Rapid detection of methicillin-resistant staphylococci by multiplex PCR

Influence of Nisin-Biogel at Subinhibitory Concentrations on Virulence Expression in Staphylococcus aureus Isolates from Diabetic Foot Infections

A new approach to diabetic foot infections (DFIs) has been investigated, using a nisin-biogel combining the antimicrobial peptide (AMP) nisin with the natural polysaccharide guar-gum. Since in in vivo conditions bacteria may be exposed to decreased antimicrobial concentrations, known as subinhibitory concentrations (sub-MICs), effects of nisin-biogel sub-MIC values corresponding to 1/2, 1/4 and 1/8 of nisin's minimum inhibitory concentration (MIC) on virulence expression by six Staphylococcus aureus DFI isolates was evaluated by determining bacteria growth rate; expression of genes encoding for staphylococcal protein A (spA), coagulase (coa), clumping factor A (clfA), autolysin (atl), intracellular adhesin A (icaA), intracellular adhesin D (icaD), and the accessory gene regulator I (agrI); biofilm formation; Coa production; and SpA release. Nisin-biogel sub-MICs decreased bacterial growth in a strain- and dose-dependent manner, decreased agrI, atl and clfA expression, and increased spA, coa, icaA and icaD expression. Biofilm formation increased in the presence of nisin-biogel at 1/4 and 1/8 MIC, whereas 1/2 MIC had no effect. Finally, nisin-biogel at sub-MICs did not affect coagulase production, but decreased SpA production in a dose-dependent manner. Results highlight the importance of optimizing nisin-biogel doses before proceeding to in vivo trials, to reduce the risk of virulence factor's up-regulation due to the presence of inappropriate antimicrobial concentrations.

Susceptibility to chlorhexidine and mupirocin among methicillin-resistant Staphylococcus aureus clinical isolates from a teaching hospital

Despite the widespread use of chlorhexidine (CHX) to prevent infection, data regarding the in vitro action of CHX against methicillin-resistant Staphylococcus aureus(MRSA) are limited. Clinical isolates from Hospital das Clinicas, Sao Paulo, Brazil, identified during 2002/2003 and 2012/2013 were studied to describe the susceptibility to CHX and mupirocin, molecular characteristics, and virulence profile of MRSA. Susceptibility test to Mupirocin was performed by the disk diffusion method and to CHX by the agar dilution technique. PCR for virulence genes, mecA gene and Staphylococcal Cassette Chromosome mec (SCCmec) types were investigated as well. Mupirocin- and CHX-resistant isolates were sequenced using the Illumina^TM plataform. Two hundred and sixteen MRSA clinical isolates were evaluated: 154 from infected and 62 from colonized patients. Resistance to mupirocin was observed in four isolates assigned as SCCmec type III and STs (ST05; ST239 and ST105) carrying mupA and blaZ, two of them co-harboring the ileS gene. Only one isolate assigned as SCCmec type III was resistant to CHX (MIC of 8.0 μg.mL^-1) and harbored the qacA gene. Resistance to chlorhexidine and mupirocin were found in isolates carrying qacA and mupA in our hospital. Since these genes are plasmid-mediated, this finding draws attention to the potential spread of resistance to mupirocin in our hospital.

Panton-Valentine leukocidin-positive novel sequence type 5959 community-acquired methicillin-resistant Staphylococcus aureus meningitis complicated by cerebral infarction in a 1-month-old infant

Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a pathogen of major importance in pediatric patients. CA-MRSA can cause skin and soft tissue infection in children and young active adults with no predisposing factors, and life-threatening infections such as meningitis or necrotizing pneumonia have been reported. We report here a case of CA-MRSA meningitis complicated by acute left middle cerebral artery (MCA) infarction and necrotizing pneumonia in a previously healthy 1-month-old Vietnamese boy. He was firstly treated with vancomycin, but changed to linezolid because of persistent fever and low vancomycin trough level. He recovered successfully with residual right-sided hemiparesis. The mode of transmission of CA-MRSA and the mechanism of cerebral infarction (thrombotic or embolic) were unknown. The isolate was genotyped as staphylococcal cassette chromosome (SCC) mec type V with a novel sequence type (ST) 5959 harboring the Panton-Valentine leukocidin (PVL) gene. ST 5959 is a double locus variant of ST 59, which is a major PVL-positive CA-MRSA strain isolated in invasive disease in Asian countries. This case report may serve as a warning about the dissemination of PVL-positive CA-MRSA in and around Japan, with the possibility of causing serious life-threatening disease. The potential of linezolid for the treatment of MRSA meningitis as one of the alternative MRSA therapeutic drugs is also discussed.

Detection of the mecA gene and identification of Staphylococcus directly from blood culture bottles by multiplex polymerase chain reaction

INTRODUCTION

Staphylococcus spp. - both S. aureus, including methicillin-resistant strains (MRSA) and coagulase negative staphylococci (CoNS) - are relevant agents of healthcare-associated infections. Therefore, the rapid recognition of MRSA and methicillin-resistant CoNS from blood stream infections is critically important for patient management. It is worth noting that inappropriate empiric therapy has been associated with higher in-hospital mortality.

MATERIAL AND METHODS

In this study we evaluated a multiplex polymerase chain reaction (multiplex PCR) standardized to detect Staphylococcus spp., S. aureus, and mecA gene-encoded oxacillin resistance directly from blood culture bottles. A total of 371 blood cultures with Gram-positive microorganisms confirmed by Gram-stain were analyzed. Results from multiplex PCR were compared to phenotypic characterization of isolates.

RESULTS

Staphylococcus aureus was detected in 85 (23.0%) blood cultures and CoNS in 286 (77.0%). There was 100% agreement between phenotypic and multiplex PCR identification. Forty-three (50.6%) of the 85 S. aureus carried the mecA gene and among the 286 CoNS, 225 (78.7%) were positive for the mecA gene.

CONCLUSIONS

The multiplex PCR assay developed here was found to be sensitive, specific, rapid, and showed good agreement with the phenotypic results besides being less expensive. This PCR method could be used in clinical laboratories for rapid identification and initiation of specific and effective treatment, reducing patient mortality and morbidity. Furthermore, this method may reduce misuse of antimicrobial classes that are more expensive and toxic, thus contributing to the selection of antibiotic-resistant Staphylococcus spp.

Vancomycin-intermediate livestock-associated methicillin-resistant Staphylococcus aureus ST398/t9538 from swine in Brazil

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has been mainly related with pig farming, in Europe and North America, with the ST398 as the most commonly identified type of LA-MRSA. Here we present the draft genome of the first vancomycin-intermediate MRSA ST398/t9538 isolated from a swine presenting exudative epidermitis in Brazil.

