Comparison of DNA sequencing of the protein A gene polymorphic region with other molecular typing techniques for typing two epidemiologically diverse collections of methicillin-resistant Staphylococcus aureus

Antibiotics Resistance and Virulence of Staphylococcus aureus Isolates Isolated from Raw Milk from Handmade Dairy Retail Stores in Hefei City, China

Handmade dairy products, which retain the nutrients in milk to the greatest extent, have become popular in China recently. However, no investigation regarding the characteristics of Staphylococcus aureus (S. aureus) in raw milk of handmade dairy retail stores has been reported. Here, we investigated the antimicrobial susceptibility, virulence, biofilm formation, and genetic diversity of S. aureus in raw milk from handmade dairy retail stores in Hefei, China. After 10 months of long-term monitoring, 50 S. aureus strains were isolated from 69 different raw milk samples, of which 6 were positive for methicillin-resistant S. aureus (MRSA). The resistance rates of these isolates to ampicillin, erythromycin, kanamycin, tetracycline, sulfamethoxazole-trimethoprim, gentamicin, ofloxacin, oxacillin, chloramphenicol, and doxycycline were 56, 54, 40, 24, 22, 22, 18, 14, 8 and 6%, respectively. All 50 isolates were susceptible to vancomycin and 29 strains (58%) showed multidrug resistance phenotype. For enterotoxins genes, selp (14%) was detected the most frequently, followed by sea (6%), sec (4%), sei (4%), ser (4%), selj (4%), and seh (2%). By microplate assay, 32 and 68% of the strains showed moderate and strong biofilm formation ability, respectively. Fifty isolates were discriminated into nine spa types, and the most common spa typing was t034 (42%). The results of this study indicate that S. aureus from raw milk may constitute a risk concerning food poisoning, and more attention must be given to awareness and hygienic measures in the food industry.

Characterization of SCCmec, Spa Types and Multidrug Resistant of Methicillin-Resistant Staphylococcus aureus Isolates in Ahvaz, Iran

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most pathogens associated with health care. Molecular typing methods are vital for outbreak investigations of MRSA. The aim of this study was characterization of SCCmec, spa types and multidrug resistant of methicillin-resistant Staphylococcus aureus isolates in Ahvaz, Iran.

Methods

A total of 50 MRSA isolates were determined by using the phenotypic method and mecA gene. Antibiotic resistance profile and SCCmec types were screened using disc diffusion method and PCR, respectively. For spa typing of MRSA isolates, two molecular typing methods including the PCR-sequencing and high-resolution melting (HRM) analysis were used.

Results

In the present study, the highest sensitivity of MRSA was to vancomycin and linezolid and the lowest to clindamycin. In the MRSA isolates, 22% were XDR and 78% were MDR. SCCmec type III was found commonly among MRSA. Based on PCR-sequencing and HRM results, 10 different spa types were identified. The spa types t037 and t030 were the most common in this study.

Conclusion

This study emphasizes the spa variation among MRSA isolates, which may be considered as an important criterion when treating staphylococcal infections. Accurate and early detection of MDR, XDR, or even PDR MRSA isolates strains must be commenced by all clinical microbiology laboratories to reduce the menace of antimicrobial resistance.

Methicillin-Resistant Staphylococcus aureus ST80 Clone: A Systematic Review

This review assessed the molecular characterization of the methicillin-resistant Staphylococcus aureus (MRSA)-ST80 clone with an emphasis on its proportion of total MRSA strains isolated, PVL production, spa-typing, antibiotic resistance, and virulence. A systematic review of the literature was conducted on MRSA-ST80 clone published between 1 January 2000 and 31 August 2019. Citations were chosen for a review of the full text if we found evidence that MRSA-ST80 clone was reported in the study. For each isolate, the country of isolation, the sampling period, the source of isolation (the type of infection, nasal swabs, or extra-human), the total number of MRSA strains isolated, number of MRSA-ST80 strains, antibiotic resistance patterns, PVL production, virulence genes, and spa type were recorded. The data from 103 articles were abstracted into an Excel database. Analysis of the data showed that the overall proportion of MRSA-ST80 has been decreasing in many countries in recent years. The majority of MRSA-ST80 were PVL positive with spa-type t044. Only six reports of MRSA-ST80 in extra-human niches were found. This review summarizes the rise of MRSA-ST80 and the evidence that suggests that it could be in decline in many countries.

Molecular Characterization of Methicillin Resistant Staphylococcus aureus in West Bank-Palestine

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a public health threat and a major cause of hospital-acquired and community-acquired infections. This study aimed to investigate the genetic diversity of MRSA isolates from 2015 to 2017 and to characterize the major MRSA clones and anti-biogram trends in Palestine.

Methodology: Isolates were obtained from 112 patients admitted to different hospitals of West Bank and East Jerusalem, originating from different clinical sources. Antibiotic susceptibility patterns, staphylococcal chromosomal cassette mec (SCCmec) typing, and Staphylococcus aureus protein A (spa) typing were determined. Also, a panel of toxin genes and virulence factors was studied, including: Panton-Valentine Leukocidin (PVL), ACME-arcA, Toxic Shock Syndrome Toxin-1 (TSST-1), and Exfoliative Toxin A (ETA).

Results: Of the 112 confirmed MRSA isolates, 100% were resistant to all β-lactam antibiotics. Resistance rates to other non- β-lactam classes were as the following: 18.8% were resistant to trimethoprim-sulfamethoxazole, 23.2% were resistant to gentamicin, 34.8% to clindamycin, 39.3% to ciprofloxacin, and 63.4% to erythromycin. All MRSA isolates were susceptible to vancomycin (100%). Of all isolates, 32 isolates (28.6%) were multidrug- resistant (MDR). The majority of the isolates were identified as SCCmec type IV (86.6%). The molecular typing identified 29 spa types representing 12 MLST-clonal complexes (CC). The most prevalent spa types were: spa type t386 (CC1)/(12.5%), spa type t044 (CC80)/(10.7%), spa type t008 (CC8)/(10.7%), and spa type t223 (CC22)/(9.8%). PVL toxin gene was detected in (29.5%) of all isolates, while ACME-arcA gene was present in 18.8% of all isolates and 23.2% had the TSST-1 gene. The two most common spa types among the TSST-1positive isolates were the spa type t223 (CC22)/(Gaza clone) and the spa type t021 (CC30)/(South West Pacific clone). All isolates with the spa type t991 were ETA positive (5.4%). USA-300 clone (spa type t008, positive for PVL toxin gene and ACME-arcA genes) was found in nine isolates (8.0%).

Conclusions: Our results provide insights into the epidemiology of MRSA strains in Palestine. We report a high diversity of MRSA strains among hospitals in Palestine, with frequent SCCmec type IV carriage. The four prominent clones detected were: t386-IV/ CC1, the European clone (t044/CC80), Gaza clone (t223/CC22), and the USA-300 clone (t008/CC8).

