Diversity of staphylocoagulase and identification of novel variants of staphylocoagulase gene in Staphylococcus aureus

Clonal Diversity and Molecular Characteristics of Methicillin-Susceptible and -Resistant Staphylococcus aureus from Pediatric Patients in Myanmar

The spread of multidrug-resistant and virulent Staphylococcus aureus among children is a public health concern, but the actual conditions in Myanmar have not been characterized. In this study, a total of 244 clinical isolates of S. aureus collected from pediatric patients in Yangon Children's Hospital during a 1-year period were analyzed for their drug resistance and genetic features. Methicillin-resistant S. aureus (MRSA) accounted for 19.7% of isolates associated with staphylococcal cassette chromosome mec (SCCmec) type III, IV, or V. Panton-Valentine leukocidin (PVL) genes were detected in 61.5% of all isolates, with a significantly higher prevalence in methicillin-susceptible S. aureus (MSSA; 67.9%) than in MRSA (35.4%) isolates. Sequence type (ST) 239/SCCmec-III was the most common MRSA clone lacking PVL genes, while PVL-positive MRSA belonged to mostly ST361/SCCmec-V and ST772/SCCmec-V. Among MSSA isolates, ST121, ST2990, ST88, and ST1930 were dominant, harboring mostly PVL genes. ST239 MRSA isolates exhibited the highest resistance rates to antimicrobials, and quinolone resistance was found in the dominant MRSA clones (ST239, ST361, and ST772) and some MSSA lineages. The present study revealed the prevalence and clonal diversity of MRSA/MSSA in children in Myanmar in relation to drug resistance and virulence determinants.

Distribution of Virulence Factors and Resistance Determinants in Three Genotypes of Staphylococcus argenteus Clinical Isolates in Japan

Staphylococcus argenteus, a novel staphylococcal species independent of S. aureus, causes a wide spectrum of infectious diseases. As detection of this species from humans and animals has been increasingly reported worldwide, its growing virulence and drug resistance via external genetic determinants has become concerning. In this study, the prevalence and genetic characteristics of virulence factors and drug resistance determinants were investigated for 82 S. argenteus clinical isolates in Hokkaido, Japan, for a one-year period starting in August 2019. These S. argenteus isolates corresponded to 0.66% of the total number of S. aureus isolates collected in the same period. The most prevalent genotype was sequence type (ST) 2250 and staphylocoagulase (coa) genotype XId (45.1%, n = 37), followed by ST1223-coa XV (30.5%, n = 25) and ST2198-coa XIV (24.4%, n = 20). Panton-Valentine leukocidin genes (lukS-PV-lukF-PV) were identified in a single ST2250 isolate. Only ST1223 isolates had the enterotoxin gene cluster (egc-2), seb, and selw (detection rate; 100%, 60%, and 84%, respectively), while sec, sey, sel26-sel27, tst-1 were only detected in ST2250 isolates (detection rate; 10.8%, 100%, 67.6%, and 10.8%, respectively). ST2198 isolates harbored selx at a significantly higher rate (60%) than isolates of other STs. Although most of S. argenteus isolates were susceptible to antimicrobials examined, ST2198 showed higher resistance rates to penicillin, macrolides, and aminoglycosides than other STs, and it harbored various resistance genes such as blaZ, erm(C), msr(A), lnuA, and aac(6′)-Ie-aph(2″)-Ia. Only one ST2250 isolate possessed SCCmec-IVc, showing resistance to oxacillin. blaZ was the most prevalent determinant of resistance in the three STs and belonged to two plasmid groups and a chromosomal group, suggesting its diverse origin. lnu(A) in ST2198 isolates was assigned to a major cluster with various staphylococcal species. The present study indicates that the prevalence of virulence factors and drug resistance profile/determinants differ depending on the lineage (ST) of S. argenteus.

