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J Clin Microbiol. Sep 2008; 46(9): 2938–2944.
Published online Jul 16, 2008. doi:  10.1128/JCM.00232-08
PMCID: PMC2546726

Acinetobacter baylyi as a Pathogen for Opportunistic Infection[down-pointing small open triangle]


There are no previous reports of human infection due to Acinetobacter baylyi. In this study, we report on six patients with bacteremia due to A. baylyi, based on analysis of the 16S-23S rRNA intergenic spacer and the 16S rRNA gene. All six patients had multiple underlying diseases. The infection was nosocomially acquired in five patients. The six clinical isolates had similar ribopatterns, suggesting a clonal relationship. Compared to the reference strain, the clinical isolates were more resistant to antimicrobial agents, especially beta-lactam antibiotics. In three of the isolates, they may have undetermined plasmid mediated class C type beta-lactamases because of the positive results in a double-disk synergy test using 3-aminophenylboronic acid. Two of the clinical isolates retained a level of natural transformability similar to that of the reference strain. None of the patients died, although only three of them received appropriate antimicrobial therapy. This study demonstrates that A. baylyi is a potential human pathogen that can cause nosocomial infection in immunocompromised patients.

Classification of the Acinetobacter spp., important soil organisms and sources of infection in immunocompromised patients, is difficult because of limited knowledge of their basic biology and ecology (3). Acinetobacter species are now defined as strictly aerobic gram-negative coccobacilli that are nonmotile, catalase positive, oxidase negative, and have a DNA G+C content of 39 to 47% (3). They can survive at a wide range of temperatures on animate and inanimate surfaces and are commonly isolated in hospitals, where these organisms are emerging nosocomial pathogens.

At present, the Acinetobacter genus has at least 32 genomic species (10). Acinetobacter baumannii is the most clinically important species (22), presumably because it can rapidly develop resistance to antibiotics. Acinetobacter genomic species 13TU and 3, which are phenotypically similar to A. baumannii, are also commonly encountered in nosocomial infections. Along with an environmental species (Acinetobacter calcoaceticus), these species are classified as the A. calcoaceticus-A. baumannii complex (3). This complex is usually identified by commercially available methods based on phenotypic characteristics (4), although more reliable identification requires molecular methods.

The identification of non-A. calcoaceticus-A. baumannii complex species by phenotypic methods is more difficult (11). Therefore, the clinical significance of many non-A. calcoaceticus-A. baumannii complex species remains to be determined. However, precise identification is necessary in order to evaluate the clinical significance of a species. For example, the use of a genotypic method (16S rRNA gene analysis) enabled identification of 103 Acinetobacter isolates and showed that two species, Acinetobacter schindleri and Acinetobacter ursingii, were underreported by previous studies (11).

DNA-DNA hybridization and sequence analysis are the most widely accepted methods for identifying species, including Acinetobacter (3). DNA-DNA hybridization is considered the gold standard but is labor-intensive and impractical in most clinical laboratories (15). Sequence analysis of housekeeping genes, including the 16S rRNA gene (13), 16S-23S rRNA intergenic spacer (ITS) (6), recA gene (15), rpoB and flanking spacers (16), and gyrB gene (27), also allows identification of Acinetobacter species. Among these genes, the 16S rRNA gene is most commonly used (14). It has been suggested that an unknown isolate can be assigned to a species when its 16S rRNA sequence has a similarity of ≥99% with the reference sequence of a well-defined species and when it has at least 0.5% sequence difference to the second nearest species (4, 14).

In the present study, we used genotypic methods to identify Acinetobacter baylyi in six bacteremic patients. Previously, this species was only known to live in the soil. The identification procedures, antimicrobial susceptibility, natural transformability of the isolates and clinical features of the patients are described.


Isolates of Acinetobacter in the present study.

