Acinetobacter in Denmark: I. Taxonomy, antibiotic susceptibility, and pathogenicity of 112 clinical strains

Whole-Genome Analysis of an Extensively Drug-Resistant Acinetobacter baumannii Strain XDR-BJ83: Insights into the Mechanisms of Resistance of an ST368 Strain from a Tertiary Care Hospital in China

Acinetobacter baumannii is an important pathogen of nosocomial infections. Nosocomial outbreaks caused by antibiotic-resistant A. baumannii remain a significant challenge. Understanding the antibiotic resistance mechanism of A. baumannii is critical for clinical treatment. The purpose of this study was to determine the whole-genome sequence (WGS) of an extensively drug-resistant (XDR) A. baumannii strain, XDR-BJ83, which was associated with a nosocomial outbreak in a tertiary care hospital of China, and to investigate the antibiotic resistance mechanism of this strain. The WGS of XDR-BJ83 was performed using single-molecule real-time sequencing. The complete genome of XDR-BJ83 consisted of a 4,011,552-bp chromosome and a 69,069-bp plasmid. The sequence type of XDR-BJ83 was ST368, which belongs to clonal complex 92 (CC92). The chromosome of XDR-BJ83 carried multiple antibiotic resistance genes, antibiotic efflux pump genes, and mobile genetic elements, including insertion sequences, transposons, integrons, and resistance islands. The plasmid of XDR-BJ83 (pBJ83) was a conjugative plasmid carrying type IV secretion system. These results indicate that the presence of multiple antibiotic resistance genes, efflux pumps, and mobile genetic elements is likely associated with resistance to various antibiotics in XDR-BJ83.

In vitro activity and in vivo efficacy of clavulanic acid against Acinetobacter baumannii

Clavulanic acid (CLA) exhibits low MICs against some Acinetobacter baumannii strains. The present study evaluates the efficacy of CLA in a murine model of A. baumannii pneumonia. For this purpose, two clinical strains, Ab11 and Ab51, were used; CLA MICs for these strains were 2 and 4 mg/liter, respectively, and the imipenem (IPM) MIC was 0.5 mg/liter for both. A pneumonia model in C57BL/6 mice was used. The CLA dosage (13 mg/kg of body weight given intraperitoneally) was chosen to reach a maximum concentration of the drug in serum similar to that in humans and a time during which the serum CLA concentration remained above the MIC equivalent to 40% of the interval between doses. Six groups (n = 15) were inoculated with Ab11 or Ab51 and were allocated to IPM or CLA therapy or to the untreated control group. In time-kill experiments, CLA was bactericidal only against Ab11 whereas IPM was bactericidal against both strains. CLA and IPM both decreased bacterial concentrations in lungs, 1.78 and 2.47 log10 CFU/g (P < or = 0.001), respectively, in the experiments with Ab11 and 2.42 and 2.28 log10 CFU/g (P < or = 0.001), respectively, with Ab51. IPM significantly increased the sterility of blood cultures over that for the controls with both strains (P < or = 0.005); CLA had the same effect with Ab51 (P < 0.005) but not with Ab11 (P = 0.07). For the first time, we suggest that CLA may be used for the treatment of experimental severe A. baumannii infections.

Wastewater treatment contributes to selective increase of antibiotic resistance among Acinetobacter spp

