Novel clinically relevant antibiotic resistance genes associated with sewage sludge and industrial waste streams revealed by functional metagenomic screening

A growing body of evidence indicates that anthropogenic activities can result in increased prevalence of antimicrobial resistance genes (ARGs) in bacteria in natural environments. Many environmental studies have used next-generation sequencing methods to sequence the metagenome. However, this approach is limited as it does not identify divergent uncharacterized genes or demonstrate activity. Characterization of ARGs in environmental metagenomes is important for understanding the evolution and dissemination of resistance, as there are several examples of clinically important resistance genes originating in environmental species. The current study employed a functional metagenomic approach to detect genes encoding resistance to extended spectrum β-lactams (ESBLs) and carbapenems in sewage sludge, sludge amended soil, quaternary ammonium compound (QAC) impacted reed bed sediment and less impacted long term curated grassland soil. ESBL and carbapenemase genes were detected in sewage sludge, sludge amended soils and QAC impacted soil with varying degrees of homology to clinically important β-lactamase genes. The flanking regions were sequenced to identify potential host background and genetic context. Novel β-lactamase genes were found in Gram negative bacteria, with one gene adjacent to an insertion sequence ISPme1, suggesting a recent mobilization event and/ the potential for future transfer. Sewage sludge and quaternary ammonium compound (QAC) rich industrial effluent appear to disseminate and/or select for ESBL genes which were not detected in long term curated grassland soils. This work confirms the natural environment as a reservoir of novel and mobilizable resistance genes, which may pose a threat to human and animal health.

Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment

Objectives

Multidrug-resistant Enterobacteriaceae pose a significant threat to public health. We aimed to study the impact of sewage treatment effluent on antibiotic resistance reservoirs in a river.

Methods

River sediment samples were taken from downstream and upstream of a waste water treatment plant (WWTP) in 2009 and 2011. Third-generation cephalosporin (3GC)-resistant Enterobacteriaceae were enumerated. PCR-based techniques were used to elucidate mechanisms of resistance, with a new two-step PCR-based assay developed to investigate bla_CTX-M-15 mobilization. Conjugation experiments and incompatibility replicon typing were used to investigate plasmid ecology.

Results

We report the first examples of bla_CTX-M-15 in UK river sediment; the prevalence of bla_CTX-M-15 was dramatically increased downstream of the WWTP. Ten novel genetic contexts for this gene were identified, carried in pathogens such as Escherichia coli ST131 as well as indigenous aquatic bacteria such as Aeromonas media. The bla_{CTX-M-15 ­}gene was readily transferable to other Gram-negative bacteria. We also report the first finding of an imipenem-resistant E. coli in a UK river.

Conclusions

The high diversity and host range of novel genetic contexts proves that evolution of novel combinations of resistance genes is occurring at high frequency and has to date been significantly underestimated. We have identified a worrying reservoir of highly resistant enteric bacteria in the environment that poses a threat to human and animal health.

Changing epidemiology of Clostridium difficile infection following the introduction of a national ribotyping-based surveillance scheme in England

BACKGROUND

Marked increases in Clostridium difficile infection (CDI) incidence, driven by epidemic strain spread, is a global phenomenon.

METHODS

The Clostridium difficile Ribotyping Network (CDRN) was established in 2007 as part of enhanced CDI surveillance in England, to facilitate the recognition and control of epidemic strains. We report on changes in CDI epidemiology in England in the first 3 years of CDRN.

RESULTS

CDRN received 12,603 fecal specimens, comprising significantly (P < .05) increasing numbers and proportions of national CDI cases in 2007-2008 (n = 2109, 3.8%), 2008-2009 (n = 4774, 13.2%), and 2009-2010 (n = 5720, 22.3%). The C. difficile recovery rate was 90%, yielding 11,294 isolates for ribotyping. Rates of 9 of the 10 most common ribotypes changed significantly (P < .05) during 2007-2010. Clostridium difficile ribotype 027 predominated, but decreased markedly from 55% to 36% and 21% in 2007-2008, 2008-2009, and 2009-2010, respectively. The largest regional variations in prevalence occurred for ribotypes 027, 002, 015, and 078. Cephalosporin and fluoroquinolone use in CDI cases was reported significantly (P < .05) less frequently during 2007-2010. Mortality data were subject to potential reporting bias, but there was a significant decrease in CDI-associated deaths during 2007-2010, which may have been due to multiple factors, including reduced prevalence of ribotype 027.

CONCLUSIONS

Access to C. difficile ribotyping was associated with significant changes in the prevalence of epidemic strains, especially ribotype 027. These changes coincided with markedly reduced CDI incidence and related mortality in England. CDI control programs should include prospective access to C. difficile typing and analysis of risk factors for CDI and outcomes.

Reducing Clostridium difficile through early identification of clusters and the use of a standardised set of interventions

In recent years the rates of Clostridium difficile infection (CDI) have increased worldwide with several large outbreaks occurring within the UK. New guidance from the UK Department of Health describes measures to investigate periods of increased incidence (PII) of CDI which include informing staff, ribotyping isolates, enhanced cleaning, audits and monitoring of antibiotic prescribing. This study aimed to determine whether a standardised set of measures could be used to control the incidence of CDI within an acute hospital setting over an 18 month period. During the study period a total of 102 PII involving 439 patients were investigated. The number of PII per month ranged from 14 in February 2008 to one in June 2009. From January 2008 to September 2008, ribotyping of patient isolates was only carried out on PII involving more than 10 patients, but from October 2008 it was carried out on all PII. During the period October 2008 to June 2009, 28 PII were investigated on 21 different wards, with seven wards having two PII. Ribotyping of the isolates confirmed nine (32%) of these PII to be outbreaks, with three being due to ribotype 027, two ribotype 078 and the others distinct ribotypes. Use of a set of standardised interventions has resulted in a decrease in the incidence of PII and a reduction in the number of patients involved. By taking early action with a set of standardised measures the incidence of hospital-acquired CDI can be reduced.

