Molecular characterization of methicillin-resistant Staphylococcus aureus: characterization of major clones and emergence of epidemic clones of sequence type (ST) 36 and ST 121 in Tehran, Iran

Hospital-Related Lineage of USA300 Methicillin-Resistant Staphylococcus aureus (MRSA) to Cause Bacteremia in Iran

Staphylococcus aureus is an important pathogen that causes bloodstream infections. This study is aimed at assessing the genotypic characteristics of S. aureus strains responsible for bloodstream infections. An epidemiological study was conducted using 85 S. aureus strains isolated from bloodstream infections. Susceptibility was tested using the broth microdilution method and disk diffusion. All detected methicillin-resistant S. aureus (MRSA) isolates were confirmed by mecA PCR assays. S. aureus isolated from bacteremia were characterized using SCCmec, spa, and multilocus sequence typing methods. The prevalence of S. aureus strains responsible for bloodstream infections was 38.8%. All isolates were MRSA. Multidrug resistance (MDR) was present in 84.7% of isolates. MRSA isolated categorized within six clonal complexes including CC8 (60%), CC22 (22.4%), CC5 (5.9%), CC30 (4.7%), CC45 (4.7%), and CC59 (2.3%). The main lineages found were USA300/CC8-MRSA-IV/t008 (41.2%), followed by ST22-SCCmecIV/t790 (9.4%), ST239-SCCmecIII/t037 (7.1%), ST22-SCCmecIV/t032 (7.1%), ST239-SCCmecIII/t631 (5.9%), ST239-SCCmecIII/t860 (5.9%), ST22-SCCmecIV/t852 (5.9%), ST5-SCCmecIV/t002 (4.7%), ST45-SCCmecIV/t038 (4.7%), ST30-SCCmecIV/t318 (4.7%), ST59-SCCmecIV/t437 (2.3%), and ST225-SCCmecII/t045 (1.1%). Resistance to vancomycin amounted to 5.9% of isolates that belonged to ST239-SCCmecIII/t037 (80%) and ST8-SCCmecIV/t008 (20%). The emergence of USA300 strains in bloodstream infections in our country is a serious alarm and highlights the significant invasion of this lineage into the healthcare system. MDR patterns among these strains appear to be becoming the biggest problem in healthcare treatment.

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

Background

Some Staphylococcus aureus strains produce Panton-Valentine leukocidin (PVL), a bi-component pore-forming toxin, which causes leukocyte lysis and tissue necrosis. Currently, there is very limited information on the molecular epidemiology of PVL-encoding S. aureus strains in Iran. This study aimed to determine the molecular epidemiology and genetic background of PVL-positive S. aureus clinical strains isolated from Iranian patients.

Methods

A total of 28 PVL-positive S. aureus strains were detected from 600 S. aureus isolates between February 2015 and March 2018 from different hospitals in Tehran, Iran. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Molecular genotyping was performed using SCCmec and accessory gene regulator (agr) typing, PVL haplotyping, multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE).

Results

The highest antibiotic resistance rate was found to be against erythromycin (57.1%), followed by ciprofloxacin (42.8%) and clindamycin (35.7%). Moreover, 19 (67.9%) out of 28 S. aureus isolates were identified as MRSA, including CA-MRSA (14/19, 73.7%) and HA-MRSA (5/19, 26.3%). SCCmec type IVa was detected as the predominant type (10/19, 52.6%), followed by type III (5/19, 26.3%) and type V (4/19, 21.1%). The agr type I was identified as the most common type (14/28, 50%), and H and R haplotype groups were observed at frequencies of 67.9 and 32.1%, respectively. Among H variants, the predominant variant was H2 (78/9%). The isolates encompassed 21 different sequence types (STs), including 16 new STs (ST5147 to ST5162). Based on eBURST analysis, the isolates were clustered into five CCs, including CC30, CC22, CC1, CC8, and CC5 (ST5160), and nine singletons. PFGE typing showed that 24 isolates were clustered into A (4 pulsotypes), B (9 pulsotypes), and C (11 pulsotypes) clusters.

