Comparative Analysis of Two Commercial Automated Systems with Agar Dilution for Oxacillin Susceptibility and Their Association with Genotypes of Invasive Staphylococcus aureus Isolates (2011-2021)

Background

Determining oxacillin susceptibility using reference methods and automated systems is crucial for treating invasive infections caused by Staphylococcus aureus. This study compares the oxacillin susceptibility results from the two automated systems with agar dilution and correlates them with genotypes of invasive S. aureus.

Methods

Non-duplicate S. aureus invasive isolates were collected over an 11-year period. The oxacillin susceptibility was determined with Phoenix 100 (Jan 2011 to Aug 2018) or Vitek 2 (Sep 2018 to Dec 2021), and susceptibility for oxacillin and cefoxitin was determined with agar dilution. Methicillin-resistant S. aureus (MRSA) was confirmed with mecA existence, and the genotype was determined using SCCmec. The association between genotype and antibiotic susceptibility using two automated systems and agar dilution was evaluated.

Results

A total of 842 invasive S. aureus, including 443 mecA+ MRSA and 399 mecA- MSSA, were collected. The susceptibility rates of oxacillin determined by two automated systems and agar dilution were 68.8% (76.8% for Phoenix 100 and 57.6% for Vitek 2) and 54.0%, respectively. When compared with the oxacillin susceptibility using agar dilution, the categorical agreement for Phoenix 100 and Vitek 2 were 0.46% and 0.88%, respectively (p < 0.001). One hundred and forty-three isolates were misinterpreted as oxacillin-susceptible S. aureus (OSSA) using automated systems while comparing with agar dilution, among which molecularly community-associated MRSA (CA-MRSA) outnumbered healthcare-associated MRSA (HA-MRSA) (99 vs 34, p < 0.001). There were 70 mecA+ OSSA (OS-MRSA) using agar dilution, among which 42 harbored SCCmec types were predominantly categorized as CA-MRSA (38, p < 0.001).

Conclusion

The categorical agreement of Vitek 2 in determining oxacillin susceptibility and predicting mecA existence is comparable with agar dilution, whereas Phoenix 100 is not. Most of those ORSA determined by agar dilution but misinterpreted as OSSA by automated systems and OS-MRSA are categorized as CA-MRSA.

Emergence and Genomic Characterization of a spa Type t4407 ST6-SCCmec Type IVa Methicillin-Resistant Staphylococcus aureus Strain Isolated from Al-Karak Hospital, Jordan

Background and Objectives: Methicillin-resistant Staphylococcus aureus (MRSA) is a major concern in Jordanian hospitals in terms of infection control. The purpose of this study was to identify the resistance patterns of Staphylococcus aureus strains isolated from surfaces of critical locations within the Al-Karak Governmental Hospital in 2019. Additionally, the study aimed to conduct whole-genome sequencing on the isolates. Materials and Methods: In February 2019, fourteen S. aureus strains were isolated from surfaces in critical sites in the Al-Karak Governmental Hospital. These isolates underwent antibiogram testing to determine their resistance profile. Genome sequencing using the Illumina MiSeq platform was applied to the extracted DNA from these isolates. The genomic data, including coding sequences, were analyzed to identify lineage, resistance genes, and plasmids. Results: The antibiogram results revealed that 11 of the 14 isolates were resistant to oxacillin, 6 to linezolid, and 1 to rifampicin, while none showed resistance to chloramphenicol. Eleven isolates were identified as MRSA, with a novel spa type (t4407) not previously reported in Jordan. High-quality sequencing data were obtained for only one isolate, i.e., A29, the genome showed 2,789,641 bp with a 32.7% GC content and contained 2650 coding sequences. Genomic analysis indicated the ST6 lineage, mecA gene (SCCmec type IVa(2B)), and a hybrid plasmid (pJOR_blaZ) carrying the blaZ gene for β-lactam resistance. Genomic data were deposited in NCBI (CP104989). The A29 genome closely resembled an MRSA genome isolated from a Danish hospital in 2011. The SNP analysis revealed identical antimicrobial resistance genes in these two genomes. Conclusions: This study unveils the first genomic sequence of an MRSA isolate from Jordan, marked by distinctive genotypic traits. The findings enhance our understanding of the MRSA types circulating in Jordan and the region and substantiate the phenomenon of intercontinental MRSA transmission.

Global distribution of heterogeneous vancomycin-intermediate Staphylococcus aureus strains (1997-2021): a systematic review and meta-analysis

BACKGROUND

Heterogeneous vancomycin-intermediate Staphylococcus aureus is considered one of the main causes in treatment failure of vancomycin, which leads to poor clinical outcomes. Herein, we comprehensively evaluated characteristics such as global prevalence, trend, and genetic backgrounds of these strains.

METHODS

In this study, we conducted a meta-analysis based on PRISMA checklist 2020. In the beginning, global databases were searched to achieve the studies related to the prevalence of hVISA in clinical isolates of methicillin-resistant Staphylococcus aureus. After retrieving the eligible English studies, the prevalence of hVISA isolates and their trend changes were assessed using event rate with 95% confidence intervals.

RESULTS

In the present study, the prevalence of 114 801 MRSA isolates (of 124 studies) was 64%. According to our results, although the frequency of infection with hVISA is increasing in recent years, there is not a significant difference between Asian countries and Europe/America (6.1% vs. 6.8%). In addition, infection with hVISA bacteria was higher in bacteraemic patients than other infections (9.4% vs. 5.5%), which increases hospitalization, treatment costs, and mortality in these patients. Isolates harbouring SCCmec types II and III are most common genotypes in hVISA strains.

CONCLUSIONS

The prevalence of hVISA is increasing, which will reduce the effectiveness of vancomycin treatment in the coming years. The presence of hVISA stains in blood samples was higher than the other samples, which is threatening for bacteraemic patients. The results of the current study indicate a universal program to identify and control the spread of such strains in nosocomial infections.

Staphylococcus capitis Bloodstream Isolates: Investigation of Clonal Relationship, Resistance Profile, Virulence and Biofilm Formation

Staphylococcus capitis has been recognized as a relevant opportunistic pathogen, particularly its persistence in neonatal ICUs around the world. Therefore, the aim of this study was to describe the epidemiological profile of clinical isolates of S. capitis and to characterize the factors involved in the persistence and pathogenesis of these strains isolated from blood cultures collected in a hospital in the interior of the state of São Paulo, Brazil. A total of 141 S. capitis strains were submitted to detection of the mecA gene and SCCmec typing by multiplex PCR. Genes involved in biofilm production and genes encoding enterotoxins and hemolysins were detected by conventional PCR. Biofilm formation was evaluated by the polystyrene plate adherence test and phenotypic resistance was investigated by the disk diffusion method. Finally, pulsed-field gel electrophoresis (PFGE) was used to analyze the clonal relationship between isolates. The mecA gene was detected in 99 (70.2%) isolates, with this percentage reaching 100% in the neonatal ICU. SCCmec type III was the most prevalent type, detected in 31 (31.3%) isolates and co-occurrence of SCCmec was also observed. In vitro biofilm formation was detected in 46 (32.6%) isolates but was not correlated with the presence of the ica operon genes. Furthermore, biofilm production in ICU isolates was favored by hyperosmotic conditions, which are common in ICUs because of the frequent parenteral nutrition. Analysis of the clonal relationship between the isolates investigated in the present study confirms a homogeneous profile of S. capitis and the persistence of clones that are prevalent in the neonatal ICU and disseminated across the hospital. This study highlights the adaptation of isolates to specific hospital environments and their high clonality.

Methicillin Resistance Elements in the Canine Pathogen Staphylococcus pseudintermedius and Their Association with the Peptide Toxin PSM-mec

Staphylococcus pseudintermedius is a frequent cause of infections in dogs. Infectious isolates of this coagulase-positive staphylococcal species are often methicillin- and multidrug-resistant, which complicates therapy. In staphylococci, methicillin resistance is encoded by determinants found on mobile genetic elements called Staphylococcal Chromosome Cassette mec (SCCmec), which, in addition to methicillin resistance factors, sometimes encode additional genes, such as further resistance factors and, rarely, virulence determinants. In this study, we analyzed SCCmec in a collection of infectious methicillin-resistant S. pseudintermedius (MRSP) isolates from predominant lineages in the United States. We found that several lineages characteristically have specific types of SCCmec elements and Agr types and harbor additional factors in their SCCmec elements that may promote virulence or affect DNA uptake. All isolates had SCCmec-encoded restriction-modification (R-M) systems of types I or II, and sequence types (STs) ST84 and ST64 had one type II and one type I R-M system, although the latter lacked a complete methylation enzyme gene. ST68 isolates also had an SCCmec-encoded CRISPR system. ST71 isolates had a psm-mec gene, which, in all but apparently Agr-dysfunctional isolates, produced a PSM-mec peptide toxin, albeit at relatively small amounts. This study gives detailed insight into the composition of SCCmec elements in infectious isolates of S. pseudintermedius and lays the genetic foundation for further efforts directed at elucidating the contribution of identified accessory SCCmec factors in impacting SCCmec-encoded and thus methicillin resistance-associated virulence and resistance to DNA uptake in this leading canine pathogen.

aureus and/or MRSA in hospitalized patients with diabetic foot and establishment of LAMP methods for rapid detection of the SCCmec gene

BACKGROUND

Patients with diabetic feet are prone to be infected due to the impaired immune system. However, the prognostic outcome of different microbial infections remains controversial. Identification and rapid screening of the pathogenic microorganisms that pose the greatest threat to the prognosis of patients with diabetic foot infections (DFIs) is critical.

METHODS

Clinical data were statistically analyzed, which were obtained from 522 patients with DFIs, including pathogenic bacterial culture results and treatment outcomes at the last return visit. In addition, a loop-mediated isothermal amplification (LAMP) detection method was developed to identify the prevalent subtype of methicillin-resistant Staphylococcus aureus (MRSA) in DFIs patients. This study was approved by the Ethics Committee of Nanfang Hospital (NFEC-202012-K6) and registered on ClinicalTrials.gov (NCT04916457) on June 1, 2021.

