Repeated introduction and spread of the MRSA clone t304/ST6 in northern Europe

Insights from a decade of surveillance: Molecular epidemiology of methicillin-resistant Staphylococcus aureus in Norway from 2008 to 2017

AIM

Norway has a low prevalence of methicillin-resistant Staphylococcus aureus (MRSA) and reporting of all MRSA cases has been mandatory, including infections and carriage, since 1995 and 2005 accordingly. This provides a unique window to study the spread of MRSA in Norway over time. The aim of this study was to analyze the nationwide trends in the molecular epidemiology of MRSA in Norway over a period of 10 years.

METHODS

Clinical and epidemiological data as well as bacterial genotype (spa-type and PVL) were analyzed for all reported MRSA cases in Norway in the period 2008-2017.

RESULTS

During the study period, there were 15,200 MRSA cases reported in Norway, from 14,386 patients. The notification rate per 100,000 population increased by 15% annually, rising from 14.2 in 2007 to 48.6 in 2017. This increase was primarily driven by MRSA carriage and community-associated MRSA cases. The incidence of invasive infections remained stable and low, at less than 0.5. The incidence of healthcare-associated MRSA showed an increasing trend, while the number of outbreak-related cases, particularly those associated with nursing homes, decreased. Overall, there were significantly more MRSA infections in males than females. Interestingly, there was a significantly higher prevalence of MRSA infections in female young adolescents compared to males. spa-typing revealed a very heterogeneous MRSA population (D = 0.97), predominantly impacted by international travel and migration patterns, and less by domestic spread in the community.

CONCLUSIONS

This study highlights that Norway, while still classified as a low-prevalence country, has experienced a significant increase in the incidence of MRSA between 2008 and 2017, which can predominantly be attributed to CA-MRSA and MRSA carriage.

Genetic characterization of methicillin-resistant / susceptible Staphylococcus aureus (MRSA/MSSA) and Staphylococcus argenteus clinical isolates in Bangladesh: Dominance of ST6-MRSA-IV/t304 and detection of cfr/fexA in ST8-MSSA/t008

Objectives

Coagulase-positive staphylococcus (CoPS), represented by Staphylococcus aureus, is a major cause of infections in humans. This study aimed to investigate molecular epidemiological characteristics, antimicrobial resistance, and their trends of CoPS in Bangladesh.

Methods

Clinical isolates of CoPS were collected from two medical institutions in Bangladesh for a 2-year period and analyzed for their species, genotypes, virulence factors, antimicrobial susceptibility, and resistance determinants.

Results

172 CoPS isolates collected were identified as S. aureus or S. argenteus (170 and two, respectively). Methicillin-resistant S. aureus (MRSA) accounted for 36% (n = 61), having Staphylococcal cassette chromosome mec (SCCmec)-IV (82%) or V (18%). Panton-Valentine leukocidin (PVL) genes were detected at higher rate in methicillin-susceptible S. aureus (MSSA) (62%) than MRSA (26%). MRSA comprised 11 STs, including a dominant type ST6 (46%) associated with mostly SCCmec-IVa/spa-t304, and one isolate had genetic features of the USA300 clone (ST8/SCCmec-IVa/coa-IIIa/spa-t008/ACME-I/ΦSa2USA). STs of CC1, CC88, and CC398 were common in MSSA, with CC88 showing the highest PVL-positive rate. One MSSA isolate (ST8/spa-t008) harbored fexA and cfr showing susceptibility to linezolid. S. argenteus was methicillin-susceptible and belonged to ST2250/coa-XId.

Conclusions

Genetic characteristics of current MRSA/MSSA in Bangladesh were revealed, with first identification of S. argenteus at low prevalence.

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.

Methicillin-Resistant Staphylococcus aureus (MRSA) in a Tertiary Care Hospital in Kuwait: A Molecular and Genetic Analysis

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen that causes serious infections in healthcare facilities and in communities. The purpose of this study was to investigate MRSA isolates obtained in a tertiary hospital in Kuwait to assess their antibiotic susceptibility profile and clonal composition. Sixty MRSA isolates collected in 2020 were tested through antibiotic susceptibility testing, spa typing, and DNA microarray analysis. All isolates were found to be susceptible to vancomycin (MIC: ≤3 µg/mL), teicoplanin (MIC: ≤3 µg/mL), rifampicin, and mupirocin, but were resistant to fusidic acid (n = 43, 72%), trimethoprim (n = 27, 45%), ciprofloxacin (n = 31, 51.7%), gentamicin (n = 14; 23.3%), kanamycin (n = 20; 33.3%), chloramphenicol (n = 7; 11.7%), tetracycline (n = 17; 28.3%), erythromycin (n = 19; 31.6%), inducible clindamycin (n = 13; 21.7%), and constitutive clindamycin (n = 2; 3.3%). The isolates belonged to 30 spa types and 13 clonal complexes (CCs). The dominant spa types were t304, t442, t311, t688, and t1234, collectively constituting 28.3% of the isolates. The dominant CCs were CC5 and CC6, which together constituted 46.7% of the isolates. This study provides updated research on antibiotic resistance and changes in the clonal composition of MRSA in a Kuwait hospital, including the disappearance of the ST239-MRSA-III clone that was previously the dominant clone in this hospital.

