Comparison of Outer Membrane Protein Genesompandpmpin the Whole Genome Sequences ofChlamydia pneumoniaeIsolates from Japan and the United States

ABSTRACT Anaplasma phagocytophilum, a recently reclassified bacteria in the order Rickettsiales, infects many different animal species and causes an emerging tick-borne disease of humans. The genome contains a large number of related genes and gene fragments encoding partial or apparently full-length outer membrane protein MSP2 (P44). Previous data using strains isolated from humans in the United States suggest that antigenic diversity results from RecF-mediated conversion of a single MSP2 (P44) expression site by partially homologous donor sequences. However, whether similar mechanisms operate in naturally infected animal species and the extent of global diversity in MSP2 (P44) are unknown. We analyzed the structure and diversity of the MSP2 (P44) expression site in strains derived from the United States and Europe and from infections of different animal species, including wildlife reservoirs. The results show that a syntenic expression site is present in all strains of A. phagocytophilum investigated. This genomic locus contained diverse MSP2 (P44) variants in all infected animals sampled, and variants also differed at different time points during infection. Although similar variants were found among different populations of U.S. origin, there was little sequence identity between U.S. strain variants (including genomic copies from a completely sequenced U.S. strain) and expression site variants infecting sheep and dogs in Norway and Sweden. Finally, the possibility that combinatorial mechanisms can generate additional diversity beyond the basic donor sequence repertoire is supported by the observation of shared sequence blocks throughout the MSP2 (P44) hypervariable region in reservoir hosts. These data suggest similar genetic mechanisms for A. phagocytophilum variation in all hosts but worldwide diversity of the MSP2 (P44) outer membrane protein.

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Complete Genome Sequences of Three Streptococcus agalactiae Serotype Ia Isolates Obtained from Disease Outbreaks in Nile Tilapia (Oreochromis niloticus)

Genome Announcements ◽

10.1128/genomea.01432-17 ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Anita Jaglarz ◽

Artur Gurgul ◽

William J. Leigh ◽

Janina Z. Costa ◽

Kim D. Thompson

Keyword(s):

United States ◽

Streptococcus Agalactiae ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Disease Outbreaks ◽

The United States ◽

The Other ◽

Whole Genome ◽

Genome Sequences ◽

Nile Tilapia Oreochromis Niloticus

ABSTRACT This paper describes the whole-genome sequences for three Streptococcus agalactiae serotype Ia isolates. The isolates were recovered from the brains of clinically sick tilapia, Oreochromis niloticus, that were suffering from streptococcosis. One isolate was from tilapia in the United States and the other two from fish in China.

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Estimation of Full-Length TprK Diversity in Treponema pallidum subsp. pallidum

mBio ◽

10.1128/mbio.02726-20 ◽

2020 ◽

Vol 11 (5) ◽

Author(s):

Amin Addetia ◽

Michelle J. Lin ◽

Quynh Phung ◽

Hong Xie ◽

Meei-Li Huang ◽

...

Keyword(s):

Immune System ◽

Membrane Protein ◽

Outer Membrane ◽

Deep Sequencing ◽

Outer Membrane Protein ◽

Treponema Pallidum ◽

The United States ◽

Full Length ◽

Variable Regions ◽

Content Type

ABSTRACT Immune evasion and disease progression of Treponema pallidum subsp. pallidum are associated with sequence diversity in the hypervariable outer membrane protein TprK. Previous attempts to study variation within TprK have sequenced at depths insufficient to fully appreciate the hypervariable nature of the protein, failed to establish linkage between the protein’s seven variable regions, or were conducted on isolates passed through rabbits. As a consequence, a complete profile of tprK during infection in the human host is still lacking. Furthermore, prior studies examining how T. pallidum subsp. pallidum uses its repertoire of genomic donor sites to generate diversity within the variable regions of the tprK have yielded a partial understanding of this process due to the limited number of tprK alleles examined. In this study, we used short- and long-read deep sequencing to directly characterize full-length tprK alleles from T. pallidum subsp. pallidum collected from early lesions of patients attending two sexually transmitted infection clinics in Italy. We demonstrate that strains collected from cases of secondary syphilis contain significantly more unique variable region sequences and full-length TprK sequences than those from cases of primary syphilis. Our data, combined with recent data available on Chinese T. pallidum subsp. pallidum specimens, show the near-complete absence of overlap in TprK sequences among the 41 specimens profiled to date. We further estimate that the potential antigenic variability carried by TprK rivals that of current estimates of the human adaptive immune system. These data underscore the immunoevasive ability of TprK that allows T. pallidum subsp. pallidum to establish lifelong infection. IMPORTANCE Syphilis continues to be a significant public health issue in both low- and high-income countries, including the United States where the rate of syphilis infection has increased over the past 5 years. Treponema pallidum subsp. pallidum, the causative agent of syphilis, carries the outer membrane protein TprK that undergoes segmental gene conversion to constantly create new sequences. We performed full-length deep sequencing of TprK to examine TprK diversity in clinical T. pallidum subsp. pallidum strains. We then combined our results with data from all samples for which TprK deep sequencing results were available. We found almost no overlap in TprK sequences between different patients. Moreover, our data allowed us to estimate the total number of TprK variants that T. pallidum subsp. pallidum can potentially generate. Our results support how the T. pallidum subsp. pallidum TprK antigenic variation system is an equal adversary of the human immune system leading to pathogen persistence in the host.

