Figures
Abstract
Many sequenced strains of Acinetobacter baumannii are established nosocomial pathogens capable of resistance to multiple antimicrobials. Community-acquired A. baumannii in contrast, comprise a minor proportion of all A. baumannii infections and are highly susceptible to antimicrobial treatment. However, these infections also present acute clinical manifestations associated with high reported rates of mortality. We report the complete 3.70 Mbp genome of A. baumannii D1279779, previously isolated from the bacteraemic infection of an Indigenous Australian; this strain represents the first community-acquired A. baumannii to be sequenced. Comparative analysis of currently published A. baumannii genomes identified twenty-four accessory gene clusters present in D1279779. These accessory elements were predicted to encode a range of functions including polysaccharide biosynthesis, type I DNA restriction-modification, and the metabolism of novel carbonaceous and nitrogenous compounds. Conversely, twenty genomic regions present in previously sequenced A. baumannii strains were absent in D1279779, including gene clusters involved in the catabolism of 4-hydroxybenzoate and glucarate, and the A. baumannii antibiotic resistance island, known to bestow resistance to multiple antimicrobials in nosocomial strains. Phenomic analysis utilising the Biolog Phenotype Microarray system indicated that A. baumannii D1279779 can utilise a broader range of carbon and nitrogen sources than international clone I and clone II nosocomial isolates. However, D1279779 was more sensitive to antimicrobial compounds, particularly beta-lactams, tetracyclines and sulphonamides. The combined genomic and phenomic analyses have provided insight into the features distinguishing A. baumannii isolated from community-acquired and nosocomial infections.
Citation: Farrugia DN, Elbourne LDH, Hassan KA, Eijkelkamp BA, Tetu SG, Brown MH, et al. (2013) The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii. PLoS ONE 8(3): e58628. https://doi.org/10.1371/journal.pone.0058628
Editor: Valerie de Crécy-Lagard, University of Florida, United States of America
Received: November 6, 2012; Accepted: February 5, 2013; Published: March 19, 2013
Copyright: © 2013 Farrugia et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported in part by the National Health and Medical Research Council of Australia Grant No. 535053 awarded to MHB and ITP, and by Macquarie University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Introduction
Acinetobacter baumannii is a significant nosocomial pathogen [1], known for its high intrinsic and laterally acquired resistance to antimicrobials [2], [3] as well as its persistence on various abiotic surfaces [4]-[6]. The complete genome sequences of ten A. baumannii strains have been determined to date: 1656-2 [7], AB0057 [8], AB307-0294 [8], ACICU [9], ATCC 17978 [10], AYE [11], MDR-TJ [12], MDR-ZJ06 [13], SDF [11] and TCDC-AB0715 [14]. Nine of these are nosocomial isolates, whereas A. baumannii SDF was isolated from a human body louse [11]. These genome sequences have demonstrated extensive divergence due to the acquisition and accretion of various mobile genetic elements, particularly those contributing to antimicrobial resistance [15]. One mobile element of clinical import is the A. baumannii antibiotic resistance island (AbaR), that encodes resistance to a multitude of antibiotics and heavy metals [15].
Research regarding A. baumannii has occurred primarily within the context of the clinical milieu, with little known about potential environmental reservoirs of this organism. Several non-nosocomial niches of A. baumannii have been identified, including human lice [16], [17], hydrocarbon contaminated soils [18], [19], the plant rhizosphere [20], [21] and estuaries [22], [23]. A. baumannii is also known to exist outside the hospital environment as a commensal of the skin [24] and nasopharynx [25] of humans. This organism is also a public health issue outside of the hospital setting, in the form of community-acquired A. baumannii (CA-AB) infections.
Infections caused by CA-AB are clinically and epidemiologically distinct from their nosocomial counterparts [26]. CA-AB infections are uncommon and highly fatal, comprising less than 10% of all A. baumannii infections [27], [28] but resulting in mortalities ranging from 30–62% [27]–[30]. These infections are also antimicrobial susceptible [26], [30] and present a more acute clinical manifestation [30], but are thought not to be reservoirs of nosocomial outbreaks [26].
The majority of CA-AB infections occur in individuals with underlying comorbidities, who reside in tropical and subtropical climates [28]. Incidences of CA-AB infection have been reported within various regions of the Asia Pacific such as Taiwan [31], Hong-Kong [30], Singapore [32], Korea [33] and Australia [34]. To a lesser extent, CA-AB infections have also been observed in non-tropical regions [27] and in otherwise healthy children and adults [35]–[39]. Indigenous Australians in the Northern Territory are overrepresented relative to the general population in rates of community-acquired bacteraemic pneumonia caused by A. baumannii and other pathogens [29], [34]. This disparity has been attributed to the interaction of both monsoonal climate and a high prevalence of comorbidities in the indigenous Australian population including alcoholism, diabetes mellitus, chronic obstructive pulmonary disease and cigarette smoking [25], [34], [40].
To explore the underlying basis of epidemiological and phenotypic differences between nosocomial and community-acquired strains of A. baumannii, we determined the complete genome sequence of the CA-AB isolate D1279779 and phenotypically profiled this strain using phenotype microarrays. The genome and phenome of D1279779 was subsequently compared to completely sequenced nosocomial A. baumannii strains.
Materials and Methods
Bacterial strains, culture conditions and genomic DNA extraction
The A. baumannii strain D1279779 was kindly provided by the Menzies School of Health Research (Darwin, Australia). This strain was isolated in 2009 from a bacteraemic infection of an indigenous Australian male at the Royal Darwin Hospital, where the identity and antimicrobial susceptibilities of this isolate were previously determined with a VITEK 2 System (bioMérieux). A. baumannii D1279779 was cultured in lysogeny broth (LB) and lysogeny broth agar (LBA) (both without glucose) at 37 °C. Genomic DNA was extracted with the Wizard Genomic DNA Purification Kit (Promega) from 1 mL of overnight culture as per the manufacturer’s protocol.
