Novel genetic context of multiple bla OXA-58 genes in Acinetobacter genospecies 3.

OBJECTIVES: The detection in Acinetobacter genospecies 3 isolates of OXA-type carbapenemases, resulting in reduced susceptibility to carbapenem antibiotics, is increasingly reported. We identified an Acinetobacter genospecies 3 isolate carrying the gene for OXA-58 and aimed to resolve the genetic environment surrounding the bla(OXA-58) gene. METHODS: Species identification was confirmed by 16S-23S rRNA restriction analysis. MICs of imipenem, meropenem and ertapenem were determined, and the isolate was screened by PCR for bla(OXA-23-like), bla(OXA-40-like), bla(OXA-51-like) and bla(OXA-58-like) genes. The sequence surrounding bla(OXA-58) was determined through amplification by inverse PCR and genome walking followed by sequencing. Genetic localization was investigated by Southern blotting. RESULTS: Isolate A164 was confirmed as belonging to Acinetobacter genospecies 3 and had reduced susceptibility to the carbapenems. The isolate was found to encode two bla(OXA-58) genes that may have been duplicated by the insertion sequence ISAba125, two copies of which were inserted into ISAba3 elements. The bla(OXA-58) genes appear to be plasmid borne. CONCLUSIONS: This is the first report of beta-lactamase duplication in Acinetobacter genospecies 3 and of gene duplication mediated by ISAba125.

Acinetobacter: an old friend, but a new enemy.

Acinetobacter emerged as a significant nosocomial pathogen during the late 1970s, probably as a consequence, at least in part, of increasing use of broad-spectrum antibiotics in hospitals. Most clinically significant isolates belong to the species Acinetobacter baumannii or its close relatives, with many infections concentrated in intensive care, burns or high dependency units treating severely ill or debilitated patients. Large outbreaks can occur in such units, involving the infection or colonisation of numerous patients by specific epidemic strains of A. baumannii. Recently, a particular problem has concerned cross-infection of injured military patients repatriated from combat regions of the world (e.g. Iraq and Afghanistan). Carbapenems have previously been the treatment of choice for infected patients, but increasing reports worldwide now describe A. baumannii isolates resistant to all conventional antimicrobial regimens. Data to support therapeutic use of the limited number of new antimicrobial agents (e.g. tigecycline) with in-vitro activity against these pathogens are still very limited. Detailed advice concerning prevention and control of outbreaks caused by multidrug-resistant strains of acinetobacter is available from the UK Health Protection Agency. In addition to antibiotic prescribing policies and audit, these measures focus on reinforcing standard infection control procedures and precautions, with particular attention to thorough cleaning of patient areas to take account of the long-term survival of acinetobacter after drying and inadequate disinfection. Despite these measures, the problem continues to escalate, with many hospitals worldwide now reporting outbreaks caused by multidrug-resistant strains of acinetobacter.

OXA-51-like beta-lactamases and their association with particular epidemic lineages of Acinetobacter baumannii.

Sixty diverse clinical Acinetobacter baumannii isolates of worldwide origin were assigned to sequence groups, based on a multiplex PCR for the ompA, csuE and bla(OXA-51-like) genes. The majority (77%) of isolates belonged to sequence groups 1 and 2 (SG1 and SG2), with sequence group 3 (SG3) and non-grouped isolates accounting for the remainder. The isolates were not closely related according to pulsed-field gel electrophoresis (PFGE), and the majority were sensitive to imipenem and meropenem. The construction of a linkage map of OXA-51-like beta-lactamase sequence relationships revealed two closely related clusters of enzymes, one focused around OXA-66 and the other around OXA-69. Isolates belonging to SG1 encoded an enzyme from the OXA-66 cluster, while those belonging to SG2 encoded an enzyme from the OXA-69 cluster. All SG3 isolates encoded OXA-71, which does not form part of a close enzyme grouping. Major multinational lineages accounted for a significant proportion of A. baumannii clinical isolates, and the evolution of the OXA-51-like enzymes appears to be an ongoing process.

Genetic diversity of carbapenem-resistant isolates of Acinetobacter baumannii in Europe.