Low-level glycopeptide resistance in methicillin-resistant Staphylococcus aureus and how to test it

Vancomycin resistance in Staphylococcus aureus has emerged over the last ten years due to varying mechanisms and giving variable levels of resistance to vancomycin. The most resistant strains (fortunately rare) bear the vanA gene cluster and these are generally recognisable as MICs of vancomycin are usually found to be in the range 32-64mg/L. It should be noted that some automated systems have failed to detect these isolates. The much more commonly encountered GISA and hGISA vancomycin resistant strains of MRSA and methicillin sensitive Staph. aureus (MSSA) exhibit lower levels of resistance and difficulty is encountered in reliably defining and identifying these strains in clinical laboratories. No single completely reliable, convenient test either phonotypical genetic currently exists which can be readily applied in the clinical laboratory for the detection of hGISA/GISA. The population analysis profile (PAP) method is currently regarded as the reference method but is slow and tedious to perform on a large number of isolates. This enables the differentiation of hGISA and GISA from fully vancomycin sensitive strains. In the clinical laboratory the use of Meuller-Hinton agar with 5mg/L teicoplanin and a 10microL innoculum of MacFarland 0.5 incubated for 48h represents the most reliable and economical screening test. Further confirmation would be required using either macrodilution Etest methodology using an MIC >or= 8mg/L of vancomycin and/or teicoplanin as the cut off for hGISA or the newer GRD (glycopeptide resistance detection) strip.

Beta-lactams and beta-lactamase-inhibitors in current- or potential-clinical practice: a comprehensive update

The use of successive generations of beta-lactams has selected successive generations of beta-lactamases including CTX-M ESBLs, AmpC beta-lactamases, and KPC carbapenamases in Enterobacteriaceae. Moreover, this cephalosporin resistance, along with rising resistance to fluoroquinolones, is now driving the use of carbapenems and unfortunately the carbapenem resistance has emerged markedly, especially in Acinetobacter spp. due to OXA- and metallo-carbapenemases. The industry responded to the challenge of rising resistance and recently developed some novel beta-lactams such as ceftobiprole, ceftaroline etc. and many beta-lactam compounds, including beta-lactamase-inhibitors, such as BMS-247243, S-3578, RWJ-54428, CS-023, SMP-601, NXL 104, BAL 30376, LK 157, and so on are under trials. This review provides the comprehensive accounts of the developments in penicillins, cephalosporins, carbapenems, and beta-lactamase-inhibitors, and the insight about medicinal chemistry, mechanism(s) of action and resistance, potential strategies to overcome resistance due to beta-lactamases, and also the recent advancements in the development of newer beta-lactam compounds; some of which are still under trials and yet to be classified. This review will fill the gap since previously published reviews and will serve as a comprehensive update on the current topic.

Laboratory tools and strategies for methicillin-resistant Staphylococcus aureus screening, surveillance and typing: state of the art and unmet needs

The public health burden caused by methicillin-resistant Staphylococcus aureus (MRSA) infections is now widely recognized, and is a cause of public alarm. Effective MRSA risk management in the healthcare system as well as in the community should rely on accurate detection of reservoirs and sources of transmission, as well as on close monitoring of the impact of interventions on disease incidence and bacterial dissemination. MRSA carrier screening and disease surveillance, coupled with molecular typing, are key information tools for integrated MRSA control and individual risk assessment. These tools should be tailored to the distinct needs of local interventions and national prevention programmes. Surveillance schemes should primarily inform local staff and serve as quality assurance about MRSA risk management. New technologies, including the use of selective culture media and real-time PCR assays, allow faster detection of MRSA carriers upon admission or during stay in healthcare institutions. More research is needed to ascertain their cost-effectiveness for MRSA control. Likewise, tremendous progress has been made concerning molecular typing methods, with optimization and standardization of sequence-based technologies offering broad applicability and high throughput. However, no single S. aureus typing method is yet providing fully reliable information within the range of discrimination needed for public health action. Further refinement of genotyping methods and international harmonization of surveillance and typing schemes must be achieved to facilitate global MRSA control.

