Sequence analysis of dru regions from methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates

Prevalence, biofilm formation, and mass spectrometric characterization of linezolid-resistant Staphylococcus capitis isolated from a tertiary hospital in China

OBJECTIVES

Linezolid-resistant Staphylococcus capitis (LRSC) has become a new challenge for clinical anti-infective therapy. The present study aimed to investigate the trends of LRSC prevalence in a tertiary hospital of China 2017-2020. The resistance mechanisms, virulence genes, biofilm formation, and mass spectrometric characteristics of LRSC isolates were also analysed.

METHODS

This study retrospectively analysed the antibiotic resistance trends of coagulase negative staphylococci (CoNS) isolated from clinical samples collected between 2017-2020. Antimicrobial resistance profiles were tested by micro-broth dilution and the E-test method. Antimicrobial resistance genes and virulence genes were detected by polymerase chain reaction, and dru-typing sequences were obtained by Sanger sequencing. Crystal violet staining in 96-well plates was used to detect biofilm formation ability. Mass spectrometric characterization of LRSC was analysed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) coupled with ClinProTools.

RESULTS

The linezolid resistance rate in 3575 CoNS clinical strains was 1.6%, wherein the great majority of was LRSC (91.1%, n = 51/56), with a resistant rate of 15.5% (n = 51/328) in all S. capitis isolates. In this study, 48 out of the 51 LRSC strains and 54 of 277 linezolid-susceptible S. capitis (LSSC) strains were enrolled. G2576T, C2104T, T2130A, C2163T, and T2319C mutations in the 23S rRNA V region and acquisition of cfr were the main linezolid resistant mechanisms in LRSC. The biofilm-forming ability of LRSC was more potent than LSSC, with a higher detection rate of bap (P < 0.05). Eleven mass spectrometric peaks of interest were identified by using MALDI-TOF MS and ClinProTools, which were differently distributed between LRSC and LSSC strains, with the area under the receiver operating characteristic curve of more than 0.8, especially for 5465.37 m/z.

CONCLUSIONS

Linezolid resistance was mediated by mutations in the 23S rRNA V region and presence of the cfr gene in LRSC strains. LRSC strains have stronger biofilm-forming ability than LSSC strains, which maybe associated with the adhesion-related gene of bap. Further, linezolid-resistant and linezolid-susceptible S. capitis could be rapidly identified with mass spectrometric characterization. To the best of our knowledge, this study is the first to document the biofilm formation ability of LRSC and the potential usefulness of MALDI-TOF MS for the discrimination of LRSC and LSSC.

Assessment of inducible clindamycin resistance and Hyper Variable Region (HVR) of mecA gene in clinical staphylococci

Objective:

To study the prevalence of inducible clindamycin along with vancomycin and methicillin resistance and assessment of hyper variable region (HVR) of mecA gene among different clinical isolates of Staphylococcus spp.

Methods:

A total of 176 clinical isolates of Staphylococci were collected from Pakistan Institute of Medical Sciences (PIMS), Islamabad during 2014-2015. The sample sources were pus, blood, urine, sputum, tracheal secretions and tissue fluids. Bacterial identification was done by colony morphology and biochemical tests. Kirby-Bauer disc-diffusion method was carried out to assess the susceptibility against different antibiotics. Minimal inhibitory concentrations (MICs) were done for vancomycin resistance. Double Disk Diffusion test (D-test) was used to detect the clindamycin inducible resistance. PCR was performed to detect erm(C), mecA and HVR genes.

Results:

Clindamycin inducible resistance among Staphylococcal isolates was found to be 7%, whereas in S. aureus it was 4%, and in coagulase negative Staphylococci (CoNS) it was 11%. The highest resistance was observed against fosfomycin, fusidic acid and cefoxitin. Vancomycin resistance was observed in 23 isolates (13%) of Staphylococci. erm(C), mecA and HVR genes were found in 18%, 50% and 42% respectively.

Conclusions:

D-test must be performed routinely to avoid clindamycin failure. A high level of resistance against vancomycin in Staphylococcal isolates is a concern for public health.