In total, 96 carbapenem-resistant isolates of Acinetobacter baumannii were obtained from 25 hospitals in 17 European countries. Imipenem MICs ranged from <4 to 128 mg/L on retesting by Etest, with MICs > or =16 mg/L being associated with the carriage of genes encoding at least one other class D carbapenemase in addition to the intrinsic OXA-51-like enzyme. Molecular typing results obtained by random amplified polymorphic DNA analysis, followed by pulsed-field gel electrophoresis (PFGE) of ApaI-digested chromosomal DNA, were highly congruent, with 17 different PFGE types being delineated at a cut-off similarity level of 85%. With few exceptions, multiple isolates from a single hospital belonged to the same PFGE type. Seven sequence groups were identified among the 96 A. baumannii isolates, with the majority of isolates (n = 81) belonging to the previously defined sequence groups 1 and 2, which each included eight PFGE types. These two multinational lineages included the previously defined European clones II and I, respectively, but the problem of resistant A. baumannii in Europe appeared not to be confined solely to these two European clones. Rather, two broader lineages of carbapenem-resistant A. baumannii now seem to be spreading throughout Europe.

Emergence and spread of carbapenem-resistant strains of Acinetobacter baumannii in a tertiary-care hospital in Poland.

This study analysed the occurrence of carbapenem resistance among Acinetobacter baumannii isolates from a tertiary-care hospital in Poland, together with the molecular epidemiology of these isolates and the risk-factors for their acquisition and possible nosocomial spread. The medical charts of 21 patients with Acinetobacter infection or colonisation revealed that A. baumannii isolates were obtained most frequently from intensive care unit and surgical patients (particularly those receiving transplantation surgery). First isolation occurred, on average, on day 21 following admission (range 5-45 days). Infection with Acinetobacter contributed directly to the death of seven patients. Several patients were infected with more than one strain, and molecular typing revealed the co-circulation of three predominant clones, of which two belonged to the Acinetobacter lineages designated as European clones I and II. All three clones encoded an OXA-51-type carbapenemase, but were negative for carbapenemases belonging to the OXA-23, OXA-24 and OXA-58 families. The OXA-51 gene was found in both resistant and susceptible isolates, and was not associated directly with carbapenem resistance. Etests with imipenem and imipenem plus EDTA indicated production of a metallo-beta-lactamase (MBL) in carbapenem-resistant isolates. PCRs for IMP-type MBLs were negative, but PCR using consensus primers for VIM-type MBLs were positive for carbapenem-resistant isolates belonging to the European clone II lineage. The occurrence of a VIM-type MBL in association with one of the epidemic lineages of A. baumannii is a cause for concern. Further studies are needed to evaluate possible inter-hospital spread of resistant A. baumannii strains in Poland.

Evaluation of the sensitivity of a rapid polymerase chain reaction for detection of group B streptococcus.

The objective of this study was to compare detection of group B streptococcal (GBS) carriage using 'real-time' polymerase chain reaction (PCR) and microbiological standard culture. The study design was a test accuracy study comparing a novel molecular technique against the standard microbiological cultural technique in normal pregnant women. The setting and population consisted of 143 pregnant women with pre-labour rupture of the membranes, recruited from two large teaching hospitals in the UK. The study examined the efficacy of a polymerase chain reaction (PCR) assay for screening pregnant women who presented with term rupture of the membranes. Low vaginal specimens were obtained from the women. The specimens were tested for GBS by conventional culture and with a GBS-specific real-time PCR assay. The main outcome measure was the sensitivity and specificity of the PCR assay with 95% confidence intervals (CI) compared with the standard culture. The length of time to obtain a result was also reported for both methods. Among the 143 women, the results of the culture were positive (at least one colony) for GBS in 20 women (14%). The PCR assay detected GBS carriage in 10 women (7%). As compared with the culture method, the sensitivity and specificity of the PCR assay were 45% and 99%, respectively. The positive and negative predictive values of the PCR assay were 90% and 92%, respectively. The length of time required to obtain results for the majority of women (94%) was <2.5 h for the PCR assay and at least 24 h for culture. While a rapid result (within 3 h) of carriage of GBS can be obtained by the PCR assay, at present, it cannot replace conventional culture without further optimisation of the DNA extraction method. The sensitivity may further be improved by testing both low vaginal and rectal specimens.

Report of the Consensus Conference on Antibiotic Resistance; Prevention and Control (ARPAC).