DNA sequencing, genome assembly and annotation
A. baumannii D1279779 genomic DNA was prepared and sequenced by 454 FLX pyrosequencing (Roche Diagnostics) at the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney). The sequences reads were assembled de novo with MIRA [41] using the default parameters. The ninety-four contiguous sequences of D1279779 were reordered relative to the ten currently complete genomes of A. baumannii using MAUVE [42]. The highest level of synteny was observed with the A. baumannii ACICU genome [9], which was subsequently utilised as a reference in Projector2 [43] to design oligonucleotides for gap closure by PCR and sequencing. Amplicons for gap closure were generated using AccuPrime Pfx Mastermix (Invitrogen) or GoTaq DNA Polymerase (Promega) as per the manufacturer’s protocol, with variations in the annealing temperature (45 °C to 65 °C) and extension time (2 to 12 min) according to estimated gap sizes. The resultant amplicons were purified using the QIAquick PCR Purification Kit (Qiagen) and cloned into pGEM-T Easy (Promega), or directly sequenced using bidirectional dideoxysequencing performed by the Macquarie University DNA Analysis Facility (Sydney, Australia). The resultant chromatograms were edited and assembled in ChromasPro (Technelysium Pty. Ltd.) and crosschecked against the D1279779 genome by use of the BLASTN [44] application integrated into BioEdit [45]. The presence and directionality of the six rRNA operons in the genome was confirmed by amplification of the gap and sequencing of small junctions flanking this region. The genome assembly was finalised with the aid of CLC Sequence Viewer 6 (CLCbio). Genome annotation was conducted with the RAST automated annotation engine [46] and manual curation was performed with the aid of Artemis [47]. UGENE was routinely utilised for genome browsing and analysis [48]. The nucleotide sequences of the D1279779 chromosome and the plasmid pD1279779 have been deposited into GenBank with the accession numbers CP003967 and CP003968 respectively.
Comparative genomics and accessory element identification
A. baumannii D1279779 was compared to the ten published A. baumannii genomes by a reciprocal BLASTP [49] search to identify putative orthologs at an e-value cutoff of 10-5. Trinucleotide composition of the DNA sequence was computed by χ2 analysis using a 2000 bp sliding window with a 1000 bp overlap [50]; regions containing χ2 values >500 were suggestive of atypical trinucleotide composition. Evidence derived from BLASTP and χ2 analysis was used to identify regions of genomic plasticity (RGPs) [51], [52], defined as either any putative mobile genetic element or contiguous cluster of genes present in D1279779 and three or less strains. Genes clusters absent in D1279779 but present in more than three other strains were also considered RGPs. The identity of insertion sequences present in the D1279779 genome were elucidated with BLASTP searches conducted in ISFinder [53].
The phylogenetic relationship of D1279779 to sequenced A. baumannii strains was inferred with a bootstrapped neighbour-joining analysis in MEGA5 [54] based on the concatenated nucleotide sequences of six of the seven reference genes utilised in the multilocus sequence typing (MLST) of A. baumannii [55]. The fusA gene was excluded from this analysis as it displayed atypical trinucleotide composition in D1279779, suggesting potential lateral acquisition of this gene.
Phenotype microarray testing
The phenomes of A. baumannii D1279779 and three nosocomial strains, ACICU, ATCC 17978 and AYE, were assayed with the Biolog Phenotype MicroArray™ (PM) system [56] to identify compounds that could serve as sole carbon (PM1-2; 190 compounds) or nitrogen sources (PM3; 95 compounds). Additionally, sensitivities to stress conditions (PM9-10; 192 conditions) and various antimicrobials compounds (PM11-20; 240 antimicrobials) were also investigated. All phenotypic tests were performed as per the manufacturer’s protocol, except cryogenic stocks of A. baumannii were streaked onto either LBA medium (PM1-2 and PM9-20) or Reasoner’s 2A agar (Difco) (PM3). The bacterial suspension for nitrogen source testing was supplemented with D-xylose as the sole carbon source at a concentration of 20 mM. Following inoculation, all PM plates were incubated in an OmniLog reader (Biolog) aerobically at 37 °C for 48 h. Reduction of the tetrazolium-based dye (colourless) to formazan (violet) was monitored and recorded at 15 min intervals by an integrated charge-coupled device camera. The resultant data were analysed with the supplied manufacturer’s software, resulting in a time-course curve for colorimetric change equating to respiration rate. The phenotypes were classified on the basis of the maximal curve height; a phenotype was considered positive if the height was greater than 115 and 101 OmniLog units for nitrogen sources and all other phenotypes, respectively. Data that exceeded these cutoff values as the result of colouration from certain compounds was excluded from analysis. Observed phenotypic differences between the strains were linked to differences in genotype through a combined analysis of the EcoCyc [57], MetaCyc [58], and KEGG [59] metabolic databases and additional literature searching.
Independent confirmatory testing of phenotype microarray data
Five millilitres of M9 minimal media (Sigma-Aldrich), supplemented with varied carbon source compounds (20 mM), was inoculated with a single colony of A. baumannii D1279779 or ACICU previously streaked on LBA medium. Cultures were incubated with shaking at 37 °C for 24 h, with the observation of turbidity from cellular replication deemed to signify a positive phenotype. A minimum of three temporally distinct replicates were performed for each tested compound, in addition to substrate and inoculation negative controls. The carbon sources tested were: L-arabinose, bromosuccinic acid, (±)-carnitine hydrochloride, L-carnitine hydrochloride, disodium fumarate, α-D-glucose, L-histidine monohydrochloride monohydrate, polysorbate 80, putrescine dihydrochloride, L-pyroglutamic acid, quinic acid, sodium 4-hydroxybenzoate, sodium acetate trihydrate, trisodium citrate dihydrate, sodium D-gluconate, and D-xylose. All chemicals were sourced from Sigma-Aldrich (purity ≥96%), dissolved in sterile distilled water and filter-sterilised. Phenotypic testing of α-D-glucose and D-gluconic acid utilisation was further conducted in inoculation fluid zero (IF-0) [56] (without sodium pyruvate and tetrazolium dye). Further experiments with α-D-glucose were supplemented with 10 µM methoxatin disodium salt (pyrroloquinoline quinone) with the corresponding negative control.
Results and Discussion
Genomic features
The complete genome of A. baumannii D1279779 was determined and found to consist of a 3704285 bp circular chromosome and a plasmid of 7416 bp, dubbed pD1279779. A total of 3479 genes were annotated on the chromosome including 65 tRNAs, 6 rRNA operons and 3388 predicted protein coding sequences (CDS) (Table 1, Figure 1), which included 1019 annotated CDS (30%) predicted to encode hypothetical proteins. The plasmid pD1279779, unlike many previously sequenced A. baumannii plasmids, does not encode any insertion sequences or genes involved in antimicrobial resistance [60]. Plasmid pD1279779 appears to be of mosaic origin, with a replication repA gene sharing 100% nucleotide sequence identity with the A. baumannii plasmid p203 [60] and a 2609 bp segment sharing 99% nucleotide identity with a region from the otherwise unrelated organic peroxide resistance plasmid pMAC of A. baumannii ATCC 19606 [61].
