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

An improved MLVF method and its comparison with traditional MLVF, spa typing, MLST/SCCmec and PFGE for the typing of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) has become an important nosocomial pathogen, causing considerable morbidity and mortality. During the last 20 years, a variety of genotyping methods have been introduced for screening the prevalence of MRSA. In this study, we developed and evaluated an improved approach capillary gel electrophoresis based multilocus variable-number tandem-repeat fingerprinting (CGE/MLVF) for rapid MRSA typing. A total of 42 well-characterized strains and 116 non-repetitive clinical MRSA isolates collected from six hospitals in northeast China between 2009 and 2010 were tested. The results obtained by CGE/MLVF against clinical isolates were compared with traditional MLVF, spa typing, Multilocus sequence typing/ staphylococcal cassette chromosome mec (MLST/SCCmec) and pulse field gel electrophoresis (PFGE). The discriminatory power estimated by Simpson's index of diversity was 0.855 (28 types), 0.855 (28 patterns), 0.623 (11 types), 0.517 (8 types) and 0.854 (28 patterns) for CGE/MLVF, traditional MLVF, spa typing, MLST/SCCmec and PFGE, respectively. All methods tested showed a satisfied concordance in clonal complex level calculated by adjusted Rand's coefficient. CGE/MLVF showed better reproducibility and accuracy than traditional MLVF and PFGE methods. In addition, the CGE/MLVF has potential to produce portable results. In conclusion, CGE/MLVF is a rapid and easy to use MRSA typing method with lower cost, good reproducibility and high discriminatory power for monitoring the outbreak and clonal spread of MRSA isolates.

Fine typing of methicillin-resistant Staphylococcus aureus isolates using direct repeat unit and staphylococcal interspersed repeat unit typing methods

BACKGROUND/PURPOSE

Methicillin-resistant Staphylococcus aureus (MRSA) typing is an important epidemiologic tool for monitoring trends and preventing outbreaks. However, the efficiency of various MRSA typing methods for each SCCmec MRSA isolate is rarely evaluated.

MATERIALS AND METHODS

A total of 157 MRSA isolates from four different regions in Taiwan were typed with five different molecular methods, including SCCmec typing, multilocus sequence typing (MLST), spa typing, mec-associated direct repeat unit (dru) copy number determination, and staphylococcal interspersed repeat unit (SIRU) profiling.

RESULTS

There were four SCCmec types, eight MLST types, 15 spa types, 11 dru types, and 31 SIRU profiles. The most common type determined by each molecular typing method was SCCmec III (115 isolates, 73.2%), ST239 (99 isolates, 63.1%), t037 (107 isolates, 68.2%), 14 dru copies (76 isolates, 48.4%), and SIRU profile 3013722 (102 isolates, 65%), respectively. When using the combination of MLST, spa typing, and dru copy number, ST5-t002-4 (n = 8), ST239-t037-14 (n = 68), ST59-t437-9 (n = 9), and ST59-t437-11 (n = 6) were found to be the most common types of SCCmec types II (n = 9), III (n = 115), IV (n = 21), and VT (n = 11) isolates, respectively. SCCmec type III isolates were further classified into 11 dru types. Of the 21 SCCmec type IV isolates, 14 SIRU profiles were found. Seven SIRU patterns were observed in the 11 SCCmec type VT isolates.

CONCLUSION

Different typing methods showed a similar Hunter-Gaston discrimination index among the 157 MRSA isolates. However, dru and SIRU typing methods had a better discriminatory power for SCCmec type III and SCCmec types IV and VT isolates, respectively, suggesting that dru and SIRU can be used to further type these isolates.

A combined multi-virulence-locus sequence typing and Staphylococcal Cassette Chromosome mec typing scheme possesses enhanced discriminatory power for genotyping MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) remains a major threat to human populations worldwide. Knowing the extent of MRSA genetic diversity within a healthcare facility may provide important insights into the epidemiology of this important pathogen. MRSA isolates recovered from nasal swabs of patients entering the Intensive Care Unit of the Penn State Milton S. Hershey Medical Center, USA, from 2008 to 2009 were genotyped using Staphylococcal Cassette Chromosome mec (SCCmec), multilocus sequence typing (MLST) and a newly developed multi-virulence-locus sequence typing (MVLST) scheme. Sequence data for seven housekeeping genes (arcC, aroE, glpF, gmk, pta, tpi and yqiL) and six virulence genes (alt, essC, geh, hlgA, htrA and sdrC) were used for MLST and MVLST analyses, respectively. MLST identified 12 sequence types (STs) within the hospital isolates. One ST designated ST5 was the most common subtype (38.8%) followed by ST105 (22.4%) and ST8 (16.4%). In contrast, MVLST identified 29 STs (Virulence Types, VTs) from the same set of isolates, with VT6 (32.8%) being the predominant subtype followed by VT9 (8.9%) and VT2 (8.9%). Subsequent analysis of 25 MRSA isolates associated with an outbreak at a Pennsylvania state prison revealed all isolates were VT2 and SCCmec type IVa. These results suggest that a combination of MVLST and SCCmec typing may clarify the epidemiology of MRSA. Additional research with a more diverse set of strains and correlation with conventional epidemiologic data are needed to validate this new subtyping strategy.

