Lack of efflux mediated quinolone resistance in Salmonella enterica serovars Typhi and Paratyphi A.

International audienceSalmonella enterica serovars Typhi and Paratyphi A isolates from human patients in France displaying different levels of resistance to quinolones or fluoroquinolones were studied for resistance mechanisms to these antimicrobial agents. All resistant isolates carried either single or multiple target gene mutations (i.e., in gyrA, gyrB, or parC) correlating with the resistance levels observed. Active efflux, through upregulation of multipartite efflux systems, has also been previously reported as contributing mechanism for other serovars. Therefore, we investigated also the occurrence of non-target gene mutations in regulatory regions affecting efflux pump expression. However, no mutation was detected in these regions in both Typhi and Paratyphi isolates of this study. Besides, no overexpression of the major efflux systems was observed for these isolates. Nevertheless, a large deletion of 2334 bp was identified in the acrS-acrE region of all S. Typhi strains but which did not affect the resistance phenotype. As being specific to S. Typhi, this deletion could be used for specific molecular detection purposes. In conclusion, the different levels of quinolone or FQ resistance in both S. Typhi and S. Paratyphi A seem to rely only on target modifications

Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

International audienceSalmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database-Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 ± 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures

Ecr, une protéine potentiellement impliquée dans la résistance hétérogène à la colistine des clusters I et IV du complexe Enterobacter cloacae

International audienceObjectif - Introduction : La colistine (COS), antibiotique longtemps délaissé, est devenue une alternative de dernier recours pour le traitement des infections à entérobactéries multirésistantes, notamment productrices de carbapénémases. Le complexe Enterobacter cloacae (CEC) comprend plusieurs clusters étroitement liés et non différenciables phénotypiquement, dont certains présentent un phénotype d’hétérorésistance (HR) à la COS. Même si plusieurs gènes ont été identifiés (ex. tolC, phoP et soxS-soxR) dans cette HR, les mécanismes restent en grande partie inconnus. En 2019, Huang et al. ont décrit le gène ecr qui serait également impliqué dans l’HR en régulant positivement l’expression de phoP et de l’opéron arnBCADTEF. Le but de ce travail a été de rechercher la présence du gène ecr par PCR en temps réel dans une collection de souches de CEC déjà caractérisées et par une approche in silico à partir des séquences génomiques disponibles.Matériels et méthodes : Une collection de 100 souches cliniques uniques représentatives des différents clusters du CEC (C-I à C-XIV) a été étudiée. Les souches identifiées par séquençage partiel du gène hsp60 ont été caractérisées pour l’HR à la COS par CMI par microdilution et analyse de population. Après le design d’amorces spécifiques, une technique de PCR en temps réel a été développée. Parallèlement, le gène ecr a été recherché par une analyse in silico sur 1560 souches du CEC.Résultats : Sur les 100 souches, 48 présentaient une HR à la COS et appartenaient aux clusters hsp60suivants : C-I (7/8), C-II (16/16), C-III (1/14), C-IV (8/9), CVII (2/4), C-IX (3/3), C-X (1/2), C-XI (8/9), C-XII (2/2). Le gène ecr a été retrouvé uniquement pour les clusters C-I (7/7, 100%), C-IV (7/8, 87,5%), C-VII (1/2) et C-X (1/1) par PCR. L’analyse in silico des 1560 génomes a montré la présence du gène ecr uniquement pour les clusters C-I (87/87, 100%) et C-IV (86/92, 93,5%). Conclusion : Dans cette étude, nous avons pu montrer que le gène ecr semble particulièrement présent chez les clusters C-I et C-IV. Ces résultats montrent l’importance de la détermination précise du cluster en matière d’interprétation de la sensibilité à la COS. L’analyse génomique doit être étendue aux 100 souches cliniques de ce panel pour confirmer cette association exclusive à certains clusters et redéfinir ainsi précisément le cluster des 2 souches ecr positif non C-I ou C-IV

Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

Twenty-six Salmonella enterica serovar Eko isolated from various sources in Nigeria were investigated by whole genome sequencing to identify the source of human infections. Diversity among the isolates was observed and camel and cattle were identified as the primary reservoirs and the most likely source of the human infections

Melioidosis in Tsunami Survivors

Eugene Athan, Anthony M. Allworth, Catherine Engler, Ivan Bastian, and Allen C. Chen

Global Genomic Epidemiology of <i>Salmonella enterica</i> Serovar Typhimurium DT104

International audienceIt has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella entericaserovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315S Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonellafrom pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections

Ceftazidime-Resistant Salmonella enterica, Morocco

International audienceTo the Editor: Many thanks for your interesting and informative special section on infectious diseases in the Amazon Region (1). Your readers should also be interested in a little known, but extremely successful, sustainable health program that had its start in the Amazon. In 1942, the governments of Brazil and the United States agreed to establish a special service for public health (called the Serviço Especial de Saúde Pública). The purpose of this program was to improve health conditions in key areas in the Amazon, expedite the collection and export of native rubber, and counteract the growing influence of Nazi Germany in Latin America (2). The program spread to the Vale do Rio Doce, where there were resources of iron ore, mica, and optical quartz, which were important for the war effort. Although the program eventually moved to all states of Brazil, the Amazon program remained an important activity for ≈50 years before it was integrated into the Brazilian Ministry of Health (3). The program in the Amazon fo-cused primarily on infectious disease. It comprised programs of immunization , provision of small sustainable water systems, development of privy programs (sewer systems in the larger centers of population), malaria control , improvement of residences and living conditions for Chagas disease control, epidemiologic intelligence, and extensive training for auxiliary and professional personnel. The effects of this program are shown by the increase in life expectancy for all age groups, with an increase of >10 years for those childhood age groups for whom infectious disease control would have the greatest effect from 1939–1941 to 1950–1951 (4). This program contains many lessons for the planners of health and disease control projects in tropical, low-income countries