"species complex" in the genomic era

Topics with information and discussion about published studies related to Lyme disease and other tick-borne diseases.
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panda
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"species complex" in the genomic era

Post by panda » Mon 3 Dec 2012 2:24

Infection, Genetics and Evolution 13 (2013) 67–75
http://dx.doi.org/10.1016/j.meegid.2012.08.011. [Epub ahead of print]
Highlights on molecular identification of closely related species.
Almeida LA, Araujo R.
IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal; ICBAS, Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira n.° 228, 4050-313 Porto, Portugal. Electronic address: almeida.ligia.mca@gmail.com.
Abstract
The term "complex" emerged in the literature at the beginning of the genomic era associated to taxonomy and grouping organisms that belong to different species but exhibited similar patterns according to their morphological, physiological and/or other phenotypic features. DNA-DNA hybridization values ⩾70% and high identity on 16S rRNA gene sequences were recommended for species delineation. Electrophoretic methods showed in some cases to be useful for species identification and population structure but the reproducibility was questionable. Later, the implementation of polyphasic approaches involving phenotypic and molecular methods brought new insights into the analysis of population structure and phylogeny of several "species complexes", allowing the identification of new closely related species. Likewise, the introduction of multilocus sequence typing and sequencing analysis of several genes offered an evolutionary perspective to the term "species complex". Several centres worldwide have recently released increasing genetic information on distinct microbial species. A brief review will be presented to highlight the definition of "species complex" for selected microorganisms, mainly the prokaryotic Acinetobacter calcoaceticus -Acinetobacter baumannii, Borrelia burgdorferi sensu lato, Burkholderia cepacia, Mycobacterium tuberculosis and Nocardia asteroides complexes, and the eukaryotic Aspergillus fumigatus, Leishmania donovani and Saccharomyces sensu stricto complexes. The members of these complexes may show distinct epidemiology, pathogenicity and susceptibility, turning critical their correct identification. Dynamics of prokaryotic and eukaryotic genomes can be very distinct and the term "species complex" should be carefully extended.
http://www.ncbi.nlm.nih.gov/pubmed/22982158 [abstract]

http://www.sciencedirect.com/science/ar ... 4812002808 [abstract]

p. 69:
2.3. Borrelia burgdorferi sensu lato complex
Borrelia burgdorferi sensu stricto (B. burgdorferi s. s.) is a gram-negative, spiral-shaped or helical bacteria, belonging to the family of spirochaetaceae (Kelly, 1984). B. burgdorferi s. s. belongs to a group of spirochaetes also known as Lyme disease spirochaetes, which are kept in nature by numerous vertebrate hosts and are transmitted by different ticks from the Ixodes persulcatus species complex (Margos et al., 2010). B. burgdorferi s. s., was first retrieved from Ixodes dammini ticks by Burgdorfer et al. (1982) and later recovered from skin, blood and cerebrospinal fluid of patients suffering from Lyme disease (Steere et al., 1983) and named B. burgdorferi sp. nov. by Johnson et al. (1984). Currently, the B. burgdorferi s. l. complex comprises 18 species (B. afzelii, B. americana, B. andersonii, B. bavariensis, B. bissettii, B. burgdorferi s. s., B. californiensis, B. carolinensis, B. garinii, B. japonica, B. kurtenbachii, B. lusitaniae, B. sinica, B. spielmanii, B. tanukii, B. turdae, B. valaisiana, B. yangtze) and several of them, namely B. afzelii, B. burgdorferi s. s., B. garinii, and B. spielmanii, have been associated with human Lyme disease (Kurtenbach et al., 2006; Margos et al., 2010).
The B. burgdorferi s.l. spirochaetes have been shown to evolve clonally (Dykhuizen et al., 1993). Yet, they have also been described as a heterogeneous group of bacteria with frequent occurrence of lateral transfer events (Fraser et al., 2007; Marconi et al., 1996). This heterogeneity has been demonstrated by different approaches including serotyping, MLEE, electrophoretic and sequencing methods (Boerlin et al., 1992; Wilske et al., 1995, 1993b). These methodologies targeted, respectively, the expression of proteins encoded by plasmid genes (i.e. the outer surface proteins: ospA, ospB, ospC), genomic markers (clpA, clpX, nifS, pepX, pyrG, recA, rplB, uvrA, groEL, hbborflaB) or the ribosomal regions of the bacterial genome for instance, 16S rRNA, 23S rRNA and 16S-to-23S rRNA interspersed region (ITS) (Brisson and Dykhuizen, 2004; Liveris et al., 1995; Richter et al., 2006; Rudenko et al., 2009). Serotyping was the first widely used method to characterize B. burgdorferi s. l. complex strains based on the heterogeneity of the outer surface proteins (OspA and OspC) (Wilske et al., 1993a,b). However, false positive results due to lack or altered proteins following culture were observed (Wang et al., 1999). DDH and sequence analysis of the 16S rRNA locus showed limited ability to discriminate within the B. burgdorferi s. l. complex (Gevers et al., 2005; Stackebrandt and Jonas, 2006). Thus, multilocus approaches, namely MLST scheme (Margos et al., 2011), have been shown to improve the accuracy towards identification of B. burgdorferi s. l. complex species. MLSA was proposed by Richter et al. (2006) to replace DDH as an excellent alternative for B. burgdorferi s. l. species delineation. This proposal was based on the analysis of seven genes in a large number of B. burgdorferi s. l. strains. MLSA successfully enabled the identification of six new species within B. burgdorferi s. l. complex: B. spielmanii sp. nov., B. californiensis sp. nov., B. americana sp. nov., B. carolinensis sp., nov., B. bavariensis sp. nov., Borrelia kurtenbachii sp. nov. (Margos et al., 2010).
Remarkably, Crowder et al. (2010) have reported the successful identification of various species within the B. burgdorferi s. l. by PCR/ESI-MS. In this assay the authors targeted seven Borrelia genes, six genes from the chromosomal region (gyrB, rpoC, rplB, leuS, flaB, hbb) and one gene from the hypervariable region (ospC) to identify simultaneous infection by different species of B. burgdorferi s. l. in the same host (Crowder et al., 2010). This methodology still needs to be tested in multiple laboratories.
Best wishes,
Panda