Leukocidin genes lukF-P83 and lukM are associated with Taphylococcus aureus clonal complexes 151, 479 and 133 isolated from bovine udder infections in Thuringia, Germany

Staphylococcus aureus is one of the most important causal agents of bovine mastitis. Population studies on bovine Staphylococcus aureus isolates have identified considerable genetic heterogeneity among strains causing mastitis. The aim of this study was to investigate the contribution of different clonal complexes and the occurrence of virulence factors and resistance determinants within bovine Staphylococcus aureus isolates.

A total of 189 Staphylococcus aureus isolates obtained from milk samples of 34 dairy herds in the German Federal State of Thuringia were characterised by microarray technology.

The isolates were assigned to eleven different clonal complexes with CC151, CC479 and CC133 being dominant (together 80.5%). The methicillin resistance gene mecA was found in four isolates (2.1%), which belonged to CC398. Enterotoxin genes could be detected in 79.3% of analysed Staphylococcus aureus and 19 isolates (10.1%) harboured a distinct allele of the toxic shock syndrome toxin gene, tst-RF122. The most striking finding of the present study was that almost all except one isolate (151/152) belonging to CC151, CC479 and CC133 harboured the leukocidin genes lukF-P83 and lukM, whereas no further isolates from other lineages possessed these genes.

The consistent occurrence of lukF-P83/lukM in the dominating clonal complexes suggests an essential role of this leukocidin in the etiology of bovine mastitis.

From types to trees: reconstructing the spatial spread of Staphylococcus aureus based on DNA variation

Tracing the spatial spread of pathogens is a key objective of molecular infectious disease epidemiology. Accordingly, a wide range of genotyping approaches have been used to monitor the dissemination of Staphylococcus aureus strains, from localized outbreaks to global spread. We provide a critical review of available methods, revealing that molecular markers currently in use for typing S. aureus acquire changes so slowly that they monitor evolutionary change over timescales that are largely irrelevant to epidemiology. Moreover, the more variable markers frequently do not reflect the pathogen's evolutionary history and, hence, provide potentially misleading information about spread. More recent work has demonstrated that staphylococcal evolution proceeds sufficiently fast that the dynamics of S. aureus spatial spread can be elucidated at great detail on the basis of genome-wide single-nucleotide polymorphisms.

Comparison of PCR ribotyping and multilocus variable-number tandem-repeat analysis (MLVA) for improved detection of Clostridium difficile

Background

Polymerase chain reaction (PCR) ribotyping is one of the globally accepted techniques for defining epidemic clones of Clostridium difficile and tracing virulence-related strains. However, the ambiguous data generated by this technique makes it difficult to compare data attained from different laboratories; therefore, a portable technique that could supersede or supplement PCR ribotyping should be developed. The current study attempted to use a new multilocus variable-number tandem-repeat analysis (MLVA) panel to detect PCR-ribotype groups. In addition, various MLVA panels using different numbers of variable-number tandem-repeat (VNTR) loci were evaluated for their power to discriminate C. difficile clinical isolates.

Results

At first, 40 VNTR loci from the C. difficile genome were used to screen for the most suitable MLVA panel. MLVA and PCR ribotyping were implemented to identify 142 C. difficile isolates. Groupings of serial MLVA panels with different allelic diversity were compared with 47 PCR-ribotype groups. A MLVA panel using ten VNTR loci with limited allelic diversity (0.54-0.83), designated MLVA10, generated groups highly congruent (98%) with the PCR-ribotype groups. For comparison of discriminatory power, a MLVA panel using only four highly variable VNTR loci (allelic diversity: 0.94-0.96), designated MLVA4, was found to be the simplest MLVA panel that retained high discriminatory power. The MLVA10 and MLVA4 were combined and used to detect genetically closely related C. difficile strains.