The occurrence and spread of multi-drug resistant bacteria is a pressing public health problem. The emergence of bacterial resistance to antibiotics is common in areas where antibiotics are heavily used, and antibiotic-resistant bacteria also increasingly occur in aquatic environments. The purpose of the present study was to evaluate the impact of the wastewater treatment process on the prevalence of antibiotic resistance in Acinetobacter spp. in the wastewater and its receiving water. During two different events (high-temperature, high-flow, 31 degrees C; and low-temperature, low-flow, 8 degrees C), 366 strains of Acinetobacter spp. were isolated from five different sites, three in a wastewater treatment plant (raw influent, second effluent, and final effluent) and two in the receiving body (upstream and downstream of the treated wastewater discharge point). The antibiotic susceptibility phenotypes were determined by the disc-diffusion method for 8 antibiotics, amoxicillin/clavulanic acid (AMC), chloramphenicol (CHL), ciprofloxacin (CIP), colistin (CL), gentamicin (GM), rifampin (RA), sulfisoxazole (SU), and trimethoprim (TMP). The prevalence of antibiotic resistance in Acinetobacter isolates to AMC, CHL, RA, and multi-drug (three antibiotics or more) significantly increased (p<0.01) from the raw influent samples (AMC, 8.7%; CHL, 25.2%; RA, 63.1%; multi-drug, 33.0%) to the final effluent samples (AMC, 37.9%; CHL, 69.0%; RA, 84.5%; multi-drug, 72.4%), and was significantly higher (p<0.05) in the downstream samples (AMC, 25.8%; CHL, 48.4%; RA, 85.5%; multi-drug, 56.5%) than in the upstream samples (AMC, 9.5%; CHL, 27.0%; RA, 65.1%; multi-drug, 28.6%). These results suggest that wastewater treatment process contributes to the selective increase of antibiotic resistant bacteria and the occurrence of multi-drug resistant bacteria in aquatic environments.

Distinct antimicrobial resistance patterns and antimicrobial resistance-harboring genes according to genomic species of Acinetobacter isolates

Using 58 isolates of Acinetobacter species recovered from a university hospital between August 2004 and March 2005, we performed genomic identification by amplified rRNA gene restriction analysis (ARDRA) and investigated the existence of metallo-beta-lactamase (MBL) producers and extended-spectrum beta-lactamase (ESBL) producers. Genomic species identification of Acinetobacter strains using ARDRA showed that 40 strains were genomic species 2 (Acinetobacter baumannii), 9 were 13 sensu Tjernberg and Ursing (13TU), 5 were Acinetobacter phenon 6/ct 13TU, and 4 were Acinetobacter genospecies 3. Among 58 strains, 13 isolates were MBL producers carrying bla(IMP-1) or bla(VIM-2) and 13 isolates were ESBL producers carrying bla(PER-1). Notably, the MBL producers were mostly 13TU, Acinetobacter phenon 6/ct 13TU, and Acinetobacter genospecies 3, which showed susceptibility to ciprofloxacin and ampicillin-sulbactam. However, 12 of 13 strains carrying bla(PER-1) were A. baumannii, showing multidrug resistance. The data revealed that the antimicrobial resistance patterns and resistance-harboring genes of Acinetobacter species are remarkably distinct according to the genomic species of Acinetobacter isolates.

Comparison of a repetitive extragenic palindromic sequence-based PCR method and clinical and microbiological methods for determining strain sources in cases of nosocomial Acinetobacter baumannii bacteremia

Using a repetitive extragenic palindromic PCR (REP-PCR), we genotypically characterized strains causing nosocomial Acinetobacter baumannii infections and analyzed the source of bacteremia in 67 patients from an institution in which infections by this bacterium were endemic. Six different genotypes were found, including 21, 27, 3, 9, 3, and 4 strains. The probable source of bacteremia, according to clinical and/or microbiological criteria, was known in 42 patients (63%): respiratory tract (n = 19), surgical sites (n = 12), intravascular catheters (n = 5), burns (n = 3), and urinary tract (n = 3). The definite source of bacteremia, according to REP-PCR, could be established in 30 (71%) out of the 42 patients with strains from blood and other sites; in these cases clinical and microbiological criteria for the source of bacteremia were thus confirmed. In the remaining 12 patients (29%) the probable source was refuted by the REP-PCR method. The definite sources of bacteremia according to genotype were as follows: respiratory tract in 13 patients (31%), surgical sites in 8 (19%), intravascular catheters in 4 (9%), burns in 3 (7%), and urinary tract in 2 (5%). A comparison of strains from blood cultures and other sites with regard to their REP-PCR and antimicrobial resistance profiles was also made. Taking the REP-PCR as the "gold standard," the positive predictive value of antibiotype was 77% and the negative predictive value was 42%. In summary, the utility of the diagnosis of the source of nosocomial A. baumannii bacteremia using clinical and/or microbiological criteria, including antibiotyping, is limited, as demonstrated by REP-PCR.

