Staphylococcal Cassette Chromosome Research Articles

ST105 Lineage of MRSA: An Emerging Implication for Bloodstream Infection in the American and European Continents

Sequence-type 5 (ST5) of methicillin-resistant Staphylococcus aureus (MRSA), harboring the staphylococcal chromosomal cassette mec type IV (SCCmecIV), was first detected in Portugal. It emerged as a significant cause of healthcare-associated (HA) infection in pediatric units and was hence named the pediatric clone. Another ST5 lineage, which carries SCCmecII, also prevailed in the USA and Japan for multiple years. More recently, another MRSA lineage, ST105-SCCmecII, part of the evolution of clonal complex 5 (CC5) MRSA, has emerged as the cause of hospital-acquired bloodstream infection outbreaks in countries including Portugal, the USA, and Brazil. This article reviews studies on the epidemiology and evolution of these newly emerging pathogens. To this end, a search of PUBMED from inception to 2024 was performed to find articles reporting the occurrence of ST105 MRSA in epidemiologic studies. A second search was performed to find studies on MRSA, CC5, ST5, and SCCmecII. A search of PUBMED from 1999 to 2024 was also performed to identify studies on the genomics and evolution of ST5, CC5, and ST105 MRSA. Further studies were identified by analyzing the references of the previously selected articles from PUBMED. Most articles on ST105 MRSA were included in this review. Only articles written in English were included. Furthermore, only studies that used a reliable genotyping method (e.g., whole genome sequencing, or MLST) to classify the CC5 lineages were selected. The quality and selection of articles were based on the consensus assessment of the three authors in independent evaluations. In conclusion, ST105-SCCmecII is an emerging MRSA in several countries, being the second/third most important CC5 lineage, with a relatively high frequency in bloodstream infections. Of concern is the increased mortality from BSI in patients older than 15 years and the higher prevalence of ST105-SCCmecII in the blood of patients older than 60 years reported in some studies.

Genomic portraits of methicillin-resistant staphylococci (MRS) from food fish unveiled the genes associated with staphylococcal food poisoning (SFP), virulence and antimicrobial resistance

BackgroundCharacteristics of non-clinical strains of methicillin-resistant Staphylococcus aureus (MRSA) especially from fishery environment are poorly understood. This research, in addition to comprehensive characterisation, sought to delineate the genetic relatedness between the MRSA strains originating from clinical as well as non-clinical settings. Out of 39 methicillin-resistant staphylococcal isolates from 197 fish samples, 6 (Three each of methicillin-resistant S. haemolyticus (MRSH) and MRSA) with distinct resistance profiles were selected for whole-genome sequencing. Using respective bioinformatics tools, MRSA genomes were comprehensively characterized for resistome, virulomes, molecular epidemiology and phylogenetic analysis. Simultaneously, MRSH genomes were specifically examined to characterize antimicrobial resistance genes (ARGs), owing to the fact that MRSH is often recognized as a reservoir for resistance determinants.ResultsThree MRSA clones identified in this study include ST672-IVd/t13599 (sequence type-SCCmec type/spa type), ST88-V/t2526, and ST672-IVa/t1309. Though, the isolates were phenotypically vancomycin-sensitive, five of the six genomes carried vancomycin resistance genes including the VanT (VanG cluster) or VanY (VanM cluster). Among the three MRSA, only one harbored the gene encoding Panton-Valentine Leukocidin (PVL) toxin, while staphylococcal enterotoxin (SEs) genes such as sea and seb, associated with staphylococcal food poisoning were identified in two other MRSA. Genomes of MRSH carried a composite of type V staphylococcal cassette chromosome mec (SCCmec) elements (5C2 & 5). This finding may be explained by the inversion and recombination events that may facilitate the integration of type V elements to the SCC elements of S. aureus with a methicillin-susceptible phenotype. Phylogenetically, MRSA from a non-clinical setting displayed a considerable relatedness to that from clinical settings.ConclusionThis study highlights the genetic diversity and resistance profiles of MRSA and MRSH, with non-clinical MRSA showing notable relatedness to clinical strains. Future research should explore resistance gene transfer mechanisms and environmental reservoirs to better manage MRSA spread.

