Unconventional SCCmec types and low prevalence of the Panton-Valentine Leukocidin exotoxin in South African blood culture Staphylococcus aureus surveillance isolates, 2013-2016
Abstract:Staphylococcus aureus is a healthcare-associated pathogen that can harbour multiple antimicrobial resistance determinants and express multiple virulence factors e.g. Panton-Valentine Leukocidin (PVL). Unknown staphylococcal cassette chromosome mec (SCCmec) typing patterns were previously observed among 11% (n = 52) of methicillin-resistant S. aureus (MRSA) isolates; we further investigated these as well as the proportion of PVL, encoded by lukS/F-PV, in 761 S. aureus isolates from patients with a diagnosis of … Show more
“…We observed that, in addition to β-lactam resistance, the isolates classified as t064/t1257/t6238-CC8 harbouring the SCC mec IV element also possessed genes ( aacA-aphD , dfrA , and ermC ) mediating resistance to aminoglycosides, trimethoprim and macrolides, respectively. The presence of these resistance determinants in our archived isolates support existing data [20,21] that this multi-resistant lineage is established and well adapted in the hospital environment in South Africa.…”
Staphylococcus aureus is an important human pathogen with an arsenal of virulence factors and a propensity to acquire antibiotic resistance genes. The understanding of the global epidemiology of S. aureus through the use of various typing methods is important in the detection and tracking of novel and epidemic clones in countries and regions. However, detailed information on antibiotic resistance and virulence genes of S. aureus, and its population structure is still limited in Africa. In this study, S. aureus isolates collected in South Africa (n=38) and Nigeria (n=2) from 2001-2004 were characterized using DNA microarray. The combination of spa typing and DNA microarray classified the isolates into seven spa types and three clonal complexes (CCs) i.e. t064-CC8 (n=17), t037-CC8 (n=8), t1257-CC8 (n=6), t045-CC5 (n=5), t951-CC8 (n=1), t2723-CC88 (n=1), t6238-CC8 (n=1), and untypeable-CC8 (n=1). There was excellent agreement (only two discordant results) between antibiotic susceptibility testing and the detection of the corresponding resistance genes by DNA microarray. Antibiotic and virulence gene markers were associated with specific clones. The detection of the collagen-binding adhesion (cna) gene was unique for t037-CC8-MRSA, the enterotoxin gene cluster (egc) and staphylococcal complement inhibitor (scn) gene for t045-CC5-MRSA, and the combination of genes encoding enterotoxin (entA, entB, entK, entQ) were noted with most of the CC8 isolates. The t045-CC5-MRSA clone was positive for the mercury resistance (mer) operon. DNA microarray assay provides information on antibiotic resistance and virulence gene determinants and can be a useful tool to identify gene markers of specific S. aureus clones in Africa.
“…We observed that, in addition to β-lactam resistance, the isolates classified as t064/t1257/t6238-CC8 harbouring the SCC mec IV element also possessed genes ( aacA-aphD , dfrA , and ermC ) mediating resistance to aminoglycosides, trimethoprim and macrolides, respectively. The presence of these resistance determinants in our archived isolates support existing data [20,21] that this multi-resistant lineage is established and well adapted in the hospital environment in South Africa.…”
Staphylococcus aureus is an important human pathogen with an arsenal of virulence factors and a propensity to acquire antibiotic resistance genes. The understanding of the global epidemiology of S. aureus through the use of various typing methods is important in the detection and tracking of novel and epidemic clones in countries and regions. However, detailed information on antibiotic resistance and virulence genes of S. aureus, and its population structure is still limited in Africa. In this study, S. aureus isolates collected in South Africa (n=38) and Nigeria (n=2) from 2001-2004 were characterized using DNA microarray. The combination of spa typing and DNA microarray classified the isolates into seven spa types and three clonal complexes (CCs) i.e. t064-CC8 (n=17), t037-CC8 (n=8), t1257-CC8 (n=6), t045-CC5 (n=5), t951-CC8 (n=1), t2723-CC88 (n=1), t6238-CC8 (n=1), and untypeable-CC8 (n=1). There was excellent agreement (only two discordant results) between antibiotic susceptibility testing and the detection of the corresponding resistance genes by DNA microarray. Antibiotic and virulence gene markers were associated with specific clones. The detection of the collagen-binding adhesion (cna) gene was unique for t037-CC8-MRSA, the enterotoxin gene cluster (egc) and staphylococcal complement inhibitor (scn) gene for t045-CC5-MRSA, and the combination of genes encoding enterotoxin (entA, entB, entK, entQ) were noted with most of the CC8 isolates. The t045-CC5-MRSA clone was positive for the mercury resistance (mer) operon. DNA microarray assay provides information on antibiotic resistance and virulence gene determinants and can be a useful tool to identify gene markers of specific S. aureus clones in Africa.
