT 1A may cause an illness.

Water samples were collected in August 2001 and 2002 from the eutrophic Lake Joutikas during cyanobacterial blooms. DNA and RNA were isolated from size fractionated samples and the diversity of the bacteria present in each fraction was studied by PCR amplification of partial 16S rRNA and denaturing gradient gel electrophoresis (DGGE) fingerprinting. Major bands from the gels were sequenced for further identification. Cyanobacteria were also identified and counted under the microscope. Anabaena/Aphanizomenon were the most abundant cyanobacteria in both years, although the dominant species was different each year. When comparing the 2 techniques, equal numbers of abundant Anabaena/Aphanizomenon morphotypes were detected by microscopy and phylotypes by DGGE. The genera Microcystis and Synechococcus appeared more abundant in the DGGE analysis than under the microscope. In the heterotrophic bacterial community variation was observed between the bloom samples from the 2 years. Verrucomicrobia was the most abundant group in both years in both DNA-and RNA-derived profiles. Otherwise the patterns based on DNAand RNA-derived DGGE-profiles differed, especially in 2002. The presence of Actinobacteria and Chloroflexi was less pronounced in RNA-based than in DNA-based analysis. This indicates that their relative biomass was smaller than estimated by DNA-analysis. It might also indicate that they were metabolically inactive. In contrast, in 2002, the CFB group (Cytophaga-Flavobacterium-Bacteroides) and δ-Proteobacteria were more prominent in the RNA-based than in the DNA-based profiles. Thus they probably formed a substantial fraction of biomass and/or were active members in the blooms. KEY WORDS: Cyanobacteria · Heterotrophic bacteria · DGGE · DNA · RNA · DiversityResale or republication not permitted without written consent of the publisher Aquat Microb Ecol 36: 201-211, 2004 bacteria in cyanobacterial blooms whereas freshwater bacterial communities in general have been studied extensively (e.g. Hiorns et al. 1997, Konopka et al. 1999, Crump et al. 1999, Casamayor et al. 2000, Glöckner et al. 2000, Lindström & Leskinen 2002, Zwart et al. 2002.In spite of improved culturing techniques, most microorganisms in aquatic ecosystems still remain uncultured (Zwart et al. 2002). Therefore, molecular biology techniques such as denaturing gradient gel electrophoresis (DGGE) using the 16S rRNA as a molecular marker are commonly used for diversity studies. In DGGE, DNA fragments of the same length can be separated on the basis of melting domain structure and nucleotide composition (Muyzer & Smalla 1998). In studies of aquatic bacterial communities both 16S rRNA gene and reverse transcribed rRNA have been used in the DGGE analysis. Several authors have used RNA-derived DGGE patterns to infer the potentially active bacterial population (Teske et al. 1996, Bernard et al. 2000, Schäfer et al. 2001, Winter et al. 2001, Troussellier et al. 2002. Although active cells tend to have more RNA than inactive ones, the RNA content varies...

The diversity and phylogeny of nodA andnifH genes were studied by using 52 rhizobial isolates fromAcacia senegal, Prosopis chilensis, and related leguminous trees growing in Africa and Latin America. All of the strains had similar host ranges and belonged to the generaSinorhizobium and Mesorhizobium, as previously determined by 16S rRNA gene sequence analysis. The restriction patterns and a sequence analysis of the nodA and nifHgenes divided the strains into the following three distinct groups: sinorhizobia from Africa, sinorhizobia from Latin America, and mesorhizobia from both regions. In a phylogenetic tree also containing previously published sequences, the nodA genes of our rhizobia formed a branch of their own, but within the branch no correlation between symbiotic genes and host trees was apparent. Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries. Most strains had plasmids, and the presence of plasmid-bornenifH was demonstrated by hybridization for some examples. The nodA and nifH genes of Sinorhizobium teranga ORS1009T grouped with the nodAand nifH genes of the other African sinorhizobia, butSinorhizobium saheli ORS609T had a totally different nodA sequence, although it was closely related based on the 16S rRNA gene and nifH data. This might be because this S. saheli strain was originally isolated fromSesbania sp., which belongs to a different cross-nodulation group than Acacia and Prosopis spp. The factors that appear to have influenced the evolution of rhizobial symbiotic genes vary in importance at different taxonomic levels.

Tropical forests have a high diversity of plant species; are they associated with a correspondingly rich microbial flora? We addressed this question by examining the symbiotic rhizobium bacteria that nodulate a diverse pool of forest legume species in Brazil. The 44 strains studied had been isolated from 29 legume tree species representing 13 tribes including all three subfamilies of the Leguminosae, and were chosen to represent major groups from a larger sample that had previously been characterized by SDS-PAGE of total proteins. Partial 16S rRNA gene sequence was determined, corresponding to positions 44-303 in the Escherichia coli sequence. Fifteen sequences were found, including six novel ones. However, all but one of them could be assigned to a genus because they grouped closely with sequences from previously described rhizobial species. Fast-growing strains had sequences similar to Rhizobium spp., Sinorhizobium spp. or Mesorhizobium spp., while the slow-growing strains had sequences similar to Bradyrhizobium spp. One strain with an intermediate growth rate had a unique sequence which indicated that the strain might belong to the genus Azorhizobium. Although the strains showed a variety of sequences, it was surprising that these strains isolated from taxonomically very diverse host plants in previously unexplored environments were mostly very similar to strains described previously, largely from agricultural systems.

Cyanobacteria of the genus Nodularia form toxic blooms in brackish waters worldwide. In addition, Nodularia spp. are found in benthic, periphytic, and soil habitats. The majority of the planktic isolates produce a pentapeptide hepatotoxin nodularin. We examined the morphologic, toxicologic, and molecular characters of 18 nodularin-producing and nontoxic Nodularia strains to find appropriate markers for distinguishing the toxic strains from the nontoxic ones in field samples. After classical taxonomy, the examined strains were identified as Nodularia sp., Nodularia spumigena, N. baltica, N. harveyana, and N. sphaerocarpa. Morphologic characters were ambiguous in terms of distinguishing between the toxic and the nontoxic strains. DNA sequences from the short 16S-23S rRNA internally transcribed spacer (ITS1-S) and from the phycocyanin operon intergenic spacer and its flanking regions (PC-IGS) were different for the toxic and the nontoxic strains. Phylogenetic analysis of the ITS1-S and PC-IGS sequences from strains identified as N. spumigena, and N. baltica, and N. litorea indicated that the division of the planktic Nodularia into the three species is not supported by the ITS1-S and PC-IGS sequences. However, the ITS1-S and PC-IGS sequences supported the separation of strains designated N. harveyana and N. sphaerocarpa from one another and the planktic strains. HaeIII digestion of PCR amplified PC-IGS regions of all examined 186 Nodularia filaments collected from the Baltic Sea produced a digestion pattern similar to that found in toxic isolates. Our results suggest that only one planktic Nodularia species is present in the Baltic Sea plankton and that it is nodularin producing.