Molecular surveillance of European quinolone-resistant clinical isolates of Pseudomonas aeruginosa and Acinetobacter spp. using automated ribotyping

Detection of biofilm production and antimicrobial susceptibility in clinical isolates of Acinetobacter baumannii and Pseudomonas aeruginosa

Acinetobacter baumannii and Pseudomonas aeruginosa are commensal which commonly colonize humans. As a result of their ubiquitous nature, reservoirs in hospital environment and resistance to many antimicrobial agents they are responsible for hospital – acquired infections. Additionally treatment of these infections is difficult because of the ability for biofilm formation. Aim of the paper was to determine the association between biofilm formation on medical devices and antibiotic resistance profile, compared to respiratory samples in clinical isolates of Acinetobacter baumannii and Pseudomonas aeruginosa. Material and methods: The study comprised 50 clinical samples (36 from medical devices and 14 as а control group from respiratory secretions). Acinetobacter baumannii and Pseudomonas aeruginosa were identified by routine microbiological methods. Modification of the microtiter plate assay described by Stepanovic et al. was used to investigate the formation of biofilm. The antimicrobial susceptibility testing was performed according to EUCAST guidelines. Results:  Of the 50 analyzed strains, 16 (32%) were non-biofilm producers, and 34 (68%) were producing biofilms. Out of these, 29 (58%) were from medical devices, and 5 (10%) from the control group. Acinetobacter baumannii showed biofilm formation in 19 (67.9%), of which 17 (60.7%) from medical devices, and 2 (7.1%) from control group. Pseudomonas aeruginosa produced biofilm in 15 (68.1%), of which 12 (54.5%) from medical devices, and  3 (13.6%) from the control group. Multidrug resistance was detected in 40 (80%). All strains of Acinetobacter baumannii were multidrug resistant (MDR). For Pseudomonas aeruginosa, 11 (73.3%) biofilm forming isolates were MDR, and 1 (14.2%) non-biofilm forming isolate was MDR. Conclusion: Biofilm production was higher in strains from medical devices. Eighty percent of isolates were MDR. This is a serious challenge for treatment of these hospital-acquired infections.

Antimicrobial activities of sitafloxacin and comparators against the clinical isolates of less common nonfermenting Gram-negative bacteria

The in vitro antimicrobial activities of sitafloxacin and comparators against 320 clinical isolates of less common nonfermenting Gram-negative bacteria (NFGNB) were assessed by determining the minimum inhibitory concentrations (MICs) using broth microdilution method. In terms of MIC_50/90 values, sitafloxacin was highly active against Stenotrophomonas maltophilia (0.25/1 mg/L), Burkholderia cepacia complex (0.25/2 mg/L), Achromobacter xylosoxidans (0.25/1 mg/L), and Chryseobacterium gleum (1/2 mg/L), but less active for Elizabethkingia (1/8 mg/L) and Chryseobacterium indologenes (16/32 mg/L). Sitafloxacin was more active than other fluoroquinolones against these NFGNB except Chryseobacterium. The results are helpful for clinicians to be aware of the role of sitafloxacin in managing the infections caused by these NFGNB.

In Vitro Activities of Colistin and Sitafloxacin Combinations against Multidrug-, Carbapenem-, and Colistin-Resistant Acinetobacter baumannii Using the Broth Microdilution Checkerboard and Time-Kill Methods

Drug-resistant Acinetobacter baumannii (A. baumannii) infections are a critical global problem, with limited treatment choices. This study aims to determine the in vitro activities of colistin–sitafloxacin combinations against multidrug-, carbapenem- and colistin-resistant A. baumannii (MDR-AB, CRAB, CoR-AB, respectively) clinical isolates from tertiary care hospitals. We used the broth microdilution checkerboard and time-kill methods in this study. Synergy was found using both methods. The colistin–sitafloxacin combination showed synergy in MDR-AB, CRAB, and CoR-AB isolates (3.4%, 3.1%, and 20.9%, respectively). No antagonism was found in any type of drug-resistant isolate. The majority of CoR-AB isolates became susceptible to colistin (95.4%). The time-kill method also showed that this combination could suppress regrowth back to the initial inocula of all representative isolates. Our results demonstrated that the colistin–sitafloxacin combination might be an interesting option for the treatment of drug-resistant A. baumannii. However, further in vivo and clinical studies are required.

Comparative in vitro activity of sitafloxacin against bacteremic isolates of carbapenem resistant Acinetobacter baumannii complex

BACKGROUND

The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) complex has posed a great challenge to clinicians worldwide. Sitafloxacin has been shown to have in vitro activity against pathogens resistant to other fluoroquinolones. However, data comparing the anti-CRAB activity of sitafloxacin with that of other antimicrobial agents are limited.

METHODS

Genospecies were identified by 16S-23S ribosomal RNA intergenic spacer sequencing. Minimum inhibitory concentrations (MICs) were determined by an agar dilution method. Isolates with sitafloxacin MICs ≤ 2 mg/L were provisionally considered as susceptible to sitafloxacin. The MIC breakpoint for tigecycline susceptibility was 2 mg/L.

RESULTS

A total of 167 CRAB complex blood isolates (146 A. baumannii, 7 Acinetobacter pittii, and 14 Acinetobacter nosocomialis) were collected from January 2009 to December 2011. Around 90% of the A. baumannii isolates were resistant to amikacin, cefepime, ceftazidime, piperacillin/tazobactam, ampicillin/sulbactam, ciprofloxacin, and levofloxacin. By contrast, the rate of resistance to colistin, sitafloxacin, and tigecycline was relatively low (0%, 41.1%, and 65.1%, respectively). The MIC50 and MIC90 of ciprofloxacin, levofloxacin, and sitafloxacin were 128 mg/L and >128 mg/L; 16 mg/L and 64 mg/L; 2 mg/L and 8 mg/L, respectively. Compared with ciprofloxacin and levofloxacin, sitafloxacin had a significantly lower MIC (p < 0.001), and the rate of resistance to sitafloxacin was significantly lower than that to ciprofloxacin (97.9% vs. 41.1%, p < 0.001), levofloxacin (97.3% vs. 41.1%, p < 0.001), and tigecycline (p < 0.001).

