scholarly journals Characterization of HypermutatorPseudomonas aeruginosaIsolates from Patients with Cystic Fibrosis in Australia

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Vanessa E. Rees ◽  
Deanna S. Deveson Lucas ◽  
Carla López-Causapé ◽  
Yuling Huang ◽  
Tom Kotsimbos ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Health Care ◽  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Phylogenetic Analyses ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type

ABSTRACTHypermutablePseudomonas aeruginosaisolates (hypermutators) have been identified in patients with cystic fibrosis (CF) and are associated with reduced lung function. Hypermutators display a greatly increased mutation rate and an enhanced ability to become resistant to antibiotics during treatment. Their prevalence has been established among patients with CF, but it has not been determined for patients with CF in Australia. This study aimed to determine the prevalence of hypermutableP. aeruginosaisolates from adult patients with CF from a health care institution in Australia and to characterize the genetic diversity and antibiotic susceptibility of these isolates. A total of 59 P. aeruginosaclinical isolates from patients with CF were characterized. For all isolates, rifampin (RIF) mutation frequencies and susceptibility to a range of antibiotics were determined. Of the 59 isolates, 13 (22%) were hypermutable. Whole-genome sequences were determined for all hypermutable isolates. Core genome polymorphisms were used to assess genetic relatedness of the isolates, both to each other and to a sample of previously characterizedP. aeruginosastrains. Phylogenetic analyses showed that the hypermutators were from divergent lineages and that hypermutator phenotype was mostly the result of mutations inmutLor, less commonly, inmutS. Hypermutable isolates also contained a range of mutations that are likely associated with adaptation ofP. aeruginosato the CF lung environment. Multidrug resistance was more prevalent in hypermutable than nonhypermutable isolates (38% versus 22%). This study revealed that hypermutableP. aeruginosastrains are common among isolates from patients with CF in Australia and are implicated in the emergence of antibiotic resistance.

scholarly journals Genotypic Characterization of Multidrug-Resistant Pseudomonas aeruginosa Using Whole-Genome Sequencing

2021 ◽  
Vol 10 (32) ◽  
Author(s):  
Baha Abdalhamid ◽  
Itidal Reslane ◽  
Emily Mccutchen ◽  
Peter C. Iwen
Keyword(s):  
Health Care ◽  
Pseudomonas Aeruginosa ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Significant Morbidity ◽  
Genome Sequences ◽  
Content Type ◽  
Human Infections

Multidrug-resistant Pseudomonas aeruginosa is a serious threat worldwide causing health care-acquired infections and is associated with significant morbidity and mortality. This report describes the draft genome sequences of five multidrug-resistant Pseudomonas aeruginosa strains isolated from human infections.

scholarly journals Clostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Aakash Balaji ◽  
Egon A. Ozer ◽  
Larry K. Kociolek
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Core Genome ◽  
Genetic Relatedness ◽  
The Other ◽  
Whole Genome ◽  
Content Type ◽  
Clostridioides Difficile ◽  
Host Genetic

ABSTRACT Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events. To evaluate the likelihood of missed transmission events using WGS of single colonies from culture, we examined within-host genetic diversity among C. difficile isolates collected from children. We performed WGS using an Illumina MiSeq instrument on 8 C. difficile colonies randomly selected from each culture performed on stool collected from 10 children (8 children diagnosed with C. difficile infection and 2 children with asymptomatic carriage); 77/80 (96%) isolate sequences were successfully assembled. Among 8/10 (80%) children, all isolates were the same sequence type (ST). The other 2 children each had mixed infection with two STs, although one ST predominated. Among 9/10 (90%) children, isotypic isolates differed by ≤2 SNVs; an isotypic isolate in the remaining child differed by 3 to SNVs relative to the other isolates from that child. Overall, among the 77 isolates collected from 10 stool cultures, 74/77 (96%) were clonal (i.e., same ST and ≤2 core genome SNVs) to other isolates in stool culture. In summary, we identified rare C. difficile within-host genetic diversity in children, suggesting that WGS of a single colony from stool is likely to appropriately characterize isolate clonality and putative transmission events in the majority of cases.

Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients

2019 ◽  
Vol 14 (16) ◽  
pp. 1357-1367
Author(s):  
Jumamurat R Bayjanov ◽  
Miquel B Ekkelenkamp ◽  
Malbert RC Rogers ◽  
Rafael Cantón ◽  
Barry J Benaissa-Trouw ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Characterization ◽  
Novel Species ◽  
Antibiotic Resistance Genes ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Acquired Antibiotic Resistance

Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.

Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 357-365 ◽  
Author(s):  
Gilda Rose S. Amaral ◽  
Graciela M. Dias ◽  
Michiyo Wellington-Oguri ◽  
Luciane Chimetto ◽  
Mariana E. Campeão ◽  
...  
Keyword(s):  
Phenotypic Characterization ◽  
Whole Genome ◽  
Genome Sequences ◽  
Diagnostic Features ◽  
Phenotypic Data ◽  
Content Type ◽  
Ecological Relationships ◽  
Phenotypic Information ◽  
Specific Proteins