Camp Other
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Re: "species complex" in the genomic era

Post by Camp Other » Mon 3 Dec 2012 2:45

Thanks, Panda.

Just a few thoughts about this, briefly, until I have more:

I thought that more than burgdorferi, garinii, afzelii, and spielmanii caused human Lyme disease?

The recent Nadelman et al reinfection study used MLST in addition to OspC RST genotyping. I found it interesting, and one of the questions that has come to mind has been just how much lateral gene transfer occurs between Borrelia. Steven Norris has written about promiscuous recombination, but suggested lateral or horizontal gene transfer didn't occur that often. Will have to review Marconi and Fraser papers.

A while back, I ran different strains of Bb sl Osp A through BLAST and found out how much they alone could differ. It was a fun exercise. I didn't run other proteins or markers through it, though.

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inmacdonald
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Re: "species complex" in the genomic era

Post by inmacdonald » Mon 3 Dec 2012 16:04

Dear Panda,

thanks for you exceptional and thought provoking contributions to this forum.
the promiscuous" borrelia genome and the Genome in Flux of borreliae
are now more frequently discussed , and these discussions are long overdue.

With a microbe with a manifest unstable genome, the entire concept of a Vaccine
is and always has been flawed.

OspC is among the least stable components of Genome borreliae.
Rates of nucleotide switching of the OspC ORF of borrelia
of up to 25% have been demonstrated by Qui . Dr Alan Barbour has
defined 5 different Lateral Gene Transfer mechanisms for the OspC
ORF of OspC for borrelia burgdorferi ss.

In addition to conjugation, the physical transfer of genomic units from and between borrelia genotypes
is also accomplished by the microvesicles [liposome] which are continuously shed by borrelia
throughout their lifetimes. Even te much maligned and ofter disbeleied Borrelia Cystic forms
have been demonstrated Beerman to shed liposomes into the space where they reside.

Liposomes are sub microscopic, visible only by Electron microscopy, and are
packets of DNA surrounded by an external layer of outer surface membrane of borrelia
- this release by "budding" which does not involve cell division or the death of the Shedding
parent organism. Liposome release is a true biologic Multiplier of infection.

best to you, Panda,
alan

Pandora
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Re: "species complex" in the genomic era

Post by Pandora » Wed 12 Dec 2012 18:21

You will find the new pics of HeLa cells very interesting in those cases.
https://www.facebook.com/LIFEMolecularProbes

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