The two outermost circles denote positions of protein coding sequences (CDSs) on the positive (circle 1) and negative (circle 2) strands coloured according to clusters of orthologous groups (COGs) [99] functional category: A (lavender), B (apricot), C (olive), D (light brown), E (dark green), F (electric pink), G (electric green), H (peach), I (red), J (dark red), K (midnight blue), L (plum), M (teal), N (blue), O (aquamarine), P (orange), Q (yellow), R (dark grey), S (grey), T (light purple), U (light green), V (light yellow), and unknown COG (black). Circle 3 represents positions of identified regions of genomic plasticity (red) and ISAb13s (black) ordered clockwise from the origin of chromosomal replication as outlined in Table 2 and Table 4, respectively. Circle 4 denotes the calculated chi-squared values based on the trinucleotide composition of the DNA sequence. Circles 5-14 show DNA conservation between D1279779 and other sequenced A. baumannii strains based on pairwise BLASTN alignments (evalue threshold 1e-10). Strain comparisons (outermost to innermost): 1656-2 (teal), ACICU (aquamarine), MDR-ZJ06 (orange), MDR-TJ (light purple), TCDC-AB0715 (red), AB307-0294 (blue), AB0057 (olive), AYE (green-brown), ATCC 17978 (teal) and SDF (aquamarine). The innermost circle denotes positive (green) and negative (purple) GC-skew and the scale in kilobase pairs. The CGView software [100] was utilised to construct the genome map.
The phylogeny and synteny of A. baumannii
The phylogeny of A. baumannii D1279779, with respect to other sequenced A. baumannii isolates, was inferred using a MLST approach [55]. The allelic profile of this strain is 12-37-2-2-3-2-14, but it does not match any previously assigned STs; the closest allelic profile in the MLST database belonged to an ST117 isolate (12-37-2-2-9-2-14), differing only in the recA allele. This MLST-based analysis suggested that the nearest phylogenetic relatives of D1279779 were A. baumannii strains of the international clonal (IC) lineage II, though this strain did not fall within either the A. baumannii ICI or ICII lineages (Figure 2). This observation was congruent with our own previous PCR typing, which indicated this strain did not belong to any of the three major A. baumannii lineages [62]. The phylogenetic relationship of D1279779 to other A. baumannii strains was also consistent with the notion that community-acquired isolates are epidemiologically distinct from nosocomial isolates [26].
The phylogenetic relationship of all completely sequenced A. baumannii strains was inferred by the neighbour-joining method conducted in MEGA5 [54] using concatenated nucleotide sequences of six reference genes based on the multilocus sequence tag scheme of A. baumannii (cpn60, gltA, pyrG, recA, rplB and rpoB). Numerals adjacent to strain names represent the number of unique genes (determined by BLASTP) and the numerals adjacent to the brackets represent the size of the core genome of A. baumannii or within clonal lineages. The interior values are bootstrap probabilities based on 1000 replicates, and the tree was drawn using TreeGraph2 [101].
Genomic alignments using MAUVE indicated that A. baumannii D1279779 shares a high degree of genome synteny with other completely sequenced strains of A. baumannii, with the exception of A. baumannii SDF (Figure S1), which is known to have undergone both extensive genome reduction and rearrangement [11]. In A. baumannii D1279779, a 50.8 kb region of sequence situated between the first and sixth rRNA operons was inverted relative to other A. baumannii genomes (Figure 3). We confirmed this rearrangement in D1279779 by PCR analysis conducted on the original cryogenic stock. The inversion of this region resulted in reversing the orientation of a number of critical housekeeping genes as well as the origin of chromosomal replication (oriC) (Figure 3). It is of note that the opposing directionality of both rRNA operons flanking the inversion was maintained, which would otherwise potentially result in replicative blockage [63]. Presumably this genomic rearrangement was mediated by homologous recombination between the two oppositely oriented rRNA operons [64]. Such rRNA operon-mediated rearrangements in genome architecture have been known to occur in other organisms and between more distal rRNA operons [64], [65], resulting in even larger inversions than observed here.
The DNA region between rRNA operons one and six in A. baumannii D1279779 is conserved (≥96% nucleotide identity) but is inverted relative to other A. baumannii genomes (represented by ACICU), as depicted by the grey shading. Genes on positive and negative strands are depicted on the top and bottom row of rectangles, respectively. Conserved regions (≥99% nucleotide identity) in the same orientation are depicted by black shading. Locations of several conserved genes and the origin of chromosomal replication (oriC) are indicated. This figure was generated using the combined outputs of MAUVE [42] and the Artemis Comparison Tool [102].
The core and accessory genome of A. baumannii
The predicted proteome for all currently complete genomes of A. baumannii was compared by means of a reciprocal BLASTP search, which enabled estimation of the A. baumannii core genome size. The numbers overlaid on the phylogenetic tree in Figure 2 (adjacent to the brackets) indicate the various sizes of the core genome. A total of 1944 predicted CDS are shared between all A. baumannii genomes in this analysis; this increases to 2603 CDS when strain SDF is excluded from this analysis group (Figure 2). The lineage-specific core genomes of ICI and ICII is larger than the A. baumannii core genome, with 3098 and 3167 CDS shared respectively (Figure 2), supporting the notion that ICI and ICII constitute recent clonal lineages [55]. A. baumannii strains ATCC 17978 and SDF were the two deepest branching strains in the phylogenetic tree, each displaying over 500 strain-specific genes (Figure 2). A. baumannii D1279779 encoded 172 unique genes not present in the other sequenced strains. The majority of these genes were associated with features indicative of recent lateral acquisition, such as atypical trinucleotide composition and the presence of mobile genetic elements.
Eighteen copies of the insertion sequence ISAba13 and twenty-four regions of genomic plasticity (RGPs) were identified in the genome of D1279779, including two prophages and four genomic islands (Table 2). Unlike RGPs located in genomes of nosocomial isolates, those in D1279779 do not appear to encode known antibiotic resistance or virulence-associated functions (Table 2). One RGP of interest, D1279779_RGP05, contains genes encoding a type I DNA restriction-modification system and genes associated with the catabolic degradation of nitrogenous compounds. Analysis indicated the gene encoding the specificity subunit (hsdS) of the restriction-modification system contained a frameshift mutation. However, a truncated hsdS can still potentially translate and dimerize into a functional HsdS subunit, albeit with an altered DNA specificity [66]-[68]. Nevertheless, the presence of a DNA restriction-modification system in this genomic island may act as a ‘selfish’ genetic element to ensure its dissemination [69] and/or may function in bacteriophage defence and hindrance of lateral gene transfer [70].
