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Friday, July 19, 2019

New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis.

Acinetobacter baumannii is a globally important nosocomial pathogen characterized by an increasing incidence of multidrug resistance. Routes of dissemination and gene flow among health care facilities are poorly resolved and are important for understanding the epidemiology of A. baumannii, minimizing disease transmission, and improving patient outcomes. We used whole-genome sequencing to assess diversity and genome dynamics in 49 isolates from one United States hospital system during one year from 2007 to 2008. Core single-nucleotide-variant-based phylogenetic analysis revealed multiple founder strains and multiple independent strains recovered from the same patient yet was insufficient to fully resolve strain relationships, where gene content…

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Friday, July 19, 2019

Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage.

Lactobacillus hokkaidonensis is an obligate heterofermentative lactic acid bacterium, which is isolated from Timothy grass silage in Hokkaido, a subarctic region of Japan. This bacterium is expected to be useful as a silage starter culture in cold regions because of its remarkable psychrotolerance; it can grow at temperatures as low as 4°C. To elucidate its genetic background, particularly in relation to the source of psychrotolerance, we constructed the complete genome sequence of L. hokkaidonensis LOOC260(T) using PacBio single-molecule real-time sequencing technology.The genome of LOOC260(T) comprises one circular chromosome (2.28 Mbp) and two circular plasmids: pLOOC260-1 (81.6 kbp) and pLOOC260-2 (41.0…

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Sunday, July 7, 2019

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas…

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Sunday, July 7, 2019

Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode.

Serratia nematodiphila DSM 21420(T) (=CGMCC 1.6853(T), DZ0503SBS1(T)), isolated from the intestine of Heterorhabditidoides chongmingensis, has been known to have symbiotic-pathogenic life cycle, on the multilateral relationships with entomopathogenic nematode and insect pest. In order to better understanding of this rare feature in Serratia species, we present here the genome sequence of S. nematodiphila DSM 21420(T) with the significance of first genome sequence in this species. Copyright © 2014 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Ceftriaxone-resistant Salmonella enterica serotype Typhimurium sequence type 313 from Kenyan patients is associated with the blaCTX-M-15 gene on a novel IncHI2 plasmid.

Multidrug-resistant bacteria pose a major challenge to the clinical management of infections in resource-poor settings. Although nontyphoidal Salmonella (NTS) bacteria cause predominantly enteric self-limiting illness in developed countries, NTS is responsible for a huge burden of life-threatening bloodstream infections in sub-Saharan Africa. Here, we characterized nine S. Typhimurium isolates from an outbreak involving patients who initially failed to respond to ceftriaxone treatment at a referral hospital in Kenya. These Salmonella enterica serotype Typhimurium isolates were resistant to ampicillin, chloramphenicol, cefuroxime, ceftriaxone, aztreonam, cefepime, sulfamethoxazole-trimethoprim, and cefpodoxime. Resistance to ß-lactams, including to ceftriaxone, was associated with carriage of a combination of…

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Sunday, July 7, 2019

Complete genome sequence of Haloarcula sp. CBA1115 isolated from non-purified solar salts.

Haloarcula sp. CBA1115, isolated from non-purified solar salts from South Korea, is a halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the strain Haloarcula sp. CBA1115 (4,225,046bp, with a G+C content of 61.98%), which is distributed over one chromosome and five plasmids. A comparison of the genome sequence of Haloarcula sp. CBA1115 with those of members of its closely related taxa showed that the closest neighbor is Haloarcula hispanica Y27, a popular model organism for archaeal studies. The strain was found to possess a number of genes predicted to be involved in osmo-regulatory…

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Sunday, July 7, 2019

Complete genome sequence of Paenibacillus beijingensis 7188(T) (=DSM 24997(T)), a novel rhizobacterium from jujube garden soil.

We present here the complete genome sequence of a novel species Paenibacillus beijingensis 7188(T) (=DSM 24997(T)) from jujube rhizosphere soil that consists of one circular chromosome of 5,749,967bp with a GC content of 52.5%. On the significance of first genome information in this species, the genome sequence of strain 7188(T) will provide a better comprehension of Paenibacillus species for the practical uses as a biofertilizer in agriculture. Copyright © 2015 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Genome sequence analysis of the naphthenic acid degrading and metal resistant bacterium Cupriavidus gilardii CR3.

Cupriavidus sp. are generally heavy metal tolerant bacteria with the ability to degrade a variety of aromatic hydrocarbon compounds, although the degradation pathways and substrate versatilities remain largely unknown. Here we studied the bacterium Cupriavidus gilardii strain CR3, which was isolated from a natural asphalt deposit, and which was shown to utilize naphthenic acids as a sole carbon source. Genome sequencing of C. gilardii CR3 was carried out to elucidate possible mechanisms for the naphthenic acid biodegradation. The genome of C. gilardii CR3 was composed of two circular chromosomes chr1 and chr2 of respectively 3,539,530 bp and 2,039,213 bp in…

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Sunday, July 7, 2019

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

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Sunday, July 7, 2019

Complete genome sequence of the heavy metal resistant bacterium Altererythrobacter atlanticus 26DY36(T), isolated from deep-sea sediment of the North Atlantic Mid-ocean ridge.

Altererythrobacter atlanticus 26DY36(T) (CGMCC 1.12411(T)=JCM 18865(T)) was isolated from the North Atlantic Mid-Ocean Ridge. The strain is resistant to heavy metals, such as Mn(2+) (200 mM), Co(2+) (2.0mM), Cu(2+) (1mM), Zn(2+) (1mM), Hg(2+) (0.1mM) and Cd(2+) (0.5mM). Here we describe the genome sequence and annotation, as well as the features of the organism. A. atlanticus 26DY36(T) harbors a chromosome (3,386,291 bp) and a circular plasmid (88,815 bp). The genome contains 3322 protein-coding genes (2483 with predicted functions), 47 tRNA genes and 6 rRNA genes. A. atlanticus 26DY36(T) encodes dozens of genes related to heavy metal resistance and has potential applications…

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Sunday, July 7, 2019

Clonal dissemination of Enterobacter cloacae harboring blaKPC-3 in the upper midwestern United States.

Carbapenemase-producing, carbapenem-resistant Enterobacteriaceae, or CP-CRE, are an emerging threat to human and animal health, because they are resistant to many of the last-line antimicrobials available for disease treatment. Carbapenemase-producing Enterobacter cloacae harboring blaKPC-3 recently was reported in the upper midwestern United States and implicated in a hospital outbreak in Fargo, North Dakota (L. M. Kiedrowski, D. M. Guerrero, F. Perez, R. A. Viau, L. J. Rojas, M. F. Mojica, S. D. Rudin, A. M. Hujer, S. H. Marshall, and R. A. Bonomo, Emerg Infect Dis 20:1583-1585, 2014, http://dx.doi.org/10.3201/eid2009.140344). In early 2009, the Minnesota Department of Health began collecting and screening…

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Sunday, July 7, 2019

Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria.

In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. However, understanding the natural variation and possible differences between pathogens and beneficials is the main challenge in furthering these possibilities. The genus Stenotrophomonas contains representatives found to be associated with human and plant host.We used comparative genomics as well as transcriptomic and physiological approaches to detect significant borders between the Stenotrophomonas strains: the multi-drug resistant pathogenic S.…

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