scholarly journals Comparative genomics of two Shewanella xiamenensis strains isolated from a pilgrim before and during travels to the Hajj

Gut Pathogens ◽  
2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Thongpan Leangapichart ◽  
Linda Hadjadj ◽  
Philippe Gautret ◽  
Jean-Marc Rolain
Keyword(s):  
Genome Size ◽  
Pathogenic Bacteria ◽  
Capsular Polysaccharide ◽  
Draft Genome ◽  
Water Environment ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genome Sequences

Abstract Background Shewanella xiamenensis has been reported in water environment and in patients and can act as the originator of oxacillinase in gram-negative bacteria. In order to assess genome plasticity and its functional properties related diarrhea symptoms in pilgrim, comparisons of draft genome sequences of the two isolates were conducted with other closely related genomes. Results We isolated S. xiamenensis 111B and 111D strains from a pilgrim before travels to the Hajj and during travels with diarrhea symptom, respectively. Whole-genome sequencing showed that draft genome size of 111B strain was 5,008,191 bp, containing 49 kb of a putative plasmid. The genome size of 111D was 4,964,295 bp containing 225 kb of a putative plasmid that shared the backbone sequences with the hospital wastewater strain T17. Comparatively, two Hajj strains are identical at 97.3% identity and 98.7% coverage. They are closely related to river water strain, AS58 by SNPs analysis. Notably, a novel blaOXA-48 allele blaOXA-547 was identified in 111D, sharing 99.5% identity with blaOXA-546 and blaOXA-894. Multiple copies of virulence specific genes, such as capsular polysaccharide biosynthesis, O-antigen and lasB (vibriolysin related gene) have been identified specifically in 111D, but absent in 111B strain. Conclusions The whole genome sequences of S. xiamenensis strain 111B and 111D, including comparative genomic analysis, highlight here the potential for virulence factors that might be related to the cause of diarrhea in humans and also indicate the possible acquisition of pathogenic bacteria, including antibiotic resistance genes or plasmids during the Hajj.

scholarly journals Whole-Genome Sequences and Classification of Streptococcus agalactiae Strains Isolated from Laboratory-Reared Long-Evans Rats (Rattus norvegicus)

2017 ◽  
Vol 5 (1) ◽  
Author(s):  
C. Bodi Winn ◽  
J. Dzink-Fox ◽  
Y. Feng ◽  
Z. Shen ◽  
V. Bakthavatchalu ◽  
...  
Keyword(s):  
Streptococcus Agalactiae ◽  
Genomic Analysis ◽  
Opportunistic Pathogen ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Long Evans ◽  
Fatal Septicemia

ABSTRACT In collaboration with the CDC’s Streptococcus Laboratory, we report here the whole-genome sequences of seven Streptococcus agalactiae bacteria isolated from laboratory-reared Long-Evans rats. Four of the S. agalactiae isolates were associated with morbidity accompanied by endocarditis, metritis, and fatal septicemia, providing an opportunity for comparative genomic analysis of this opportunistic pathogen.

scholarly journals Draft Genome Sequences of Lactobacillales Isolated from the International Space Station

2020 ◽  
Vol 9 (39) ◽  
Author(s):  
Achintya R. Bharadwaj ◽  
Nitin K. Singh ◽  
Jason M. Wood ◽  
Marilyne Debieu ◽  
Niamh B. O’Hara ◽  
...  
Keyword(s):  
International Space Station ◽  
Pathogenic Bacteria ◽  
Draft Genome ◽  
Space Station ◽  
Space Environment ◽  
Extreme Conditions ◽  
Whole Genome ◽  
Genome Sequences ◽  
International Space

ABSTRACT Nineteen strains from the order Lactobacillales were isolated from the International Space Station and commercial resupply vehicle, and whole-genome sequences (WGS) were generated. WGS would permit the characterization of these potentially pathogenic bacteria that have been adapting to the extreme conditions of the space environment.