Catabolism-associated genes in this RGP included a gene cluster encoding a glutamate dehydrogenase and a near-complete arginine succinyltransferase (AST) pathway [71]. Complete and partial copies of the AST pathway are encoded elsewhere in the core genome of A. baumannii D1279779. Also present in D1279779_RGP05 are genes encoding an acetylpolyamine amidohydrolase (AphA) and an allantoate amidohydrolase (AllC). AphA performs the deacetylation of varied acetylpolyamines [72], and AllC functions in the degradation of allantonate to S-ureidoglycolate [73]. The core genome of A. baumannii D1279779 also encodes an allantoicase (Alc) which functions in a similar manner to AllC, except degradation of allantoate is performed by a single-step catalytic mechanism, rather than a dual-step one [73].
Two other RGPs, D1279779_RGP01 and D1279779_RGP22, encode enzymes involved in capsule polysaccharide biosynthesis. The RGP D1279779_RGP03 encodes additional copies of three enzymes (diaminopimelate decarboxylase, a ribulose-phosphate 3-epimerase, and an uroporphyrinogen decarboxylase) encoded elsewhere in the core genome.
The D1279779 genome encodes two putative prophages, one of which encodes paralogues of the error-prone DNA polymerase V subunits UmuC and UmuD; these genes are frequently associated with prophages and other mobile genetic elements such as genomic islands and plasmids [74]. The second prophage encodes a paralogue of lipid A phosphoethanolamine transferase (EptA) which facilitates the covalent modification of lipid A. Overexpression of eptA in A. baumannii has previously been associated with increased colistin resistance [75]. However, strain D1279779 appears to exhibit greater colistin sensitivity than nosocomial isolates (discussed below).
Notably, A. baumannii D1279779 does not encode the AbaR genomic island (Table 3), a drug resistance island present in the majority of published A. baumannii genomes. AbaRs are characteristically found inserted within the comM gene [76], and associated with the accretion of multiple insertion sequences and genomic islands [77], [78]. When present, AbaRs are capable of encoding resistance to a multitude of antibiotics (aminoglycosides, beta-lactams, sulphonamides, tetracyclines) and heavy metals (arsenic and mercury) [2]. A. baumannii D1279779 has an intact comM gene and lacks an AbaR island, which may partially explain the antimicrobial susceptibility phenotype observed for this CA-AB isolate.
Nineteen other gene clusters, present in the genomes of other A. baumannii isolates, are also absent from D1279779. Ten of the missing gene clusters are unique to A. baumannii strains of the ICI and ICII lineages. Six other gene clusters absent in D1279779 were replaced with RGPs unique to this strain or additionally present only in ATCC 17978 (Table 2, Table 3). Some of the absent genes included those involved in the β-ketoadipate pathway [79], the D-glucarate degradation pathway [80] and potentially, the catabolism of carnitine and vanillate (Table 3). The loss of these metabolic genes very likely correlates with the observed inability of this strain to utilise glactarate, glucarate and 4-hydroxybenoazte as carbon sources but does not prevent the utilisation of carnitine (see below).
Comparison of known or predicted virulence genes amongst A. baumannii sequences indicated strain D1279779 lacks several genes conserved amongst previously sequenced A. baumannii strains. These include a type VI secretion system gene cluster [81] (Table 3), a gene encoding the Acinetobacter trimeric autotransporter protein (Ata) [82] (which is truncated in D1279779), haem acquisition (Table 3) and a gene encoding for the biofilm-associated protein (Bap) [83], [84]. The loss of these genes may correlate with the observation that D1279779 has only a modest capacity for biofilm formation and adherence to nasopharyngeal cells [62]. Nevertheless, this strain still carries other potential virulence-associated genes, including those coding for acinetobactin biosynthesis [85], capsular polysaccharide polymerisation/export [86], type I and type IV pili biogeneses [87] and phospholipases C and D [88], [89].
Multiple copies of ISAba13 are present in the genome
Eighteen copies of the transposon ISAba13, previously identified in A. baumannii AB0057 [8], are present throughout the D1279779 chromosome (Figure 1). All insertion sequences, with the exception of one, are of an identical isoform (Table 4). The two insertion sequence isoforms have nucleotide identities of 99% and 96% to the ISAba13 in AB0057. Thirteen copies of ISAba13 are inserted within annotated genes, including some potentially encoding virulence and competence functions such as a fimbrial adhesin, a type I secretion domain protein, bacterial capsule synthesis protein and competence-damaged induced protein CinA (Table 4). One of the copies of ISAba13 replaced an approximately 44 kb region, present in some other A. baumannii strains, that carries genes for the catabolism of glucarate, galactarate and vanillate (Table 3, Table 4).
The catabolic phenome of A. baumannii D1279779
Biolog Phenotype MicroArrays are a respiration-based assay system that can test up to 2000 phenotypic traits simultaneously [56], [90]. This system uses 96 well plates with each well testing a separate phenotype using a tetrazolium dye that produces a colour change in response to cellular respiration. The phenome of A. baumannii D1279779 was investigated with the Biolog Phenotype MicroArray System and compared with an ICI strain (AYE), an ICII strain (ACICU) and ATCC 17978, a nosocomial isolate from 1951, predating the emergence of the major global clonal lineages as the dominant nosocomial strains.
The four A. baumannii strains tested were similar in their utilization of sole carbon (Figure 4) and nitrogen sources (Figure S2). They utilized a combined total of 80 carbon sources out of the 190 tested, encompassing a range of amino acids, carboxylic acids, saccharides and miscellaneous compounds (Figure 4). Strains D1279779 and ATCC 17978 were able to utilise a greater breadth of sole carbon and nitrogen sources compared to ICI and ICII strains, particularly in relation to amino acids including alaninamide, asparagine, isoleucine, glutamate and homoserine (Figure 4, Figure S2). The observed phenotypic profiles suggest the emergence of ICI and ICII lineages in nosocomial settings has coincided with a narrowing of their substrate utilisation capabilities. Furthermore, A. baumannii ACICU displayed a higher respiration rate on substrates arginine, ornithine, phenylalanine, pyroglutamic acid, quinic acid and ribonolactone (Figure 4), suggesting a possible specialization in terms of carbon utilization preferences.
Strengths of carbon utilisation phenotypes of A. baumannii strains D1279779, ACICU, AYE and ATCC 17978 were determined using Biolog Phenotype Microarray plates PM1 and PM2. The maximal kinetic curve height was expressed as a greyscale ranging from 101 (light grey) to 320 OmniLog units (black). Phenotypes are arranged from strongest to weakest relative to A. baumannii D1279779. Phenotypes <101 OmniLog units (white) were considered negative.