RESULTS

We found that the proportion of patients with infections of Staphylococcus aureus (S. aureus) and MRSA was 27.7% (145/522) and 33.7% (49/145), respectively. Additionally, the incidence of osteomyelitis was 46.9% (23/49) and amputation/disability was 40.8% (20/49) in patients with MRSA infection, which were significantly higher compared to patients with other types of bacterial infections such as methicillin-susceptible Staphylococcus aureus (MSSA). Notably, we demonstrated that the main prevalent subtype of MRSA in DFIs patients in our hospital was Staphylococcal chromosomal cassettes mec (SCCmec) type II. In addition, it only takes 1.5 h to complete the entire experimental procedure in this LAMP assay, providing high sensitivity (100%) and specificity (77.8%) in hospitalized patients with DFIs.

CONCLUSIONS

We demonstrated there is a very high rate of MRSA isolation in patients with DFIs and revealed that patients infected with MRSA are at a higher risk of developing osteomyelitis, and amputation or disability. Importantly, we have developed a method for quickly screening newly admitted patients for MRSA.

Unearthing new ccr genes and SCC elements in staphylococci through genome mining

The SCCmec typing is crucial for investigating methicillin-resistant S. aureus, relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB and 3 ccrC) through mining of the NCBI database, which forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of five groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.

Phylogenetic analysis and virulence characteristics of methicillin-resistant Staphylococcus aureus ST764-SCCmec II: an emerging hypervirulent clone ST764-t1084 in China

Previous studies have shown that the increased prevalent ST764 clone in China, Japan, and other Asian areas. However, the knowledge of the genetic features and virulence characteristics of methicillin-resistant Staphylococcus aureus (MRSA) ST764 in China is still limited. In this study, we identified 52 ST764-SCCmec type II isolates collected from five cities in China between 2014 and 2021. Whole genome sequencing showed that the most common staphylococcal protein A (spa) types of ST764 in China were t002 (55.78%) and t1084 (40.38%). Virulence assays showed that ST764-t1084 isolates had high haemolytic activity and α-toxin levels. Of the critical regulatory factors affecting α-toxin production, only the SaeRS was highly expressed in ST764-t1084 isolates. Mouse abscess model indicated that the virulence of ST764-t1084 isolates was comparable to that of S. aureus USA300-LAC famous for its hypervirulence. Interestingly, ST764-t002 isolates exhibited stronger biofilm formation and cell adhesion capacities than ST764-t1084 isolates. This seems to explain why ST764-t002 subclone has become more prevalent in China in recent years. Phylogenetic analysis suggested that all ST764 isolates from China in Clade III were closely related to KUN1163 (an isolate from Japan). Notably, genomic analysis revealed that the 52 ST764 isolates did not carry arginine catabolic mobile element (ACME), which differed from ST764 isolates in Japan. Additionally, most ST764 isolates (69.23%) harboured an obvious deletion of approximately 5 kb in the SCCmec II cassette region compared to KUN1163. Our findings shed light on the potential global transmission and genotypic as well as phenotypic characteristics of ST764 lineage.

Nasal staphylococci microbiota and resistome in healthy adults in La Rioja, northern Spain: High frequency of toxigenic S. aureus and MSSA-CC398 subclade

This study determined the nasal staphylococci diversity and characterized their resistome, with a focus on the mobilome of methicillin-susceptible Staphylococcus aureus (MSSA)-CC398 subclade from healthy adults in La Rioja (northern Spain). Nasal staphylococci recovered from 57 healthy individuals (HI) were identified (MALDI-TOF-MS) and their antimicrobial resistance, virulence determinants and genetic lineages were studied. The relatedness of MSSA-CC398 isolates was assessed by core-genome single-nucleotide-polymorphisms (SNPs). One-hundred-forty-three non-repetitive staphylococci were obtained from most HI (98.2%), of which S. epidermidis (87.7%) and S. aureus (36.8%) were the predominant species. About 15% of the 27 S. aureus and 30.1% of the 116 coagulase-negative staphylococci (CoNS) isolates presented a multidrug resistance (MDR) phenotype. All S. aureus isolates were MSSA but 30.2% of CoNS isolates were mecA-positive and carried SCCmec types III, IV, and V. The highest non-beta-lactam resistance (frequency/genes) in S. aureus and CoNS were: erythromycin-clindamycin-inducible (25.9%/ermT, ermC) and mupirocin (30.1%/mupA), respectively. About 85% of S. aureus isolates carried relevant virulence genes. Eight clonal complexes (CCs) of MSSA were identified, of which CC398 was the predominant (33.3%). About 78% of the CC398 isolates harboured rep13-bound ermT gene, however, one carried a rep10-bound ermC gene. Only the ermT-positive MSSA-CC398 isolates were closely related (<50 SNPs) and carried the φSa3. Diverse MDR-S. epidermidis isolates were identified which included the lineages ST59 and ST210. The high rate of toxigenic S. aureus and of MSSA-CC398 subclade highlight the ability of HI to carry and transmit virulent isolates. Moreover, the high frequency of MDR-CoNS, often linked with SCCmec, needs to be monitored for their potential human health implications.

Identification and characterization of SCCmec typing with psm-mec positivity in staphylococci from patients with coagulase-negative staphylococci peritoneal dialysis-related peritonitis

BACKGROUND

Peritonitis is the most important complication of peritoneal dialysis (PD) and coagulase-negative staphylococci (CNS) are a frequent cause of dialysis-related infections. The association between SCCmec typing with psm-mec positivity in staphylococci and PD-related infections has not been identified. We aim to investigate the molecular epidemiology of CNS isolated from PD-peritonitis in a single Chinese center, focusing on the genetic determinants conferring methicillin resistance.

METHODS

We collected 10 genetically unrelated CNS isolates from 10 patients with CNS PD-related peritonitis. The patients were divided into two groups based on the results of MIC to oxacillin: the methicillin-resistant CNS (MRCNS) and methicillin-sensitive CNS (MSCNS) groups. The biofilm formation group (BFG) and the non-biofilm formation group (NBFG) were used as the control groups. Phenotypic and molecular methods were used to analyze SCCmec types I, II and III, associated genes and biofilm formation and the existence of psm-mec. The demographic data and clinical indicators were collected.

RESULTS

Ten CNS PD-related peritonitis patients were enrolled for this study. There were 6 MRCNS and 4 MRCNS isolates. SCCmec types were fully determined in 10 isolates. Seven staphylococci (70%) carried SCCmec, of which 4 isolates carried single SCCmec type I (40%) and 3 isolates had multiple SCCmec elements (I + III). Of the 6 MRCNS isolates, 3 carried SCCmec type I (50%) and 2 isolates carried SCCmec type I + III (33.3%). A high diversity of ccr types, mec complexes and ccr-mec complex combinations was identified among the 10 CNS isolates. The psm-mec gene was detected in 2/10 (20%) CNS isolates. There was no mutation in the psm-mec gene.

CONCLUSIONS

The majority of isolates were hospital-associated isolates. Furthermore, 2 psm-mec positive isolates were MRCNS in the NBFG. The PD patients frequent exposure to hospital would be the main risk factor. The presence of the psm-mec signal in the spectra of the MRCNS tested here demonstrates the presence of certain SCCmec cassettes that convey methicillin resistance.

Genetic diversity of Staphylococcus aureus isolated from ear infections in Iran: Emergence of CC8/ST239-SCCmec III as major genotype

Increase in antibiotic resistance in Staphylococcus aureus isolated from ear infection is a serious public health problem. The objective of this investigation was to determine the antibacterial resistance profile and genetic variability of the S. aureus isolated from adult patients with otitis externa (OE) and otitis media (OM) infections, Tehran- Iran. The disk diffusion was employed to detect the susceptibility of 45 S. aureus strains. Biofilm production was evaluated by microtiter plate assay. Genetic diversity of the isolates was determined by staphylococcal cassette SCCmec, spa, and MLST techniques. Resistance to mupirocin and vancomycin were identified in 40 and 2.2% of isolates. Out of the 45 S. aureus isolates, 41 (91.2%) strains were considered as positive biofilm strains at different levels. According to our results, S. aureus isolated from OM (44.4%, 20/45) were including CC8/ST239-SCCmecIII corresponded to spa types t860, t030, t037, t234, t421 (70%, 14/20) and CC/ST30-SCCmecIV corresponded to spa types t605 and t019 (30%, 6/20) while S. aureus isolated from OE (55.6%, 25/45) were including CC/ST30-SCCmecIV corresponded to spa types t605, t345 and t1130 (52%, 13/25), CC/ST22-SCCmecIV corresponded to spa type t790 (20%, 5/25), CC8/ST8-SCCmecIV corresponded to spa type t008 (16%, 4/25), and CC/ST45-SCCmecIV corresponded to spa types t004 and t038 (12%, 3/25). This study highlighted genetic variability and strong biofilm formation ability among our isolates revealing its crucial role in enhancing the resistance of this bacteria to drugs. Thus, it is necessary to continue the epidemiological analysis to improve the control of ear infections related to S. aureus.

An Endogenous Staphylococcus aureus CRISPR-Cas System Limits Phage Proliferation and Is Efficiently Excised from the Genome as Part of the SCCmec Cassette

CRISPR-Cas is an adaptive immune system that allows bacteria to inactivate mobile genetic elements. Approximately 50% of bacteria harbor CRISPR-Cas; however, in the human pathogen Staphylococcus aureus, CRISPR-Cas loci are less common and often studied in heterologous systems. We analyzed the prevalence of CRISPR-Cas in genomes of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated in Denmark. Only 2.9% of the strains carried CRISPR-Cas systems, but for strains of sequence type ST630, over half were positive. All CRISPR-Cas loci were type III-A and located within the staphylococcal cassette chromosome mec (SCCmec) type V(5C2&5), conferring β-lactam resistance. Curiously, only 23 different CRISPR spacers were identified in 69 CRISPR-Cas positive strains, and almost identical SCCmec cassettes, CRISPR arrays, and cas genes are present in staphylococcal species other than S. aureus, suggesting that these were transferred horizontally. For the ST630 strain 110900, we demonstrate that the SCCmec cassette containing CRISPR-Cas is excised from the chromosome at high frequency. However, the cassette was not transferable under the conditions investigated. One of the CRISPR spacers targets a late gene in the lytic bacteriophage phiIPLA-RODI, and we show that the system protects against phage infection by reducing phage burst size. However, CRISPR-Cas can be overloaded or circumvented by CRISPR escape mutants. Our results imply that the endogenous type III-A CRISPR-Cas system in S. aureus is active against targeted phages, albeit with low efficacy. This suggests that native S. aureus CRISPR-Cas offers only partial immunity and in nature may work in tandem with other defense systems. IMPORTANCE CRISPR-Cas is an adaptive immune system protecting bacteria and archaea against mobile genetic elements such as phages. In strains of Staphylococcus aureus, CRISPR-Cas is rare, but when present, it is located within the SCCmec element, which encodes resistance to methicillin and other β-lactam antibiotics. We show that the element is excisable, suggesting that the CRISPR-Cas locus is transferable. In support of this, we found almost identical CRISPR-Cas-carrying SCCmec elements in different species of non-S. aureus staphylococci, indicating that the system is mobile but only rarely acquires new spacers in S. aureus. Additionally, we show that in its endogenous form, the S. aureus CRISPR-Cas is active but inefficient against lytic phages that can overload the system or form escape mutants. Thus, we propose that CRISPR-Cas in S. aureus offers only partial immunity in native systems and so may work with other defense systems to prevent phage-mediated killing.