Conclusions

A high prevalence of PVL-positive CA-MRSA strains was detected in Iran. The majority of PVL-positive isolates were of H (mostly H2) variant, while R variant was harbored by 100% of PVL-positive MRSA strains. Also, CC8, CC22, and CC30 were identified as the dominant clones among PVL-encoding S. aureus strains. This study promotes a better understanding of the molecular epidemiology and evolution of PVL-positive S. aureus strains in Iran.

The Expression of Efflux Pump Genes in Methicillin-Resistant Staphylococcus aureus (MRSA) Strains Isolated from Blood Cultures in Iran

Background: Efflux pump is a significant resistance mechanism in Staphylococcus aureus. A total of 100 patients with bacteremia from Shahid Beheshti University Hospitals of Tehran in Iran were tested for the expression of efflux pump genes, contributing to S. aureus antimicrobial resistance. Objectives: This study was conducted to identify antibiotic resistance pattern, and to evaluate the inhibitory effect of efflux pump, MIC of ciprofloxacin, and expression levels of norA, norB, and norC efflux pump genes in the presence of an efflux pump inhibitor against MDR S. aureus. Methods: A total of 100 MRSA isolates were investigated in different hospitals of Shahid Beheshti University of Medical Sciences from April 2017 - 2018. Owing to new consensus guidelines from the Clinical and Laboratory Standards Institute (CLSI), both the Kirby-Bauer disk diffusion test and micro-dilution method were used to evaluate antimicrobial susceptibility. Efflux pump activity using carbonyl cyanide 3-chlorophenylhydrazone (CCCP) was identified as a chemical efflux pump inhibitor. E-test was used to determine vancomycin-resistant antibiotic. Broth micro-dilution method for S. aureus isolates resistant to ciprofloxacin has been developed for minimum inhibitory concentration (MIC) of ciprofloxacin and CCCP and their composition. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to investigate the expression level of norA, norB, and norC efflux pump genes. Results: A total of 38 of 45 MRSA isolates (84.4%) showed resistance to ciprofloxacin. Moreover, 100% of isolates had the norA and norB genes. Further, 95% of S. aureus isolates had the norC gene. According to this study, ciprofloxacin MIC has decreased by CCCP compared to ciprofloxacin. There was an increase in the expression level of norA, norB, and norC efflux pump genes in methicillin-resistant and ciprofloxacin-resistant S. aureus strains based on RT- PCR. In this study, four different spA types were obtained as the most prevalent type of spA by t037and t790 (23.3%) and t030 (14.1%) and t044 (12.2%). Conclusions: This study indicates that the prevalence of ciprofloxacin-resistant S. aureus strains has a rising trend among MRSA clinical isolates. The ability of S. aureus isolates to be converted into drug-resistant strains using efflux pump mechanism has become a widespread concern.

Characteristics of methicillin-resistant Staphylococcus aureus carrying the toxic shock syndrome toxin gene: high prevalence of clonal complex 22 strains and the emergence of new spa types t223 and t605 in Iran

Methicillin-resistant Staphylococcus aureus (MRSA) strains that carry the tst gene are disseminated worldwide with varying regional incidences and different genetic backgrounds. The data on molecular characteristics of these strains is insufficient in Iran. The present study aimed to assess the characteristics and distribution of spa types of tst-positive MRSA strains. We investigated 89 MRSA isolates carrying the tst gene with spa typing, resistance gene detection and in vitro antimicrobial susceptibility. Of the 89 tested isolates, 61 (68.5%) were confirmed as multidrug resistant (MDR). The isolates were distributed across seven clonal complexes (CCs) including CC22 (42.7%), CC8 (28.1%), CC5 (11.2%), CC59 (5.6%), CC30 (4.5%), CC80 (4.5%) and CC15 (3.4%). spa typing identified 11 distinct types, with t223 (16.9%) and t790 (15.7%) being the most prevalent. All high-level mupirocin-resistant strains belonged to t002 (n = 8) and low-level mupirocin-resistant strains belonged to t790 (n = 6) spa types. Fusidic-acid-resistant isolates belonged to t437 (n = 3). iMLS_B phenotype was observed in t005 (6.7%), t002 (5.6%), t790 (3.4%), and t030, t044 and t084 (each 2.2%). It was found that in the tst-carrying MRSA strains, there were genetic diversities with a majority of the t223 spa type. Indeed, there is a necessity for more constructive surveillance/infection control strategies to address the prevalence and prevention of the emerging spa types.

