scholarly journals Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements

2020 ◽  
Vol 12 (2) ◽  
pp. 3850-3856
Author(s):  
William G Miller ◽  
Emma Yee ◽  
James L Bono
Keyword(s):  
Genome Sequencing ◽  
Ribosomal Rna ◽  
Mobile Elements ◽  
Genomic Rearrangements ◽  
Clinical Samples ◽  
Insertion Sequences ◽  
Is Element ◽  
Is Elements ◽  
Antimicrobial Resistance Genes ◽  
Type Strains

Abstract Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.

scholarly journals Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jacqueline King ◽  
Anne Pohlmann ◽  
Kamila Dziadek ◽  
Martin Beer ◽  
Kerstin Wernike
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Bovine Viral Diarrhea ◽  
Sequence Information ◽  
Whole Genome ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

scholarly journals Defining the Rhizobium leguminosarum Species Complex

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 111 ◽  
Author(s):  
J. Peter W. Young ◽  
Sara Moeskjær ◽  
Alexey Afonin ◽  
Praveen Rahi ◽  
Marta Maluk ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Species Complex ◽  
Rhizobium Leguminosarum ◽  
Housekeeping Genes ◽  
Single Species ◽  
Natural Unit ◽  
Genome Sequences ◽  
Distinct Entity ◽  
Type Strains ◽  
Core Genes

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

scholarly journals Molecular detection and phylogenetic relationship of wild-type strains of canine distemper virus in symptomatic dogs from Uberlândia, Minas Gerais

2015 ◽  
Vol 67 (6) ◽  
pp. 1510-1518
Author(s):  
S.A. Headley ◽  
T.R. Santos ◽  
L. Bodnar ◽  
J.P.E. Saut ◽  
A.P. Silva ◽  
...  
Keyword(s):  
Canine Distemper Virus ◽  
Phylogenetic Analyses ◽  
Clinical Manifestations ◽  
N Gene ◽  
Clinical Samples ◽  
Canine Distemper ◽  
Wild Type ◽  
Age Related ◽  
Relationship Of ◽  
Type Strains

This study investigated the occurrence of canine distemper virus (CDV) by evaluating the presence of viral RNA within urine samples of dogs from Uberlândia, MG, with clinical manifestations suggestive of infection by CDV by targeting the CDV N gene. Of the clinical samples collected ( n =33), CDV viruria was detected in 45.5%. Five dogs died spontaneously; all had characteristic CDV-associated histopathological alterations and demonstrated CDV viruria. Statistical analyses revealed that the age, gender, breed, or the organ system of the dog affected had no influence on the occurrence of canine distemper. Myoclonus and motor incoordination were the most significant neurological manifestations observed. A direct association was observed between keratoconjunctivitis and dogs with CDV viruria. These findings suggest that CDV viruria in symptomatic dogs might not be age related, and that symptomatic dogs can demonstrate clinical manifestations attributed to CDV without viruria identified by RT-PCR. Additionally, the results of the sequence identities analysed have suggested that all Brazilian wild-type strains of CDV currently identified are closely related and probably originated from the same lineage of CDV. Nevertheless, phylogenetic analyses suggest that there are different clusters of wild-type strains of CDV circulating within urban canine populations in Brazil.

scholarly journals Putative Integrative Mobile Elements That Exploit the Xer Recombination Machinery Carrying blaIMI-Type Carbapenemase Genes in Enterobacter cloacae Complex Isolates in Singapore

2017 ◽  
Vol 62 (1) ◽  
Author(s):  
Tse H. Koh ◽  
Nurdyana Binte Abdul Rahman ◽  
Jeanette W. P. Teo ◽  
My-Van La ◽  
Balamurugan Periaswamy ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multilocus Sequence Typing ◽  
Enterobacter Cloacae ◽  
Mobile Elements ◽  
Whole Genome ◽  
Content Type ◽  
Flanking Regions ◽  
Enterobacter Cloacae Complex

ABSTRACT Whole-genome sequencing was performed on 16 isolates of the carbapenemase-producing Enterobacter cloacae complex to determine the flanking regions of bla IMI-type genes. Phylogenetic analysis of multilocus sequence typing (MLST) targets separated the isolates into 4 clusters. The bla IMI-type genes were all found on Xer-dependent integrative mobile elements (IMEX). The IMEX elements of 5 isolates were similar to those described in Canada, while the remainder were novel. Five isolates had IMEX elements lacking a resolvase and recombinase.

scholarly journals Detection of Nocardia by 16S Ribosomal RNA Gene PCR and Metagenomic Next-Generation Sequencing (mNGS)

