scholarly journals Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Han Ming Gan ◽  
Ganeswrie Rajasekaram ◽  
Wilhelm Wei Han Eng ◽  
Priyatharisni Kaniappan ◽  
Amreeta Dhanoa
Keyword(s):  
Tertiary Hospital ◽  
Clinical Isolates ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Extended Spectrum

ABSTRACT We report the whole-genome sequences of two carbapenem-resistant clinical isolates of Klebsiella quasipneumoniae subsp. similipneumoniae obtained from two different patients. Both strains contained three different extended-spectrum β-lactamase genes and showed strikingly high pairwise average nucleotide identity of 99.99% despite being isolated 3 years apart from the same hospital.

scholarly journals Draft Genome Sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor, Purple Sulfur Photosynthetic Bacteria in the Gammaproteobacterial Family Chromatiaceae

2020 ◽  
Vol 9 (14) ◽  
Author(s):  
Fabiola A. Aviles ◽  
Terry E. Meyer ◽  
John A. Kyndt
Keyword(s):  
Photosynthetic Bacteria ◽  
Draft Genome ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

We have determined the draft genome sequences of Thiorhodococcus mannitoliphagus and Thiorhodococcus minor for comparison with those of T. drewsii and Imhoffiella purpurea. According to average nucleotide identity (ANI) and whole-genome phylogenetic comparisons, these two species are clearly distinct from the Imhoffiella species and T. drewsii.

scholarly journals Genome Sequences of Allochromatium palmeri and Allochromatium humboldtianum Expand the Allochromatium Family Tree of Purple Sulfur Photosynthetic Bacteria within the Gammaproteobacteria and Further Refine the Genus

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
John A. Kyndt ◽  
Terry E. Meyer
Keyword(s):  
Photosynthetic Bacteria ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Family Tree ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Allochromatium Vinosum ◽  
Content Type ◽  
The Family ◽  
Identity Based

ABSTRACT New genomes of two Allochromatium strains were sequenced. Whole-genome and average nucleotide identity based on BLAST (ANIb) comparisons show that Allochromatium humboldtianum is the nearest relative of Allochromatium vinosum (ANIb, 91.5%), while both Allochromatium palmeri and Thermochromatium tepidum are more distantly related (ANIb, <87%). These new sequences firmly establish the position of Allochromatium on the family tree.

scholarly journals Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Toshiyuki Moriya ◽  
Natsuko Tokito ◽  
Tairo Oshima ◽  
Kei Yura ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Hot Spring ◽  
Thermus Thermophilus ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

ABSTRACT We isolated Thermus thermophilus strains HB5002 and HB5008 from Mine Hot Spring in Japan. Whole-genome sequencing revealed that they showed ∼100% average nucleotide identity to each other, ≥98.53% to the T. thermophilus strains originating from the same spot but ≤97.64% to the T. thermophilus strains from geographically different places in Japan.

scholarly journals Comparative Genomics of Klebsiella pneumoniae Strains with Different Antibiotic Resistance Profiles

2011 ◽  
Vol 55 (9) ◽  
pp. 4267-4276 ◽  
Author(s):  
Vinod Kumar ◽  
Peng Sun ◽  
Jessica Vamathevan ◽  
Yong Li ◽  
Karen Ingraham ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Multidrug Resistance ◽  
Klebsiella Pneumoniae ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Susceptible Strain ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Content Type ◽  
Extended Spectrum