Comparative Genotypes, Staphylococcal Cassette Chromosome mec (SCCmec) Genes and Antimicrobial Resistance amongst Staphylococcus epidermidis and Staphylococcus haemolyticus Isolates from Infections in Humans and Companion Animals

This study compares the characteristics of Staphylococcus epidermidis (SE) and Staphylococcus haemolyticus (SH) isolates from epidemiologically unrelated infections in humans (Hu) (28 SE-Hu; 8 SH-Hu) and companion animals (CpA) (12 SE-CpA; 13 SH-CpA). All isolates underwent antimicrobial susceptibility testing, multilocus sequence typing and DNA microarray profiling to detect antimicrobial resistance and SCCmec-associated genes. All methicillin-resistant (MR) isolates (33/40 SE, 20/21 SH) underwent dru and mecA allele typing. Isolates were predominantly assigned to sequence types (STs) within a single clonal complex (CC2, SE, 84.8%; CC1, SH, 95.2%). SCCmec IV predominated among MRSE with ST2-MRSE-IVc common to both Hu (40.9%) and CpA (54.5%). Identical mecA alleles and nontypeable dru types (dts) were identified in one ST2-MRSE-IVc Hu and CpA isolate, however, all mecA alleles and 2/4 dts detected among 18 ST2-MRSE-IVc isolates were closely related, sharing >96.5% DNA sequence homology. Although only one ST-SCCmec type combination (ST1 with a non-typeable [NT] SCCmec NT9 [class C mec and ccrB4]) was common to four MRSH-Hu and one MRSH-CpA, all MRSH isolates were closely related based on similar STs, SCCmec genes (V/V_T or components thereof), mecA alleles and dts. Overall, 39.6% of MR isolates harbored NT SCCmec elements, and ACME was more common amongst MRSE and CpA isolates. Multidrug resistance (MDR) was detected among 96.7% of isolates but they differed in the prevalence of specific macrolide, aminoglycoside and trimethoprim resistance genes amongst SE and SH isolates. Ciprofloxacin, rifampicin, chloramphenicol [fexA, cat-pC221], tetracycline [tet(K)], aminoglycosides [aadD, aphA3] and fusidic acid [fusB] resistance was significantly more common amongst CpA isolates. SE and SH isolates causing infections in Hu and CpA hosts belong predominantly to STs within a single lineage, harboring similar but variable SCCmec genes, mecA alleles and dts. Host and staphylococcal species-specific characteristics were identified in relation to antimicrobial resistance genes and phenotypes, SCCmec and ACME.

Associations between dru Types and SCCmec cassettes

Molecular typing is an important tool in the investigation of methicillin resistant Staphylococcus aureus (MRSA) outbreaks and in following the evolution of MRSA. The staphylococcal cassette chromosome mec (SCCmec) contains a hypervariable region with a variable number of 40 bp repeats named direct repeat units (dru). The dru region has been suggested as a supplementary typing method for MRSA and an international nomenclature exists. The purpose of this study was to investigate the diversity and variability of the dru region in a diverse collection of MRSA. We studied 302 MRSA isolates harbouring SCCmec types I to VI. The isolates represented a broad genetic background based on Staphylococcal protein A (spa) typing and multilocus sequence typing (MLST) and included 68 isolates (68 patients) from an outbreak with t024-ST8-IVa and 26 isolates from the same patient. Sequencing identified 53 dru types (dt) in 283 isolates, while eighteen isolates contained no dru repeats and one isolate resisted sequencing. The most common dru type, dt10a, was present in 53% of the sequenced isolates and was found in all SCCmec types, except type II. Seven (10%) of the 68 epidemiologically related patients had isolates with dru type variants indicating that dru typing is not useful as a first line epidemiological typing tool. However, MRSA isolates cultured from a single patient over a three year period exhibited a single dru type. The finding of dt10a in most SCCmec types suggests that dru and mecA originate from the same Staphylococcus species.

