Prevalence and diversity of Salmonella enterica in water, fish and lettuce in Ouagadougou, Burkina Faso

Background: This study investigated the prevalence, serotypes and antimicrobial sensitivity patterns of Salmonella enterica in environment in Ouagadougou, Burkina Faso. A total of 476 samples, consisting of 36 samples of tap water, 51 samples of well water, 87 samples of channel water, 44 samples of reservoir water, 238 samples of fish, and 20 samples of lettuce were examined using standard bacteriological procedures for Salmonella. Results: Salmonella were isolated from 98 samples. Salmonella were rare in drinking water, since they were not found at all from the tap water, and only in 2 % of well water. Salmonella were more common in the water of reservoir of Tanghin (15 %), reservoir of Yamtenga (20 %), and in the water channels in the city (from 20 to 31 %). Salmonella were commonly isolated from the fish (24 %) caught from the reservoir of Tanghin and from the lettuce (50 %) irrigated with water from Tanghin. The Salmonella isolates were found to represent 50 different serotypes. The 11 most common serotypes were Salmonella Bredeney and S. Colindale (both 8.2 %), S. Muenster (6.1 %), S. Korlebu (5.1 %), S. Eastbourne and S. Poona (both 4.1 %), and S. Agona, S. Derby, S. Drac, S. Senftenberg, S. Waycross (each 3.1 %), accounting for 51.3 % of all the isolates. In general, the Salmonella strains were sensitive to the antimicrobials tested, but two strains were resistant to streptomycin and many more intermediate to streptomycin or sulphonamide. Conclusion: This study highlights the common prevalence of Salmonella and the high diversity of Salmonella serotypes in aquatic environment in Ouagadougou, Burkina Faso. Therefore, various human activities linked to water and consumption of water-related products, such as fish and lettuce, can lead to human Salmonella infections.Peer reviewe

Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland

The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic resistance crisis.Antibiotic resistance is a global threat to human health, with the most severe effect in low- and middle-income countries. We explored the presence of antibiotic resistance genes (ARGs) in the hospital wastewater (HWW) of nine hospitals in Benin and Burkina Faso, two low-income countries in West Africa, with shotgun metagenomic sequencing. For comparison, we also studied six hospitals in Finland. The highest sum of the relative abundance of ARGs in the 68 HWW samples was detected in Benin and the lowest in Finland. HWW resistomes and mobilomes in Benin and Burkina Faso resembled each other more than those in Finland. Many carbapenemase genes were detected at various abundances, especially in HWW from Burkina Faso and Finland. The bla(GES) genes, the most widespread carbapenemase gene in the Beninese HWW, were also found in water intended for hand washing and in a puddle at a hospital yard in Benin. mcr genes were detected in the HWW of all three countries, with mcr-5 being the most common mcr gene. These and other mcr genes were observed in very high relative abundances, even in treated wastewater in Burkina Faso and a street gutter in Benin. The results highlight the importance of wastewater treatment, with particular attention to HWW.IMPORTANCE The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic resistance crisis. However, this information is scarce in many low- and middle-income countries (LMICs), such as those in West Africa. In this study, we describe the resistomes of hospital wastewater in Benin and Burkina Faso and, as a comparison, Finland. Our results help to understand the hitherto unrevealed resistance in Beninese and Burkinabe hospitals. Furthermore, the results emphasize the importance of wastewater management infrastructure design to minimize exposure events between humans, HWW, and the environment, preventing the circulation of resistant bacteria and ARGs between humans (hospitals and community) and the environment.Peer reviewe

Rotavirus in various animal species in Ouagadougou, Burkina Faso: detection of genotype G9.