CONCLUSION

Sitafloxacin has acceptable in vitro activity against CRAB, even against isolates resistant to other fluoroquinolones. Sitafloxacin may be considered an alternative drug of choice in treating CRAB related infections.

Single-locus-sequence-based typing of blaOXA-51-like genes for rapid assignment of Acinetobacter baumannii clinical isolates to international clonal lineages

Single-locus blaOXA-51-like sequence-based typing (SBT) was evaluated for its ability to determine correctly sequence types (STs) in Acinetobacter baumannii clinical isolates, in comparison with the Pasteur's multilocus sequence typing (MLST) reference method and 3-locus sequence typing (3-LST). The comparative study was performed in 585 multidrug-resistant (MDR) A. baumannii clinical isolates recovered from 21 hospitals located throughout Greece, Italy, Lebanon, and Turkey. The isolates belonged to nine clonal complexes (CCs) that correspond to 12 distinct sequence types (STs) and to one singleton ST. These clonal lineages predominate worldwide among nosocomial MDR A. baumannii strains. The most common clone was CC2 (ST2 and ST45; n=278 isolates) followed by CC1 (ST1 and ST20; n=155), CC25 (n=65), ST78 (n=62), CC15 (ST15 and ST84; n=9), CC10 (n=4), CC3 (n=4), CC6 (n=3), CC54 (n=3), and CC83 (n=2). Using the blaOXA-51-like SBT method, all 585 isolates of the study were typed and assigned correctly to the nine CCs and the singleton ST78. The 3-LST method was not able to classify isolates belonging to CC6, CC10, CC54, and CC83, which are not yet characterized in its database. The low-cost and convenient blaOXA-51-like SBT method, compared with 3-LST and MLST, discriminated all epidemic and sporadic lineages of our collection and could be effectively applied to type rapidly A. baumannii strains.

The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii

The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool

Outbreaks of hospital infections caused by multidrug resistant Acinetobacter baumannii strains are of increasing concern worldwide. Although it has been reported that particular outbreak strains are geographically widespread, little is known about the diversity and phylogenetic relatedness of A. baumannii clonal groups. Sequencing of internal portions of seven housekeeping genes (total 2,976 nt) was performed in 154 A. baumannii strains covering the breadth of known diversity and including representatives of previously recognized international clones, and in 19 representatives of other Acinetobacter species. Restricted amounts of diversity and a star-like phylogeny reveal that A. baumannii is a genetically compact species that suffered a severe bottleneck in the recent past, possibly linked to a restricted ecological niche. A. baumannii is neatly demarcated from its closest relative (genomic species 13TU) and other Acinetobacter species. Multilocus sequence typing analysis demonstrated that the previously recognized international clones I to III correspond to three clonal complexes, each made of a central, predominant genotype and few single locus variants, a hallmark of recent clonal expansion. Whereas antimicrobial resistance was almost universal among isolates of these and a novel international clone (ST15), isolates of the other genotypes were mostly susceptible. This dichotomy indicates that antimicrobial resistance is a major selective advantage that drives the ongoing rapid clonal expansion of these highly problematic agents of nosocomial infections.

Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii

The recent emergence of multidrug resistance (MDR) in Acinetobacter baumannii has raised concern in health care settings worldwide. In order to understand the repertoire of resistance determinants and their organization and origins, we compared the genome sequences of three MDR and three drug-susceptible A. baumannii isolates. The entire MDR phenotype can be explained by the acquisition of discrete resistance determinants distributed throughout the genome. A comparison of closely related MDR and drug-susceptible isolates suggests that drug efflux may be a less significant contributor to resistance to certain classes of antibiotics than inactivation enzymes are. A resistance island with a variable composition of resistance determinants interspersed with transposons, integrons, and other mobile genetic elements is a significant but not universal contributor to the MDR phenotype. Four hundred seventy-five genes are shared among all six clinical isolates but absent from the related environmental species Acinetobacter baylyi ADP1. These genes are enriched for transcription factors and transporters and suggest physiological features of A. baumannii that are related to adaptation for growth in association with humans.

Antibiotic susceptibility patterns and clones of Pseudomonas aeruginosa in Swedish ICUs

Pseudomonas aeruginosa is 1 of the bacteria most adaptive to anti-bacterial treatment. Previous studies have shown nosocomial spread and transmission of clonal strains of P. aeruginosa in European hospitals. In this study we investigated antibiotic susceptibility and clonality in 101 P. aeruginosa isolates from 88 patients admitted to 8 Swedish ICUs during 2002. We also compared phenotypes and genotypes of P. aeruginosa and carried out cluster analysis to determine if phenotypic data can be used for surveillance of clonal spread. All isolates were collected on clinical indication as part of the NPRS II study in Sweden and were subjected to AFLP analysis for genotyping. 68 isolates with unique genotypes were found. Phenotyping was performed using MIC values for 5 anti-pseudomonal agents. Almost 6% of the isolates were multi-drug resistant (MDR), and this figure rose to almost 8% when intermediate isolates were also included. We found probable clonal spread in 9 cases, but none of them was found to be an MDR strain. Phenotypical cluster analysis produced 40 clusters. Comparing partitions did not demonstrate any significant concordance between the typing methods. The conclusion of our study is that cross-transmission and clonal spread of MDR P. aeruginosa does not present a clinical problem in Swedish ICUs, but probable cross-transmission of non-MDR clones indicate a need for improved hygiene routines bedside. The phenotype clusters were not concordant with genotype clusters, and genotyping is still recommended for epidemiological tracking.