Pre-clinical experience with daptomycin

Daptomycin is a broad-spectrum, bactericidal agent active against Gram-positive bacteria, acting largely and unusually through membrane depolarization. Activity is markedly affected in vitro by the availability of calcium ions, and its high molecular weight with associated poor diffusion means that conventional disc diffusion testing is not reliable (and as a consequence not available). In order to allow susceptibility categorization, it is recommended that the MIC be determined in the presence of a defined calcium concentration. The activity of daptomycin is concentration-dependent with a prolonged post-antibiotic effect. It has linear pharmacokinetics, with a half-life of 8-9 h, the primary route of excretion is renal, it exhibits serum protein binding of approximately 92% and there is no interaction with the P450 cytochrome. Daptomycin is inactivated by surfactant in the lung and, in consequence, is not recommended for the treatment of respiratory infections. Daptomycin is currently licensed for the treatment of complicated skin and soft tissue infections and for bacteraemia and right-sided endocarditis due to methicillin-susceptible and -resistant Staphylococcus aureus. To date, daptomycin-resistant bacteria have rarely been isolated from patients, although increases in vancomycin MIC may be linked to reduced susceptibility to daptomycin. Close monitoring of resistance is essential to maintain the clinical utility of the drug. Using once-daily dosing, daptomycin has been generally well tolerated; however, weekly monitoring of creatinine phosphokinase is recommended, as myopathy in skeletal muscles has been seen, albeit rarely. The rapid bactericidal action of daptomycin makes it a useful addition to the therapeutic armamentarium for the treatment of Gram-positive infections, providing a valuable alternative to vancomycin when it is inappropriate or resistance is a problem.

Prevalence and clonality of extended-spectrum beta-lactamases in Asia

Asia is almost certainly a part of the world in which extended-spectrum beta-lactamases (ESBLs) have emerged de novo, with some early antimicrobial resistance studies showing high levels of the ESBL phenotype, particularly among Klebsiella, and most notably in China, Korea, Japan and India. There is a lack of genotyping studies but work from the late 1990s suggests that SHV-5 and SHV-12 were most common then, with only very rare reports of TEM-related ESBL genes. As in other parts of the world, quite marked differences have since been seen in the pattern of ESBL genes, particularly in relation to the CTX-M family. The early emergence of TOHO CTX-M-2 in Japan contrasted with CTX-M-3 and -14 in China and many other parts of the Far East, suggesting the separate transfer of genes from the genome of Kluyvera spp. to mobile genetic elements in human-associated Enterobacteriaceae. ESBL production rates are now very high compared with Europe. In most countries, there are mixtures of CTX-M types, with VEB appearing significantly in Vietnam and Thailand, and ESBL isolates from India being completely dominated by the presence of bla(CTX-M-15) alone, with no other CTX-M types reported. With the total population of India and China being c. 2.4 billion and with faecal carriage rates of, probably, c. 10%, these countries represent major reservoirs of bla(CTX-M) genes. Increasing international travel and trade will lead to the movement of many of these ESBL genes. The high prevalence of ESBL genes in Asia means that the empirical treatment of serious infections with beta-lactam antibiotics, except carbapenems, is seriously compromised.

Molecular epidemiology of clinically significant antibiotic resistance genes

Antimicrobials were first introduced into medical practice a little over 60 years ago and since that time resistant strains of bacteria have arisen in response to the selective pressure of their use. This review uses the paradigm of the evolution and spread of beta-lactamases and in particular beta-lactamases active against antimicrobials used to treat Gram-negative infections. The emergence and evolution particularly of CTX-M extended-spectrum beta-lactamases (ESBLs) is described together with the molecular mechanisms responsible for both primary mutation and horizontal gene transfer. Reference is also made to other significant antibiotic resistance genes, resistance mechanisms in Gram-negative bacteria, such as carbepenamases, and plasmid-mediated fluoroquinolone resistance. The pathogen Staphylococcus aureus is reviewed in detail as an example of a highly successful Gram-positive bacterial pathogen that has acquired and developed resistance to a wide range of antimicrobials. The role of selective pressures in the environment as well as the medical use of antimicrobials together with the interplay of various genetic mechanisms for horizontal gene transfer are considered in the concluding part of this review.

An IS6110-targeting fluorescent amplified fragment length polymorphism alternative to IS6110 restriction fragment length polymorphism analysis for Mycobacterium tuberculosis DNA fingerprinting

A rapid, simple and highly discriminatory DNA fingerprinting methodology which produces data that can be easily interpreted, compared and transported is the ultimate goal for studying the epidemiology of Mycobacterium tuberculosis. A novel TaqI fluorescent amplified fragment length polymorphism (fAFLP) approach to M. tuberculosis DNA fingerprinting that targeted the variable IS6110 marker was developed in this study. The new method was tested for specificity and reproducibility, and compared with the standard reference IS6110 restriction fragment length polymorphism (RFLP) method for a panel of 78 isolates. Clustering conflicts between the two methods were resolved using mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) data. Comparison with an in-silico digestion of strain H37Rv showed that fAFLP-detected fragments were highly specific in vitro. The reproducibility of repeated digestions of strain H37Rv was 100%. Clustering results obtained by fAFLP and RFLP were highly congruent, with fAFLP allocating 97% of RFLP-clustered isolates to the same eight clusters as RFLP. Two single-copy isolates that had been clustered by RFLP were not clustered by fAFLP, but the MIRU-VNTR patterns of these isolates were different, indicating that the RFLP data had falsely clustered these isolates. Analysis by fAFLP will allow rapid screening of isolates to confirm or refute epidemiological links, and thereby provide insights into the frequency, conservation and consequences of specific transposition events.