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Finished Whole-Genome Sequences of Two Clostridium botulinum Type A(B) Isolates

Genome Announcements ◽

10.1128/genomea.00381-17 ◽

2017 ◽

Vol 5 (21) ◽

Cited By ~ 1

Author(s):

Jessica L. Halpin ◽

Karen Hill ◽

Shannon L. Johnson ◽

David Carlton Bruce ◽

T. Brian Shirey ◽

...

Keyword(s):

United States ◽

Clostridium Botulinum ◽

Type A ◽

The United States ◽

Whole Genome ◽

Genome Sequences ◽

Content Type ◽

Botulinum Type ◽

Clinically Significant

ABSTRACT Clostridium botulinum secretes a potent neurotoxin that causes devastating effects when ingested, including paralysis and death if not treated. In the United States, some clinically significant strains produce toxin type A while also harboring a silent B gene. These are the first two closed genome sequences published for this subset.

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Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted Chia and Flax Seed Powders

Genome Announcements ◽

10.1128/genomea.00963-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 2

Author(s):

Jennifer Ronholm ◽

Nicholas Petronella ◽

Sandeep Tamber

Keyword(s):

United States ◽

Salmonella Enterica ◽

Draft Genome ◽

The United States ◽

Whole Genome ◽

Flax Seed ◽

Genome Sequences ◽

Chia Seed ◽

First Time

A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the first time, sprouted chia seed powder as the vehicle of transmission. Here, we report the draft whole genome sequences of two Salmonella enterica strains isolated from sprouted powders related to the aforementioned outbreak.

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Genome Sequences of Mycobacterium Strains Recovered from Captive Elephants with Tuberculosis

Microbiology Resource Announcements ◽

10.1128/mra.00671-21 ◽

2021 ◽

Vol 10 (36) ◽

Author(s):

Evan P. Brenner ◽

Syeda A. Hadi ◽

Beth Harris ◽

Suelee Robbe-Austerman ◽

Srinand Sreevatsan

Keyword(s):

United States ◽

Mycobacterium Tuberculosis ◽

Endangered Species ◽

Human Health ◽

The United States ◽

Whole Genome ◽

Genome Sequences ◽

Asian Elephants ◽

Content Type

Members of the Mycobacterium tuberculosis complex cause tuberculosis, infamous for enormous impacts on human health. As zoonoses, they also threaten endangered species like African/Asian elephants. We report the whole-genome sequences of Mycobacterium tuberculosis biovars tuberculosis and bovis from two zoo elephants in the United States.

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Complete Genome Sequences of Three Fish-Associated Streptococcus agalactiae Isolates

Genome Announcements ◽

10.1128/genomea.00025-18 ◽

2018 ◽

Vol 6 (6) ◽

pp. e00025-18 ◽

Cited By ~ 3

Author(s):

Anita Jaglarz ◽

Artur Gurgul ◽

William J. Leigh ◽

Janina Z. Costa ◽

Kim D. Thompson

Keyword(s):

United States ◽

Costa Rica ◽

Streptococcus Agalactiae ◽

Oreochromis Niloticus ◽

Complete Genome ◽

The United States ◽

Whole Genome ◽

Genome Sequences ◽

Group B

ABSTRACTThe whole-genome sequences are described here for three group B Streptococcus (GBS) (S. agalactiae) serotype Ib isolates obtained from tilapia (Oreochromis niloticus) farmed at sites in Honduras, Costa Rica, and the United States. The bacteria were isolated from the brains of fish displaying signs of streptococcosis.

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Sequence typing reveals extensive strain diversity of the Lyme borreliosis agents Borrelia burgdorferi in North America and Borrelia afzelii in Europe

Microbiology ◽

10.1099/mic.0.26944-0 ◽

2004 ◽

Vol 150 (6) ◽

pp. 1741-1755 ◽

Cited By ~ 217

Author(s):

Jonas Bunikis ◽

Ulf Garpmo ◽

Jean Tsao ◽

Johan Berglund ◽

Durland Fish ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Membrane Protein ◽

