Comparison of MIDI Sherlock system and pulsed-field gel electrophoresis in characterizing strains of methicillin-resistant Staphylococcus aureus from a recent hospital outbreak

Mass Spectrometry and Microbial Diagnostics in the Clinical Laboratory

Over the past decade, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry has revolutionized the practice of clinical microbiology and infectious disease diagnostics. Rapid advancement has occurred through the development and implementation of mass spectrometric protein profiling technologies that are widely available. Ease of sample preparation, rapid turnaround times, and high throughput accuracy have accelerated acceptance within the clinical laboratory. New mass spectrometric technologies centered on multiple microbial diagnostic markers are in development. Such new applications, reviewed in this article and on the near horizon, stand to greatly enhance the capabilities and utility for improved mass spectrometric microbial identification and patient care.

The Various Roles of Fatty Acids

Lipids comprise a large group of chemically heterogeneous compounds. The majority have fatty acids (FA) as part of their structure, making these compounds suitable tools to examine processes raging from cellular to macroscopic levels of organization. Among the multiple roles of FA, they have structural functions as constituents of phospholipids which are the "building blocks" of cell membranes; as part of neutral lipids FA serve as storage materials in cells; and FA derivatives are involved in cell signalling. Studies on FA and their metabolism are important in numerous research fields, including biology, bacteriology, ecology, human nutrition and health. Specific FA and their ratios in cellular membranes may be used as biomarkers to enable the identification of organisms, to study adaptation of bacterial cells to toxic compounds and environmental conditions and to disclose food web connections. In this review, we discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. We briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.

Combining Environmental Investigation and a Dual-Analytical Strategy to Isolate the Legionella longbeachae Strain Linked to Two Occupational Cases of Legionellosis

Legionella has a global distribution, mainly in aquatic and man-made environments. Under the right conditions, this bacterium is a notorious human pathogen responsible for severe pulmonary illnesses. Legionellosis outbreaks are reported around the world, and exposure to water droplet aerosols containing Legionella pneumophila is usually the mechanism of its transmission. Even if L. pneumophila causes most outbreaks, Legionella longbeachae also accounts for some cases. Unlike most other Legionella strains, L. longbeachae is typically found in soil. Given the wide diversity and high concentration of microorganisms found in soil, isolating L. longbeachae by culture can be challenging. Because the chances of successfully isolating the strain are low, it is often not even attempted. This study reports the strategies used to successfully isolate L. longbeachae strain that was responsible of the two occupational legionellosis in Quebec. Fifteen random samples were collected from the soil of the metal recycling plant where the diagnosed workers were employed, covering 1.5% of the accessible surface of the plant. All samples were analyzed with both the quantitative polymerase chain reaction (qPCR) and culture methods. Four qPCR detection systems targeting Legionella spp, L. pneumophila, L. pneumophila serogroup 1, and L. longbeachae were used. Acid, heat, and acid/heat treatments were used for the culture method. For the qPCR method, all samples were positives for Legionella spp but only four were positives for L. longbeachae. For the culture method, only one isolate could be confirmed to be L. longbeachae. However, that strain proves to be the same one that caused the occupational legionellosis. Detecting the presence of L. longbeachae using the qPCR method made it possible to target the right samples to enable the cultivable strain of L. longbeachae to be isolated from the soil of the metal recycling plant. The complementarity of the two methods was established. This paper demonstrated the advantages of selecting the proper sampling and analytical strategies to achieve the isolation of the strain responsible for the infections. It also highlights for the first time in Quebec the potential occupational risks associated with L. longbeachae from soil and should motivate questioning soil exposures when all sources of water contamination have been eliminated from the causal analysis of legionellosis.

Analysis of Chemical Signatures of Alkaliphiles using Fatty Acid Methyl Ester Analysis

BACKGROUND

Fatty acids occur in nearly all living organisms as the important predominant constituents of lipids. While all fatty acids have essentially the same chemical nature, they are an extremely diverse group of compounds.

MATERIALS AND METHODS

To test the hypothesis, fatty acids of alkaliphiles isolates, Bacillus subtilis SVUNM4, Bacillus licheniformis SVUNM8, Bacillus methylotrohicus SVUNM9, and Paenibacillus dendritiformis SVUNM11, were characterized compared using gas chromatography-mass spectrometry (GC-MS) analysis.

RESULTS

The content of investigated ten fatty acids, 1, 2-benzenedicarboxylic acid butyl 2-methylpropyl ester, phthalic acid, isobutyl 2-pentyl ester, dibutyl phthalate, cyclotrisiloxane, hexamethyl, cyclotetrasiloxane, octamethyl, dodecamethyl, heptasiloxane 1,1,3,3,5,5,7,7,9,9,11,11,13,13-etradecamethyl, 7,15-dihydroxydehydroabietic acid, methyl ester, di (trimethylsilyl) ether, hentriacontane, 2-thiopheneacetic acid, undec-2-enyl ester, obviously varied among four species, suggesting each species has its own fatty acid pattern.

CONCLUSIONS

These findings demonstrated that GC-MS-based fatty acid profiling analysis provides the reliable platform to classify these four species, which is helpful for ensuring their biotechnological interest and novel chemotaxonomic.

Electronic Prediction Rules for Methicillin-ResistantStaphylococcus aureusColonization

Background.

Considerable hospital resources are dedicated to minimizing the number of methicillin-resistantStaphylococcus aureus(MRSA) infections. One tool that is commonly used to achieve this goal is surveillance for MRSA colonization. This process is costly, and false-positive test results lead to isolation of individuals who do not carry MRSA. The performance of this technique would improve if patients who are at high risk of colonization could be readily targeted.