Virulence, Susceptibility Profile, and Clinical Characteristics of Pathogenic Coagulase-Negative Staphylococci.

Background Coagulase-negative staphylococci (CoNS) are emerging as clinically significant pathogens. A high proportion of methicillin resistance along with intensebiofilm-producing abilityrender CoNS-related infections challenging to treat. This study was undertaken to investigate the mechanisms of methicillin resistance, identify genes encoding for virulence, and their association with clinical outcomes among clinical isolates of Staphylococci in a tertiary care center. Methods A total of 203 clinical isolates were included in this study. Susceptibility to various antibiotics was determined by the disc diffusion method. Methicillin resistance was screened using cefoxitin disc, mecAand mecC genes were detected using polymerase chain reaction (PCR). PCR was performed to detect five virulence genes:atlE, aap, fbe, embp, and icaAB. Staphylococcal cassette chromosome mec (SCCmec) types were identified by multiplex PCR. Statistical analysis was performed using SPSS software (IBM Inc., Armonk, New York). The Chi-squared test was used to compare the distribution of virulence genes among methicillin-susceptible resistant CoNS. A p-value of less than 0.5 was considered significant. Results In the current study, 60% (122/203) of CoNS were methicillin-resistant, and SCCmec type Iwas the most common. Among the 203 CoNS, 24.6% (50/203) isolates harbored one or more virulence genes in them. Conclusion CoNS have relatively low virulence as only 24.6% of isolates carried the virulence genes. Nevertheless, the variety of diseases linked to these species indicates the necessity for accurate identification and precise reporting ofantimicrobial susceptibility to avoid adverse outcomes.

ST913-IVa-t991 Methicillin-Resistant Staphylococcus aureus among Pediatric Patients, Israel.

In Israel, prevalence of sequence type 913, staphylococcal cassette chromosome mecIVa, spa type t991 methicillin-resistant Staphylococcus aureus lineage has surged among pediatric populations, predominantly in Arab and Orthodox Jewish communities. Antimicrobial resistance patterns vary by demographics. This lineage's spread and microevolution in the Middle East underscore the need for ongoing surveillance.

Characterization of staphylococcal cassette chromosome mec in Staphylococcus haemolyticus ST3 and ST42 isolates from bovine mastitis milk: identification of novel variant in class C1 mec complex.

Methicillin-resistant Staphylococcus haemolyticus (MRSH) is an important pathogenic agent of bovine mastitis. Among the prominent clone lineages in dairy cows are MRSH sequence types ST3 and ST42. Little information is available on the complete characterization of SCCmec elements in MRSH. In this study, two clinical isolates of MRSH ST3 and ST42 from bovine mastitis milk were selected, and their nontypable SCCmec structures were compared. Two MRSH strains, MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1, were identified from bovine mastitis milk in Thailand in 2022. Minimum inhibitory concentration was used to screen for antimicrobial resistance susceptibility. Oxford Nanopore Technologies and Illumina sequencing were performed in combination to complete the genome. Their gene organization and structure of SCCmec types were analysed and compared with the whole sequences of other strains in the same sequence types. Both MRSH-ST3 strain M62.3 and MRSH-ST42 strain M81.1 possessed the class C1 mec complex but lacked the ccr gene complex. Notably, MRSH-ST42 strain M81.1 contained a novel variant of C1 mec complex, which consisted of IS431-mecA-ISSha1-paaZ-upgQ-IS431, with IS431 organized in the same orientation. Apart from class C1 mec and the heavy metal-resistant cluster, the gene composition and order of the SCCmec element varied. In ST3, variations in the SCCmec type, gene content and organization were observed. The distinct evolution of the MRSH lineage was indicated by the various SCCmec elements. The insertion of ISSha1 resulted in a unique variant of class C1 mec complex that demonstrated the important role of the insertion sequence in SCCmec diversification.