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec₅₇₃₉₅ were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

A Multimodal Approach towards Genomic Identification of Protein Inhibitors of Uracil-DNA Glycosylase

DNA-mimicking proteins encoded by viruses can modulate processes such as innate cellular immunity. An example is Ung-family uracil-DNA glycosylase inhibition, which prevents Ung-mediated degradation via the stoichiometric protein blockade of the Ung DNA-binding cleft. This is significant where uracil-DNA is a key determinant in the replication and distribution of virus genomes. Unrelated protein folds support a common physicochemical spatial strategy for Ung inhibition, characterised by pronounced sequence plasticity within the diverse fold families. That, and the fact that relatively few template sequences are biochemically verified to encode Ung inhibitor proteins, presents a barrier to the straightforward identification of Ung inhibitors in genomic sequences. In this study, distant homologs of known Ung inhibitors were characterised via structural biology and structure prediction methods. A recombinant cellular survival assay and in vitro biochemical assay were used to screen distant variants and mutants to further explore tolerated sequence plasticity in motifs supporting Ung inhibition. The resulting validated sequence repertoire defines an expanded set of heuristic sequence and biophysical signatures shared by known Ung inhibitor proteins. A computational search of genome database sequences and the results of recombinant tests of selected output sequences obtained are presented here.

Progress in the Prevalence, Classification and Drug Resistance Mechanisms of Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus is a common human pathogen with a variety of virulence factors, which can cause multiple infectious diseases. In recent decades, due to the constant evolution and the abuse of antibiotics, Staphylococcus aureus was becoming more resistant, the infection rate of MRSA remained high, and clinical treatment of MRSA became more difficult. The genetic diversity of MRSA was mainly represented by the continuous emergence of epidemic strains, resulting in the constant changes of epidemic clones. Different classes of MRSA resulted in different epidemics and resistance characteristics, which could affect the clinical symptoms and treatments. MRSA had also spread from traditional hospitals to community and livestock environments, and the new clones established a relationship between animals and humans, promoting further evolution of MRSA. Since the resistance mechanism of MRSA is very complex, it is important to clarify these resistance mechanisms at the molecular level for the treatment of infectious diseases. We firstly described the diversity of SCCmec elements, and discussed the types of SCCmec, its drug resistance mechanisms and expression regulations. Then, we described how the vanA operon makes Staphylococcus aureus resistant to vancomycin and its expression regulation. Finally, a brief introduction was given to the drug resistance mechanisms of biofilms and efflux pump systems. Analyzing the resistance mechanism of MRSA can help study new anti-infective drugs and alleviate the evolution of MRSA. At the end of the review, we summarized the treatment strategies for MRSA infection, including antibiotics, anti-biofilm agents and efflux pump inhibitors. To sum up, here we reviewed the epidemic characteristics of Staphylococcus aureus, summarized its classifications, drug resistance mechanisms of MRSA (SCCmec element, vanA operon, biofilm and active efflux pump system) and novel therapy strategies, so as to provide a theoretical basis for the treatment of MRSA infection.

aureus

BACKGROUND

In blood cultures that test positive for staphylococcal bacteria, rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) or methicillin-susceptible Staphylococcus aureus (MSSA) by molecular assay is useful for appropriate antimicrobial treatment of bloodstream infections. Although the Xpert MRSA/SA BC assay is widely available in clinical settings in Japan, its efficacy has not yet evaluated thoroughly.

METHODS

We retrospectively studied 100 blood culture cases positive for S. aureus at Sapporo Medical University Hospital between March 2019 to May 2022. Cycle threshold (CT) values for target genes from the Xpert MRSA/SA BC assay were compared to phenotypic results. Genotyping and genetic analysis of the orfX-SCCmec junction region was performed for selected isolates.

RESULTS

We analyzed 25 and 75 isolates assigned to MRSA and MSSA, respectively, using the Xpert MRSA/SA BC assay. Of these, 99 isolates from agar cultures showed compatible susceptibility to oxacillin. One genetically misidentified case of MRSA was found to be caused by the mixed growth of MSSA and methicillin-resistant S. hominis on agar culture. Of the 73 MSSA with pure growth on agar culture, 45 (61.6%) were found to be orfX-SCCmec-positive, spa-positive, and mecA-negative in this assay. These MSSA belong to diverse spa and coa types.

CONCLUSION

The Xpert MRSA/SA BC assay accurately identified MRSA and MSSA in positive blood cultures. However, over half of the MSSA isolates showed positive results for orfX-SCCmec, presumably due to genetic diversity in the orfX-associated region of MSSA. Therefore, the coexistence of MSSA and mecA-harboring coagulase-negative staphylococci may cause confusion about identification of MRSA.

Characterization of oxacillin-resistant Staphylococcus lugdunensis isolated from sterile body fluids in a medical center in Taiwan: A 12-year longitudinal epidemiological study

BACKGROUND

In this study, our objective was to characterize Staphylococcus lugdunensis isolated from sterile body fluids (SBFs) in a medical center in Taiwan between 2009 and 2020.

METHODS

We used MALDI-TOF MS, disk diffusion testing, agar dilution assay, SCCmec typing, and antibiotic resistance gene screening to identify and investigate the characteristics of oxacillin-resistant S. lugdunensis (ORSL).

RESULTS

A total of 438 S. lugdunensis isolates were collected and 146 (33.3%) isolates were identified as ORSL. SCCmec type V was dominant (65.7%) in our ORSL isolates, followed by SCCmec type II (18.5%), and type IV (8.9%). After 2013, a slight increase in SCCmec types IV and V was revealed. Moreover, all ORSL isolates with type II and untypable SCCmec were highly resistant to oxacillin (MIC >32 μg/mL), compared to ORSL that had SCCmec types IV, V, and VT. All 146 ORSL isolates were resistant to penicillin and susceptible to teicoplanin and vancomycin. High resistance rates of ORSL to clindamycin (43.2%), erythromycin (43.2%), gentamicin (78.1%) and tetracycline (46.6%) was observed. Moreover, only two (1.4%) and six (4.1%) ORSL isolates were resistant to trimethoprim/sulfamethoxazole and ciprofloxacin, respectively. The erythromycin-resistant ORSL isolates mostly exhibited constitutive MLS_B resistant phenotype (61/63, 96.8%) and contained either ermC alone (27/63, 42.9%) or a combination of ermC with ermA (28/63, 44.4%).

CONCLUSION

Our present study showed a stable rate of ORSL from SBFs during 2009-2020. Moreover, teicoplanin, vancomycin, trimethoprim/sulfamethoxazole, and ciprofloxacin were shown to be highly efficient for the treatment of ORSL in vitro.

First report of Staphylococcus pseudintermedius ST71-SCCmec III and ST45-ΨSCCmec57395 from canine pyoderma in Argentina

Staphylococcus pseudintermedius is an opportunistic pathogen commonly associated with skin infections in dogs. Twenty-three methicillin-resistant S. pseudintermedius (MRSP) isolated in Argentina from dogs with pyoderma were analyzed using whole genome sequencing (WGS) and classified into sequence types (ST) by multilocus sequence typing (MLST) and staphylococcal chromosome cassette mec (SCCmec) types.Based on the WGS analysis, MLST, and SCCmec type results, we report for the first time in Argentina two MRSP strains, one each, belonging to ST71-SCCmec III and ST45-ΨSCCmec₅₇₃₉₅ from dogs with pyoderma. We also identified seven isolates with ST339, which had been previously reported in only two isolates in Argentina. Additionally, we identified ten MRSP isolates harboring variants of the SCCmec V found in S. aureus, seven SCCmec V (5C2&5) with two ccrC1 recombinases, and three SCCmec V (5C2) with one ccrC1 recombinase.Our findings provide important insights into the evolution and geographic spread of these hypervirulent dominant clones that threaten the health of our companion animals and represent a significant risk for zoonotic infections.

Antimicrobial Resistance, SCCmec, Virulence and Genotypes of MRSA in Southern China for 7 Years: Filling the Gap of Molecular Epidemiology

As the prevalence of Staphylococcus aureus infections is of worldwide concern, phenotype and genotype in prevalent MRSA strains require longitudinal investigation. In this study, the antibiotic resistance, virulence gene acquisition, and molecular type were determined on a large scale of nosocomial S. aureus strains in Southern China during 2009-2015. Bacterial identification and antimicrobial susceptibility to 10 antibiotics were tested by Vitek-2. Virulence genes encoding staphylococcal enterotoxins (SEA, SEB, SEC, SED, and SEE), exfoliative toxins (ETA and ETB), Panton-Valentine leukocidin (PVL), and toxic shock syndrome toxin (TSST) were detected by PCR, with SCCmec typing also conducted by multiplex PCR strategy. Genotypes were discriminated by MLST and spaA typing. MLST was performed by amplification of the internal region of seven housekeeping genes. PCR amplification targeting the spa gene was performed for spa typing. No resistance to vancomycin, linezolid, or quinupristin and increase in the resistance to trimethoprim/sulfamethoxazole (55.5%) were identified. A total of nine SCCmec types and subtypes, thirteen STs clustered into thirteen spa types were identified, with ST239-SCCmec III-t037 presenting the predominant methicillin-resistant S. aureus (MRSA) clone. Typically, SCCmec type IX and ST546 were emergent types in China. Isolates positive for both pvl and tsst genes and for both eta and etb genes were also identified. Important findings in this study include: firstly, we have provided comprehensive knowledge on the molecular epidemiology of MRSA in Southern China which fills the gap since 2006 or 2010 from previous studies. Secondly, we have presented the correlation between virulence factors (four major groups) and genotypes (SCCmec, ST and spa types). Thirdly, we have shown evidence for earliest emergence of type I SCCmec from 2012, type VI from 2009 and type XI from 2012 in MRSA from Southern China.