Virulence and resistance profiles of MRSA isolates in pre- and post-liver transplantation patients using microarray

Methicillin-resistant Staphylococcus aureus (MRSA) screening plays a great role in preventing infections in surgical patients. This study aims to evaluate clonality, virulence and resistance of MRSA in pre- and post-liver transplantation (LT) patients. Nasal and groin swabs of 190 patients were collected. PCR for virulence genes and staphylococcal cassette chromosome mec (SCCmec) types, microarray, PFGE, multilocus sequence typing and MIC were performed. MRSA carriers were detected in 20.5 % (39/190) of the patients. However, only three colonized patients developed infections post-LT. Sixty-nine MRSA isolates were identified, and the most frequent SCCmec type was type II (29/69; 42.0 %). Most isolates (57/69; 82.6 %) were susceptible to trimethoprim-sulfamethoxazole (TMP/SMX) and harboured the lukD, lukE, clf and fnbA genes as determined by PCR. Five sequence types (ST) were identified among nine clones; 36.2 % (25/69) isolates belonged to a predominant clone (ST105 and SCCmec type II) that was susceptible to TMP/SMX, mupirocin and chlorhexidine, which had 87.9 % similarity with the New York/Japan clone. The array showed virulence difference in isolates of the same clone and patients and that colonized isolates (pre-LT patients) were less virulent than those post-LT and those infected. Therefore, despite the high frequency of MRSA colonization, infection due to MRSA was uncommon in our LT unit. MRSA isolates presented great diversity. Isolates of the same clone expressed different virulence factors by array. Colonizing isolates pre-LT expressed less virulent factors than post-LT and infecting isolates.

A Study of the Relationship Between Environmental Contamination with Methicillin-ResistantStaphylococcus aureus(MRSA) and Patients' Acquisition of MRSA

Objective.

The study aimed to examine the presence of methicillin-resistantStaphylococcus aureus(MRSA) in the environment and its relationship to patients' acquisition of MRSA.

Design.

A prospective study was conducted in a 9-bed intensive care unit for 14 months. At every environmental screening, samples were obtained from the same 4 sites in each bed space. Patients were screened at admission and then 3 times weekly. All environmental and patient strains were typed using pulsed-field gel electrophoresis.

Results.

MRSA was isolated from the environment at every environmental screening, when both small and large numbers of patients were colonized. Detailed epidemiological typing of 250 environmental and 139 patient isolates revealed 14 different pulsed-field gel electrophoresis profiles, with variants of EMRSA-15 being the predominant type. On only 20 (35.7%) of 56 occasions were the strains isolated from the patients and the strains isolated from their immediate environment indistinguishable. There was strong evidence to suggest that 3 of 26 patients who acquired MRSA while in the intensive care unit acquired MRSA from the environment.

Conclusions.

This study reveals widespread contamination of the hospital environment with MRSA, highlights the complexities of the problem of contamination, and confirms the need for more-effective cleaning of the hospital environment to eliminate MRSA.

Staphylococcus aureus isolates colonizing and infecting cirrhotic and liver-transplantation patients: comparison of molecular typing and virulence factors

BACKGROUND

S. aureus is an important agent of colonization and infection in liver transplant patients. It harbors several virulence factors that can increase its pathogenicity. However, studies of virulence and molecular typing of MRSA in cirrhotic and liver transplantation patients are scarce.

RESULTS

Here we use SCCmec, PFGE, spa typing, MLST and virulence factors to characterize MRSA isolates in pre and post liver transplantation patients. Sixteen (13%) of 126 cirrhotic and 15 of the 64 liver-transplanted patients (23%) were colonized by MRSA (p=0.091). SCCmec types I, II and III that are generally associated with nosocomial infections were identified in 91% of the isolates. None of the isolates carried PVL, adhesion factors and fib gene. Only three MRSA colonized isolates carried tst gene and were characterized as SCCmec type I and t149. Ten spa types and five STs were identified; t002 and ST105 were the most frequent profiles. Spa types and ST1510 never described in Brazil and a new spa type t14789 were identified. Nineteen PFGE subtypes were found and grouped into nine types. There was a predominant cluster, which was related to the New York/Japanese epidemic clone and harboured SCCmec type II identified in both cirrhotic and post-transplantation patients. Based on SCCmec and virulence factors the MRSA isolates belonged to NY/Jpn clone seen be more similar to the USA100 MRSA isolates.

CONCLUSIONS

Although without significance, liver-transplantation was more frequently colonized by MRSA than cirrhotic patients. The most frequent SCCmec was type II, and the predominant cluster was related to the New York/Japanese clone. A new spa t14789, and ST1510 never reported in Brazil were identified.

Genotypic and phenotypic characteristics of Methicillin-resistant Staphylococcus aureus (MRSA) strains, isolated on three different geography locations

Staphylococcus aureus is a major cause of hospital-acquired infections worldwide. Increased frequency of methicillin-resistant Staphylococcus aureus (MRSA) in hospitalized patients and possibility of vancomycin resistance requires rapid and reliable characterization of isolates and control of MRSA spread in hospitals. Typing of isolates helps to understand the route of a hospital pathogen spread. The aim of this study was to investigate and compare genotypic and phenotypic characteristics of MRSA samples on three different geography locations. In addition, our aim was to evaluate three different methods of MRSA typing: spa-typing, agr-typing and GenoType MRSA.  We included 104 samples of MRSA, isolated in 3 different geographical locations in clinical hospitals in Zagreb, Mostar, and Heidelberg, during the period of six months. Genotyping and phenotyping were done by spa-typing, agr-typing and dipstick assay GenoType MRSA. We failed to type all our samples by spa-typing.  The most common spa-type in clinical hospital Zagreb was t041, in Mostar t001, and in Heidelberg t003.We analyzed 102/104 of our samples by agr-typing method. We did not find any agr-type IV in our locations. We analyzed all our samples by the dipstick assay GenoType MRSA. All isolates in our study were MRSA strains. In Zagreb there were no positive strains to PVL gene. In Mostar we have found 5/25 positive strains to PVL gene, in Heidelberg there was 1/49. PVL positive isolates were associated with spa-type t008 and agr-type I, thus, genetically, they were community-associated MRSA (CA-MRSA). Dipstick assay GenoType MRSA has demonstrated sufficient specificity, sensibility, simple performance and low cost, so we could introduce it to work in smaller laboratories. Using this method may expedite MRSA screening, thus preventing its spread in hospitals.

Identification of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from burn patients by multiplex PCR

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative staphylococci (MRCoNS) as important human pathogens are causes of nosocomial infections worldwide. Burn patients are at a higher risk of local and systemic infections with these microorganisms.

OBJECTIVE

A screening method for MRSA by using a multiplex polymerase chain reaction (PCR) targeting the 16S ribosomal RNA (rRNA), mecA, and nuc genes was developed. The aim of the present study was to investigate the potential of this PCR assay for the detection of MRSA strains in samples from burn patients.