Acinetobacter baumannii: emergence of a successful pathogen

Acinetobacter baumannii has emerged as a highly troublesome pathogen for many institutions globally. As a consequence of its immense ability to acquire or upregulate antibiotic drug resistance determinants, it has justifiably been propelled to the forefront of scientific attention. Apart from its predilection for the seriously ill within intensive care units, A. baumannii has more recently caused a range of infectious syndromes in military personnel injured in the Iraq and Afghanistan conflicts. This review details the significant advances that have been made in our understanding of this remarkable organism over the last 10 years, including current taxonomy and species identification, issues with susceptibility testing, mechanisms of antibiotic resistance, global epidemiology, clinical impact of infection, host-pathogen interactions, and infection control and therapeutic considerations.

Molecular epidemiology of clinical Acinetobacter baumannii and Acinetobacter genomic species 13TU isolates using a multilocus sequencing typing scheme

To further expand the limited multilocus sequence typing (MLST) database for Acinetobacter baumannii, 53 clinical isolates from various outbreaks in Europe and the USA, collected between 1991 and 2004, plus the A. baumannii reference strain ATCC 19606(T) and 20 clinical Acinetobacter genomic species 13TU isolates from the same period, were analyzed using a new MLST scheme based on fragments of the gltA, gyrB, gdhB, recA, cpn60, gpi and rpoD genes. Data were compared with typing results generated using pulsed-field gel electrophoresis (PFGE) and randomly amplified polymorphic DNA (RAPD)-PCR. In total, 50 sequence types (STs) were distinguished among the A. baumannii isolates investigated, and the MLST data were in high concordance with the PFGE and RAPD-PCR results. Only five clonal complexes were identified by eBURST analysis, including the 21 STs listed in a previous study, suggesting high diversity among the A. baumannii isolates. With one exception, there was no relatedness among isolates from outbreaks in different countries (Europe) or regions (USA). No intercontinental spread was revealed. Acinetobacter genomic species 13TU isolates could also be analyzed using the A. baumannii MLST scheme (18 different STs) and could be distinguished from A. baumannii isolates according to characteristic sequences. It was concluded that the MLST scheme provides a high level of resolution and is a promising tool for studying the epidemiology of A. baumannii and Acinetobacter genomic species 13TU.

Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group

The whole-genome sequence of an epidemic, multidrug-resistant Acinetobacter baumannii strain (strain ACICU) belonging to the European clone II group and carrying the plasmid-mediated bla(OXA)(-)(58) carbapenem resistance gene was determined. The A. baumannii ACICU genome was compared with the genomes of A. baumannii ATCC 17978 and Acinetobacter baylyi ADP1, with the aim of identifying novel genes related to virulence and drug resistance. A. baumannii ACICU has a single chromosome of 3,904,116 bp (which is predicted to contain 3,758 genes) and two plasmids, pACICU1 and pACICU2, of 28,279 and 64,366 bp, respectively. Genome comparison showed 86.4% synteny with A. baumannii ATCC 17978 and 14.8% synteny with A. baylyi ADP1. A conspicuous number of transporters belonging to different superfamilies was predicted for A. baumannii ACICU. The relative number of transporters was much higher in ACICU than in ATCC 17978 and ADP1 (76.2, 57.2, and 62.5 transporters per Mb of genome, respectively). An antibiotic resistance island, AbaR2, was identified in ACICU and had plausibly evolved by reductive evolution from the AbaR1 island previously described in multiresistant strain A. baumannii AYE. Moreover, 36 putative alien islands (pAs) were detected in the ACICU genome; 24 of these had previously been described in the ATCC 17978 genome, 4 are proposed here for the first time and are present in both ATCC 17978 and ACICU, and 8 are unique to the ACICU genome. Fifteen of the pAs in the ACICU genome encode genes related to drug resistance, including membrane transporters and ex novo acquired resistance genes. These findings provide novel insight into the genetic basis of A. baumannii resistance.

New antibacterial agents for treating infections caused by multi-drug resistant Gram-negative bacteria

BACKGROUND

Infections caused by multi-drug resistant (MDR) Gram-negative bacteria represent an ever-growing area of unmet medical need. To address this need, it is imperative that novel classes of antibiotics demonstrating activity against bacterial strains resistant to established antibiotics are introduced into the clinic.

OBJECTIVES

To examine the current status of the Gram-negative antibacterial pipeline, ranging from the more advanced preclinical candidates to drugs recently launched, and look to the future of anti-Gram-negative drug development.

METHODS

Information was compiled from scientific and patent literature, conference proceedings and company publications/websites.

RESULTS/CONCLUSIONS

None of the antibacterial agents currently in clinical trials that encompass Gram-negative bacteria in their spectrum of activity possess sufficiently novel modes of action to circumvent extant antibiotic resistance mechanisms. Furthermore, although some interesting anti-Gram-negative drug candidates are nearing the beginning of clinical trials, they are limited in number and, even in the best-case scenario, many years away from the clinic.