Molecular Characteristics of Methicillin-Resistant Staphylococcus aureus (MRSA) Isolated from Diabetic Foot Infection

Background & Objective:

Diabetic foot ulcer (DFU), is one of the most frequent causes for hospitalizations in patients with diabetes. A major problem in the treatment of DFU is the increased-incidence of methicillin-resistant Staphylococcus aureus (MRSA). The aim of this study was to determine the SCCmec types of MRSA isolates and their epidemiology among patients with diabetes.

Methods:

This study was carried out on 145 diabetic patients with DFUs. The antibiotic susceptibility tests (ASTs) were performed using the disk diffusion method and E-test technique. SCCmec typing was done by multiplex PCR. Moreover, the presence of virulence toxin genes, including pvl and lukED was detected by PCR assay.

Results:

In 145 samples from which S. aureus was predominantly isolated, 19.48% were MRSA. Analysis of MRSA isolates revealed that the most prevalent SCCmec type was type IV (46.7%) followed by type III (30.0%) and type V (20.0%). One strain (3.3%) was untypeable. The prevalence of pvl and lukED was 56.7% and 100%, respectively.

Conclusion:

The high prevalence of MRSA in DFUs represents the high levels of antibiotic usage among patients with diabetes. In this study, resistance to other important clinical antibiotics was detected among MRSA isolates. The high proportion of SCCmec type IV and V strains, even in former hospitalized patients, indicates the entrance of these clones to the clinical setting.

Genetic Diversity Analysis of Methicillin-resistant Staphylococcus aureus Strains Isolated from Intensive Care Unit in Iran

Objectives

Staphylococcus aureus has emerged as a major public health concern. It is a common pathogen in high-risk hospital intensive care units (ICUs). We analyzed the molecular characteristics on the SCCmec and spa genes of S. aureus isolates gathered from ICUs. The antibiotic resistance patterns and carriage of resistance and virulence determinants were also identified.

Methods

In this cross-sectional study, 84 non-duplicated S. aureus strains isolated from ICU patients in were genotyped using SCCmec and spa typing. The Kirby-Bauer disk diffusion and micro-broth dilution methods were used to determine resistance patterns. Virulence and resistance gene profiling were also determined using the polymerase chain reaction technique.

Results

All isolates were methicillin-resistant S. aureus and belonged to seven spa types: t388 (36.9%), t852 (14.3%), t924 (13.1%), t790 (11.9%), t064 (10.7%), t037 (9.5%), and t084 (3.6%). They differed in the carriage of resistance and toxin genes. The most common SCCmec type was III detected in 50 isolates (59.5%), followed by type IV in 34 isolates (40.5%). The pvl gene was detected in 14.3% (n = 12) of isolates, of which 66.7% (n = 8) belonged to t852 and 33.3% (n = 4) belonged to t790. Among the tested strains, 9.5% (n = 8) carried the mupA gene and belonged to the t064 spa type.

Conclusions

The data revealed a high resistance rate to antibiotics, which could be a threat to ICU patients. It is necessary to detect antimicrobial resistance and resistance and toxin-encoding of gene profiles in different molecular types.

Real-time PCR followed by high-resolution melting analysis - a new robust approach to evaluate SCCmec typing of methicillin-resistant Staphylococcus aureus

AIM

We designed a novel approach based on real-time PCR followed by high-resolution melting (HRM) analysis to determine the Staphylococcal cassette chromosome mec (SCCmec) types of methicillin-resistant Staphylococcus aureus  strains, which we compared against the results of conventional multiplex PCR SCCmec typing.