Characterization of Staphylococcus aureus faecal isolates associated with food-borne disease in Korea

AIMS

To characterize Staphylococcus aureus faecal isolates from people suspected to be infected with food poisoning by using antimicrobial susceptibility testing and molecular techniques.

METHODS AND RESULTS

A total of 340 Staph. aureus isolates from 6226 people suspected to be infected with food poisoning were identified and characterized by biochemical methods, antimicrobial susceptibility testing and PCR. Samples were obtained from January 2006 to December 2008 from the National Notifiable Diseases Surveillance System at the Research Institute of Public Health and Environment in Seoul Metropolitan, Korea. All strains carried at least one of the eight staphylococcal enterotoxin (se) genes tested and a total of 27 se profiles were produced; the most frequent se profile was seg-sei and the next was sea. Among the total isolates, 36 methicillin-resistant Staphylococcus aureus (MRSAs) isolates were further analysed by multilocus sequence typing (MLST), Staphylococcal cassette chromosome mec (SCCmec) typing, pulsed-field gel electrophoresis (PFGE) and PCR detection for pvl. ST72-SCCmec type IV was the most predominant clone (27 isolates, 75%) followed by ST1-SCCmec type IV (five isolates, 13·8%), ST20-SCCmec type IV (one isolate, 2·8%), ST493-SCCmec type IV (one isolate, 2·8%), ST903-SCCmec type IV (one isolate, 2·8%) and ST5-SCCmec type II (one isolate, 2·8%). By PFGE typing, MRSAs isolated during the same period were grouped together although they were isolated from different regions. None of MRSAs had PVL gene and nine MRSAs were multidrug resistant.

CONCLUSIONS

Analysis of MRSAs by MLST, SCCmec typing, PFGE and pvl detection showed that the majority of strain associated with food-borne diseases belonged to a Korean community-acquired (CA) MRSA clone with ST72-SCCmec type IV-PVL negative-SEG/SEI and its variations while one strain was hospital-acquired (HA) MRSA.

SIGNIFICANCE AND IMPACT OF THE STUDY

CA-MRSA clone which possessed ST72-SCCmec type IV-PVL negative-SEG/SEI was spread most commonly among MRSAs that were associated with food-borne diseases. This is the first report of ST903 strain in Korea.

Epidemiological and molecular characteristics of meticillin-resistant Staphylococcus aureus in Turkey: A multicentre study

The aim of this study was to investigate the epidemiological and molecular features of clinical meticillin-resistant Staphylococcus aureus (MRSA) isolates in Turkey. MRSA isolates were collected from six regions of Turkey. The mecA and nuc genes were detected by PCR. Antimicrobial susceptibilities were determined by the disk diffusion method. Staphylococcal cassette chromosome mec (SCCmec) and staphylococcal protein A (spa) typing were performed by the sequencing method for 270 randomly selected MRSA isolates. The US Centers for Disease Control and Prevention (CDC) definition was used for epidemiological diagnosis of community-associated MRSA (CA-MRSA). Resistance rates of MRSA to ciprofloxacin, gentamicin, clindamycin, erythromycin, rifampicin, trimethoprim/sulfamethoxazole and tetracycline were 93.4%, 81.2%, 38.5%, 57.8%, 93.9%, 1.1% and 93.1%, respectively. The most frequent SCCmec type was SCCmec III (91.1%). SCCmec type IV was found in 5.2% of the isolates. The most frequent spa type was t030 (81.1%). Five isolates were CA-MRSA if only the epidemiological definition was used (5/725; 0.7%). Two isolates were defined as CA-MRSA both by epidemiological features and SCCmec typing (2/270; 0.7%). Of 14 SCCmec type IV isolates, 12 were not defined as CA-MRSA by epidemiological features. In conclusion, this is the most comprehensive multicentre study in Turkey investigating MRSA using both epidemiological and genotypic features. The CA-MRSA rate is low in Turkey. Combined use of epidemiological and genotypic methods is the most accurate approach for the diagnosis of CA-MRSA.

Contribution of peptidoglycan amidation to beta-lactam and lysozyme resistance in different genetic lineages of Staphylococcus aureus

The enzymes responsible for peptidoglycan amidation in Staphylococcus aureus, MurT and GatD, were recently identified and shown to be required for optimal expression of resistance to beta-lactams, bacterial growth, and resistance to lysozyme. In this study, we analyzed the impact of peptidoglycan amidation in representative strains of the most widespread clones of methicillin resistant S. aureus (MRSA). The inhibition of the expression of murT-gatD operon resulted in different phenotypes of resistance to beta-lactams and lysozyme according to the different genetic backgrounds. Further, clonal lineages CC1 and CC398 (community-acquired MRSA [CA-MRSA]) showed a stronger dependency on MurT-GatD for resistance to beta-lactams, when compared to the impact of the impairment of the cell wall step catalyzed by MurF. In the remaining backgrounds similar phenotypes of beta-lactam resistance were observed upon the impairment of both cell-wall-related genes. Therefore, for CA-related backgrounds, the predominant beta-lactam resistance mechanism seems to involve genes associated with secondary modifications of peptidoglycan. On the other hand, the lack of glutamic acid amidation had a more substantial impact on lysozyme resistance for cells of CA-MRSA backgrounds, than for hospital-acquired MRSA (HA-MRSA). However, no significant differences were found in the resistance level of the respective peptidoglycan structure, suggesting that the lysozyme resistance mechanism involves other factors. Taken together, these results suggested that the different genetic lineages of MRSA were able to develop different molecular strategies to overcome the selective pressures experienced during evolution.

The use of high-resolution melting analysis for rapid spa typing on methicillin-resistant Staphylococcus aureus clinical isolates

Methicillin-resistant Staphylococcus aureus (MRSA) has been endemic in Hong Kong for three decades. This study evaluated the practical use of high-resolution melting (HRM) real-time PCR analysis on MRSA staphylococcal Protein A (spa) typing on local MRSA isolates. Among 55 clinical MRSA isolates collected in 2011, 12 different spa types were observed by the conventional PCR-sequencing method including the locally predominant spa type t1081 and two locally predominant community acquired MRSA spa types t019 and t437. By using the HRM method, it could differentiate all 12 spa genotypes by distinct melting curves and HRM difference plot analysis. These two methods demonstrated 100% concordance whereas the HRM method required only 3h of turnaround time and one-fifth of reagent cost compared to the conventional method. Our study confirmed that the cost effective and rapid HRM typing approach is practically useful for MRSA community transmission monitoring and nosocomial outbreak control in Hong Kong.