Methods.

Five MRSA colonization prediction rules of varying complexity were derived in a population of 23,314 patients who were consecutively admitted to a US hospital and tested for colonization. Rules incorporated only prospectively collected, structured electronic data found in a patient's record within 1 day of hospital admission. These rules were tested in a validation cohort of 26,650 patients who were admitted to 2 other hospitals.

Results.

The prevalence of MRSA at hospital admission was 2.2% and 4.0% in the derivation and validation cohorts, respectively. Multivariable modeling identified predictors of MRSA colonization among demographic, admission-related, pharmacologic, laboratory, physiologic, and historical variables. Five prediction rules varied in their performance, but each could be used to identify the 30% of patients who accounted for greater than 60% of all cases of MRSA colonization and approximately 70% of all MRSA-associated patient-days. Most rules could also identify the 20% of patients with a greater than 8% chance of colonization and the 40% of patients among whom colonization prevalence was 2% or less.

Conclusions.

We report electronic prediction rules that can fully automate triage of patients for MRSA-related hospital admission testing and that offer significant improvements on previously reported rules. The efficiencies introduced may result in savings to infection control programs with little sacrifice in effectiveness.

Antibiotic susceptibility and resistance of Staphylococcus aureus isolated from fresh porcine skin xenografts: risk to recipients with thermal injury

The previous use of fresh porcine xenografts at the Prague Burn Centre had raised concerns over the transmission of zoonotic pathogens. This study examines the risk of zoonotic Staphylococcus aureus colonisation of burn patients from fresh porcine skin xenografts. Samples were collected from the nares, skin and perineum of commercial pigs (n=101) and were screened for methicillin sensitive S. aureus (MSSA) and resistant S. aureus (MRSA). The efficacy of the antibiotic wash used in decontamination of the pigskin was tested against planktonic- and biofilm-grown isolates. The spa type of each isolate was also confirmed. All pig swabs were negative for MRSA but 86% positive for MSSA. All planktonic-grown isolates of MSSA were sensitive to chloramphenicol and nitrofurantoin and 44% of isolates were resistant to streptomycin. Isolates grown as biofilm exhibited higher rates of antimicrobial resistance. Sequence analysis revealed three distinct spa types of the MRSA ST398 clonal type. This finding demonstrates the existence of a MSSA reservoir containing spa types resembling those of well-known MRSA strains. These MSSA exhibit resistance to antibiotics used for decontamination of the pigskin prior to xenograft. Amended use of procurement could allow the use of fresh pigskin xenografts to be reinstated.

MRSA decolonization of cotton rat nares by a combination treatment comprising lysostaphin and the antimicrobial peptide ranalexin

OBJECTIVES

To evaluate the in vivo effectiveness of a combination treatment containing ranalexin (a natural antimicrobial peptide) and lysostaphin (an antistaphylococcal endopeptidase) for reducing nasal burden of methicillin-resistant Staphylococcus aureus (MRSA).

METHODS

The community-acquired MRSA strain S. aureus NRS384 (USA300-0114) was used in the present study because it is commonly isolated from human nares and it established consistent and reproducible colonization of cotton rat nares. This model was used to evaluate the efficacy of ranalexin/lysostaphin gels (0.1%-1% w/v; administered intranasally once or once per day for 3 consecutive days) for reducing nasal MRSA burden. Control animals were administered vehicle gel only (0.5% hydroxypropyl methylcellulose) or 2% mupirocin, which is used clinically for nasal decolonization of MRSA. Nasal MRSA burden was assessed at 192 h post-inoculation, which was at least 72 h after the final treatment had been administered. An additional study assessed the efficacy of 0.1% ranalexin/lysostaphin against a mupirocin-resistant MRSA strain (MUP20), which had been selected by serial passage of S. aureus NRS384 through subinhibitory concentrations of mupirocin.

RESULTS

Gels containing 0.1% ranalexin/lysostaphin consistently reduced median nasal burden of MRSA to an extent similar to or greater than 2% mupirocin. Treatment with 0.1% ranalexin/lysostaphin was also effective against the MUP20 strain. There was evidence for only minimal irritancy in cotton rat nares administered three doses of 0.1% ranalexin/lysostaphin, suggesting that this agent is suitable for short-course therapy such as is employed currently for nasal decolonization with mupirocin.

CONCLUSIONS

Ranalexin/lysostaphin could serve as an alternative to mupirocin for nasal decolonization of MRSA.

Dose-ranging study to assess the application of intranasal 2% mupirocin calcium ointment to eradicate Staphylococcus aureus nasal colonization

BACKGROUND

Mupirocin nasal ointment may be prescribed for decolonization prior to surgical procedures, especially for carriers of methicillin-resistant Staphylococcus aureus (MRSA). The approved regimen for decolonization of S. aureus from the anterior nares is twice daily for 5 d (10 doses). We performed a two-center, randomized, open-label study to compare the utility of six and 10 doses for decolonization of S. aureus.

METHODS

Patients expecting to undergo surgery were screened for S. aureus nasal carriage approximately three weeks prior to the procedure. Those found to be positive were offered enrollment in the study. In the first arm (n=41), patients were randomized to receive 2, 3, or 5 d (six or 10 doses) of treatment prior to their operation. Their anterior nares were swabbed for culture and S. aureus polymerase chain reaction (PCR) during the decolonization therapy period as well as for four weeks after surgery. In the second arm (n=60), all patients were given 5 d (10 doses) of nasal mupirocin treatment, and the patient's anterior nares were swabbed for culture and S. aureus PCR for four weeks after surgery. Data from six of the patients were excluded from analysis because of failure to submit swabs after operation. All S. aureus isolates were tested for susceptibility to mupirocin and the presence of the mecA gene to detect MRSA.