scholarly journals Draft Genome Sequences of Enterobacteriales Strains Isolated from the International Space Station

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Achintya R. Bharadwaj ◽  
Robert Daudu ◽  
Nitin K. Singh ◽  
Jason M. Wood ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
International Space Station ◽  
Pathogenic Bacteria ◽  
Draft Genome ◽  
Space Station ◽  
Space Environment ◽  
Whole Genome ◽  
Genome Sequences ◽  
International Space

ABSTRACT The whole-genome sequences of 26 strains isolated from the International Space Station were generated, and the strains were identified as being members of the order Enterobacteriales. Characterization of these whole-genome sequences might enable the identification of potential pathogenic bacteria that have been adapting to the space environment.

scholarly journals Draft Genome Sequences for Seven Streptococcus parauberis Isolates from Wild Fish in the Chesapeake Bay: TABLE 1 

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Ashley Haines ◽  
Emily Nebergall ◽  
Elvira Besong ◽  
Kimaya Council ◽  
Onaysha Lambert ◽  
...  
Keyword(s):  
Chesapeake Bay ◽  
Draft Genome ◽  
Morone Saxatilis ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Streptococcus Iniae ◽  
Genome Sequences ◽  
Streptococcus Uberis ◽  
Animal Hosts ◽  
Streptococcus Parauberis

Streptococcus parauberis is a pathogen of cattle and fish, closely related Streptococcus uberis and Streptococcus iniae . We report the genomes of seven S. parauberis strains recovered from striped bass ( Morone saxatilis ) in the Chesapeake Bay. The availability of these genomes will allow comparative genomic analysis of Chesapeake Bay S. parauberis strains versus S. parauberis cultured from other animal hosts and geographic regions.

scholarly journals Responses of the Human GutEscherichia coliPopulation to Pathogen and Antibiotic Disturbances

mSystems ◽  
2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Taylor K. S. Richter ◽  
Jane M. Michalski ◽  
Luke Zanetti ◽  
Sharon M. Tennant ◽  
Wilbur H. Chen ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Antibiotic Treatment ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Gastrointestinal Tract ◽  
Content Type ◽  
E Coli ◽  
Pathogen Invasion

ABSTRACTStudies ofEscherichia coliin the human gastrointestinal tract have focused on pathogens, such as diarrhea-causing enterotoxigenicE. coli(ETEC), while overlooking the resident, nonpathogenicE. colicommunity. Relatively few genomes of nonpathogenicE. colistrains are available for comparative genomic analysis, and the ecology of these strains is poorly understood. This study examined the diversity and dynamics of resident human gastrointestinalE. colicommunities in the face of the ecological challenges presented by pathogen (ETEC) challenge, as well as of antibiotic treatment. Whole-genome sequences obtained fromE. coliisolates from before, during, and after ETEC challenge were used in phylogenomic and comparative genomic analyses to examine the diversity of the residentE. colicommunities, as well as the dynamics of the challenge strain, H10407, a well-studied ETEC strain (serotype O78:H11) that produces both heat-labile and heat-stable enterotoxins. ETEC failed to become the dominantE. coliclone in two of the six challenge subjects, each of whom exhibited limited or no clinical presentation of diarrhea. TheE. colicommunities of the remaining four subjects became ETEC dominant during the challenge but reverted to their original, subject-specific populations following antibiotic treatment, suggesting resiliency of the residentE. colipopulation following major ecological disruptions. This resiliency is likely due in part to the abundance of antibiotic-resistant ST131E. colistrains in the resident populations. This report provides valuable insights into the potential interactions of members of the gastrointestinal microbiome and its responses to challenge by an external pathogen and by antibiotic exposure.IMPORTANCEResearch on human-associatedE. colitends to focus on pathogens, such as enterotoxigenicE. coli(ETEC) strains, which are a leading cause of diarrhea in developing countries. However, the severity of disease caused by these pathogens is thought to be influenced by the microbiome. The nonpathogenicE. colicommunity that resides in the human gastrointestinal tract may play a role in pathogen colonization and disease severity and may become a reservoir for virulence and antibiotic resistance genes. Our study used whole-genome sequencing ofE. colibefore, during, and after challenge with an archetype ETEC isolate, H10407, and antibiotic treatment to explore the diversity and resiliency of the residentE. colipopulation in response to the ecological disturbances caused by pathogen invasion and antibiotic treatment.