Prevalence, risk factors and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) colonization in residents of long-term care facilities in Luxembourg, 2010

A prevalence survey of methicillin-resistant Staphylococcus aureus (MRSA) was performed in 2010 in 19 long-term care facilities in Luxembourg. Of the 954 participating residents, 69 (7·2%) were colonized by MRSA. Previous history of MRSA [odds ratio (OR) 7·20, 95% confidence interval (CI) 3·19-16·27], quinolone therapy in the previous year (OR 2·27, 95% CI 1·17-4·41) and ≥24 h care administered per week (OR 4·29, 95% CI 1·18-15·56) were independent risk factors for MRSA colonization. More than 75% of strains were of clonal complex (CC)5, mainly spa-type t003 or sequence type (ST)225 and ST710, which is a rapidly emerging lineage prevalent in central Europe. Five residents were colonized by livestock-associated genotypes belonging to CC398. Previously dominant CC8 strains have recently been replaced by more resistant CC5 strains in Luxembourg.

Molecular epidemiology and nasal carriage of Staphylococcus aureus and methicillin-resistant S. aureus among young children attending day care centers and kindergartens in Hong Kong

OBJECTIVES

To investigate the prevalence and molecular epidemiology of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) nasal carriage in children.

METHODS

We collected nasal and nasopharyngeal swabs from 2211 children aged 2-5 years attending 79 day care centers (DCCs) and 113 kindergartens (KGs) in all 18 geographical districts in Hong Kong.

RESULTS

The overall carriage rates of S. aureus and MRSA were 27.6% (95% confidence interval [CI], 24.8-28.5%) and 1.3% (95% CI, 0.8-1.8%), respectively. Molecular typing (staphylococcal cassette chromosome mec [SCCmec], sequence type [ST], clonal cluster [CC]) showed that all the 28 MRSA isolates had SCCmec IV (n = 13) or V (n = 15) including 12 isolates with community-associated-MRSA genotypes (ST59-IV/V, ST30-IV and ST88-V), 10 isolates with healthcare-associated-MRSA genotypes (ST45-IV/V, CC5-IV and ST630-V) and six isolates with novel genotypes (ST10-V and CC1-IV). Spa typing indicated that there was some within and between DCCs/KGs transmission of certain MRSA and methicillin-sensitive S. aureus strains but this was not extensive.

CONCLUSION

Our findings indicate the potential for DCCs to be a reservoir for emerging MRSA genotypes and highlight the need to enhance education and infection control measures to reduce their cross-transmission in this population.

Shedding of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus from adult and pediatric bathers in marine waters

Background

Staphylococcus aureus including methicillin resistant S. aureus, MRSA, are human colonizing bacteria that commonly cause opportunistic infections primarily involving the skin in otherwise healthy individuals. These infections have been linked to close contact and sharing of common facilities such as locker rooms, schools and prisons Waterborne exposure and transmission routes have not been traditionally associated with S. aureus infections. Coastal marine waters and beaches used for recreation are potential locations for the combination of high numbers of people with close contact and therefore could contribute to the exposure to and infection by these organisms. The primary aim of this study was to evaluate the amount and characteristics of the shedding of methicillin sensitive S. aureus, MSSA and MRSA by human bathers in marine waters.

Results

Nasal cultures were collected from bathers, and water samples were collected from two sets of pools designed to isolate and quantify MSSA and MRSA shed by adults and toddlers during exposure to marine water. A combination of selective growth media and biochemical and polymerase chain reaction analysis was used to identify and perform limited characterization of the S. aureus isolated from the water and the participants. Twelve of 15 MRSA isolates collected from the water had identical genetic characteristics as the organisms isolated from the participants exposed to that water while the remaining 3 MRSA were without matching nasal isolates from participants. The amount of S. aureus shed per person corresponded to 10⁵ to 10⁶ CFU per person per 15-minute bathing period, with 15 to 20% of this quantity testing positive for MRSA.

Conclusions

This is the first report of a comparison of human colonizing organisms with bacteria from human exposed marine water attempting to confirm that participants shed their own colonizing MSSA and MRSA into their bathing milieu. These findings clearly demonstrate that adults and toddlers shed their colonizing organisms into marine waters and therefore can be sources of potentially pathogenic S. aureus and MRSA in recreational marine waters. Additional research is needed to evaluate recreational beaches and marine waters as potential exposure and transmission pathways for MRSA.

Vancomycin MIC creep in MRSA isolates from 1997 to 2008 in a healthcare region in Hong Kong

OBJECTIVES

To assess whether vancomycin MIC creeps among blood methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from 5 hospitals in Hong Kong from 1997 to 2008.

METHODS

Blood cultures MRSA isolates from 1997 to 1999 (period 1), 2004 (period 2) and 2006-2008 (period 3) were retrieved. Etest method was used to determine their vancomycin MIC. The genotypic features were determined by PCR and sequencing.

RESULTS

247 blood MRSA isolates were studied. The vancomycin MIC were 0.375, 0.5, 0.75 and 1 mg/L for 15 (6.1%), 68 (27.5%), 89 (36%) and 75 (30.4%) isolates, respectively. There was an increase in the percentage of isolates with an MIC=1mg/L from 10.4% (5/48) during period 1 to 21.6% (8/37) during period 2 and 38.3% (62/162) during period 3 (period 1 vs. period 3, P<0.001). Molecular typing showed that this was due to increased percentages of clonal cluster (CC) 8/SCCmec III/IIIA (agr group I), CC45/SCCmec IV/V (agr group IV) and other minor clones with elevated MIC over time.

CONCLUSION

This study found vancomycin MIC creep among blood MRSA isolates over time. As elevated MIC within the susceptible range may reduce vancomycin efficacy, clinical laboratories should adopt methods with the required precision to accurately determine MICs.

Isolation from sewage influent and characterization of novel Staphylococcus aureus bacteriophages with wide host ranges and potent lytic capabilities

Staphylococcus aureus is a gram-positive pathogen that causes a variety of diseases, including bovine mastitis, which has severe economic consequences. Standard antibiotic treatment results in selection of resistant strains, leading to a need for alternative treatments, such as bacteriophage therapy. Forty-nine S. aureus isolates were obtained from the milk of mastitic cows for use in screening of staphylococcal phages. Fifteen isolates which were positive for both coagulase and hemolysin were assayed by PCR for variation in the X region and the immunoglobulin G-binding region of the protein A gene (spa) and in the carboxy terminus of the coagulase gene (coa) and for the presence of enterotoxin C, G, H, and I genes. The host ranges of 52 phages isolated from sewage influent were determined by performing spot tests with the 15 S. aureus isolates, and two phages were subsequently chosen for further analysis. PhiSA039 had the widest host range, producing clear plaques on 13 of the 15 isolates (87%), while PhiSA012 produced clear plaques on 8 isolates (53%) and was the only phage that produced a clear plaque on a nonmastitic S. aureus strain. Transmission electron microscopy revealed that the phages were similar sizes and belonged to the Myoviridae family. Measurement of optical densities during coculture with S. aureus isolates confirmed the breadth of the PhiSA039 host range and showed that PhiSA012 had potent lytic capability. PhiSA012-resistant bacteria did not appear for three of seven isolates tested (43%) after 65 h of incubation. These two phages are proposed as candidates for phage therapy of bovine mastitis.