METHODS

During an 11-month period, 230 isolates (53.11%) of Staphylococcus spp. were collected from burn patients. The isolates were identified as S. aureus by using standard culture and biochemical tests. DNA was extracted from bacterial colonies and multiplex PCR was used to detect MRSA and MRCoNS strains.

RESULTS

Of the staphylococci isolates, 149 (64.9%) were identified as S. aureus and 81 (35.21%) were described as CoNS. Among the latter, 51 (62.97%) were reported to be MRCoNS. From the total S. aureus isolates, 132 (88.6%) were detected as MRSA and 17 (11.4%) were methicillin-susceptible S. aureus (MSSA). The presence of the mecA gene in all isolates was confirmed by using multiplex PCR as a gold standard method.

CONCLUSION

This study presented a high MRSA rate in the region under investigation. The 16S rRNA-mecA-nuc multiplex PCR is a good tool for the rapid characterization of MRSA strains. This paper emphasizes the need for preventive measures and choosing effective antimicrobials against MRSA and MRCoNS infections in the burn units.

Non-multidrug-resistant, methicillin-resistant Staphylococcus aureus in a neonatal unit

BACKGROUND

In the last decade, non-multiresistant methicillin-resistant Staphylococcus aureus (NM-MRSA) has been described as an important agent in bloodstream infections in our hospital.

METHODS

This prospective cohort study, conducted from February 2009 through January 2010 in the neonatal unit, evaluated 403 newborns (NB), their 382 mothers and 148 health care workers (HCW).

RESULTS

Approximately 217 NB (54%), 187 mothers (48%) and 87 HCW (59%) were colonized by S. aureus (SA). MRSA colonization was greater among NB (15%) than mothers (4.7%) and HCW (3.4%). Although mother-to-NB transmission occurred, in most cases mothers were not responsible for NB colonization. There were 2 predominant PFGE patterns among the NB and some mothers and HCW became colonized by them. Factors significantly associated with MRSA carriage by NB were lower level of maternal schooling (risk factor: odds ratio: 2.99; 95% confidence interval: 1.10-8.07) and maternal rhinosinusitis (protective factor: odds ratio: 0.33; 95% confidence interval:0.12-0.88). Among NB who remained hospitalized for more than 72 hours, breast feeding was protective (odds ratio: 0.22; 95% confidence interval: 0.05-0.98). All the isolates were NM-MRSA, carried few virulence factors and SCCmec types IVa and type IVd predominated.

CONCLUSIONS

Although there were no cases of infection, nosocomial transmission of MRSA clearly occurred in the neonatal unit, and this highlights the need for infection control practices such as hand hygiene to prevent cross-dissemination. Other healthcare practices, which are very basic but also ample in scope, may play a role, such as general education of women and breast feeding.

Differentiation between Staphylococcus aureus and coagulase-negative Staphylococcus species by real-time PCR including detection of methicillin resistants in comparison to conventional microbiology testing

BACKGROUND

Staphylococcus aureus has long been recognized as a major pathogen. Methicillin-resistant strains of S. aureus (MRSA) and methicillin-resistant strains of S. epidermidis (MRSE) are among the most prevalent multiresistant pathogens worldwide, frequently causing nosocomial and community-acquired infections.

METHODS

In the present pilot study, we tested a polymerase chain reaction (PCR) method to quickly differentiate Staphylococci and identify the mecA gene in a clinical setting.

RESULTS

Compared to the conventional microbiology testing the real-time PCR assay had a higher detection rate for both S. aureus and coagulase-negative Staphylococci (CoNS; 55 vs. 32 for S. aureus and 63 vs. 24 for CoNS). Hands-on time preparing DNA, carrying out the PCR, and evaluating results was less than 5 h.

CONCLUSIONS

The assay is largely automated, easy to adapt, and has been shown to be rapid and reliable. Fast detection and differentiation of S. aureus, CoNS, and the mecA gene by means of this real-time PCR protocol may help expedite therapeutic decision-making and enable earlier adequate antibiotic treatment.

Oxacillin resistance and antimicrobial susceptibility profile of Staphylococcus saprophyticus and other staphylococci isolated from patients with urinary tract infection

BACKGROUND

Staphylococcus saprophyticus is the second most frequent community-acquired causative agent of urinary tract infection (UTI). The objective of this study was to evaluate the susceptibility profile and resistance detection in Staphylococcus species. isolated from patients with UTI.

MATERIALS AND METHODS

The isolates were investigated using the disk diffusion method, Vitek I system, E-test®, and detection of the mecA gene.

RESULTS

Most isolates (76.2%) were resistant to oxacillin by the disk diffusion method, followed by those resistant to penicillin (72.2%). The oxacillin disk diffusion method, E-test, and Vitek I method showed higher sensitivity (94.4%) and lower specificity (28.9, 26.5, and 24.0%, respectively) than the cefoxitin disk diffusion test (sensitivity: 83.5%, specificity: 85.5%) for the detection of oxacillin resistance.

CONCLUSIONS

The large number of oxacillin-resistant isolates indicates that the breakpoint value recommended by the Clinical and Laboratory Standards Institute may overestimate oxacillin resistance in S. saprophyticus. Thus, changes in these guidelines are necessary for the correct detection of this resistance.

Identification of Staphylococcus saprophyticus isolated from patients with urinary tract infection using a simple set of biochemical tests correlating with 16S-23S interspace region molecular weight patterns

The emergence of Staphylococcus spp. not only as human pathogens, but also as reservoirs of antibiotic resistance determinants, requires the development of methods for their rapid and reliable identification in medically important samples. The aim of this study was to compare three phenotypic methods for the identification of Staphylococcus spp. isolated from patients with urinary tract infection using the PCR of the 16S-23S interspace region generating molecular weight patterns (ITR-PCR) as reference. All 57 S. saprophyticus studied were correctly identified using only the novobiocin disk. A rate of agreement of 98.0% was obtained for the simplified battery of biochemical tests in relation to ITR-PCR, whereas the Vitek I system and novobiocin disk showed 81.2% and 89.1% agreement, respectively. No other novobiocin-resistant non-S. saprophyticus strain was identified. Thus, the novobiocin disk is a feasible alternative for the identification of S. saprophyticus in urine samples in laboratories with limited resources. ITR-PCR and the simplified battery of biochemical tests were more reliable than the commercial systems currently available. This study confirms that automated systems are still unable to correctly differentiate CoNS species and that simple, reliable and inexpensive methods can be used for routine identification.

