Adapting spa typing for national laboratory-based surveillance of methicillin-resistant Staphylococcus aureus

Whole genome sequencing reveals new links between spa t172/CC59 methicillin-resistant Staphylococcus aureus cases in low-endemicity region of Southwest Finland, 2007‒2016

Methicillin-resistant Staphylococcus aureus (MRSA) rates have remained relatively low in Finland. In Southwest Finland, however, annual MRSA incidence increased from 12 to 25/100,000 between 2007 and 2016 with spa t172 strain causing one fourth (237/983) of all cases. This provoked us to study the molecular epidemiology of t172-MRSA, aiming to better understand the transmission of this strain type. We combined epidemiological data and whole genome sequencing (WGS) of a set of 64 (27%, 64/237) t172-MRSA isolates covering 10 years. Isolates represented sporadic and index cases of all identified healthcare-associated outbreaks (HAOs) and family clusters (FCs). Among the included 62 isolates, core-genome MLST analysis revealed eight genomic clusters comprising 24 (38.7%) isolates and 38 (61.3%) non-clustered isolates. Cluster 1 comprised ten and the remaining seven clusters two isolates each, respectively. Two epidemiologically distinct HAOs were linked in cluster 1. FCs were involved in all clusters. All strains were associated with epidemic clonal complex CC59. We were able to confirm the spread of several successful t172-MRSA subclones in regional healthcare and the community. WGS complemented routine surveillance by revealing undetected links between t172-MRSA cases. Targeted, WGS-based typing could enhance MRSA surveillance without the need for routine WGS diagnostics.

Increasing Incidences and Clonal Diversity of Methicillin-Resistant Staphylococcus aureus in the Nordic Countries - Results From the Nordic MRSA Surveillance

Methicillin-resistant Staphylococcus aureus (MRSA) is notifiable in Denmark, Finland, Iceland, Norway and Sweden. The prevalence of MRSA in this region has been low for many years, but all five countries experience increasing numbers of new cases. The aim of the study was to describe the molecular epidemiology in the Nordic countries 2009-2016. Numbers of new cases of MRSA from 1997 to 2016 were compared, and a database containing information on spa-type and place of residence or acquisition, for all new MRSA isolates from 2009 to 2016 was established. A website was developed to visualize the geographic distribution of the spa-types. The incidence of new MRSA cases increased in all Nordic countries with Denmark having 61.8 new cases per 100,000 inhabitants in 2016 as the highest. The number of new cases 2009 to 2016 was 60,984. spa-typing revealed a high genetic diversity, with a total of 2,344 different spa-types identified. The majority of these spa-types (N = 2,017) were found in 1-10 cases. The most common spa-types t127/CC1, t223/CC22, and t304/CC6:8 increased significantly in all Nordic countries during the study period, except for Iceland, while spa-type t002/CC5 decreased in the same four countries. The trends of other common spa-types were different in each of the Nordic countries. The Nordic countries were shown to share similar trends but also to have country-specific characteristics in their MRSA populations. A continued increasing numbers of MRSA will challenge the surveillance economically. A more selected molecular surveillance will probably have to be employed in the future.

Virulence Determinants Are Required for Brain Abscess Formation Through Staphylococcus aureus Infection and Are Potential Targets of Antivirulence Factor Therapy

Bacterial brain abscesses (BAs) are difficult to treat with conventional antibiotics. Thus, the development of alternative therapeutic strategies for BAs is of high priority. Identifying the virulence determinants that contribute to BA formation induced by Staphylococcus aureus would improve the effectiveness of interventions for this disease. In this study, RT-qPCR was performed to compare the expression levels of 42 putative virulence determinants of S. aureus strains Newman and XQ during murine BA formation, ear colonization, and bacteremia. The alterations in the expression levels of 23 genes were further confirmed through specific TaqMan RT-qPCR. Eleven S. aureus genes that persistently upregulated expression levels during BA infection were identified, and their functions in BA formation were confirmed through isogenic mutant experiments. Bacterial loads and BA volumes in mice infected with isdA, isdC, lgt, hla, or spa deletion mutants and the hla/spa double mutant strain were lower than those in mice infected with the wild-type Newman strain. The therapeutic application of monoclonal antibodies against Hla and SpA decreased bacterial loads and BA volume in mice infected with Newman. This study provides insights into the virulence determinants that contribute to staphylococcal BA formation and a paradigm for antivirulence factor therapy against S. aureus infections.

