scholarly journals The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

2017 ◽  
Vol 199 (8) ◽  
Author(s):  
Michael R. Weigand ◽  
Yanhui Peng ◽  
Vladimir Loparev ◽  
Dhwani Batra ◽  
Katherine E. Bowden ◽  
...  
Keyword(s):  
United States ◽  
Nucleotide Sequence ◽  
Bordetella Pertussis ◽  
Gene Order ◽  
Complete Genome ◽  
Whooping Cough ◽  
The United States ◽  
Content Type ◽  
Nucleotide Sequence Diversity ◽  
Genome Assemblies

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.

scholarly journals Complete Genome Sequence of Bordetella pertussis Strain VA-190 Isolated from a Vaccinated 10-Year-Old Patient with Whooping Cough

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Joshua C. Eby ◽  
Lauren Turner ◽  
Bryan Nguyen ◽  
June Kang ◽  
Carly Neville ◽  
...  
Keyword(s):  
United States ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
Bordetella Pertussis ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whooping Cough ◽  
The United States ◽  
Laboratory Studies ◽  
Long Read

The number of cases of pertussis has increased in the United States despite vaccination. We present the genome of an isolate of Bordetella pertussis from a vaccinated patient from Virginia. The genome was sequenced by long-read methodology and compared to that of a clinical isolate used for laboratory studies, D420.

scholarly journals Complete Genome Sequences of Bordetella pertussis Isolates with Novel Pertactin-Deficient Deletions

2017 ◽  
Vol 5 (37) ◽  
Author(s):  
Michael R. Weigand ◽  
Yanhui Peng ◽  
Pamela K. Cassiday ◽  
Vladimir N. Loparev ◽  
Taccara Johnson ◽  
...  
Keyword(s):  
United States ◽  
Bordetella Pertussis ◽  
Complete Genome ◽  
The United States ◽  
Clinical Isolates ◽  
Respiratory Pathogen ◽  
Genome Sequences ◽  
Vaccine Immunogen ◽  
Content Type ◽  
Acellular Vaccine

ABSTRACT Clinical isolates of the respiratory pathogen Bordetella pertussis in the United States have become predominantly deficient for the acellular vaccine immunogen pertactin through various independent mutations. Here, we report the complete genome sequences for four B. pertussis isolates that harbor novel deletions responsible for pertactin deficiency.

scholarly journals Conserved Patterns of Symmetric Inversion in the Genome Evolution of Bordetella Respiratory Pathogens

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Michael R. Weigand ◽  
Yanhui Peng ◽  
Dhwani Batra ◽  
Mark Burroughs ◽  
Jamie K. Davis ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Bordetella Pertussis ◽  
Gene Order ◽  
Chromosome Structure ◽  
Whooping Cough ◽  
The United States ◽  
Respiratory Pathogens ◽  
Structure Variation ◽  
Content Type ◽  
Is Elements

ABSTRACT Whooping cough (pertussis), primarily caused by Bordetella pertussis, has resurged in the United States, and circulating strains exhibit considerable chromosome structural fluidity in the form of rearrangement and deletion. The genus Bordetella includes additional pathogenic species infecting various animals, some even causing pertussis-like respiratory disease in humans; however, investigation of their genome evolution has been limited. We studied chromosome structure in complete genome sequences from 167 Bordetella species isolates, as well as 469 B. pertussis isolates, to gain a generalized understanding of rearrangement patterns among these related pathogens. Observed changes in gene order primarily resulted from large inversions and were only detected in species with genomes harboring multicopy insertion sequence (IS) elements, most notably B. holmesii and B. parapertussis. While genomes of B. pertussis contain >240 copies of IS481, IS elements appear less numerous in other species and yield less chromosome structural diversity through rearrangement. These data were further used to predict all possible rearrangements between IS element copies present in Bordetella genomes, revealing that only a subset is observed among circulating strains. Therefore, while it appears that rearrangement occurs less frequently in other species than in B. pertussis, these clinically relevant respiratory pathogens likely experience similar mutation of gene order. The resulting chromosome structural fluidity presents both challenges and opportunity for the study of Bordetella respiratory pathogens. IMPORTANCE Bordetella pertussis is the primary agent of whooping cough (pertussis). The Bordetella genus includes additional pathogens of animals and humans, including some that cause pertussis-like respiratory illness. The chromosome of B. pertussis has previously been shown to exhibit considerable structural rearrangement, but insufficient data have prevented comparable investigation in related species. In this study, we analyze chromosome structure variation in several Bordetella species to gain a generalized understanding of rearrangement patterns in this genus. Just as in B. pertussis, we observed inversions in other species that likely result from common mutational processes. We used these data to further predict additional, unobserved inversions, suggesting that specific genome structures may be preferred in each species.

scholarly journals Complete Genome Sequences of Mycobacteriophages OKaNui and DroogsArmy

2020 ◽  
Vol 9 (33) ◽  
Author(s):  
Kayla M. Fast ◽  
Kadaisha G. Johnson ◽  
Kaitlyn N. Mayfield ◽  
Leah A. Stephens ◽  
T. Hunter Reid ◽  
...  
Keyword(s):  
United States ◽  
Mycobacterium Smegmatis ◽  
Complete Genome ◽  
The United States ◽  
Genome Sequences ◽  
Bacterial Host ◽  
Content Type