Performance of surveillance cultures at different body sites to identify asymptomatic Staphylococcus aureus carriers

The objective was to evaluate the performance of surveillance cultures at various body sites for Staphylococcus aureus colonization in pregnant women and newborns (NB) and the factors associated with nasal colonization. For NB, 4 sites were evaluated: nares, oropharynx, perineum, and umbilical stump (birth, third day, and weekly). For pregnant women, 4 sites during labor: anterior nares, anus, perineum, and oropharynx. Nasally colonized patients were compared with colonized only extranasally. Colonization was 53% of 392 pregnant women (methicillin-resistant S. aureus [MRSA]: 4%) and 47% of 382 NB (MRSA: 9%). For newborn patients, the best body site was the umbilical stump (methicillin-susceptible S. aureus [MSSA]: 64%; MRSA: 68%) and the combination of nares + umbilical (MSSA: 86%; MRSA: 91%). Among pregnant women, the best body site was the anterior nares (MSSA: 59%; MRSA: 67%) and the combination of nares + oropharynx (MSSA: 83%; MRSA: 80%). A smaller number of household members were associated with MRSA carriage in pregnant women (2.2 ± 0.6 versus 3.6 ± 1.8; P = 0.04). In conclusion, multiple culture sites are needed. Control programs based on surveillance cultures may be compromised.

[Oxacillin-resistant coagulase-negative Staphylococci bacteremia at a teaching hospital in Santa Maria, State of Rio Grande do Sul, Brazil]

INTRODUCTION

This study aimed to characterize the prevalence and susceptibility profile to oxacillin-resistant Coagulase-negative Staphylococci strains isolated from blood cultures in a teaching hospital, located in Santa Maria, RS. In addition, different methodologies for phenotypic characterization of mecA-mediated oxacillin resistance were compared with genotypic reference testing.

METHODS

After identification (MicroScan - Siemens), the isolates were tested for antimicrobial sensitivity using disk diffusion and automation (MicroScan - Siemens). The presence of mecA gene was identified by the polymerase chain reaction molecular technique.

RESULTS

The most common species was Staphylococcus epidermidis (n=40, 67%). The mecA gene was detected in 54 (90%) strains, while analysis of the sensitivity profiles revealed a high rate of resistance to multiple classes of antimicrobial drugs. However, all isolates were uniformly sensitive to vancomycin and tigecycline. The cefoxitin disk was the phenotypic method that best correlated with the gold standard.

CONCLUSIONS

Analysis of the clinical significance of CoNS isolated from hemocultures and the precise detection of oxacillin resistance represent decisive factors for the correct choice of antibiotic therapy. Although vancomycin constitutes the normal treatment in most Brazilian hospitals, reduction in its use is recommended.

Molecular detection of enterotoxins E, G, H and I in Staphylococcus aureus and coagulase-negative staphylococci isolated from clinical samples of newborns in Brazil

AIMS

The objective of this study was to investigate the detection of SEE, SEG, SEH and SEI in strains of Staphylococcus aureus and coagulase-negative staphylococci (CNS) using RT-PCR.

METHODS AND RESULTS

In this study, 90 Staph. aureus strains and 90 CNS strains were analysed by PCR for the detection of genes encoding staphylococcal enterotoxins (SE) E, G, H and I. One or more genes were detected in 54 (60%) Staph. aureus isolates and in 29 (32.2%) CNS isolates. Staphylococcus epidermidis was the most frequently isolated CNS species (n = 64, 71.1%), followed by Staphylococcus warneri (n = 8, 8.9%) and other species (Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus lugdunensis, Staphylococcus simulans, Staphylococcus saprophyticus and Staphylococcus xylosus: n = 18, 20%). The genes studied were detected in Staph. epidermidis, Staph. warneri, Staph. haemolyticus, Staph. hominis, Staph. simulans and Staph. lugdunensis. The highest frequency of genes was observed in Staph. epidermidis and Staph. warneri, a finding indicating differences in the pathogenic potential between CNS species and highlighting the importance of the correct identification of these micro-organisms. RT-PCR used for the detection of mRNA revealed the expression of SEG, SEH and/or SEI in 32 (59.3%) of the 90 Staph. aureus isolates, whereas expression of some of these genes was observed in 10 (34.5%) of the 90 CNS isolates.

CONCLUSIONS

Staphylococcus epidermidis was the most toxigenic CNS species. Among the other species, only Staph. warneri and Staph. lugdunensis presented a positive RT-PCR result. PCR was efficient in confirming the toxigenic capacity of Staph. aureus and CNS.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study permitted to confirm the toxigenic capacity of CNS to better characterize the pathogenic potential of this group of micro-organisms. In addition, it permitted the detection of SEG, SEH and SEI, enterotoxins that cannot be detected by commercially available immunological methods.

Urine cultures from indwelling bladder catheters in nursing home patients: a point prevalence study in a Swedish county

OBJECTIVES

To survey the bacterial flora and antibiotic resistance in urinary strains from patients with indwelling bladder catheters residing in nursing homes within a geographically defined region.

MATERIAL AND METHODS

Urine was sampled for culture from 163 catheter patients (126 men and 37 women) during a 2 week period in March 2010. Susceptibility testing of the isolated bacteria was compared with all urinary strains (n = 9994) from hospitals and primary healthcare in the same geographical area cultured during the first 6 months of 2010 (control group).

RESULTS

Bacteriuria was found in 159 of 163 urine samples (98%). Enterococcus faecalis and Escherichia coli were the most common species, one or both being detected in 72% of the urine samples, while Proteus species were found in10% and a single isolate of Providentia species was seen.Strains in the study patients were more resistant to antibiotics than in the control group. Particularly large differences were noted for ciprofloxacinin in E. coli (16.9% vs 7.9%) and for trimethoprim-sulfamethoxazole in E. faecalis (39.1% vs 24.8%). One extended spectrum β-lactamase (ESBL)-producing E. coli was cultured (1.3%), compared with 1.6% in the control group. No vancomycin-resistant enterococci (VRE) or methicillin-resistant Staphylococcus aureus (MRSA) were detected.

CONCLUSIONS

Proteus mirabilis and Providentia species were rarely isolated, in sharp contrast to previous studies from geriatric hospital wards where they have often been in the majority. The limited incidence of ESBL and the absence of VRE and MRSA is gratifying, but the high resistance to antibiotics needs to be assessed on a continuous basis.

Methicillin-resistant Staphylococcus aureus (MRSA) carriage in a dermatology unit

OBJECTIVE

The aim of this study was to characterize Staphylococcus aureus (MRSA) carriage in a dermatology unit.

METHODS

This was a prospective and descriptive study. Over the course of 26 weeks, surveillance cultures were collected weekly from the anterior nares and skin of all patients hospitalized in a 20-bed dermatology unit of a tertiary-care hospital. Samples from healthcare workers (HCWS) were cultured at the beginning and end of the study. Colonized patients were put under contact precautions, and basic infection control measures were enforced. Staphylococcus aureus colonization pressure was determined monthly. Colonized and non-colonized patients were compared, and isolates were evaluated for antimicrobial susceptibility, SCCmec type, virulence factors, and type.