Molecular Epidemiology and Characterization of Multidrug-Resistant MRSA ST398 and ST239 in Himachal Pradesh, India

Aim

Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of severe and difficult-to-treat infections in humans and animals. We aimed to identify the predominant lineages of methicillin-resistant S. aureus in Himachal Pradesh, India, to understand the genomic epidemiology along with the genotypic and phenotypic characteristics.

Methods

We isolated 250 S. aureus from two district hospitals in Himachal Pradesh, India. Methicillin-Resistant S. aureus (MRSA) isolates were subjected to MLST, SCCmec typing, and resistance as well as virulence determinants were determined by PCR and sequencing. Bio-typing was also performed for source tracking.

Results

A 17.6% (44/250) of isolates were classified as MRSA by both the MRSA detection kit and disc diffusion methods. Antimicrobial Susceptibility Testing of MRSA isolates (n = 44) showed high resistance to oxacillin (77.27%), erythromycin (77.27%), tetracycline (75%), cefoxitin (65.9%), and gentamicin (61.36%), while low resistance was observed for teicoplanin (36.36%), vancomycin and levofloxacin (31.81%) and fusidic acid (18.18%). All isolates were sensitive to linezolid, quinupristin-dulfopristin, dalbavancin, and cefazoline. The SCCmec-II was observed in 20.45% of isolates, SCCmec-I in 11.36%, SCCmec-III in 9%, SCCmec-IV in 40.9% and SCCmec-V in 18.18%. The mecA gene was present in all isolates (n = 44) and 50% also had the vanA gene. 35% of isolates had the lukS-PV/lukf-PV toxin gene and 11.36% had the co-existence of mecA, vanA, and lukS-PV/lukf-PV. The major strain was ST398 (39%) followed by ST239 (27%), ST217 (16%), ST121 (11%), and ST338 (7%). The MRSA isolates produced staphylokinase and β-hemolysis but were negative for bovine plasma coagulation tests.

In Conclusion

The predominant MRSA clones in Himachal Pradesh, India, were hospital-associated multi-drug resistant-MRSA ST239 with PVL and community-associated MRSA ST398.

Biofilm formation of two genetically diverse Staphylococcus aureus isolates under beta-lactam antibiotics

PURPOSE

Our aim was to evaluate the biofilm formation of 2 genetically diverse Staphylococcus aureus isolates, 10379 and 121940, under different concentrations of beta-lactam antibiotics on biomass content and biofilm viability.

METHODS

Biofilm formation and methicillin resistance genes were tested using PCR and multiplex PCR. PCR was combined with bioinformatics analysis to detect multilocal sequence typing (MLST) and SCCmec types, to study the genetical correlation between the tested strains. Then, the crystal violet (CV) test and XTT were used to detect biomass content and biofilm activity. Antibiotic susceptibility was tested using a broth dilution method. According to their specific MIC, different concentrations of beta-lactam antibiotics were used to study its effect on biomass content and biofilm viability.

RESULTS

Strain 10379 carried the icaD, icaBC, and MRSA genes, not the icaA, atl, app, and agr genes, and MLST and SCCmec typing was ST45 and IV, respectively. Strain 121940 carried the icaA, icaD, icaBC, atl, and agr genes, not the aap gene, and MLST and SCCmec typed as ST546 and IV, respectively. This suggested that strains 10379 and 121940 were genotypically very different. Two S. aureus isolates, 10379 and 121940, showed resistance to beta-lactam antibiotics, penicillin, ampicillin, meropenem, streptomycin and kanamycin, some of which promoted the formation of biofilm and biofilm viability at low concentrations.

CONCLUSION

Despite the large differences in the genetic background of S. aureus 10379 and 121940, some sub-inhibitory concentrations of beta-lactam antibiotics are able to promote biomass and biofilm viability of both two isolates.

Genetic Diversity, Antibiotic Resistance, and Virulence Gene Features of Methicillin-Resistant Staphylococcus aureus Epidemics in Guiyang, Southwest China

Purpose

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common pathogens of community- and hospital-acquired infections, and its prevalence is increasing globally. Guiyang is the capital city of Guizhou Province, Southwest China; as the transport and tourism centre of Southwest China, Guizhou Province is bordered by Yunnan, Sichuan, Chongqing, and Guangxi Provinces. Although MRSA prevalence is increasing, little is known about its aspects in the area. The purpose of this study was to analyse MRSA molecular characteristics, antimicrobial resistance, and virulence genes in Guiyang.

Methods

In total, 209 MRSA isolates from four hospitals (2019-2020) were collected and analysed by antimicrobial susceptibility testing and molecular classification by the MLST, spa, and SCCmec typing methods. Isolate antibiotic resistance rates were detected by a drug susceptibility assays. PCR amplification was used to detect the virulence gene-carrying status.

Results

Twenty-four STs, including 4 new STs (ST7346, ST7347, ST7348, and ST7247) and 3 new allelic mutations, were identified based on MLST. The major prevalent ST type and clone complex were ST59 (49.8%) and CC59 (62.7%), respectively. Spa type t437 (42.1%) and SCCmec IV (55.5%) were identified by spa and SCCmec typing methods as the most important types. Drug sensitivity data showed that the multidrug resistance rate was 79.0%. There were significant differences in multidrug resistance rates and virulence gene-carrying rates for seb, hla, hlb, cna and bap between ST59 and non-ST59 types.

Conclusion

ST59-SCCmecIV-t437 is a major epidemic clone in Guiyang that should be monitored by local medical and health institutions. The situation differs from other adjacent or middle provinces of China, which may be due to the special geographical location of the region and the trend in antibiotic use or lifestyle. This study provides empirical evidence for local medical and health departments to prevent and control the spread of MRSA.

Molecular epidemiology and phenotypes of invasive methicillin-resistant vancomycin-intermediate Staphylococcus aureus in Taiwan

BACKGROUND

Patients with invasive infections caused by methicillin-resistant Staphylococcus aureus (MRSA), especially those with an elevated minimal inhibitory concentration (MIC) of vancomycin (VA), are likely to have treatment failure and poor outcomes. The aim of this study was to delineate and correlate the genotypes and phenotypes of clinical VA-intermediate S. aureus (VISA) from invasive infections in Taiwan.

METHODS

Between 2006 and 2010, a total of 670 non-duplicate MRSA isolates were collected from patients with invasive infections, mostly from blood, as part of a nationwide antimicrobial surveillance program named Tigecycline in vitro Surveillance in Taiwan. Among them, 10 (1.5%) VISA (VA MIC = 4 mg/L) isolates were identified. Molecular typing with staphylococcal cassette chromosome mec (SCCmec), multilocus sequence typing, staphylococcal protein A (spa), mec-associated hypervariable region (dru), accessory gene regulator (agr), and pulse-field gel electrophoresis, and phenotypic analysis including antibiotic susceptibility testing, gene encoding Panton-Valentine leukocidin (pvl), and superantigenic toxin profiles, were analyzed.

RESULTS

All but one isolate was defined as molecular health-care-associated MRSA: 6 as SCCmecIII-ST239-spa t037-agrI-dru7 (1 isolate) and dru14 (5 isolates), 2 as SCCmecII-ST5-spa t586-agrII-dru4, and one as SCCmecII-ST89-spa t3520-agrIII-dru7. One isolate was defined as SCCmecIV-ST59-spa t437-agrI-dru8, which was categorized as molecular community-associated MRSA. Five pulsotypes were identified; only one had a positive D-test and 3 were insusceptible to daptomycin (MIC ≧1 mg/L). Five isolates possessed sea-selk-selq, among them 4 belonged to SCCmecIII-ST239-spa t037-agrI.

CONCLUSION

In this study, VISA was rarely isolated from invasive MRSA infections, and most cases harbored limited genotypes and corresponding phenotypes.

How to survive pig farming: Mechanism of SCCmec element deletion and metabolic stress adaptation in livestock-associated MRSA

Previous research on methicillin susceptible Staphylococcus aureus (MSSA) belonging to livestock-associated (LA-) sequence type (ST) 398, isolated from pigs and their local surroundings, indicated that differences between these MSSA and their methicillin resistant predecessors (MRSA) are often limited to the absence of the staphylococcal cassette chromosome mec (SCCmec) and few single nucleotide polymorphisms. So far, our understanding on how LA-MRSA endure the environmental conditions associated with pig-farming as well as the putative impact of this particular environment on the mobilisation of SCCmec elements is limited. Thus, we performed in-depth genomic and transcriptomic analyses using the LA-MRSA ST398 strain IMT38951 and its methicillin susceptible descendant. We identified a mosaic-structured SCCmec region including a putative replicative SCCmecVc which is absent from the MSSA chromosome through homologous recombination. Based on our data, such events occur between short repetitive sequences identified within and adjacent to two distinct alleles of the large cassette recombinase genes C (ccrC). We further evaluated the global transcriptomic response of MRSA ST398 to particular pig-farm associated conditions, i.e., contact with host proteins (porcine serum) and a high ammonia concentration. Differential expression of global regulators involved in stress response control were identified, i.e., ammonia-induced alternative sigma factor B-depending activation of genes for the alkaline shock protein 23, the heat shock response and the accessory gene regulator (agr)-controlled transcription of virulence factors. Exposure to serum transiently induced the transcription of distinct virulence factor encoding genes. Transcription of genes reported for mediating the loss of methicillin resistance, especially ccrC, was not significantly different compared to the unchallenged controls. We concluded that, from an evolutionary perspective, bacteria may save energy by incidentally dismissing a fully replicative SCCmec element in contrast to the induction of ccr genes on a population scale. Since the genomic SCCmec integration site is a hot-spot of recombination, occasional losses of elements of 16 kb size may restore capacities for the uptake of foreign genetic material. Subsequent spread of resistance, on the other hand, might depend on the autonomous replication machinery of the deleted SCCmec elements that probably enhance chances for reintegration of SCCmec into susceptible genomes by mere multiplication.