Characteristics of clinical Acinetobacter spp. strains

Resistance to 13 antimicrobial agents, resistance to the bactericidal activity of human serum, hydrophobic properties, lipolytic activity and production of histamine were determined in a total of 50 clinical Acinetobacter spp. strains (A. baumannii, A. lwoffii, A. calcoaceticus, A. haemolyticus). None of the tested isolates showed resistance to meropenem and none of A. lwoffii, A. calcoaceticus and A. haemolyticus strains were resistant to amikacin. Forty-six strains (92%) manifested resistance to ampicillin, 90% to cefuroxime, 68% to ciprofloxacin, 58% to piperacillin, gentamicin and cotrimaxazole, 50% to cefotaxime, 44% to amikacin, 42% to ceftazidime, 38% to piperacillin/tazobactam, 24% to netilmicin and 16% to ampicillin/sulbactam. In particular, A. baumannii and A. calcoaceticus strains showed considerable antibiotic resistance. Thirty-one isolates (62%) showed serum resistance; intermediate sensitivity was found in 19 isolates (38%). The majority of the strains (72%) demonstrated a strongly hydrophobic character; 16% of isolates exhibited moderate hydrophobic properties. All strains showed lipolytic activity; production of histamine was detected in 14 of 43 strains examined.

RAPD-PCR typing of Acinetobacter isolates from activated sludge systems designed to remove phosphorus microbiologically

AIMS

This study investigated whether there were differences in RAPD fingerprints between already described genomic species of Acinetobacter and those from activated sludge systems. Whether plant-specific populations of acinetobacters exist was also examined.

METHODS AND RESULTS

Fifty-two isolates of Acinetobacter from four biological phosphorus removal (EBPR) systems of different configurations, and the known genomic species, were characterized using RAPD-PCR, and fragments separated on agarose gels. Patterns were analysed using Gel Pro software and data analysed numerically. RAPD-PCR produced patterns suggesting that many environmental isolates differ from known genomic species. In two cases, strains from individual plants clustered closely enough together to imply that there may be plant-specific populations of acinetobacters.

CONCLUSION

The data suggest that current understanding of the taxonomic status of Acinetobacter may need modifying to accommodate non-clinical isolates, as many of the clusters emerging after numerical analysis of RAPD-PCR fragments from activated sludge isolates were quite separate from the clusters containing the already described genomic species. Some evidence was also obtained from the clusters generated to support a view that particular populations of Acinetobacter may occur in individual activated sludge plants.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data suggest that the current understanding of the systematics of Acinetobacter, based as it is almost exclusively on clinical isolates, may need drastic revision to accommodate environmental strains. They also suggest that a re-examination of the importance and role of Acinetobacter in the activated sludge process may be appropriate.

Outer-membrane proteins pattern and detection of beta-lactamases in clinical isolates of imipenem-resistant Acinetobacter baumannii from Brazil

In order to compare imipenem-sensitive and -resistant Acinetobacter baumannii strains isolated from three patients, ribotyping, plasmid, beta-lactamase detection and outer-membrane analysis were performed. Ribotyping and the use of a beta-lactam during the period when the strains were isolated suggested that they had a common origin and that resistance occurred in vivo. Outer membrane analysis showed no difference between susceptible and resistant strains with the exception of an A2 imipenem-resistant strain that lost a protein band of 31-36 kDa. Beta-lactamases were detected using isoelectric focusing in all strains (pI of 7.4). In addition, two beta-lactamases (pI of 5.9 and 6.7) were found in imipenem-resistant isolates. The double-disc technique demonstrated the presence of a beta-lactamase capable of imipenem inactivation in resistant strains. Plasmid analysis showed that all susceptible strains had the same pattern, one resistant strain did not have any plasmid, one had the same plasmid pattern of its susceptible pair and only one had a different pattern when compared with its susceptible pair.

