Etude de la contribution des salmonelles aviaires aux salmonelloses humaines au Tchad : Cas de la ville capitale, N'Djamena

Salmonella are linked to many food-borne diseases worldwide. They are also considered to be one of the main pathogens causing human gastroenteritis. The main objective of this study was to update the prevalence and antimicrobial resistance characteristics of Salmonella isolated from poultry and from humans experiencing gastroenteritis in N'Djamena, Chad. The results collected during this study provide the first baseline data on the prevalence of contamination by Salmonella in humans suffering from diarrhoea, as well as in laying hens and broiler chicken farms in N'Djamena. Samples were collected on one hand from five hospitals another and on another hand from sixteen poultry farms, both over two periods of six months each: from August 2010 to January 2011 and from September 2011 to February 2012. Diagnostic methods carried out during this study led to the isolation of one hundred and thirty nine Salmonella strains, belonging to forty two different serotypes. Salmonella Colindale was the most prevalent serovar (13.6 % of the isolates belonged to this serovar), followed by Salmonella Minnesota (10.8 %), Salmonella Stanleyville (5.8 %), Salmonella Havana and Kottbus (5 % each), Salmonella Idikan (4.3 %), Salmonella Riggil and Anatum (3.6 % each). Other serotypes were under-represented. The majority of these isolates were susceptible to all antibiotics tested (CLSI Standards), except some Salmonella Colindale avian isolates that exhibited a decreased susceptibility to nalidixic acid, ofloxacin and enrofloxacin, two S. Enteritidis human isolates resistant to nalidixic acid, ofloxacin and ciprofloxacin, a S. Limete avian isolate resistant to three antibiotics and 15 S. Minnesota avian isolates resistant to five different antimicrobial classes. In order to evaluate the phylogenetic relationships and to find epidemiological links between human and avian strains isolated in the same period of time and in the same region, a total of 139 Salmonella isolates found in humans and poultry in this study were characterised by ERIC-PCR and IS200-PCR. The PCR analysis was followed by macrorestriction analysis (PFGE) of genomic DNA from 22 common isolates of Salmonella serotypes encountered in both humans and poultry with XbaI enzyme. PCR results demonstrated that, in the context of this epidemiological study, ERIC- and IS200-PCR methods can be used effectively to limit the number of isolates that have to be serotyped. The comparison of ERIC-PCR, IS200-PCR, PFGE and antimicrobial susceptibility profiles among isolates from human and avian origins has highlighted, on one hand, the indirect evidence of human contamination sources by Salmonella serovars from poultry farms, and on the other hand the diversity of sources and potential reservoirs of Salmonella strains in the N'Djamena city.Les salmonelles sont liées à de nombreuses maladies infectieuses d'origine alimentaire dans le monde. Elles sont aussi considérées comme l'un des principaux agents pathogènes responsables de gastro-entérite humaine. L'objectif principal de notre étude était de mettre à jour la prévalence de contamination et l'état de l'antibio-résistance des souches Salmonella isolées chez les humains et chez les volailles dans la ville de N'Djamena, capitale du Tchad. Les résultats obtenus au terme de cette étude, offrent les premières données de prévalence de contamination par les salmonelles chez les humains et dans les élevages de poules pondeuses et de poulets de chair à N'Djamena. Tous les échantillons étaient collectés au sein de 5 hôpitaux et de 16 fermes avicoles, sur deux périodes de six mois chacune: de Août 2010 à Janvier 2011 et de Septembre 2011 à Février 2012. L'ensemble des méthodes et techniques de diagnostics réalisées a permis d'isoler chez les humains et chez les volailles, cent trente neuf souches de salmonelles, appartenant à quarante deux sérotypes différents. Salmonella Colindale était le sérotype majoritaire (13,6 %), suivi par S. Minnesota (10,8 %), S. Stanleyville (5,8 %), S. Havana, Kottbus (5 %), S. Idikan (4,3 %), S. Riggil, Anatum (3,6 %). Les autres sérotypes étaient très peu représentés. La majorité de ces sérotypes était sensible à la gamme d'antibiotiques testée (Normes CLSI), sauf quelques isolats aviaires de S. Colindale qui avaient présenté une sensibilité diminuée à l'acide nalidixique, à l'ofloxacine et à l'enrofloxacine, 1 isolat aviaire de Salmonella Limete résistant à trois antimicrobiens, deux isolats humains de Salmonella Enteritidis résistants à l'acide nalidixique, à l'ofloxacine et à la ciprofloxacine et 15 isolats aviaires de Salmonella Minnesota résistants à au moins cinq classes différentes d'antimicrobiens. Dans le but d‘évaluer les relations phylogénétiques et de trouver des liens épidémiologiques entre les souches humaines et aviaires isolées au cours de la même période et dans la même ville, 139 isolats de Salmonella trouvés chez les humains et chez les volailles dans cette étude ont été caractérisés par ERIC-PCR et IS200-PCR. L'analyse PCR a été suivie par l'analyse de macrorestriction (PFGE) de l'ADN génomique issu de 22 isolats communs de sérovars de Salmonella rencontrés à la fois chez les humains et chez les volailles avec l'enzyme XbaI. Les résultats de la PCR ont montré que, dans le cadre de cette étude épidémiologique, les méthodes Eric- et IS200-PCR peuvent être utilisées efficacement pour limiter le nombre d'isolats qui doivent être sérotypés. La comparaison des profils d'Eric-types, d'IS-types, de pulsotypes et de susceptibilité aux antimicrobiens des isolats d'origines humaines et aviaires a mis en évidence, d'une part, la preuve indirecte des sources de contamination humaine par les sérovars de Salmonella à partir des fermes de volailles et d'autre part, la diversité des sources et réservoirs potentiels des souches de Salmonella dans la ville de N'Djamena