Antimicrobial resistance is a key public health concern in Europe. It is known that there are significant variations in the prevalence of resistance across Europe, and methods to reduce the problem are also assumed to vary significantly. The 'Antibiotic Resistance; Prevention and Control (ARPAC)' Concerted Action project was funded by the European Commission and conducted by four study groups of the European Society of Clinical Microbiology and Infectious Diseases (ESCMID). The project established a network of European hospitals and collated data on antimicrobial resistance prevalence, antimicrobial susceptibility testing methods, typing methods employed, antimicrobial use, antibiotic policies and practices, and infection control policies and practices. The ARPAC Consensus Conference, entitled 'Control of antibiotic resistance in European hospitals-informing future evidence-based practice', was held in Amsterdam in November 2004. The conference was co-hosted by the European Commission, ESCMID and the Dutch Working Party on Antibiotic Policy (SWAB). Key ARPAC findings were presented and discussed in the context of the worldwide situation. The conference delivered a set of high-priority recommendations likely to have a significant impact on antimicrobial resistance. This report summarises these recommendations.

Rapid detection of methicillin-resistant Staphylococcus aureus from screening enrichment broths by real-time PCR.

The aim of this study was to evaluate real-time PCR (LightCycler) kits for the detection of methicillin-resistant Staphylococcus aureus in enrichment broth using 200 sets of patient screening swab samples. One hundred sets were processed using a lysostaphin/lysozyme extraction method and a further 100 were tested using a column extraction kit. The PCR kits with lysostaphin/lysozyme lysis showed 95.7% sensitivity, 90.8% specificity, and negative and positive predictive values of 98.6% and 75.9%, respectively, compared with 88%, 95.9%, 84.6% and 95.9%, respectively, with the column extraction kit.

Prevalence of Acinetobacter baumannii and other Acinetobacter spp. in faecal samples from non-hospitalised individuals.

In total, 226 individuals from the community were investigated for faecal carriage of Acinetobacter spp. by broth enrichment culture, followed by growth on blood agar and/or Leeds Acinetobacter Medium (LAM). Acinetobacter baumannii was isolated on both LAM and blood agar from one of 100 specimens in the UK and one of 126 specimens in The Netherlands. The predominant species were Acinetobactor johnsonii and genomic sp. 11, which were cultured from 22 and five specimens, respectively. A. baumannii did not seem to be widespread in the faecal flora of individuals in the community.

Evaluation of a real-time PCR hybridization assay for rapid detection of Legionella pneumophila in hospital and environmental water samples.

A real-time LightCycler assay for Legionella pneumophila was evaluated with 120 water samples potentially contaminated with PCR inhibitors. Results were obtained within five hours, with a detection limit equivalent to 800 cells/L. However, 11 of 22 culture-positive samples containing < 100 CFU/L were also positive by LightCycler assay, indicating the presence of significant numbers of non-viable cells. Following extraction, amplification inhibitors remained in four culture-positive samples, but only one contained > 800 CFU/L. The assay seemed suitable for rapidly screening large sample numbers for heavy contamination with L. pneumophila, but conventional culture should continue to be used to detect low contamination levels.

Endemic carbapenem resistance associated with OXA-40 carbapenemase among Acinetobacter baumannii isolates from a hospital in northern Spain.

Eighty-two carbapenem-resistant isolates of Acinetobacter baumannii from a single hospital in Bilbao were typed into two major clusters and several subclusters. Disk synergy tests and PCR indicated the production of a zinc-independent OXA-class carbapenemase. Sequencing identified this enzyme, OXA-40, as a variant of the OXA-24-OXA-25-OXA-26 cluster.

Diversity of Staphylococcus aureus strains isolated from two European regions with different prevalences of methicillin resistance.

The genodiversity of Staphylococcus aureus isolates from the Nottingham region of the United Kingdom was compared with isolates from the Freiburg region of Germany. The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) isolates was higher in Nottingham than in Freiburg. In patients from Nottingham hospitals, 80% of MRSA isolates were classical epidemic MRSA-15, but genotypic variants of epidemic MRSA-15 comprised 72% of isolates from Nottingham community-based patients. In contrast, MRSA isolates from Freiburg showed greater diversity, but 47% and 23% of isolates, respectively, belonged to two predominant MRSA genotypes found in isolates from both hospitalised and community-based patients. The results suggest that genodiversity becomes increasingly more confined in settings with a higher frequency and longer duration of MRSA prevalence.

Detection of Legionella pneumophila using a real-time PCR hybridization assay.