Molecular characterization of methicillin-resistant Staphylococcus aureus strains by spa typing and pulsed field gel electrophoresis methods

BACKGROUND

Rapid detection of sources and transmission routes by molecular methods provides key data for risk management of methicillin-resistant Staphylococcus aureus-induced infections acquired in both the community and hospitals. This study aimed to determine the clonal relationship of methicillin-resistant S. aureus strains isolated from our hospital by pulsed-field gel electrophoresis (PFGE) and Staphylococcal protein A (spa) typing methods and to identify the predominant clones in Cukurova Region, Turkey.

RESULTS

All isolates analyzed by PFGE were distributed among 11 clusters. Clusters A (n = 19) and B (n = 27) were 84.1% similar and accounted for 61% of all samples. All isolates were distributed among 18 spa types, with the most common type being t030 with 31 isolates (41.3%), followed by t223 with nine isolates (12%) and t127 with seven isolates (9.3%).

CONCLUSIONS

We found that t030 was the most common spa type in the area where the study was conducted, as also previously shown in studies undertaken in Turkey. However, the rate of t030 in our study was below the rates reported in the literature. We also detected some rare or sporadic spa types like t127, which has not been previously defined in our country. We consider that the spa typing and PFGE methods are useful for research on clonal relations in monitoring the changing prevalent clones in specific regions.

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.

Combined interventions are effective in MRSA control

BACKGROUND

A large healthcare-associated epidemic mainly caused by one methicillin-resistant Staphylococcus aureus (MRSA) strain broke out in Pirkanmaa County, Finland, in 2001. This study describes the impact of infection control and screening practices on the epidemic.

METHODS

The number of hospital-acquired (HA)-MRSA findings obtained from clinical and screening samples during the epidemic was calculated. Strains were typed by pulsed-field electrophoresis (PFGE) or spa typing. Strain type distribution was studied in relation to sample type, year of the epidemic and site of transmission. Several infection control interventions were launched stepwise and screening protocols were expanded.

RESULTS

A total of 4118 cases were identified during 2001-2014, of which 3527 were classified as HA. One strain (spa t067) dominated in the epidemic. HA-MRSA cases decreased constantly from the year 2011. The number of new HA-MRSA cases was 57% less in the year 2014 (n = 171) as compared with the year 2011 (n = 399). The proportion of the epidemic strain declined significantly over the years. Screening samples comprised 71% (2439/3527) and clinical samples 29% (1034/3527) of HA-MRSA findings. The number of HA-MRSA cases found from clinical samples started to decrease when screening was expanded. An increase in hand-rub consumption was associated with a decrease in transmissions in Tampere University Hospital (TAUH).

CONCLUSION

Implementation of universal screening together with several other interventions is effective in containing an MRSA epidemic. The proportion of other than Pirkanmaa epidemic (PE)-MRSA strain findings increased throughout the period, indicating the changing epidemiology of MRSA.

Evaluation of repetitive element polymerase chain reaction for surveillance of methicillin-resistant Staphylococcus aureus at a large academic medical center and community hospitals

Repetitive element polymerase chain reaction (rep-PCR) typing has been used for methicillin-resistant Staphylococcus aureus (MRSA) strain characterization. The goal of this study was to determine if a rapid commercial rep-PCR system, DiversiLab™ (DL; bioMérieux, Durham, NC, USA), could be used for MRSA surveillance at a large medical center and community hospitals. A total of 1286 MRSA isolates genotyped by the DL system were distributed into 84 distinct rep-PCR patterns: 737/1286 (57%) were clustered into 6 major rep-PCR patterns. A subset of 220 isolates was further typed by pulsed-field gel electrophoresis (PFGE), spa typing, and SCCmec typing. The 220 isolates were distributed into 80 rep-PCR patterns, 94 PFGE pulsotypes, 27 spa, and 3 SCCmec types. The DL rep-PCR system is sufficient for surveillance, but the DL system alone cannot be used to compare data to other institutions until a standardized nomenclature is established and the DL MRSA reference library is expanded.