Hand carriage, antimicrobial resistance and molecular characterisation of methicillin-resistant coagulase-negative staphylococci isolated from gynaecological surgical staff

Sepsis caused by methicillin-resistant coagulase-negative staphylococci (MRCoNS) seriously affects the morbidity and mortality of neonates. However, the hand carriage and genotypic diversity of MRCoNS within surgical staff remain unclear in China. In the study, antimicrobial susceptibility tests and genotypic characterisation were applied to MRCoNS. One hundred and one samples were collected from the hands of gynaecological surgical staff. Eighty staphylococcal isolates were identified, of which 75 (94%) were resistant to at least one antibiotic. mecA gene was determined in 50 (62.5%) staphylococcal isolates. Panton-Valentine leukocidin (pvl) and ica genes were determined in 17 (21%) and 12 (15%) staphylococcal isolates, respectively. About 52% of staphylococci carried SCCmec IV and V, followed by SCCmec type I, II, and III (38%). In addition, two new STs types were assigned as ST844 and ST845. The high level of hand MRCoNS colonisation rate in gynaecological surgical staff is of concern, and hand hygiene management should be emphasised among surgical assistants.Impact statementWhat is already known on this subject? Coagulase-negative staphylococci (CoNS) are the predominant cause of neonatal sepsis. Exposure to antimicrobial-resistant CoNS might put neonates at increased risk of infection. However, little is known about the carriage and genetic diversity of methicillin-resistant CoNS (MRCoNS) of gynaecological surgeons and surgical assistants.What do the results of this study add? This is the first study on the molecular characterisation of MRCoNS recovered from gynaecological surgeons and surgical assistants in China. MRCoNS carriage rate in surgical assistants was significantly higher than in surgeons. Seventy-five (94%) coagulase-negative staphylococci were resistant to at least one antibiotic. SCCmec I, II and III was the dominant types identified in MRCoNS that were recovered from surgical staff. Fifty (62.5%) staphylococcal isolates that were recovered from surgical staff harboured the mecA gene. Pathogenic clones of MRCoNS were disseminated in surgical staff, and half of mecA-positive Staphylococcus epidermidis harboured the ica gene.What are the implications of these findings for clinical practice and/or further research? The high level of hand MRCoNS colonisation rate among gynaecological surgical staff is of concern. The alarming outcome of this study suggested that hygiene measures should be emphasised among gynaecological surgical assistants.

Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs

Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis are common coagulase-negative staphylococcus opportunistic pathogens. In Thailand, the clinical strains S. haemolyticus 1864 and 48 and S. hominis subsp. hominis 384 and 371 have been recovered from sick dogs. These strains were methicillin resistant with the nontypeable staphylococcal cassette chromosome mec (NT-SCCmec). The SCCmec element distribution in the clinical isolates from dogs was analyzed using whole-genome sequencing, which revealed the presence of different SCCmec composite islands (CIs) and gene structure. The SCCmec-CIs of ψSCCmec1864 (13 kb) and ψSCC1864 (11 kb) with a class C1 mec complex but no ccr gene were discovered in S. haemolyticus 1864. The CIs of ψSCCmec48 with a C1 mec complex (28 kb), SCC48 with ccrA4B4 (23 kb), and ψSCC48 (2.6 kb) were discovered in S. haemolyticus 48. In SCC48, insertion sequence IS256 contained an aminoglycoside-resistant gene [aph(2″)-Ia]. Two copies of IS431 containing the tetracycline-resistant gene tet(K) were found downstream of ψSCC48. In S. hominis subsp. hominis, the SCCmec-CI in strain 384 had two separate sections: ψSCCmec384 (20 kb) and SCCars (23 kb). ψSCCmec384 lacked the ccr gene complex but carried the class A mec complex. Trimethoprim-resistant dihydrofolate reductase (dfrC) was discovered on ψSCCmec384 between two copies of IS257. In strain 371, SCCmec VIII (4A) (37 kb) lacking a direct repeat at the chromosomal end was identified. This study found SCCmec elements in clinical isolates from dogs that were structurally complex and varied in their genetic content, with novel organization. IMPORTANCE In Thailand, the staphylococcal cassette chromosome mec (SCCmec) element, which causes methicillin resistance through acquisition of the mec gene, has been studied in clinical coagulase-negative Staphylococcus isolates from various companion animals, and Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis were found to have the most nontypeable (NT)-SCCmec elements. These species are more prone to causing illness and more resistant to a variety of antimicrobials than other coagulase-negative staphylococci. However, full characterization of NT-SCCmec in clinical S. haemolyticus and S. hominis subsp. hominis isolates from such animals has been limited. Our findings support the use of full nucleotide sequencing rather than PCR designed for Staphylococcus aureus in further research of novel SCCmec elements. Moreover, several antimicrobial resistance and heavy metal resistance genes were identified on the SCCmec elements; these are important as they could limit the therapeutic options available in veterinary medicine.

Clonality and Persistence of Multiresistant Methicillin-Resistant Coagulase-Negative Staphylococci Isolated from the Staff of a University Veterinary Hospital

The aim of this study was to characterize methicillin-resistant coagulase-negative staphylococci (MRCoNS) isolates from the healthy staff of a university veterinary hospital in order to assess their importance as a reservoir of antimicrobial resistance and to determine their population structure and evolution. The study duration was over two years (2020–2021), 94 individuals were analyzed in duplicate, and 78 strains were obtained. The overall prevalence of methicillin-resistant strains detected throughout the study was 61.7%, with point prevalence values of 53.2% in 2020 and 31.5% in 2021. A total of 19.1% of the individuals analyzed were carriers throughout the study. The most frequently identified MRCoNs were Staphylococcus epidermidis (92.3%) and S. warneri (3.8%). A total of 75.6% of the isolates obtained showed the development of multi-resistance, preferentially against erythromycin, gentamicin, and tetracycline, and to a lesser extent against fusidic acid, norfloxacin, and clindamycin; these antimicrobials are frequently used in the veterinary field. Although most of the S. epidermidis isolates obtained showed wide genetic variability and low dispersion, which are characteristic of community-associated isolates, a small number of strains spread between individuals in close physical proximity and were maintained over time, forming stable clones. These clones generally maintained the same type of staphylococcal cassette chromosome mec (SCCmec) and had a similar antimicrobial resistance pattern.

Characterization of SCCmec Instability in Methicillin-Resistant Staphylococcus aureus Affecting Adjacent Chromosomal Regions, Including the Gene for Staphylococcal Protein A (spa)

Staphylococcal cassette chromosome mec (SCCmec) represents a sequence of clear clinical and diagnostic importance in staphylococci. At a minimum the chromosomal cassette contains the mecA gene encoding PBP2a but frequently also includes additional antibiotic resistance genes (e.g., ermA and aadC; macrolide and aminoglycoside resistance, respectively). Certain regions within SCCmec elements are hot spots for sequence instability due to cassette-specific recombinases and a variety of internal mobile elements. SCCmec changes may affect not only cassette stability but the integrity of adjacent chromosomal sequences (e.g., the staphylococcal protein A gene; spa). We investigated SCCmec stability in methicillin-resistant Staphylococcus aureus (MRSA) strains carrying one of four SCCmec types cultured in the absence of antimicrobial selection over a 3-month period. SCCmec rearrangements were first detected in cefoxitin-susceptible variants after 2 months of passage, and most commonly showed precise excision of the SCCmec element. Sequence analysis after 3 months revealed both precise SCCmec excision and a variety of SCCmec internal deletions, some including extensive adjacent chromosomal loss, including spa. No empty cassettes (i.e., loss of just mecA from SCCmec) were observed among the variants. SCCmec stability was influenced both by internal mobile elements (IS431) as well as the host cell environment. Genotypically similar clinical isolates with deletions in the spa gene were also included for purposes of comparison. The results indicate a role for host-cell influence and the IS431 element on SCCmec stability.

Molecular Epidemiological Survey of Staphylococcus lugdunensis Isolates With Variable Number of Repeats in the von Willebrand Factor-Binding Protein Gene

The von Willebrand factor binding protein in Staphylococcus lugdunensis (vWbl) comprises four major regions: the signal peptide (S), the non-repetitive (A) region, the repeat (R) region, and the wall-associated (W) region. Previous studies have demonstrated that the R region contains 10 copies of repeating sequences; however, we reveal that the copy number of repeats in the vWbl gene varies among different S. lugdunensis isolates. In this study, an epidemiological surveillance was conducted to determine whether the copy number of repeats in vWbl in different isolates of S. lugdunensis correlates with their infectivity. The number of repeats was estimated in a total of 212 isolates, consisting of 162 isolates of oxacillin-sensitive S. lugdunensis (OSSL) and 50 isolates of oxacillin-resistant S. lugdunensis (ORSL). Our data showed that 72.5% (116/162) of OSSL isolates contained 9 (25, 15.4%), 12 (43, 26.5%), or 13 (48, 29.6%) repeats, and 90% (45/50) of ORSL isolates had 9 (32, 64%) or 13 (13, 26%) repeats. In addition, 89.6% (26 of 29) of the sequence type (ST)27 strain had 12 repeats, and 86.8% (13 of 15) of the ST4 strain had 14 repeats. Twenty-seven of the 28 isolates with nine repeats were of the staphylococcal cassette chromosome mec (SCCmec) V or V_t type and belonged to ST3, and all isolates with 13 repeats were of SCCmec II type and belonged to ST6. All isolates with nine repeats had a stop codon at the 18^th codon of the third repeat, suggesting that these isolates coded for nonfunctional vWbl. Further, western blot analysis confirmed that all strains translated vWbl, and only vWbl proteins coded by genes with nine repeats were exported outside the cell. These results suggest that number of vWbl repeats in S. lugdunensis have clonal specificities and may correlate with potential pathogenicity.

