Limited value of routine spa typing: a cross-sectional study of methicillin-resistant Staphylococcus aureus-positive patients in an Austrian hospital

Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections

108 isolates of Staphylococcus aureus, belonging to six large ribogroups according to the automated Ribo-Printer^® system, were studied with two highly used molecular methods for epidemiological studies, namely multi-locus sequence typing (MLST) and spa typing, followed by BURP and eBURST v3 analysis for clustering spa types and sequence (ST) types. The aim was to evaluate whether automated ribotyping could be considered a useful screening tool for identifying S. aureus genetic lineages with respect to spa typing and MLST. Clarifying the relationship of riboprinting with these typing methods and establishing whether ribogroups fit single clonal complexes were two main objectives. Further information on the genetic profile of the isolates was obtained from agr typing and the search for the mecA, tst genes, and the IS256 insertion sequence. Automated ribotyping has been shown to predict spa clonal complexes and MLST clonal complexes. The high cost and lower discriminatory power of automated ribotyping compared to spa and MSLT typing could be an obstacle to fine genotyping analyzes, especially when high discriminatory power is required. On the other hand, numerous advantages such as automation, ease and speed of execution, stability, typeability and reproducibility make ribotyping a reliable method to be juxtaposed to gold standard methods.

Evaluation of high-resolution melting analysis for spa-typing of methicillin-resistant and -susceptible Staphylococcus aureus isolates

Molecular characterization of Staphylococcus aureus isolates from nosocomial and community-acquired infections using accurate, reproducible, and rapid typing methods is essential for the fast identification of prevalent and epidemic strains. Although sequence-based spa typing is highly effective, PCR-based techniques (such as high-resolution melting curve analysis, HRM) are simpler, less expensive, faster, and can be performed in a single and closed-tube assay format, thereby reducing the risk of contamination. A total of 51 methicillin-resistant S. aureus (MRSA) (n = 26) and methicillin-sensitive S. aureus (MSSA) (n = 25) isolates from Karaj (n = 10) and Yasuj (n = 41), Iran, were subjected to HRM. All selected isolates were identified by the standard spa-typing method. Among the 51 tested isolates, 11 genotype profiles were distinguished from 12 spa types. Strains t1077 and t1816 exhibited the highest and lowest melting temperatures (81.8°C and 79.4°C), with 46.7% and 39.8% G + C contents, respectively. Strains t706 and t1816, with almost identical G + C contents, had the same HRM genotypes, but their curves differed due to different G + C distributions. Four standard spa types (strains t030, t037, t701 and t5598) were differentiated correctly and their melting temperatures were 81.2°C, 81.4°C, 80.4°C and 80.1°C, respectively. We demonstrated that HRM profiling is a rapid method which enables the accurate screening of certain strains (especially the endemic ones), and may be used for bacterial surveillance. However, it cannot replace sequence-based spa typing, especially for newly emerging spa types, and therefore cannot be used as a standardized global method.

Molecular characterization of clonal lineage and staphylococcal toxin genes from S. aureus in Southern Nigeria

Background

Staphylococcus aureus is a human colonizer with high potential for virulence, and the spread of the virulent strains from the colonized hosts to non-carriers in the community is on the increase. However, there are few reports on comprehensive analysis of staphylococcal enterotoxin (SE) genes with clonal lineage in S. aureus in Africa. This is essential because of diversity of cultures and habits of the people. This study analyzed spa types and enterotoxin genes in S. aureus strains previously isolated from the human nostrils, poultry and clinical samples in Southern Nigeria.

Methods

Forty-seven S. aureus isolates were obtained from humans nostrils (n = 13), clinical strains (n = 21) and poultry (n = 13) from previous studies in Southern Nigeria. The strains were analyzed for mecA gene, selected toxins genes (sea, seb, sec, sed, see, seg, seh, sei, sej, sek, sel, sem, sen, seo, sep, seq, ser, seu) and Panton-Valentine leukocidin (PVL) gene (lukS-PV/lukF-PV) by PCR. Population structures of the strains were detected by Staphylococcal protein A (spa) typing.

Results

Twenty different spa types were obtained with the highest percentages, 17% observed in spa type t091 from clinical, nasal and poultry samples while t069 was the most prevalent spa type in poultry. Two MRSA were only detected in human strains. The poultry strains had the highest occurrence of SE genes (18%) followed by nasal strains (15%) and clinical strains (10%). Eighty-nine percent of all tested isolates harbored at least one SE gene; seo was the most prevalent (34%) followed by seg (30%) and sea (21%), while sec, see and sej were absent in all strains. Spa type t355 was associated with lukS-PV/lukF-PV gene and complete absence of all studied SE. Sea, seq, seb, sek were associated with spa type t069; sea was associated with t127 while sep was associated with spa type t091. There were coexistences of seo/seg and sei/seg.

Conclusions

The higher carriage of staphylococci enterotoxin genes by the nasal and poultry S. aureus strains suggests a high potential of spread of staphylococcal food poisoning through poultry and healthy carriers in the community. This is the first report of high occurrence of staphylococcal enterotoxins genes in poultry from Nigeria.

Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review

Background:Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies.

Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.”

Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence.

Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.