Prevalence and Molecular Characterization of Methicillin-Resistant Staphylococci (MRS) and Mammaliicocci (MRM) in Dromedary Camels from Algeria: First Detection of SCCmec-mecC Hybrid in Methicillin-Resistant Mammaliicoccus lentus

Dromedary camels are an important source of food and income in many countries. However, it has been largely overlooked that they can also transmit antibiotic-resistant bacteria. The aim of this study was to identify the Staphylococcaceae bacteria composition of the nasal flora in dromedary camels and evaluate the presence of methicillin-resistant Mammaliicoccus (MRM) and methicillin-resistant Staphylococcus (MRS) in dromedary camels in Algeria. Nasal swabs were collected from 46 camels from seven farms located in two different regions of Algeria (M'sila and Ouargla). We used non-selective media to determine the nasal flora, and antibiotic-supplemented media to isolate MRS and MRM. The staphylococcal isolates were identified using an Autoflex Biotyper Mass Spectrometer (MALDI-TOF MS). The mecA and mecC genes were detected by PCR. Methicillin-resistant strains were further analysed by long-read whole genome sequencing (WGS). Thirteen known Staphylococcus and Mammaliicoccus species were identified in the nasal flora, of which half (49.2%) were coagulase-positive staphylococci. The results showed that four out of seven farms were positive for MRS and/or MRM, with a total of 16 isolates from 13 dromedary camels. The predominant species were M. lentus, S. epidermidis, and S. aureus. Three methicillin-resistant S. aureus (MRSA) were found to be ST6 and spa type t304. Among methicillin-resistant S. epidermidis (MRSE), ST61 was the predominant ST identified. Phylogenetic analysis showed clonal relatedness among M. lentus strains, while S. epidermidis strains were not closely related. Resistance genes were detected, including mecA, mecC, ermB, tet(K), and blaZ. An SCCmec type VIII element was found in a methicillin-resistant S. hominis (MRSH) belonging to the ST1 strain. An SCCmec-mecC hybrid element was detected in M. lentus, similar to what was previously detected in M. sciuri. This study highlights that dromedary camels may be a reservoir for MRS and MRM, and that they contain a specific set of SCCmec elements. This emphasizes the need for further research in this ecological niche from a One Health perspective.

Escalation of antimicrobial resistance among MRSA part 1: focus on global spread

INTRODUCTION

Staphylococcus aureus produce numerous virulence factors that influence tissue invasion, cytotoxicity, membrane damage, and intracellular persistence allowing them to be very common human pathogens. S. aureus isolates exhibit considerable diversity though specific genotypes have been associated with antimicrobial resistance (AMR) and toxin gene profiles. MRSA is an important pathogen causing both community-acquired (CA) and healthcare-acquired (HCA) infections. Importantly, over the past several decades, both HCA-MRSA and CA-MRSA have spread all over the globe. Even more concerning is that CA-MRSA clones have disseminated into hospitals and HCA-MRSA have entered the community. Factors that enhance spread of MRSA include: poor antimicrobial stewardship and inadequate infection control. The emergence and spread of multidrug resistant (MDR) MRSA has limited therapeutic options.

AREAS COVERED

The authors discuss the escalation of MRSA, both HCA-MRSA and CA-MRSA across the globe. A literature search of MRSA was performed via PubMed (up to September 2022), using the key words: antimicrobial resistance; β-lactams; community-associated MRSA; epidemiology; infection; multidrug resistance; Staphylococcus aureus.

EXPERT OPINION

Over the past several decades, MRSA has spread all over the globe. We encourage the judicious use of antimicrobials in accordance with antimicrobial stewardship programs along with infection control measures to minimize the spread of MRSA.