RESULTS

In Arm 1, 16 patients received 10 doses of mupirocin, 18 received six doses (twice daily for 3 d), and 7 received six doses (thrice daily for 2 d). In the second arm, all patients received 10 doses of mupirocin (twice a day for 5 d). Overall, 89.5% patients who received 10 doses of mupirocin remained decolonized for at least four weeks after surgery versus 68.0% of patients who received six doses (p=0.016). There was no difference between arms 1 and 2 for those given mupirocin twice daily for 5 d.

CONCLUSION

The ten-dose regimen is superior to any six-dose regimen for de-colonizing S. aureus from the anterior nares of patients and for maintaining the decolonized state for at least four weeks after therapy.

Use of fatty acid methyl ester profiles for discrimination of Bacillus cereus T-strain spores grown on different media

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 omega9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation.

Community-acquired methicillin-resistant Staphylococcus aureus emerging as an important cause of necrotizing fasciitis

BACKGROUND

Necrotizing fasciitis (NF) is an uncommon fulminant soft tissue infection characterized by extensive fascial necrosis. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) isolates producing the Panton-Valentine leukocidin (PVL) cytotoxin have been associated with serious necrotizing infections, but NF caused by CA-MRSA has been described only recently. We reviewed our NF experience at Denver Health Medical Center, where CA-MRSA accounts for more than 50% of community S. aureus clinical isolates.

METHODS

Patients treated for NF from January 2004 to February 2006 were identified by review of pathology records and diagnostic codes, and their medical records were reviewed. Isolates of MRSA from monomicrobial NF underwent testing for the PVL gene and pulsed-field gel electrophoresis to determine relatedness to CA-MRSA strains.

RESULTS

Five of 30 NF cases during the study period, all involving the extremities, were caused by MRSA. Monomicrobial MRSA NF accounted for three cases, with all of the patients reporting a distinct "spider bite" lesion 2-3 days prior to admission. The median age was 32 years (range 28-55 years). Resistance to erythromycin and levofloxacin was present in four isolates. None of the isolates displayed inducible clindamycin resistance. Within 12 hours of admission, all patients received empiric antibiotics to which their isolate was susceptible. Patients required a median of six surgical procedures (range 2-7 operations). All patients survived. The MRSA isolates tested positive for PVL and had the USA 300 CA-MRSA deoxyribonucleic acid banding pattern.

CONCLUSIONS

Community-acquired MRSA is an important cause of NF in our region, accounting for > 15% of NF cases. This infection was associated with significant morbidity necessitating multiple surgical interventions. Given the propensity of PVL-positive CA-MRSA to cause severe necrotizing infections, it is reasonable to administer empiric MRSA coverage for NF in endemic locations.

Use of Fatty Acid Methyl Ester Profiles to Compare Copper-Tolerant and Copper-Sensitive Strains of Pantoea ananatis

ABSTRACT A survey was conducted to evaluate differences in fatty acid methyl ester (FAME) profiles among strains of Pantoea ananatis, causal agent of center rot of onion (Allium cepa), isolated from 15 different onion cultivars in three different sites in Georgia. Differences in FAME composition were determined by plotting principal components (PCs) in two-dimensional plots. Euclidean distance squared (ED(2)) values indicated a high degree of similarity among strains. Plotting of PCs calculated from P. ananatis strains capable of growing on media amended with copper sulfate pentahydrate (200 mug/ml) indicated that copper-tolerant strains grouped into tight clusters separate from clusters formed by wild-type strains. However, unlike copper-sensitive strains, the copper-tolerant strains tended to cluster by location. A total of 80, 60, and 73% of the strains from Tift1, Tift2, and Tattnall, respectively, exhibited either confluent growth or partial growth on copper-amended medium. However, all strains were sensitive to a mixture of copper sulfate pentahydrate (200 mug/ml) and maneb (40 mug/ml). When copper-tolerant clones were analyzed and compared with their wild-type parents, in all cases the plotting of PCs developed from copper-tolerant clones formed tight clusters separate from clusters formed by the parents. Eigenvalues generated from these tests indicated that two components provided a good summary of the data, accounting for 98, 98, and 96% of the standardized variance for strains Pna 1-15B, Pna 1-12B, and Pna 2-5A, respectively. Furthermore, feature 4 (cis-9-hexadecenoic acid/2-hydroxy-13-methyltetradecanoic acid) and feature 7 (cis-9/trans-12/cis-7-octadecenoic acid) were the highest or second highest absolute values for PC1 in all three strains of the parents versus copper-tolerant clones, and hexadecanoic acid was the highest absolute value for PC2 in all three strains. Along with those fatty acids, dodecanoic acid and feature 3 (3-hydroxytetradecanoic acid/14-methylpentadecenoic acid) also had an impact on the differences observed between copper-sensitive parents and copper-resistant mutants. Finding these changes in bacterial fatty acid composition could lead to the development of a laboratory assay to identify copper-tolerant strains using gas chromatography as well as providing clues to further elucidate the mode of action of copper tolerance.