Heterogeneity of Molecular Characteristics among Staphylococcus argenteus Clinical Isolates (ST2250, ST2793, ST1223, and ST2198) in Northern Taiwan

Staphylococcus argenteus is an emerging pathogen that is recognized as non-pigmented Staphylococcus aureus. However, the molecular characteristics of S. argenteus and its virulence factors have not been well studied. The present study analyzed 96 isolates of S. argenteus recovered from blood. Identification of S. argenteus was based on results of MALDI-TOF MS and lacking crtM gene. All 96 isolates were methicillin-susceptible. Multilocus sequence typing (MLST) revealed four sequence types: ST2250 (n = 72), ST2793 (n = 12), ST1223 (n = 10), and ST2198 (n = 2). All 72 ST2250 isolates harbored CRISPR loci with polymorphism of direct repeats and spacers, but no other STs carried CRISPR loci. To date, ST2793 isolates have rarely been reported in other countries. Collagen-binding adhesin gene (cna) and staphylococcal enterotoxin type C (sec) were detected in 12 (100%) and 8 (67%) ST2793 isolates, respectively. ST1223 has been reported as food poisoning pathogens, and enterotoxin gene clusters (egc) were detected in all 10 isolates, while seb gene was detected in three isolates. Two ST2198 isolates carried bone sialoprotein-binding protein gene (bbp), belonging to agr type IV. Our focus on the heterogeneity of molecular characterization in four ST types of S. argenteus revealed that S. argenteus had been isolated as early as 2000. Each ST type of S. argenteus harbors particular genetic markers that may contribute to their virulence.

Molecular Characterization of Methicillin-Susceptible and -Resistant Staphylococcus aureus Harboring Panton-Valentine Leukocidin-Encoding Bacteriophages in a Tertiary Care Hospital in Myanmar

Panton-Valentine leukocidin (PVL) is a pore-forming toxin encoded by genes on bacteriophages distributed to Staphylococcus aureus, associated with its increased virulence to humans. In this study, molecular epidemiological characteristics were investigated for 239 clinical isolates of S. aureus collected in a tertiary care hospital in Yangon, Myanmar, particularly with regard to methicillin resistance and PVL genes. Methicillin-resistant S. aureus (MRSA) accounted for 13.8% (33/239) and possessed mostly types IV- and V-SCCmec, while types III- and IX-SCCmec were identified in a few isolates. PVL genes were detected in 66.7% and 28.6% in MRSA and methicillin-susceptible S. aureus (MSSA), respectively. Among PVL-positive MRSA, ST772/SCCmec-V isolates (i.e., Bengal Bay clone) were predominant (73%, 16/22), and harbored PVL gene-encoding bacteriophage ΦSa119. Furthermore, two ST8-MRSA-SCCmec-IVa isolates harbored type-I arginine catabolic mobile element and ΦSa2usa: these isolates were considered the USA300 clone first identified in Myanmar. ΦPVL was the most frequent PVL phage among MSSA (56%, 33/59), and distributed to various genotypes, with ST88 and ST121 being dominant. In contrast, ΦSa2usa and ΦSa119 were also detected in MSSA with genotypes other than ST8 or ST772, suggesting the spread of these PVL phages to MSSA. The present study revealed potentially high prevalence of PVL phages among diverse clones of MRSA and MSSA in Myanmar.

Molecular Epidemiological Characterization of Staphylococcus argenteus Clinical Isolates in Japan: Identification of Three Clones (ST1223, ST2198, and ST2550) and a Novel Staphylocoagulase Genotype XV

Staphylococcus argenteus, a novel emerging species within Staphylococcus aureus complex (SAC), has been increasingly reported worldwide. In this study, prevalence of S. argenteus among human clinical isolates, and their clonal diversity and genetic characteristics of virulence factors were investigated in Hokkaido, the northern main island of Japan. During a four-month period starting from March 2019, twenty-four S. argenteus and 4330 S. aureus isolates were recovered from clinical specimens (the ratio of S. argenteus to S. aureus :0.0055). Half of S. argenteus isolates (n = 12) belonged to MLST sequence type (ST) 2250 and its single-locus variant, with staphylocoagulase genotype (coa-) XId, while the remaining isolates were assigned to ST2198/coa-XIV (n = 6), and ST1223 with a novel coa-XV identified in this study (n = 6). All the isolates were mecA-negative, and susceptible to all the antimicrobials tested, except for an ST2198 isolate with blaZ and an ST2250 isolate with tet(L) showing resistance to ampicillin and tetracyclines, respectively. Common virulence factors in the S. argenteus isolates were staphylococcal enterotoxin (-like) genes sey, selz, sel26, and sel27 in ST2250, selx in ST2198, and enterotoxin gene cluster (egc-1: seg-sei-sem-sen-seo) in ST1223 isolates, in addition to hemolysin genes (hla, hlb, and hld) distributed universally. Elastin binding protein gene (ebpS) and MSCRAMM family adhesin SdrE gene (sdrE) detected in all the isolates showed high sequence identity among them (> 97%), while relatively lower identity to those of S. aureus (78–92%). Phylogenetically, ebpS, sdrE, selx, sey, selw, sel26, and sel27 of S. argenteus formed clusters distinct from those of S. aureus, unlike sec, selz, tst-1, and staphylokinase gene (sak). The present study revealed the prevalence of S. argenteus among clinical isolates, and presence of three distinct S. argenteus clones (ST2250; ST2198 and ST1223) harboring different virulence factors in northern Japan. ST2198 S. argenteus, a minor clone (strain BN75-like) that had been rarely reported, was first identified in Japan as human isolates.