Rapid recontamination with MRSA of the environment of an intensive care unit after decontamination with hydrogen peroxide vapour

Meticillin-resistant Staphylococcus aureus (MRSA) persists in the hospital environment and conventional cleaning procedures do not necessarily eliminate contamination. A prospective study was conducted on an intensive care unit to establish the level of environmental contamination with MRSA, assess the effectiveness of hydrogen peroxide vapour (HPV) decontamination and determine the rate of environmental recontamination. MRSA was isolated from 11.2% of environmental sites in the three months preceding the use of HPV and epidemiological typing revealed that the types circulating within the environment were similar to those colonising patients. After patient discharge and terminal cleaning using conventional methods, MRSA was isolated from five sites (17.2%). After HPV decontamination but before the readmission of patients, MRSA was not isolated from the environment. Twenty-four hours after readmitting patients, including two colonized with MRSA, the organism was isolated from five sites. The strains were indistinguishable from a strain with which a patient was colonized but were not all confined to the immediate vicinity of the colonized patient. In the eight weeks after the use of HPV, the environment was sampled on a weekly basis and MRSA was isolated from 16.3% sites. Hydrogen peroxide vapour is effective in eliminating bacteria from the environment but the rapid rate of recontamination suggests that it is not an effective means of maintaining low levels of environmental contamination in an open-plan intensive care unit.

Subtyping of ST22-MRSA-IV (Barnim epidemic MRSA strain) at a university clinic in Germany from 2002 to 2005

Emergence of the meticillin-resistant Staphylococcus aureus (MRSA) Barnim epidemic strain (ST22-MRSA-IV) was demonstrated recently at University Hospital in Magdeburg, Germany. To aid the study of transmission events, it is important to have an epidemiological typing method with the ability to distinguish among MRSA isolates. The aim of this study was to determine the ability of phenotypic and genotypic methods to type ST22-MRSA-IV strains within a hospital for microevolution events. Forty-two ST22-MRSA-IV strains collected from 2002 to 2005 were analysed using antimicrobial testing, toxin gene analysis, PFGE, spa typing, fluorescent amplified fragment length polymorphism (fAFLP) and determination of staphylococcal interspersed repeat units (SIRUs). Four different antimicrobial patterns were observed. The majority of the isolates (n=31) were resistant towards erythromycin, ciprofloxacin and clindamycin, in addition to penicillin and oxacillin. All strains harboured the sec gene and showed a homogeneous profile of toxin genes. One isolate was typed as spa t022, two as spa t474 and the remainder belonged to spa type t032. PFGE yielded eight profiles and SIRU typing resulted in six different patterns. The fAFLP technique subdivided the individual PFGE profiles, but the grouping of isolates differed from that obtained by PFGE or SIRU typing. These results showed a diversity of ST22-MRSA-IV strains within a narrow clinical setting, indicating microevolution of the Barnim MRSA clone. The ability to distinguish among MRSA strains within an endemic setting will lead to a greater understanding of the transmission of MRSA and is necessary to be able to control the spread of various clones.

A novel reverse-line hybridization assay for identifying genotypes of CTX-M-type extended-spectrum β-lactamases

OBJECTIVES

To develop a reverse-line hybridization assay to identify CTX-M genotypes, potentially useful for large-scale investigation of surveillance collections.

METHODS

Isolates carrying previously characterized bla(CTX-M) genes were used to develop the method. In addition, 334 isolates from five separate surveys were used to validate the method. CTX-M group was known from an independent multiplex PCR for 122 isolates and genotype was confirmed for 80 isolates by DNA sequencing. A multiplex PCR was designed to amplify a genotype-specific region within the bla(CTX-M) open-reading frame. Oligonucleotides were designed to hybridize to regions within each amplicon, covering mutations that distinguish among bla(CTX-M) genotypes.

RESULTS

CTX-M phylogenetic groups were identified by the multiplex PCR with 100% concordance. The reverse-line hybridization assay specifically identified commonly-reported variants within these groups (98.7% concordance).

CONCLUSIONS

The hybridization method enabled precise identification of CTX-M genes, rather than just to group level, without the need for DNA sequencing. In its present format, the method enables 43 isolates to be processed per membrane, giving results within one working day. It is a useful tool for the epidemiological investigation of bla(CTX-M) genes among survey collections of Enterobacteriaceae.

Occurrence, prevalence and genetic environment of CTX-M beta-lactamases in Enterobacteriaceae from Indian hospitals

OBJECTIVES

To determine occurrence, prevalence and CTX-M genotypes produced by Enterobacteriaceae from clinical samples from three geographically distant Indian hospitals and to detect linkage of IS26 with bla(CTX-M) and map its precise insertion position.

METHODS

A total of 130, non-duplicate Escherichia coli and Klebsiella pneumoniae resistant to a third-generation cephalosporin (3GC) from three Indian centres were screened for extended-spectrum beta-lactamase (ESBL) production using phenotypic detection methods. All isolates were screened for bla(CTX-M) using multiplex PCR. Precise CTX-M genotype was identified using reverse-line hybridization. All CTX-M-producing isolates were screened for linkage of IS26 with bla(CTX-M). DNA sequencing was used to map the exact insertion position of this mobile element.

RESULTS

Ninety-five of 130 3GC-resistant (73%) (73% of total E. coli, 72% of total K. pneumoniae) isolates were found to carry bla(CTX-M-15). No other CTX-M genotype was detected. IS26 linkage with bla(CTX-M-15) was detected in 31% of isolates carrying bla(CTX-M-15). DNA sequencing revealed variable insertion of this mobile element within tnpA of ISEcp1. RAPD-PCR typing demonstrated great diversity in isolates carrying bla(CTX-M-15); no predominant clone was identified.