Impact of infection control interventions and antibiotic use on hospital MRSA: a multivariate interrupted time-series analysis

Hospitals in the northeast of Scotland have experienced methicillin-resistant Staphylococcus aureus (MRSA) outbreaks since 1997. Several infection control measures were introduced sequentially to control MRSA, and antibiotic use has been monitored. From January 1997 to December 2004, data on the monthly percentage of non-duplicate MRSA infections (%MRSA) were collated from an intervention hospital (IH) and a control hospital (CH). Both hospitals introduced the use of alcohol hand gel in November 2002. Furthermore, the IH introduced an environmental MRSA swabbing programme in March 2001, chlorine disinfection of the environment in September 2001, discharge screening in December 2001, admission screening in November 2003 and environmental audits in March 2004. Multivariate dynamic regression analysis was used to evaluate the longitudinal effects of these interventions as measured by new clinical cases of MRSA. At the IH, the %MRSA increased between January 1998 and January 2001 and then decreased. At the CH, the %MRSA increased from January 1997 to December 2004. Introduction of alcohol hand gel was associated with an absolute decrease in %MRSA of 21% and 30%, respectively, for the IH and CH. At the IH, introduction of chlorine disinfection and environmental swabbing were, respectively, associated with a decrease in %MRSA of 27% immediately and 32% 3 months later. Discharge screening and environmental audit did not significantly affect %MRSA, whereas admission screening was associated with a 22% decrease in %MRSA 4 months later. Increasing macrolide use was associated with increasing %MRSA in both hospitals, and increasing quinolone use was associated with increasing %MRSA in the CH. Implementation of stepwise infection control measures was associated with a decrease in %MRSA in the IH. Introduction of an alcohol gel for hand hygiene was associated with a decrease in %MRSA in both hospitals. Antibiotic use also affects %MRSA, in particular that of macrolides and quinolones.

Spread of a single multiresistant methicillin-resistant Staphylococcus aureus clone carrying a variant of staphylococcal cassette chromosome mec type III isolated in a university hospital

The purpose of the study was the molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) isolates cultured from patients treated in seven wards of a university hospital in Lublin, Poland, over a 14-month period. Eleven nosocomial MRSA isolates were analyzed. Phenotypic identification of the isolates as MRSA was confirmed by the detection of the nuc and mecA genes using a multiplex PCR assay. The MRSA isolates were further characterized by pulsed-field gel electrophoresis, 16S-23S rRNA spacer length polymorphism analysis, and the simplex and multiplex SCCmec PCR assays. The MRSA isolates were found to be multiresistant: in addition to resistance to beta-lactam agents, they demonstrated resistance to ciprofloxacin, tetracycline, erythromycin, and gentamicin. The MRSA isolates were genetically identical and shared common pulsed-field gel electrophoresis profiles and 16S-23S rRNA spacer length polymorphism profiles. The PCR-based method revealed that the profile of the Lublin clone was identical to that of the Brazilian pandemic MRSA isolates. By SCCmec typing, all MRSA isolates harbored the C variant of the SCCmec type III that differed from the typical SCCmec type III pattern by the lack of locus F (414 bp). The results of this study indicate the spread of a single, multiresistant, MRSA clone in various wards of a university hospital over a 14-month period. The SCCmec structure harbored by the Lublin clone has previously been identified among Polish MRSA isolates representing the HoMRSA-Pol1 clone. The data from this study indicate that the Lublin MRSA clone is most probably genetically related to the HoMRSA-Pol1 clone. Moreover, this latter clone belongs to ST239, the same sequence type as the Hungarian and Brazilian pandemic MRSA isolates.

The investigation of Staphylococcus aureus and coagulase-negative staphylococci nasal carriage among patients undergoing haemodialysis

The frequency of nasal staphylococcal colonization among haemodialysed patients was investigated. The swabs were collected in 1998 and 2004 from 28 and 43 patients, respectively. Staphylococcus aureus colonization rates were 57.1% and 27.9% in 1998 and 2004, respectively. Twenty-six coagulase-negative staphylococci (CNS) isolates were cultured: S. epidermidis (21), S. lugdunensis (2), single S. haemolyticus, S. warneri, and S. capitits isolates. One S. aureus and 10 CNS isolates were methicillin resistant. The methicillin-resistant S. aureus (MRSA) was resistant to beta-lactams, tetracycline, and harbored the pvl gene encoding the Panton-Valentine leukocidin. The decrease in S. aureus colonization at 6-year interval was observed. The presence of the pvl gene and a favorable antibiotic susceptibility pattern of the MRSA suggest that the isolate was a member of community-acquired MRSA (CA-MRSA). Concluding, screening of haemodialysed patients for staphylococcal colonization accompanied by characterization of cultured isolates is important to understand its epidemiology and to develop infection prevention measures and treatment strategies.

Cooperative catabolic pathways within an atrazine-degrading enrichment culture isolated from soil

Atrazine degradation previously has been shown to be carried out by individual bacterial species or by relatively simple consortia that have been isolated using enrichment cultures. Here, the degradative pathway for atrazine was examined for a complex 8-membered enrichment culture. The species composition of the culture was determined by PCR-DGGE. The bacterial species included Agrobacterium tumefaciens, Caulobacter crescentus, Pseudomonas putida, Sphingomonas yaniokuyae, Nocardia sp., Rhizobium sp., Flavobacterium oryzihabitans, and Variovorax paradoxus. All of the isolates were screened for the presence of known genes that function for atrazine degradation including atzA,-B,-C,-D,-E,-F and trzD,-N. Dechlorination of atrazine, which was obligatory for complete mineralization, was carried out exclusively by Nocardia sp., which contained the trzN gene. Following dechlorination, the resulting product, hydroxyatrazine was further degraded via two separate pathways. In one pathway Nocardia converted hydroxyatrazine to N-ethylammelide via an unidentified gene product. In the second pathway, hydroxyatrazine generated by Nocardia sp. was hydrolyzed to N-isopropylammelide by Rhizobium sp., which contained the atzB gene. Each member of the enrichment culture contained atzC, which is responsible for ring cleavage, but none of the isolates carried the atzD,-E, or -F genes. Each member further contained either trzD or exhibited urease activity. The enrichment culture was destabilized by loss of Nocardia sp. when grown on ethylamine, ethylammelide, and cyanuric acid, after which the consortium was no longer able to degrade atrazine. The analysis of this enrichment culture highlights the broad level bacterial community interactions that may be involved in atrazine degradation in nature.

