Genetic relationship between methicillin-sensitive and methicillin-resistant Staphylococcus aureus strains from France and from international sources: delineation of genomic groups

Arana D, Monereo A, Domingo D, Cordero J, Sánchez Romero MI, García Viejo MÁ, Lora-Tamayo J, Chaves F. Genotypic and Phenotypic Characteristics of Staphylococcus aureus Prosthetic Joint Infections: Insight on the Pathogenesis and Prognosis of a Multicenter Prospective Cohort

BACKGROUND

Staphylococcus aureus is the leading cause of prosthetic joint infection (PJI). Beyond the antibiogram, little attention has been paid to the influence of deep microbiological characteristics on patient prognosis. Our aim was to investigate whether microbiological genotypic and phenotypic features have a significant influence on infection pathogenesis and patient outcome.

METHODS

A prospective multicenter study was performed, including all S. aureus PJIs (2016-2017). Clinical data and phenotypic (agr functionality, β-hemolysis, biofilm formation) and genotypic characteristics of the strains were collected. Biofilm susceptibility to antimicrobials was investigated (minimal biofilm eradication concentration [MBEC] assay).

RESULTS

Eighty-eight patients (39.8% men, age 74.7 ± 14.1 years) were included. Forty-five had early postoperative infections (EPIs), 21 had chronic infections (CPIs), and 19 had hematogenous infections (HIs). Twenty (22.7%) were caused by methicillin-resistant S. aureus. High genotypic diversity was observed, including 16 clonal complexes (CCs), with CC5 being the most frequent (30.7%). agr activity was greater in EPI than CPI (55.6% vs 28.6%; P = .041). Strains causing EPI were phenotypically and genotypically similar, regardless of symptom duration. Treatment failure (36.5%) occurred less frequently among cases treated with implant removal. In cases treated with debridement and implant retention, there were fewer failures among those who received combination therapy with rifampin. No genotypic or phenotypic characteristics predicted failure, except vancomycin minimal inhibitory concentration ≥1.5 mg/L (23.1% failure vs 3.4%; P = .044). MBEC50 was >128 mg/L for all antibiotics tested and showed no association with prognosis.

CONCLUSIONS

S. aureus with different genotypic backgrounds is capable of causing PJI, showing slight differences in clinical presentation and pathogenesis. No major microbiological characteristics were observed to influence the outcome, including MBEC.

Pulsed-field gel electrophoretic analysis and some characteristics of Staphylococcus aureus isolated from retail foods and human hands

This study investigates whether there is a predominant Staphylococcus aureus strain in retail foods and healthy human hands, and examines the relationship between pulsed-field gel electrophoresis (PFGE) banding patterns and the S. aureus characteristics of staphylococcal enterotoxin (SE) type, coagulase type, and β-lactamase activity. Ninety-four strains of S. aureus isolated from retail foods and healthy human hands were analyzed by PFGE. Several strains isolated from the same shop or a chain store showed identical patterns, indicating that the origins of these strains were identical. After excluding these strains showing identical patterns, 54 strains were used for the PFGE analysis. No spread of a particular clone in the environment surrounding the food was apparent. The PFGE analysis of these 54 strains was classified in 6 lineages (L1-L6). There was no relationship between the PFGE banding pattern and coagulase type or SE type. Eleven (84.6%) of the 13 isolates in PFGE banding pattern L5 did not produce β-lactamase, suggesting that the production of β-lactamase influenced a specific PFGE banding pattern.

Prevalent genotypes of meticillin-resistant Staphylococcus aureus: report from Pakistan

Meticillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial pathogen in Pakistan and is emerging in the community. This is one of the first reports of the prevalent genotypes of MRSA in both hospital and community settings in Pakistan. Isolates collected in 2006–2007 were characterized by PFGE, staphylococcal cassette chromosome mec (SCCmec) typing and multilocus sequence typing (MLST). PFGE identified nine pulsotypes, the majority of isolates belonging to pulsotypes A (n=70) and B (n=38), which were predominant among hospital-onset MRSA (HO-MRSA) and community-onset MRSA (CO-MRSA) isolates, respectively. Among the HO-MRSA isolates, variants of SCCmec type III were prevalent, whilst SCCmec type IV or variants were predominant in the CO-MRSA isolates. MLST identified two principal sequence types, ST8 and ST239. An association was observed between ST8, PFGE pulsotype B and SCCmec type IV in the CO-MRSA (ST8-MRSA-IV). Similarly, ST239, PFGE pulsotype A and SCCmec type III were associated with HO-MRSA (ST239-MRSA-III). Therefore, the prevalent genotypes circulating in Pakistan at the time of study were ST8-MRSA-IV and ST239-MRSA-III in the community and hospital settings, respectively. A set of HO-MRSA isolates collected in 1997 were characterized by PFGE and SCCmec typing for comparison. The isolates belonged to two PFGE pulsotypes (A, n=28; B, n=11) and contained just two SCCmec types. These results suggest that an increase in genetic diversity occurred over the period 1997–2007 as a result of either microevolution or the importation of strains from surrounding areas.

Cooccurrence of predominant Panton-Valentine leukocidin-positive sequence type (ST) 152 and multidrug-resistant ST 241 Staphylococcus aureus clones in Nigerian hospitals

Ninety-six clinical isolates of Staphylococcus aureus from Nigeria were characterized phenotypically and genetically. Twelve multidrug-resistant methicillin (meticillin)-resistant S. aureus (MRSA) isolates carrying a new staphylococcal cassette chromosome mec element and a high proportion of Panton-Valentine leukocidin (PVL)-positive methicillin-susceptible S. aureus (MSSA) isolates were observed. The cooccurrence of multidrug-resistant MRSA and PVL-positive MSSA isolates entails the risk of emergence of a multidrug-resistant PVL-positive MRSA clone.

Comparison of Austrian, Hungarian and Macedonian methicillin-resistant and methicillin-sensitive Staphylococcus aureus strains in relation to prevalence of cytotoxin genes

Cytotoxin genes in 128 Austrian (AT) MSSA, 48 MRSA, 94 Hungarian (HU) MSSA, 110 MRSA and 67 Macedonian (MK) MSSA, 81 MRSA strains were examined. The presence of alfa-haemolysin gene (hla) was more common in HU MSSA strains compared to AT and MK (99%, 86%, 72%: p<0.001). AT and MK MRSA harboured hlb genes more frequently compared to HU (60%, 62%, 33%: p<0.001). HU and MK MRSA strains carried gamma-haemolysin gene (hlg) in higher percentage in contrast to AT (88%, 83%, 69%: p=0.01). Haemolysin gamma-variant gene (hlgv) was more prevalent in HU MSSA compared to AT and MK (84%, 56%, 69%: p<0.001). Panton-Valentine leukocidin genes were found only in AT, HU, MK MSSA and MK MRSA in 2.3%, 4%, 1.5% (p=0.53) and 1% (p=0.38), respectively. The 3-gene combination pattern comprising of hla, hlg and hld genes showed increased prevalence among AT MSSA compared to HU (27%, 11%: p<0.001). The 4-gene pattern composed of hla, hlg, hlgv and hld genes was significantly characteristic for HU MRSA in contrast to AT and MK MRSA (56%, 12.5%, 27%: p<0.001). Frequency of certain cytotoxin genes and combinations differed significantly in Staphylococcus aureus strains according to geographical origin and methicillin-resistance.

Molecular typing of Staphylococcus aureus clinical isolates by pulsed-field gel electrophoresis, staphylococcal cassette chromosome mec type determination and dissemination of antibiotic resistance genes

Pulsed-field gel electrophoresis (PFGE) of SmaI macrorestriction fragments of genomic DNA as well as staphylococcal cassette chromosome mec (SCCmec) typing for mecA-carrying isolates were used to study the distribution of clonal types among 177 Staphylococcus aureus clinical isolates recovered in a Spanish hospital between 2000 and 2003. Five major clonal types (P1 to P5) were identified by PFGE, with one of them (P1) comprising the majority of strains (47.5%). According to SCCmec typing, SCCmec type IVA was the most prevalent type, showing increasing prevalence in the hospital setting with respect to other pandemic clones. One SCCmec pattern was detected in different PFGE types, which demonstrates that the latter is a major discriminative typing method. Three novel SCCmec elements or variants were found, each in a different PFGE type. Oxacillin (methicillin)-resistant and -susceptible S. aureus (MRSA and MSSA, respectively) strains were detected showing identical PFGE patterns, suggesting horizontal transfer of mecA to MSSA and/or mecA deletion from MRSA. Persistence of several S. aureus clones throughout the years within the same hospital environment was also observed.