Mammaliicoccus sciuri's Pan-Immune System and the Dynamics of Horizontal Gene Transfer Among Staphylococcaceae: a One-Health CRISPR Tale.

Recently emancipated from the Staphylococcus genus due to genomic differences, Mammaliicoccus sciuri, previously classified as an occasional pathogen, emerges as a significant player in the landscape of resistance gene dissemination among Staphylococcaceae. Despite its classification, its role remained enigmatic. In this study, we delved into the genomic repertoire of M. sciuri to unravel its contribution to resistance and virulence gene transfer in the context of One Health. Through comprehensive analysis of publicly available genomes, we unveiled a diverse pan-immune system adept at defending against exogenous genetic elements, yet concurrently fostering horizontal gene transfer (HGT). Specifically, exploration of CRISPR-Cas systems, with spacer sequences as molecular signatures, elucidated a global dissemination pattern spanning environmental, animal, and human hosts. Notably, we identified the integration of CRISPR-Cas systems within SCCmecs (Staphylococcal Cassette Chromosome mec), harboring key genes associated with pathogenicity and resistance, especially the methicillin resistance gene mecA, suggesting a strategic adaptation to outcompete other mobile genetic elements. Our findings underscored M. sciuri's active engagement in HGT dynamics and evolutionary trajectories within Staphylococcaceae, emphasizing its central role in shaping microbial communities and highlighting the significance of understanding its implications in the One Health framework, an interdisciplinary approach that recognizes the interconnectedness of human, animal, and environmental health to address global health challenges.

Genotypic Shift and Diversification of MRSA Blood Stream Isolates in a University Hospital Setting: Evidence from a 12-Year Observational Study.

There have been few reports regarding the long-term trends in the genotypes of methicillin-resistant Staphylococcus aureus (MRSA) bloodstream isolates. Therefore, this study was performed to investigate the longitudinal trends in the genotypes of MRSA bloodstream isolates obtained from hospitalized patients during a 12-year study period from 2010 to 2021 at a tertiary care university hospital. Over the 12-year period from 2010 to 2021, we conducted a genetic investigation focusing on 245 MRSA strains isolated from the blood of hospitalized patients. The genotypes of the MRSA bloodstream isolates were determined by Staphylococcal Cassette Chromosome mec (SCCmec) typing, accessory gene regulator (agr) typing, PCR-based ORF typing (POT), and multilocus sequence typing (MLST). Strains with the same POT type detected in two or more isolates were designated as epidemic clones, while strains without a common POT type were classified as sporadic clones. Until 2015, isolates with SCCmec II/agr II were prevalent, but isolates with SCCmec IV/agr III increased from 2016. A total of 128 strains (52%) were identified as epidemic clones, while 117 strains (48%) were classified as sporadic clones. The detection rate of sporadic clones increased significantly since 2016 (p < 0.05). The epidemic clones were classified into three clusters, with MRSA of clonal complex (CC) 1 being prominent after 2016. This study showed that the genotypes of MRSA bloodstream isolates underwent a shift from SCCmec II/agr II type to SCCmec IV/agr III type, with a notable increase in MRSA of CC1, after 2016. There was a significant increase in the proportion of sporadic strains among the isolates, suggesting the diversification of genotypes.

Isolation of community-associated methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 30 from house rats (Rattus tanezumi) in Hong Kong.