Molecular typing indicates an important role for two international clonal complexes in dissemination of VIM-producing Pseudomonas aeruginosa clinical isolates in Hungary

VIM metallo-beta-lactamase-producing serotype O11 or O12 Pseudomonas aeruginosa isolates infecting or colonising 19 patients from seven hospitals were reported in Hungary between 2003 and 2005. In this study we characterised VIM-producing Pseudomonas spp. clinical isolates from two novel locations in Hungary; we identified three new bla(VIM) carrying integron types and the presence of the bla(VIM-2) allele in Hungary. By applying various typing techniques, including multilocus sequence typing, we revealed an important role of two international clonal complexes, CC4 and CC11, in the dissemination of bla(VIM)-positive P. aeruginosa in hospitals in Hungary. Isolate P12-Q, a representative strain from France of the major European multiresistant P12 clone, displayed ST111 which, according to eBURST analysis, is the presently calculated founder sequence type of CC4. This is in accordance with the wide geographic distribution of the P12 clone. Our data indicate that, although the CC4 clonal complex includes serotype O1 and O6 isolates as well, it also contains the P12 clone. We characterised a P. aeruginosa nosocomial clone with a singleton sequence type (ST313), that may have acquired bla(VIM-2) and bla(VIM-4) gene cassettes from a yet unidentified local gene pool in Hungary.

The increasing role of Acinetobacter species as nosocomial pathogens

Among gram-negative organisms playing a significant role in nosocomial infections, Acinetobacter species have attracted increasing attention in intensive care units during the past two decades. Acinetobacter species are implicated in a wide spectrum of infections (eg, bacteremia, nosocomial pneumonia, urinary tract infections, secondary meningitis, superinfections in burn patients). One of the most striking features of Acinetobacter species is their extraordinary ability to develop multiple resistance mechanisms against major antibiotic classes. They have become resistant to broad-spectrum β-lactams (third-generation cephalosporins, carboxypenicillins, and increasingly to carbapenems); they produce a wide range of aminoglycoside-inactivating enzymes; and most strains are resistant to fluoroquinolones. In Acinetobacter nosocomial infections, the major problems confronting clinicians in intensive care units are related to the severity of Acinetobacter nosocomial infections and to resistance to major antibiotic classes of these organisms.

Use of the DiversiLab semiautomated repetitive-sequence-based polymerase chain reaction for epidemiologic analysis on Acinetobacter baumannii isolates in different Italian hospitals

Acinetobacter baumannii is typically a nosocomial pathogen. Epidemiologic tools that can rapidly trace the spread of hospital-associated infections due to this microorganism are essential. Currently, amplified fragment length polymorphism and pulsed-field gel electrophoresis using ApaI, a macrorestriction enzyme, are the molecular techniques most widely used to type this microorganism. Unfortunately, they are technically demanding, requiring also well-trained personnel, and are time consuming. The aims of this study are 1) to evaluate the usefulness of the semiautomated repetitive-sequence-based polymerase chain reaction (rep-PCR) for typing A. baumannii, comparing this method with another semiautomated technique, such as ribotyping, and 2) to acquire information about the incidence, the clinical significance, and the susceptibility patterns of this microorganism in 13 different Italian hospitals in a 4-week period (total study population, >14000 beds). Twenty-eight A. baumannii were isolated in 7 different hospitals; 21 strains were analyzed with molecular methods. Automated ribotyping distinguished 6 different clusters of isolates, whereas rep-PCR appeared to be more discriminating, allowing us to distinguish 8 different clusters. Our study confirms the good discriminatory power of the semiautomated rep-PCR. Although expensive, this method is simple, fast, and reproducible, and in our opinion, it could be used in a hierarchic approach as a 1st-line typing tool if results of analysis are required in a short period or if a large number of isolates have to be analyzed.

Resistance to disinfectants in epidemiologically defined clinical isolates of Acinetobacter baumannii

Decreased susceptibility to biocides may contribute to epidemic spread of Acinetobacter baumannii in the hospital. This study was conducted to evaluate the susceptibility of different clinical A. baumannii strains to disinfectants. Twenty A. baumannii strains were examined, ten of which were outbreak-related and ten that were sporadic. Clinical isolates were selected on the basis of demonstrating a unique pulsed-field gel electrophoresis pattern. The in-vitro activities of propanol, combination of 1-propanol, 2-propanol and mecetronium ethylsulphate, polyvinylpyrrolidone (PVP)-iodine, triclosan and chlorhexidine were determined using a broth macrodilution method. Exposure times to the disinfectant ranged from 15 s to 2 min and concentrations ranged from undiluted to a 1:4000 dilution in order to investigate the impact of inadvertent dilution that might occur in clinical practice. Five American Type Culture Collection (ATCC) type strains (A. baumannii, Escherichia coli, Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus aureus) were used as controls. All disinfectants inhibited growth of all isolates at concentrations and contact times recommended by the respective manufacturer. With most of the disinfectants tested, a relevant number of viable bacteria remained if contact times < 30s or diluted agents were used. No significant differences in susceptibility between outbreak-related and sporadic strains were detected, but larger studies would be required to confirm this. Resistance to currently used disinfectants is probably not a major factor in the epidemic spread of A. baumannii. However, even minor deviations from the recommended procedures leading to decreased concentrations or exposure times may play a role in nosocomial cross-transmission.

Comparison of one-tube multiplex PCR, automated ribotyping and intergenic spacer (ITS) sequencing for rapid identification of Acinetobacter baumannii

Acinetobacter baumannii has emerged as a serious cause of nosocomial infections. Rapid identification of this pathogen is required so that appropriate therapy can be given and outbreaks controlled. This study evaluated a multiplex PCR and an automated ribotyping system for the rapid identification of Acinetobacter baumannii. In total, 22 different reference strains and 138 clinical isolates of Acinetobacter spp., identified by 16S-23S rRNA intergenic spacer (ITS) sequence analysis, were evaluated. All A. baumannii isolates (82 clinical isolates and one reference strain) were identified by the multiplex PCR method (specificity 100%). The sensitivity and specificity of the ribotyping system for identification of A. baumannii were 85.5% (71/83) and 93.5% (72/77), respectively. An additional 100 clinical isolates belonging to the Acinetobacter calcoaceticus-A. baumannii complex were used to compare these two methods for identification of A. baumannii, and this comparison revealed a level of disagreement of 14% (14 isolates). The accuracy of the multiplex PCR was 100%, which was confirmed by sequence analysis of the ITS and recA gene of these isolates. Thus, the multiplex PCR method dramatically increased the efficiency and speed of A. baumannii identification.