Evaluation of the Antibacterial Activity of Quinoxaline Derivative Compound Against Methicillin-Resistant Staphylococcus aureus

Background

While the frequency of methicillin-resistant Staphylococcus aureus (MRSA) continues to rise globally, there is a fear regarding an increase in vancomycin resistance among S. aureus strains. As far back as the 1960s, MRSA was one of the world's most prevalent antibiotic-resistant bacteria. Among hospitalized patients and community members, MRSA is the cause of a significant number of infections. As a result of its resistance to classical beta-lactam and, in some cases, vancomycin antibiotics, efforts must be made as soon as feasible to find a new approach to fighting MRSA.

Purpose

This study is designed to evaluate the antibacterial activity of quinoxaline derivative compound against MRSA in comparison with vancomycin as a reference drug.

Methods

Sixty MRSA isolates were subjected to susceptibility testing by broth microdilution method for quinoxaline derivative compound and vancomycin. Each drug's minimal inhibitory concentration (MIC) was determined and compared.

Results

Among the sixty MRSA isolates, most of the quinoxaline derivative compound MIC findings (56.7%) were 4 µg/mL compared to vancomycin MIC values (63.3%) of 4 µg/mL. In comparison, 20% of quinoxaline derivative compound MIC readings were 2 µg/mL, while the vancomycin MIC results were 6.7%. However, the overall proportion of MIC readings at ≤2 µg/mL for both antibacterial agents was equal (23.3%). None of the isolates were resistant to vancomycin.

Conclusion

This experiment revealed that most MRSA isolates were associated with low MICs (1-4 μg/mL) for quinoxaline derivative compound. Overall, the susceptibility of the quinoxaline derivative compound signifies a promising efficacy against MRSA and may set a novel treatment approach.

spa Typing of Methicillin-Resistant Staphylococcus aureus Based on Whole-Genome Sequencing: the Impact of the Assembler

Sequencing of the spa gene of methicillin-resistant Staphylococcus aureus (MRSA) is used for assigning spa types to e.g., detect transmission and control outbreaks. Traditionally, spa typing is performed by Sanger sequencing but has in recent years been replaced by whole-genome sequencing (WGS) in some laboratories. Spa typing by WGS involves de novo assembly of millions of short sequencing reads into larger contiguous sequences, from which the spa type is then determined. The choice of assembly program therefore potentially impacts the spa typing result. In this study, WGS of 1,754 MRSA isolates was followed by de novo assembly using the assembly programs SPAdes (with two different sets of parameters) and SKESA. The spa types were assigned and compared to the spa types obtained by Sanger sequencing, regarding the latter as the correct spa types. SPAdes with the two different settings resulted in assembly of the correct spa type for 84.8% and 97.6% of the isolates, respectively, while SKESA assembled the correct spa type in 98.6% of cases. The misassembled spa types were generally two spa repeats shorter than the correct spa type and mainly included spa types with repetition of the same repeats. WGS-based spa typing is thus very accurate compared to Sanger sequencing, when the best assembly program for this purpose is used. IMPORTANCE spa typing of methicillin-resistant Staphylococcus aureus (MRSA) is widely used by clinicians, infection control workers, and researchers both in local outbreak investigations and as an easy way to communicate and compare MRSA types between laboratories and countries. Traditionally, spa types are determined by Sanger sequencing, but in recent years a whole-genome sequencing (WGS)-based approach has become increasingly used. In this study, we compared spa typing by WGS using different methods for assembling the genome from short sequencing reads and compared to Sanger sequencing as the gold standard. We find substantial differences in correct assembly of spa types between the assembly methods. Our findings are therefore important for the quality of WGS based spa typing data being exchanged by clinical microbiology laboratories.

First Finding of a Methicillin-Resistant Staphylococcus aureus (MRSA) t304/ST6 from Bovine Clinical Mastitis

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) comprises a global threat to humans and animals. Here, we report and characterize the MRSA t304/ST6 variant which, to our knowledge, represents the first case found in bovine clinical mastitis. In general, the MRSA t304/ST6 variant is rarely described in livestock, contrary to humans where it is widely recognized. Phenotypic and genotypic resistance profiling showed that the bovine-MRSA t304/ST6 isolate expressed low susceptibility toward cefoxitin (MIC_cefoxitin = 16 µg/mL) and carried the mecA resistance gene in the SCCmec IVa. The bovine-MRSA t304/ST6 isolate carried a plasmid similar to that which has been frequently observed among human-MRSA t304/ST6 isolates in Denmark (GenBank accession no. NZ_CP047022). In addition, a Staphylococcus prophage 3 (ϕSA3) was detected, encoding an immune evasion cluster (IEC) of putative virulence genes associated with human host-specificity (sea, sak, and scn). Taken together, these findings suggest that the MRSA t304/ST6 found in this study represents a recent host-jump event, with human to cow transmission. This study emphasizes the importance of and the need for performance of antimicrobial resistance surveillance among bovine mastitis pathogens, including S. aureus and MRSA.