CONCLUSIONS

In contrast with other studies where greater diversity exists, CTX-M-15 was the only CTX-M ESBL produced in this Indian collection of unrelated E. coli and K. pneumoniae. This is the first systematic survey report from India detecting CTX-M-type beta-lactamases This is also the first report indicating such high mobility/diversity of insertion of IS26 in close association with bla(CTX-M) in a single bacterial collection.

Examination of specimens for mycobacteria in clinical laboratories in 21 countries: a 10-year review of the UK National Quality Assessment Scheme for Mycobacteria Culture

Results from clinical diagnostic microbiology laboratories taking part in the UK National Quality Assessment Service (UK NEQAS) scheme for Mycobacteria Culture between 1993 and 2003 were evaluated and assessed to determine whether the perceived increase in the use of rapid methods is improving time-to-positive reporting of results. Four simulated sputum specimens containing mycobacteria in mixed cultures with normal commensal organisms were distributed three times a year. Participating laboratories were required to report on the presence of 'mycobacteria' and on the time required to obtain a positive result. The overall level of performance with the mycobacteria culture external quality assessment specimens remained consistently high, with an average success rate of 94% over 10 years. The mean time-to-positive decreased from 24 to 17 days during the previous 8 years. A survey questionnaire, circulated in 2002, addressed the use of continuous automated mycobacterial liquid culture (CAMLiC) and molecular methods. The increase in the use of rapid culture methods for the detection of Mycobacterium tuberculosis has resulted in an overall reduction in time-to-positive data reported by participants, and has provided an indication of participants' ability to meet the 21-day target recommended by the CDC for the detection and identification of M. tuberculosis.

Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment

Samples of effluent and soil were collected from a reed bed system used to remediate liquid waste from a wool finishing mill with a high use of quaternary ammonium compounds (QACs) and were compared with samples of agricultural soils. Resistance quotients of aerobic gram-negative and gram-positive bacteria to ditallowdimethylammomium chloride (DTDMAC) and cetyltrimethylammonium bromide (CTAB) were established by plating onto nutrient agar containing 5 microg/ml or 50 microg/ml DTDMAC or CTAB. Approximately 500 isolates were obtained and screened for the presence of the intI1 (class 1 integrase), qacE (multidrug efflux), and qacE Delta1 (attenuated qacE) genes. QAC resistance was higher in isolates from reed bed samples, and class 1 integron incidence was significantly higher for populations that were preexposed to QACs. This is the first study to demonstrate that QAC selection in the natural environment has the potential to coselect for antibiotic resistance, as class 1 integrons are well-established vectors for cassette genes encoding antibiotic resistance.

CTX-M: changing the face of ESBLs in the UK

The UK has experienced a sudden rise in extended-spectrum beta-lactamase (ESBL) rates, largely due to the appearance and spread of Escherichia coli producing CTX-M-15 type beta-lactamase. The British Society for Antimicrobial Chemotherapy organized two update meetings during 2004 to report and discuss the recognition, clinical diagnosis, treatment and control of bacteria producing these beta-lactamases. This paper reports the data and reviews made by contributors to the conferences. The historical distribution and emergence of ESBLs was reviewed along with the emergence of plasmid-mediated CTX-M ESBLs following their mobilization from the chromosome of Kluyvera spp. The first significant outbreak of CTX-M producers in the UK occurred in 2001 and involved Klebsiella pneumoniae with CTX-M-26 at one site, but by 2003, cloned and diverse E. coli with CTX-M-15 were widespread, with Shropshire one of the most affected regions. The specific experience in Shropshire was reported on and a comprehensive review made of the level of awareness of the need for ESBL detection in laboratories in England and Wales, together with a description of the variety of methods that may be applied, with recommendations for optimal methodology. The increased mortality associated with inappropriate treatment of infections caused by ESBL-producing strains was highlighted, together with discussion on potential control of cross-infection. The meeting concluded that the CTX-M genes have now become widespread in not only E. coli but other Enterobacteriaceae in the UK and this will represent a substantial threat to both the treatment of infections caused by these bacteria in the community and within hospitals.

Incidence of class 1 integrons in a quaternary ammonium compound-polluted environment

Samples of effluent and soil were collected from a reed bed system used to remediate liquid waste from a wool finishing mill with a high use of quaternary ammonium compounds (QACs) and were compared with samples of agricultural soils. Resistance quotients of aerobic gram-negative and gram-positive bacteria to ditallowdimethylammomium chloride (DTDMAC) and cetyltrimethylammonium bromide (CTAB) were established by plating onto nutrient agar containing 5 microg/ml or 50 microg/ml DTDMAC or CTAB. Approximately 500 isolates were obtained and screened for the presence of the intI1 (class 1 integrase), qacE (multidrug efflux), and qacE Delta1 (attenuated qacE) genes. QAC resistance was higher in isolates from reed bed samples, and class 1 integron incidence was significantly higher for populations that were preexposed to QACs. This is the first study to demonstrate that QAC selection in the natural environment has the potential to coselect for antibiotic resistance, as class 1 integrons are well-established vectors for cassette genes encoding antibiotic resistance.

Role of environmental cleaning in controlling an outbreak of Acinetobacter baumannii on a neurosurgical intensive care unit

An outbreak of Acinetobacter baumannii colonization and infection occurred in 19 patients over a 14-month period during 1998-1999 on a neurosurgical intensive care unit. During efforts to control the outbreak a significant correlation was observed between the number of environmental isolates of A. baumannii obtained during each monthly screening and the number of patients with A. baumannii colonization/infection in the same calendar month (P=0.004). Use of 1000 ppm hypochlorite solution and the introduction of new cleaning protocols reduced the number of environmental isolates. Failure to maintain low levels of environmental contamination with A. baumannii resulted in increases in patient colonization. This study showed that high standards of cleaning play an integral role in controlling outbreaks of A. baumannii in the intensive care unit setting.

Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

Variable-number tandem repeats (VNTRs) have been shown to be a powerful tool in the determination of evolutionary relationships and population genetics of bacteria. The sequencing of a number of Staphylococcus aureus genomes has allowed the identification of novel VNTR sequences in S. aureus, which are similar to those used in the study of the evolution of Mycobacterium tuberculosis clades. Seven VNTRs, termed staphylococcal interspersed repeat units (SIRUs), distributed around the genome are described, occurring in both unique and multiple sites, and varying in length from 48 to 159 bp. Variations in copy numbers were observed in all loci, within both the sequenced genomes and the UK epidemic methicillin-resistant S. aureus (EMRSA) isolates. Clonally related UK EMRSA isolates were clustered using SIRUs, which provided a greater degree of discrimination than multi-locus sequence typing, indicating that VNTRs may be a more appropriate evolutionary marker for studying transmission events and the geographical spread of S. aureus clades.

Predominance and genetic diversity of community- and hospital-acquired CTX-M extended-spectrum β-lactamases in York, UK

OBJECTIVES

This study was conducted to detect the presence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae within the faecal flora of both community- and hospital-based patients in York and to characterize the bla(TEM), bla(SHV) and bla(CTX-M) genes present in these isolates.

METHODS

One thousand faeces samples were collected and screened at York Hospital during October-December 2003. Ninety-five non-duplicate Enterobacteriaceae isolates resistant to third-generation cephalosporins were recovered; 22 isolates were selected for further study on the basis of a positive double disc diffusion test for ESBL production. Antibiotic susceptibility testing was performed to a range of antibiotics. The TEM, SHV and CTX-M genes were detected by PCR and the DNA sequenced.

RESULTS

The distribution of ESBL-positive isolates from the hospital and community was 1.4:1. These included nine Escherichia coli, seven Enterobacter cloacae, four Citrobacter freundii and a single isolate each of Klebsiella spp. and Salmonella spp. A total of 17 isolates contained bla(CTX-M) (five bla(CTX-M-15), three bla(CTX-M-14) and nine bla(CTX-M-9)). ISEcp1 was present in isolates expressing CTX-M-14 and -15, but was absent upstream of In60-associated bla(CTX-M-9). E. coli isolates also contained either a bla(TEM-1) or bla(TEM-2), whereas six of the E. cloacae carried bla(SHV-12) and the Klebsiella spp. bla(SHV-36) in addition to bla(CTX-M-9). The single Salmonella spp. carried bla(SHV-12).

CONCLUSIONS

The overall prevalence of ESBL in isolates of Enterobacteriaceae from York was 1.9%. ESBL-producing isolates were found in both the community and hospital, with the CTX-M type most common. This is also the first report of an ESBL-producing Salmonella in the UK.

Role of environmental cleaning in controlling an outbreak of Acinetobacter baumannii on a neurosurgical intensive care unit

An outbreak of Acinetobacter baumannii colonization and infection occurred in 19 patients over a 14-month period during 1998-1999 on a neurosurgical intensive care unit. During efforts to control the outbreak a significant correlation was observed between the number of environmental isolates of A. baumannii obtained during each monthly screening and the number of patients with A. baumannii colonization/infection in the same calendar month (P < 0.004). Use of 1000 ppm hypochlorite solution and the introduction of new cleaning protocols reduced the number of environmental isolates. Failure to maintain low levels of environmental contamination with A. baumannii resulted in increases in patient colonization. This study showed that high standards of cleaning play an integral role in controlling outbreaks of A. baumannii in the intensive care unit setting.

Dissemination of CTX-M type β-lactamases in Enterobacteriaceae isolates in the People’s Republic of China

Previously there have been a number of reports of extended spectrum beta-lactamase (ESBL) producing isolates of the family Enterobacteriaceae in Asia. We first reported the occurrence of bla(CTX-M) in Guangzhou, China, subsequently there have been reports of bla(CTX-M) from a number of other south Asian countries. Initial surveillance study data suggested that bla(CTX-M) might be widely distributed in China. This study examines the type of bla(CTX-M) occurring in other major population centres in China. Initial disk diffusion method susceptibility testing (NCCLS) selected ESBL producing Escherichia coli and Klebsiella pneumoniae isolates from Beijing and near Wuhan, PRC. After screening in both China and the UK, 13 isolates producing CTX-M ESBLs were identified and studied, 11 also produced TEM-1, and 4 also produced SHV-1. Sequence analysis of the bla(CTX-M) containing isolates revealed these isolates contained two different bla(CTX-M), three with bla(CTX-M-3) and 10 with bla(CTX-M-14). After comparison with other previously published studies in the English language, we conclude that the most prevalent bla(CTX-M) so far reported in Asia are bla(CTX-M-14) and bla(CTX-M-3).

Methicillin resistant Staphylococcus aureus in the critically ill

Methicillin resistant Staphylococcus aureus (MRSA) is endemic within many hospitals worldwide. Critically ill patients on intensive care units have increased risk factors making them especially prone to nosocomially acquired infections. This review addresses the current situation regarding the evolution of MRSA and the techniques for identifying and epidemiologically typing it. It discusses specific risk factors, the morbidity and mortality associated with critically ill patients, and possibilities for future antibiotic treatments.