Vibrios are ubiquitous in the aquatic environment and can be found in association with animal or plant hosts. The range of ecological relationships includes pathogenic and mutualistic associations. To gain a better understanding of the ecology of these microbes, it is important to determine their phenotypic features. However, the traditional phenotypic characterization of vibrios has been expensive, time-consuming and restricted in scope to a limited number of features. In addition, most of the commercial systems applied for phenotypic characterization cannot characterize the broad spectrum of environmental strains. A reliable and possible alternative is to obtain phenotypic information directly from whole genome sequences. The aim of the present study was to evaluate the usefulness of whole genome sequences as a source of phenotypic information. We performed a comparison of the vibrio phenotypes obtained from the literature with the phenotypes obtained from whole genome sequences. We observed a significant correlation between the previously published phenotypic data and the phenotypic data retrieved from whole genome sequences of vibrios. Analysis of 26 vibrio genomes revealed that all genes coding for the specific proteins involved in the metabolic pathways responsible for positive phenotypes of the 14 diagnostic features (Voges–Proskauer reaction, indole production, arginine dihydrolase, ornithine decarboxylase, utilization of myo-inositol, sucrose and l-leucine, and fermentation of d-mannitol, d-sorbitol, l-arabinose, trehalose, cellobiose, d-mannose and d-galactose) were found in the majority of the vibrios genomes. Vibrio species that were negative for a given phenotype revealed the absence of all or several genes involved in the respective biochemical pathways, indicating the utility of this approach to characterize the phenotypes of vibrios. The absence of the global regulation and regulatory proteins in the Vibrio parahaemolyticus genome indicated a non-vibrio phenotype. Whole genome sequences represent an important source for the phenotypic identification of vibrios.

scholarly journals Investigation of the Evolutionary Development of the Genus Bifidobacterium by Comparative Genomics

2014 ◽  
Vol 80 (20) ◽  
pp. 6383-6394 ◽  
Author(s):  
Gabriele Andrea Lugli ◽  
Christian Milani ◽  
Francesca Turroni ◽  
Sabrina Duranti ◽  
Chiara Ferrario ◽  
...  
Keyword(s):  
Sequence Comparison ◽  
Core Genome ◽  
Genetic Relatedness ◽  
Single Gene ◽  
Evolutionary Development ◽  
Genome Sequences ◽  
Separate Species ◽  
Content Type ◽  
Relative Paucity ◽  
A Genome

ABSTRACTTheBifidobacteriumgenus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particularBifidobacteriumtaxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of theBifidobacteriumgenus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.

scholarly journals Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a Giant Phage Mutant Collection

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Han Ming Gan ◽  
Wilhelm Wei Han Eng ◽  
Melissa K. Barton ◽  
Lily E. Adams ◽  
Nurul Aisyah Samsudin ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Phage Mutant ◽  
Isolation And Characterization ◽  
Serovar Typhimurium ◽  
Bacterial Viruses ◽  
Mutant Collection

ABSTRACT We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097, which we utilize for genetic analyses of giant bacterial viruses. Our analyses identified several genetic variations between the two strains, most significantly confirming strain TT6675 as a serine suppressor and TT9097 as a nonsuppressor.

scholarly journals Whole-Genome Assemblies for Three Yersinia pestis Strains Isolated in Erenhot, China

2020 ◽  
Vol 9 (45) ◽  
Author(s):  
Jing Wang ◽  
Xifeng Yang ◽  
Hongyuan Zheng ◽  
Li Tian ◽  
Qi Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Yersinia Pestis ◽  
Draft Genome ◽  
Meriones Unguiculatus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Assemblies

ABSTRACT To explore the genetic diversity of Yersinia pestis strains in Erenhot, China, and their relationship with Mongolian strains, we collected and sequenced three Y. pestis strains from Erenhot, China, in 2018. Here, we report the draft genome sequences of three Y. pestis bv. Medievalis strains belonging to the 2.MED phylogroup that were circulating in Meriones unguiculatus populations.

scholarly journals Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Preetha Shibu ◽  
Frazer McCuaig ◽  
Anne L. McCartney ◽  
Magdalena Kujawska ◽  
Lindsay J. Hall ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. bla OXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis . Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii . The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four ( K. oxytoca , K. pasteurii , K. grimontii , K. michiganensis ) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

scholarly journals First Whole-Genome Characterization of Avian Nephritis Virus 2 of Broiler Chicken from Pará, Brazil

2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Ceyla Maria Oeiras Castro ◽  
Elaine Hellen Nunes Chagas ◽  
Delana Andreza Melo Bezerra ◽  
Sandro Patroca da Silva ◽  
Ana Cecília Ribeiro Cruz ◽  
...  
Keyword(s):  
Broiler Chickens ◽  
Broiler Chicken ◽  
Whole Genome ◽  
Full Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Characterization ◽  
Avian Nephritis Virus ◽  
The Family

ABSTRACT Our results show the first full-genome characterization of avian nephritis virus 2 recovered from stools of broiler chickens at a commercial farm located in Benevides, Pará, Brazil. Nucleotide analyses of whole-genome sequences showed the isolate to be a strain of Avastrovirus 2 in the family Astroviridae.

scholarly journals Whole-Genome Sequences of Mycobacterium abscessus subsp. massiliense Isolates from Brazil

2021 ◽  
Vol 10 (28) ◽  
Author(s):  
Edson Machado ◽  
Fernanda Cristina Oliveira ◽  
Rafael Silva Duarte ◽  
Ana Carolina Carvalho ◽  
Pedro Henrique Campanini Cândido ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Cystic Fibrosis Patient ◽  
Multidrug Resistant ◽  
Mycobacterium Abscessus ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Composition ◽  
Content Type ◽  
Severe Infections

The Mycobacterium abscessus complex comprises multidrug-resistant, opportunistic, and rapidly growing pathogens responsible for severe infections. Here, we report the genome composition of four Mycobacterium abscessus subsp. massiliense isolates from three sources: two from the lung of a cystic fibrosis patient, one from a mammary cyst, and one from a gutter system.

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