Borrelia Burgdorferi ◽

Outer Membrane ◽

Lyme Borreliosis ◽

Outer Membrane Protein ◽

Eastern United States ◽

The North ◽

North Eastern

The genetic polymorphism of Borrelia burgdorferi and Borrelia afzelii, two species that cause Lyme borreliosis, was estimated by sequence typing of four loci: the rrs–rrlA intergenic spacer (IGS) and the outer-membrane-protein gene p66 on the chromosome, and the outer-membrane-protein genes ospA and ospC on plasmids. The major sources of DNA for PCR amplification and sequencing were samples of the B. burgdorferi tick vector Ixodes scapularis, collected at a field site in an endemic region of the north-eastern United States, and the B. afzelii vector Ixodes ricinus, collected at a similar site in southern Sweden. The sequences were compared with those of reference strains and skin biopsy isolates, as well as database sequences. For B. burgdorferi, 10–13 alleles for each of the 4 loci, and a total of 9 distinct clonal lineages with linkage of all 4 loci, were found. For B. afzelii, 2 loci, ospC and IGS, were examined, and 11 IGS genotypes, 12 ospC alleles, and a total of 9 linkage groups were identified. The genetic variants of B. burgdorferi and B. afzelii among samples from the field sites accounted for the greater part of the genetic diversity previously reported from larger areas of the north-eastern United States and central and northern Europe. Although ospC alleles of both species had higher nucleotide diversity than other loci, the ospC locus showed evidence of intragenic recombination and was unsuitable for phylogenetic inference. In contrast, there was no detectable recombination at the IGS locus of B. burgdorferi. Moreover, beyond the signature nucleotides that specified 10 IGS genotypes, there were additional nucleotide polymorphisms that defined a total of 24 subtypes. Maximum-likelihood and parsimony cladograms of B. burgdorferi aligned IGS sequences revealed the subtype sequences to be terminal branches of clades, and the existence of at least three monophyletic lineages within B. burgdorferi. It is concluded that B. burgdorferi and B. afzelii have greater genetic diversity than had previously been estimated, and that the IGS locus alone is sufficient for strain typing and phylogenetic studies.

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High-Quality Whole-Genome Sequences for 21 Enterotoxigenic Escherichia coli Strains Generated with PacBio Sequencing

Genome Announcements ◽

10.1128/genomea.01311-17 ◽

2018 ◽

Vol 6 (2) ◽

Cited By ~ 4

Author(s):

Peyton Smith ◽

Rebecca L. Lindsey ◽

Lori A. Rowe ◽

Dhwani Batra ◽

Devon Stripling ◽

...

Keyword(s):

United States ◽

Escherichia Coli ◽

The United States ◽

Enterotoxigenic Escherichia Coli ◽

Whole Genome ◽

Cruise Ship ◽

Genome Sequences ◽

Pacbio Sequencing ◽

High Quality ◽

Surveillance Studies

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) is an important diarrheagenic pathogen. We report here the high-quality whole-genome sequences of 21 ETEC strains isolated from patients in the United States, international diarrheal surveillance studies, and cruise ship outbreaks.

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Expression and Refolding of Truncated Recombinant Major Outer Membrane Protein Antigen (r56) of Orientia tsutsugamushi and Its Use in Enzyme-Linked Immunosorbent Assays

Clinical and Diagnostic Laboratory Immunology ◽

10.1128/cdli.5.4.519-526.1998 ◽

1998 ◽

Vol 5 (4) ◽

pp. 519-526 ◽

Cited By ~ 33

Author(s):

W.-M. Ching ◽

H. Wang ◽

C. Eamsila ◽

D. J. Kelly ◽

G. A. Dasch

Keyword(s):

Membrane Protein ◽

Outer Membrane ◽

Outer Membrane Protein ◽

Scrub Typhus ◽

The United States ◽

Major Outer Membrane Protein ◽

Orientia Tsutsugamushi ◽

Whole Cell ◽

Whole Cell Lysate ◽

Cell Lysate

ABSTRACT The variable 56-kDa major outer membrane protein of Orientia tsutsugamushi is the immunodominant antigen in human scrub typhus infections. The gene encoding this protein from Karp strain was cloned into the expression vector pET11a. The recombinant protein (r56) was expressed as a truncated nonfusion protein (amino acids 80 to 456 of the open reading frame) which formed an inclusion body when expressed in Escherichia coli BL21. Refolded r56 was purified and compared to purified whole-cell lysate of the Karp strain of O. tsutsugamushi by immunoglobulin G (IgG) enzyme-linked immunosorbent assay (ELISA) for reactivity with rabbit sera prepared against eight antigenic prototypes of O. tsutsugamushi as well as several other species of Rickettsiales and nonrickettsial antigens. Refolded r56 exhibited broad reactivity with the rabbit antisera against the Orientia prototypes, and the ELISA reactions with the r56 and Karp whole-cell lysate antigens correlated well (r = 0.81, n = 22, sensitivity compared to that of standard ELISA of 91%). Refolded r56 did not react with most antisera against other rickettsial species or control antigens (specificity = 92%, n = 13) using a positive cutoff value determined with eight uninfected rabbit sera. Refolded r56 was evaluated further by ELISA, using 128 sera obtained from patients with suspected scrub typhus from Korat, Thailand, and 74 serum specimens from healthy Thai soldiers. By using the indirect immunoperoxidase assay as the reference assay, the recombinant antigen exhibited a sensitivity and specificity of 93% or greater for detection of both IgG and IgM in the ELISA at 1:400 serum dilution. These results strongly suggest that purified r56 is a suitable candidate for replacing the density gradient-purified, rickettsia-derived, whole-cell antigen currently used in the commercial dipstick assay available in the United States.

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