Molecular characterization and antibiotic susceptibility of Staphylococcus aureus from a multidisciplinary hospital in Romania

From 2004 to 2005, 60%-72% of invasive Staphylococcus aureus isolates from Romanian hospitals were resistant to methicillin (methicillin-resistant S. aureus [MRSA]), the highest frequency for any European nation. Few reports, however, have addressed the molecular characteristics of S. aureus in Romania. In this study, we utilized spa typing, multilocus sequence typing, staphylococcal cassette chromosome mec (SCCmec) typing, dru typing, pulsed-field gel electrophoresis, and detection of virulence factors to characterize 146 S. aureus strains isolated from 2004 to 2005 at the Clinic County Hospital in Braşov. Antibiotic susceptibility patterns for all MRSA isolates and patient demographic data were also obtained. Fifty-six strains (38.4%) were determined to be MRSA by susceptibility testing and SCCmec typing. All MRSA strains were resistant to beta-lactams and tetracycline, but susceptible to nitrofurans, vancomycin, and clindamycin, with inducible clindamycin resistance in 23/28 clindamycin-sensitive/erythromycin-resistant isolates. Molecular typing identified 15 clonal backgrounds (CC 1, 5, 8, 8/239, 9, 15, 20, 22, 25, 30, 45, 80, 97, 101, and 121), only 4 of which were associated with MRSA (CC 1, 8/239, 30, and 80). Spa types 35 (t127, CC 1) and 351 (t030, CC 8/239) accounted for 27.4% and 21.9% of all S. aureus strains, respectively, and 19.6% and 57.1% of all MRSA strains. Both hospital-associated (SCCmec type III) and community-associated (SCCmec type IV) elements were identified within MRSA strains, whereas Panton-Valentine leukocidin was detected in 10 MRSA and 12 methicillin-sensitive S. aureus strains. These results demonstrate the presence of various endemic S. aureus clones within the Clinic County Hospital in Braşov, suggestive of ongoing nosocomial and community transmission.

Identification of a novel transposon (Tn6072) and a truncated staphylococcal cassette chromosome mec element in methicillin-resistant Staphylococcus aureus ST239

A novel composite transposon (Tn6072) resembling staphylococcal cassette chromosome mercury (SCCHg) was identified in a collection of sequence type (ST) 239 methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) isolates from Romanian hospitals. Tn6072 is homologous to the 5' region of SCCHg found in staphylococcal cassette chromosome mec (SCCmec) type III prototype strain 85/2082 but lacks the characteristic mer operon. SCCHg has previously been reported to integrate downstream of orfX, at the same chromosomal location as SCCmec. Tn6072, by contrast, is demarcated by two IS431 elements, flanked by 8-bp direct repeats, and inserted upstream of the origin of replication, within an open reading frame homologous to SAR2700 of S. aureus strain MRSA252. Analysis of a geographically and temporally diverse collection of 111 strains from the ST239 clonal group uncovered 11 additional strains harboring Tn6072, demonstrating a lineage-specific insertion pattern. Complete sequence analysis of the SCCmec regions of two representative Romanian strains (BK16704, BK16691) revealed two additional novel structures derived from a type III SCCmec background. BK16704 possesses an SCCmec 3A.1.4 structure, with an IS256 insertion downstream of the right chromosomal junction. In contrast, the SCCmec element of BK16691 is truncated downstream of the mec gene complex, with a 24-kb deletion encompassing the right chromosomal junction and an inverted downstream IS256 element. This structure, tentatively named "psiSCCmec16691," confers methicillin resistance but lacks most of the J1/J2 region, including the ccr gene complex. Taken together, these findings provide evidence for the continuing evolution of SCC elements, as well as the ST239 clonal group.

Enhanced discrimination of highly clonal ST22-methicillin-resistant Staphylococcus aureus IV isolates achieved by combining spa, dru, and pulsed-field gel electrophoresis typing data