Lytic enzyme, labiase for a broad range of Gram-positive bacteria and its application to analyze functional DNA/RNA

The lytic activity of labiase and achromopeptidase for bacterial DNA/RNA extraction were compared. Rapid lysis of many bacterial strains was observed with labiase followed by SDS treatment. Both labiase and achromopeptidase showed high lytic activity against bacterial strains with the A1alpha chemotype (e.g., Aerococcus viridans) and the A3alpha chemotype (e.g., Staphylococcus epidermidis) for cell wall peptidoglycan structures. The lytic activity of labiase was higher than that of achromopeptidase against strains with the A1gamma chemotype (e.g., Bacillus subtilis). The activity of labiase was not detrimentally affected with increasing NaCl concentration. Labiase lysates were successfully used for rapid extraction of DNA and RNA, whereas achromopeptidase lysates degraded RNA. The DNA and RNA obtained were successfully used for 16S rRNA amplification and real-time RT-PCR detection. It is concluded that labiase is useful for rapid lysis of a wide variety of Gram-positive bacteria and can be used for DNA/RNA isolation protocols.

Clinical evaluation of the DiversiLab microbial typing system using repetitive-sequence-based PCR for characterization of Staphylococcus aureus strains

The DiversiLab System, which includes microfluidics-based detection, reagent kits, and software for data processing and analysis, is an automated method using repetitive sequence-based PCR (rep-PCR) for microbial strain typing. To assess the reliability of the DiversiLab System for strain characterization of Staphylococcus aureus, we tested clinical isolates sent to ARUP Laboratories for typing and compared results to those of pulsed field electrophoresis (PFGE) aided by the cluster analysis provided by BioNumerics software. spa typing was performed when the results of these two methods for an outbreak were not concordant. The study included 89 S. aureus isolates (65 mecA positive, 24 mecA negative) from 19 outbreaks (2 to 11 isolates/outbreak). The DiversiLab and PFGE-BioNumerics results were concordant for 15 of the 19 outbreaks. For the remaining four outbreaks, there was partial concordance between the two methods. spa typing results were the same as or more similar to rep-PCR results for three of those outbreaks and were more similar to PFGE results for one. With regard to performance, the DiversiLab system was considerably less labor intensive than PFGE and provided results in less than 24 h, compared with 2 to 3 days for PFGE. Additionally, the Web-based DiversiLab software provides standardized comparisons among isolates almost instantaneously and generates user-friendly, customized reports.

Study of proteomic changes associated with healthy and tumoral murine samples in neuroblastoma by principal component analysis and classification methods

BACKGROUND

The adrenal gland is the election organ forming primary neuroblastoma (NB) tumours, the most common extracranial solid tumours of infancy and childhood.

METHODS

Samples of adrenal gland belonging to healthy and diseased nude mouse were analysed by 2D gel-electrophoresis. The resulting 2D-PAGE maps were digitized by PDQuest and investigated by principal component analysis (PCA).

RESULTS

The analysis of the loadings of the first principal component (PC) permitted the evaluation of the spots characterising each class of samples. Moreover, the soft-independent model of class analogy (SIMCA) method confirmed the separation of the samples in the two classes and allowed the identification of the modelling and discriminating spots. Very good correlation was found between the data obtained by analysis of 2D maps via the commercial software PDQuest and the present PCA analysis. In both cases, the comparison between such maps showed up- and down-regulation of 84 polypeptide chains, out of a total of 700 spots detected by a fluorescent stain, Sypro Ruby. Spots that were differentially expressed between the two groups were analysed by matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry and 14 of these spots were identified so far.

Antimicrobial drug use and methicillin-resistant Staphylococcus aureus, Aberdeen, 1996-2000

Relationships between antimicrobial use and MRSA prevalence are analyzed in Aberdeen, Scotland.

Similar to many hospitals worldwide, Aberdeen Royal Infirmary has had an outbreak of methicillin-resistant Staphylococcus aureus (MRSA). In this setting, the outbreak is attributable to two major clones. The relationships between antimicrobial use and MRSA prevalence were analyzed by time-series analysis. From June 1997 to December 2000, dynamic, temporal relationships were found between monthly %MRSA and previous %MRSA, macrolide use, third-generation cephalosporin use, and fluoroquinolone use. This study suggests that use of antimicrobial drugs to which the MRSA outbreak strains are resistant may be an important factor in perpetuating the outbreak. Moreover, this study confirmed the ecologic effect of antimicrobial drug use (i.e., current antimicrobial use) may have an effect on resistance in future patients. Although these results may not be generalized to other hospitals, they suggest new directions for control of MRSA, which has thus far proved difficult and expensive.

Biochemical and virulence characterization of viable but nonculturable cells of Vibrio parahaemolyticus

Vibrio parahaemolyticus is a common foodborne pathogen frequently causing outbreaks in summer. Maintenance of virulence by the viable but nonculturable (VBNC) state of this pathogen would allow its threat to human health to persist. This study reports on the change in virulence and concomitant changes in activity of two enzymes and fatty acid profiles when V. parahaemolyticus ST550 entered the VBNC state in the modified Morita mineral salt-0.5% NaCl medium incubated at 4 degrees C. The major change in fatty acid composition occurred in the first week, with a rapid increase in C15:0 fatty acid and saturated/unsaturated ratio while a rapid decrease in C16:1 was observed. The activity level of the inducible protective enzyme superoxide dismutase became undetectable in the VBNC state, whereas that of constitutive glucose-6-phosphate dehydrogenase did not change in either the exponential phase or the VBNC state. Cytotoxicity against HEp-2 cells and a suckling mouse assay showed that virulence was lowered in the VBNC state compared with exponential-phase cells. Longer incubation times were required by the VBNC cells to achieve the same level of virulence as seen in exponential-phase cells. Culturable cells were recovered on selective agar medium from the VBNC cultures injected into suckling mice, probably as the result of in vivo resuscitation. Results of this study add to our understanding of the biochemical and physiological changes that have not been reported when V. parahaemolyticus enters into the VBNC state.