Phenotypic characterization and antibiotic resistance of Acinetobacter spp. isolated from aquatic sources

A total of 99 Acinetobacter isolates from sewage, freshwater aquaculture habitats, trout intestinal contents and frozen shrimps was characterized phenotypically and antibiotic susceptibility patterns determined. One group of genomic species, including Ac. johnsonii, Ac. lwoffi and spp. 15TU, was detected in all sample types and represented the majority of the isolates (n = 54). Isolates belonging to the Acb complex (Ac. calcoaceticus, Ac. baumannii and genomic species 3) were detected in sewage (n = 6) and frozen shrimps (n = 1), Ac. haemolyticus in frozen shrimps (n = 6) and trout intestinal contents (n = 2) and genomic species 11 in freshwater aquaculture habitats (n = 6) and trout intestinal contents (n = 1). Acinetobacter junii (n = 5), genomic species 10 (n = 2), 14BJ (n = 8) and 16BJ (n = 4) were only isolated from sewage. Acinetobacter isolates from sewage were generally more biochemically reactive and resistant to antimicrobial agents compared with isolates from other sample types. Different strains, often belonging to different genomic species, were isolated from sites situated upstream and downstream of the discharge point of a pharmaceutical plant. This finding supported the hypothesis that the waste effluent from the pharmaceutical plant was likely to cause a change in the distribution of Acinetobacter spp. by selecting and/or introducing antibiotic-resistant strains into the recipient sewers.

Development of bacterial resistance to the third generation cephalosporins and their clinical use

Development of Gram-negative rods resistance to the third generation cephalosporins (cefotaxime, ceftazidime, cefoperazone) in connection with their application at the University Hospital in Olomouc was evaluated in this study. The highest increase in resistance to cefotaxime was detected in Enterobacter cloacae (from 22.9% in 1995 to 49.0% in 1997) and Enterobacter agglomerans strains (28.0% - 40.5%). In addition, increased resistance to ceftazidime in Acinetobacter baumannii (12.5% - 35.1%), Enterobacter aerogenes (7.4% - 20.9%), Enterobacter cloacae (16.7% - 47.2%) and Pseudomonas aeruginosa (4.0% - 26.3%) was observed. Finally, the greatest increase in frequency of strains resistant to cefoperazone was observed in E. aerogenes (18.4% - 30.1%), E. agglomerans (31.0% - 52.3%), E. cloacae (35.5% - 47.2%) and Providencia rettgeri (26.5% - 53.2%). A 23.5% increase in third generation cephalosporin use was evident by evaluation of RDDD(ATB) parameters in 1996 and 1997. Corresponding values for individual antibiotics were 26.5% cefotaxime, 20.7% ceftriaxone, and 40.3% ceftazidime increase. However, cefoperazone use decreased by 10.9%.

Characterization of oligonucleotide probes for the identification of Acinetobacter spp., A. baumannii and Acinetobacter genomic species 3

The 16S-23S intergenic spacer regions of four Acinetobacter genomic species belonging to the A. calcoaceticus-A. baumannii (Acb) complex, i.e. genomic species 1 (A. calcoaceticus), genomic species 2 (A. baumannii), genomic species 3 and Tjernberg and Ursing (TU) genomic species 13, have been cloned and sequenced. Sequence analysis led to the discovery of a single copy of IIe and Ala tRNA genes within each spacer. Sequence comparison allowed the identification of a 192-base-pair long highly conserved sequence between the 3' end of the 16S rRNA and the 5' end of the tRNA(Ala) genes. Moreover, two short regions, which were specific to, respectively, genomic species 2 and 3, could be identified. Oligonucleotides corresponding to these sequences were constructed and tested for the ability to hybridize with chromosomal DNA extracted from Acinetobacter belonging to different genomic species and with chromosomal DNA of other bacterial genera. One of these oligonucleotides was demonstrated to be useful as a sensitive and specific probe for A. baumannii. A less sensitive probe for Acinetobacter genomic species 3 was also developed.