Identification of the clonal complexes of Staphylococcus aureus strains by determination of the conservation patterns of small genomic islets

AIMS

To investigate the clonality of Staphylococcus aureus isolates, it is important to identify their clonal complexes (CCs) with multilocus sequence typing (MLST). However, it is expensive to carry out MLST analyses for many isolates. The aim of this study, therefore, was to develop a cost-effective method to identify CCs by determining the conservation pattern of 'small genomic islets' (SGIs). SGIs are nonconserved regions between strains and have single or multiple open-reading frames (ORFs).

METHODS AND RESULTS

The whole-genome sequences of nine strains were compared in order to select 16 SGIs. The conservation patterns of the 16 SGIs (islet patterns) were investigated in 136 S. aureus isolates, which were classified into 21 CCs. The islet patterns (IPs) exhibited a one-to-one correspondence with the CCs, except for isolates belonging to CC1, CC5 and CC8. The IPs typical of strains belonging to CC1, CC5 and CC8 differed between those of sequence type 1 (ST1) and ST188 (CC1), ST5 and ST6 (CC5) and ST8 and ST239 (CC8).

SIGNIFICANCE AND IMPACT OF THE STUDY

The CCs of many isolates can be identified in an easy and inexpensive manner by detecting these 16 SGIs. Emergent clones, particularly methicillin-resistant ones, can be identified by examining numerous islets by IP analysis.

Staphylococcal interspersed repeat unit typing of Staphylococcus aureus: evaluation of a new multilocus variable-number tandem-repeat analysis typing method

The present study evaluates the performance of the staphylococcal interspersed repeat unit (SIRU) method applied to a diverse collection of 104 Staphylococcus aureus isolates previously characterized by pulsed-field gel electrophoresis (PFGE), spa typing, multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec typing for methicillin-resistant S. aureus. The SIRU method distributed the 104 strains into 81 SIRU profiles that could be clustered into 12 groups and 29 singletons. The discriminatory power of the method at the profile level, translated by Simpson's index of diversity (SID), was similar to that of PFGE subtyping (SID = 99.23% versus 99.85%) and slightly higher than that of spa typing (SID = 97.61%). At the group level, the SIRU SID (93.24%) was lower than that of PFGE typing (95.41%) but higher than that of MLST (SID = 91.77%). The adjusted Rand (AR) coefficient showed that SIRU typing at the group level had the highest congruence with MLST (AR = 0.5736) and with clonal complex (CC) (AR = 0.4963) but the lowest congruence with PFGE subtype (AR = 0.0242). The Wallace coefficient indicated that in the present collection, two strains with the same SIRU profile have a 100% probability of belonging to the same CC, a 90% probability of sharing the same spa type, and an 83% probability of being classified in the same sequence type. The high discriminatory power of the SIRU method, along with its apparent concordance with MLST results, makes it potentially valuable for S. aureus short-term epidemiological investigations and population dynamics as well.

spa typing for epidemiological surveillance of Staphylococcus aureus

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

Molecular diagnostics of clinically important staphylococci

Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.

Unusual form of oxacillin resistance in methicillin-resistant Staphylococcus aureus clinical strains

The mechanisms by which there is differential expression of resistance to oxacillin within the populations of a single strain remains to be fully understood. The purpose of this study was to evaluate and characterize 25 GOA48 methicillin-resistant Staphylococcus aureus (MRSA) oxacillin-susceptible mecA-positive strains, which were obtained by screening consecutively 832 S. aureus isolates. These 25 isolates (3% of the total strains investigated) were uniformly detected by extending the 24-h oxacillin agar screen plate to 48 h (namely, GOA48-MRSA). Twenty-two isolates tested positive for penicillin-binding protein 2a, whereas the remaining 3 isolates were inconsistently mecA positive. Inconsistent detection of mecA by polymerase chain reaction (PCR) in the mentioned 3 isolates was investigated by colony hybridization using a mecA probe (> or = 80% of colonies hybridized poorly to the probe). A PCR product that amplified the empty SCCmec insertion site (attB), present only if the element was excised, resulted positive in all 3 isolates before oxacillin exposure, whereas integrated elements were positive only for oxacillin-grown isolates. The remaining 22 strains did not reveal excision demonstrating stable mecA. We concluded that resistance to beta-lactams in MRSA-positive mecA strains susceptible to oxacillin is associated to an extreme heterogeneous expression of resistance combined in some cases to oxacillin SCCmec excision.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus in residential care homes for the elderly in Hong Kong

This territory-wide study evaluated the molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in residential care homes for elderly (RCHEs) in Hong Kong. MRSA colonization was assessed by taking swab culture from anterior nares and active skin lesions. Of 487 RCHEs surveyed, 80 MRSA strains were recovered from 1563 residents, giving a prevalence of 5.1%. Twenty-four isolates had SCCmec II, 2 had SCCmec III, 17 had SCCmec IV, 36 had SCCmec V, and 1 had a composite SCCmec type. Pulsed-field gel electrophoresis typing clustered 75 isolates into 7 clones (HKU10 to 50, HKU80, and HKU90). Two predominant types, HKU30 and HKU50, which together account for 75% of all MRSA strains, were found in 13 and 15 of the 18 geographic districts in Hong Kong, respectively. The main features for HKU50 strains were spa t1081/ST45-IV or V, capsular type 8, agrIV, and hla, seg, sei positive. On the other hand, HKU30 strains had spa t002/ST5-II, capsular type 5, agrII, and were hla, seg, sei positive. HKU30 strains were often multidrug resistant (MDR, involving ciprofloxacin, erythromycin, gentamicin, and tetracycline). In contrast, HKU50 strains exhibit both multidrug resistance (MDR) (involving ciprofloxacin, erythromycin, and tetracycline, but not gentamicin) and non-MDR patterns.

