Clonal diversity and genomic characterization of Panton-valentine Leukocidin (PVL)-positive Staphylococcus aureus in Tehran, Iran

Staphylococcus aureus (S. aureus)-associated disorders vary from skin infections to life-threatening invasive diseases, such as bacteremia, sepsis, and endocarditis, mediated by a variety of virulence factors [1, 2]. S. aureus plays an important role in the development of epidural abscesses, meningitis, toxic shock syndrome (TSS), urinary tract infections (UTIs), septic thrombophlebitis, pneumonia, etc. [3, 4]. S. aureus causes invasive infections in all age groups, but the prevalence of these infections is somewhat higher in infants and patients over 65 years of age [3]. Panton-Valentine Leukocidin (PVL) is a two-component toxin produced by some S. aureus strains in varying amounts [5, 6]. However, the majority of isolates that cause skin and soft tissue infections (SSTI) and severe necrotizing pneumonia are PVL-positive [7]. This preforming toxin is encoded by a 1.9-kb lukSF-PV locus consisting of two contiguous, but co-transcribed lukF and lukS genes [8]. It is well documented that these two components are secreted by S. aureus strains, and before they assemble into a pore-forming heptamer on neutrophil membranes, they could induce lysis of host defense cells, including human polymorphonuclear neutrophils (PMNs), monocytes, and macrophages [9, 10]. PVL causes apoptosis in neutrophils through the activation of caspase-3 and -9; the participation of TLR2 (toll like receptor 2) in causing inflammation by PVL in the lung has also been reported [4].

Generally, phages are considered as one of the major mobile genetic elements (MGEs) among S. aureus strains, which are strongly able to transfer antibiotic resistance markers and virulence attributes [11, 12]. The genes encoding PVL are also located on lysogenized bacteriophages integrated into the chromosomal content of S. aureus [9]. Currently, these phages are classified into the order Caudovirales, which could be divided into three major families based on the tail morphology, including Podoviridae, Siphoviridae, and Myoviridae [8]. To date, at least 10 PVL phages belonging to the Siphoviridae family have been identified and sequenced, including 108PVL, PVL, tp310–1, SLT, Sa2958, Sa2MW, Sa2usa, 7247PVL/ST5967PVL, TCH60, and Sa119 PVL [13‐17]. They are characterized as double-stranded, non-enveloped DNA viruses with an icosahedral head and a long non-contractile tail [5, 12].

The emergence of PVL-positive methicillin-resistant S. aureus (PVL-MRSA) isolates have been reported worldwide [18]. Previous studies have revealed a strongassociation between the presence of PVL genes and community-associated MRSA (CA-MRSA) strains, especially those carrying staphylococcal cassette chromosomemec (SCCmec) types IV [19]. Moreover, hospital-acquired MRSA (HA-MRSA) strains that carry PVL genes have been reported in various geographical regions inEurope and Asia [9, 19, 20]. Generally, infections caused by PVL-positive methicillin-sensitive S. aureus (PVL-MSSA) strains have been reported to play the role ofreservoirs for PVL-MRSA due to clonality and evolutionary relationships [21].

Some studies have shown an association between PVL genes and invasive diseases, implying that PVL is an epidemiological marker for severe infection syndrome; also, individuals with PVL-positive skin and soft-tissue infections are more likely to require surgery compared to those with PVL-negative infection. In some countries, this notion has led to the implementation of public health measures for individuals infected with PVL-producing strains. Compared with PVL-negative S. aureus, PVL-positive S. aureus strains are more likely to be truly community-acquired, infecting individuals who have not had contact with healthcare settings [10]. However, the potential risk of spreading PVL-positive S. aureus strains to hospitals is considered as a significant public health concern, as the establishment of a PVL-positive clonal lineage of HA-MRSA strains could rapidly lead to dramatically worse outcomes for HA-MRSA patients. However, there are clonal lineages from which HA-MRSA and CA-MRSA have been reported [5].

To date, at least 22 single-nucleotide polymorphisms (SNPs) have been identified in the lukSF-PV genes based on phylogenetic analysis [8, 13, 22]. Additionally, a number of non-synonymous mutations have been detected in different isoforms of PVL protein. PVL-positive S. aureus strains could be classified into four major haplotype groups (R, H1, H2, H3) based on non-synonymous variations in the PVL sequence at nucleotide positions 527, 663, and 1396 [22, 23].

