Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.

To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. n...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Christopher Maslunka, Bianca Gifford, Joseph Tucci, Volker Gürtler, Robert J Seviour
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d1e82bb6b73240f59f53acbd29171004
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:d1e82bb6b73240f59f53acbd29171004
record_format	dspace
spelling	oai:doaj.org-article:d1e82bb6b73240f59f53acbd291710042021-11-25T06:03:55ZInsertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.1932-620310.1371/journal.pone.0105390https://doaj.org/article/d1e82bb6b73240f59f53acbd291710042014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/25141005/?tool=EBIhttps://doaj.org/toc/1932-6203To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2-13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.Christopher MaslunkaBianca GiffordJoseph TucciVolker GürtlerRobert J SeviourPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 8, p e105390 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Christopher Maslunka Bianca Gifford Joseph Tucci Volker Gürtler Robert J Seviour Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
description	To determine whether ITS sequences in the rrn operon are suitable for identifying individual Acinetobacter Acb complex members, we analysed length and sequence differences between multiple ITS copies within the genomes of individual strains. Length differences in ITS reported previously between A. nosocomialis BCRC15417T (615 bp) and other strains (607 bp) can be explained by presence of an insertion (indel 13i/1) in the longer ITS variant. The same Indel 13i/1 was also found in ITS sequences of ten strains of A. calcoaceticus, all 639 bp long, and the 628 bp ITS of Acinetobacter strain BENAB127. Four additional indels (13i/2-13i/5) were detected in Acinetobacter strain c/t13TU 10090 ITS length variants (608, 609, 620, 621 and 630 bp). These ITS variants appear to have resulted from horizontal gene transfer involving other Acinetobacter species or in some cases unrelated bacteria. Although some ITS copies in strain c/t13TU 10090 are of the same length (620 bp) as those in Acinetobacter strains b/n1&3, A. pittii (10 strains), A. calcoaceticus and A. oleivorans (not currently acknowledged as an Acb member), their individual ITS sequences differ. Thus ITS length by itself can not by itself be used to identify Acb complex strains. A shared indel in ITS copies in two separate Acinetobacter species compromises the specificity of ITS targeted probes, as shown with the Aun-3 probe designed to target the ITS in A. pitti. The presence of indel 13i/5 in the ITS of Acinetobacter strain c/t13TU means it too responded positively to this probe. Thus, neither ITS sequencing nor the currently available ITS targeted probes can distinguish reliably between Acb member species.
format	article
author	Christopher Maslunka Bianca Gifford Joseph Tucci Volker Gürtler Robert J Seviour
author_facet	Christopher Maslunka Bianca Gifford Joseph Tucci Volker Gürtler Robert J Seviour
author_sort	Christopher Maslunka
title	Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
title_short	Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
title_full	Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
title_fullStr	Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
title_full_unstemmed	Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.
title_sort	insertions or deletions (indels) in the rrn 16s-23s rrna gene internal transcribed spacer region (its) compromise the typing and identification of strains within the acinetobacter calcoaceticus-baumannii (acb) complex and closely related members.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/d1e82bb6b73240f59f53acbd29171004
work_keys_str_mv	AT christophermaslunka insertionsordeletionsindelsintherrn16s23srrnageneinternaltranscribedspacerregionitscompromisethetypingandidentificationofstrainswithintheacinetobactercalcoaceticusbaumanniiacbcomplexandcloselyrelatedmembers AT biancagifford insertionsordeletionsindelsintherrn16s23srrnageneinternaltranscribedspacerregionitscompromisethetypingandidentificationofstrainswithintheacinetobactercalcoaceticusbaumanniiacbcomplexandcloselyrelatedmembers AT josephtucci insertionsordeletionsindelsintherrn16s23srrnageneinternaltranscribedspacerregionitscompromisethetypingandidentificationofstrainswithintheacinetobactercalcoaceticusbaumanniiacbcomplexandcloselyrelatedmembers AT volkergurtler insertionsordeletionsindelsintherrn16s23srrnageneinternaltranscribedspacerregionitscompromisethetypingandidentificationofstrainswithintheacinetobactercalcoaceticusbaumanniiacbcomplexandcloselyrelatedmembers AT robertjseviour insertionsordeletionsindelsintherrn16s23srrnageneinternaltranscribedspacerregionitscompromisethetypingandidentificationofstrainswithintheacinetobactercalcoaceticusbaumanniiacbcomplexandcloselyrelatedmembers
_version_	1718414249181577216

Insertions or deletions (Indels) in the rrn 16S-23S rRNA gene internal transcribed spacer region (ITS) compromise the typing and identification of strains within the Acinetobacter calcoaceticus-baumannii (Acb) complex and closely related members.

Ejemplares similares