METHODS

Multiplex PCR (for ccr and mec gene complexes) was carried out as conventional method. The HRM analysis was then designed using standard strains of each SCCmec type.

RESULTS

The M-PCR results included types III (33.33%), IV (43.33%) and V (23.33%). HRM analysis was able to distinguish all five types, which were used to set up the protocol with a sensitivity and specificity of 100% compared with the conventional method.

CONCLUSION

This novel method for SCCmec typing has high specificity and sensitivity and can be conducted in a shorter period of time at lower costs.

Molecular analysis of immune evasion cluster (IEC) genes and intercellular adhesion gene cluster (ICA) among methicillin-resistant and methicillin-sensitive isolates of Staphylococcus aureus

Introduction

Resistance to antibiotics and presence of virulence factors play an important role in increased mortality associated with infection due to Staphylococcus aureus. In this study, we determine antibiotic resistance pattern, presence of the icaADBC locus as well as biofilm formation and distribution and diversity the immune evasion cluster (IEC) genes in clinical isolate of S. aureus from Kerman, Iran.

Materials and methods

During 15 months, 100 clinical isolates S. aureus recovered from different patients were admitted to Kerman University affiliated hospitals. Resistance to different antibiotic agents was determined by disk diffusion method. Phenotypic method was used to the determination of biofilm formation ability and methicillin-resistance S. aureus (MRSA). Polymerase chain reaction technique (PCR) was used to the detection of nuc, mecA, icaA, icaD, icaB, icaC, scn, sea, sak, sep and chp genes.

Results

Forty-four isolates were considered as MRSA and all of isolates were sensitive to vancomycin and linezolid. Our results showed, 77.2% (34/44) of MRSA and 8.9 % (5/56) of MSSA isolates were multidrug resistant. The predominant IEC variant was type B and our results displayed that 77.7% of the MRSA isolates harbor loci icaD and mecA. There was no significant difference in production biofilm between MSSA and MRSA isolates (P ≥ 0.05). There was significant difference in presence IEC types between MSSA and MRSA isolates (P = 0.000).

Conclusions

The presence of icaADBC locus may not be a determining factor for biofilm formation in Staphtlocooci and other mechanisms might be involved in this process.The high prevalence IEC types in MSSA isolates can indicate that the presence of these genes can be an advantage for pathogenesis of these isolates in different infections.

Prevalence of sea, seb, sec, sed, and tsst-1 genes of Staphylococcus aureus in nasal carriage and their association with multiple sclerosis

Background

Microbial superantigens might initiate or exacerbate autoimmune responses against particular tissues, organs or systems. This study aimed to examine the prevalence of sea, seb, sec, sed, and tsst-1 genes of Staphylococcus aureus in nasal carriage and their association with multiple sclerosis (MS).

Methods

Nasal swabs were collected from 150 MS patients and 150 healthy individuals (control group) to isolate S. aureus and investigate their superantigen genes (sea, seb, sec, sed and tsst-1) using PCR.

Results

A total of 300 participants were enrolled in the study, matched for age and gender (150 patients in the MS group and 150 in the control group). The prevalence of S. aureus colonization in MS patients and control groups was 42% and 23.3%, respectively. There was a statistically significant association between S. aureus colonization and MS disease (p<0.001; odds ratio 2.4; 95% confidence interval 1.4-3.9). No significant association was observed between the presence of S. aureus harboring sea, seb, sec, sed and tsst-1 genes with MS disease.

Conclusion

The rate of S. aureus nasal carriage is higher in patients with MS. Our study's results suggest that further investigation into whether there is a connection between MS and nasal exposure to staphylococcal superantigens is warranted.

Prevalence of methicillin-resistant Staphylococcus aureus isolated from burn patients in Iran: A systematic review and meta-analysis

OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) is considered a major cause of infection and mortality in burn patients, especially when nosocomially acquired. However, limited information is available on the prevalence of MRSA among burn patients in Iran.