Molecular Characteristics of Rifampin-Sensitive and -Resistant Isolates and Characteristics of rpoB Gene Mutations in Methicillin-Resistant Staphylococcus aureus

Introduction

Methicillin-resistant Staphylococcus aureus (MRSA) infections have become a leading cause of severe infections in both healthcare and community settings. Mutations in the rpoB gene cause resistance to rifampin (RIF^R), a critical antibiotic for the treatment of multidrug-resistant Staphylococcus aureus. The aim of this study was to detect the molecular characteristics of RIF^R MRSA and analyze the rpoB gene mutations involved in RIF resistance.

Methods

A total of 49 RIF^R MRSA and 38 RIF^S MRSA isolates collected from seven cities in China were analyzed by multilocus sequence typing, staphylococcus chromosomal cassette mec (SCCmec) typing, spa typing, and rpoB gene mutations.

Results

ST239-III-t030 (35/49, 71.4%), the major clone in RIF^R MRSA isolates; ST45-IV-t116 (16/38, 42.1%), the major clone in RIF^S MRSA isolates with rpoB mutations. RIF^R MRSA isolates were resistant to erythromycin, ciprofloxacin, tetracycline, gentamicin, and clindamycin. By contrast, RIF^S MRSA isolates with rpoB mutation were more susceptible to ciprofloxacin, tetracycline, and gentamicin. Forty-three (87.8%) isolates present the mutational change H481N and L466S, conferring 128–512 μg/mL RIF resistance. The four isolates with RIF MIC ≥ 1024 μg/mL had additional amino acid substitution: H481N, L466S, A473T (n=2); H481Y (n=2), associated with a high-level RIF resistance. Of 38 RIF^S MRSA isolates, two mutations were observed, including H481N (n=37) and A477D (n=1).

Conclusion

In conclusion, the predominant RIF^R MRSA clones in China were ST239-III-t030. Molecular characteristics, antibiotic-resistant profiles, and rpoB mutations between RIF^R MRSA and RIF^S MRSA were diverse. Antibiotics for treating patients with MRSA infections can be selected based on molecular characteristics.

Methicillin-Resistant Coagulase Negative Staphylococci and Their Antibiotic Susceptibility Pattern from Healthy Dogs and Their Owners from Kathmandu Valley

This cross-sectional study was designed to identify information on the frequency, antimicrobial resistance and species diversity of methicillin-resistant coagulase negative staphylococci (MRCoNS) among pet dogs and humans within households. Fifty five nasal swabs each from dogs and their owners were collected. MRCoNS were identified based on gram staining, culture on mannitol salt agar, biochemical tests, and mecA gene amplification. The antibiotic susceptibility of the isolates was assessed by a disc diffusion test. Uniplex and multiplex polymerase chain reaction (PCR) were employed for the species identification of MRCoNS and SCCmec typing, respectively. Species were further confirmed by MALDI-TOF-MS. The prevalence of MRCoNS was 29% in dog owners and 23.6% in dogs. Four different species of MRCoNS, Staphylococci saprophyticus (48.3%), S. haemolyticus (24.1%), S. warneri (17.2%), and S. epidermidis (10.3%), were detected. Two isolates each from dog owners and dogs showed a constitutive resistance to macrolide-lincosamide-streptogramin B (cMLSB) resistance, eight isolates each from dogs and their owners showed a macrolide-streptogramin B (MSB) resistance, and only two isolates from dog owners revealed an inducible resistance to macrolide-lincosamide-streptogramin B (iMLSB) resistance. SCCmec types were SCCmec type IV (55.2%), SCCmec type V (24.1%), SCCmec III (10.3%), SCCmec II (3.4%); two isolates were non-typable. MRCoNS are prevalent and genetically diverse in companion animals and humans. Different species of MRCoNS were found in dogs and their owners.

Antimicrobial Resistance and Molecular Epidemiological Characteristics of Methicillin-Resistant and Susceptible Staphylococcal Isolates from Oral Cavity of Dental Patients and Staff in Northern Japan

The acquisition of drug resistance and virulence by staphylococcal species colonizing humans is a growing public health concern. The present study was conducted to investigate the prevalence, antimicrobial resistance and genetic characteristics of Staphylococcus isolates from the oral cavity and skin (hand) of systemically healthy subjects with dental disease and dental staff in northern Japan. Among a total of 133 subjects (91 patients and 42 staff), 87 coagulase-positive Staphylococcus (83 S. aureus/4 S. argenteus) and 162 coagulase-negative Staphylococcus (CoNS) isolates were recovered from 59 (44.4%) and 95 (71.4%) subjects, respectively. Three oral isolates were methicillin-resistant S. aureus (MRSA) (3.6%, 3/83) that were genotyped as ST8-SCCmec-IVl, ST4775(CC1)-SCCmec-IVa and ST6562(CC8)-SCCmec-IVa. Remarkably, the ST6562 isolate harbored PVL genes on ΦSa2usa and type I ACME (arginine catabolic mobile element). Four methicillin-susceptible isolates were identified as S. argenteus belonging to ST1223 and ST2250, which harbored enterotoxin genes egc-2 and sey, respectively. Among the fourteen CoNS species identified, methicillin-resistant (MR) isolates were detected in five species (11 isolates, 13.3% of CoNS), with S. saprophyticus and S. haemolyticus being the most common. ACME was prevalent in only S. epidermidis and S. capitis. These findings indicated the potential distribution of USA300 clone-like MRSA, toxigenic S. argenteus and MR-CoNS in the oral cavity of dental patients.

Insights into the epidemiology of community-associated methicillin-resistant Staphylococcus aureus in special populations and at the community-healthcare interface

The current epidemic proportions of infections caused by Staphylococcus aureus strains and especially by methicillin-resistant S. aureus (MRSA) are one of today's many threats to global public health, particularly in underdeveloped countries where significant gaps on the subject exist. The rapid spread and diversification of pandemic clones that exhibit remarkably increasing virulence and antimicrobial resistance pose a risk to the effective prevention and treatment of a wide range of infections. Undoubtedly, the remarkable versatility involving the pathogenesis and resistance of these bacteria is perpetuated through geographic and temporal factors inherent to clonal evolution and is reflected in the dramatic epidemiological changes of MRSA which, after decades prevailing in healthcare settings, have emerged in the community. Denominated community-associated [CA]-MRSA, these strains are particularly prevalent in some population groups, facilitating the spread of successful clones that are potentially capable of triggering severe community-acquired infections. Therefore, a broad approach to local epidemiological aspects in less studied regions, but nonetheless at latent risk of endemic spread that may reach global proportions, is necessary. In Brazil, despite limited molecular epidemiology data, CA-MRSA strains predominantly characterized as SCCmec IV, often classified as CC30-ST30, CC5-ST5 and CC8-ST8, seem to be spreading across different population groups in different regions of the country. Another important fact addressed in this review is the identification of the ST398-MRSA-IV/V clone and methicillin-susceptible S. aureus (MSSA) in healthy individuals from the community. Although susceptible to methicillin, the ST398 clone is associated with severe infections in humans and animals, denominated livestock-associated MRSA. It is therefore important to encourage assertive actions by all government sectors and by society, with a reassessment of current public health measures in light of the new perspectives arising from the scientific and epidemiological data on MRSA.

Environmental survey of Methicillin-Resistant Staphylococci in a Hospital in Japan

We examined the hospital-wide incidence of methicillin-resistant Staphylococcus contamination in a hospital environment to predict the risk of the nosocomial spread of infection. Samples were also taken different surfaces and medical equipment in a general hospital ward and a staff station. The isolates were identified bacterial strains and analyzed by PCR for detection of the mecA gene and staphylococcal cassette chromosome mec (SCCmec) types (I-V). Overall, out of 146 isolates that were screened, 15.7% of the samples in the hospital wards were contaminated with Staphylococcus aureus and 74.7% were isolated with coagulase-negative Staphylococci (CNS). The methicillin-resistant mecA gene was detected in all oxacillin-resistant S. aureus, and 89% of oxacillin-resistant CNS was identified as methicillin-resistant S. aureus (MRSA) and MRCNS respectively. All S. aureus and CNS from the hospital wards with MRSA patients were detected as MRSA and MRCNS. A widespread distribution of MRSA and MRCNS was detected in the Cuff. The majority of the MRSA and MRCNS isolates in this study were SCCmec type V, which are a community-acquired infection type. The increased incidence and prevalence of community-acquired MRSA and MRCNS, as well as hospital-acquired MRSA, should be recognized as serious healthcare problems.

Misidentification of meticillin-resistant Staphylococcus aureus by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021

We describe two false-negative results in the detection of meticillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 and spa type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.

Whole Genome Sequencing of Methicillin-Resistant Staphylococcus epidermidis Clinical Isolates Reveals Variable Composite SCCmec ACME among Different STs in a Tertiary Care Hospital in Oman

Staphylococcus epidermidis has been recently recognized as an emerging nosocomial pathogen. There are concerns over the increasing virulence potential of this commensal due to the capabilities of transferring mobile genetic elements to Staphylococcus aureus through staphylococcal chromosomal cassette (SCCmec) and the closely related arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER). The potential pathogenicity of S. epidermidis, particularly from blood stream infections, has been poorly investigated. In this study, 24 S. epidermidis isolated from blood stream infections from Oman were investigated using whole genome sequence analysis. Core genome phylogenetic trees revealed one third of the isolates belong to the multidrug resistance ST-2. Genomic analysis unraveled a common occurrence of SCCmec type IV and ACME element predominantly type I arranged in a composite island. The genetic composition of ACME was highly variable among isolates of same or different STs. The COMER-like island was absent in all of our isolates. Reduced copper susceptibility was observed among isolates of ST-2 and ACME type I, followed by ACME type V. In conclusion, in this work, we identify a prevalent occurrence of highly variable ACME elements in different hospital STs of S. epidermidis in Oman, thus strongly suggesting the hypothesis that ACME types evolved from closely related STs.