Genomic characterization of two community-acquired methicillin-resistant Staphylococcus aureus with novel sequence types in Kenya

Staphylococcus aureus is a clinically important bacteria with high antimicrobial resistance (AMR) challenge globally. The emergence of methicillin-resistant Staphylococcus aureus (MRSA) clones with unique sequence types have been identified in the community showing evidence that the epidemiology of MRSA globally is changing and requires continual surveillance. We utilized whole genome sequencing to characterize two community acquired-MRSA (CA-MRSA) strains isolated from wound swabs from community-onset infections in two health facilities in Kenya. The two strains belonged to multilocus sequence type (MLST) sequence type (ST) 7460, and ST 7635. The resistance genes detected showed that the novel STs are carriers of clinically relevant resistance genes. Linezolid and mupirocin resistance was observed, yet mupirocin is not commonly used in the country. Mutations within resistance genes were also detected and the pathogenicity toward the human host matched various pathogenic global S. aureus families, e.g., S. aureus subsp. aureus USA300. Multidrug efflux transporters, important in antimicrobial resistance including restriction enzymes type I and type IV were detected. Plasmids identified showed similarities with the plasmids in other clinically significant non-staphylococcal species, such as Pseudomonas aeruginosa, Escherichia coli, Morganella morganii, and Enterococcus faecium. Both STs belong to clonal complex 8 (CC8) which is the most successful MRSA clone in Kenya. Spa type t30 to which ST 7635 belongs has not been reported in the country. The results of this study further highlight the need for epidemiological studies to reveal circulating strains and antimicrobial resistance spread between hospitals and the community. The genomic research highlights resistance to anti-staphylococcal broad-spectrum antimicrobials not used frequently in the country, jeopardizing successful MRSA treatment since most health facilities do not perform genotypic resistance tests for routine patient management. Preliminary insights into unidentified STs of CA-MRSA in Kenya show the need for molecular epidemiological surveillance studies to further understand the diversity of S. aureus in Africa.

Lateral Flow Immunoassay for the Detection of Panton-Valentine Leukocidin in Staphylococcus aureus From Skin and Soft Tissue Infections in the United Arab Emirates

Introduction

Panton Valentine leukocidin (PVL) is a virulence factor which is associated with methicillin sensitive and resistant Staphylococcus aureus (MSSA/MRSA) causing skin and soft tissue infections (SSTI). This study aimed to evaluate a novel lateral flow immunoassay (LFI) for PVL detection in S. aureus cultures and to describe their genotypic characterization.

Methods

The study was carried out from January-August 2020 in Dubai, United Arab Emirates. S. aureus isolates associated with SSTI were tested for PVL detection using LFI. DNA microarray-based assays were used for molecular characterization including detection of pvl genes.

Results

One-hundred thirty-five patients with a clinical diagnosis of SSTIs were recruited. Sixty-six patients received antibiotics, mostly beta lactams (n=36) and topical fusidic acid (n=15). One-hundred twenty-nine isolates (MRSA: n=43; MSSA: n=86) were tested by LFI and DNA microarrays. All 76 (58.9%) isolates which were unambiguously negative for the PVL in LFI were negative for pvl genes using the DNA microarray. All the LFI PVL positive isolates (n=53) had pvl genes detected. This translates into 100% each for sensitivity, specificity, positive and negative predictive values for the LFI. The LFI typically takes about 15 min inclusive of a 10 min incubation period. Predominant S. aureus clonal complexes (CC) were CC30 (n=18), CC22 (n=13), CC5 (n=12), CC1 (n=11), CC152 (n=8), CC15 (n=7); CC97 (n=7); CC8 and CC20 (n=6 each). Among MRSA, the proportion of pvl-positives (35/43; 81%) was higher than among MSSA (n/N=18/86; 21%). The fusidic acid resistance gene fusC was detected in 14 MRSA (33%) compared to 8 MSSA (9%). A co-carriage of fusC and pvl genes was present in 7 MRSA and in one MSSA.

Conclusion

LFI shows excellent diagnostic accuracy indices for rapid identification of PVL in MSSA/MRSA in a setting with high prevalence of pvl^+ve strains. The high occurrence of pvl and fusC genes in MRSA strains causing SSTI is of concern and needs constant surveillance.