The population structure and clones of MRSA strains are changing in different healthcare facilities in different countries. The most prevalent PVL-MRSA types in the United States belong to ST8 (USA300), ST1 (USA400), ST59 (USA1000), and ST30 (USA1100), while ST80 clone is commonly reported in European countries [24]. Furthermore, several clones belonging to ST80, ST30, ST59, and ST22 have been reported as the most frequent clones in Asia [24‐26]. Previous studies in Iran have reported ST22, ST30, ST8, ST931, ST722, ST15, ST88, ST239, ST291, and ST585 as the predominant clones among MRSA strains [27‐29]

Currently, there is very limited data on the molecular epidemiology of PVL-encoding S. aureus clinical strains in Iran. In addition, no details have yet been reported about PVL haplotype groups of S. aureus strains in Iran. The present study aimed to obtain a more complete description about the molecular epidemiology and genetic background of PVL-positive S. aureus clinical strains isolated from Iranian patients using a combination of molecular typing techniques, including SCCmec and accessory gene regulator (agr) typing, PVL haplotyping, multilocus sequence typing (MLST) analysis, and pulsed-field gel electrophoresis (PFGE). The antibiotic susceptibility of the strains was also determined.

MALDI-TOF MS-based DOT-MGA is also able to perform antimicrobial susceptibility testing within few hours, through specific novel peaks, but is applicable to only some MRSA strains [43]. Therefore, MRSA strains were detected and confirmed by targeting the mecA gene responsible for resistance in staphylococci species, located on mobile genetic element called SCCmec.

Little information is available about the predominant STs, CCs, and particularly haplotype groups of PVL-positive S. aureus strains in Iran. In the current study, attempts were made to raise awareness about the molecular relatedness and epidemiology of PVL-positive S. aureus strains among Iranian patients by applying a number of molecular typing techniques in this setting. In this study, the majority of the isolates (67.85%) were detected to be PVL-positive MRSA. This result is consistent with several previous reports with respect to high prevalence of PVL-positive strains recovered from CA-MRSA [44, 45]. Also, previous studies in Iran have reported a high prevalence of PVL-positive strains among MRSA isolates, ranging from 12 to 60% [27, 28, 40, 42, 46].

Epidemiological studies have revealed that PVL gene is commonly carried by CA-MRSA having SCC mec type IV [47]. The majority of MRSA strains in the current (50%) and previous studies in Iran carried SCCmec IV [30, 34, 36, 38, 41, 46, 48], supporting the hypothesize that SCCmec IV is probably more mobile than other SCCmec types. This hypothesis is further supported by the fact that most public health-associated MRSA infections reported in Iran are caused by casual transmission of CA-MRSA strains. Although PVL gene is more frequently found in CA-MRSA strains, there are some reports of PVL gene recovered from HA-MRSA strains, but with a relatively lower prevalence [31, 37]. In this study, 17.9% of PVL-positive isolates were HA-MRSA. The presence of PVL gene among HA-MRSA strains and the interhospital spread of PVL encoding HA-MRSA strains support the need for system-wide implementation of patient safety and infection control initiatives.

Furthermore, PVL is carried by MSSA strains; thus, they share similar disease potential and epidemiological features with MRSA [49]. Based on most previous reports in Iran, the prevalence of PVL-positive MRSA strains is relatively higher than that of PVL-positive MSSA strains [38, 41, 50], in contrast to some European and UK countries where PVL-encoding MSSA strains are more common than PVL-positive MRSA strains [51, 52]. In agreement with most previous studies in Iran, about one third of the isolates (32.1%) were found to be PVL-positive MSSA in this study [42, 53]. However, in our previous study [54] and the study by Havaei et al. (2017) [55], the prevalence of PVL gene in MSSA strains was higher than in MRSA strains. Therefore, further in-depth studies are required to better understand the probable transfer and mobility of PVL gene among MSSA and MRSA clones.

PVL gene is highly conserved with four major variants (H1, H2, H3, R) identified based on the sequence variations at positions 527, 663, and 1396 [23]. H1 and H2 haplotype groups are more common in India and South Africa, whereas R variants are frequently found in the United States [23]. H variant (particularly the H2 group) has a broader geographical distribution and spreads within several CCs such as CC22, CC30, CC1, CC5, CC8, and CC121 [23, 55]. In this study, 53.6% of the isolates carried H2 variants, which were distributed among five CCs (CC22, CC30, CC1, and CC5). Moreover, 32.1% of R variants were allocated to three CCs including CC22, CC30, and CC8. There is very limited data about haplotype groups of S. aureus strains in Iran. In a recent study by Havaei et al. (2017), 56.6% of S. aureus isolates had H variants, and 43.3% carried R variants [55]. Their study revealed that both R and H variants were detected among S. aureus strains in Iran, consistent with the present study which showed that the mecA gene was present in 52.6% of the strains belonging to H variants. Additionally, some studies have reported that PVL-positive MRSA strains mainly belong to R variants, and only 5% of strains in H variants are mecA-positive [56]. In contrast, this may indicate controversial reports from different geographical locations.