In order to independently confirm the Biolog respiration data, the ability of A. baumannii D1279779 and ACICU to grow on minimal media in the presence of fifteen sole carbon compounds was tested. Turbidity consistent with cellular replication was observed in all tested carbon sources except for D-gluconic acid and α-D-glucose (see below) (Table S1), which was concordant with the phenotype microarray data.
Metabolic reconstructions for each of the four strains were undertaken to analyse whether the phenotypic differences detected could be ascribed to the presence or absence of specific genes. A. baumannii D1279779 was unable to utilise 4-hydroxybenzoic acid as a sole source of carbon in either the phenotype microarray (Figure 4) or minimal media (Table S1). Genomic analysis indicated that this strain lacked the pobA gene encoding a 4-hydroxybenzoate 3-hydroxylase (Table 3), required for the conversion of 4-hydroxybenzoic acid to protocatechuic acid [79]. Both this strain and A. baumannii SDF were the only genomes examined that lacked this gene.
A. baumannii ATCC 17978 was the only strain in the test group able to utilise the diastereomers saccharic acid (glucarate) and mucic acid (galactarate) as sole sources of carbon (Figure 4). This was attributable to the presence of a gene cluster involved in the glucarate degradation pathway [80] conserved in some other A. baumannii strains, but absent in D1279779, ACICU and AYE (Table 3, Table 4).
Both strains D1279779 and ATCC 17978 showed a positive result for respiration on both D-gluconic acid and α-D-glucose. Our results were concordant with the results of a previous phenotype microarray study [91], which demonstrated the capability of various Acinetobacter sp. (including A. baumannii) to respire in the presence of both these carbon sources. This is curious, since the majority of Acinetobacter species including A. baumannii have repeatedly been reported as incapable of utilising D-glucose and D-gluconate as sole carbon sources [92], [93]. All four strains encode the Entner-Doudoroff (ED) pathway, an alternative glucose assimilation route that requires the cofactor pyrroloquinoline quinone (PQQ) [94]; a PQQ biosynthetic pathway is evident in three of the strains (but not in ATCC 17978). Growth experiments in both M9 and IF-0 minimal media using D-gluconic acid and α-D-glucose as sole carbon sources, with or without PQQ supplementation, were all negative. The apparent contradiction between the genome, phenotype microarray data and growth assays may indicate these substrates are not assimilated, but rather act as energy donors [95].
A number of the differences observed in carbon and nitrogen utilization between the strains could not be accounted for at the genetic level. This could be due to differences in regulation, membrane transport activity, or the presence of novel uncharacterized catabolic pathways. For instance, strains D1279779 and ATCC 17978 were able to utilize the branched-chain amino acids leucine and isoleucine, while ACICU and AYE were only able to respire weakly on leucine. All of the strains encoded a putative branched-chain amino acid aminotransferase (IlvE) for the reversible transamination of isoleucine, leucine and valine [96], it seems likely the phenotypic differences are due to altered regulation or transport factors. It is possible the residual leucine utilisation in AYE and ACICU is due to a tyrosine aminotransferase (TyrB), which overlaps IlvE in specificity to leucine [97]. In another instance, A. baumannii AYE was found to be unable to utilise proline, ornithine and putrescine as carbon sources (Figure 4) or citrulline, ornithine and putrescine as nitrogen sources (Figure S2). This suggests potential defects in proline and arginine catabolism, but these deficiencies cannot currently be accounted for at the genetic level.
The resistance phenome of A. baumannii D1279779
The osmotolerance (Table S1), pH tolerance (Figure S2) and antimicrobial resistance (Figure 5, Table S1) of the four A. baumannii strains was also examined with Biolog Phenotype MicroArrays. A. baumannii ACICU and ATCC 17978 were found to be more sensitive to acidic pH and were only able to deaminate a limited number of compounds at pH 4.5 (Figure S2).
Select antimicrobial resistance phenotypes of A. baumannii strains D1279779, ACICU, AYE and ATCC 17978 are displayed as a five-coloured grey scale ranging from no resistance (white) to maximal resistance (dark grey). Phenotypes are arranged from strongest to weakest relative to A. baumannii D1279779. Abbreviations: Macro, macrolides; QACs, quaternary ammonium compounds; and Sulph, sulphonamides.
The four A. baumannii strains displayed high intrinsic resistance to many antimicrobial compounds. Respiration in all four strains was observed, at all concentrations, for 94 of the 240 antimicrobials tested (Table S1). No respiration was observed in any strain for five compounds: the antibiotic novobiocin and the heavy metals salts potassium chromate, cadmium chloride, sodium orthovanadate and sodium metavanadate. Differential susceptibility to a further 106 compounds was observed in the four strains (Figure 5, Table S1). Strains D1279779 and ATCC 17978 were noticeably more susceptible to a range of clinically important antibiotics, including the beta-lactams and tetracyclines. The higher levels of resistance of A. baumannii ACICU and AYE towards beta-lactams and sulphonamides is likely due to resistance determinants encoded within their respective AbaR elements [2], [9], as well as the carbapenem resistance plasmid pACICU1 [9]. Although, ATCC 17978 was also resistant to sulphonamides, it is likely that this resistance is encoded on a separate genomic island [98]. The strain AYE encodes two TetA tetracycline resistance efflux pumps [2], though in the case of ACICU, there are no characterized tetracycline resistance genes; the observed resistance may be due to the function of other efflux pumps. Resistance to the quinolone nalidixic acid can be accounted for by mutations both in gyrA and parC in strain AYE, and a mutation in gyrA for strain ACICU [8]; neither mutation is present in ATCC 17978 or D1279779. A. baumannii AYE was found to be relatively more resistant to arsenic and rifamycin SV, attributable to the respective presence of an arsenic resistance cluster and a rifampin ADP-ribosyltransferase (arr-2) in its AbaR island [2]. Strains AYE and ATCC 17978 had increased resistance to copper, very likely due to the presence of a copper resistance cluster (copABCDRS) [8], in addition to the copper resistance genes (pcoAB) present in the A. baumannii core genome.