A tale of two STs: molecular and clinical epidemiology of MRSA t304 in Norway 2008-2016

The purpose of this study was to investigate the epidemiological, molecular, and clinical characteristics of MRSA t304/ST8 and t304/ST6 in Norway from 2008 to 2016. Clinical and epidemiological data were collected for each case included in the study. Strains were characterized by PCR, spa typing, antimicrobial susceptibility testing, and whole genome sequencing. The overall number of cases of MRSA t304 increased from 27 in 2008 to 203 in 2016. Most MRSA t304/ST8 cases were defined as HA-MRSA (89.9%) and diagnosed in persons with Norwegian background, many of them living in nursing homes (62.3%). The number of t304/ST8 cases declined throughout the study period and it has not been reported in Norway since 2014. The increasing MRSA t304/ST6 genotype has mainly been introduced to Norway by immigration from the Middle East, but also from other parts of the world. The t304/ST6 clone is mostly classified as CA-MRSA (75.1%), does not seem to cause serious infections, is not multi-resistant, and has not yet caused outbreaks in Norway. This study provides an example of two MRSA clones with the same spa type found in different epidemiological settings. This is very unusual, but still a reminder that spa typing in some cases may have insufficient discriminatory power for surveillance of MRSA. Our results highlight the importance of active surveillance and characterization of emerging MRSA clones with high potential for spread in the community, which may potentially cause outbreaks in healthcare facilities.

An amplification-free ultra-sensitive electrochemical CRISPR/Cas biosensor for drug-resistant bacteria detection

Continued development of high-performance and cost-effective in vitro diagnostic tools is vital for improving infectious disease treatment and transmission control. For nucleic acid diagnostics, moving beyond enzyme-mediated amplification assays will be critical in reducing the time and complexity of diagnostic technologies. Further, an emerging area of threat, in which in vitro diagnostics will play an increasingly important role, is antimicrobial resistance (AMR) in bacterial infections. Herein, we present an amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) to detect methicillin-resistant Staphylococcus aureus (MRSA). Using a custom-designed guide RNA (gRNA) targeting the mecA gene of MRSA, the Cas12a enzyme allows highly sensitive and specific detection when employed with silver metallization and square wave voltammetry (SWV). Our biosensor exhibits excellent analytical performance, with detection and quantitation limits of 3.5 and 10 fM, respectively, and linearity over five orders of magnitude (from 10 fM to 0.1 nM). Importantly, we observe no degradation in performance when moving from buffer to human serum samples, and achieve excellent selectivity for MRSA in human serum in the presence of other common bacteria. The E-Si-CRISPR method shows significant promise as an ultrasensitive field-deployable device for nucleic acid-based diagnostics, without requiring nucleic acid amplification. Finally, adjustment to a different disease target can be achieved by simple modification of the gRNA protospacer.

An amplification-free electrochemical CRISPR/Cas biosensor utilizing silver metallization (termed E-Si-CRISPR) allows detection of methicillin-resistant Staphylococcus aureus (MRSA) with excellent sensitivity and specificity.

Genomic Insights into Methicillin-Resistant Staphylococcus aureus spa Type t899 Isolates Belonging to Different Sequence Types

This study showed the genetic diversity and population structure of S. aureus presenting the same spa type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using spa typing only.

Methicillin-resistant Staphylococcus aureus (MRSA) presenting spa type t899 is commonly associated with sequence type 9 (ST9) but is also increasingly linked to ST398. This study provides genomic insight into the diversity of t899 isolates using core genome multilocus sequence typing (cgMLST), single nucleotide polymorphism (SNP)-based phylogeny, and the description of selected antimicrobial resistance and virulence markers. The SNP-based phylogenic tree showed that isolates sharing the same spa type (t899) but different STs highly diverged in their core and accessory genomes, revealing discriminant antimicrobial resistance (AMR) and virulence markers. Our results highlighted the idea that in a surveillance context where only spa typing is used, an additional multiplex PCR for the detection of the tet(M), sak, and seg genes would be valuable in helping distinguish ST9 from ST398 isolates on a routine basis.

IMPORTANCE This study showed the genetic diversity and population structure of S. aureus presenting the same spa type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using spa typing only. Given that identical spa types can be associated with different STs and that spa typing only is not appropriate for S. aureus isolates that have undergone major recombination events which include the passage of the spa gene (such as in t899-positive MRSA), the combination of both MLST and spa typing methods is recommended. However, spa typing alone is still largely used in surveillance studies and basic characterization. Our data suggest that additional markers, such as tet(M), sak, and seg genes, could be implemented in an easy and inexpensive manner in order to identify S. aureus lineages with a higher accuracy.