Prevalence and Genetic Characteristics of Methicillin-Resistant Staphylococcus aureus and Coagulase-Negative Staphylococci Isolated from Oral Cavity of Healthy Children in Japan

Prevalence and genetic characteristics of methicillin-resistant Staphylococcus aureus (MRSA) and coagulase-negative staphylococci in oral cavity of healthy children were studied in Hokkaido, northern main island of Japan. From saliva of 526 children, a total of 248 staphylococcal isolates comprising S. aureus (n = 143), S. epidermidis (n = 84), S. warneri (n = 13), S. haemolyticus (n = 5), S. hominis (n = 2), and S. intermedius (n = 1) were recovered. Presence of mecA was confirmed in 6.3% of S. aureus, 50% of S. epidermidis, and 7.7% in S. warneri. SCCmec was mostly classified into type IV, and ACME (arginine catabolic mobile element)-arcA was detected in S. epidermidis (23.8%) and S. intermedius. Nine MRSA isolates belonged to staphylocoagulase gene (coa) type Ia, IIa, IIIa, VIIb/sequence type 1 (ST1), ST5, ST8, ST89, ST120, and were negative for PVL (Panton-Valentine leukocidin) genes. These isolates included two clones of emerging community-acquired MRSA (CA-MRSA) that had been described recently in Japan: ST5/SCCmec IVc, which resembles the "Pediatric clone," and ST8/SCCmec IVl belonging to coa-IIIa/agr-I with sasL gene, designated "CA-MRSA/J" clone. Various enterotoxin genes were found in all the MRSA and some methicillin-susceptible S. aureus (MSSA) isolates examined, while tst-1 was detected in four MRSA isolates. Notably, a variant of elastin-binding protein gene (ebpS-v) was identified in ST120 MRSA and ST45 MSSA isolates, and exfoliative toxin D gene (etd) was detected in an MSSA isolate. The present study revealed the presence of MRSA, including the novel CA-MRSA clones, and high prevalence of methicillin-resistant S. epidermidis in oral cavity of healthy children in Japan.

Molecular Epidemiological Characterization of Methicillin-Susceptible and -Resistant Staphylococcus aureus Isolated from Skin and Soft Tissue Infections in Bangladesh

Genetic background and molecular characteristics of Staphylococcus aureus collected from patients with skin and soft tissue infections were studied in the North-Central region of Bangladesh from 2015 to 2016. Among 430 clinical isolates, methicillin-resistant S. aureus (MRSA) accounted for 31% having SCCmec type IV (73%) and V (14%), and belonged mostly to coagulase (coa) genotypes IIa, IIIa, IVb, and XIa, while dominant coa type in methicillin-susceptible S. aureus (MSSA) was IIIa, followed by Va, IIa, and VIa. Panton-Valentine Leukocidin genes (pvl) were detected at higher rate in MSSA (54%) than in MRSA (24%). Based on multilocus sequence typing, pvl-positive MRSA isolates were classified into clonal complex 88 (CC88) (ST88, ST2884, ST4345), CC6 (ST6, ST4350), and CC1 (ST1, ST772), while pvl-negative MRSA into CC5, CC22, CC80, CC121, and CC672. The pvl-negative ST80 MRSA isolates had SCCmec-IVa (agr-III/coa-XIc, etd/edinB-positive, fusB-negative), indicating that they belong to the novel CC80 clade related to the European community-acquired MRSA clone. Among MSSA, genotypes ST121/spa-t645/coa-Va and ST2884 (CC88)/spa-t2393/coa-IIIa were identified in both pvl-positive and negative isolates, and all the ST772 isolates harbored pvl. All the ST121 isolates had a variant of elastin-binding protein gene (ebpS-v) with internal 180-nucleotide deletion. The present study suggested that CC88 (ST88, ST2884) and ST772 are the putative dominant lineages of pvl-positive MRSA/MSSA, while novel CC80 clade is one of the main pvl-negative MRSA lineages distributed endemically in Bangladesh.