Characterization and Clonal Diffusion of Ceftaroline Non-Susceptible MRSA in Two Hospitals in Central Italy

Background: Ceftaroline represents a novel fifth-generation cephalosporin to treat infections caused by methicillin-resistant Staphylococcus aureus (MRSA). Methods: Ceftaroline susceptibility of 239 MRSA isolates was assessed by disk diffusion and a MIC test strip following both EUCAST and CLSI guidelines. Non-susceptible isolates were epidemiologically characterized by pulsed-field gel electrophoresis, spa typing, and multilocus sequence typing, and further investigated by PCR and whole genome sequencing to detect penicillin-binding protein (PBP) mutations as well as antibiotic resistance and virulence genes. Results: Fourteen isolates out of two hundred and thirty-nine (5.8%) were non-susceptible to ceftaroline (MIC > 1 mg/L), with differences between the EUCAST and CLSI interpretations. The characterized isolates belonged to seven different pulsotypes and three different clones (ST228/CC5-t041-SCCmecI, ST22/CC22-t18014-SCCmecIV, and ST22/CC22-t022-SCCmecIV), confirming a clonal diffusion of ceftaroline non-susceptible strains. Mutations in PBPs involved PBP2a for ST228-t041-SCCmecI strains and all the other PBPs for ST22-t18014-SCCmecIV and ST22-t022-SCCmecIV clones. All isolates harbored antibiotic resistance and virulence genes with a clonal distribution. Conclusion: Our study demonstrated that ceftaroline non-susceptibile isolates belonged not only to ST228 strains (the most widespread clone in Italy) but also to ST22, confirming the increasing role of these clones in hospital infections.

The Resistome and Mobilome of Multidrug-Resistant Staphylococcus sciuri C2865 Unveil a Transferable Trimethoprim Resistance Gene, Designated dfrE, Spread Unnoticed

Methicillin-resistant Staphylococcus sciuri (MRSS) strain C2865 from a stranded dog in Nigeria was trimethoprim (TMP) resistant but lacked formerly described staphylococcal TMP-resistant dihydrofolate reductase genes (dfr). Whole-genome sequencing, comparative genomics, and pan-genome analyses were pursued to unveil the molecular bases for TMP resistance via resistome and mobilome profiling. MRSS C2865 comprised a species subcluster and positioned just above the intraspecies boundary. Lack of species host tropism was observed. S. sciuri exhibited an open pan-genome, while MRSS C2865 harbored the highest number of unique genes (75% associated with mobilome). Within this fraction, we discovered a transferable TMP resistance gene, named dfrE, which confers high-level TMP resistance in Staphylococcus aureus and Escherichia coli. dfrE was located in a novel multidrug resistance mosaic plasmid (pUR2865-34) encompassing adaptive, mobilization, and segregational stability traits. dfrE was formerly denoted as dfr_like in Exiguobacterium spp. from fish farm sediment in China but escaped identification in one macrococcal and diverse staphylococcal genomes in different Asian countries. dfrE shares the highest identity with dfr of soil-related Paenibacillus anaericanus (68%). Data analysis discloses that dfrE has emerged from a single ancestor and places S. sciuri as a plausible donor. C2865 unique fraction additionally enclosed novel chromosomal mobile islands, including a multidrug-resistant pseudo-SCCmec cassette, three apparently functional prophages (Siphoviridae), and an SaPI4-related staphylococcal pathogenicity island. Since dfrE seems not yet common in staphylococcal clinical specimens, our data promote early surveillance and enable molecular diagnosis. We evidence the genome plasticity of S. sciuri and highlight its role as a resourceful reservoir for adaptive traits.

IMPORTANCE The discovery and surveillance of antimicrobial resistance genes (AMRG) and their mobilization platforms are critical to understand the evolution of bacterial resistance and to restrain further expansion. Limited genomic data are available on Staphylococcus sciuri; regardless, it is considered a reservoir for critical AMRG and mobile elements. We uncover a transferable staphylococcal TMP resistance gene, named dfrE, in a novel mosaic plasmid harboring additional resistance, adaptive, and self-stabilization features. dfrE is present but evaded detection in diverse species from varied sources geographically distant. Our analyses evidence that the dfrE-carrying element has emerged from a single ancestor and position S. sciuri as the donor species for dfrE spread. We also identify novel mobilizable chromosomal islands encompassing AMRG and three unrelated prophages. We prove high intraspecies heterogenicity and genome plasticity for S. sciuri. This work highlights the importance of genome-wide ecological studies to facilitate identification, characterization, and evolution routes of bacteria adaptive features.

Frequency, Distribution, and Antimicrobial Resistance of Coagulase-Negative Staphylococci Isolated from Clinical Samples in Dogs and Cats

This study aimed to investigate the frequency, distribution, and antimicrobial resistance of coagulase-negative staphylococci (CoNS) obtained from clinical samples from dogs and cats and to classify any methicillin-resistant CoNS (MRCoNS). The samples were collected in 2017-2018, and species identification and antimicrobial susceptibility testing were routinely performed using the Vitek2 system. Among 1,056 staphylococci, 185 CoNS (17.5%) were obtained and included 18 species from dogs (n = 116) and 14 species from cats (n = 69). The predominant species were Staphylococcus chromogenes (31.4%), Staphylococcus hominis ssp. hominis (16.2%), Staphylococcus warneri (10.8%), and Staphylococcus epidermidis (8.1%). The primary isolation sites were the skin and urinary tract. High levels of resistance to β-lactams (65.4%), tetracycline (44.3%), clindamycin (36.8%), and erythromycin (30.8%) were observed. Twenty-five MRCoNS (13.4%), mainly Staphylococcus haemolyticus (n = 8), S. epidermidis (n = 6), and S. hominis ssp. hominis (n = 5), were identified. SCCmec type V (n = 8) was the most common type, followed by SCCmec type IV (n = 6) and SCCmec type III (n = 2), whereas nontypable SCCmec were classified into nine MRCoNS. Some CoNS have been recorded in humans, and these might be transferred to and cause subsequent infections in humans. Moreover, the diversity of SCCmec types and resistant strains suggested that they may serve as a reservoir of resistance genes among staphylococci.

Genotypic Characterization of Clinical Isolates of Staphylococcus aureus from Pakistan

In this study, we compared pulsed-field gel electrophoretic (PFGE), multilocus sequence typing (MLST), Staphylococcal cassette chromosome mec (SCCmec), spa typing, and virulence gene profiles of 19 Panton–Valentine leucocidin (PVL)-positive, multidrug-, and methicillin-resistant clinical Staphylococcus aureus (MRSA) isolates obtained from a hospital intensive care unit in Pakistan. The isolates exhibited 10 pulsotypes, contained eight adhesin genes (bbp, clfA, clfB, cna, fnbA, fnbB, map-eap, and spa), 10 toxin genes (hla, hlb, hld, hlg, pvl, sed, see, seg, seh, and tst), and two other virulence genes (cfb, v8) that were commonly present in all isolates. The spa-typing indicated seven known spa types (t030, t064, t138, t314, t987, t1509, and t5414) and three novel spa types. MLST analysis indicated eight ST types (ST8, ST15, ST30, ST239, ST291, ST503, ST772, and ST1413). All isolates belonged to the agr group 1. Most of the isolates possessed SCCmec type III, but some isolates had it in combination with types SCCmec IV and V. The presence of multidrug-resistant MRSA isolates in Pakistan indicates poor hygienic conditions, overuse of antibiotics, and a lack of rational antibiotic therapy that have led to the evolution and development of hypervirulent MRSA clones. The study warrants development of a robust epidemiological screening program and adoption of effective measures to stop their spread in hospitals and the community.

Characterization and clonal representation of MRSA strains in Tuzla Canton, Bosnia and Herzegovina, from 2009 to 2017

Aim To characterize methicillin-resistant S. aureus (MRSA) strains phenotypically and genotypically and to determine their clonal affiliation, representation and antibiotic resistance profile. Methods A total of 62 randomly selected MRSA isolates of different clinical samples collected from 2009 to 2017 were phenotypically and genotypically analysed. Phenotypic analyses were performed by standard microbiological procedures, and using VITEK 2/AES instrument as well as MALDI-TOF (matrix-assisted laser desorption/ionization) technology. Genotypic characterization included spa, MLST (multilocus sequence typing) and SCCmec typing, and detection of the Panton-Valentine leukocidin (PVL) and other enterotoxin encoding genes. Results The largest number of isolates, 21 (33.87%) belonged to ST228-MRSA-I, spa type t041, t1003 and t001. Other major clones were: ST239-MRSA-III, spa type t037 and t030 (27.41%); ST8-MRSA-IV, spa type t008 and t121 (12.9%); ST247-MRSA-I, spa type t051 (4.83%). PVL was detected in 10 isolates (SCCmec IV/V). During 2009 and 2010 the most frequent MRSA strain was South German clone, ST228-MRSA-I (80% and 90%, respectively), while in later years it was replaced with Brazilian-Hungarian clone ST239-MRSA-III (75% in 2015 and 2016). The South German clone, spa type t041 in 90.48% of cases was resistant to clindamycin, ciprofloxacin, erythromycin, cefoxitin, gentamicin, kanamycin, tobramycin and penicillin, while 70.58% samples of the Brazilian-Hungarian clone spa type t037 were additionally resistant to tetracycline and rifampicin. Conclusion This research can supplement the existing knowledge about the clonal distribution of MRSA in Bosnia and Herzegovina and their sensitivity to antibiotics in order to improve the national control of these infections.

Coagulase-Negative Staphylococci Clones Are Widely Distributed in the Hospital and Community

Coagulase-negative staphylococci (CoNS) may be considered contaminants when isolated from clinical specimens but may also be a cause of true infection. This study aimed to compare the clonality and SCCmec type of a collection of CoNS isolated from blood cultures of inpatients, nasal swabs of healthy individuals, and patients with chronic wounds, all from the same community, using SCCmec typing, pulsed-field gel electrophoresis (PFGE), and MLST. Staphylococcus epidermidis, exhibited high clonal diversity, but hospital and community clusters were observed. Nosocomial S. epidermidis clones belonged to sequence types ST2, ST6, and ST23. Some Staphylococcus haemolyticus clones were found to circulate in the hospital and community, while Staphylococcus saprophyticus exhibited very high clonal diversity. Staphylococcus lugdunensis, Staphylococcus warneri, and Staphylococcus capitis revealed several isolates belonging to the same clone in the hospital and community. The detection of different SCCmec types within the same cluster indicated high diversity. S. epidermidis was associated with SCCmec I and III, S. haemolyticus with I and II, S. capitis with type V, Staphylococcus hominis with mec complex type A and ccr1, and S. warneri and S. saprophyticus with SCCmec I. The generation of elements and new combinations of cassette genes were highly associated with CoNS isolates, suggesting that SCCmec may not be a good marker of clonality in these bacteria.