Methicillin-resistant Staphylococcus aureus (MRSA) is of major public health concern due to its resistance to multiple antibiotics. This resistance has been observed in various settings, including hospitals and communities, and has been detected in both animals and humans. Although peridomestic rat species (Rattus spp.) are well described reservoirs of several human pathogens and antimicrobial resistant bacteria, little is known about their role in MRSA epidemiology. In order to investigate whether Rattus spp. in Hong Kong are potential carriers of MRSA, 221 rats were caught from various ecological areas and nasopharyngeal samples were cultured on MRSA selective media. Genotypic characteristics of MRSA were confirmed by whole genome sequencing. Two clonal sequence type (ST) 30 MRSA isolates, harbouring mecA on staphylococcal chromosome cassette (SCC) mec type IVc, were cultured from two house rats (Rattus tanezumi) caught in two densely populated urban areas. To the best of the authors' knowledge, this is the first detection of community-associated (CA)-MRSA strain ST30 SCCmec IVc in peridomestic rodents in Hong Kong and globally. Our finding indicates that house rats can be carriers of MRSA strains that are widely distributed in the community.

Prevalence and genetic characteristics ofStaphylococcus aureus isolates from cellphones of medical students from Iran.

Although mobile phones as a rapid communication vehicle can lead to improved quality of healthcare, they can also facilitate the transmission of pathogens to patients. This current research focuses on genetic diversity, and genes involved in resistance and biofilm production of Staphylococcus aureus isolates from mobile phones of medical students. Antibiotic resistance profiling and polymerase chain reaction (PCR) amplification of antibiotic resistance and biofilm-related genes were investigated and statistically analyzed. Staphylococcal cassette chromosome mec (SCCmec) types were analyzed by multiplex PCR, and S. aureus protein A gene typing (spa typing) was done using PCR and sequencing. Sixty-four S. aureus isolates (16.8%) were obtained from 380 medical students' mobile phones who were working in hospitals. The findings showed that 71.9% of the isolates were MRSA and 78.1% were classified as MDR. All isolates exhibited sensitivity to vancomycin and linezolid. Overall, 7.8% of the isolates displayed an inducible clindamycin resistance phenotype, while 26.7% showed resistance to mupirocin. The results indicated that 68.8% of the isolates were biofilm producers, with 7 isolates (15.9%) classified as strong producers, 22 isolates (50%) as moderate producers, and 15 isolates (34.1%) as weak producers. The most prevalent type was CC8-MRSA III/t030 (18.7%), followed by CC8-MRSA III/t037 (12.5%), CC/ST22-MSSA/t790 (10.9%), CC1-MRSA IV-t114 (9.4%), CC1-MRSA IV-t127 (7.8%), CC8-MRSA V/t064 (7.8%), CC/ST15-MSSA-t360 (7.8%), CC30-MSSA/t021(6.3%), MRSA V-t355 (6.3%), CC8-MRSA III/t421 (4.7%), CC1-MRSA V-t267 (4.7%), and CC/ST15-MSSA-t084 (3.1%). The genetic diversity and prevalent multidrug resistance indicate that the resistance situation of S. aureus recovered from mobile phones in Tehran is severe, posing a potential threat to patients, the community, and healthcare settings.

Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution

An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.

Comparison of the effectiveness of core genome multilocus sequence typing and polymerase chain reaction-based open reading frame typing in tracing nosocomial methicillin-resistant Staphylococcus aureus transmission

IntroductionA clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II/ST5 methicillin-resistant Staphylococcus aureus (MRSA) to SCCmec type IV/clonal complex (CC)1 MRSA has occurred rapidly in Japan. Our previous research in a geriatric hospital found SCCmec type IV/CC1 MRSA prevalence in long-term care wards. Due to intensive personal care requirements, frequent contact with healthcare providers can potentially cause unintentional nosocomial MRSA transmission. We performed polymerase chain reaction-based open reading frame typing (POT) and core genome multilocus sequence typing (cgMLST) to investigate the occurrence of nosocomial transmission and to compare the results of these methods. MethodsPOT and whole genome sequencing were performed in 83 MRSA isolates. Commercial automated software (Ridom SeqSphere+) was used to perform cgMLST. MRSA isolates with 0–8 allelic differences were considered related, and medical records were consulted in these cases. ResultsSCCmec type IV/CC1 MRSA was the most frequently detected clone (n = 56, 67.5 %), which was divided into 14 POT types, followed by SCCmec type I/ST8 (n = 9) and SCCmec type IV/ST8 (n = 8). Identical POT types were found across 7 of 11 wards. However, cgMLST analysis identified only three cases (six strains) of high genetic similarity, indicating nosocomial transmission; only one involved SCCmec type IV/CC1 (two strains). The mean allelic difference in the core genomes between strains with identical POT types in the same ward was 55.3 ± 22.0. ConclusionsThe cgMLST method proved more effective for identifying nosocomial transmissions compared to POT, highlighting its utility in tracking MRSA spread in healthcare settings.