A real-time PCR hybridization assay for Legionella pneumophila is described; the assay uses LightCycler (Idaho Technology) methodology to specifically detect 2.5 CFU/reaction, equivalent to 1,000 CFU/liter of starting water sample. The assay, including DNA extraction and confirmation of product identity, is completed within 90 min of receipt of a sample.

Evaluation of a PCR-immunoassay technique for detection of Neisseria meningitidis in cerebrospinal fluid and peripheral blood.

A multiplex PCR-immunoassay for the rapid diagnosis of bacterial meningitis from cerebrospinal fluid (CSF) or peripheral blood was compared with conventional microbiological techniques used in the routine diagnostic laboratory. The multiplex PCR was designed to detect simultaneously a universal conserved sequence coding for bacterial 16S rRNA and the Neisseria meningitidis porA gene. The PCR-immunoassay had a detection limit of (3-5) x 10(2) cfu/ml (equivalent to 1-3 cfu/PCR) with spiked CSF or blood samples, compared with (3-5) x 10(3) cfu/ml for PCR followed by conventional agarose gel electrophoresis for detection of PCR products. Of 294 CSF samples from patients suspected on clinical grounds of suffering from meningitis, the PCR-immunoassay detected bacterial DNA in 29 CSF samples, 15 of which were also positive for N. meningitidis DNA. The 29 positive CSF samples comprised 25 samples that were also reported positive and four that were reported negative by conventional methodology; the latter four were all positive for N. meningitidis by the PCR-immunoassay. Of 173 peripheral blood samples examined, the PCR-immunoassay detected bacterial DNA in 18 samples, 14 of which were also positive for N. meningitidis DNA. In comparison, only 10 samples were reported positive for N. meningitidis by conventional methodology. All negative PCR-immunoassay results correlated with those obtained by conventional methodology for both CSF and blood samples. The sensitivity and speed of the PCR-immunoassay system indicated that it could be used as a routine diagnostic test for meningococcal meningitis, enabling a diagnosis to be made within 4 h of receipt of the specimen.

Use of RAPD-ALF analysis for investigating the frequency of bacterial cross-transmission in an adult intensive care unit.

Bacterial cross-transmission was investigated during a 12-month period in an adult intensive care unit (ICU) by the generation of random amplified polymorphic DNA (RAPD) fingerprinting profiles, combined with automated laser fluorescence (ALF) analysis. The potential episodes of cross-transmission identified, were compared with those detected by the conventional first-line screen of antibiogram typing. Over the year, 215 primary gram-negative bacterial isolates were obtained from 160 patients. In total, 22 possible episodes of cross-transmission, involving 70 (44%) of the 160 patients, were identified by RAPD-ALF analysis, and 19 of these were substantiated with epidemiological evidence. Conversely, 31 possible episodes were identified on the basis of antibiogram data, but only three of these episodes, two involving Acinetobacter baumannii and one involving Serratia marcescens, correlated with those identified by RAPD-ALF analysis. It was concluded that analysis of antibiogram data alone is an unreliable method for assessing bacterial cross-transmission, unless the organism involved has a particularly stable or unusual resistance pattern. In contrast, the technique of RAPD-ALF analysis may provide a rapid and simple technique for obtaining an insight into the population dynamics of gram-negative bacteria in adult ICUs.

Use of an automated DNA analysis system (DARAS) for sequence-specific recognition of Neisseria meningitidis DNA.

OBJECTIVES: To combine use of the polymerase chain reaction (PCR) for rapid diagnosis of meningococcal meningitis with a novel automated detection system for sequence-specific recognition of PCR products. METHODS: DNA was extracted from cerebrospinal fluid (CSF) by a quick boil-lysis method, followed by PCR with primers specific for Neisseria meningitidis. Sequence-specific recognition of N. meningitidis DNA was performed with an automated DNA analysis system (DARAS) and the data were compared with results following agarose gel electrophoresis or conventional microbiological culture. RESULTS: The DARAS system had a sensitive detection limit of 102 meningococci/mL with spiked samples, compared with a detection limit of 104 meningococci/mL following agarose gel electrophoresis. When the system was used to examine 74 CSF samples, the 19 CSF samples positive for N. meningitidis by conventional microbiological methods were also all positive in the DARAS system and the 55 samples negative by DARAS for meningococci were also negative by conventional microbiological methods. CONCLUSION: The sensitivity and specificity of the DARAS system makes it a useful tool for the diagnosis of meningococcal meningitis. The system is user-friendly, requires minimal hands-on time and generates data in an informative numerical format.