RESULTS

Of the 142 patients evaluated, 64 (45%) were colonized by MRSA (39% hospital acquired; 25% community acquired; 36% indeterminate). Despite isolation precautions, hospital-acquired Staphylococcus aureus occurred in addition to the continuous entry of Staphylococcus aureus from the community. Colonization pressure increased from 13% to 59%, and pemphigus and other bullous diseases were associated with MRSA colonization. Eleven out of 71 HCWs (15%) were Staphylococcus aureus carriers, although only one worker carried a persistent clone. Of the hospital-acquired MRSA cases, 14/28 (50%) were SCCmec type IV (3 PFGE types), 13 were SCCmec type III (46%), and one had an indeterminate type. These types were also present among the community-acquired Staphylococcus aureus isolates. SSCmec type IV isolates were shown to be more susceptible than type III isolates. There were two cases of bloodstream infection, and the pvl and tst virulence genes were absent from all isolates.

CONCLUSIONS

Dermatology patients were colonized by community- and hospital-acquired Staphylococcus aureus. Half of the nosocomial Staphylococcus aureus isolates were SCCmec type IV. Despite the identification of colonized patients and the subsequent contact precautions and room placement, Staphylococcus aureus colonization continued to occur, and colonization pressure increased. Pemphigus and other bullous diseases were associated with Staphylococcus aureus.

CE-based detection of methicillin-resistant Staphylococcus aureus

Rapid and sensitive detection of methicillin-resistant Staphylococcus aureus is crucial for effective treatment and control of clinical infections caused by this bacterium. The goal of this study is to develop a CE-based detection method for multiplexed identification of a femA sequence specific for S. aureus and a unique mecA sequence encoding methicillin resistance. Blood samples spiked with known concentrations of bacteria were used for testing. Crude cell lysates were prepared by treating the spiked blood samples with DNazol Direct reagent and used as the template for isothermal amplification of mecA and femA genes. The amplified gene products then underwent a cycling probe reaction (CPR)-based assay to generate a short fluorophore-labeled oligonucleotide for detection in a CZE-LIF system. The assay enables a gene-specific fluorophore-labeled DNA-RNA-DNA chimeric probe to hybridize with complementary target in the presence of RNase H enzyme. The RNase H enzyme specifically cleaves probe RNA residues of the duplex, releasing a fluorophore fragment for detection and the target for recycling and hybridization with another chimeric probe. Intact and cleaved probe fragments were separated and detected using a CZE-LIF system. The limit of detection for isothermal amplification and CPR-CZE-LIF was approximately 10(4) colony-forming units of bacteria/mL of blood. This method accurately detects methicillin-resistant S. aureus within 3 h.

Phenotypic and genetic antibiogram of methicillin-resistant staphylococci isolated from bovine mastitis in Korea

Staphylococcus aureus belongs to the group of major contagious mastitis pathogens, whereas the coagulase-negative staphylococci (CNS) are also capable of causing opportunistic bovine mastitis. Many of these strains are resistant to penicillin or ampicillin because of the long-term use of beta-lactam antibiotics in agricultural and healthcare settings. Based on the simple and highly specific coagulase genotyping by PCR-RFLP used for discriminating among Staph. aureus strains, the relationship between phenotypic antibiogram and the polymorphism of coagulase gene was determined in this study. The staphylococci strains (835 Staph. aureus and 763 CNS) were isolated from 3,047 bovine mastitic milk samples from 153 dairy farms in 8 provinces from 1997 to 2004 in the Republic of Korea. Twenty-one (2.5%) Staph. aureus and 19 (2.4%) CNS strains were resistant to methicillin [oxacillin minimum inhibitory concentration (MIC) > or = 4 microg/mL]. The mecA gene was also found in 13 methicillin-resistant Staph. aureus (MRSA) and 12 methicillin-resistant CNS (MRCNS) isolates with a significantly higher detection rate of the mecA gene in MRSA with high MIC (> or = 16 microg/mL) compared with those with MIC < or = 8 microg/mL. Methicillin-resistant Staph. aureus and MRCNS were also more resistant to other antibiotics (ampicillin, cephalothin, kanamycin, and gentamicin) than methicillin-susceptible staphylococci. Among 10 different coa PCR-RFLP patterns (A to J) in 706 Staph. aureus strains, the main types were A (26.9%), B (17.0%), G (10.5%), and H (15.4%), with the frequent observation of the A and H types (6 and 10 isolates) in MRSA. This study indicates that major epidemic Staph. aureus clones may be spread between different dairy farms, and the profile of coa genotype can be applied for epidemiological investigations and control of bovine mastitis, particularly one caused by MRSA with specific prevalent coa types.

Cholangiocarcinoma complicating primary sclerosing cholangitis: a 24-year experience

AIM

To report the prevalence and outcome of cholangiocarcinoma arising in primary sclerosing cholangitis for a British tertiary referral centre.

METHODS

All patients diagnosed with primary sclerosing cholangitis and concurrent cholangiocarcinoma were identified from a prospectively maintained departmental database, and the mode of presentation, management and outcome were determined.

RESULTS

Of 370 patients with primary sclerosing cholangitis, 48 patients (13%) were diagnosed with a cholangiocarcinoma within a median time of 0.51 months (range: 0-73.12) from presentation to the unit. Mode of presentation included: inoperable tumours (n = 14); incidental findings in transplant hepatectomy specimens (n = 13); primary sclerosing cholangitis follow-up (n = 9); transplant work-up (n = 5); transplant waiting list (n = 5); suspected tumour confirmed at transplant (n = 1), and incidental finding at cholecystectomy (n = 1). The diagnosis was confirmed by: radiology-guided biopsy (n = 27); MRI (n = 3); CT (n = 2); laparoscopy or laparotomy (n = 2), and frozen section at transplant (n = 1). Management consisted of: transplantation (n = 14, including 1 abandoned); hepatic resection (n = 8), and palliation through stenting (n = 26). The overall median survival of the cohort was 4.9 months (range: 0.09-104.5). Median survival ranged from 2.6 months (range: 0.09-35.3) for palliation to 7.6 months (range: 0.6-99.6) for transplantation and 52.8 months (range: 3.7-104.5) for resection. There was no difference in survival between the transplant and resection groups (p = 0.14).

CONCLUSIONS

Cholangiocarcinoma is a common finding in primary sclerosing cholangitis and regular screening of this cohort of patients at referring centres is advocated to detect early tumours, as surgical treatment at an early stage offers significantly better outcomes for this cohort of patients.