ABSTRACTThere is a global emergence of multidrug-resistant (MDR) strains ofKlebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology ofK. pneumoniaestrains and occurrences of specific antibiotic resistance genes, such as plasmid-borne extended-spectrum β-lactamases (ESBLs), have been extensively studied, only four complete genomes ofK. pneumoniaeare available. To better understand the multidrug resistance factors inK. pneumoniae, we determined by pyrosequencing the nearly complete genome DNA sequences of two strains with disparate antibiotic resistance profiles, broadly drug-susceptible strain JH1 and strain 1162281, which is resistant to multiple clinically used antibiotics, including extended-spectrum β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, and sulfamethoxazoles. Comparative genomic analysis of JH1, 1162281, and other publishedK. pneumoniaegenomes revealed a core set of 3,631 conserved orthologous proteins, which were used for reconstruction of whole-genome phylogenetic trees. The close evolutionary relationship between JH1 and 1162281 relative to otherK. pneumoniaestrains suggests that a large component of the genetic and phenotypic diversity of clinical isolates is due to horizontal gene transfer. Using curated lists of over 400 antibiotic resistance genes, we identified all of the elements that differentiated the antibiotic profile of MDR strain 1162281 from that of susceptible strain JH1, such as the presence of additional efflux pumps, ESBLs, and multiple mechanisms of fluoroquinolone resistance. Our study adds new and significant DNA sequence data onK. pneumoniaestrains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.

scholarly journals Whole-Genome Sequences of Corynebacterium macginleyi CCUG 32361T and Clinical Isolates NML 080212 and NML 120205

2018 ◽  
Vol 7 (23) ◽  
Author(s):  
Anne-Marie Bernier ◽  
Kathryn Bernard
Keyword(s):  
Draft Genome ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type

Draft genome sequences of Corynebacterium macginleyi CCUG 32361T and clinical isolates NML 080212 and NML 120205 were assembled and studied. Genome sizes ranged from 2.35 Mb to 2.42 Mb, with G+C contents ranging from 57.1% to 57.2%.

scholarly journals Genome Sequences of Two Choline-Utilizing Methanogenic Archaea, Methanococcoides spp., Isolated from Marine Sediments

2019 ◽  
Vol 8 (18) ◽  
Author(s):  
Gordon Webster ◽  
Alex J. Mullins ◽  
Andrew J. Watkins ◽  
Edward Cunningham-Oakes ◽  
Andrew J. Weightman ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Dna Hybridization ◽  
In Silico ◽  
Methanogenic Archaea ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

The genomes of two Methanococcoides spp. that were isolated from marine sediments and are capable of carrying out methanogenesis from choline and other methylotrophic substrates were sequenced. The average nucleotide identity and in silico DNA-DNA hybridization analyses demonstrate that they represent species different from those previously described.

scholarly journals Whole-Genome-Sequence-Based Characterization of Extensively Drug-Resistant Acinetobacter baumannii Hospital Outbreak

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Ghiwa Makke ◽  
Ibrahim Bitar ◽  
Tamara Salloum ◽  
Balig Panossian ◽  
Sahar Alousi ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Tertiary Hospital ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Transmission Network ◽  
Drug Resistant ◽  
Content Type ◽  
Carbapenem Resistant ◽  
Extensively Drug Resistant ◽  
Long Read

ABSTRACT Carbapenem-resistant Acinetobacter baumannii (CRAB) is an important opportunistic pathogen linked to a variety of nosocomial infections and hospital outbreaks worldwide. This study aimed at investigating and characterizing a CRAB outbreak at a large tertiary hospital in Lebanon. A total of 41 isolates were collected and analyzed using pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing (WGS) was performed on all the isolates, and long-read PacBio sequencing was used to generate reference genomes. The multilocus sequence types (MLST), repertoire of resistance genes, and virulence factors were determined from the sequencing data. The plasmid content was analyzed both in silico and using the A. baumannii PCR-based replicon typing (AB-PBRT) method. Genome analysis initially revealed two clones, one carrying blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218) and another carrying blaOXA-72 on pMAL-1 (ST-502 and ST-2059, a new ST), with the latter having two subclones, as revealed using the Bayesian transmission network. All isolates were extensively drug resistant (XDR). WGS analysis revealed the transmission pathways and demonstrated the diversity of CRAB isolates and mobile genetic elements in this health care setting. Outbreak detection using WGS and immediate implementation of infection control measures contribute to restraining the spread and decreasing mortality. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii (CRAB) has been implicated in hospital outbreaks worldwide. Here, we present a whole-genome-based investigation of an extensively drug-resistant CRAB outbreak rapidly spreading and causing high incidences of mortality at numerous wards of a large tertiary hospital in Lebanon. This is the first study of its kind in the region. Two circulating clones were identified using a combination of molecular typing approaches, short- and long-read sequencing and Bayesian transmission network analysis. One clone carried blaOXA-23 on Tn2006 (ST-1305, ST-195, and ST-218), and another carried blaOXA-72 on a pMAL-1 plasmid (ST-502 and ST-2059, a new ST). A pMAL-2 plasmid was circulating between the two clones. The approaches implemented in this study and the obtained findings facilitate the tracking of outbreak scenarios in Lebanon and the region at large.