Surveillance of infections in hospital: agents and antibiotic-resistance

The surveillance system for Hospital Acquired Infections (HAI) implemented in the S. Eugenio hospital of Rome allows to monitor the distribution of the micro-organisms by service and their resistance to antibiotics. It is based upon the data collected by the Central Analysis Laboratory of the hospital. The data of four high-risk departments (Surgical service, Intensive Care Unit, Haematology, Burn Unit) are reported. In the period October 1992-September 1993, 3909 samples have been analyzed; 1603 (43.1%) were found positive to the microbiologic analysis. The results of the antibiotic resistance concerning four micro-organisms, agents of HAI are reported and discussed. Surveillance systems are necessary to limit the frequency of HAI.

Outbreak of septicaemia in neonates caused by Acinetobacter junii investigated by amplified ribosomal DNA restriction analysis (ARDRA) and four typing methods

Septicaemia caused by Acinetobacter occurred in six infants in the neonatal unit. A total of 18 acinetobacters were isolated from blood cultures, cultures of intravascular catheters, and surveillance cultures. Twelve isolates from the six affected infants were identified as Acinetobacter junii by the use of a novel method, amplified ribosomal DNA restriction analysis (ARDRA). Typing of the organisms using the biochemical profiles of the API 20NE system, antibiogram typing, cell envelope protein electrophoresis, and PCR fingerprinting with two primer sets, ERIC1/ERIC2 and ERIC2/ 1026, showed that these 12 isolates were indistinguishable, whereas the remaining six isolates were different. The six infants recovered after therapy with ciprofloxacin alone in five cases and with a combination of ciprofloxacin and gentamicin in one case. This study showed that A. junii is capable of causing a serious, though non-fatal infection in neonates. The combined use of genotypic and phenotypic methods allowed the rapid separation of epidemic from non-epidemic isolates. It is concluded that for a better understanding of the role of the various Acinetobacter genomic species in human pathology, identification of acinetobacters according to the recent taxonomy is imperative.

Structural and serological characterisation of two O-specific polysaccharides of Acinetobacter

Extraction of dry bacteria of Acinetobacter strain 34 (DNA group 2) or Acinetobacter strain 108 (DNA group 13) by phenol/water yielded a polymer that was identified by means of serological studies and fatty acid analysis as S-form lipopolysaccharide. Degradation of the lipopolysaccharides of strains 34 and 108 in 1% acetic acid and 5% acetic acid, respectively, and gel-permeation chromatography gave the respective O-antigenic polysaccharides, the structures of which were determined, by compositional analysis and NMR spectroscopy of the polysaccharide, as [Sequence: see text] for strain 108, where D-Fucp3NBuOH represents 3-[(R)-3-hydroxybutyramido] -3,6-dideoxy-D-galactose and D-GalpANAc represents 2-acetamido-2-deoxy-D-galacturonic acid. Both structures were specifically recognised in Western blots by polyclonal rabbit antisera and there was no cross-reaction between these two structures.

Evaluation of the ability of a commercial system to identify Acinetobacter genomic species

A collection of 130 Acinetobacter strains identified by DNA hybridization to 18 different genomic species was used to assess the ability of the API 20NE system (bioMérieux, France) to identify Acinetobacter genomic species and to determine its accuracy. Fifty-eight (87%) of the 67 strains of genomic species defined in the database (version 5.1) were identified to the appropriate genomic species. The Acinetobacter baumannii strains and the Acinetobacter haemolyticus strains were all identified correctly. Three of five Acinetobacter junii strains, three of eight Acinetobacter johnsonii strains, and 11 of 13 Acinetobacter lwoffii strains were also identified correctly. The 58 correctly identified strains represented 45% of the total 130 strains. Thirty-six of the 72 inappropriately identified strains were designated Acinetobacter baumannii. Thirty-one of these 36 strains belonged to genomic species 1 (Acinetobacter calcoaceticus), 3, or 13TU. Analysis of the profiles showed that the API system does not discriminate between genomic species 1, 2, 3, and 13TU. Lumping of these groups into the Acinetobacter calcoaceticus-Acinetobacter baumannii complex in the API 20NE database would make the system considerably more accurate. Incorporation of these data into the database may improve identification of the remaining genomic species, including some that are not defined. However, the discriminative power of the tests in the API galleries is insufficient for correct identification of all Acinetobacter genomic species.