Conclusions
The CA-AB isolate D1279779, while phylogenetically related to the ICII A. baumannii global clonal lineage, phenotypically resembles ATCC 17978 in terms of carbon and nitrogen utilization, and drug susceptibility profile. Phenotypic testing of nosocomial A. baumannii suggests that the narrowing of substrate utilisation capabilities and expansion of drug resistance profiles in both ICI and ICII global clonal lineages has contributed to their success in the nosocomial milieu. Our genomic analysis of the CA-AB isolate D1279779 reveals the absence of the AbaR island common to nosocomial isolates. D1279779 does however comprise of 24 novel RGPs that encode catabolic functions, polysaccharide biosynthesis and many hypothetical proteins of unknown function. Reports in the literature have suggested that CA-AB is associated with higher mortality rates than nosocomial A. baumannii strains. Whilst there were no obvious virulence-associated genes unique to D1279779, there was however, the apparent loss of several genes associated with virulence, particularly with respect to biofilm formation and eukaryotic cell adhesion. The characteristics of D1279779 may be more representative of an environmental or pre-antibiotic era clinical A. baumannii isolate, and appears quite distinct from the current dominant lineages of nosocomial isolates.
Supporting Information
Figure S1.
Synteny of Acinetobacter baumannii. Chromosomal alignments of the A. baumannii D1279779 genome against the ten currently complete A. baumannii genomes were generated using progressive MAUVE [103]. Regions of significant synteny between the strains are shown as coloured blocks and unshared regions are seen as white gaps.
https://doi.org/10.1371/journal.pone.0058628.s001
(PNG)
Figure S2.
Phenotypic analysis of nitrogen utilisation and pH stress tolerance. Strengths of nitrogen utilisation (A) and the pH tolerance phenotypes (B) of A. baumannii strains D1279779, ACICU, AYE and ATCC 17978 were determined were determined using Biolog Phenotype Microarray plates PM3 and PM10, respectively. The maximal kinetic curve height was expressed as a greyscale ranging from 101 OmniLog units (light grey) to 310 and 360 OmniLog units (black) for nitrogen and pH tolerance phenotypes, respectively. Phenotypes are arranged from strongest to weakest relative to A. baumannii D1279779. Phenotypes <115 OmniLog units for nitrogen phenotypes and <101 OmniLog units for pH tolerance phenotypes were considered negative phenotypes and are represented in white.
https://doi.org/10.1371/journal.pone.0058628.s002
(TIF)
Table S1.
Raw phenotype microarray data. The maximal kinetic curve height for all phenotypes obtained from plates PM1-3 (carbon and nitrogen utilisation) and PM9-20 (osmotolerance, pH tolerance and antimicrobial exposure) expressed in OmniLog units.
https://doi.org/10.1371/journal.pone.0058628.s003
(XLS)
Acknowledgments
We would like to thank Matthias Maiwald for providing A. baumannii D1279779, Alessandra Carattoli for providing A. baumannii ACICU and Patrice Nordmann for providing A. baumannii AYE.
Author Contributions
Conceived and designed the experiments: DNF KAH MHB ITP. Performed the experiments: DNF LDHE KAH BAE SGT BSS. Analyzed the data: DNF LDHE BAE BSS ITP. Wrote the paper: DNF LDHE KAH MHB AYP BCM ITP.
References
- 1. Roca I, Espinal P, Vila-Farres X, Vila J (2012) The Acinetobacter baumannii oxymoron: commensal hospital dweller turned pan-drug-resistant menace. Front Microbiol 3: 148.
- 2. Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, et al. (2006) Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet 2: 62–72.
- 3. Vila J, Marti S, Sanchez-Cespedes J (2007) Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii. J Antimicrob Chemoth 59: 1210–1215.
- 4. Wendt C, Dietze B, Dietz E, Ruden H (1997) Survival of Acinetobacter baumannii on dry surfaces. J Clin Microbiol 35: 1394–1397.
- 5. Jawad A, Seifert H, Snelling AM, Heritage J, Hawkey PM (1998) Survival of Acinetobacter baumannii on dry surfaces: comparison of outbreak and sporadic isolates. J Clin Microbiol 36: 1938–1941.
- 6. Neely AN, Maley MP, Warden GD (1999) Computer keyboards as reservoirs for Acinetobacter baumannii in a burn hospital. Clin Infect Dis 29: 1358–1359.
- 7. Park JY, Kim S, Kim S-M, Cha SH, Lim S-K, et al. (2011) Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm. J Bacteriol 193: 6393–6394.
- 8. Adams MD, Goglin K, Molyneaux N, Hujer KM, Lavender H, et al. (2008) Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. J Bacteriol 190: 8053–8064.
- 9. Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, et al. (2008) Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 52: 2616–2625.
- 10. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, et al. (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Gene Dev 21: 601–614.
- 11. Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, et al. (2008) Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One 3: e1805.
- 12. Gao F, Wang Y, Liu Y-J, Wu X-M, Lv X, et al. (2011) Genome sequence of Acinetobacter baumannii MDR-TJ. J Bacteriol 193: 2365–2366.
- 13. Zhou H, Zhang T, Yu D, Pi B, Yang Q, et al. (2011) Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob Agents Chemother 55: 4506–4512.
- 14. Chen C-C, Lin Y-C, Sheng W-H, Chen Y-C, Chang S-C, et al. (2011) Genome sequence of a dominant, multidrug-resistant Acinetobacter baumannii strain, TCDC-AB0715. J Bacteriol 193: 2361–2362.
- 15. Adams MD, Chan ER, Molyneaux ND, Bonomo RA (2010) Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 54: 3569–3577.
- 16. La Scola B, Raoult D (2004) Acinetobacter baumannii in human body louse. Emerg Infect Dis 10: 1671–1673.
- 17. Bouvresse S, Socolovshi C, Berdjane Z, Durand R, Izri A, et al. (2011) No evidence of Bartonella quintana but detection of Acinetobacter baumannii in head lice from elementary schoolchildren in Paris. Comp Immunol Microb 34: 475–477.
- 18. Sarma PM, Bhattacharya D, Krishnan S, Lal B (2004) Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons. Can J Microbiol 50: 405–414.
- 19. Chang LK, Ibrahim D, Omar IC (2011) A laboratory scale bioremediation of Tapis crude oil contaminated soil by bioaugmentation of Acinetobacter baumannii T30C. Afr J Microbiol Res 5: 2609–2615.
- 20. Berg G, Roskot N, Steidle A, Eberl L, Zock A, et al. (2002) Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl Environ Microb 68: 3328–3338.
- 21. Sachdev D, Nema P, Dhakephalkar P, Zinjarde S, Chopade B (2010) Assessment of 16S rRNA gene-based phylogenetic diversity and promising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat. Microbiol Res 165: 627–638.