Use of MIDI-fatty acid methyl ester analysis to monitor the transmission of Campylobacter during commercial poultry processing

The presence of Campylobacter spp. on broiler carcasses and in scald water taken from a commercial poultry processing facility was monitored on a monthly basis from January through June. Campylobacter agar, Blaser, was used to enumerate Campylobacter in water samples from a multiple-tank scalder; on prescalded, picked, eviscerated, and chilled carcasses; and on processed carcasses stored at 4 degrees C for 7 or 14 days. The MIDI Sherlock microbial identification system was used to identify Campylobacter-like isolates based on the fatty acid methyl ester profile of the bacteria. The dendrogram program of the Sherlock microbial identification system was used to compare the fatty acid methyl ester profiles of the bacteria and determine the degree of relatedness between the isolates. Findings indicated that no Campylobacter were recovered from carcasses or scald tank water samples collected in January or February, but the pathogen was recovered from samples collected in March, April, May, and June. Processing generally produced a significant (P < 0.05) decrease in the number of Campylobacter recovered from broiler carcasses, and the number of Campylobacter recovered from refrigerated carcasses generally decreased during storage. Significantly (P < 0.05) fewer Campylobacter were recovered from the final tank of the multiple-tank scald system than from the first tank. MIDI similarity index values ranged from 0.104 to 0.928 based on MIDI-fatty acid methyl ester analysis of Campylobacterjejuni and Campylobacter coli isolates. Dendrograms of the fatty acid methyl ester profile of the isolates indicated that poultry flocks may introduce several strains of C. jejuni and C. coli into processing plants. Different populations of the pathogen may be carried into the processing plant by successive broiler flocks, and the same Campylobacter strain may be recovered from different poultry processing operations. However, Campylobacter apparently is unable to colonize equipment in the processing facility and contaminate broilers from flocks processed at later dates in the facility.

Tracking spoilage bacteria in commercial poultry processing and refrigerated storage of poultry carcasses

Four trials were conducted to examine the effect of commercial processing and refrigerated storage on spoilage bacteria in the native microflora of broiler carcasses. Prescalded, picked, eviscerated, and chilled carcasses were obtained from a commercial processing facility, and psychrotrophs in the bacterial flora were enumerated on Iron Agar, Pseudomonas Agar, and STAA Agar. The size of the population of spoilage bacteria on processed carcasses stored at 4 degrees C for 7, 10, or 14 days was also determined. Bacterial isolates were identified and dendrograms of the fatty acid profiles of the isolates were prepared to determine the degree of relatedness of the isolates. Findings indicated that although some processing steps increased the level of carcass contamination by selected bacteria, the number of spoilage bacteria recovered from processed carcasses was significantly (P< or = 0.05) less than the number of bacteria recovered from carcasses entering the processing line. Acinetobacter and Aeromonas spp. were the primary isolates recovered from carcasses taken from the processing line. During refrigerated storage, there was a significant (P < or =0.05) increase in the population of bacteria on the carcasses, and Pseudomonas spp. were the predominant bacteria recovered from these carcasses. Dendrograms of the fatty acid profiles of the isolates indicated that bacterial cross-contamination of carcasses occurs during all stages of processing and that some bacteria can survive processing and proliferate on carcasses during refrigerated storage. Furthermore, cross-contamination was detected between carcasses processed on different days at the same facility. Findings indicate that although poultry processing decreases carcass contamination by psychrotrophic spoilage bacteria, significant levels of bacterial cross-contamination occur during processing, and bacteria that survive processing may multiply on the carcasses during refrigerated storage.

New approach based on fuzzy logic and principal component analysis for the classification of two-dimensional maps in health and disease. Application to lymphomas

Two-dimensional (2D) electrophoresis is the most wide spread technique for the separation of proteins in biological systems. This technique produces 2D maps of high complexity, which creates difficulties in the comparison of different samples. The method proposed in this paper for the comparison of different 2D maps can be summarised in four steps: (a) digitalisation of the image; (b) fuzzyfication of the digitalised map in order to consider the variability of the two-dimensional electrophoretic separation; (c) decoding by principal component analysis of the previously obtained fuzzy maps, in order to reduce the system dimensionality; (d) classification analysis (linear discriminant analysis), in order to separate the samples contained in the dataset according to the classes present in said dataset. This method was applied to a dataset constituted by eight samples: four belonging to healthy human lymph-nodes and four deriving from non-Hodgkin lymphomas. The amount of fuzzyfication of the original map is governed by the sigma parameter. The larger the value, the more fuzzy theresulting transformed map. The effect of the fuzzyfication parameter was investigated, the optimal results being obtained for sigma = 1.75 and 2.25. Principal component analysis and linear discriminant analysis allowed the separation of the two classes of samples without any misclassification.