Replacement of methicillin-resistant Staphylococcus aureus clones in Hungary over time: a 10-year surveillance study

The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Hungary has been increasing and is now close to 20% among invasive isolates of S. aureus. In order to understand the evolution of MRSA in Hungary, two collections of isolates were studied: 22 representatives of a collection of 238 MRSA isolates recovered between 1994 and 1998, and a collection of 299 MRSA isolates recovered between 2001 and 2004. The isolates were first characterised by pulsed-field gel electrophoresis (PFGE) and were distributed into 19 different PFGE patterns. Representatives of each pattern were further characterised by spa typing, multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. The Hungarian clone that was predominant in 1994-1998 (PFGE E, ST239-III) had almost disappeared in 2003-2004, being replaced by the Southern German clone (PFGE B, ST228-I) and the New York/Japan epidemic clone (PFGE A, ST5-II), which represented c. 85% of the 2001-2004 isolates. Thus, this study describes, for the first time, the co-dominance and extensive spread of the New York/Japan clone in a European country.

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.

Development of a rapid strain differentiation method for methicillin-resistant Staphylococcus aureus isolated in Japan by detecting phage-derived open-reading frames

AIMS

To develop a rapid genotyping method for investigating outbreaks of methicillin-resistant strains of Staphylococcus aureus (MRSA) isolated in Japan.

METHODS AND RESULTS

Isolates were genotyped by detecting the keeping pattern of 16 open-reading frames (ORFs), a process we call phage ORF typing (POT). Thirteen of the ORFs were selected from phage genomes and one from a genomic island SaGIm in the genome of strain Mu50. The other two ORFs, one from Tn554 and one from staphylococcal cassette chromosome mec (SCCmec) type II, were used as strain markers. Three hundred and sixty-eight isolates from five hospitals were classified into 133 types by POT, whereas they were classified into 139 types by pulsed-field gel electrophoresis (PFGE) subtyping. The discriminatory power of POT (D=0.989) was equal to that of PFGE subtyping (D=0.986).

CONCLUSIONS

MRSA isolates collected in Japan can be genotyped by detecting the keeping pattern of phage-derived ORFs with a discriminatory power equal to that of PFGE subtyping.

SIGNIFICANCE AND IMPACT OF THE STUDY

MRSA isolates can be genotyped rapidly by detecting phage-derived ORFs. As particular pandemic clones can be found in a specific region, a typing method localized to a pandemic clone may be effective for the rapid genotyping of MRSA during outbreaks.

Rapid cost-effective subtyping of meticillin-resistant Staphylococcus aureus by denaturing HPLC

The importance of meticillin-resistant Staphylococcus aureus (MRSA) in hospital-acquired infection is widely acknowledged. The UK government has stated that MRSA bloodstream infection rates will have to be halved by 2008. Such radical improvements will require advances on several fronts. Screening for MRSA in high-risk patients on arrival at hospital allows isolation of carriers and reduces transmission to staff and other patients. Concurrent subtyping of MRSA could also inform outbreak investigations and long-term epidemiological studies. The variability within the staphylococcal protein A, or spaA, gene-repeat region can be used as a marker of short- and long-term genetic variation. A novel application is described of denaturing HPLC (DHPLC) for rapid, inexpensive characterization of spaA gene amplification products, without the need for DNA sequence determination. The method allowed rapid and precise sizing of spaA gene-repeat regions from 99 S. aureus strains and was combined with heteroduplex analysis, using reference PCR products, to indicate the spa type of the test isolate. The method allowed subtyping of strains in less than 5 h from receipt of a primary isolation plate. When applied to an outbreak that occurred during this study, the authors were able to demonstrate relatedness of the isolates more than 5 days before results were received from a reference laboratory. If combined with direct amplification from swabs, DHPLC analysis of spaA gene variation could prove extremely valuable in outbreak investigation and MRSA surveillance.

Classifying spa types in complexes improves interpretation of typing results for methicillin-resistant Staphylococcus aureus

A total of 382 isolates of methicillin-resistant Staphylococcus aureus originating from three Austrian regions and one adjacent Italian region (Vienna, Lower Austria, North Tyrol, and South Tyrol) were typed by DNA sequence analysis of the variable repeat region of the protein A gene (spa typing). The strain collection consisted of arbitrarily chosen isolates originating from clinical specimens taken in the years 2003 to 2005 at 17 hospitals. The most common spa types found were t001 (28.8% of all isolates), t190 (27.0%), t008 (14.1%), and t041 (11.3%). The 42 remaining spa types accounted for Collapse

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MESH Headings

• Austria
• Bacterial Typing Techniques/methods
• DNA, Bacterial/chemistry
• DNA, Bacterial/genetics
• Humans
• Italy
• Methicillin Resistance
• Molecular Epidemiology
• Repetitive Sequences, Nucleic Acid/genetics
• Sequence Analysis, DNA
• Staphylococcal Infections/microbiology
• Staphylococcal Protein A/genetics
• Staphylococcus aureus/classification
• Staphylococcus aureus/genetics
• Staphylococcus aureus/isolation & purification

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Affiliation(s)

Werner Ruppitsch Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Spargelfeldstrasse 191, A-1226 Vienna, Austria.
Alexander Indra
Anna Stöger
Barbara Mayer
Silke Stadlbauer
Günther Wewalka
Franz Allerberger

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Multilocus sequence typing: Data analysis in clinical microbiology and public health

Numerous computer-based statistical packages have been developed in recent years and it has become easier to analyze nucleotide sequence data and gather subsequent information that would not normally be available. Multilocus sequence typing (MLST) is used for characterizing isolates of bacterial and fungal species and uses nucleotide sequences of internal fragments of housekeeping genes. This method is finding a place in clinical microbiology and public health by providing data for epidemiological surveillance and development of vaccine policy. It adds greatly to our knowledge of the genetic variation that can occur within a species and has therefore been used for studies of population biology. Analysis requires the detailed interpretation of nucleotide sequence data obtained from housekeeping and nonhousekeeping genes. This is due to the amount of data generated from nucleotide sequencing and the information generated from an array of analytical tools improves our understanding of bacterial pathogens. This can benefit public health interventions and the development of enhanced therapies and vaccines. This review concentrates on the analytical tools used in MLST and their use in the clinical microbiology and public health fields.

Genotypic diversity of methicillin-resistant Staphylococcus aureus isolates in Korean hospitals

Ninety-six methicillin-resistant Staphylococcus aureus (MRSA) isolates from eight Korean hospitals were analyzed by multilocus sequence typing, SCCmec typing, and spa typing. The predominant genotype was ST5-MRSA-II of clonal complex 5, which was found in 36 isolates from six hospitals, but ST239-MRSA-III was also common. Overall, results showed a notable genotypic diversity of MRSA strains circulating in Korean hospitals.