A previous study identified 138 Acinetobacter isolates to the species level by ITS sequence analysis and verified a new multiplex PCR method for identification of A. baumannii (8). Among the 47 non-A. calcoaceticus-A. baumannii complex species, six were identified as A. baylyi. Sequence analysis of 16S rRNA gene and phylogenetic analysis confirmed this identification. The A. baylyi strain ADP1 (ATCC 33305) and A. baumannii type strain (ATCC 19606T) were purchased from the Bioresources Collection and Research Center of Taiwan and used as reference strains. The clonality of the isolates was delineated by using an automated ribotyping system (25).

Genotypic identification and phylogenetic analysis.

Amplification of 16S rRNA gene was performed as that described previously (13). The ITS and 16S rRNA gene sequences were compared to sequences in GenBank by using the BLAST program. All available ITS and 16S rRNA sequences of different Acinetobacter spp., some of which were not well characterized, were included for phylogenetic analysis. All copies of the 16S rRNA gene and the ITSs of A. baylyi strain ADP1 from the genome sequence (CR543861) were also used for comparison. Analysis of 16S rRNA gene was performed by comparison of a continuous stretch of ca. of 1,330 bp, which corresponded to nucleotide positions 102 to 1435 of the homologous Escherichia coli gene (EU014689). The phylogenetic analysis was performed with the neighbor-joining algorithm in the CLUSTAL W program (version 1.83), and the resulting phylogenic tree was displayed with TreeView software (version 1.6.6).

Phenotypic identification.

For phenotypic identification, the ID 32 GN and Vitek 2 systems (both from bioMérieux, Marcy l'Etoile, France) were used according to the manufacturer's protocols. The results from the 32 GN system were interpreted with the database version 3.1. The identification with Vitek 2 system was performed by using the colorimetric-based GN card, and the results were interpreted by the Advanced Expert system (version VT2-R04.03).

Antimicrobial susceptibility testing.

The MIC of isolates was determined by the broth dilution method with the use of an automated Sensititre susceptibility plate (TREK Diagnostic Systems, Ltd., United Kingdom) according to the recommendation of the Clinical Laboratory Standard Institute (9) or as recommended by the manufacturer. E. coli ATCC 35218 and Pseudomonas aeruginosa ATCC 27853 reference strains were included for quality control.

Detection of ESBLs, AmpC type beta-lactamases, and insertion sequences (ISs).

Beta-lactamase production was detected by the colorimetric nitrocefin disk assay (Remel, Lenexa, KS) according to the manufacturer's instructions. Phenotypic assay for extended-spectrum beta-lactamase (ESBL) production was carried out by using double-disk synergy test on the plates with or without cloxacillin (200 μg/ml) according to the method of Poirel et al. (20). Detection of the plasmid-mediated class C enzymes was performed by disk potentiation and double-disk synergy test with the use of 3-aminophenylboronic acid (APB) as previously described (26). Genes encoding ESBLs, AmpC type beta-lactamases (including Acinetobacter-derived cephalosporinase [ADC]), tnpA of IS1236, and ISAba1 were detected by PCR method using the primers listed in Table Table1.1. Templates of Enterobacteriaceae harboring different ESBL genes, AmpC genes, and A. baumannii harboring ADC gene were included in the PCR as a positive control.

Primers used for detection of genes encoding various beta-lactamases and transposase of IS1236 and ISAba1

Natural transformation assay.

An Acinetobacter-E. coli shuttle vector, pOXA58-2, was used as donor DNA in the transformation assay. This shuttle vector has a pET backbone (kanamycin resistance) and contains fragments of A. baumannii ATCC 19606T plasmid origin and blaOXA58 gene. The electrotransformation of the pOXA58-2 to A. baylyi ATCC 33305 could confer a kanamycin and imipenem resistance to the recipient cells (unpublished data). To perform the natural transformation assay, 40 μl of overnight culture was diluted 1:10 in fresh Luria-Bertani broth medium and incubated at 30°C for 2 h with shaking (180 rpm). One microgram of pOXA58-2 was then added. After incubation for another 4 h, 50 μg of DNase I was added to the culture. Aliquots of 0.1 ml were removed and plated on Mueller-Hinton plate with or without 1 μg of imipenem/ml to examine the number of transformants and viable cells, respectively. The transformation of pOXA58-2 was verified by PCR method using the primers OXA-58-F and OXA-58-B. A. baumannii ATCC 19606T was included in the assay for comparison.