METHODS

A systematic search was performed using different electronic databases including Medline (via PubMed), Embase, Web of Science and Iranian Database. A meta-analysis was performed using Comprehensive Meta-Analysis Software (BioStat v.2.2). Use of a fixed- or random-effects model was used based on a heterogeneity test, and publication bias was assessed using Begg rank correlation and Egger weighted regression methods.

RESULTS

Of 555 articles published from January 2000 to January 2016, 13 studies were included in this review. The meta-analyses showed that the prevalence of MRSA infection in burn patients was 77.9% (95% confidence interval 70.2-84.0%) among culture-positive cases.

CONCLUSIONS

The results of this study indicate that the prevalence of MRSA among burn patients is very high in Iran. Thus, a comprehensive infection control strategy based on hand hygiene, education and training in antibiotic prescribing, environmental cleaning, contact precautions, good antibiotic stewardship and an active surveillance system on the basis of international criteria is urgently needed.

Molecular characterization of nasal methicillin resistant Staphylococcus aureus isolates from workers of an automaker company in southeast Iran

Colonization of methicillin resistant Staphylococccus aureus (MRSA) can occur more commonly in healthy people who live in close together or are in close physical contact with each other. Having knowledge about the molecular characteristics of these strains provides considerable discernment into the epidemiology of this important microorganism. A total of 806 nasal swabs were collected from healthy workers of an automaker company in the southeast of Iran and were analyzed to detect MRSA isolates. Multilocus sequence typing (MLST), spa typing, and detection of staphylococcal cassette chromosome mec (SCCmec) were performed. The presence of genes encoding Panton-Valentine Leukocidin (PVL) and Arginine Catabolic Mobile Element (ACME) were also investigated. Carriage rate of S. aureus was 20%. Among 10 identified MRSA, no acme was found while high prevalence of pvl (60%) was of great concern. Seven different spa types including five new ones were identified. The most frequent sequence type was the novel one; ST 3373 (n = 3), followed by each of ST22, ST88, ST859 (n = 2) and ST1955 (n = 1). MRSA isolates were clustered into two main clonal complexes; CC22 (n = 6) and CC88 (n = 4). Low genetic diversity with the dominance of CC22, SCCmecIV was found. Distribution of previously found hospital-associated MRSA was demonstrated among our isolates.

Staphylococcus aureus Toxins and Diabetic Foot Ulcers: Role in Pathogenesis and Interest in Diagnosis

Infection of foot ulcers is a common, often severe and costly complication in diabetes. Diabetic foot infections (DFI) are mainly polymicrobial, and Staphylococcus aureus is the most frequent pathogen isolated. The numerous virulence factors and toxins produced by S. aureus during an infection are well characterized. However, some particular features could be observed in DFI. The aim of this review is to describe the role of S. aureus in DFI and the implication of its toxins in the establishment of the infection. Studies on this issue have helped to distinguish two S. aureus populations in DFI: toxinogenic S. aureus strains (harboring exfoliatin-, EDIN-, PVL- or TSST-encoding genes) and non-toxinogenic strains. Toxinogenic strains are often present in infections with a more severe grade and systemic impact, whereas non-toxinogenic strains seem to remain localized in deep structures and bone involving diabetic foot osteomyelitis. Testing the virulence profile of bacteria seems to be a promising way to predict the behavior of S. aureus in the chronic wounds.