Study of the avian salmonella contribution to human salmonellosis in Chad : Example of the capital, N'Djamena

Les salmonelles sont liées à de nombreuses maladies infectieuses d'origine alimentaire dans le monde. Elles sont aussi considérées comme l'un des principaux agents pathogènes responsables de gastro-entérite humaine. L'objectif principal de notre étude était de mettre à jour la prévalence de contamination et l'état de l'antibio-résistance des souches Salmonella isolées chez les humains et chez les volailles dans la ville de N'Djamena, capitale du Tchad. Les résultats obtenus au terme de cette étude, offrent les premières données de prévalence de contamination par les salmonelles chez les humains et dans les élevages de poules pondeuses et de poulets de chair à N'Djamena. Tous les échantillons étaient collectés au sein de 5 hôpitaux et de 16 fermes avicoles, sur deux périodes de six mois chacune: de Août 2010 à Janvier 2011 et de Septembre 2011 à Février 2012. L'ensemble des méthodes et techniques de diagnostics réalisées a permis d'isoler chez les humains et chez les volailles, cent trente neuf souches de salmonelles, appartenant à quarante deux sérotypes différents. Salmonella Colindale était le sérotype majoritaire (13,6 %), suivi par S. Minnesota (10,8 %), S. Stanleyville (5,8 %), S. Havana, Kottbus (5 %), S. Idikan (4,3 %), S. Riggil, Anatum (3,6 %). Les autres sérotypes étaient très peu représentés. La majorité de ces sérotypes était sensible à la gamme d'antibiotiques testée (Normes CLSI), sauf quelques isolats aviaires de S. Colindale qui avaient présenté une sensibilité diminuée à l'acide nalidixique, à l'ofloxacine et à l'enrofloxacine, 1 isolat aviaire de Salmonella Limete résistant à trois antimicrobiens, deux isolats humains de Salmonella Enteritidis résistants à l'acide nalidixique, à l'ofloxacine et à la ciprofloxacine et 15 isolats aviaires de Salmonella Minnesota résistants à au moins cinq classes différentes d'antimicrobiens. Dans le but d‘évaluer les relations phylogénétiques et de trouver des liens épidémiologiques entre les souches humaines et aviaires isolées au cours de la même période et dans la même ville, 139 isolats de Salmonella trouvés chez les humains et chez les volailles dans cette étude ont été caractérisés par ERIC-PCR et IS200-PCR. L'analyse PCR a été suivie par l'analyse de macrorestriction (PFGE) de l'ADN génomique issu de 22 isolats communs de sérovars de Salmonella rencontrés à la fois chez les humains et chez les volailles avec l'enzyme XbaI. Les résultats de la PCR ont montré que, dans le cadre de cette étude épidémiologique, les méthodes Eric- et IS200-PCR peuvent être utilisées efficacement pour limiter le nombre d'isolats qui doivent être sérotypés. La comparaison des profils d'Eric-types, d'IS-types, de pulsotypes et de susceptibilité aux antimicrobiens des isolats d'origines humaines et aviaires a mis en évidence, d'une part, la preuve indirecte des sources de contamination humaine par les sérovars de Salmonella à partir des fermes de volailles et d'autre part, la diversité des sources et réservoirs potentiels des souches de Salmonella dans la ville de N'Djamena.Salmonella are linked to many food-borne diseases worldwide. They are also considered to be one of the main pathogens causing human gastroenteritis. The main objective of this study was to update the prevalence and antimicrobial resistance characteristics of Salmonella isolated from poultry and from humans experiencing gastroenteritis in N'Djamena, Chad. The results collected during this study provide the first baseline data on the prevalence of contamination by Salmonella in humans suffering from diarrhoea, as well as in laying hens and broiler chicken farms in N'Djamena. Samples were collected on one hand from five hospitals another and on another hand from sixteen poultry farms, both over two periods of six months each: from August 2010 to January 2011 and from September 2011 to February 2012. Diagnostic methods carried out during this study led to the isolation of one hundred and thirty nine Salmonella strains, belonging to forty two different serotypes. Salmonella Colindale was the most prevalent serovar (13.6 % of the isolates belonged to this serovar), followed by Salmonella Minnesota (10.8 %), Salmonella Stanleyville (5.8 %), Salmonella Havana and Kottbus (5 % each), Salmonella Idikan (4.3 %), Salmonella Riggil and Anatum (3.6 % each). Other serotypes were under-represented. The majority of these isolates were susceptible to all antibiotics tested (CLSI Standards), except some Salmonella Colindale avian isolates that exhibited a decreased susceptibility to nalidixic acid, ofloxacin and enrofloxacin, two S. Enteritidis human isolates resistant to nalidixic acid, ofloxacin and ciprofloxacin, a S. Limete avian isolate resistant to three antibiotics and 15 S. Minnesota avian isolates resistant to five different antimicrobial classes. In order to evaluate the phylogenetic relationships and to find epidemiological links between human and avian strains isolated in the same period of time and in the same region, a total of 139 Salmonella isolates found in humans and poultry in this study were characterised by ERIC-PCR and IS200-PCR. The PCR analysis was followed by macrorestriction analysis (PFGE) of genomic DNA from 22 common isolates of Salmonella serotypes encountered in both humans and poultry with XbaI enzyme. PCR results demonstrated that, in the context of this epidemiological study, ERIC- and IS200-PCR methods can be used effectively to limit the number of isolates that have to be serotyped. The comparison of ERIC-PCR, IS200-PCR, PFGE and antimicrobial susceptibility profiles among isolates from human and avian origins has highlighted, on one hand, the indirect evidence of human contamination sources by Salmonella serovars from poultry farms, and on the other hand the diversity of sources and potential reservoirs of Salmonella strains in the N'Djamena city