Clinical information.

All patient data were retrospectively retrieved from medical records. A patient's antimicrobial therapy was considered to be appropriate if the isolate of A. baylyi demonstrated in vitro susceptibility to at least one of the antimicrobial agents used within 3 days. The present study was conducted under the approved protocol of Joint Institutional Review Board of Taipei Veterans General Hospital. Since the data were obtained from retrospective chart review, informed consent was not required.


Genotypic identification and ribotyping of the A. baylyi isolates.

The ITS sequences of the six clinical isolates showed 98 to 99% identity with that of several A. baylyi reference strains deposited in GenBank. In the genome of A. baylyi strain ADP1, there were seven copies of ITSs. They can be divided into two groups based on length and sequence (86.59% sequence similarity between each group). In the phylogenetic analysis, the ITSs from both groups were grouped together with those from the six clinical isolates and other reference strains of A. baylyi (data not shown).

In the comparison of the 16S rRNA gene sequences, the six clinical isolates also had the highest similarity (99% for four isolates; 100% for two isolates, accession no. EU604244 and EU604245) with several reference strains of A. baylyi. The seven copies of the 16S rRNA gene from strain ADP1 is nearly identical to one another, except in one copy the nucleotide changed from A to G at nucleotide position 949. For phylogenetic study, the clinical isolates and the A. baylyi strains formed a separate cluster within the Acinetobacter genus (Fig. (Fig.1).1). The 16S rRNA sequences of these six clinical isolates had 97.31 to 97.87% similarity with that of Acinetobacter genomic 13TU (ATCC 17922) and 97.15 to 97.71% similarity with that of A. baumannii (ATCC 19606T). These were the second and third nearest species. The ribopatterns of the six clinical isolates were similar to one another but different from the reference strain (Fig. (Fig.22).

FIG. 1.
Neighbor-joining phylogenetic tree based on 16S rRNA gene sequences of 37 Acinetobacter reference (including 16 type) strains. Note the cluster of six clinical isolates with the A. baylyi strains. Selected bootstrap analysis (100×) values are ...
FIG. 2.
Dendrogram of ribopatterns generated from clinical isolates and reference strain of A. baylyi. The dendrogram was constructed by unweighted pair-group method for arithmetic averages clustering analysis.

Phenotypic identification.

The 32 GN system identified five of the clinical isolates as A. baumannii (actually equivalent to A. calcoaceticus-A. baumannii complex) but had a low discriminatory level (<80% probability). The major difference in the assimilation test between A. baylyi and A. calcoaceticus-A. baumannii complex was l-arabinose and d-ribose, which were negative for A. baylyi but positive in 93 and 77%, respectively, of the A. calcoaceticus-A. baumannii complex isolates (provided by the database). One clinical isolate was identified as A. johnsonii (91.8% probability). Unexpectedly, the reference strain ATCC 33305 was repeatedly identified as Ralstonia pickettii. Indeed, R. pickettii was the second nearest species identified for two of the clinical isolates but had a low probability (28.5%). The identification obtained by Vitek 2 assigned three isolates as A. baumannii with an “excellent” or “very good” confidence level (>90% probability). Three of the clinical isolates were identified as Pseudomonas spp., and the reference strain was identified as A. lwoffii with a “good” confidence level.

Antimicrobial susceptibility testing.

The reference strain was susceptible to all of the tested antibiotics except aztreonam, to which it showed intermediate resistance (Table (Table2).2). Compared to the reference strain, the clinical isolates were more resistant to antimicrobial agents, especially to many classes of beta-lactams. All clinical isolates were susceptible to imipenem, aminoglycosides, levofloxacin, trimethoprim-sulfamethoxazole, and chloramphenicol.

Antimicrobial susceptibility of a reference strain and 6 clinical isolates of A. baylyi

Detection of ESBL, AmpC type beta-lactamase, ISs, and transformation assay.