Application of three-way principal component analysis to the evaluation of two-dimensional maps in proteomics

Three-way PCA has been applied to proteomic pattern images to identify the classes of samples present in the dataset. The developed method has been applied to two different datasets: a rat sera dataset, constituted by five samples of healthy Wistar rat sera and five samples of nicotine-treated Wistar rat sera; a human lymph-node dataset constituted by four healthy lymph-nodes and four lymph-nodes affected by a non-Hodgkin's lymphoma. The method proved to be successful in the identification of the classes of samples present in both of the groups of 2D-PAGE images, and it allowed us to identify the regions of the two-dimensional maps responsible for the differences occurring between the classes for both rat sera and human lymph-nodes datasets.

Enumeration and identification of yeasts associated with commercial poultry processing and spoilage of refrigerated broiler carcasses

Yeasts associated with broiler carcasses taken from various stages of commercial poultry processing operations and broiler carcasses stored at refrigerated temperatures were enumerated and identified. Whole carcass rinses were performed to recover yeasts from carcasses taken from a processing facility and processed carcasses stored at 4 degrees C for up to 14 days. Yeasts in the carcass rinsates were enumerated on acidified potato dextrose agar and identified with the MIDI Sherlock Microbial Identification System. Dendrograms of fatty acid profiles of yeast were prepared to determine the degree of relatedness of the yeast isolates. Findings indicated that as the carcasses are moved through the processing line, significant decreases in the number of yeasts associated with broiler carcasses usually occur, and the composition of the yeast flora of the carcasses is altered. Significant (P < 0.05) increases in the yeast population of the carcasses generally occur during storage at 4 degrees C, however. Furthermore, it was determined that the same strain of yeast may be recovered from different carcasses at different points in the processing line and that the same strain of yeast may be isolated from carcasses processed on different days in the same processing facility.

Rapid pulsed-field gel electrophoresis method for group B streptococcus isolates

We developed a rapid pulsed-field gel electrophoresis (PFGE) method that required 3 days to complete, an improvement over the standard method that required as many as 8 days. The accuracy and reproducibility of the rapid method were verified by analysis of DNA band sizes of our control group B streptococcus isolate. The rapid method was superior to the standard method, providing more precise molecular sizing and gels of higher image quality. The reproducibility of rapid PFGE substantiated its value and continued use.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus strains: state of affairs and tomorrow' s possibilities

Methicillin-resistant strains of Staphylococcus aureus (MRSA) have posed a clinical threat for nearly 40 years. During these years, an array of additional technologies suited for identification of MRSA below the species level has become available. The technologies, whether they assess phenotype or genotype, provide data that can be used for elucidation of the routes of dissemination of individual MRSA types. This review summarizes the current state of affairs with respect to the quality of the various laboratory techniques and includes descriptions of novel strategies such as binary typing and multilocus sequence typing (MLST). Drawbacks of procedures will be compared, and the value of molecular typing in the elucidation of complex biological phenomena, such as epidemicity, carriage, and reduced vancomycin susceptibility, will be indicated. Means for integrated assessment of bacterial biology, epidemiology, and population structure will be discussed.

A community pseudo-outbreak of invasive Staphylococcus aureus infection

Outbreaks of invasive infection caused by methicillin-susceptible and methicillin-resistant Staphylococcus aureus occur in hospitals, long term care institutions, and in patients discharged from these settings. In contrast, epidemic S. aureus infection has not been reported in well persons in the community. Here, we describe a group of healthy young adults who resided in the same neighborhood and participated together in school sports, and who developed serious S. aureus infections within 3 weeks of each other, suggesting a true community outbreak. Timely use of molecular epidemiological tools, however, demonstrated that their illnesses were caused by unrelated bacterial strains.

Tracing the origin of an outbreak of methicillin-resistant Staphylococcus aureus infections in a Portuguese hospital by molecular fingerprinting methods

Seventy-six methicillin-resistant Staphylococcus aureus (MRSA) isolates were collected from July 1992 to May 1995 at a 400-bed district hospital in the northeast of Portugal. During the second half of the surveillance period, in July of 1994, an outbreak was detected in the orthopedic ward. Thirty-three (out of the 76) MRSA strains were recovered only in this ward during the outbreak period. All strains were characterized by a variety of genomic fingerprints. Hybridization of ClaI and SmaI restriction digests with the mecA- and Tn554-specific DNA probes was used to identify polymorphism and determine chromosomal location of these determinants, and pulsed-field gel electrophoretic analysis of SmaI digests was used to determine chromosomal backgrounds. All strains recovered during the outbreak in the orthopedic ward were found to belong to a single clone that carried the mecA polymorph I, Tn554 type E in a macrorestriction background called H (clone I::E::H1), which was identified in 18 patients, and 5 health care personnel and from a fomite sample, and was traced to a single transfer patient admitted to the hospital at the beginning of the outbreak. The new clone I::E::H1 differed only in the macrorestriction profile from the MRSA clone previously dominant in this hospital, known as Iberian epidemic clone I::E::A, which has already been identified in several Spanish and Portuguese hospitals.

Cationic peptide antimicrobials induce selective transcription of micF and osmY in Escherichia coli

Cationic antimicrobial peptides, such as polymyxin and cecropin, activated transcription of osmY and micF in growing Escherichia coli independently of each other. The micF response required the presence of a functional rob gene. It is intriguing that in this and other assays an identical response profile was also seen with hyperosmotic salt or sucrose gradient, two of the most commonly used traditional food preservatives. The osmY and micF transcription was not induced by hypoosmotic gradient, ionophoric peptides, uncouplers, or with other classes of membrane perturbing agents. The antibacterial peptides did not promote transcription of genes that respond to macromolecular or oxidative damage, fatty acid biosynthesis, heat shock, or depletion of proton or ion gradients. These and other results show that the antibacterial cationic peptides induce stasis in the early growth phase, and the transcriptional efficacy of antibacterial peptides correlates with their minimum inhibitory concentration, and also with their ability to mediate direct exchange of phospholipids between vesicles. The significance of these results is developed as the hypothesis that the cationic peptide antimicrobials stress growth of Gram-negative organisms by making contacts between the two phospholipid interfaces in the periplasmic space and prevent the hyperosmotic wrinkling of the cytoplasmic membrane. Broader significance of these results, and of the hypothesis that the peptide mediated contacts between the periplasmic phospholipid interfaces are the primary triggers, is discussed in relation to antibacterial resistance.