Comparison of antibiogram, staphylococcal enterotoxin productivity, and coagulase genotypes among Staphylococcus aureus isolated from animal and vegetable sources in Korea

Staphylococcal food poisoning is caused by enterotoxin-producing Staphylococcus aureus. We investigated the prevalence of such organisms in samples of bovine mastitic milk (n = 714), raw meat (n = 139), and vegetables (n = 616). We determined the degrees of relatedness of isolates as indicated by antibiogram, staphylococcal enterotoxin (SE) productivity, and coagulase gene restriction fragment length polymorphism analysis. We examined 297 S. aureus isolates and found SE production in 57 (31.8%), 4 (7.8%), and 49 (73.1%) isolates from raw milk, raw meat, and vegetables, respectively. A high proportion of the isolates obtained from milk produced more than two types of toxins (mainly SEA, SEB, and/or SEC), whereas isolates from raw meat and vegetables primarily produced SEA alone. Most isolates were sensitive to cephalothin (97.6%), gentamicin (80.8%), erythromycin (79.5%), and tetracycline (72.7%), but were resistant to penicillin (90.2%) and ampicillin (88.9%). The proportion of antibiotic-resistant isolates differed according the source of the bacteria; the milk and vegetable isolates were more resistant to penicillin and ampicillin than were the meat isolates (P < 0.05), whereas tetracycline resistance was limited to the milk and vegetables isolates. The coagulase genotypes (I to XII) varied with the source of the organism, and only a few genotypes prevailed in each source: II (42.4%) and IV (24%) types in isolates from milk, IX (35.3%) and XI (45%) from raw meat, and III (40.3%) and XII (32.8%) from vegetables. These findings suggest that remarkable differences exist in antibiogram, SE productivity, and coagulase genotypes, resulting in limited clonal transmission of S. aureus into various food sources. As enterotoxin production only occurs when S. aureus grows to high numbers, staphylococcal food poisoning can be prevented by proper refrigeration.

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.

Genome content determination in methicillin-resistant Staphylococcus aureus

Staphylococcus aureus is a major pathogen responsible for both nosocomial and community-acquired infections. While the first S. aureus isolates displaying resistance to methicillin were reported in the early 1960s, endemic strains of methicillin-resistant S. aureus (MRSA) carrying multiple resistance determinants only became a worldwide nosocomial problem in the early 1980s, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteremia. Recent efforts in the field of high-throughput sequencing resulted in the release of several MRSA genome sequences enabling the development of massively parallel tools to study clinical isolates of MRSA at the organism scale. Microarrays covering whole genomes and high-throughput sequencing devices are the two main techniques currently utilizable for whole-genome characterization. These tools not only provide information for the development of genotyping assays but also allow evaluation of potential virulence of the strains, by enumerating genetic-encoded resistance markers and toxin content. This appears particularly attractive for understanding the epidemiology of MRSA and the relationship between genome content on one side and virulence potential or epidemicity on the other side. In addition, sequence information is mandatory for the development of molecular tests allowing the rapid identification, genotyping and characterization of clinical isolates.

Detection of methicillin- and aminoglycoside-resistant genes and simultaneous identification of S. aureus using triplex real-time PCR Taqman assay

In this study we describe a triplex real-time PCR assay that enables the identification of S. aureus and detection of two important antibiotic resistant genes simultaneously using real-time PCR technology in a single assay. In this triplex real-time PCR assay, the mecA (methicillin resistant), femA (species specific S. aureus) and aacA-aphD (aminoglycoside resistant) genes were detected in a single test using dual-labeled Taqman probes. The assay gives simultaneous information for the identification of S. aureus and detection of methicillin and aminoglycoside resistance in staphylococcal isolates. 152 clinical isolates were subjected to this triplex real-time PCR assay. The results of the triplex real-time PCR assay correlated with the results of the phenotypic antibiotic susceptibility testing. The results obtained from triplex real-time PCR assay shows that the primer and probe sets were specific for the identification of S. aureus and were able to detect methicillin- and aminoglycoside-resistant genes. The entire assay can be performed within 3 h which is a very rapid method that can give simultaneous information for the identification of S. aureus and antibiotic resistance pattern of a staphylococcal isolate. The application of this rapid method in microbiology laboratories would be a valuable tool for the rapid identification of the S. aureus isolates and determination of their antibiotic resistance pattern with regards to methicillin and aminoglycosides.

Simultaneous species identification and detection of methicillin resistance in staphylococci using triplex real-time PCR assay

For rapid identification of methicillin-resistant Staphylococcus aureus, molecular methods are generally targeting mecA and species-specific genes. Sa442 DNA fragment is a popular species-specific target. However, recently, there have been few reports on S. aureus isolates that are negative for Sa442 fragment; therefore, use of single gene or DNA-fragment-specific polymerase chain reaction (PCR) for identification of microbial isolate may result in misidentification. This study includes CoA gene in parallel with Sa442 marker for identification of S. aureus. This further improves the specificity of the assay by checking for 2 determinants simultaneously for the identification of S. aureus and can prevent misidentification of S. aureus isolates lacking Sa442 DNA fragment. In this study, the newly developed triplex real-time PCR assay was compared with a quadruplex conventional gel-based PCR assay using the same primer sets in both assays. The dual-labeled TaqMan probes (ProOligo, France) for these primers were specifically designed and used in a real-time PCR assay. The clinical isolates (n = 152) were subjected to both PCR assays. The results obtained from both assays proved that the primer and probe sets were 100% sensitive and 100% specific for identification of S. aureus and detection of methicillin resistance. This triplex real-time PCR assay represents a rapid and powerful method for S. aureus identification and detection of methicillin resistance.

Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains

Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.

Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA)

These evidence-based guidelines have been produced after a literature review of the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). We have considered the detection of MRSA in screening samples and the detection of reduced susceptibility to glycopeptides in S. aureus. Recommendations are given for the identification of S. aureus and for suitable methods of susceptibility testing and screening for MRSA and for S. aureus with reduced susceptibility to glycopeptides. These guidelines indicate what tests should be used but not when the tests are applicable, as aspects of this are dealt with in guidelines on control of MRSA. There are currently several developments in screening media and molecular methods. It is likely that some of our recommendations will require modification as the new methods become available.

Rapid detection of antibacterial resistance in emerging Gram-positive cocci

Effective infection control efforts obviously depend on the performance of the laboratory to detect emerging resistant pathogens accurately and confirm resistance patterns by additional methods to conventional or automated systems. Conventional methods still remain the predominant approaches for detection and identification of bacteria and resistance patterns. However, the estimated time for conventional tests to detect resistance is at least 24-48 h for methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and other epidemiologically important pathogens. Most of the tests used for rapid detection require bacterial growth in culture. There is an important clinical need for rapid detection of bacteria directly from patient samples. Rapid methods based on immunological or molecular technologies have contributed significantly. Molecular assays for several resistance markers are reliable, such as for mecA in staphylococci and vanA in enterococci. However, for other resistance markers, there is a lack of field testing. Cost-effectiveness of rapid detection of antibacterial resistance is another concern. Molecular assays would be useful for tertiary hospitals considering the investment costs and requirement of expert laboratory staff. For smaller centres, rapid tests based on immunological techniques may be a better choice.

