Estimation of ribosomal RNA operon (rrn) copy number in Acinetobacter isolates and potential of patterns of rrn operon-containing fragments for typing strains of members of this genus

Maslunka, Christopher; Carr, E.; Gürtler, Volker; Kämpfer, Peter; Seviour, Robert J.

doi:10.1016/j.syapm.2005.07.015

Cited by 9 publications

(15 citation statements)

References 52 publications

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“…Like in the case of tRNAs, the missing rRNA cluster may have been lost during one of the numerous recombination events probably mediated by Insertion Sequences (ISs; see below). As reported in the literature, the 16S–23S Intergenic Spacer Region (16S–23S ISR) of A. baylyi strain ADP1 rRNA clusters is of variable length and probably resulted from recombination between rRNA operons [12]. This does not seem to be a feature shared by species belonging to the Acinetobacter genus since rRNA clusters 16S–23S ISRs in both A. baumannii strains are of constant length (663 bp).…”

Section: Resultsmentioning

confidence: 74%

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

et al. 2008

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Acinetobacter baumannii is the source of numerous nosocomial infections in humans and therefore deserves close attention as multidrug or even pandrug resistant strains are increasingly being identified worldwide. Here we report the comparison of two newly sequenced genomes of A. baumannii. The human isolate A. baumannii AYE is multidrug resistant whereas strain SDF, which was isolated from body lice, is antibiotic susceptible. As reference for comparison in this analysis, the genome of the soil-living bacterium A. baylyi strain ADP1 was used. The most interesting dissimilarities we observed were that i) whereas strain AYE and A. baylyi genomes harbored very few Insertion Sequence elements which could promote expression of downstream genes, strain SDF sequence contains several hundred of them that have played a crucial role in its genome reduction (gene disruptions and simple DNA loss); ii) strain SDF has low catabolic capacities compared to strain AYE. Interestingly, the latter has even higher catabolic capacities than A. baylyi which has already been reported as a very nutritionally versatile organism. This metabolic performance could explain the persistence of A. baumannii nosocomial strains in environments where nutrients are scarce; iii) several processes known to play a key role during host infection (biofilm formation, iron uptake, quorum sensing, virulence factors) were either different or absent, the best example of which is iron uptake. Indeed, strain AYE and A. baylyi use siderophore-based systems to scavenge iron from the environment whereas strain SDF uses an alternate system similar to the Haem Acquisition System (HAS). Taken together, all these observations suggest that the genome contents of the 3 Acinetobacters compared are partly shaped by life in distinct ecological niches: human (and more largely hospital environment), louse, soil.

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Section: Resultsmentioning

confidence: 74%

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

et al. 2008

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“…These were A. calcoaceticus strains ATCC23055 T , 97366, 97420, 97424; A. baumannii strains ATCC19606 T , 97429, 97434, 16842; A. pittii ATCC19004 T ; ‘close to 13TU’ strains 5804 and 10090 (hereafter referred to as c/t13TU 5804 and c/t13TU 10090); ‘between1&3’ strains 10095 and 10169 (hereafter referred to as b/n1&3 10095 and b/n1&3 10169); Acinetobacter BENAB127. Thirteen of these Acb strains were speciated by DNA-DNA hybridization [19], [20], [5], and 11 were isolated from clinical samples, as detailed by Maslunka et al [10]. The exceptions were A. calcoaceticus strains 97366 and 97420, both isolated from soil, and Acinetobacter strain BENAB127, which was isolated from activated sludge.…”

Section: Methodsmentioning

confidence: 99%

“…Although all Acinetobacter spp. are known to possess multiple ITS copies [10], [11], ITS targeted probes have been designed to identify Acb members [12]–[17] on the premise that the extent of Acb intra-species ITS copy sequence variance is low.…”

Section: Introductionmentioning

confidence: 99%

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

Maslunka

Gifford²,

Tucci³

et al. 2014

PLoS ONE

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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.

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“…Only a single ITS sequence is publicly available for most of these, including those with variable length ITS copies (Chang et al, 2005). ITS consensus sequences for A. baylyi ADP1 (593 and 683 bp) and A. baylyi 93A2 (629 and 668 bp) were constructed based upon sequence data discussed in Maslunka et al (2006Maslunka et al ( , 2008. Unpublished ITS sequences of A. bereziniae LMG10600 (614 bp) and A. guillouiae LMG10603 (593 bp) were kindly provided by Professor T. C. Chang (National Cheng Kung University, Tainan, Taiwan).…”

Section: Methodsmentioning

confidence: 99%

“…It is known that each Acinetobacter species may contain between three and seven rrn operons (Maslunka et al, 2006), and this is important because one or more of the individual internal 16S-23S rRNA internal transcribed spacer region (ITS) copies can vary in its length and, hence, sequence between rrn operons. For example, Acinetobacter baylyi strains ADP1/B2 (Barbe et al, 2004;Carr et al, 2004) each contain ITS copies of two lengths, which are quite different to the two copies in A. baylyi strain 93A2 (Maslunka et al, 2008).…”

Section: Introductionmentioning

confidence: 99%