2022 ◽  
Vol 11 ◽  
Author(s):  
Juanjuan Ding ◽  
Bing Ma ◽  
Xupeng Wei ◽  
Ying Li
Keyword(s):  
16S Rrna ◽  
Ribosomal Rna ◽  
Human Herpesvirus ◽  
Antibiotic Sensitivity ◽  
Common Species ◽  
16S Ribosomal Rna ◽  
Clinical Samples ◽  
Klebsiella Pneumonia ◽  
Antimicrobial Drugs ◽  
Detection And Identification

In this study, the aim was to investigate the discriminatory power of molecular diagnostics based on mNGS and traditional 16S ribosomal RNA PCR among Nocardia species. A total of fourteen clinical isolates from patients with positive Nocardia cultures and clinical evidence were included between January 2017 and June 2020 in HeNan Provincial People’s Hospital. DNA extraction and 16S rRNA PCR were performed on positive cultures, and pathogens were detected by mNGS in these same samples directly. Among the 14 Nocardia isolates, four species were identified, and N. cyriacigeorgica (8 cases) is the most common species. Twelve of the 14 Nocardia spp. isolates were identified by the two methods, while two strains of N. cyriacigeorgica were not identified by mNGS. All tested isolates showed susceptibility to trimethoprim-sulfamethoxazole (SXT), amikacin and linezolid. Apart from Nocardia species, other pathogens such as Acinetobacter baumannii, Klebsiella pneumonia, Aspergillus, Enterococcus faecalis, Human herpesvirus, etc., were detected from the same clinical samples by mNGS. However, these different pathogens were considered as colonization or contamination. We found that it is essential to accurately identify species for determining antibiotic sensitivity and, consequently, choosing antibiotic treatment. 16S rRNA PCR was useful for identification of nocardial infection among species, while this technique needs the clinicians to make the pre-considerations of nocardiosis. However, mNGS may be a putative tool for rapid and accurate detection and identification of Nocardia, beneficial for applications of antimicrobial drugs and timely adjustments of medication.

scholarly journals A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus

2021 ◽  
Vol 12 ◽  
Author(s):  
Kwan Woo Kim ◽  
Sungmi Choi ◽  
Su-Kyoung Shin ◽  
Imchang Lee ◽  
Keun Bon Ku ◽  
...  
Keyword(s):  
Public Health ◽  
Middle East ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Middle East Respiratory Syndrome ◽  
Universal Primers ◽  
Clinical Samples ◽  
Primary Concern ◽  
Whole Genome ◽  
Serum Samples

Recent coronavirus (CoV) outbreaks, including that of Middle East respiratory syndrome (MERS), have presented a threat to public health worldwide. A primary concern in these outbreaks is the extent of mutations in the CoV, and the content of viral variation that can be determined only by whole genome sequencing (WGS). We aimed to develop a time efficient WGS protocol, using universal primers spanning the entire MERS-CoV genome. MERS and synthetic Neoromicia capensis bat CoV genomes were successfully amplified using our developed PCR primer set and sequenced with MinION. All experimental and analytical processes took 6 h to complete and were also applied to synthetic animal serum samples, wherein the MERS-CoV genome sequence was completely recovered. Results showed that the complete genome of MERS-CoV and related variants could be directly obtained from clinical samples within half a day. Consequently, this method will contribute to rapid MERS diagnosis, particularly in future CoV epidemics.

scholarly journals Detection of colistin resistance mcr-1 gene in Salmonella enterica serovar Rissen isolated from mussels, Spain, 2012­ to 2016

2019 ◽  
Vol 24 (16) ◽  
Author(s):  
Antonio Lozano-Leon ◽  
Carlos Garcia-Omil ◽  
Jacobo Dalama ◽  
Rafael Rodriguez-Souto ◽  
Jaime Martinez-Urtaza ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Sequence Type ◽  
Monitoring Programme ◽  
Colistin Resistance ◽  
North West ◽  
Antimicrobial Resistance Genes

Nineteen Salmonella strains were isolated from 5,907 randomly selected mussel samples during a monitoring programme for the presence of Salmonella in shellfish in Galicia, north-west Spain (2012–16). Serovars, sequence type and antimicrobial resistance genes were determined through genome sequencing. Presence of the mcr-1 gene in one strain belonging to serovar Rissen and ST-469 was identified. The mcr-1 gene had not been isolated previously in environmental Salmonella isolated from mussels in Spain.

scholarly journals Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Steven Van Borm ◽  
Toon Rosseel ◽  
Andy Haegeman ◽  
Mpolokang Elliot Fana ◽  
Latoa Seoke ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Clinical Samples ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Genome Sequences ◽  
Foot And Mouth

The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

scholarly journals Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Kevin Cole ◽  
Dona Foster ◽  
Julie E. Russell ◽  
Tanya Golubchik ◽  
Martin Llewelyn ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Accurate Identification ◽  
Access To Data ◽  
Type Strains

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.

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