Dataset Information

Enterobacter hormaechei subsp. hoffmannii UCICRE 3

ABSTRACT: Carbapenem Resistance

PROVIDER: PRJNA201986 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR867695_1.fastq.gz	Fastqsanger.gz
	SRR867695_2.fastq.gz	Fastqsanger.gz
	SRR960869_1.fastq.gz	Fastqsanger.gz
	SRR960869_2.fastq.gz	Fastqsanger.gz

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Project description:Persian walnut (Juglans regia) has a considerable economic importance worldwide. However, the vigor and vitality of walnut trees were heavily affected by bark canker during the last few years. Irregular longitudinal cankers in the outer bark, stem tissue necrosis, and bleeding with black-colored exudates walnut trees were observed in Kermanshah, Hamedan, Markazi, Alborz, Isfahan, Qom, Semnan, and Razavi Khorasan provinces in western, central and eastern Iran during 2018 and 2019. A total of 150 symptomatic samples were collected from affected walnut trees in order to identify bacteria associated with walnut decline. Two-hundred sixty strains with a metallic green sheen were isolated on EMB-agar medium. The pathogenicity of all strains was proved by inoculating a suspension of the bacterial strains under the bark of immature walnut fruits cv. 'Hartley'. Ninety-five strains caused necrosis and a dark-colored region in the mesocarp around the inoculation site 14 days post-inoculation. Moreover, 12 representative strains induced necrotic and black-colored tissues in the bark of young green twigs of two-year old walnut seedling cv. 'Chandler'. The strains were classified into four categories based on conventional phenotypic characters confirmed with the 16S rRNA gene sequences. A phylogenetic tree based on the concatenated sequences of two housekeeping gene fragments, gyrB and infB, indicated that strains including I1, Q6, and S6 were grouped in a cluster with Gibbsiella quercinecans FBR97T as well as strains I2, I5, and KE6 were clustered with Rahnella victoriana FRB 225T. Moreover, strains MR1, MR3, and MR5 were grouped with the Enterobacter hormaechei subsp. hoffmannii DSM 14563T. The phylogenetic analyses based on the partial sequencing of housekeeping genes including fusA, pyrG, and leuS revealed that strains KH1, KH3, and KH7 belong to Citrobacter braakii species. To the best of our knowledge, this is the first report of C. braakii and E. hormaechei as plant pathogens and R. victoriana associated with walnut decline.

Project description:Six species and six additional genovars are combined within the so-called Enterobacter cloacae complex, with one of them being the species Enterobacter hormaechei. In a recent population genetic study, two genetic clusters were found in close phylogenetic proximity to the genetic cluster of E. hormaechei. In order to prove the hypothesis that these three genetic clusters belong to the same species, we performed cross-hybridization experiments in microplates with DNAs of representatives of each genetic cluster. The close phylogenetic relationship among the clusters was reflected by their relatively low deltaT(m) values, ranging from 0.3 to 4.8, confirming the hypothesis that the clusters are parts of the same species. These clusters can be distinguished from the other species of the E. cloacae complex, which have deltaT(m) values of 5.6 to 10.3. Forty-eight E. hormaechei strains from the different genetic clusters were phenotypically characterized with 129 biochemical tests. In this way, E. hormaechei could be differentiated from the other species of the E. cloacae complex because it tests negative in the 3-hydroxy-butyrate test. The three genetic clusters of E. hormaechei could also be differentiated from each other by using phenotypic tests. Hence, we propose three new subspecies of E. hormaechei corresponding to genetic clusters VI, VII, and VIII of the E. cloacae complex. E. hormaechei subsp. hormaechei comb. nov. corresponds to the original species description, as it gives negative results for the adonitol, d-arabitol, d-sorbitol, and d-melibiose tests and a positive result for the dulcitol test. E. hormaechei subsp. oharae subsp. nov. gives negative results for the dulcitol, adonitol, and d-arabitol tests and positive results for the d-sorbitol and d-melibiose tests. E. hormaechei subsp. steigerwaltii subsp. nov. gives a negative result for the dulcitol test and positive results for the adonitol, d-arabitol, d-sorbitol, and d-melibiose tests. Among the members of the E. cloacae complex, E. hormaechei seems to be the species most frequently recovered from clinical specimens.

Dataset Information

Enterobacter hormaechei subsp. hoffmannii UCICRE 3

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