Imipenem/cilastatin: an update of its antibacterial activity, pharmacokinetics and therapeutic efficacy in the treatment of serious infections

The prototype carbapenem antibacterial agent imipenem has a very broad spectrum of antibacterial activity, encompassing most Gram-negative and Gram-positive aerobes and anaerobes, including most beta-lactamase-producing species. It is coadministered with a renal dehydropeptidase inhibitor, cilastatin, in order to prevent its renal metabolism in clinical use. Extensive clinical experience gained with imipenem/cilastatin has shown it to provide effective monotherapy for septicaemia, neutropenic fever, and intra-abdominal, lower respiratory tract, genitourinary, gynaecological, skin and soft tissues, and bone and joint infections. In these indications, imipenem/cilastatin generally exhibits similar efficacy to broad-spectrum cephalosporins and other carbapenems and is at least equivalent to standard aminoglycoside-based and other combination regimens. Imipenem/cilastatin is generally well tolerated by adults and children, with local injection site events, gastrointestinal disturbances and dermatological reactions being the most common adverse events. Seizures have also been reported, occurring mostly in patients with impaired renal function or CNS pathology, or with excessive dosage. Although it is no longer a unique compound, as newer carbapenems such as meropenem are becoming available, imipenem/cilastatin nevertheless remains an important agent with established efficacy as monotherapy for moderate to severe bacterial infections. Its particular niche is in treating infections known or suspected to be caused by multiresistant pathogens.

Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis

A total of 53 field and reference strains, including the type strains of the seven named species (nomenspecies) and belonging to the 18 described genomic species (DNA groups) of the genus Acinetobacter, were studied by amplified ribosomal DNA restriction analysis (ARDRA). Restriction analysis with the enzymes AluI, CfoI, MboI, RsaI, and MspI of the enzymatically amplified 16S rRNA genes allowed us to identify all species except the genomic species 4 (Acinetobacter haemolyticus) and 7 (A. johnsonii), 5 (A. junii) and 17, and 10 and 11, which clustered pairwise in three respective groups. Further analysis with the enzyme HaeIII, HinfI, NciI, ScrFI, or TaqI did not allow us to differentiate the species within these three clusters. However, use of a few additional simple phenotypic tests (hemolysis, growth at 37 degrees C, production of acid from glucose, and gelatin hydrolysis) can be used to differentiate between the species within these clusters. ARDRA proved to be a rapid and reliable method for the identification of most of the Acinetobacter genomic species, including the closely related DNA groups 1 (A. calcoaceticus), 2 (A. baumannii), 3, and 13. The results of this study suggest that ARDRA can be used for the identification of Acinetobacter species and as such may help to elucidate the ecology and clinical significance of the different species of this genus. Since ARDRA uses universal 16S rRNA gene primers, it is expected to be applicable to the identification of most bacterial species. Furthermore, ARDRA is less prone to contamination problems than PCR for detection, since the use of cultured organisms results in a large initial quantity of target DNA.

Description of Leeds Acinetobacter Medium, a new selective and differential medium for isolation of clinically important Acinetobacter spp., and comparison with Herellea agar and Holton's agar

Acinetobacter spp. are responsible for an increasing number of opportunistic, nosocomial infections. They have been isolated from diverse inanimate objects in the hospital environment and are resistant to most of the commonly used antibiotics. Existing media for the isolation of Acinetobacter spp. are either nonselective, allowing the growth of unwanted bacteria, or too inhibitory, inhibiting the growth of many Acinetobacter strains. For the rapid isolation and effective control of Acinetobacter infection, a new selective and differential medium, Leeds Acinetobacter Medium (LAM), has been developed to isolate Acinetobacter spp. from clinical and environmental sources. The concentration of antibiotics and other ingredients in this medium have been determined according to the results of MIC and viable counts performed for these ingredients. LAM was compared with other selective and differential media for the isolation of Acinetobacter spp. from a local hospital environment and proved to be better in terms of recovery and selectivity.