Identification of staphylococcal cassette chromosome mec encoding methicillin resistance in Staphylococcus aureus isolates at Charles Nicolle Hospital of Tunis

Staphylococcal cassette chromosome is a mobile element that carries the gene mecA mediating the methicillin resistance in staphylococci. In Staphylococcus aureus five types of SCCmec have been described, which differs in size and genetic composition among strains. SCCmec typing of 34 non redundant methicillin-resistant S. aureus (MRSA) recovered in 2004 at Charles Nicolle Hospital of Tunis was carried out. The isolates were identified by conventional methods. Methicillin resistance was detected by oxacillin and cefoxitin disks and confirmed by mecA PCR. The SCCmec complex types were determined by using PCR which amplify a sequence overlapping the right SCCmec chromosome junction. Strains were recovered mainly from cutaneous pus (61.7%) and blood cultures (17.64%). They were isolated from different wards: medicine (53.1%) especially from dermatology (41.2%); surgery (40.6%) and pediatrics (3.1%). Only two strains were community-acquired MRSA. Two strains (5.9%) were harboring SCCmec type I; five (14.7%) SCCmec type II and 27 (79.4%) SCCmec type III. The two community-acquired MRSA were harboring type II and III SCCmec, usually found in hospital acquired MRSA. Our findings indicate that there are only three SCCmec types at Charles Nicolle Hospital. However, the existence of SCCmec types II and III in community incite us to investigate more community-acquired MRSA.

Comparison of genetic backgrounds of methicillin-resistant and -susceptible Staphylococcus aureus isolates from Portuguese hospitals and the community

In order to understand the origins of the dominant methicillin-resistant Staphylococcus aureus (MRSA) clones in Portuguese hospitals, we compared the genetic backgrounds of nosocomial MRSA with methicillin-susceptible S. aureus (MSSA) isolates from the same hospitals (n=155) and from the community (n=157) where they were located. Pulsed-field gel electrophoresis, spa typing, multilocus sequence typing, and agr type analysis revealed that the genetic backgrounds correspondent to the dominant MRSA clones in Portuguese hospitals during the last 15 years (Iberian ST 247, Brazilian ST 239, and EMRSA-15 ST 22) were scarcely or not found among the present MSSA collection. The four major MSSA clones encountered (A-ST 30, B-ST 34, C-ST 5, and H-ST 45) correspond, or are very similar, to the background of other international MRSA pandemic clones, i.e., EMRSA-16, New York/Japan, Pediatric, and Berlin clones. However, with the exception of the Pediatric clone, none of these MRSA clones has been detected in Portugal. Our findings suggest the three major MRSA clones identified in Portuguese hospitals have not originated from the introduction of SCCmec into dominant MSSA backgrounds present in the Portuguese nosocomial or community environment but were probably imported from abroad. In contrast, the MRSA Pediatric clone might have originated in our country by the acquisition of SCCmec type IV into MSSA clone C. Furthermore, we provide evidence that the introduction of SCCmec into sensitive clones is most likely a relatively infrequent event that seems to depend not exclusively on the presence of a successful MSSA lineage.