Utility and limitations of Spa-typing in understanding the epidemiology of Staphylococcus aureus bacteraemia isolates in a single University Hospital

Background

Staphylococcus aureus (SA) is a recognized cause of nosocomial infections with 8,767 SA bacteraemia (SAB) cases reported in England only in 2012. Different typing methods have been developed but they are not generally performed as a routine investigation in hospital laboratories.

Findings

We collected epidemiological data and spa-typed all SAB isolates over a 12 months period. Spa-typing was useful to detect two potential outbreaks of methicillin-sensitive SA (MSSA). In addition, the analysis of spa-types from individuals with multiple bacteriaemias helped to distinguish between relapse and re-infection.

Conclusions

Spa-typing could be used as a rapid tool to understand the epidemiology of SAB, in particular the detection of hospital clusters and to distinguish relapse from re-infection, but clinicians should be aware of its possible limitations.

Methicillin-resistant Staphylococcus aureus epidemic restricted to one health district in Finland: a population-based descriptive study in Pirkanmaa, Finland, years 2001-2011

BACKGROUND

The incidence of methicillin-resistant Staphylococcus aureus (MRSA) has been low in the Scandinavian countries, including Finland.

METHODS

We report a population-based, prospective survey of an exceptionally large ongoing MRSA epidemic in a Finnish health district (HD), Pirkanmaa HD, during 2001-2011 caused by 1 strain, spa t067 (FIN-16).

RESULTS

The first FIN-16 case in the HD was identified in 2000. Ten years later, 2447 carriers had been found in 95 different institutions. MRSA in carriers was mostly health care-associated (98%). The epidemic emerged in long-term care facilities and gradually spread to acute hospitals. The majority of carriers were elderly people (median age 78 y). Fifty-two percent of new carriers had an infection with MRSA at the time of detection.

CONCLUSIONS

The incidence of MRSA in Pirkanmaa HD is substantially higher than the incidence for all of Finland. Temporary projects to control MRSA have not proved sufficient to contain this large epidemic.

High throughput multiple locus variable number of tandem repeat analysis (MLVA) of Staphylococcus aureus from human, animal and food sources

Staphylococcus aureus is a major human pathogen, a relevant pathogen in veterinary medicine, and a major cause of food poisoning. Epidemiological investigation tools are needed to establish surveillance of S. aureus strains in humans, animals and food. In this study, we investigated 145 S. aureus isolates recovered from various animal species, disease conditions, food products and food poisoning events. Multiple Locus Variable Number of Tandem Repeat (VNTR) analysis (MLVA), known to be highly efficient for the genotyping of human S. aureus isolates, was used and shown to be equally well suited for the typing of animal S. aureus isolates. MLVA was improved by using sixteen VNTR loci amplified in two multiplex PCRs and analyzed by capillary electrophoresis ensuring a high throughput and high discriminatory power. The isolates were assigned to twelve known clonal complexes (CCs) and –a few singletons. Half of the test collection belonged to four CCs (CC9, CC97, CC133, CC398) previously described as mostly associated with animals. The remaining eight CCs (CC1, CC5, CC8, CC15, CC25, CC30, CC45, CC51), representing 46% of the animal isolates, are common in humans. Interestingly, isolates responsible for food poisoning show a CC distribution signature typical of human isolates and strikingly different from animal isolates, suggesting a predominantly human origin.

Identification of predominant SNPs as a novel method for genotyping bovine Staphylococcus aureus isolates

Staphylococcus aureus is a formidable pathogen of both human and animal. Infection often gives rise to an economic loss resulting from the extended cost of treatment and hospitalization for humans, and loss of usable agriculture animal products from infected animals and treatment regiments. We describe here a protocol for the amplification and sequencing of predominant single nucleotide polymorphisms within the promoter region of hla (encoding α-toxin) that confers a hyper-producing α-toxin phenotype to S. aureus isolates associated with chronic and severe bovine mastitis infections. We validated our findings with a second round of analysis, confirming the SNPs as a valid genotypic marker for α-toxin hyper-producing bovine isolates. The identification of highly virulent isolates will allow for aggressive treatment of the infection and limit the disease and economic impact. With readily available reagents and facilities, this protocol can be completed in as little as 72 h once samples are isolated.