“…A number of unknown types was noted from 2010 to 2017. We subsequently further investigated a proportion ( n = 52) of the unknown types from 2013 to 2016 and found that the majority of the isolates were interpreted as type I-like, type II-like and type III-like [ 30 ]. Fig.…”
Background
The prevalence of Staphylococcus aureus varies depending on the healthcare facility, region and country. To understand its genetic diversity, transmission, dissemination, epidemiology and evolution in a particular geographical location, it is important to understand the similarities and variations in the population being studied. This can be achieved by using various molecular characterisation techniques. This study aimed to provide detailed molecular characterisation of South African mecA-positive S. aureus blood culture isolates by describing the SCCmec types, spa types and to lesser extent, the sequence types obtained from two consecutive national surveillance studies.
Methods
S. aureus blood culture isolates from a national laboratory-based and enhanced surveillance programme were identified and antimicrobial susceptibility testing was performed using automated systems. A real-time PCR assay confirmed the presence of the methicillin-resistance determinant, mecA. Conventional PCR assays were used to identify the SCCmec type and spa type, which was subsequently analysed using the Ridom StaphType™ software. Multilocus sequence typing was performed on selected isolates using conventional methods. MRSA clones were defined by their sequence type (ST), SCCmec type and spa type.
Results
A detailed description of findings is reported in this manuscript. SCCmec type III predominated overall followed by type IV. A total of 71 different spa types and 24 novel spa types were observed. Spa type t037 was the most common and predominated throughout followed by t1257. Isolates were multidrug resistant; isolates belonging to all SCCmec types were resistant to most of the antibiotics with the exception of type I; isolates with spa type t045 showed resistance to all antibiotics except vancomycin. The most diverse SCCmec-spa type complex was composed of the SCCmec type IV element and 53 different spa types.
Conclusion
Although ST data was limited, thereby limiting the number of clones that could be identified, the circulating clones were relatively diverse.
“…In another study, Singh-Moodley et al have characterized MRSA isolates from blood cultures from 2013 to 2016 in South Africa, and reported pvl positivity rate to be 25% [39]. PVL-MRSA has been also linked to nosocomial infections in which hospital transmission of CA-MRSA had occurred in the US [40], highlighting the important source of CA-MRSA as a public health threat in hospitals.…”
Objective
Panton-Valentine leukocidin (PVL)-positive methicillin-resistant Staphylococcus aureus (MRSA) is a healthcare problem worldwide. There are no reports on the virulence characteristics of MRSA in Northern Cyprus (NC). This study aimed to determine the presence of pvl among MRSA isolates from patients admitted to a university hospital in NC using molecular methods. Fifty S. aureus strains were included in this study. BD Phoenix automated identification system was used for bacterial identification and antibiotic susceptibility testing. Methicillin resistance was confirmed by disc diffusion assay. Presence of nuc and mecA genes was tested by multiplex PCR. Detection of pvl gene was performed by single-target PCR.
Results
Out of 50 S. aureus isolates identified as MRSA by BD Phoenix system, 3 were susceptible to cefoxitin with disc diffusion assay and were confirmed as methicillin-sensitive S. aureus (MSSA). All isolates (n = 50, 100%) tested positive for the presence nuc gene and 68% (n = 34/50) were mecA positive. pvl was detected in 27.7% (n = 13/47) of the MRSA isolates. Among PVL-positive MRSA isolates, 69.2% (9/13) were inpatients. PVL-MRSA was more common in isolates from deep tracheal aspirate (30.8%, 4/13) and abscess/wound (23.1%, 3/13). This represents the first study of PVL presence among MRSA in hospital setting in NC.
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