Identification and functional activity of a staphylocoagulase type XI variant originating from staphylococcal food poisoning isolates

Staphylocoagulase, an extracellular protein secreted by Staphylococcus aureus, has been used as an epidemiological marker. At least 12 serotypes and 24 genotypes subdivided on the basis of nucleotide sequence have been reported to date. In this study, we identified a novel staphylocoagulase nucleotide sequence, coa310, from staphylococcal food poisoning isolates that had the ability to coagulate plasma, but could not be typed using the conventional method. The protein encoded by coa310 contained the six fundamental conserved domains of staphylocoagulase. The full-length nucleotide sequence of coa310 shared the highest similarity (77·5%) with that of staphylocoagulase-type (SCT) XIa. The sequence of the D1 region, which would be responsible for the determination of SCT, shared the highest similarity (91·8%) with that of SCT XIa. These results suggest that coa310 is a novel variant of SCT XI. Moreover, we demonstrated that coa310 encodes a functioning coagulase, by confirming the coagulating activity of the recombinant protein expressed from coa310. This is the first study to directly demonstrate that Coa310, a putative SCT XI, has coagulating activity. These findings may be useful for the improvement of the staphylocoagulase-typing method, including serotyping and genotyping.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to identify a novel variant of staphylocoagulase type XI based on its nucleotide sequence and to demonstrate coagulating activity in the variant using a recombinant protein. Elucidation of the variety of staphylocoagulases will provide suggestions for further improvement of the staphylocoagulase-typing method and contribute to our understanding of the epidemiologic characterization of Staphylococcus aureus.

Detection of ST772 Panton-Valentine leukocidin-positive methicillin-resistant Staphylococcus aureus (Bengal Bay clone) and ST22 S. aureus isolates with a genetic variant of elastin binding protein in Nepal

Genetic characteristics were analysed for recent clinical isolates of methicillin-resistant and -susceptible Staphylococcus aureus (MRSA and MSSA respectively) in Kathmandu, Nepal. MRSA isolates harbouring Panton-Valentine leukocidin (PVL) genes were classified into ST1, ST22 and ST88 with SCCmec-IV and ST772 with SCCmec-V (Bengal Bay clone), while PVL-positive MSSA into ST22, ST30 and ST772. ST22 isolates (PVL-positive MRSA and MSSA, PVL-negative MRSA) possessed a variant of elastin binding protein gene (ebpS) with an internal deletion of 180 bp, which was similar to that reported for ST121 S. aureus previously outside Nepal. Phylogenetic analysis indicated that the ebpS variant in ST22 might have occurred independently of ST121 strains. This is the first report of ST772 PVL-positive MRSA in Nepal and detection of the deletion variant of ebpS in ST22 S. aureus.

Drug resistance and genetic characteristics of clinical isolates of staphylococci in Myanmar: high prevalence of PVL among methicillin-susceptible Staphylococcus aureus belonging to various sequence types