Increase of genetic diversity and clonal replacement of epidemic methicillin-resistant Staphylococcus aureus strains in South-East Austria

Spa-typing and microarray techniques were used to study epidemiological changes in methicillin-resistant Staphylococcus aureus (MRSA) in South-East Austria. The population structure of 327 MRSA isolated between 2002 and 2012 was investigated. MRSA was assigned to 58 different spa types and 14 different MLST CC (multilocus sequence type clonal complexes); in particular, between 2007 and 2012, an increasing diversity in MRSA clones could be observed. The most abundant clonal complex was CC5. On the respective SCCmec cassettes, the CC5 isolates differed clearly within this decade and CC5/SCCmecI, the South German MRSA, predominant in 2002, was replaced by CC5/SCCmecII, the Rhine-Hesse MRSA in 2012. Whereas in many European countries MLST CC22-MRSA (EMRSA 15, the Barnim epidemic MRSA) is predominant, this clone occurred in Austria nearly 10 years later than in neighbouring countries. CC45, the Berlin EMRSA, epidemic in Germany, was only sporadically found in South-East Austria. The Irish ST8-MRSA-II represented by spa-type t190 was frequently found in 2002 and 2007, but disappeared in 2012. Our results demonstrate clonal replacement of MRSA clones within the last years in Austria. Ongoing surveillance is warranted for detection of changes within the MRSA population.

Changes in the epidemiology of MRSA clones in Austria.

Multiple-locus variable number tandem repeat analysis is superior to spa typing and sufficient to characterize MRSA for surveillance purposes

AIM

Assess the best approach to type methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcal protein A (spa) typing, multiple-locus variable number tandem repeat analysis (MLVA) or both.

MATERIALS & METHODS

Discriminatory power of spa typing and MLVA was determined using 20,771 MRSA isolates.

RESULTS

There were twice as many MLVA types (MTs) as spa types present in the collection. Among the top 70% of the isolates, 37 spa types and 139 MTs were found. MLVA diversity among the top-10 spa types was high (diversity index 0.96), while spa diversity among the top-10 MTs was much lower (diversity index 0.83). The probability that two MRSA isolates with the same spa type also had the same MT was low (Wallace's coefficient 0.27). By contrast, most MRSA isolates yielding the same MT also had the same spa type (Wallace's coefficient 0.90).

CONCLUSION

MLVA is superior to spa typing and will suffice to characterize MRSA isolates for surveillance.

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.

Molecular Characterization of a Prevalent Ribocluster of Methicillin-Sensitive Staphylococcus aureus from Orthopedic Implant Infections. Correspondence with MLST CC30

Staphylococcus aureus is the leading etiologic agent of orthopedic implant infections. Here a ribocluster of 27 S. aureus strains underwent further molecular characterization and subtyping by multilocus sequence typing (MLST) and spa-typing. This cluster had been detected by automated ribotyping (with the EcoRI restriction enzyme) of 200 S. aureus isolates from periprosthetic infections of patients who underwent revision at the Rizzoli Orthopaedic Institute. The ribocluster, consisting of agr type III strains, with a 74% co-occurrence of bone sialoprotein-binding (bbp) and collagen-binding (cna) genes, lacked mecA and IS256, and exhibited a high prevalence of the toxic shock syndrome toxin gene (tst, 85%). Strains' relatedness was analyzed by BURP and eBURST. Two predominant spa types, t012 (32%) and t021 (36%), and one predominant sequence type, ST30 (18/27, 67%) were identified: a S. aureus lineage spread worldwide belonging to MLST CC30. Two new sequence types (ST2954, ST2960) and one new spa type (t13129) were detected for the first time. Interestingly, the 27-strain cluster detected by ribotyping corresponded exactly to MLST CC30, the sole CC identified by eBURST.

Improved protocol for rapid identification of certain spa types using high resolution melting curve analysis

Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital.

Epidemiology of MRSA in southern Sweden: strong relation to foreign country of origin, health care abroad and foreign travel

All notified MRSA cases in Skåne County have been followed since 2000. We have investigated the MRSA epidemiology over time, method of acquisition, whether some spa types are more prone to spread, and/or cause more infections, and the connection between spa type and country of acquisition/origin. All cases between 2000 and 2010 were included. Infection or colonization and the presence of PVL genes were noted. The spa types of the index cases were correlated with community or healthcare acquisition, proportion of MRSA-positive household contacts, country of origin of families and country of acquisition of MRSA. The number of cases increased from 31 in 2000 to 315 in 2010. Most cases were community-acquired and the median age was 30 years. Thirty-two per cent of the MRSA cases were found because of a clinical infection. Of the household contacts 35 % were MRSA-positive. Only 24 % of the MRSA cases were both of Swedish origin and had contracted MRSA in Sweden. An association between spa type and certain regions of acquisition/origin was noted. Spa types t044, t002 and t008 were the most predominant strains. PVL-positive spa types t008, t019 and t044 caused more skin infections than the other spa types. Our results support screening for MRSA in patients with health care contacts abroad, culturing of patients with skin infections contracted outside Sweden and performing contact tracing among household members. Knowledge of spa type might give guidance in the process of contact tracing. Eradication treatment of MRSA spa types causing more skin infections may be warranted.