scholarly journals Draft Genome Sequences of Klebsiella Species Isolated from the International Space Station

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Samuel A. Solomon ◽  
Achintya R. Bharadwaj ◽  
Nitin K. Singh ◽  
Jason M. Wood ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
International Space Station ◽  
Draft Genome ◽  
Space Station ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Bacterial Strains ◽  
Genome Sequences ◽  
Klebsiella Species ◽  
International Space

ABSTRACT Isolated across four locations aboard the International Space Station (ISS), 10 bacterial strains were compared using whole-genome sequencing analysis and were phylogenetically identified as Klebsiella. The whole-genome sequences will aid in comparative genomic studies of ISS Klebsiella strains with Earth counterparts to gain insight into their adaptation to space conditions.

scholarly journals Comparative Genomic Analysis of Members of the GeneraMethanosphaeraandMethanobrevibacterReveals Distinct Clades with Specific Potential Metabolic Functions

Archaea ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Anja Poehlein ◽  
Dominik Schneider ◽  
Melissa Soh ◽  
Rolf Daniel ◽  
Henning Seedorf
Keyword(s):  
Draft Genome ◽  
Genomic Analysis ◽  
Methanogenic Archaea ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Genomic Features ◽  
Metabolic Functions ◽  
Core Set ◽  
Cofactor Biosynthesis ◽  
Genome Analyses

MethanobrevibacterandMethanosphaeraspecies represent some of the most prevalent methanogenic archaea in the gastrointestinal tract of animals and humans and play an important role in this environment. The aim of this study was to identify genomic features that are shared or specific for members of each genus with a special emphasis of the analysis on the assimilation of nitrogen and acetate and the utilization of methanol and ethanol for methanogenesis. Here, draft genome sequences ofMethanobrevibacter thaueristrain DSM 11995T,Methanobrevibacter woeseistrain DSM 11979T, andMethanosphaera cuniculistrain 4103Tare reported and compared to those of 16 otherMethanobrevibacterandMethanosphaeragenomes, including genomes of the 13 currently available types of strains of the two genera. The comparative genome analyses indicate that among other genes, the absence of molybdopterin cofactor biosynthesis is conserved inMethanosphaeraspecies but reveals also that the three species share a core set of more than 300 genes that distinguishes the genusMethanosphaerafrom the genusMethanobrevibacter. Multilocus sequence analysis shows that the genusMethanobrevibactercan be subdivided into clades, potentially new genera, which may display characteristic specific metabolic features. These features include not only the potential ability of nitrogen fixation and acetate assimilation in a clade comprised ofMethanobrevibacterspecies from the termite gut andMethanobrevibacter arboriphilusstrains but also the potential capability to utilize ethanol and methanol in a clade comprisingMethanobrevibacter woliniistrain DSM 11976T,Mbb.sp. AbM4, andMbb. boviskoreanistrain DSM 25824T.

scholarly journals Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi

2021 ◽  
Vol 53 (4) ◽  
Author(s):  
Jean N. Hakizimana ◽  
Jean B. Ntirandekura ◽  
Clara Yona ◽  
Lionel Nyabongo ◽  
Gladson Kamwendo ◽  
...  
Keyword(s):  
Complete Genome ◽  
African Swine Fever Virus ◽  
Gc Content ◽  
Genomic Analysis ◽  
African Swine Fever ◽  
Eastern Africa ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Domestic Pigs

AbstractSeveral African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.

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