Guidelines for the validation and application of typing methods for use in bacterial epidemiology

For bacterial typing to be useful, the development, validation and appropriate application of typing methods must follow unified criteria. Over a decade ago, ESGEM, the ESCMID (Europen Society for Clinical Microbiology and Infectious Diseases) Study Group on Epidemiological Markers, produced guidelines for optimal use and quality assessment of the then most frequently used typing procedures. We present here an update of these guidelines, taking into account the spectacular increase in the number and quality of typing methods made available over the past decade. Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages. Criteria for their evaluation and application and the interpretation of their results are proposed. Finally, the issues of reporting, standardisation, quality assessment and international networks are discussed. It must be emphasised that typing results can never stand alone and need to be interpreted in the context of all available epidemiological, clinical and demographical data relating to the infectious disease under investigation. A strategic effort on the part of all workers in the field is thus mandatory to combat emerging infectious diseases, as is financial support from national and international granting bodies and health authorities.

First report of Salmonella enterica serotype panama meningitis associated with consumption of contaminated breast milk by a neonate

Salmonella enterica serotype Panama is capable of causing severe infection in children and is often transmitted via contaminated food. Here, we present the first documented case of serotype Panama infection that was acquired through the consumption of contaminated breast milk. The mother excreted the organism asymptomatically for at least 2 weeks.

[Epidemiology of nosocomial infections due to Pseudomonas aeruginosa, Burkholderia cepacia and Stenotrophomonas maltophilia]

Non-fermentative Gram negative rods are opportunistic pathogens responsible for nosocomial infections. Using phenotypic markers (serotypes for Pseudomonas aeruginosa and antibiotic susceptibility) allows a preliminary screening of epidemiologically-related strains. However, genotypic markers are necessary to better characterize nosocomial strains for the investigation of outbreaks or cross-transmissions in the hospital setting. Infections due to P. aeruginosa, Burkholderia. cepacia or Stenotrophomonas. maltophilia are usually hospital-acquired and responsible for a high mortality rate as illustrated by the lethality of nosocomial pneumonia due to P. aeruginosa. The severity of these infections is due to the virulence factors of the bacteria and to their occurrence in debilitated patients in whom invasives devices are used. The hospital environment can act as a reservoir with a rate of exogeneous transmission of these bacteria as high as 50% in some studies. To better prevent nosocomial infections related to Gram negative non fermentative rods, the control of the aqueous hospital environment, the strict application of hand disinfection and the investigation of potential cross-transmission in the hospital setting are needed.

Acinetobacter as a causative agent in preseptal cellulitis

BACKGROUND

The bacterial genus Acinetobacter, once viewed as inconsequential, has been increasingly implicated as a significant pathogen. Acinetobacter is becoming progressively more resistant to older and newer-generation antibiotics. The primary species encountered in infections is Acinetobacter baumannii.

CASE REPORT

A 39-year-old woman came in for treatment of a preseptal cellulitis and conjunctivitis. She was referred to W.W. Hastings Optometry Clinic eleven days after first being diagnosed with a hordeolum that developed into a preseptal cellulitis, despite the use of oral cephalexin anazithromycin. After being referred, the patient was placed on oral regimen of gatifloxacin and topical ciprofloxacin. The patient gradually improved over the next 10 days, with full resolution occurring 21 days after the first presentation. Culturing revealed the offending organism to be Acinetobacter.

DISCUSSION

Most ocular infections are still caused by common organisms such as Staphylococcus. However, atypical bacteria such as Acinetobacter are responsible for a minority of infections. Careful consideration of patient history and clinical signs must be made to differentiate preseptal cellulitis and orbital cellulitis.

CONCLUSION

This case emphasizes that clinicians need to be aware of emerging and resistant bacteria in ocular infections. Infections that do not respond to traditional therapy should be treated aggressively with the latest-generation antibiotics. Ocular infections that do not resolve in a timely manner should be cultured for the offending organism and these organisms should be tested for susceptibility to anti-microbial drugs.

Variable resistance patterns of integron-associated multidrug-resistant Acinetobacter baumannii isolates in a surgical intensive care unit

Between 1998 and 2000, we characterized 91 nosocomial isolates of Acinetobacter baumannii by antibiotyping and genotyping. A total of 25 ribotypes were obtained among these 91 isolates. When the isolates from surgical intensive care units (ICUs) and other wards were compared, multiresistant A. baumannii isolates with the same ribotype 25 (R-25) were significantly more prevalent in nosocomial infections among the surgical patients. Further subtyping of the strains by pulsed-field gel electrophoresis confirmed that strains of the same ribotype in surgical ICUs and a few isolates from other wards were identical or clonally related. Different antibiotic resistance profiles were observed among these R-25 isolates. All R-25 isolates contained intI1 integrase, and two clusters of integron cassettes were found. These clusters of cassettes were encoded by an open reading frame (ORF) of -5'CS-aac(3)Ia-aadA1a-unknown or f-3'CS or 5'CS-aacA4-aadA1-catB8-3'CS, indicating the involvement of different resistant genes. Two isolates contained bla (IMP-1), which was acquired from a conjugatively transferable plasmid and did not involve integron-associated resistance. In conclusion, an epidemic of nosocomial infections associated with A. baumannii strains that have different resistance profiles was identified. Resistance profiles can change by a combination of plasmid- and integron-associated acquisition, especially in a unit with high antibiotic selective pressures. Infectious control personnel should be alert to the change in resistance profiles during routine monitoring.