All clinical isolates produced beta-lactamase based on nitrocefin test, but the phenotypic assays failed to demonstrate the production of ESBL, and the inhibitory zone around the disk containing extended-spectrum cephalosporin did not increase in size in the presence of cloxacillin. Three of the clinical isolates (isolates 133, 9255, and 1477) showed positive results in the double-disk synergy test with the use of APB. With the PCR methods, only the reference strain but none of the clinical isolates gave a band corresponding to blaADC-8 gene. In addition, no known ESBL and other AmpC beta-lactamase genes could be detected in the reference or clinical isolates. IS1236 was detected in the reference stain and all but one of the clinical isolate (723), but ISAba1 was found only in isolate 9255. Among the six clinical isolates, two retained a similar level of natural competence as the reference strain (Table (Table3).3). Three clinical isolates showed a decrease in competence but were still more transformable than the A. baumannii type strain (Table (Table33).

Results of natural transformation assay

Patients' clinical features.

All patients were adults, and four were males (Table (Table4).4). The patients had multiple underlying diseases and/or invasive devices. All of the patients, except case 3, acquired the infection nosocomially. Three patients suffered from intracranial hemorrhage and developed bacteremia in the neurological intensive care unit. Case 3, who complained local tenderness over the port-A insertion side, had a purulent discharge, and the pus culture also tested positive for A. baylyi. The bacteremia in case 2 was most probably associated with a biliary tract infection, in which the bacteria may have entered via the percutaneous transhepatic cholangial drainage tube. We were unable to determine the routes of infection in the remaining four patients.

Clinical characteristics of patients with A. baylyi bacteremiaa

All patients presented with fever during bacteremia, with body temperature from 38.2 to 39.7°C (median, 38.8°C). Cases 2 and 4 developed septic shock. Leukocytosis (white blood cell count of >1010 cells/liter) was found in cases 1, 2, and 6, and leukopenia (white blood cell count of <4 × 109 cells/liter) was found in cases 3 and 5. The value of C-reactive protein, which was available in four patients, ranged from 28.1 to 99.2 mg/liter. Bacterial cultures were monomicrobial in cases 3, 4, 5, and 6. In cases 1 and 2, Acinetobacter genomic species 13TU was concomitantly isolated from blood samples. All patients received antimicrobial therapy with a broad-spectrum beta-lactam antibiotic, with or without an aminoglycoside. Based on our retrospective analysis (Table (Table4),4), only three patients received appropriate antimicrobial therapy. None of the patients died from the bacteremia.


A. baylyi strain ADP1 is highly competent in natural genetic transformation and metabolic versatility (23) and is the most widely investigated species of Acinetobacter. This species is generally considered an environmental bacterium and is frequently isolated from soil and activated sludge (10). There is a recent report of A. baylyi being isolated from clinical samples (17). To our knowledge, there have been no reports of A. baylyi infection of humans. With the use of genotypic identification method, we were able to identify six clinical isolates of A. baylyi from 47 non-A. calcoaceticus-A. baumannii complex species.

Currently, there is no quantitative definition of Acinetobacter species based on ITS sequence analysis. Chang et al. showed that the similarity score between the nearest species of Acinetobacter is 92% (6). Although the intraspecies similarities of members of the A. calcoaceticus-A. baumannii complex are very high (99 to 100%), the intraspecies similarities of species in the non-A. calcoaceticus-A. baumannii complex are unknown. The ITSs of our clinical isolates best matched those of A. baylyi, with a similarity of 98 to 99%. We found two groups of ITSs, with diverse sequence and length, in A. baylyi strain ADP1. A. haemolyticus and A. johnsonii also have heterogeneity in the number of copies of ITSs (6). However, our phylogenetic analysis clusters the ITSs from both groups in A. baylyi. This indicates that analysis of the ITS from either group of A. baylyi will not lead to misidentification.

Compared to ITS analysis, analysis of the 16S rRNA gene is a better way to identify A. baylyi. The 16S rRNA sequence of the 6 clinical isolates yielded a similarity score of ≥99% with sequences of several reference strains of A. baylyi. Moreover, there was ≥0.5 sequence diversity with the nearest Acinetobacter spp. Therefore, based on criteria adopted by most taxonomists (4, 14), the six clinical isolates were confirmed as A. baylyi.