Description and clinical treatment of an early outbreak of severe acute respiratory syndrome (SARS) in Guangzhou, PR China

Severe acute respiratory syndrome (SARS), now known to be caused by a coronavirus, probably originated in Guangdong province in southern China in late 2002. The first major outbreak occurred in Guangzhou, the capital of Guangdong, between January and March 2003. This study reviews the clinical presentation, laboratory findings and response to four different treatment protocols. Case notes and laboratory findings were analysed and outcome measures were collected prospectively. The SARS outbreak in Guangdong province and the outbreak in Guangzhou associated with hospitals in the city are described, documenting clinical and laboratory features in a cohort of 190 patients randomly allocated to four treatment regimens. Patients were infected by close contact in either family or health-care settings, particularly following procedures likely to generate aerosols of respiratory secretions (e.g. administration of nebulized drugs and bronchoscopy). The earliest symptom was a high fever followed, in most patients, by dyspnoea, cough and myalgia, with 24 % of patients complaining of diarrhoea. The most frequent chest X-ray changes were patchy consolidation with progression to bilateral bronchopneumonia over 5-10 days. Thirty-six cases developed adult respiratory distress syndrome (ARDS), of whom 11 died. There was no response to antibiotics. The best response (no deaths) was seen in the group of 60 patients receiving early high-dose steroids and nasal CPAP (continuous airway positive pressure) ventilation; the other three treatment groups had significant mortality. Cross-infection to medical and nursing staff was completely prevented in one hospital by rigid adherence to barrier precautions during contact with infected patients. The use of rapid case identification and quarantine has controlled the outbreak in Guangzhou, in which more than 350 patients have been infected. Early administration of high-dose steroids and CPAP ventilation appears to offer the best supportive treatment with a reduced mortality compared with other treatment regimens.

Predominant VNTR family of strains of Mycobacterium tuberculosis isolated from South Asian patients

SETTING

Despite the low incidence of tuberculosis in the UK, some minority ethnic groups, particularly those originating from South Asia, experience very high incidence rates.

OBJECTIVE

Comparison of the variable number tandem repeat (VNTR) profiles of strains of Mycobacterium tuberculosis circulating in an immigrant community in the UK with those found in the country of ethnic origin.

DESIGN

Isolates of M. tuberculosis were collected from samples obtained from patients attending clinics in Leeds and Bradford, UK and Rawalpindi, Pakistan. Strains were compared using VNTR analysis and mixed-linker PCR.

RESULTS

Comparison of VNTR profiles found that one profile (42235) represented 37% of patient isolates from Rawalpindi and 23% of patient isolates in Leeds and Bradford, where it was associated exclusively with patients with South Asian names. A second profile (02235) represented 15% of patient isolates in Leeds and Bradford, and was also exclusively associated with the South Asian community. These profiles could be subdivided by mixed-linker PCR analysis.

CONCLUSION

The VNTR profile 42235 may represent a family of strains commonly found in communities associated with South Asia.

SHV-12, SHV-5, SHV-2a and VEB-1 extended-spectrum beta-lactamases in Gram-negative bacteria isolated in a university hospital in Thailand

Sixty-one extended-spectrum beta-lactamase (ESBL)-producing isolates were collected from Srinagarind Hospital, Thailand. These included 43 Enterobacteriaceae and 18 Pseudomonadaceae. The 43 Enterobacteriaceae were found to produce the following ESBLs: 26 (60.5%) SHV-12, 13 (30.2%) SHV-5, two (4.7%) SHV-2a, one (2.3%) VEB-1 and one (2.3%) unidentified. Twenty-four isolates (55.8%) also carried bla(TEM-1B), as well as bla(SHV) or bla(VEB-1). Plasmid DNA from transconjugants carrying the bla(SHV-12) gene showed various restriction patterns, indicating the distribution of the bla(SHV-12) gene among different antibiotic resistance plasmids. In contrast, bla(SHV-5) in 13 isolates was found on a single plasmid of c. 130 kb. Pulsed-field gel electrophoresis (PFGE) analysis of genomic DNA from these isolates revealed that nine of 11 Klebsiella pneumoniae gave the same pattern, indicating clonal spread of the strain within the hospital, together with the occasional spread of the plasmid to other strains. Among the pseudomonad isolates, 16 Pseudomonas aeruginosa and one Pseudomonas putida had bla(VEB-like) and one P. aeruginosa had bla(SHV-12). Nine of the 16 isolates carrying bla(VEB-like) (56.3%) had identical PFGE patterns, suggesting the dissemination of this gene, also by clonal spread. At least six different bla(VEB-like-)containing integrons were found among the 18 isolates. This is the first report of bacteria producing SHV-12 and SHV-2a in Thailand and the first report of SHV-12 in P. aeruginosa, of VEB-1 in Citrobacter freundii and a VEB-1-like beta-lactamase in P. putida. These findings indicate that ESBL genes in the Far East are part of a gene pool capable of broad horizontal gene transfer, in that these genes can transfer between different families of Gram-negative bacilli.