ST22-methicillin-resistant Staphylococcus aureus type IV (ST22-MRSA-IV) is endemic in Irish hospitals and is designated antibiogram-resistogram type-pulsed-field group (AR-PFG) 06-01. Isolates of this highly clonal strain exhibit limited numbers of pulsed-field gel electrophoresis (PFGE) patterns and spa types. This study investigated whether combining PFGE and spa typing with DNA sequencing of the staphylococcal cassette chromosome mec element (SCCmec)-associated direct repeat unit (dru typing) would improve isolate discrimination. A total of 173 MRSA isolates recovered in one Irish hospital during periods in 2007 and 2008 were investigated using antibiogram-resistogram (AR), PFGE, spa, dru, and SCCmec typing. Isolates representative of each of the 17 pulsed-field group 01 (PFG-01) spa types identified underwent multilocus sequence typing, and all isolates were ST22. Ninety-seven percent of isolates (168 of 173) exhibited AR-PFG 06-01 or closely related AR patterns, and 163 of these isolates harbored SCCmec type IVh. The combination of PFGE, spa, and dru typing methods significantly improved discrimination of the 168 PFG-01 isolates, yielding 65 type combinations with a Simpson's index of diversity (SID) of 96.53, compared to (i) pairwise combinations of spa and dru typing, spa and PFGE typing, and dru and PFGE typing, which yielded 37, 44, and 43 type combinations with SIDs of 90.84, 91.00, and 93.57, respectively, or (ii) individual spa, dru, and PFGE typing methods, which yielded 17, 17, and 21 types with SIDs of 66.9, 77.83, and 81.34, respectively. Analysis of epidemiological information for a subset of PFG-01 isolates validated the relationships inferred using combined PFGE, spa, and dru typing data. This approach significantly enhances discrimination of ST22-MRSA-IV isolates and could be applied to epidemiological investigations of other highly clonal MRSA strains.

Usefulness of mec-associated direct repeat unit (dru) typing in the epidemiological analysis of highly clonal methicillin-resistant Staphylococcus aureus in Scotland

The incidence of the epidemic methicillin-resistant Staphylococcus aureus (EMRSA) strains EMRSA-15 and EMRSA-16 in Scotland has increased dramatically, now accounting for c. 70% and c. 20% of isolates, respectively. Epidemiological tracking of these EMRSA strains is difficult, as c. 50% of EMRSA-15 and c. 35% of EMRSA-16 isolates are indistinguishable using pulsed-field gel electrophoresis (PFGE) and other typing methods. The usefulness of mec-associated direct repeat unit (dru) sequence analysis as a more sensitive approach to tracking the persistence and spread of these 'clonal' EMRSA strains in Scotland was evaluated. Analysis of 47 EMRSA-15 and 57 EMRSA-16 isolates (including two separately cultured isolates of the Harmony collection type strain) obtained from 22 hospital laboratories over an 8-year period (1997-2005) revealed 13 and 12 different dru types, respectively. Whereas some types appeared to be endemic in multiple hospitals, subtypes that may represent specific strain movement among hospitals in a given geographical region were identified in other instances. These results suggest that mec-associated dru typing may have potential for identifying and tracking specific subtypes of otherwise indistinguishable epidemic MRSA isolates such as those in Scotland.

Molecular diagnostics of clinically important staphylococci

Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.

Epidemiology of European community-associated methicillin-resistant Staphylococcus aureus clonal complex 80 type IV strains isolated in Denmark from 1993 to 2004

In Europe, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections have been caused predominantly by isolates belonging to the "European CA-MRSA" clone (sequence type 80, staphylococcal cassette chromosome mec type IV). In this study, the epidemiology of European CA-MRSA was investigated on a nationwide scale, covering the period from 1993 to 2004. Denmark has been a low-prevalence country regarding MRSA since the mid-1970s but has experienced an increase in the number of new MRSA cases in recent years. Our results show that European CA-MRSA contributed to this increase. The isolates primarily caused skin and soft tissue infections (SSTIs) in patients outside hospitals, and transmission between household members was the predominant mode of spread. Although some of the isolates were found in hospitalized patients, nosocomial transmission seemed likely in only one instance, pointing to endogenous infections as an important factor. Compared to the CA-MRSA clone most common in the United States (USA300), the European CA-MRSA clone seems less well adapted to persist in hospital environments. Patients with a recent history of travel or family relation to the Mediterranean or Middle East were highly overrepresented. The epidemiological data indicated that the European CA-MRSA isolates were introduced into Denmark on multiple occasions, paralleled by an increasing level of genetic diversity of the isolates found during the study period. European CA-MRSA has previously been described as a rather uniform clone. However, we found pronounced, diverse pulsed-field gel electrophoresis subtypes, staphylococcal protein A gene (spa) types, and susceptibility patterns.