The frequency of genetic recombination in A. baylyi might cause different ribopatterns between reference strains and clinical isolates, as previously noted in A. baumannii (8). Although the ribopatterns of our six clinical isolates were not useful for species identification, they were all very similar, indicating a clonal relationship.

It was well known that phenotypic methods have the limitation for the identification of Acinetobacter spp. However, the 32 GN system had a better chance of identifying A. baylyi than the Vitek 2 system from clinical samples. We found that the 32 GN system correctly identified all six of the clinical isolates to the genus level, and five were identified as A. baumannii, but with low discrimination. The Vitek 2 system identified three isolates as Acinetobacter with high probability but misidentified these isolates as belonging to the A. calcoaceticus-A. baumannii complex. The Vitek 2 misidentified the other three clinical isolates at the genus level. Previous research has also demonstrated that the Vitek 2 fails in the identification of other Acinetobacter species, such as A. ursingii (11) and A. lwoffii (12).

It was previously demonstrated that genome of A. baylyi strain ADP1 contains very few traits that are associated with pathogenesis (2). The genome lacks virulence-related genes such as toxins, invasins, and secretory systems, even though it does contain 10 open reading frames encoding hemolysin-like proteins (2). Nevertheless, infection with clinical isolates of A. baylyi can result in systemic signs of infection and even septic shock. Notably, four of our bacteremia patients were infected with A. baylyi alone, indicating that this species can be pathogenic. All of our affected patients had severe underlying diseases (five with either diabetes mellitus or malignancy), only three patients received appropriate therapy, and yet none of the patients died. Although our sample size is very small, this suggests that A. baylyi is an opportunistic pathogen with low virulence.

Interestingly, five of our cases acquired the pathogen nosocomially, in which the reservoir was unknown. Although the clinical isolates of A. baylyi were not as resistant to antimicrobial agents as species in the A. calcoaceticus-A. baumannii complex, they were more antibiotic resistant than the reference strain, especially to beta-lactams, and all of them demonstrated a production of beta-lactamase. Although IS1236 was detected in five isolates and ISAba1 was detected in one isolate, none had the known ESBL or AmpC type beta-lactamase gene located downstream of these ISs. Although the inhibitory zones of the extended-spectrum cephalosporins did not increase in size in the presence of cloxacillin, the presence of undetermined plasmid-mediated class C beta-lactamases in some of the isolates cannot be excluded owing to the positive result in APB test.

Our clinical isolates of A. baylyi were susceptible to imipenem, aminoglycosides, levofloxacin, trimethoprim-sulfamethoxazole, and chloramphenicol. The susceptibility to chloramphenicol might differentiate A. baylyi from species of the A. calcoaceticus-A. baumannii complex since 98% (146/149) of the A. calcoaceticus-A. baumannii complex strains isolated from the same hospital were resistant to chloramphenicol (7). Four of the clinical isolates had diminished transformability. Bacher et al. had also demonstrated the loss of natural competence in A. baylyi in an evolutionary experiment (1). Loss of transformability might be due to a corresponding increase in fitness (1).

In conclusion, the present study demonstrated that A. baylyi is a potential human pathogen. Based on our study, A. baylyi appears to be an opportunistic pathogen that can cause nosocomial infection with a favorable outcome. Clinicians should suspect infection by A. baylyi when an isolate from a clinical sample is identified by the 32 GN system as A. calcoaceticus-A. baumannii complex with low discrimination and the isolate shows susceptibility to chloramphenicol. The isolates can then be subjected to sequence analysis for accurate identification. The high competence of natural transformation and the increasing antibiotic resistance in some of the clinical isolates suggests that this species may become a significant threat in the future.


This study was supported by grants from the National Science Council of Taiwan (NSC 95-2314-B-010-061-MY2), Taipei Veterans General Hospital (VGH-96-B1-011), and the National Health Research Institutes (Taiwan).


[down-pointing small open triangle]Published ahead of print on 16 July 2008.


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