Prevalence, drug resistance and genetic characteristics were analysed for a total of 128 clinical isolates of staphylococci obtained from a tertiary hospital in Myanmar. The dominant species were S. aureus (39%) and S. haemolyticus (35%), followed by S. epidermidis (6%) and S. saprophyticus (5%). The majority of S. haemolyticus isolates (71.1%) harboured mecA, showing high resistance rates to ampicillin, cephalosporins, erythromycin and levofloxacin, while methicillin-resistant S. aureus (MRSA) was only 8% (four isolates) among S. aureus with type IV SCCmec. Panton-Valentine leukocidin (PVL) genes were detected in 20 isolates of S. aureus (40%), among which only one isolate was MRSA belonging to sequence type (ST) 88/agr-III/coa-IIIa, and the other 19 methicillin-susceptible S. aureus (MSSA) isolates were classified into six STs (ST88, ST121, ST1153, ST1155, ST1930, ST3206). An ST1153 MSSA isolate with PVL was revealed to belong to a novel coa type, XIIIa. ST121 S. aureus was the most common in the PVL-positive MSSA (47%, 9/19), harbouring genes of bone sialoprotein and variant of elastin binding protein as a distinctive feature. Although PVL-positive MSSA was susceptible to most of the antimicrobial agents examined, ST1930 isolates were resistant to erythromycin and levofloxacin. ST59 PVL-negative MRSA and MSSA had more resistance genes than other MRSA and PVL-positive MSSA, showing resistance to more antimicrobial agents. This study indicated higher prevalence of mecA associated with multiple drug resistance in S. haemolyticus than in S. aureus, and dissemination of PVL genes to multiple clones of MSSA, with ST121 being dominant, among hospital isolates in Myanmar.

Detection and genetic characterization of PVL-positive ST8-MRSA-IVa and exfoliative toxin D-positive European CA-MRSA-Like ST1931 (CC80) MRSA-IVa strains in Bangladesh

Severe skin lesions caused by Staphylococcus aureus infection are associated with production from bacterial cells of Panton-Valentine leukocidin (PVL), a typical virulence factor of community-acquired methicillin-resistant S. aureus (CA-MRSA), as well as other toxins represented by exfoliative toxins. Through a retrospective study of 26 S. aureus strains isolated from skin lesions of diabetic patients admitted to a hospital in Bangladesh, 2 PVL-gene-positive MRSA-IVa strains and 8 PVL-negative, exfoliative toxin D (ETD) gene (etd)-positive MRSA-IVa strains were isolated. A PVL-positive MRSA-IVa strain had a type I arginine catabolic mobile element (ACME), belonged to ST8/agr-type I/spa-type t121 (a variant of t008), and harbored blaZ, tet(K), msrA, and aph(3')-IIIa, which are mostly typical characteristics found in USA300, a predominant CA-MRSA clone in the United States. Another PVL-positive MRSA strain, belonging to ST1929 (CC88)/agr-type III/spa-type t3341, was negative for ACME, but possessed blaZ and tet(K). The etd-positive MRSA-IVa strains possessed the epidermal cell differentiation inhibitor B (EDIN-B)-encoding gene (edinB) and belonged to ST1931 (CC80)/agr-type III/spa-type t11023 (a variant of t044), which was genetic trait similar to that of the European CA-MRSA ST80 clone. However, unlike the European ST80 strains, the etd-positive MRSA strains detected in the present study harbored seb, sek, and seq, while they were negative for tet(K), aph(3')-IIIa, and fusB, showing susceptibility to fusidic acid. These findings suggested that etd-positive ST1931 MRSA strains belong to the same lineage as the European ST80 MRSA clone, evolving from a common ancestral clone via acquisition of a different pathogenicity island. This is the first report of a USA300-like MRSA-IV strain, PVL-positive ST1929 (CC88) MRSA-IV, and European ST80 CA-MRSA-like etd-positive ST1931 (CC80) MRSA-IV strains isolated in Bangladesh.

Contribution of coagulases towards Staphylococcus aureus disease and protective immunity

The bacterial pathogen Staphylococcus aureus seeds abscesses in host tissues to replicate at the center of these lesions, protected from host immune cells via a pseudocapsule. Using histochemical staining, we identified prothrombin and fibrin within abscesses and pseudocapsules. S. aureus secretes two clotting factors, coagulase (Coa) and von Willebrand factor binding protein (vWbp). We report here that Coa and vWbp together are required for the formation of abscesses. Coa and vWbp promote the non-proteolytic activation of prothrombin and cleavage of fibrinogen, reactions that are inhibited with specific antibody against each of these molecules. Coa and vWbp specific antibodies confer protection against abscess formation and S. aureus lethal bacteremia, suggesting that coagulases function as protective antigens for a staphylococcal vaccine.