Characterization of a strain of community-associated methicillin-resistant Staphylococcus aureus widely disseminated in the United States

A highly stable strain of Staphylococcus aureus with a pulsed-field gel electrophoresis type of USA300 and multilocus sequence type 8 has been isolated from patients residing in diverse geographic regions of the United States. This strain, designated USA300-0114, is a major cause of skin and soft tissue infections among persons in community settings, including day care centers and correctional facilities, and among sports teams, Native Americans, men who have sex with men, and military recruits. The organism is typically resistant to penicillin, oxacillin, and erythromycin (the latter mediated by msrA) and carries SCCmec type IVa. This strain is variably resistant to tetracycline [mediated by tet(K)]; several recent isolates have decreased susceptibility to fluoroquinolones. S. aureus USA300-0114 harbors the genes encoding the Panton-Valentine leucocidin toxin. DNA sequence analysis of the direct repeat units within the mec determinant of 30 USA300-0114 isolates revealed differences in only a single isolate. Plasmid analysis identified a common 30-kb plasmid that hybridized with blaZ and msrA probes and a 3.1-kb cryptic plasmid. A 4.3-kb plasmid encoding tet(K) and a 2.6-kb plasmid encoding ermC were observed in a few isolates. DNA microarray analysis was used to determine the genetic loci for a series of virulence factors and genes associated with antimicrobial resistance. Comparative genomics between USA300-0114 and three other S. aureus lineages (USA100, USA400, and USA500) defined a set of USA300-0114-specific genes, which may facilitate the strain's pathogenesis within diverse environments.

Genetic Diversity among Methicillin-ResistantStaphylococcus epidermidis(MRSE)

We selected 106 methicillin-resistant Staphylococcus epidermidis (MRSE) and 22 methicillin-susceptible S. epidermidis (MSSE) hospital isolates--each with a different PFGE pattern--for more detailed documentation of genetic diversity. The 106 MRSE isolates showed extensive variation in the SmaI DNA fragments hybridizing with the DNA probe for mecA, the molecular size of which varied from as low as 20 kb up to over 500 kb. Parallel variation was also observed in the size of DNA fragments hybridizing with the chromosomal genes orfX and gyrA, and this was also observed in MSSE isolates. In contrast, SmaI fragments associated with the housekeeping genes murE and aroE, both located distantly from orfX, showed little size variation. Typing for the mec complex and ccr identified 10 different SCCmec structures and a large number of strains (21 isolates) that were non-typeable. The majority of strains studied (36%) carried a SCCmec type IV-like structure, including strains with non-related PFGE profiles. On the other hand, closely related strains often carried different types of SCCmec. The findings indicate that the acquisition and/or loss of mobile genetic elements, including various structural types of SCCmec, may occur frequently in the vicinity of the orfX gene on the S. epidermidis chromosome.

Evaluation of a multilocus sequence typing system for Staphylococcus epidermidis

Staphylococcus epidermidis is a significant cause of nosocomial disease. However, the taxonomy of this pathogen, particularly at subspecies level, is unclear. A multilocus sequence typing (MLST) scheme has therefore been investigated as a tool to elucidate taxonomic relationships within this group, based on genetic relatedness. DNA sequences for internal fragments of seven housekeeping genes were compared in 47 geographically and temporally diverse S. epidermidis isolates that were obtained from clinical infections. Twenty-three different allelic profiles were detected; 17 of these were represented by single strains and the largest profile group contained 17 isolates. Diversity of the same collection of isolates was investigated by using PFGE of SmaI-digested genomic DNA to test the discrimination and validity of the MLST approach. Isolates within the largest profile group were resolved into four distinct PFGE clusters on the basis of their SmaI digest patterns. Isolates within other profile groups that contained multiple isolates had matching PFGE SmaI patterns within each group. It appears that MLST is an effective method for grouping S. epidermidis strains at the subspecies level; however, it is not as discriminatory as it has been for other species for which MLST schemes have been established and, used alone, would not be a useful method for epidemiological studies. In addition, it was demonstrated that this method was effective for confirming the identity of S. epidermidis CoNS (coagulase-negative) isolates.