It has been reported that PVL-positive MSSA and MRSA strains belong to diverse clones worldwide [49]. Although different clones were identified in this study, CC30 (31.6%) and CC22 (21%) were the predominant clones and PVL-positive S. aureus strains belonged to five CCs (CC30, CC22, CC8, CC1, CC5). The established four dominant MRSA clones consisted of CC30, CC22, CC1 and CC80. Two and three different SCCmec types were found in CC22 (III, IV) and CC30 (III, IV, V), respectively, and the majority of the strains (60%) in CC22 carried SCCmec type III. Moreover, most PVL-positive CA-MRSA strains belonged to CC30, whereas most PVL-positive HA-MRSA strains belonged to CC22. As previously reported, CC8, CC22, and CC30 are the dominant clones in Iran [28, 30, 42]. PVL-positive MRSA strains belonging to CC30 have been isolated in America, Europe, Asia, and the Southwest Pacific [57‐59], while PVL-positive MRSA strains belonging to CC22 have been reported in England, Saudi Arabia, Germany, Ireland, Australia, and Nepal [58, 60, 61]. However, both CC22 and CC30 clones have been reported to be predominant in Asian countries [58, 62]. Based on the previous reports and also this study, it could be concluded that the most prevalent CA-MRSA clones in Asian countries including Iran are CC22 and CC30 clones [63, 64]. The predominance of CC22 and CC30 clones among PVL-positive MRSA strains in Iran is of great concern, as these clones appear to be highly transmissible with a propensity to spread worldwide. In the present study, 10.7% of S. aureus strains were related to CC8, and only one of them had SCCmec IV and was assigned to H2 variant. PVL-positive MRSA strains with CC8 and SCCmec IV have been previously reported in Iran [65]. CC8 is one of the most prevalent CCs worldwide and mainly contains nosocomial epidemic MRSA isolates [66]. The highest antibiotic resistance was observed in one PVL-positive HA-MRSA strain belonging to CC8. ST8 SCCmec type IV (USA300 clone) is the predominant clone in the United States but has also been reported in other countries including Anglophone, Pakistan, UK, and some of the Gulf States countries [67]. CC1 was another CC that was detected among PVL-positive strains in this study, accounting for 66.7% of R variant. According to the previous studies results, R variant of PVL is mainly found in CC1, CC8, and CC93 strains [68]. The present study results showed that R variant was harbored by 100% of PVL-positive MRSA strains primarily belonging to CC30, followed by CC1 and CC5, which were different from those CCs (CC8, CC1, and CC93) reported in previous studies [23, 55, 69]. This finding supports the findings of previous studies in Iran, in which CC30, CC22, CC8, and CC1 were detected as the predominant CCs among PVL-positive isolates [29].

In this study, the majority of the isolates (50%) belonged to agr type I. The agr locus belongs to the core variable genome and thus is linked to CCs. The agr typing results were consistent with the findings of previous studies in Iran and China [46, 47, 70]. In the current study, agr I and agr III were detected as the most common types and were linked to CC30, CC22, CC8, and CC1.

To the best of our knowledge, this is the first comprehensive study investigating the molecular epidemiology and characteristics of PVL-encoding S. aureus clinical strains in Iran using several typing methods. The findings revealed i) a high prevalence of PVL-positive MRSA strains in Iran, ii) the majority of MRSA strains in the current study carried SCCmec IV, iii) both R and H variants were detected among S. aureus strains in Iran, iv) the mecA gene was present in 52.6% of the strains with H variants, v) CC8, CC22, and CC30 were found as the dominant clones among PVL-encoding S. aureus strains, vi) agr I and agr III were detected as the most common types and were linked to CC30, CC22, CC8, and CC1. The most important limitation of the present work was the relatively small sample size, because of low prevalence of MRSA strains. Taken together, the present study results may contribute to the understanding of the molecular epidemiology and evolution of PVL-positive S. aureus in Iran.