Nosocomial transmission of CTX-M-2 beta-lactamase-producing Acinetobacter baumannii in a neurosurgery ward

Three strains of cefotaxime (CTX)-resistant Acinetobacter baumannii, FM0209680, FM0300106, and FM0301433, were isolated from transtracheal aspirate cultures of three patients with probable nosocomial infections in a neurosurgery ward in Japan. The CTX MICs for these isolates were greater than 128 microg/ml but were drastically reduced in the presence of 4 microg of clavulanic acid per ml. These strains were also resistant to ceftriaxone, cefpodoxime, and aztreonam but were susceptible to ceftazidime and imipenem. The profile of resistance to various broad-spectrum beta-lactams was transferred by conjugation. Strain FM0209680 was not eradicated from case patient 1 by administration of imipenem, ceftazidime, and levofloxacin, even after a 6-month hospitalization period. Strains FM0300106 and FM0301433 were isolated from case patients 2 and 3 during the sixth week following admission, respectively, and then each patient was colonized for 3 weeks. Eradication of FM0300106 was successfully obtained from case patient 2 by imipenem treatment, while administration of imipenem was continued to prevent pneumonia. Prophylactic antimicrobial therapy was discontinued in case patient 3 because of the lack of pneumonic symptoms, and FM0301433 disappeared after the discontinuation of antimicrobial chemotherapy. All three strains carried the bla(CTX-M-2) gene, and the appearance of colonies in the growth-inhibitory zones around disks of CTX and aztreonam in double-disk synergy tests suggested inducible beta-lactamase production in these A. baumannii strains. The ribotyping investigation suggested that all these strains belong to the same clonal lineage. The plasmids harbored by A. baumannii had the same restriction profile as those harbored by Proteus mirabilis strains previously isolated in a urology ward of the Funabashi Medical Center.

Antibiotic rotation and development of gram-negative antibiotic resistance

To attain a better understanding of antibiotic cycling and its effects on the epidemiology of antibiotic resistance in gram-negative microorganisms, two different antibiotic classes (quinolone and beta-lactam) were cycled during four 4-month periods in a surgical intensive care unit. Respiratory aspirates and rectal swabs were obtained and DNA fingerprinting was performed. Primary endpoint of the study was the acquisition rate with gram-negative bacteria resistant to the antibiotic of choice during each cycle. Secondary endpoints were changes in endemic prevalence of resistant bacteria and the relative importance of cross-transmission. In all, 388 patients were included and 2,520 cultures analyzed. Adherence to antibiotic protocol was 96%. Overall antibiotic use increased with 24%. Acquisition rates with resistant bacteria were highest during levofloxacin exposure (relative risk [RR] 3.2; 95% confidence interval [CI]: 1.4-7.1) and piperacillin/tazobactam exposure (RR 2.4; 95% CI 1.2-4.8). The relative importance of cross-transmission decreased during the study. For individual patients, treatment with levofloxacin was the only independent risk factor for acquisition of levofloxacin-resistant bacteria (hazard ratio 12.6; 95% CI 3.8-41.6). Potential for selection of antibiotic-resistant gram-negative bacteria during periods of homogeneous exposure increased from cefpirome to piperacillin/tazobactam to levofloxacin. Cycling of homogeneous antibiotic exposure is unlikely to control the emergence of gram-negative antimicrobial resistance in intensive care units.

Automated ribotyping, a rapid typing method for analysis of Erysipelothrix spp. strains

Automated ribotyping classified 70 Erysipelothrix species strains, previously classified into 14 RAPD patterns and into 63 PFGE patterns, into 27 ribogroups. Twenty-three strains of the 70 analyzed and classified into 13 ribogroups were previously classified into six ribotypes by the traditional ribotyping method. Moreover, automated ribotyping differentiated seven strains that were not differentiated by PFGE. Therefore, automated ribotyping was more sensitive than RAPD and traditional ribotyping, and it might be a useful method for a rapid screening in epidemiological study of strains of this genus, and more accurate results can be obtained when this method is used together with PFGE.

Outbreak of nosocomial meningitis caused by Acinetobacter baumannii in neurosurgical patients

An outbreak of nosocomial meningitis caused by Acinetobacter baumannii, which developed postoperatively in seven neurosurgical patients is described. The clinical isolates of A. baumannii were typed by biochemical profiles and antibiogram patterns, and by random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) and amplified fragment length polymorphism (AFLP) fingerprinting. The implicated strain was multi-drug resistant, however, susceptibility to imipenem and netilmicin was detected. An extensive search for the environmental source of the epidemic strain was carried out. Two of several isolates from hospital environment, corresponded to the A. baumannii outbreak strain, one being cultured from the suctioning equipment used in the care of these patients. The introduction of multiresistant epidemic A. baumannii into a neurosurgical unit is a severe risk factor for patients undergoing neurosurgical procedures. Genotypic typing methods are important for definitive identification of these strains in patients and their environment.