Bacillus cereus infections among oncology patients at a children's hospital

BACKGROUND

Bacillus cereus can cause severe infections in immunocompromised persons.

METHODS

We report 3 cases of bacteremia/septicemia (1 fatal) among oncology patients in a children's hospital. Because all cases occurred during a 10-day period, a common source outbreak was suspected. An epidemiologic investigation was performed. Molecular comparison of patient and environmental isolates was performed by using pulsed-field gel electrophoresis.

RESULTS

After an extensive investigation, no common hospital source could be found. Pulsed-field gel electrophoresis proved that the isolates were not related.

CONCLUSION

Sporadic infections in immunocompromised persons do occur and can be associated with significant morbidity.

Rapid pulsed-field gel electrophoresis protocol for typing of Escherichia coli O157:H7 and other gram-negative organisms in 1 day

Genomic DNA patterns generated by pulsed-field gel electrophoresis are highly specific for different strains of an organism and have significant value in epidemiologic investigations of infectious-disease outbreaks. Unfortunately, time-consuming and tedious specimen processing is an inherent problem which limits the use of this powerful technology as a real-time epidemic investigational tool. Here, I describe a rapid method to improve the response time and provide specific bacterial strain identification for the typing of Escherichia coli O157:H7 and other gram-negative organisms in a single day.

Rapid lysis of gram-positive cocci for pulsed-field gel electrophoresis using achromopeptidase

To adapt pulsed-field gel electrophoresis (PFGE) to a busy clinical laboratory, we evaluated the use of achromopeptidase (ACP) as the sole agent for lysis of a variety of gram-positive cocci. Growth in an appropriate broth media was adjusted to a 3.0 McFarland density before aliquotting for washing and plug preparation. ACP incorporated into the agarose plugs, or added to the buffer solution, lysed cells in < 1 h when suspended in a Tris-NaCl buffer. Two 30-min washes in a Tris-EDTA buffer were sufficient to remove cellular debris without additional deproteination. Final PFGE results were obtained in approximately 48 h, including the initial broth subculturing.

Investigation of nosocomial infection caused by arbekacin-resistant, methicillin-resistant Staphylococcus aureus

An outbreak of coagulase VII-producing, arbekacin (ABK)-resistant, methicillin-resistant Staphylococcus aureus (MRSA) occurred between September 1994 and December 1995, involving five different wards. Twenty-one patients developed skin, wound, drainage, or respiratory tract colonization with coagulase VII-producing, (ABK)-resistant MRSA. Phenotypic characteristics (production of enterotoxin and TSST-1, antimicrobial susceptibility) and molecular-typing procedure (plasmid DNA profile, pulsed-field gel electrophoresis [PFGE] and arbitrarily primed polymerase chain reaction [AP-PCR] of chromosomal DNA) in isolated strains were compared. Plasmid analysis identified four different profiles and 19 of 22 strains recovered had identical patterns. PFGE of chromosomal DNA identified three different subtypes and 18 (81.8%) isolates shared the same subtype. AP-PCR also demonstrated that most strains had the same phenotypic characteristics. Although traditional epidemiological methods; for example, coagulase typing, plays a central role in hospital infection control, combination of plasmid DNA profile, AP-PCR, and PFGE may prove to be a particularly informative means of tracking the nosocomial spread of MRSA.

Distinction ofPrevotella intermediaandPrevotella nigrescensfrom Endodontic Bacteremia through their Fatty Acid Contents

Prevotella nigrescens has recently been recognized as a new species distinct from Prevotella intermedia. The distinction is based largely on DNA-DNA hybridization, electrophoretic migration of malate and glutamate dehydrogenase, and peptidase and lipase activities of type strains. Gas chromatography of cellular fatty acids can be a useful adjunct for characterization and identification of bacterial species. In the present study, cellular fatty acid profiles were determined for seven strains of P. intermedia and six strains of P. nigrescens. Six of these 13 strains were isolated from the root canal and blood of three patients during endodontic therapy of teeth with Asymptomatic apical periodontitis. The bacteria were cultivated anaerobically in 10 mL prereduced anaerobically sterilized peptone-yeast extract-glucose broth for 24 h. Dried cells of each isolate were methanolysed and their fatty acid contents determined by the Microbial Identification System software package by MIDI. The data were treated by principal component analysis, which distinguished P. nigrescensfromP. intermedia. Cellular fatty acid profiles of these strains of the species in blood matched the profiles of their respective root canal isolates, as demonstrated by Euclidean Distance Square assessment. This suggested that the organisms in the root canal had spread to the bloodstream during endodontic treatment.

Rapid preparation of bacterial DNA for pulsed-field gel electrophoresis

A disadvantage of genotyping bacterial strains by pulsed-field gel electrophoresis is that the procedure requires up to 6 days to complete. We modified a standard pulsed-field gel electrophoresis method (B.E. Murray, K.V. Singh, J.D. Health, B.R. Sharma, and G.M. Weinstock, J.Clin. Microbiol. 28:2059-2063, 1990) so that it could be completed in less than 3 days. We successfully applied this method to the analysis of a variety of gram-positive and gram-negative bacteria.