Conclusions

For the epidemiological investigations of C. difficile, we recommend that MLVA10 be used in coordination with the PCR-ribotype groups to detect epidemic clones, and that the MLVA4 could be used to detect outbreak strains. MLVA10 and MLVA4 could be combined in four multiplex PCR reactions to save time and obtain distinguishable data.

First identification of methicillin-resistant Staphylococcus aureus MLST types ST5 and ST45 and SCCmec types IV and Vt by multiplex PCR during an outbreak in a respiratory care ward in central Taiwan

We used molecular typing methods to investigate an outbreak of methicillin-resistant Staphylococcus aureus (MRSA) infections in a respiratory care ward in Taiwan. From March to June 2006, the incidence of MRSA infection increased 3.75-fold. The overall carrier rates among the health care workers (HCWs) were 31.3% (total S. aureus), 16.4% (MRSA), and 14.9% (methicillin-sensitive SA, MSSA). Pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), antibiograms derived from susceptibility testing of MRSA isolates, and multiplex polymerase chain reaction (PCR) provided strong epidemiologic and microbiologic evidence that the outbreak of MRSA infections at our hospital was linked to the same PFGE pulsotype A SCCmec type II, pvl-negative, MLST ST5 strain of MRSA isolated from seven HCWs and five patients. The outbreak was controlled by application of topical fucidin ointment to the anterior nares in all colonized HCWs. Multiplex PCR combined with PFGE and MLST is a feasible method for outbreak investigations in routine clinical laboratories.

Comparison of two multilocus variable-number tandem-repeat methods and pulsed-field gel electrophoresis for differentiating highly clonal methicillin-resistant Staphylococcus aureus isolates

In the United Kingdom, EMRSA-15 and EMRSA-16 account for the majority (∼90%) of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections. Currently, the standard typing technique, pulsed-field gel electrophoresis (PFGE), is laborious and insufficient for discriminating between closely related subtypes of EMRSA-15 and -16. The objective of the present study was to compare the usefulness of multilocus variable-number tandem-repeat fingerprinting (MLVF) and multilocus variable-number tandem-repeat analysis (MLVA) with PFGE for subtyping these highly clonal MRSA lineages. A panel of 85 MRSA isolates (41 EMRSA-15, 20 EMRSA-16, and 24 MRSA isolates with diverse PFGE patterns) was investigated. In addition, a further 29 EMRSA-15s with identical PFGE patterns from two geographically linked but epidemiologically distinct outbreaks and several sporadic cases were analyzed. PFGE, MLVF, and MLVA resolved 66 (Simpson's index of diversity [SID] = 0.984), 51 (SID = 0.95), and 42 (SID = 0.881) types, respectively, among the 85 MRSA isolates. MLVF was more discriminatory than MLVA for EMRSA-15 and -16 strains, but both methods had comparable discriminatory powers for distinguishing isolates in the group containing diverse PFGE types. MLVF was comparable to PFGE for resolving the EMRSA-15s but had a lower discriminatory power for the EMRSA-16s. MLVF and MLVA resolved the 29 isolates with identical PFGE patterns into seven and six subtypes, respectively. Importantly, both assays indicated that the two geographically related outbreaks were caused by distinct subtypes of EMRSA-15. Taken together, the data suggest that both methods are suitable for identifying and tracking specific subtypes of otherwise-indistinguishable MRSA. However, due to its greater discriminatory power, MLVF would be the most suitable alternative to PFGE for hospital outbreak investigations.

Comparisons between geographically diverse samples of carried Staphylococcus aureus

Approximately one-third of the human population is asymptomatically colonized by Staphylococcus aureus. However, much of the global diversity within the carriage populations remains uncharacterized, and it is unclear to what degree the variation is geographically partitioned. We isolated 300 carriage isolates from 1,531 adults contemporaneously in four countries: France, Algeria, Moldova, and Cambodia. All strains were characterized by multilocus sequence typing. Six clonal complexes (CCs) were present in all four samples (CC30, -45, -121, -15, -5, and -8). Analyses based on the genotype frequencies revealed the French and Algerian samples to be most similar and the Cambodian sample to be most distinct. While this pattern is consistent with likely rates of human migration and geographic distance, stochastic clonal expansion also contributes to regional differences. Phylogenetic analysis revealed a highly divergent and uncharacterized genotype (ST1223) within Cambodia. This lineage is related to CC75, which has previously been observed only in remote aboriginal populations in northern Australia.