Objectives: Rotaviruses have a wide host range, infecting many animal species as well as humans. The segmented nature of the genome suggests that rotaviruses are able to form new strains by a mechanism of reassortment. Animal rotaviruses are regarded as a potential reservoir for genetic diversity of human rotaviruses. The aim of this study was to determine the incidence and molecular characteristics of rotavirus in various healthy animals in Ouagadougou, Burkina Faso.Methodology and results: A total of 618 faeces samples from various animal species with different living environments were collected between June 2009 and August 2011, and analyzed for rotavirus group A antigen detection by immunochromatographic test (SD Bioline Rota/Adeno®; Standard diagnostics, Inc., Korea). A second sample collection between February and March 2015 involved only farm animals (n= 138) and analyzed for rotavirus group A antigen detection by ELISA test (Ridascreen®, R-Biopharm AG, Darmstadt Germany). The rotaviruses antigen-positives samples for ELISA were further confirmed and characterized by reversetranscription (RT-PCR). For immunochromatographic detection, the prevalence of rotavirus A and adenovirus antigens were found in 7.4% of pig, 31% of poultry, 33.4% of pigeon, 35.7% of rabbit, 46-58% in bovine, 13.8% of shrimps, 14.8% of snails and 28.6% of captain (Lates niloticus). The detection of rotavirus antigen by ELISA reported rates of 7.4% in pigs, 4.1% in cattle and 14.3% in poultry and no case of rotavirus was detected in sheep. The molecular characterization of the strains established that they belong to the G9 genotype (3/ 7; 42.9%).Conclusion and application of results: This study provides evidence asymptomatic hosts of rotavirus. This study report for the first time rotaviruses detection and presence of the emerged genotype G9 in farms animals in Burkina Faso. These results justify the need to monitoring animals’ rotaviruses in Burkina Faso.Keywords: Rotavirus group A, Animals, molecular characterization, Burkina Faso

Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso.

Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263) and without (n = 50) diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-)PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%), adenovirus (31.2%) and genogroup II norovirus (18.2%) were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively). Sapovirus (10.3%), astrovirus (4.9%), genogroup I norovirus (2.7%) and Aichivirus A (0.8%) were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%), and the predominant norovirus strain was GII.4 variant 2012 (71.4%). Among sapovirus, the genogroup II (87.5%) predominated. Astrovirus type 1 (41.7%) was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C). Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children

Diversity and antimicrobial drug resistance of non-typhoid Salmonella serotypes isolated in lettuce, irrigation water and clinical samples in Burkina Faso

Introduction: The contamination of fresh vegetables by non-typhoid Salmonella species present in irrigation water and animal feces could causes of many diarrheal infections and diseases. The aim of this study was to determine the diversity of non-typhoidal Salmonella serotypes and their antimicrobial resistance profile from lettuce, irrigation water and human samples. Methods: This study concern 57 Salmonella isolated from 134 lettuce and irrigation water samples and 416 stool samples. All Salmonella isolated were characterized used serotyping antisera according to Kauffman-White-Le Minor scheme. Salmonella strains were characterized by simplex PCR using specific primers. Results: Out of 57 Salmonella isolated, (42/134) 31.34% were from lettuce and irrigation water and (15/416) 03.6% from human. A total of 36 different serotypes were identified. Highest prevalence was obtained with S. Cubana, S. Jodhpur and S. Kentucky 05/57 (08.77% each) followed by S. Poona 04/57 (07%). Resistance genes CTX-M1, aadA1, dfrAI, were obtained with S. Jodhpur and CTX-M2, aac(3-Id), aadA7 with S. Kentucky. However, resistance genes gyrA, gyrB and parE were found in S. Essen, S. Poona and S. Senftenberg. Virulence gene such as invA, pipD and misL were found in 91% globally, followed by orfL 81% and spvR 12%. Conclusion: This study highlighted the diversity of non-typhoid Salmonella serotypes and resistance genes circulating in environment and hospital center in BF. Gardening products should be a potential source of transmission of Salmonella causing diarrhea among human in BF. Microbiological and antimicrobial resistance plans must be implemented so that they are tools for infection prevention

Distribution of rotavirus G and P genotypes among Children under 5 years of age in Burkina Faso, November 2011-September 2012.

<p>Distribution of rotavirus G and P genotypes among Children under 5 years of age in Burkina Faso, November 2011-September 2012.</p

Phylogenetic analysis based on the partial nucleotide sequences (285 bp) of the RNA-dependent RNA polymerase coding gene of the norovirus strains detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.

<p>The tree was constructed using Maximum Likelihood method. Reference strains of norovirus were selected from the GenBank database.</p

Comparison between mean Ct-values of genotyped viruses typed and mean Ct-values of untyped viruses.

<p>Comparison between mean Ct-values of genotyped viruses typed and mean Ct-values of untyped viruses.</p

Phylogenetic analysis based on the partial nucleotide sequences (373 bp) of an area located in the open-reading frame (ORF2) of Astrovirus detected in Ouagadougou, Burkina Faso, between November 2011 and September 2012.

<p>The tree was constructed using Maximum Likelihood method. Reference strains of astrovirus were selected from the GenBank database.</p