Prevalence of the ST239 clone of methicillin-resistant Staphylococcus aureus and differences in antimicrobial susceptibilities of ST239 and ST5 clones identified in a Korean hospital

A total of 188 nonduplicate methicillin-resistant Staphylococcus aureus (MRSA) isolates obtained between 2001 and 2004 in a university hospital in Daegu, Korea, were analyzed for their clonal types by molecular typing techniques, including multilocus sequence typing, spaA typing, staphylococcal chromosomal cassette mec (SCCmec) typing, and pulsed-field gel electrophoresis (PFGE). They were examined for their antimicrobial susceptibilities. The majority (87%) of MRSA isolates belonged to sequence type 239 (ST239; n = 100; 53%) and ST5 (n = 63, 34%) on the basis of sequence typing. MRSA isolates belonging to ST239 were genotypically homogeneous, while those belonging to ST5 showed variations in spaA type, SCCmec type, and PFGE patterns. The rates of resistance of the MRSA isolates belonging to ST239 to trimethoprim, sulfamethoxazole, tobramycin, gentamicin, erythromycin, and tetracycline were significantly higher than those of the isolates belonging to ST5 (P < 0.05). This study demonstrated that the ST239 clone, while rarely detected in Korea, was prevalent and that the antimicrobial susceptibility of the ST239 clone was significantly different from that of the ST5 clone.

Genetic relatedness of Staphylococcus epidermidis from infected infants and staff in the neonatal intensive care unit

BACKGROUND

The genetic relatedness of Staphylococcus epidermidis associated with infections in infants and cultured from the hands of nurses was assessed.

METHODS

From March 2001 to January 2002, infections caused by S. epidermidis were prospectively monitored. Participating nurses had hand cultures performed quarterly following hand hygiene. Pulsed-field gel electrophoresis was performed to determine genetic relatedness of strains from infants and nurses.

RESULTS

During the study period, S. epidermidis caused 42 of 143 (29%) and 26 of 100 (26%) infant infections and was cultured from the clean hands of 51 of 61 (84%) and 53 of 58 (91%) nurses in neonatal intensive care unit (NICU)-1 and NICU-2, respectively. Fifty-eight clones of S. epidermidis were identified among 173 isolates typed: 38 of 173 isolates (22%) were unique clones detected in a single infant (n=10) or nurse (n=28); 42 of 173 (24%) isolates were defined as belonging to small cluster clones (n=15), ie, were detected in 2 to 4 nurses and/or infants; and 93 of 173 (54%) isolates belonged to large cluster clones (n=4), ie, detected in 7 to 64 nurses and/or infants.

CONCLUSIONS

These data suggested that most S. epidermidis isolates were shared between infants and nurses. Hand hygiene alone is inadequate to prevent S. epidermidis infections, and additional strategies are needed to prevent cross transmission in NICU populations.

Clonal Structure of the Methicillin-ResistantStaphylococcus aureus(MRSA) Population in Poland: Revision and Update

The clonal structure of the methicilin-resistant Staphylococcus aureus (MRSA) population in Poland has been analyzed in several reports since the mid-1990s. The present study was performed on 253 MRSA isolates (146 archival and 107 new isolates) recovered in 26 hospitals between 1990 and 2001. Whereas all isolates were typed by pulsed-field gel electrophoresis (PFGE) and the analysis of the ClaI::mecA and ClaI::Tn554 RFLP polymorphism, selected isolates were also subjected to multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) comparisons. Based on the PFGE data, 15 MRSA clones were discerned, seven of which were observed in multiple hospitals. Five of these were related to the pandemic Hungarian (MLST clonal complex, CC8), Iberian (CC8), Pediatric (CC5), Mexican (CC30), and Brazilian clones (CC8). MLST confirmed the earlier reports on the similarity of the Hungarian and Brazilian clones, and it revealed that one of the two remaining epidemic clones was related to the Hungarian/Brazilian, and the other--to the Berlin clones. A local strain from the Northeastern part of the country was found to be similar to a minor Greek clone. The MRSA clonal structure and the increasing complexity of the relationships between the genetic and phenotypic traits of this micro-organism in Poland has now been firmly established.

Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) isolates have previously been classified into major epidemic clonal types by pulsed-field gel electrophoresis in combination with multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec typing. We aimed to investigate whether genetic variability in potentially polymorphic domains of virulence-related factors could provide another level of differentiation in a diverse collection of epidemic MRSA clones. The target regions of strains representative of epidemic clones and genetically related methicillin-susceptible S. aureus isolates from the 1960s that were sequenced included the R domains of clfA and clfB; the D, W, and M regions of fnbA and fnbB; and three regions in the agr operon. Sequence variation ranged from very conserved regions, such as those for RNAIII and the agr interpromoter region, to the highly polymorphic R regions of the clf genes. The sequences of the clf R domains could be grouped into six major sequence types on the basis of the sequences in their 3' regions. Six sequence types were also observed for the fnb sequences at the amino acid level. From an evolutionary point of view, it was interesting that a small DNA stretch at the 3' clf R-domain sequence and the fnb sequences agreed with the results of MLST for this set of strains. In particular, clfB R-domain sequences, which had a high discriminatory capacity and with which the types distinguished were congruent with those obtained by other molecular typing methods, have potential for use for the typing of S. aureus. Clone- and strain-specific sequence motifs in the clf and fnb genes may represent useful additions to a typing methodology with a DNA array.

International clones of methicillin-resistant Staphylococcus aureus in two hospitals in Miami, Florida

A total of 202 methicillin-resistant Staphylococcus aureus (MRSA) single-patient isolates recovered between January and June 1998 in two hospitals in Miami, Florida, were characterized by a combination of several molecular typing techniques: multilocus sequence typing, spaA typing, pulsed-field gel electrophoresis, and determination of the structure of the SCCmec element. The overwhelming majority of the isolates-187 of 202, or 93%-belonged to one of three internationally spread epidemic clones which were identified on the basis of their multilocus sequence type (ST) as E-MRSA-16 (ST36), the New York clone V (ST8), and the New York/Japan clone (ST5; SCCmec II) and its single- and double-locus variants. The rest of the isolates (15 of 202, or 7%) were more genetically diverse and were each recovered from a few patients only. Of the 23 MRSA strains isolated from confirmed human immunodeficiency virus-positive patients, as many as 17 (or 70%) belonged to a single ST8 clone carrying SCCmec type IV. The data provide further evidence for the conclusion of earlier studies that most MRSA disease in hospitals is caused by relatively few pandemic clones.

