Background Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles. Methodology/Principle findings We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella , and found that a diverse range of serovars ( n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae , enterica , houtanae and salamae . Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S . diarizonae , S . enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo -inositol and allantoin. Significance We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella , including serovars which have been associated with disease in humans such as S . Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.
Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P. baetica strain a390T was sequenced using a unique combination of Ion Torrent semiconductor and Oxford Nanopore methods as part of a collaborative community-led project. The use of high-quality Ion Torrent sequences with long Nanopore reads gave rapid, high-contiguity and -quality, 16-contig genome sequence. Whole genome phylogenetic analysis places P. baetica within the P. koreensis clade of the P. fluorescens group. Comparison of the main genomic features of P. baetica with a variety of other Pseudomonas spp. suggests that it is a highly adaptable organism, typical of the genus. This strain was originally isolated from the liver of a diseased wedge sole fish, and genotypic and phenotypic analyses show that it is tolerant to osmotic stress and to oxytetracycline.
30 Background 31 Reptile-associated Salmonella are a major, but often neglected cause of both 32 gastrointestinal and bloodstream infection globally. The diversity of Salmonella enterica has33 not yet been determined in venomous snakes, however other cold-blooded animals have 34 been reported to carry a broad range of Salmonella bacteria. We investigated the 35 prevalence and assortment of Salmonella in a collection of venomous snakes in comparison 36 with non-venomous reptiles. 3738 Methodology/Principle Findings 39 We used a combination of selective enrichment techniques and whole-genome sequencing.40 We established a unique dataset of reptilian isolates to study Salmonella enterica species-41 level evolution and ecology and investigated differences between phylogenetic groups. We 42 observed that 91% of venomous snakes carried Salmonella, and found substantial diversity 43 between the serovars (n=58) carried by reptiles. The Salmonella serovars belonged to four 44 of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae.45 Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, 46 previously described as clade A (52%) and clade B (48%). We identified metabolic 47 differences between S. diarizonae, S. enterica clade A and clade B involving growth on 48 lactose, tartaric acid, dulcitol, myo-inositol and allantoin. 49 50 Significance 51 We present the first whole genome-based comparative study of the Salmonella bacteria that 52 colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution.53 The findings raise the possibility that venomous snakes are a reservoir for human 54 Salmonellosis in Africa. The proximity of venomous snakes to human dwellings in rural Africa 55 may result in contaminated faecal matter being shed on surfaces and in water sources used 3 56 for human homes and to irrigate salad crops. Because most of the venomous snakes had 57 been captured in Africa, we conclude that the high level of Salmonella diversity reflects the 58 African environmental niches where the snakes have inhabited. 59 60 Author Summary 61 Salmonella enterica is a remarkable bacterial species that causes Neglected Tropical 62 Diseases globally. The burden of disease is greatest in some of the most poverty-afflicted 63 regions of Africa, where salmonellosis frequently causes bloodstream infection with fatal 64 consequences. The bacteria have the ability to colonise the gastrointestinal tract of a wide 65 range of animals including reptiles. Direct or indirect contact between reptiles and humans 66 can cause Salmonellosis. In this study, we determined the prevalence and diversity of 67 Salmonella in a collection of African venomous snakes for the first time. Using the power of 68 genomics, we showed that the majority of venomous snakes (91%) carry Salmonella, two 69 thirds of which belonged to a subspecies of S. enterica called enterica, which is associated 70 with most cases of human salmonellosis. Within the S. enterica subspecies we identi...
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