An epidemiologic survey of methicillin-resistant Staphylococcus aureus by combined use of mec-HVR genotyping and toxin genotyping in a university hospital in Japan

OBJECTIVE

To evaluate the usefulness of an assay using two polymerase chain reaction-based genotyping methods in the practical surveillance of methicillin-resistant Staphylococcus aureus (MRSA).

METHODS

Nosocomial infection and colonization were surveyed monthly in a university hospital in Japan for 20 months. Genotyping with mec-HVR is based on the size of the mec-associated hypervariable region amplified by polymerase chain reaction. Toxin genotyping uses a multiplex polymerase chain reaction method to amplify eight staphylococcal toxin genes.

RESULTS

Eight hundred nine MRSA isolates were classified into 49 genotypes. We observed differing prevalences of genotypes for different hospital wards, and could rapidly demonstrate the similarity of genotype for outbreak isolates. The incidence of genotype D: SEC/TSST1 was significantly higher in isolates causing nosocomial infections (49.5%; 48 of 97) than in nasal isolates (31.4%; 54 of 172) (P = .004), suggesting that this genotype may represent the nosocomial strains.

CONCLUSION

The combined use of these two genotyping methods resulted in improved discriminatory ability and should be further investigated.

Isolation of methicillin-resistant coagulase-negative staphylococci from patients undergoing continuous ambulatory peritoneal dialysis (CAPD) and comparison of different molecular techniques for discriminating isolates of Staphylococcus epidermidis

Coagulase-negative staphylococci (CNS) have emerged as an important pathogen in nosocomial infections. About 80%-90% of CNS isolates associated with hospital infections are methicillin-resistant coagulase-negative staphylococci (MRCNS). The aims of this study were to screen for MRCNS isolates in the flora of a small population of patients undergoing continuous ambulatory peritoneal dialysis (CAPD) and to evaluate the discriminatory power of different molecular methods: pulsed-field gel electrophoresis (PFGE), mecA location, ClaI/mecA polymorphism and arbitrarily primed polymerase chain reaction (AP-PCR) for characterizing isolates of methicillin-resistant Staphylococcus epidermidis (MRSE). Seventy-nine CNS isolates were recovered from the 11 CAPD patients studied. Using a methicillin screening agar and a DNA specific mecA probe we verified that 30 of the 79 (38%) CNS isolates were resistant to methicillin (MRCNS). Twenty-two of the 30 MRCNS (73%) were MRSE, 7 (23%) methicillin-resistant S. haemolyticus (MRSH(ae)) and 1 (3%) methicillin-resistant S. hominis (MRSH(om)). All patients analyzed carried MRCNS in their flora, in one or more sites. Since CAPD patients have high risk for developing peritonitis, the colonization of these patients with MRCNS might represent an additional problem, due to the therapeutic restrictions imposed by these multiresistant isolates. A wide genetic diversity was verified when the PFGE of the MRSE isolates was analyzed. The 22 MRSE isolates displayed a total of 15 PFGE different patterns (11 PFGE types and 4 subtypes). The location of mecA in the SmaI-fragmented genome DNA did not bring any additional advantage for epidemiologic characterization of the isolates. The ClaI/mecA polymorphism was able to correctly discriminate 12 from the 15 PFGE patterns. In addition, the DNA of 20 MRSE isolates were used for AP-PCR typing. These isolates belonged to 14 PFGE patterns (11 types and 3 subtypes) and displayed 15 genotypes (for the association of PFGE, mecA location and ClaI/mecA polymorphism). A total of 17 different amplification patterns was verified using the primer 1. Only for 2 genotypes, strains having identical genetic backgrounds were further discriminated by AP-PCR (2 of 15 genotypes (87%) for AP-PCR and 1 of 15 genotypes for PFGE; (93%). Concluding, our results indicated that the AP-PCR can be an alternative and useful tool for monitoring and genotyping MRSE colonization and also to molecular characterizing MRSE outbreaks in hospitals.