- 22. Girlich D, Poirel L, Nordmann P (2010) First isolation of the blaOXA-23 carbapenemase gene from an environmental Acinetobacter baumannii isolate. Antimicrob Agents Chemother 54: 578–579.
- 23. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, et al. (2011) Metagenomics of the water column in the pristine upper course of the Amazon River. PLoS One 6: e23785.
- 24. Chu YW, Leung CM, Houang ET, Ng KC, Leung CB, et al. (1999) Skin carriage of Acinetobacters in Hong Kong. J Clin Microbiol 37: 2962–2967.
- 25. Anstey NM, Currie BJ, Hassell M, Palmer D, Dwyer B, et al. (2002) Community-acquired bacteremic Acinetobacter pneumonia in tropical Australia is caused by diverse strains of Acinetobacter baumannii, with carriage in the throat in at-risk groups. J Clin Microbiol 40: 685–686.
- 26. Zeana C, Larson E, Sahni J, Bayuga SJ, Wu F, et al. (2003) The epidemiology of multidrug-resistant Acinetobacter baumannii: Does the community represent a reservoir? Infect Cont Hosp Ep 24: 275–279.
- 27. Chen HP, Chen TL, Lai CH, Fung CP, Wong WW, et al. (2005) Predictors of mortality in Acinetobacter baumannii bacteremia. J Microbiol Immunol Infect 38: 127–136.
- 28. Falagas ME, Karveli EA, Kelesidis I, Kelesidis T (2007) Community-acquired Acinetobacter infections. Eur J Clin Microbiol 26: 857–868.
- 29. Elliott JH, Anstey NM, Jacups SP, Fisher DA, Currie BJ (2005) Community-acquired pneumonia in northern Australia: low mortality in a tropical region using locally-developed treatment guidelines. Int J Infect Dis 9: 15–20.
- 30. Leung AS, Chu CM, Tsang KY, Lo FH, Lo KF, et al. (2006) Fulminant community-acquired Acinetobacter baumannii pneumonia as a distinct clinical syndrome. Chest 129: 102–109.
- 31. Wang JT, McDonald LC, Chang SC, Ho M (2002) Community-acquired Acinetobacter baumannii bacteremia in adult patients in Taiwan. J Clin Microbiol 40: 1526–1529.
- 32. Ong CWM, Lye DCB, Khoo KL, Chua GSW, Yeoh SF, et al. (2009) Severe community–acquired Acinetobacter baumannii pneumonia: An emerging highly lethal infectious disease in the Asia-Pacific. Respirology 14: 1200–1205.
- 33. Chong YP, Jung K-S, Lee KH, Kim M-N, Moon SM, et al. (2010) The bacterial etiology of community-acquired pneumonia in Korea: a nationwide prospective multicenter study. Infect Chemother 42: 397–403.
- 34. Anstey NM, Currie BJ, Withnall KM (1992) Community-acquired Acinetobacter pneumonia in the Northern Territory of Australia. Clin Infect Dis 14: 83–91.
- 35. Gradon JD, Chapnick EK, Lutwick LI (1992) Infective endocarditis of a native valve due to Acinetobacter: case report and review. Clin Infect Dis 14: 1145–1148.
- 36. Bick JA, Semel JD (1993) Fulminant community-acquired Acinetobacter pneumonia in a healthy woman. Clin Infect Dis 17: 820–821.
- 37. Reindersma P, Nohlmans L, Korten JJ (1993) Acinetobacter, an infrequent cause of community acquired bacterial meningitis. Clin Neurol Neurosurg 95: 71–73.
- 38. Ozaki T, Nishimura N, Arakawa Y, Suzuki M, Narita A, et al. (2009) Community-acquired Acinetobacter baumannii meningitis in a previously healthy 14-month-old boy. J Infect Chemother 15: 322–324.
- 39. Moreira Silva G, Morais L, Marques L, Senra V (2012) Acinetobacter community-acquired pneumonia in a healthy child. Rev Port Pneumol 18: 96–98.
- 40. Einsiedel LJ, Woodman RJ (2010) Two nations: racial disparities in bloodstream infections recorded at Alice Springs Hospital, central Australia, 2001–2005. Med J Aust 192: 567–571.
- 41. Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99: 45–56.
- 42. Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394–1403.
- 43. van Hijum SAFT, Zomer AL, Kuipers OP, Kok J (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 33: W560–W566.
- 44. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
- 45. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95–98.
- 46. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75.
- 47. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944–945.
- 48. Okonechnikov K, Golosova O, Fursov M (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28: 1166–1167.
- 49. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
- 50. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, et al. (2002) The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci USA 99: 13148–13153.
- 51. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 105: 3100–3105.
- 52. Ogier J-C, Calteau A, Forst S, Goodrich-Blair H, Roche D, et al. (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11: 568.
- 53. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34: D32–D36.
- 54. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739.
- 55. Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S (2010) The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 5: e10034.
- 56. Bochner BR, Gadzinski P, Panomitros E (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 11: 1246–1255.
- 57. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39: D583–D590.
- 58. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742–D753.
- 59. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277–D280.
- 60. Bertini A, Poirel L, Mugnier PD, Villa L, Nordmann P, et al. (2010) Characterization and PCR-based replicon typing of resistance plasmids in Acinetobacter baumannii. Antimicrob Agents Chemother 54: 4168–4177.
- 61. Dorsey CW, Tomaras AP, Actis LA (2006) Sequence and organization of pMAC, an Acinetobacter baumannii plasmid harboring genes involved in organic peroxide resistance. Plasmid 56: 112–123.
- 62. Eijkelkamp BA, Stroeher UH, Hassan KA, Papadimitrious MS, Paulsen IT, et al. (2011) Adherence and motility characteristics of clinical Acinetobacter baumannii isolates. FEMS Microbiol Lett 323: 44–51.
- 63. Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD (2010) Co-orientation of replication and transcription preserves genome integrity. PLoS Genetics 6: e1000810.
- 64. Hill CW, Harnish BW (1981) Inversions between ribosomal RNA genes of Escherichia coli. Proc Natl Acad Sci USA 78: 7069–7072.
- 65. Klockgether J, Munder A, Neugebauer J, Davenport CF, Stanke F, et al. (2010) Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J Bacteriol 192: 1113–1121.
- 66. Abadjieva A, Patel J, Webb M, Zinkevich V, Firman K (1993) A Deletion Mutant of the Type-IC Restriction-Endonuclease EcoR124I Expressing a Novel DNA Specificity. Nucleic Acids Res 21: 4435–4443.
- 67. Meister J, MacWilliams M, Hubner P, Jutte H, Skrzypek E, et al. (1993) Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition. EMBO J 12: 4585–4591.