Community-acquired methicillin-resistant Staphylococcus aureus: community transmission, pathogenesis, and drug resistance

Methicillin-resistant Staphylococcus aureus (MRSA) is able to persist not only in hospitals (with a high level of antimicrobial agent use) but also in the community (with a low level of antimicrobial agent use). The former is called hospital-acquired MRSA (HA-MRSA) and the latter community-acquired MRSA (CA-MRSA). It is believed MRSA clones are generated from S. aureus through insertion of the staphylococcal cassette chromosome mec (SCCmec), and outbreaks occur as they spread. Several worldwide and regional clones have been identified, and their epidemiological, clinical, and genetic characteristics have been described. CA-MRSA is likely able to survive in the community because of suitable SCCmec types (type IV or V), a clone-specific colonization/infection nature, toxin profiles (including Pantone-Valentine leucocidin, PVL), and narrow drug resistance patterns. CA-MRSA infections are generally seen in healthy children or young athletes, with unexpected cases of diseases, and also in elderly inpatients, occasionally surprising clinicians used to HA-MRSA infections. CA-MRSA spreads within families and close-contact groups or even through public transport, demonstrating transmission cores. Re-infection (including multifocal infection) frequently occurs, if the cores are not sought out and properly eradicated. Recently, attention has been given to CA-MRSA (USA300), which originated in the US, and is growing as HA-MRSA and also as a worldwide clone. CA-MRSA infection in influenza season has increasingly been noted as well. MRSA is also found in farm and companion animals, and has occasionally transferred to humans. As such, the epidemiological, clinical, and genetic behavior of CA-MRSA, a growing threat, is focused on in this study.

Genetic variation among Staphylococcus aureus strains from bovine milk and their relevance to methicillin-resistant isolates from humans

In genetic analysis of bovine Staphylococcus aureus isolates that are recognized as an important pathogenic bacterium in bovine mastitis, multilocus sequence typing (MLST) showed strong correlation to the results of pulsed-field gel electrophoresis, coa PCR-restriction fragment length polymorphism (RFLP), spa typing, and the coagulase serotyping method. According to MLST results, strains derived from sequence type 97 (ST97) and ST705 were suggested as not only dominant bovine S. aureus lineages in Japan but also pandemic bovine S. aureus lineages. Although both lineages seem to be distantly related to each other by phylogenetic analysis, both had common characteristics, i.e., lukM/lukF'-PV and coagulase serotype VI. These characteristics were very rare among minor bovine strains and human strains and may contribute to the host specificity of these lineages. Four methicillin-resistant S. aureus (MRSA) isolates were first confirmed from bovine milk in Japan; these isolates showed geno- and serotypes that were identical or similar to those of human MRSA isolates in Japan (ST5, staphylococcal cassette chromosome mec type II [SCCmec II], Spa type t002 or t375, and coagulase serotype II, and ST89, SCCmec IIIa, Spa type t5266, and coagulase serotype I). ST5 and ST89 are uncommon among bovine isolates in the world, whereas these STs are common among human MRSA isolates in Japan.

Genetic diversity of staphylocoagulase genes (coa): insight into the evolution of variable chromosomal virulence factors in Staphylococcus aureus

Background

The production of staphylocoagulase (SC) causing the plasma coagulation is one of the important characteristics of Staphylococcus aureus. Although SCs have been classified into 10 serotypes based on the differences in the antigenicity, genetic bases for their diversities and relatedness to chromosome types are poorly understood.

Methodology/Principal Findings

We compared the nucleotide sequences of 105 SC genes (coa), 59 of which were determined in this study. D1 regions, which contain prothrombin-activating and -binding domains and are presumed to be the binding site of each type-specific antiserum, were classified into twelve clusters having more than 90% nucleotide identities, resulting to create two novel SC types, XI and XII, in addition to extant 10 types. Nine of the twelve SC types were further subdivided into subtypes based on the differences of the D2 or the central regions. The phylogenetical relations of the D1 regions did not correlate exactly with either one of agr types and multilocus sequence types (STs). In addition, genetic analysis showed that recombination events have occurred in and around coa. So far tested, STs of 126 S. aureus strains correspond to the combination of SC type and agr type except for the cases of CC1 and CC8, which contained two and three different SC types, respectively.

Conclusion

The data suggested that the evolution of coa was not monophyletic in the species. Chromosomal recombination had occurred at coa and agr loci, resulting in the carriage of the combinations of allotypically different important virulence determinants in staphylococcal chromosome.