Coagulase negative Staphylococcus bacteremia in hematopoietic stem cell transplant recipients: Clinical features and molecular characterization

The purpose of our study was to investigate the epidemiology of coagulase negative staphylococci (CoNS) responsible for bacteremia in hematopoietic stem cell transplant (HSCT) recipients and to determine the prevalence and the genetic background of methicillin resistance. The prevalence of CoNS bacteremia was 7.4% (54/728), higher in allograft (10.7%) than in autograft (4.7%) recipients. A sepsis or a septic shock were observed in 9% of cases. No deaths were attributable to CoNS bacteremia. The methicillin resistance rate was 81%. All MR-CoNS, harbored mecA gene and 90% were typeable with SCCmec typing using PCR amplification. The SCCmec type IV was the most frequent (44%). Clonal dissemination of MR- Staphylococcus epidermidis strains was limited. Our study showed a low prevalence and favorable outcome of CoNS bacteremia in HSCT recipients with limited clonal diffusion. However, they were associated with a significant rate of severe infections and a high rate of methicillin resistance, mediated by SCCmec IV element in most cases.

Characterisation of Staphylococcus aureus isolates from bovine mastitis in Ningxia, Western China

OBJECTIVES

The aim of this study was to explore the antimicrobial resistance, virulence genes and molecular characteristics of Staphylococcus aureus from bovine mastitis cases.

METHODS

A total of 125 non-duplicate S. aureus isolates from bovine mastitis cases in Ningxia, China, were characterised by antimicrobial susceptibility and molecular testing to determine the antimicrobial resistance, virulence genes and molecular characteristics.

RESULTS

All methicillin-resistant S. aureus (MRSA) isolates were resistant to ampicillin, oxacillin, ceftiofur, erythromycin, gentamicin and clindamycin, with resistance to nine different categories of antibiotics observed amongst the MRSA isolates. Of the methicillin-susceptible S. aureus (MSSA) isolates, 62.1% were resistant to ampicillin and sulfisoxazole. Nine clonal complexes (CCs) and 16 spa types were identified by multilocus sequence typing (MLST) and spa typing. The dominant CCs were CC97 (51.2%) and CC50 (30.4%), while t224 (30.4%), t518 (20.0%) and t359 (16.8%) were the most common spa types. A relatively high proportion (27.2%) of the S. aureus isolates belonged to ST4053, a novel sequence type identified in this study. In addition, two CC30 MSSA isolates and two CC59 MRSA isolates were positive for Panton-Valentine leukocidin, while one CC239 MRSA isolate and three CC5 MSSA isolates were positive for TSST-1. All MRSA isolates carried the immune evasion cluster (IEC) genes, including scn (100%; 9/9) and sak (100%; 9/9), which were classified into type E.

CONCLUSION

Our study indicates severe antibiotic resistance and complicated molecular characterisation of S. aureus causing bovine mastitis. Additional studies should be conducted to monitor infection and transmission of S. aureus.

Investigation of SCCmec types I-IV in clinical isolates of methicillin-resistant coagulase-negative staphylococci in Ahvaz, Southwest Iran

Today methicillin resistant coagulase-negative staphylococci (MR-CoNS) are important in terms of causing significant nosocomial infections. Besides, MR-CoNS are confirmed as the reservoir of SCCmec elements that carry mecA (methicillin-resistant) gene. Hence, the present study was designed to evaluate the susceptibility pattern, prevalence and diversity of SCCmec types I, II, III, and IV in MR-CoNS strains. In this cross-sectional study, 44 clinical isolates of MR-CoNS were identified using the cefoxitin disc method and further confirmation by polymerase chain reaction (PCR) amplification of the mecA gene. Antimicrobial susceptibility of isolates was investigated by disc diffusion. The identification of CoNS was done by amplification and sequencing of the tuf gene. Multiplex PCR method was done for the determination of SCCmec types. In the present study, the Staphylococcus epidermidis and Staphylococcus haemolyticus were the most predominant isolates with a prevalence of 45.4%. The highest resistance rates were observed against erythromycin (84.1%) and clindamycin (75%). Multiplex PCR revealed the SCCmec type I as the predominant type in the present study. Our study showed that there was no significant relationship between the presence of different types of SCCmec elements and resistance to antibiotics. The present study highlighted a frequent prevalence of MR-CoNS harboring SCCmec type genes in Ahvaz, southwest of Iran. Thus, the molecular typing and periodical monitoring of their drug resistance pattern should be considered in national stewardship programs to designing useful antibiotic prescription strategies.

Accurate detection of oxacillin-resistant Staphylococcus lugdunensis by use of agar dilution

BACKGROUND/PURPOSE

Staphylococcus lugdunensis is a Gram-positive coagulase-negative bacterium and is recognized as a critical pathogenic species recently. Here, we aimed to evaluate the cefoxitin disk diffusion (CDD), oxacillin agar dilution (OAD), and mecA PCR for detecting oxacillin-resistant S. lugdunensis (ORSL) isolates.

METHODS

Multilocus sequence typing (MLST) analysis was performed to determine the clonality of 117 S. lugdunensis isolates isolated between May 2009 and Jul 2014. CDD, OAD, and mecA PCR were used to identify oxacillin-resistant S. lugdunensis (ORSL).

RESULTS

MLST results showed that the most common sequence type (ST) of our S. lugdunensis isolates was ST6 (35.9%) followed by ST3 (28.2%), ST27 (17.9%), and ST4 (6.8%). CDD and OAD showed that 39 and 43 isolates were ORSL, respectively. 4 ST3 CDD-susceptible S. lugdunensis (OSSL) isolates had MIC values ≥ 4 for oxacillin. mecA PCR results showed that 43 OAD-resistant S. lugdunensis and 3 OAD-susceptible ST27 S. lugdunensis had the mecA gene. Therefore, OAD was used as the gold standard to evaluate the performance of CDD and mecA PCR for identifying ORSL. The overall sensitivity, specificity, and accuracy of CCD for ORSL detection was 90.7%, 100%, and 96.8%, respectively. The sensitivity, specificity, and accuracy of mecA PCR for identifying ORSL was 100%, 95.9%, and 97.44%, respectively.

CONCLUSION

Our results indicate that OAD shows higher accuracy for ORSL detection compared with CDD and mecA PCR.

Distribution of virulence genes and SCCmec types among methicillin-resistant Staphylococcus aureus of clinical and environmental origin: a study from community of Assam, India

Objective

This study was designed to discover the dissemination of virulence genes in Methicillin-resistant Staphylococcus aureus from clinical, community and environmental settings.

Results

This study includes 1165 isolates collected from hospital, community and environmental settings. Among them sixty three were confirmed as MRSA with varied SCCmec types viz; type I, type II, type III, type IV, type V, type VI, type VII, type VIII and type XII. The virulence gene such as sea (n = 54), seb (n = 21), eta (n = 27), etb (n = 2), cna (n = 24), ica (n = 2) and tst (n = 30) was also revealed from this study. The study underscores coexistence of resistance cassette and virulence genes among clinical and environment isolates which is first of its kind from this part of the world.

Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence

There is increased awareness of the worldwide spread of specific epidemic multidrug-resistant (MDR) lineages of the human commensal Staphylococcus epidermidis. Here, using bioinformatic analyses accounting for population structure, we determined genomic traits (genes, SNPs and k-mers) that distinguish S. epidermidis causing prosthetic-joint infections (PJIs) from commensal isolates from nares, by analysing whole-genome sequencing data from S. epidermidis from PJIs prospectively collected over 10 years in Sweden, and contemporary S. epidermidis from the nares of patients scheduled for arthroplasty surgery. Previously suggested virulence determinants and the presence of genes and mutations linked to antimicrobial resistance (AMR) were also investigated. Publicly available S. epidermidis sequences were used for international extrapolation and validation of findings. Our data show that S. epidermidis causing PJIs differed from nasal isolates not by virulence but by traits associated with resistance to compounds used in prevention of PJIs: β-lactams, aminoglycosides and chlorhexidine. Almost a quarter of the PJI isolates did not belong to any of the previously described major nosocomial lineages, but the AMR-related traits were also over-represented in these isolates, as well as in international S. epidermidis isolates originating from PJIs. Genes previously associated with virulence in S. epidermidis were over-represented in individual lineages, but failed to reach statistical significance when adjusted for population structure. Our findings suggest that the current strategies for prevention of PJIs select for nosocomial MDR S. epidermidis lineages that have arisen from horizontal gene transfer of AMR-related traits into multiple genetic backgrounds.

First Report on the Characteristics of Methicillin-Resistant Staphylococcus Capitis Isolates and an NRCS-A-clone Related Isolate Obtained from Iranian Children

BACKGROUND

Methicillin-resistant staphylococcus capitis (MRSC) NRCS-A clone (Multi- resistant and vancomycin-non susceptible) has been recently described as an emerging cause of nosocomial bacteremia, especially in neonatal intensive-care units (NICUs).

OBJECTIVE

The objective of this study was to evaluate the antibiotic and antiseptic resistance patterns, biofilm-producing ability and the prevalence of SCCmec and ACME types among MRSC isolates as well as to check the possible presence of NRCS-A clone at Tehran's Children's Medical Center, Iran.

METHODS

A total of 256 coagulase-negative Staphylococcal isolates were collected, of which 10 S. capitis isolates were obtained and tested for susceptibility against 13 antimicrobial and 3 antiseptic agents, as well as biofilm production. The presence of 15 distinct resistance genes, staphylococcal cassette chromosome mec (SCCmec), and arginine catabolic mobile elements (ACMEs) were tracked.

RESULTS

Seven out of 10 S. capitis isolates were MRSC (MIC90 van=8μg/mL) and resistant to trimethoprim/sulfamethoxazole, produced biofilm, (3 as strong biofilm producers) and carried ACME types I and II. Despite the identification of mec and ccr complexes in some isolates, all the SCCmec cassettes were untypeable (UT).

CONCLUSION

According to the studied features, only one isolate belonged to the NRSC-A clone. The results indicate that MRSC with high antibiotic resistance and unknown SCCmec might become a serious problem in the future for the treatment of patients, particularly children.