- 68. Adamczyk-Poplawska M, Lower M, Piekarowicz A (2011) Deletion of one nucleotide within the homonucleotide tract present in the hsdS gene alters the DNA sequence specificity of type I restriction-modification system NgoAV. J Bacteriol 193: 6750–6759.
- 69.
Kobayashi I (2004) Restriction-modification systems as minimal forms of life. In: Pingoud AM, editor. Restriction Endonucleases: Springer Berlin Heidelberg. pp. 19–62.
- 70. Waldron DE, Lindsay JA (2006) Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages. J Bacteriol 188: 5578–5585.
- 71. Schneider BL, Kiupakis AK, Reitzer LJ (1998) Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J Bacteriol 180: 4278–4286.
- 72. Sakurada K, Ohta T, Fujishiro K, Hasegawa M, Aisaka K (1996) Acetylpolyamine amidohydrolase from Mycoplana ramosa: gene cloning and characterization of the metal-substituted enzyme. J Bacteriol 178: 5781–5786.
- 73. Agarwal R, Burley SK, Swaminathan S (2007) Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics. J Mol Biol 368: 450–463.
- 74. Permina EA, Mironov AA, Gelfand MS (2002) Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene 293: 133–140.
- 75. Beceiro A, Llobet E, Aranda J, Bengoechea JA, Doumith M, et al. (2011) Phosphoethanolamine modification of lipid A in colistin-resistant variants of Acinetobacter baumannii mediated by the pmrAB two-component regulatory system. Antimicrob Agents Chemother 55: 3370–3379.
- 76. Bonnin RA, Poirel L, Nordmann P (2012) AbaR-type transposon structures in Acinetobacter baumannii. J Antimicrob Chemoth 67: 234–236.
- 77. Post V, White PA, Hall RM (2010) Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii. J Antimicrob Chemoth 65: 1162–1170.
- 78. Krizova L, Dijkshoorn L, Nemec A (2011) Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I. Antimicrob Agents Chemother. 55: 3201–3206.
- 79. Park SH, Kim JW, Yun SH, Leem SH, Kahng HY, et al. (2006) Characterization of β-ketoadipate pathway from multi-drug resistance bacterium, Acinetobacter baumannii DU202 by proteomic approach. J Microbiol 44: 632–640.
- 80. Aghaie A, Lechaplais C, Sirven P, Tricot S, Besnard-Gonnet M, et al. (2008) New insights into the alternative D-glucarate degradation pathway. J Biol Chem 283: 15638–15646.
- 81. Henry R, Vithanage N, Harrison P, Seemann T, Coutts S, et al. (2012) Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-acetylglucosamine. Antimicrob Agents Chemother 56: 59–69.
- 82. Bentancor LV, Camacho-Peiro A, Bozkurt-Guzel C, Pier GB, Maira-Litrán T (2012) Identification of Ata, a multifunctional trimeric autotransporter of Acinetobacter baumannii. J Bacteriol 194: 3950–3960.
- 83. Loehfelm TW, Luke NR, Campagnari AA (2008) Identification and characterization of an Acinetobacter baumannii biofilm-associated protein. J Bacteriol 190: 1036–1044.
- 84. Brossard KA, Campagnari AA (2012) The Acinetobacter baumannii biofilm-associated protein plays a role in adherence to human epithelial cells. Infect Immun 80: 228–233.
- 85. Gaddy JA, Arivett BA, McConnell MJ, López-Rojas R, Pachón J, et al. (2012) Role of acinetobactin-mediated iron acquisition functions in the interaction of Acinetobacter baumannii strain ATCC 19606T with human lung epithelial cells, Galleria mellonella caterpillars, and mice. Infect Immun 80: 1015–1024.
- 86. Russo TA, Luke NR, Beanan JM, Olson R, Sauberan SL, et al. (2010) The K1 capsular polysaccharide of Acinetobacter baumannii strain 307-0294 is a major virulence factor. Infect Immun 78: 3993–4000.
- 87. Eijkelkamp B, Hassan K, Paulsen I, Brown M (2011) Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions. BMC Genomics 12: 126.
- 88. Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M (2010) Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 6: e1000834.
- 89. Jacobs AC, Hood I, Boyd KL, Olson PD, Morrison JM, et al. (2010) Inactivation of phospholipase D diminishes Acinetobacter baumannii pathogenesis. Infect Immun 78: 1952–1962.
- 90. Johnson DA, Tetu SG, Phillippy K, Chen J, Ren Q, et al. (2008) High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. PLoS Genet 4: e1000211.
- 91. Bernards AT, Dijkshoorn L, Vandertoorn J, Bochner BR, Vanboven CPA (1995) Phenotypic characterization of Acinetobacter strains of 13 DNA-DNA hybridization groups by means of the Biolog system. J Med Microbiol 42: 113–119.
- 92. Baumann P, Doudoroff M, Stanier RY (1968) A study of the Moraxella group. II. oxidative-negative species (genus Acinetobacter). J Bacteriol 95: 1520–1541.
- 93. Nemec A, Krizova L, Maixnerova M, van der Reijden TJK, Deschaght P, et al. (2011) Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp nov (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp nov (formerly Acinetobacter genomic species 13TU). Res Microbiol 162: 393–404.
- 94. Peekhaus N, Conway T (1998) What's for dinner?: Entner-Doudoroff metabolism in Escherichia coli. J Bacteriol 180: 3495–3502.
- 95. Müller RH, Babel W (1986) Glucose as an energy donor in acetate growing Acinetobacter calcoaceticus. Arch Microbiol 144: 62–66.
- 96. Lee-Peng FC, Hermodson MA, Kohlhaw GB (1979) Transaminase B from Escherichia coli: quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-alpha-ketoglutarate activity. J Bacteriol 139: 339–345.
- 97. Powell JT, Morrison JF (1978) Role of the Escherichia coli aromatic amino acid aminotransferase in leucine biosynthesis. J Bacteriol 136: 1–4.
- 98. Nigro SJ, Hall RM (2011) GIsul2, a genomic island carrying the sul2 sulphonamide resistance gene and the small mobile element CR2 found in the Enterobacter cloacae subspecies cloacae type strain ATCC 13047 from 1890, Shigella flexneri ATCC 700930 from 1954 and Acinetobacter baumannii ATCC 17978 from 1951. J Antimicrob Chemother 66: 2175–2176.
- 99. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278: 631–637.
- 100. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21: 537–539.
- 101. Stover BC, Muller KF (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11: 7.
- 102. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, et al. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422–3423.
- 103. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147.