Major epidemic clones of Staphylococcus aureus in Nigeria

Clinical isolates of Staphylococcus aureus (n=276) were collected in 10 different hospitals located in the Southwest (cities of Ibadan and Lagos) and North-Central (city of Jos) parts of Nigeria. Resistance profiling of these strains revealed that the vast majority was still susceptible to methicillin (98.6% MSSA). Pulsed field gel electrophoresis (PFGE) performed for these strains identified 45 different genotypes, nine of which were identified in four or more different hospitals. The major PFGE type (genotype 2) comprised 23% of all isolates. In addition, several other strains were shown to be endemic in individual hospitals. Three out of four multi-resistant MRSA strains that were detected were sequence type 8 (ST8) as determined by array-based multi-locus sequence typing (MLST). PCRs for cataloguing the staphylococcal cassette chromosome (SCCmec) type were negative for two of these, suggesting the existence of a new methicillin-resistance gene complex in the ST8 genetic background. In conclusion, major clones of MSSA circulate in Nigeria, and the MRSA incidence is still low. However, the occurrence of old and new versions of SCCmec in some of the ecologically abundant MSSA strains should be taken as a serious warning since clonal expansion of this type of strains is not unprecedented.

Genetic diversity of Staphylococcus aureus isolated from ovine intramammary infections in Norway

Three hundred and eighty-four Staphylococcus aureus isolates obtained from mammary secretions from 332 ewes kept for meat production were typed by pulsed-field gel electrophoresis (PFGE). The ewes were from 242 flocks located in 13 counties distributed in four regions of Norway. In total, 64 different pulsotypes were identified, 31 of these were represented by a single isolate. Fifty-nine percent of the isolates belonged to one of five closely related pulsotypes. This group of pulsotypes occurred in all the counties. Although widely disseminated, the proportions of the prevalent and closely related pulsotypes differed between the regions. Nine pulsotypes were unique to single regions but the number of isolates belonging to each of these pulsotypes was low. Resistance to penicillin was found in only 3 of the 384 S. aureus isolates. These represented three different single banding patterns, not related to any of the prevalent pulsotypes found.

Distribution of major genotypes among methicillin-resistant Staphylococcus aureus clones in Asian countries

To investigate the evolutionary pattern and genotypic characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains in the Asian region, 74 MRSA strains isolated from 12 Asian countries were analyzed by multilocus sequence typing (MLST) and SCCmec typing. Overall, a total of 16 genotypes based on sequence type and SCCmec types were identified among MRSA strains from Asian countries. Data revealed two major genotypes of MRSA strains in Asia, with unique geographic distributions. By MLST analysis, all strains from Korea and Japan except one belonged to clonal complex 5 (CC5) while most MRSA isolates from other Asian countries belonged to CC239. SCCmec typing showed that most isolates from Korea and Japan were SSmec type II whereas SCCmec type III (or IIIA) was the most common type in strains from other Asian countries. Our data documented a unique geographic distribution and evolutionary pattern of MRSA clones in Asia.

Molecular characteristics of nosocomial and Native American community-associated methicillin-resistant Staphylococcus aureus clones from rural Wisconsin

In central and northern Wisconsin methicillin-resistant Staphylococcus aureus (MRSA) was first detected in 1989. Over the next 10-year period, 581 MRSA isolates were collected, 17.2% of which came from patients who were treated at five Native American clinics. These isolates were typed by SmaI-macrorestricted pulsed-field gel electrophoresis (PFGE). The PFGE patterns clustered the isolates into six major clonal groups (MCGs), i.e., MCGs 1 to 6, and 19 minor clonal groups (mCGs). The 25 clonal groups were represented by 109 unique PFGE types. Sixty-five percent of the MCG-2 isolates were recovered from patients who were treated at Native American clinics. Ninety-four percent of the MCG-2 isolates harbored the staphylococcal cassette chromosome mec (SCCmec) IVa. These isolates also had PFGE profiles that were clonally related to the midwestern community-associated MRSA (CA-MRSA) strain, MW2. The representative isolates from MCG-2 had the multilocus sequence type allelic profile 1-1-1-1-1-1-1 and contained pvl genes. They were also susceptible to various antibiotics, a finding consistent with the CA-MRSA phenotype. SCCmec IV was also present in other mCGs. Unlike MCG-2, isolates from the remaining five MCGs harbored SCCmec II and were resistant to multiple antibiotics, suggesting their nosocomial origin. The 19 mCGs were represented by diverse SCCmec types and three putative new variants referred to as SCCmec Ib, IIa, and IIb.