Evaluation of an impedance method for subtyping of P seudomonas aeruginosa

Eight isolates (no. 1 to 8) of Pseudomonas aeruginosa isolated from 8 burn patients were typed by pulsed-field gel electrophoresis (PFGE), arbitrarily primed polymerase chain reaction (PCR) (AP-PCR), biotyping, antimicrobial susceptibility testing, and a newly developed technique-impedance method. By both PFGE and AP-PCR, isolates 1 and 2 were designated type A, while isolates 3 to 8 were designated type B. However, isolates 3 to 8 could be further divided into three distinct subtypes (B, C, and D) by the impedance method. Four antibiograms were obtained by testing the 8 isolates against six antimicrobial agents and designation of antibiogram to each of the 8 isolates was in accordance with those obtained by the impedance method. The results of biotyping did not agree with any of the above typing methods. In conclusion, the impedance technique had a high discriminatory ability to differentiate genetically related clones into subtypes. The method is simple, reproducible, and has a high typeability.

Identification of a new geographically widespread multiresistant Acinetobacter baumannii clone from European hospitals

The aim of the study was to investigate the genetic diversity of Acinetobacter baumannii clinical strains that had previously been allocated to three major groups based on automated ribotyping. Forty-seven isolates from European hospitals and one isolate from a South African hospital, geographically representative of the three ribogroups (ribogroups 1, 2 and 3 with 10, 23 and 15 isolates, respectively), were analysed using the highly discriminatory fingerprinting methods AFLP and pulsed-field gel electrophoresis (PFGE). Based on AFLP data, the isolates clustered into three main groups, each corresponding to one ribogroup. Inclusion of reference strains of the previously described clones I and II, responsible for outbreaks in northwestern European hospitals, showed that ribogroups 1 and 2 correspond to clones I and II, respectively, whereas ribogroup 3 apparently represents a new clone. This clone III was found in France, The Netherlands, Italy and Spain. Clones I and II were not limited to northwestern European countries, as they were also recovered from Spain, South Africa, Poland and Italy (clone I) and from Spain, Portugal, South Africa, France, Greece and Turkey (clone II). Combined AFLP and PFGE data showed intraclonal diversity and led to the distinction of 23 different genotypes. Three genotypes, two of them belonging to clone II and one to clone III, were found in different hospitals and may correspond to subsets of isolates with a more recent clonal relationship, which emphasizes the epidemic potential of these organisms.

Long-term predominance of two pan-European clones among multi-resistant Acinetobacter baumannii strains in the Czech Republic

In a recent study, a large proportion of multi-drug-resistant (MDR) Acinetobacter baumannii strains that were isolated from hospitalized patients in the Czech Republic was found to belong to two major groups (A and B). These groups appeared to be similar to epidemic clones I and II, respectively, which were identified previously among outbreak strains from north-western European hospitals. The aim of the present study was to assess in detail the genetic relatedness of Czech A. baumannii strains and those of epidemic clones I and II by using ribotyping with HindIII and HincII and by AFLP fingerprinting. The study collection included 70 MDR strains that were isolated in 30 Czech hospitals in 1991–2001, 15 susceptible Czech strains from 1991 to 1996 and 13 reference strains of clones I and II from 1982 to 1990. One major HindIII/HincIII ribotype (R1-1) was observed in 38 MDR Czech strains and eight reference strains of clone I, whereas another major ribotype (R2-2) was observed in 11 MDR Czech strains and in three reference strains of clone II. A selection of 59 Czech strains (representative of all ribotypes) and the 13 reference strains were investigated by AFLP fingerprinting. At a clustering level of 83 %, two large clusters could be distinguished: cluster 1 included all reference strains of clone I and 25 MDR Czech strains, whilst cluster 2 contained all reference strains of clone II and 11 MDR Czech strains. There was a clear correlation between the groupings by AFLP analysis and by ribotyping, as all strains with ribotype R1-1 and four strains with slightly different ribotypes were found in AFLP cluster 1, whereas all strains with ribotype R2-2 and seven strains with similar ribotypes were in AFLP cluster 2. Thus, 41 and 21 MDR Czech strains could be classified as belonging to clones I and II, respectively. The remaining eight MDR and 15 susceptible strains were highly heterogeneous and were distinct from clones I and II by both AFLP fingerprinting and ribotyping. These results indicate that the two predominant groups observed among MDR Czech A. baumannii strains from the 1990s are genetically congruent with the north-western European epidemic clones that were found in the 1980s. Recognition of these clinically relevant, widespread clones is important in infection prevention and control; they are also interesting subjects to study genetic mechanisms that give rise to their antibiotic resistance and epidemic behaviour.

Evaluation of the polymorphisms associated with tandem repeats for Pseudomonas aeruginosa strain typing

We report on the development of a scheme for the typing of Pseudomonas aeruginosa, multiple-locus variable number of tandem repeat (VNTR) analysis (MLVA). We first evaluated the polymorphisms of 201 tandem repeat loci selected from more than 3,000 such sequences present in strain PAO1 with a test collection of 12 genotypically distinct clinical strains. Seven VNTR loci which can be easily scored with the technology used here were identified and used to genotype a collection of 89 clinical isolates that had previously been classified into 46 ribotypes, including 2 widespread ribotypes. Seventy-one different MLVA genotypes could be distinguished. With only two exceptions, strains with identical ribotypes were grouped together upon cluster analysis of the MLVA data. The 27 isolates with the most frequent ribotype were divided into 14 MLVA types, and the 18 isolates with the second most frequent ribotype were divided into 15 MLVA types. Analysis of a subset of 17 strains belonging to the major ribotype by pulsed-field gel electrophoresis with the enzyme SpeI distinguished seven types, identical to the number of MLVA types in this subset. Our data show that MLVA typing of P. aeruginosa based on the first set of loci has a high discriminatory power. Because MLVA is highly reproducible and easily portable among laboratories, it represents a very promising tool for the molecular surveillance of P. aeruginosa. A free, online strain identification service based on the genotyping data produced herein has been developed.