Molecular genetic methods in diagnosis and direct characterization of acute bacterial central nervous system infections

Acute bacterial infection of the central nervous system requires rapid and adequate management. Etiological diagnosis is hence crucial. Moreover, the epidemic threat of certain bacteria necessitates a reliable characterization of the involved bacterial strains to follow the spread of epidemic strains. Conventional identification and characterization of etiological agents are basically based on culture and identification of bacterial markers most frequently by serological assays. Molecular identification and characterization of bacteria have been employed. They provide more reliable analysis of bacterial isolates. Molecular methods for non-culture diagnosis of bacterial infections have recently been developed. In many cases, the molecular assays have decreased the identification time of positive cultures and rescued detection of pathogens in culture-negative clinical samples.

A PCR method for the identification of methicillin-resistant Staphylococcus aureus (MRSA) from screening swabs

AIM

The aim of this study was to assess the discriminatory power and potential turn around time (TAT) of a PCR-based method for the detection of methicillin-resistant Staphylococcus aureus (MRSA) from screening swabs.

METHODS

Screening swabs were examined using the current laboratory protocol of direct culture on mannitol salt agar supplemented with oxacillin (MSAO-direct). The PCR method involved pre-incubation in broth for 4 hours followed by a multiplex PCR with primers directed to mecA and nuc genes of MRSA. The reference standard was determined by pre-incubation in broth for 4 hours followed by culture on MSAO (MSAO-broth).

RESULTS

A total of 256 swabs was analysed. The rates of detection of MRSA using MSAO-direct, MSAO-broth and PCR were 10.2, 13.3 and 10.2%, respectively. For PCR, the sensitivity, specificity, positive predictive value and negative predictive values were 66.7% (95%CI 51.9-83.3%), 98.6% (95%CI 97.1-100%), 84.6% (95%CI 76.2-100%) and 95.2% (95%CI 92.4-98.0%), respectively, and these results were almost identical to those obtained from MSAO-direct. The agreement between MSAO-direct and PCR was 61.5% (95%CI 42.8-80.2%) for positive results, 95.6% (95%CI 93.0-98.2%) for negative results and overall was 92.2% (95%CI 88.9-95.5%).

CONCLUSIONS

(1) The discriminatory power of PCR and MSAO-direct is similar but the level of agreement, especially for true positive results, is low. (2) The potential TAT for the PCR method provides a marked advantage over conventional methods. (3) Further modifications to the PCR method such as increased broth incubation time, use of selective broth and adaptation to real-time PCR may lead to improvement in sensitivity and TAT.

New real-time PCR assay for rapid detection of methicillin-resistant Staphylococcus aureus directly from specimens containing a mixture of staphylococci

Molecular methods for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) are generally based on the detection of an S. aureus-specific gene target and the mecA gene. However, such methods cannot be applied for the direct detection of MRSA from nonsterile specimens such as nasal samples without the previous isolation, capture, or enrichment of MRSA because these samples often contain both coagulase-negative staphylococci (CoNS) and S. aureus, either of which can carry mecA. In this study, we describe a real-time multiplex PCR assay which allows the detection of MRSA directly from clinical specimens containing a mixture of staphylococci in <1 h. Five primers specific to the different staphylococcal cassette chromosome mec (SCCmec) right extremity sequences, including three new sequences, were used in combination with a primer and three molecular beacon probes specific to the S. aureus chromosomal orfX gene sequences located to the right of the SCCmec integration site. Of the 1,657 MRSA isolates tested, 1,636 (98.7%) were detected with the PCR assay, whereas 26 of 569 (4.6%) methicillin-susceptible S. aureus (MSSA) strains were misidentified as MRSA. None of the 62 nonstaphylococcal bacterial species or the 212 methicillin-resistant or 74 methicillin-susceptible CoNS strains (MRCoNS and MSCoNS, respectively) were detected by the assay. The amplification of MRSA was not inhibited in the presence of high copy numbers of MSSA, MRCoNS, or MSCoNS. The analytical sensitivity of the PCR assay, as evaluated with MRSA-negative nasal specimens containing a mixture of MSSA, MRCoNS, and MSCoNS spiked with MRSA, was approximately 25 CFU per nasal sample. This real-time PCR assay represents a rapid and powerful method which can be used for the detection of MRSA directly from specimens containing a mixture of staphylococci.

Multiplex PCR assay for simultaneous detection of nine clinically relevant antibiotic resistance genes in Staphylococcus aureus

In this study we describe a multiplex PCR assay for the detection of nine clinically relevant antibiotic resistance genes of Staphylococcus aureus. Conditions were optimized to amplify fragments of mecA (encoding methicillin resistance), aacA-aphD (aminoglycoside resistance), tetK, tetM (tetracycline resistance), erm(A), erm(C) (macrolide-lincosamide-streptogramin B resistance), vat(A), vat(B), and vat(C) (streptogramin A resistance) simultaneously in one PCR amplification. An additional primer pair for the amplification of a fragment of the staphylococcal 16S rDNA was included as a positive control. The multiplex PCR assay was evaluated on 30 different S. aureus isolates, and the PCR results correlated with the phenotypic antibiotic resistance data obtained by the broth microdilution assay. The multiplex PCR assay offers a rapid, simple, and accurate identification of antibiotic resistance profiles and could be used in clinical diagnosis as well as for the surveillance of the spread of antibiotic resistance determinants in epidemiological studies.

Evaluation of an isothermal signal amplification method for rapid detection of methicillin-resistant Staphylococcus aureus from patient-screening swabs

A new molecular assay (CytAMP) utilizing isothermal signal-mediated amplification of RNA was evaluated for rapid detection of methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA). The assay targeted the coa (coagulase) and mecA genes, thereby simultaneously identifying S. aureus and methicillin (oxacillin) resistance. Results were obtained in approximately 3.5 h as a color signal in 96-well microtiter plates. The detection limit was between 2 x 10(5) and 10(6) CFU/assay, equivalent to 4 x 10(6) to 2 x 10(7) CFU/ml in an overnight broth. This level of growth was obtained with an initial inoculum of 10 to 50 CFU. The CytAMP assay and a mecA-femB PCR assay both detected 113 MRSA strains among 396 clinical isolates of bacteria (CytAMP sensitivity and specificity were both 100% relative to those of PCR). Conventional culture detected 109 MRSA strains, but with 19 false-positive and 23 false-negative results relative to both molecular methods. Discrepancies were also observed for 100 enrichment broths containing MRSA screening swabs, with 11 broths culture negative but PCR positive. CytAMP and PCR were more in agreement, but six broths were CytAMP negative and PCR positive. Five of these contained 10(2) to 10(5) CFU/assay (below the CytAMP detection limit of 2 x 10(5) CFU/assay), and the sixth contained 10(6) CFU/assay. Overall, culture and CytAMP had similar sensitivities and specificities relative to those of PCR, but the CytAMP assay enabled swabs to be analyzed as a batch following overnight incubation in enrichment broth, with results reported before 12 noon the next day.

Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay

A rapid procedure was developed for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) directly from sterile sites or mixed flora samples (e.g., nose or inguinal swabs). After a rapid conditioning of samples, the method consists of two main steps: (i) immunomagnetic enrichment in S. aureus and (ii) amplification-detection profile on DNA extracts using multiplex quantitative PCR (5'-exonuclease qPCR, TaqMan). The triplex qPCR assay measures simultaneously the following targets: (i) mecA gene, conferring methicillin resistance, common to both S. aureus and Staphylococcus epidermidis; (ii) femA gene from S. aureus; and (iii) femA gene from S. epidermidis. This quantitative approach allows discrimination of the origin of the measured mecA signal. qPCR data were calibrated using two reference strains (MRSA and methicillin-resistant S. epidermidis) processed in parallel to clinical samples. This 96-well format assay allowed analysis of 30 swab samples per run and detection of the presence of MRSA with exquisite sensitivity compared to optimal culture-based techniques. The complete protocol may provide results in less than 6 h (while standard procedure needs 2 to 3 days), thus allowing prompt and cost-effective implementation of contact precautions.

Validation of rapid screening tests for the identification of methicillin resistance in staphylococci

The Velogene Rapid MRSA Identification Assay (Alexon-Trend Inc., Ramsey, MN), a commercially available 90-min genotypic test using a chimeric probe for the cycling-mediated recognition of the mecA gene in staphylococci, was compared with the MRSA-Screen latex agglutination test, a 15-min phenotypic test (Denka Seiken Co., Tokyo, Japan) for the identification of the mecA gene product PBP 2a. The results of both techniques were compared with mecA gene PCR. A total of 210 stock-culture strains were tested, consisting of 108 methicillin-susceptible Staphylococcus aureus (MSSA) strains and 92 methicillin-resistant S. aureus (MRSA) strains. The performance of the assays was good, displaying sensitivities and specificities for Velogene and MRSA Screen of 96.7% and 100% and 96.7% and 100%, respectively. Both Velogene and MRSA Screen could not correctly identify three of the MRSA strains each. Repeat testing with a larger inoculum or exposure of the three distinct strains to methicillin, respectively, resolved these problems. All MSSA strains as well as the other genera were correctly addressed by both techniques. The 10 methicillin-resistant Staphylococcus epidermidis strains were detected by both techniques. Both the Velogene and the MRSA Screen assays accurately identified mecA-positive staphylococcal strains and can be successfully used for routine application in clinical microbiology laboratories.

Detection of methicillin-resistant Staphylococcus aureus and simultaneous confirmation by automated nucleic acid extraction and real-time PCR

A molecular assay for the simultaneous detection of a Staphylococcus aureus-specific gene and the mecA gene, responsible for the resistance to methicillin in staphylococci, was evaluated. The assay included an automated DNA extraction protocol conducted with a MagNA Pure instrument and real-time PCR conducted with a LightCycler instrument. The performance and robustness of the assay were evaluated for a suspension of methicillin-resistant S. aureus (MRSA) strain with a turbidity equivalent to a McFarland standard of 0.5, which was found to be the ideal working concentration. The specificity of the new molecular assay was tested with a panel of 30 gram-negative and gram-positive bacterial strains other than MRSA. No cross-reactivity was observed. In a clinical study, 109 isolates of MRSA were investigated. All clinical MRSA isolates gave positive results for the S. aureus-specific genomic target, and all but one were positive for the mecA gene. In conclusion, the new molecular assay was found to be quick, robust, and laborsaving, and it proved to be suitable for a routine molecular diagnostic laboratory.

Multiplex PCR strategy for rapid identification of structural types and variants of the mec element in methicillin-resistant Staphylococcus aureus

Full characterization of methicillin-resistant Staphylococcus aureus (MRSA) requires definition of not only the bacterial genetic background but also the structure of the complex and heterologous mec element these bacteria carry, which is associated with drug resistance determinant mecA. We report the development, validation, and application of a multiplex PCR strategy that allows quick presumptive characterization of the mec element types based on the structural features that were shown to be typical of mec elements carried by several MRSA clones. The strategy was validated by using a representative collection of pandemic MRSA clones in which the full structure of the associated mec elements was previously determined by hybridization and PCR screenings and also by DNA sequencing. The method was tested together with multilocus sequence typing and other typing methods for the characterization of 18 isolates representative of the MRSA clones recovered during a hospital outbreak in Barcelona, Spain. The multiplex PCR was shown to be rapid, robust, and capable in a single assay of identifying five structural types of the mec element among these strains, three major and two minor variants, each one of which has been already been seen among MRSA characterized earlier. This technique should be a useful addition to the armamentarium of molecular typing tools for the characterization of MRSA clonal types and for the rapid tentative identification of structural variants of the mec element.

Evaluation of a triplex PCR assay to discriminate Staphylococcus aureus from coagulase-negative Staphylococci and determine methicillin resistance from blood cultures

A triplex PCR targeting the 16S rRNA, mecA, and nuc genes was developed for identification of staphylococci and detection of methicillin resistance. After validation of the assay with a collection of strains of staphylococci and enterococci (n = 169), the assay was evaluated with cultures of blood with gram-positive cocci from 40 patients. Accurate results were obtained for 59 (98%) of 61 cultures within 6 h of growth detection.

Molecular detection of antimicrobial resistance

The determination of antimicrobial susceptibility of a clinical isolate, especially with increasing resistance, is often crucial for the optimal antimicrobial therapy of infected patients. Nucleic acid-based assays for the detection of resistance may offer advantages over phenotypic assays. Examples are the detection of the methicillin resistance-encoding mecA gene in staphylococci, rifampin resistance in Mycobacterium tuberculosis, and the spread of resistance determinants across the globe. However, molecular assays for the detection of resistance have a number of limitations. New resistance mechanisms may be missed, and in some cases the number of different genes makes generating an assay too costly to compete with phenotypic assays. In addition, proper quality control for molecular assays poses a problem for many laboratories, and this results in questionable results at best. The development of new molecular techniques, e.g., PCR using molecular beacons and DNA chips, expands the possibilities for monitoring resistance. Although molecular techniques for the detection of antimicrobial resistance clearly are winning a place in routine diagnostics, phenotypic assays are still the method of choice for most resistance determinations. In this review, we describe the applications of molecular techniques for the detection of antimicrobial resistance and the current state of the art.