Update on the major clonal types of methicillin-resistant Staphylococcus aureus in the Czech Republic

The purpose of our study was the molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in 21 hospitals in the Czech Republic in the period 2000-2002 and comparison with previous results from 1996-1997. Strains were analyzed by pulsed-field gel electrophoresis (PFGE) of SmaI digests and ribotyping of HindIII digests hybridized with a 16S-23S DNA probe. The prevalence of the most clinically important macrolide (ermA, ermB, ermC, and msrA) and aminoglycoside (aph3', ant4', and aac6'-aph2") resistance genes was evaluated as well. Selected isolates representative of each clonal type were analyzed by multilocus sequence typing and by a multiplex PCR method capable of identifying the structural type of the staphylococcal cassette chromosome mec (SCCmec) carried by the bacteria. Our results document the displacement of the Brazilian clone (ST239, SCCmec type IIIA, PFGE type B, ribotype H1) by a new clone that we named "Czech clone" (ST239, SCCmec type IIIA, PFGE type F, ribotype H6) and the maintenance of the Iberian clone (ST247, SCCmec type IA, PFGE type A, ribotype H2) exclusively in one hospital in the Czech Republic. In addition, we found a correlation between the distribution of aminoglycoside resistance genes and MRSA clonal types.

Evolution of sporadic isolates of methicillin-resistant Staphylococcus aureus (MRSA) in hospitals and their similarities to isolates of community-acquired MRSA

Forty-one methicillin-resistant Staphylococcus aureus (MRSA) hospital isolates that clearly differed from the six major pandemic clones of MRSA in pulsed-field gel electrophoresis type, mecA and Tn554 polymorphism, and epidemic behavior were selected from an international strain collection for more detailed characterization. SpaA typing, multilocus sequence typing, and SCCmec (staphylococcal cassette chromosome mec) typing demonstrated extensive diversity among these sporadic isolates both in genetic background and also in the structure of the associated SCCmec elements. Nevertheless, the isolates could be grouped into restricted clonal complexes by using the BURST (i.e., based upon related sequence types) program algorithm, which predicted that most sporadic MRSA isolates evolved from pandemic MRSA clones. Several of the sporadic MRSA resembled community-acquired MRSA isolates in properties that included a relatively limited multiresistance pattern, faster growth rates, diversity of genetic backgrounds, and a frequent association with SCCmec type IV.

Clonal and antibiotic resistance profiles of methicillin-resistant Staphylococcus aureus (MRSA) from a Portuguese hospital over time

Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from a general hospital in Oporto, Portugal, during two periods (1992-1993 and 1996-2000) were characterized by pulsed-field gel electrophoresis (PFGE) of SmaI fragments, and by hybridization of ClaI digests with mecA and Tn554 probes, discriminating the isolates in mecA::Tn554::PFGE genotypes. In addition, a representative sample of the defined genotypes was characterized by multilocus sequence typing (MLST) and SCCmec (staphylococcal cassette chromosome mec) typing, generating the corresponding ST-SCCmec types. In 1992-1993, 77% of MRSA belonged to the Iberian clone (genotype I::E::A or ST247-IA). In 1996-2000, the frequency of this clone decreased to 19% and the majority (69%) of the isolates belonged to another international clone, the Brazilian MRSA (genotype XI::B::B or ST239-IIIA). Trimethoprim/sulfamethoxazole (SXT) was confirmed to be an important phenotypic marker to distinguish the Iberian (SXT-susceptible) and the Brazilian (SXT-resistant) clones in MRSA isolates from Portugal. Our observations document major shifts in the dominant MRSA clonal types that occurred in this hospital since 1992, suggesting a selective advantage of the Brazilian relatively to the Iberian clone. In addition to these two MRSA clones that are the most frequent in Portuguese hospitals since the early 1990s, sporadic MRSA clones (representing 14% of the total) were identified and characterized.

An outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit

OBJECTIVE

To describe the epidemiologic and molecular investigations that successfully contained an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) in a neonatal intensive care unit (NICU).

DESIGN

Isolates of MRSA were typed by pulsed-field gel electrophoresis (PFGE) and S. aureus protein A (spa).

SETTING

A level III-IV, 45-bed NICU located in a children's hospital within a medical center.

PATIENTS

Incident cases had MRSA isolated from clinical cultures (eg, blood) or surveillance cultures (ie, anterior nares).

INTERVENTIONS

Infected and colonized infants were placed on contact precautions, cohorted, and treated with mupirocin. Surveillance cultures were performed for healthcare workers (HCWs). Colonized HCWs were treated with topical mupirocin and hexachlorophene showers.

RESULTS

From January to March 2001, the outbreak strain of MRSA, PFGE clone B, was harbored by 13 infants. Three (1.3%) of 235 HCWs were colonized with MRSA. Two HCWs, who rotated between the adult and the pediatric facility, harbored clone C. One HCW, who exclusively worked in the children's hospital, was colonized with clone B. From January 1999 to November 2000, 22 patients hospitalized in the adult facility were infected or colonized with clone B. Spa typing and PFGE yielded concordant results. PFGE clone B was identified as spa type 16, associated with outbreaks in Brazil and Hungary.

CONCLUSIONS

A possible route of MRSA transmission was elucidated by molecular typing. MRSA appears to have been transferred from our adult facility to our pediatric facility by a rotating HCW. Spa typing allowed comparison of our institution's MRSA strains with previously characterized outbreak clones.

Two international methicillin-resistant Staphylococcus aureus clones endemic in a university hospital in Patras, Greece

Pulsed-field gel electrophoresis (PFGE) of SmaI macrofragments and hybridization of ClaI digests with the mecA- and Tn554-specific DNA probes were used to define the endemic clones of methicillin-resistant Staphylococcus aureus (MRSA) among strains collected in 1993 and 1998 to 2000 at the University Hospital of Patras, Patras, Greece. Representatives of each clonal type were analyzed by spaA typing, multilocus sequence typing (MLST), and staphylococcal chromosomal cassette mec (SCCmec) typing. The results indicated the existence of two successive international MRSA clones: (i) a clonal type with PFGE type A, sequence type (ST) 30 (ST30), and SCCmec type IV, which was very similar to a clone widely spread in the United Kingdom, Mexico, and Finland, and (ii) a clonal type with PFGE type B, ST239, and SCCmec III, which was related to the Brazilian clone. Both clones seem to be widespread in Greece as well. A novel MRSA clone is also described and is characterized by a new MLST type (ST80) associated with SCCmec type IV and with the presence of Panton-Valentine leukocidin genes.

Frequent recovery of a single clonal type of multidrug-resistant Staphylococcus aureus from patients in two hospitals in Taiwan and China

One hundred thirty-two methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from patients with S. aureus infections between January 1998 and February 1999 in two hospitals, one located in Taipei, Taiwan, and another in Nanjing, People's Republic of China, were examined for antibiotic susceptibility and for clonal type by a combination of three methods: hybridization of ClaI restriction digests with mecA- and Tn554-specific DNA probes and pulsed-field gel electrophoresis of chromosomal SmaI digests. Selected isolates representing each clonal type were also analyzed by spaA typing, multilocus sequence typing, and a multiplex PCR method capable of identifying the structural type of the staphylococcal cassette chromosome mec (SCCmec) carried by the bacteria. The overwhelming majority of isolates (126 of 132 or 95%) belonged to minor variants of a single clonal type resembling the Brazilian and Hungarian epidemic MRSA clones, which showed a common spaA type and which were either sequence type 239 (ST239) or ST241 (a single-locus variant of ST239) in association with SCCmec type III or IIIA.