Genomic typing of Pseudomonas aeruginosa isolates by comparison of Riboprinting and PFGE: correlation of experimental results with those predicted from the complete genome sequence of isolate PAO1

The whole genomic typing of 21 isolates of Pseudomonas aeruginosa from 15 intensive care unit (ICU) patients was performed by pulsed-field gel electrophoresis (PFGE using SpeI) and Riboprinting (using EcoRI and PvuII), and then the results were compared with predictions made from the whole genome sequence of P. aeruginosa PAO1. The analysis of electronic images from PFGE and Riboprinting by GelComparII demonstrated similar discrimination between PFGE and Riboprinting with PvuII enzyme; however, Riboprinting by EcoRI had reduced banding patterns and was shown to be of lower discrimination than PvuII. When analyzing isolates from patients, both PFGE and Riboprinting using PvuII enzyme gave equivalent results, with the exception of two isolates that were closely related by PvuII Riboprinting and unrelated by PFGE. These discrepancies in typing results can be explained and adjusted for by comparisons with the rrn properties and the SpeI restriction fragments predicted from the whole genome of P. aeruginosa PAO1. Properties of the rrn operon that need to be taken into account include: (i) restriction enzyme sites that produce one or two fragments for each rrn operon; (ii) genomic variability in ISR sequence length; (iii) different enzymes need to be used to determine differences in rrn operon copy number from Riboprints; and (iv) choice of a restriction enzyme that produces riboprinter bands derived from rrn operon regions that are highly variable within the genome and between isolates. This knowledge has ramifications for PFGE and Riboprinter design and analysis so that for each new species to be typed comparisons can be made using the whole genome sequence.

Outbreak of a susceptible strain of Acinetobacter species 13 (sensu Tjernberg and Ursing) in an adult neurosurgical intensive care unit

Between December 1999 and June 2000, an outbreak caused by Acinetobacter emerged on the neurosurgical intensive care unit of our hospital. It was shown using automated ribotyping using Eco RI and pulsed-field gel electrophoresis that the outbreak was caused by spread of a single strain, which was identified by ribotyping and amplified ribosomal DNA restriction analysis as Acinetobacter DNA group 13TU (sensu Tjernberg and Ursing). The outbreak strain, which showed no antibiotic resistance, was identified in 23 patients, five of whom developed an infection. The organism was also isolated from various environmental sites. Cross-transmission among patients continued despite contact isolation of colonized patients and reinforcement of basic disinfection procedures. Eventually, after implementation of additional stringent measures such as cohorting of positive patients and daily disinfection of the floor, the outbreak was brought under control. This study demonstrates that apart from Acinetobacter baumanii, Acinetobacter 13TU strains, even when they are fully susceptible, may cause outbreaks that are difficult to control. Correct identification to the species level of Acinetobacter by genotypic methods is necessary to get insight in the importance of the different Acinetobacter genomic species in hospital epidemiology.

CTX-M-14, a plasmid-mediated CTX-M type extended-spectrum beta-lactamase isolated from Escherichia coli

Four Escherichia coli isolates harboring CTX-M-14, with a single Ala231-->Val substitution compared to CTX-M-9, had three different ribotypes. Cefotaxime resistance was plasmid encoded and conjugatively transferable. Three isolates had the same plasmid restriction enzyme digestion profile, suggesting clonal spread of a resistant plasmid. A high k(cat)/K(m) value for cefotaxime (20.3 microM(-1) s(-1)) but low values for ceftazidime and aztreonam (< 0.02 microM(-1) s(-1)) were observed in hydrolysis assays, indicating resistance to cefotaxime (MIC > or = 64 microg/ml) but susceptibility to ceftazidime (MIC < or = 2 microg/ml).

Diversity of SHV and TEM beta-lactamases in Klebsiella pneumoniae: gene evolution in Northern Taiwan and two novel beta-lactamases, SHV-25 and SHV-26

A total of 113 blood culture isolates of Klebsiella pneumoniae from 10 hospitals in northern Taiwan were studied for SHV and TEM beta-lactamase production. bla(SHV) was amplified from all isolates by PCR. TEM-type resistance, was found in 32 of the isolates and was of the TEM-1 type in all isolates. SHV-1, -2, -5, -11, and -12 and two novel enzymes were identified. These novel enzymes were designated SHV-25 and SHV-26 and had pIs of 7.5 and 7.6, respectively. Amino acid differences in comparison to the amino acid sequence of bla(SHV-1) were found at positions T18A (ThrACC-->AlaGCC), L35Q (LeuCTA-->GluCAA), and M129V (MetATG-->ValGTG) for SHV-25 and at position A187T (AlaGCC-->ThrACC) for SHV-26. The results of substrate profiles and MIC determinations showed that the novel enzymes did not hydrolyze extended-spectrum cephalosporins, rendering the isolates susceptible to these agents. Inhibition profiles revealed that the 50% inhibitory concentration for SHV-26 was higher than those for SHV-1 and SHV-25, resulting in an intermediate resistance to amoxicillin-clavulanic acid. Forty-nine ribotypes were identified, suggesting that major clonal spread had not occurred in any of the hospitals. According to the amino acid sequence, SHV beta-lactamases in Taiwan may basically be derived through stepwise mutation from SHV-1 or SHV-11 and further subdivided by four routes. The stepwise mutations initiated from SHV-1 or SHV-11 to SHV-2, SHV-5, and SHV-12 comprise the evolutionary change responsible for extended-spectrum beta-lactamase (ESBL) production in Taiwan. The stepwise mutations that lead to a non-ESBL (SHV-25) and the beta-lactamase (SHV-26) with reduced susceptibility to clavulanic acid are possibly derived from SHV-11 and SHV-1, respectively. The results suggest a stepwise evolution of SHV beta-lactamases in Taiwan.