Discrimination of SHV beta-lactamase genes by restriction site insertion-PCR

Restriction site insertion-PCR (RSI-PCR) is a simple, rapid technique for detection of point mutations. This technique exploits primers with one to three base mismatches near the 3' end to modulate a restriction site. We have developed this technique to identify described mutations of the bla(SHV) genes for differentiation of SHV variants that cannot be distinguished easily by other techniques. To validate this method, eight standard strains were used, each producing a different SHV beta-lactamase: SHV-1, SHV-2, SHV-3, SHV-4, SHV-5, SHV-6, SHV-8, and SHV-18. Mismatch primers were designed to detect mutations affecting amino acids at positions 8 (SspI), 179 (HinfI), 205 (PstI), 238 (Gly-->Ala) (BsrI), and 240 (NruI) of bla(SHV) genes. All amplimers of the bla(SHV) genes used in this study yielded the predicted restriction endonuclease digestion products. In addition, this study also makes theoretical identification of bla(SHV-6), bla(SHV-8), and 12 novel bla(SHV) variants using the PCR-restriction fragment length polymorphism (RFLP) technique possible. By using a combination of PCR-RFLP and RSI-PCR techniques, up to 27 SHV variants can now be distinguished rapidly and reliably. These simple techniques are readily applied to epidemiological studies of the SHV beta-lactamases and may be extended to the characterisation of other resistance determinants.

Comparison of variable number tandem repeat and IS6110-restriction fragment length polymorphism analyses for discrimination of high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates

The present study was designed to evaluate the use of variable number tandem repeat (VNTR) and IS6110-restriction fragment length polymorphism (RFLP) analyses in combination as a two-step strategy for discrimination (as measured by the Hunter-Gaston Discrimination Index [HGDI]) of both high- and low-copy-number IS6110 Mycobacterium tuberculosis isolates compared to IS6110-RFLP alone with an unselected collection of isolates. Individually, IS6110-RFLP fingerprinting produced six clusters that accounted for 69% of the low-copy-number IS6110 isolates (five clusters) and 5% of the high-copy-number IS6110 isolates (one cluster). A total of 39% of all the isolates were clustered (HGDI = 0.97). VNTR analysis generated a total of 35 different VNTR allele profile sets from 93 isolates (HGDI = 0.938). Combining IS6110-RFLP analysis with VNTR analysis reduced the overall percentage of clustered isolates to 29% (HGDI = 0.988) and discriminated a further 27% of low-copy-number isolates that would have been clustered by IS6110-RFLP alone. The use of VNTR analysis as an initial typing strategy facilitates further analysis by IS6110-RFLP, and more importantly, VNTR analysis subdivides some IS6110-RFLP-defined clusters containing low- and single-copy IS6110 isolates.

Occurrence of a new metallo-beta-lactamase IMP-4 carried on a conjugative plasmid in Citrobacter youngae from the People's Republic of China

During the course of an antimicrobial resistance surveillance programme in Guangzhou, the People's Republic of China, single strains of Citrobacter youngae and Pseudomonas aeruginosa were identified which were resistant to imipenem and found to carry the carbapenemase gene bla(IMP). PCR screening of the citrobacter strain with specific primers for the bla(IMP) type genes gave a 587-bp product which when sequenced gave 100% homology with the bla(IMP-4) sequence reported recently from Acinetobacter spp. The determinant in the C. youngae strain was found to be located on a 156-kb plasmid capable of transfer to Escherichia coli UB1637 by conjugation. Sequencing of the bla(IMP-4) open reading frame in the C. youngae strain and adjacent sequences not only confirmed the presence of bla(IMP-4) but also identified that a conserved core site found within the 59-bp element of integrons was present and the same as the one described in the only other occurrence of bla(IMP-4) in Acinetobacter spp. isolated from an intensive care unit in Hong Kong. This is the second report of transferable carbapenemase genes in Enterobacteriaciae outside of Japan and the first in the People's Republic of China. Under the selective pressure of carbapenems and extended spectrum cephalosporins use we might expect this gene to spread and widespread surveillance should be instituted.

Rapid identification of laboratory contamination with Mycobacterium tuberculosis using variable number tandem repeat analysis

Compared with solid media, broth-based mycobacterial culture systems have increased sensitivity but also have higher false-positive rates due to cross-contamination. Systematic strain typing is rarely undertaken because the techniques are technically demanding and the data are difficult to organize. Variable number tandem repeat (VNTR) analysis by PCR is rapid and reproducible. The digital profile is easily manipulated in a database. We undertook a retrospective study of Mycobacterium tuberculosis isolates collected over an 18-month period following the introduction of the BACTEC MGIT 960 system. VNTR allele profiles were determined with early positive broth cultures and entered into a database with the specimen processing date and other specimen data. We found 36 distinct VNTR profiles in cultures from 144 patients. Three common VNTR profiles accounted for 45% of true-positive cases. By combining VNTR results with specimen data, we identified nine cross-contamination incidents, six of which were previously unsuspected. These nine incidents resulted in 34 false-positive cultures for 29 patients. False-positive cultures were identified for three patients who had previously been culture positive for tuberculosis and were receiving treatment. Identification of cross-contamination incidents requires careful documentation of specimen data and good communication between clinical and laboratory staff. Automated broth culture systems should be supplemented with molecular analysis to identify cross-contamination events. VNTR analysis is reproducible and provides timely results when applied to early positive broth cultures. This method should ensure that patients are not placed on unnecessary tuberculosis therapy or that cases are not falsely identified as treatment failures. In addition, areas where existing procedures may be improved can be identified.