Molecular detection and genotyping of pathogens: more accurate and rapid answers

Rapid molecular methods have enhanced the capabilities of laboratories to identify and characterize microbial pathogens in greater detail. Nucleic acid amplification strategies and advances in amplicon detection have been key aspects in the progress of molecular microbiology. Sophisticated new amplification-detection combinations are resulting in many applications in laboratory testing for infectious diseases. These applications include qualitative detection, sub-species-level DNA fingerprinting, molecular resistance testing and genotyping, and quantitative (viral load) testing. When applied selectively in the laboratory, these applications can enhance diagnostic approaches and clinical management and will probably evolve into standard laboratory and point-of-care testing protocols.

The evolution of pandemic clones of methicillin-resistant Staphylococcus aureus: identification of two ancestral genetic backgrounds and the associated mec elements

Previous surveillance studies carried out by our laboratories, primarily in Southern and Eastern Europe, Latin America, and the United States, have characterized 3,067 methicillin-resistant Staphylococcus aureus (MRSA) hospital isolates by a combination of molecular typing methods. Nearly 70% of these isolates could be classified into five clonal types showing extensive geographic spread. Representative isolates of these clonal types were now reexamined for their genetic relatedness by multilocus sequence typing (MLST) and by sequencing the polymorphic region of protein A (spaA typing), and also for the type of the Staphylococcal Chromosomal Cassette (SCCmec) resident in the bacteria. Three of the previously classified clonal types (Iberian, Brazilian, and Hungarian clones) shared a common or closely related genetic background A, which was the same as the background of the earliest European isolates of MRSA from England and Denmark. The Pediatric and New York/Japan clones belonged to a completely different genetic background B. The three recently described SCCmec types were specifically associated with different pandemic clones: types I and III with isolates of genetic background A and type II with isolates of genetic background B. A novel SCCmec related to type I, called SCCmec type IV, was identified in some MRSA strains belonging to genetic background A as well as B. Structural variations in SCCmec types I and III were also observed. The data allow tentative identification of an evolutionary pathway for the emergence of pandemic MRSA clones and also provide evidence for the multiple, yet restricted, numbers of acquisition of the mec element by S. aureus.

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.

Low prevalence of methicillin-resistant strains among Staphylococcus aureus colonizing young and healthy members of the community in Portugal

Recent reports suggest that methicillin-resistant Staphylococcus aureus (MRSA) may be emerging as a community pathogen. In Portuguese hospitals, the incidence of MRSA among disease causing isolates is extremely high (48-50%). To determine the prevalence of MRSA in the Portuguese community, nasal samples were obtained from 823 draftees, 484 nonmedical university students, and 107 high-school students. In addition, throat samples were obtained from the 823 draftees and S. aureus isolates were also recovered from 283 (13%) nasopharyngeal samples obtained from 2,111 children attending day-care centers. The rate of nasal colonization of S. aureus was 34%, 25%, and 46% for draftees, nonmedical university students, and high-school students, respectively. The rate of pharyngeal colonization of the draftees was 33%. Of the 1,001 S. aureus isolates obtained, seven were MRSA and eight were borderline oxacillin-resistant S. aureus (BORSA). By molecular typing techniques, five of the seven MRSA were identified as belonging to one of three highly epidemic clones, the Brazilian, Iberian, and Pediatric clones of MRSA, which were identified as endemic in Portuguese hospitals. The eight BORSA were all members of clones previously identified in international samples. In spite of the extremely high prevalence of MRSA in Portuguese hospitals, the carriage rate of MRSA in healthy and young individuals remains low.

Molecular typing of selected Enterococcus faecalis isolates: pilot study using multilocus sequence typing and pulsed-field gel electrophoresis

The present study compared the recently developed multilocus sequence typing (MLST) approach with a well-established molecular typing technique, pulsed-field gel electrophoresis (PFGE), for subspecies differentiation of Enterococcus faecalis isolates. We sequenced intragenic regions of three E. faecalis antigen-encoding genes (ace, encoding a collagen and laminin adhesin; efaA, encoding an endocarditis antigen; and salA, encoding a cell wall associated antigen) and one housekeeping gene (pyrC) of 22 E. faecalis isolates chosen largely for their temporal and geographical diversity, but also including some outbreak isolates. MLST analysis of polymorphic regions of these four genes identified 13 distinct sequence types (STs) with different allelic profiles; the composite sequences generated from the four sequenced gene fragments of individual isolates showed 98.3 to 100% identity among the 22 isolates. We also found that the allelic profiles from two sequences, ace and salA, were sufficient to distinguish all 13 STs of this study. The 13 STs corresponded to 12 different PFGE types, with one previously designated PFGE clone (a widespread U.S. clone of beta-lactamase-producing isolates) being classified into two highly related STs which differed at 2 of 2,894 bases, both in the same allele. MLST also confirmed the clonal relationships among the isolates of two other PFGE clonal groups, including vancomycin resistant isolates. Thus, this pilot study with representative E. faecalis isolates suggests that, similar to PFGE, the sequence-based typing method may be useful for differentiating isolates of E. faecalis to the subspecies level in addition to identifying outbreak isolates.

Three-year assessment of methicillin-resistant Staphylococcus aureus clones in Latin America from 1996 to 1998

Four hundred ninety-nine methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from 1996 to 1998 from 22 hospitals in five countries of Latin America-Argentina, Brazil, Chile, Uruguay and Mexico-were examined for antimicrobial susceptibility and clonal type in order to define the endemic clones in those hospitals. The hybridization of ClaI restriction digests with the mecA- and Tn554-specific DNA probes combined with pulsed-field gel electrophoresis of chromosomal SmaI digests (ClaI-mecA::ClaI-Tn554::PFGE clonal types) documented not only the predominance and persistence of the Brazilian clone (XI::B::B) in Brazil (97%) and Argentina (86%) but also its massive dissemination to Uruguay (100%). Moreover, a close relative of the Brazilian clone (XI::kappa::B) was highly represented in Chile (53%) together with a novel clone (47%) (II::E'::F) resistant to pencillin, oxacillin, ciprofloxacin, chloramphenicol, clindamycin, erythromycin, and gentamicin. A unique clonal type (I::NH::M) was detected in Mexico among pediatric isolates and was resistant to penicillin, oxacillin, and gentamicin only. This study clearly documented the very large capacity for geographic expansion and the persistence of the Brazilian clone, contributing not only to the increasing uniformity of the MRSA in South America but worldwide as well.