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Are Salmonella-Induced Gastroenteritis Neglected in Developing Countries? Feedback from Microbiological Investigations in N'Djamena Hospitals, Chad.

Salmonella is considered to be one of the main pathogens causing human gastroenteritis worldwide. Looking for Salmonella in Africa in patients suffering from gastroenteritis is rather unusual, and the use of antibiotics is not subject to any regulation. This study intends for stressing the possible prominent importance of Salmonella in digestive diseases in Africa as well as identifying antimicrobial resistance of Salmonella isolates from faeces samples of human origin. All samples were collected from five N'Djamena hospitals, from patients suffering from diarrhoea. The collecting was undertaken over two periods of six months each: from August 2010 to January 2011 and from September 2011 to February 2012. Salmonella isolates were obtained by standard cultivation and serotyping methods. A total of 43 Salmonella isolates were identified, belonging to 21 different serovars. The most prevalent serovar was Salmonella Stanleyville (n = 7), followed by S. Anatum (n = 4) and S. Kottbus (n = 3). The other serovars were under-represented. The majority of these isolates were susceptible to all antibiotics tested (CLSI Standards), except two S. Enteritidis isolates that exhibited resistance to fluoroquinolones. The different serovars and antibiotic resistance profiles that were observed highlight the substantial diversity of Salmonella in N'Djamena, Chad. Roughly, one out of ten patients who consulted for gastroenteritis was shedding Salmonella spp. and none of them would have been diagnosed outside the context of this research program. This study may encourage local clinicians to explore more often salmonellosis suspicion in their daily practice

Distribution and antimicrobial susceptibility profiles of <i>Salmonella</i> serovars isolated from 5 N’Djamena hospitals, Chad.

<p>Distribution and antimicrobial susceptibility profiles of <i>Salmonella</i> serovars isolated from 5 N’Djamena hospitals, Chad.</p

Prevalence of <i>Salmonella</i> strains isolated in 5 N’Djamena hospitals, Chad.

<p>Prevalence of <i>Salmonella</i> strains isolated in 5 N’Djamena hospitals, Chad.</p

Author Correction: Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance (Nature Communications, (2022), 13, 1, (7251), 10.1038/s41467-022-34312-7)

In this article, the author name Antoinette Ngandjio was incorrectly written as Antoinette Ngandijo. In this article, the affiliation details for Author Sara Cuadros-Orellana were incorrectly given as ‘Centro de Biotecnologνa de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’ but should have been ‘Universidad Catolica del Maule, Centro de Biotecnología de los Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Talca, Chile’. The original article has been corrected

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.</p