Comparative whole genome analysis of three consecutive Salmonella diarizonae isolates

Gerlach, Roman G.; Walter, Steffi; McClelland, Michael; Schmidt, Christiane; Steglich, Matthias; Prager, Rita; Bender, Jennifer K.; Fuchs, Stephan; Schoerner, Christoph; Rabsch, Wolfgang; Lang, Werner

doi:10.1016/j.ijmm.2017.09.001

Cited by 15 publications

(20 citation statements)

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“…Although the strain was susceptible to eleven tested antibiotics, two antibiotic resistance genes homologous to aac(6′) - Iaa (Accession: NC_003197), an aminoglycoside acetyltransferase, and mdfA (Accession: Y08743), a macrolide–lincosamide–streptogramin B (MLS) resistance gene were identified. We found that the strain possesses the major pathogenicity islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-18 and GI-2 [22]. Furthermore, by comparing the sequence based similarity of the 16-SA00356 genome to five other S. enterica subsp.…”

Section: Resultsmentioning

confidence: 99%

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

et al. 2019

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Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.

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Section: Resultsmentioning

confidence: 99%

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

et al. 2019

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“…While S. enterica subsp salamae is not associated with human infections, S. enterica subsp. diarizonae was responsible for acute gastroenteritis in a 77-year-old man affected by advanced rectal cancer, who later died due to multiple morbidities, including Salmonella infection [ 82 ], as well as for a case of gastroenteritis in a 10-day-old female infant with bloody mucous stools [ 83 ]. Furthermore, S. enterica subsp.…”

Section: Discussionmentioning

confidence: 99%

Salmonella Infection in Turtles: A Risk for Staff Involved in Wildlife Management?

Casalino

Bellati

Pugliese

et al. 2021

Animals

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Monitoring of infections that may be transmitted to humans by animals in wildlife rescue centres is very important in order to protect the staff engaged in rehabilitation practices. Salmonella may be a natural inhabitant of the intestinal tract of turtles, rarely causing disease. This may represent a potential risk for humans, increasing the sanitary risk for operators in wildlife rescue centres. In this paper, the occurrence of non-typhoidal Salmonella among terrestrial turtles housed in a wildlife rescue centre in Southern Italy was investigated, in order to assess the serovars more frequently carried by turtles and identify those that may represent a risk for operators involved in wildlife management. Sixty-nine adult turtles (Testudo hermanni hermanni, T. h. boettgeri, T. graeca, and T. marginata) were tested. Detection and serotyping of Salmonella strains were performed according to ISO 6579-1 and ISO/TR 6579-3:2013, respectively. The distribution of Salmonella spp. was significantly higher in T. hermanni hermanni than in other species, independent of the age and gender of the animals. Two different Salmonella species, S. enterica and S. bongori, three S. enterica subspecies (enterica, diarizonae, salamae), and five different serovars (Hermannswerder, Abony, Ferruch, Richmond, Vancouver) within the group S. enterica subspecies enterica were identified. Different combinations of Salmonella types were simultaneously found in specimens of T. h. hermanni. Most of detected Salmonella types may represent a potential risk for public health. Adopting correct animal husbandry procedures and informing on potential sanitary risks may be useful for minimising the risk of transmission of Salmonella to workers involved in wildlife management.

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“…Pet snakes are common reservoirs of diarizonae and, consequently, potential transmission sources. However, invasive infections in humans are rarely reported [10, 15, 17, 18]. Accordingly, we were interested in analyzing the genome of two diarizonae strains isolated from two human samples in the city of Santa Cruz, Bolivia.…”

Section: Resultsmentioning

confidence: 99%

“…Although there are few human clinical reports from S. enterica isolates not belonging to subsp. enterica [7, 18], diarizonae has been found sporadically responsible for maxillary sinusitis, bacteremia, cervical lymphadentitis and gastroenteritis in adults and children [15, 17, 28, 29]. Our whole genome comparison revealed that diarizonae SBO13 and SBO27 harbor 10 known Salmonella pathogenicity islands (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-11, SPI-13, SPI-18, and SPI-21) and a significant portion of SPI-7 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

et al. 2019

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BackgroundSalmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown.ResultsWe report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a ~ 10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport related-genes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates.ConclusionsThe comparative genomic study of two diarizonae strains isolated in Bolivia from human patients uncovered the presence of many genes putatively related to virulence. The statistically-significant acquisition of a unique combination of these functions by diarizonae strains isolated from humans may have impacted the ability of these isolates to successfully infect the human host.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5352-z) contains supplementary material, which is available to authorized users.

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Comparative whole genome analysis of three consecutive Salmonella diarizonae isolates

Cited by 15 publications

References 46 publications

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

Salmonella Infection in Turtles: A Risk for Staff Involved in Wildlife Management?

Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

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