Molecular characterization of Staphylococcus aureus isolates from southwest of Iran using spa and SCCmec typing methods

Staphylococcus aureus remains a major cause of nosocomial infection worldwide. Characterization of S. aureus isolates circulating in the southwest of Iran will contribute to understand and control the spread of the strains in this area. spa and SCCmec typing methods were used for genotyping of 125 S. aureus isolates obtained from two teaching hospitals in Ahvaz. Drug susceptibility testing was performed by using disk diffusion method. Frequency of the methicillin resistant S. aureus (MRSA) isolates was 39% (n = 34) and 27% (n = 10) in Emam Khomeini and Golestan hospitals, respectively. Except for Erythromycin, MRSA strains showed high rate of resistance to antimicrobial agents including penicillin (100%), norfloxacine (80%), azitromycin (80%), ciprofloxacin (80%), gentamycin (77%), cotrimoxazole (75%), cephotaxime. All isolates were sensitive to vancomycin. Out of 44 MRSA strains, 39 (88.5%) were SCCmec III, three (7%) were IVc and two (4.5%) of them were nontypeable. spa types t037 (26 isolates; 59%), and t1149 (25 isolates; 31%) were the most dominant types found in MRSA and methicillin sensitive S. aureus (MSSA) strains, respectively. We found SCCmec type III as the most prominent type indicating that most of the studied bacterial population had hospital origin. spa type t037, the most frequent genotype in this study were significantly (100%) associated with MRSA. For the first time we are reporting spa types t692, t706 and t018 from Iran and t342, t704, t2622, t5598, t11270 and t2864 from Asia. Moreover we are reporting types t6871 and t2684 for the second time in the world.

Molecular characterization of Staphylococcus aureus isolates causing skin and soft tissue infections in patients from Malakand, Pakistan

Comparatively few studies have been published describing Staphylococcus aureus/MRSA epidemiology in Central Asia including Pakistan. Here, we report the genotyping of Staphylococcus aureus strains (that include both methicillin-susceptible and methicillin-resistant Staphylococcus aureus) from community- and hospital-acquired skin and soft-tissue infections in a tertiary care hospital in the Malakand district of the Khyber Pakhtunkhwa Province of Pakistan. Forty-five isolates of Staphylococcus aureus were characterized by microarray hybridization. Twenty isolates (44 %) were MRSA, whereas 22 (49 %) were PVL-positive. Fourteen isolates (31 %) harboured both mecA and PVL genes. The dominant clones were CC121-MSSA (n = 15, 33 %) and the PVL-positive "Bengal Bay Clone" (ST772-MRSA-V; n = 13, 29 %). The PVL-positive CC8-MRSA-IV strain "USA300" was found once. The pandemic ST239-MRSA-III strain was absent, although it has previously been observed in Pakistan. These observations require a re-assessment of schemes for initial antibiotic therapy to cover MRSA and they emphasise the need for a rapid and non-molecular test for PVL.

High frequency of multidrug-resistant Staphylococcus aureus with SCCmec type III and Spa types t037 and t631 isolated from burn patients in southwest of Iran

Methicilin resistance Staphylococcus aureus (MRSA) infections are the major challenges in hospitals, especially in the burn units. The use of molecular typing methods is essential for tracking the spread of S. aureus infection and epidemiological investigations. The aim of this study was to find the profile of the spa types and also the prevalence of each SCCmec type of S. aureus strains in a central burn hospital in southwest of Iran. A total of 81 non-duplicate S. aureus were isolated from burn patients between April 2011 and February 2012. The susceptibility of the isolates against 13 different antibiotics was tested by disk agar diffusion (DAD) method. MRSA strains were identified by amplification of mecA gene. Multiplex-polymerase chain reaction (PCR) technique was used to determine the SCCmec types of MRSA strains and all the S. aureus isolates were typed by spa typing method. Detection of mecA gene showed that 70 (86.4%) of the isolates were MRSA. The highest rate of resistance was observed for penicillin (97.5%) and erythromycin (77.8%). None of the isolates were resistant to vancomycin. Sixty-seven of the 70 MRSA isolates harbored only SCCmec type III and three untypeable isolates. Five different spa types were detected. The most common spa types were t037 (42.5%) and t631 (34.5%) and were only found in MRSA isolates. Only SCCmec type III was found in burn patients which emphasizes the HA-MRSA origin of these strains. Only five different spa types identified in this study are in accordance with one SCCmec type which indicates that a limited number of bacterial colons are circulated in the burn unit in this hospital.