ABSTRACT Mycobacteriophages OKaNui and DroogsArmy were isolated from soil using the bacterial host Mycobacterium smegmatis mc2155, which belongs to the phylum Actinobacteria. OKaNui was discovered in east Mississippi and DroogsArmy in west Alabama in the United States. The genomes of OKaNui and DroogsArmy were 51,424 bp and 53,254 bp long, respectively.

scholarly journals Complete Genome Sequence of Houston Virus, a Newly Discovered Mosquito-Specific Virus Isolated from Culex quinquefasciatus in Mexico

2018 ◽  
Vol 7 (10) ◽  
Author(s):  
Nohemi Cigarroa-Toledo ◽  
Carlos M. Baak-Baak ◽  
Rosa C. Cetina-Trejo ◽  
Carlos Cordova-Fletes ◽  
Mario A. Martinez-Nuñez ◽  
...  
Keyword(s):  
United States ◽  
North America ◽  
Culex Quinquefasciatus ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Geographic Range ◽  
Southern Mexico ◽  
Content Type ◽  
Specific Virus

We fully sequenced the genome of Houston virus, a recently discovered mosquito-associated virus belonging to the newly established family Mesoniviridae. The isolate was recovered from Culex quinquefasciatus in southern Mexico, which shows that the geographic range of Houston virus is not restricted to the United States in North America.

scholarly journals Complete Genome Sequences of Two Avilamycin-Resistant Enterococcus faecium Strains Isolated from Chicken in the United States

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
S. Zhao ◽  
C. Li ◽  
S. Mukherjee ◽  
C. H. Hsu ◽  
R. Singh ◽  
...  
Keyword(s):  
United States ◽  
Enterococcus Faecium ◽  
Complete Genome ◽  
The United States ◽  
Multidrug Resistant ◽  
Genome Sequences ◽  
Content Type ◽  
Young Chicken

Avilamycin-resistant Enterococcus spp. have never been reported in the United States. Here, we report the complete genome sequences of two avilamycin-resistant (Avir) Enterococcus faecium strains isolated from a retail chicken and a cecal sample from a young chicken. Both isolates are multidrug resistant (MDR) and carry emtA on MDR plasmids.

scholarly journals Complete Genome Sequence of a Carbapenem-Resistant Escherichia coli Isolate with blaNDM-5 from a Dog in the United States

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Gregory H. Tyson ◽  
Cong Li ◽  
Olgica Ceric ◽  
Renate Reimschuessel ◽  
Stephen Cole ◽  
...  
Keyword(s):  
United States ◽  
Escherichia Coli ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Carbapenem Resistance ◽  
The United States ◽  
Multidrug Resistant ◽  
Content Type ◽  
E Coli

The carbapenem resistance gene bla NDM-5 was identified in an Escherichia coli strain isolated from a dog. We report here the complete genome sequence of this E. coli strain; the bla NDM-5 gene was present on a large IncFII multidrug-resistant plasmid. This is the first bla NDM-5-carrying E. coli strain from an animal in the United States.

scholarly journals Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain, Isolated from the Abscess of a Californian Horse

2012 ◽  
Vol 194 (23) ◽  
pp. 6620-6621 ◽  
Author(s):  
Rommel Thiago Jucá Ramos ◽  
Artur Silva ◽  
Adriana Ribeiro Carneiro ◽  
Anne Cybelle Pinto ◽  
Siomar de Castro Soares ◽  
...  
Keyword(s):  
United States ◽  
Genome Sequence ◽  
North American ◽  
Complete Genome ◽  
The United States ◽  
Corynebacterium Pseudotuberculosis ◽  
Economic Losses ◽  
Content Type ◽  
Veterinary Importance

ABSTRACTThe bacteriumCorynebacterium pseudotuberculosisis of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of theCorynebacterium pseudotuberculosisCp316 strain, biovar equi, isolated from the abscess of a North American horse.

scholarly journals Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States

2013 ◽  
Vol 21 (2) ◽  
pp. 119-125 ◽  
Author(s):  
L. C. Pawloski ◽  
A. M. Queenan ◽  
P. K. Cassiday ◽  
A. S. Lynch ◽  
M. J. Harrison ◽  
...  
Keyword(s):  
United States ◽  
Bordetella Pertussis ◽  
Stop Codon ◽  
The United States ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Content Type ◽  
Routine Surveillance ◽  
Nucleotide Insertion ◽  
Positive Isolate

ABSTRACTPertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s.Bordetella pertussisisolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting thatB. pertussisis losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting andprnsequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481in theprngene (prnIS481positive). The firstprnIS481-positive isolate was found in 1994, and the nextprnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in theprngene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found inprn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficientB. pertussisisolates throughout the United States.

scholarly journals Complete Genome Sequences of Four Salmonella enterica subsp. enterica Serovar Senftenberg and Montevideo Isolates Associated with a 2016 Multistate Outbreak in the United States

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Julie Haendiges ◽  
Tyann Blessington ◽  
Jie Zheng ◽  
Gordon Davidson ◽  
Jesse D. Miller ◽  
...  
Keyword(s):  
United States ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
The United States ◽  
Genome Sequences ◽  
Content Type ◽  
Pistachio Nuts

A multistate outbreak of 11 Salmonella infections linked to pistachio nuts occurred in 2016. In this announcement, we report the complete genome sequences of four Salmonella enterica subsp.

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