scholarly journals Draft Genome Sequences of Plant-Pathogenic Klebsiella variicola Strains Isolated from Plantain in Haiti

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
James C. Fulton ◽  
Jeannie M. Klein ◽  
Sladana Bec ◽  
Joubert Fayette ◽  
Karen A. Garrett ◽  
...  
Keyword(s):  
Type Strain ◽  
Draft Genome ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

ABSTRACT The genus Klebsiella includes pathogenic and nonpathogenic species. We report the 5.57-Mb genome sequences of two Klebsiella variicola strains, G18-1365 and G18-1376, isolated from symptomatic plantain plants in Haiti. These strains are genetically closely related (average nucleotide identity [ANI] > 99%) to the previously described type strain of K. variicola, DSM 15968.

scholarly journals Re-identification of strains deposited as Pseudomonas aeruginosa, Pseudomonas fluorescens and Pseudomonas putida in GenBank based on whole genome sequences

2020 ◽  
Vol 70 (11) ◽  
pp. 5958-5963
Author(s):  
Yuh Morimoto ◽  
Mari Tohya ◽  
Zulipiya Aibibula ◽  
Tadashi Baba ◽  
Hiroyuki Daida ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequencing ◽  
Dna Hybridization ◽  
Type Species ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

The taxonomic classification of Pseudomonas species has been revised and updated several times. This study utilized average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) cutoff values of 95 and 70 %, respectively, to re-identify the species of strains deposited in GenBank as P. aeruginosa , P. fluorescens and P. putida . Of the 264 deposited P. aeruginosa strains, 259 were correctly identified as P. aeruginosa , but the remaining five were not. All 28 deposited P. fluorescens strains had been incorrectly identified as P. fluorescens . Four of these strains were re-identified, including two as P. kilonensis and one each as P. aeruginosa and P. brassicacearum , but the remaining 24 could not be re-identified. Similarly, all 35 deposited P. putida strains had been incorrectly identified as P. putida . Nineteen of these strains were re-identified, including 12 as P. alloputida , four as P. asiatica and one each as P. juntendi , P. monteilii and P. mosselii . These results strongly suggest that Pseudomonas bacteria should be identified using ANI and dDDH analyses based on whole genome sequencing when Pseudomonas species are initially deposited in GenBank/DDBJ/EMBL databases.

scholarly journals Genome Sequences of Five Streptomyces Bacteriophages Forming Cluster BG

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Richard Donegan-Quick ◽  
Zane A. Gibbs ◽  
Patricia O. Amaku ◽  
Joshua T. Bernal ◽  
Dana A. M. Boyd ◽  
...  
Keyword(s):  
Streptomyces Griseus ◽  
The Other ◽  
Nucleotide Identity ◽  
Strain Atcc ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

ABSTRACT Cluster BG of the actinobacteriophage was formed upon discovery of five novel bacteriophages isolated by enrichment from their host, Streptomyces griseus subsp. griseus strain ATCC 10137. Four members of this cluster (BabyGotBac, Maih, TP1605, and YDN12) share over 89% average nucleotide identity, while the other (Xkcd426) has only 72% similarity to other cluster members.

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