Prevalence, Diversity, and Antimicrobial Susceptibility Profiles of Methicillin-Resistant Staphylococcus aureus Among Patients with Diabetic Foot Infections in a Referral Hospital in Tehran, Iran

Background: The increasing incidence of methicillin-resistant Staphylococcus aureus (MRSA) poses a significant challenge in the treatment of diabetic foot infections (DFIs). Objectives: This study aimed to investigate the prevalence and diversity of clonal groups of MRSA strains isolated from patients with DFIs in a major referral hospital in Tehran. Methods: We determined the prevalence, diversity, and antibiotic susceptibility profiles of MRSA isolated from patients with DFIs attending a referral hospital in Tehran, Iran, during 2019 - 2020. Staphylococcal cassette chromosome mec (SCCmec) typing, ccr typing, PhP typing, and detection of the Panton-Valentine Leukocidin (pvl) gene were performed to explore the diversity of the strains. Antibiotic susceptibility profiles of the strains were determined using the disk diffusion method and broth microdilution assay. Results: Of the 238 S. aureus strains isolated, 73 were identified as MRSA. The highest antibiotic resistance was observed against ciprofloxacin (86%), followed by kanamycin and tobramycin (84%). Additionally, 49.3% of the strains exhibited high-level oxacillin resistance (MIC ≥ 256 µg/mL). SCCmec type III and type 3 ccr were detected in 86.3% of the strains, classifying them as hospital-acquired (HA)-MRSA. PhP typing revealed the presence of 8 common types (CTs) and 11 single types (STs), with CT2 comprising 41.1% of the strains. Conclusions: Our data suggest that MRSA strains isolated from DFIs in this region are diverse and resistant to clinically important antibiotics. Diabetic patients can serve as a reservoir for the dissemination of these bacteria between community and clinical environments.

Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins.

To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.

Phenotypic and genotypic characterization of Staphylococcus aureus strains isolated from otitis externa: Emergence of CC30-spa t019-SCCmec IV carrying PVL as major genotype

The increasing emergence of Staphylococcus aureus as the primary causative agent of otitis externa has been noted; however, detailed information regarding the molecular characteristics of these strains in Iran remains scarce. The current study aims to investigate both genotypic and phenotypic attributes of S. aureus strains implicated in ear infections. In the present work, we analyzed 60 S. aureus strains isolated from cases of otitis externa over a period of 45 months. The resistance patterns were determined using disk diffusion and microbroth dilution methods. All S. aureus isolates were confirmed by the nucA polymerase chain reaction assay, and their biofilm production was assessed by a microtiter plate assay. Molecular characterization of the isolates was performed using the staphylococcal cassette chromosome mec, multilocus sequence typing, and staphylococcus protein A typing methods. Overall, the results indicated that 44 out of 60 S. aureus isolates (73.3 %) were methicillin-resistant Staphylococcus aureus. Resistance to mupirocin and vancomycin was observed in 13.3 % and 1.7 % of the tested isolates, respectively. Furthermore, out of the 60 S. aureus isolates, 56 strains (93.4 %) were classified as positive biofilm strains at different levels. Twelve distinct clonal lineages were identified. The vast majority of S. aureus isolates belonged to CC30/ST30-MRSA IV/t019 (41.7 %). Among the 31 strong biofilm producers, the majority (64.5 %) belonged to CC30/ST30-MRSA IV/t019 clone. Biofilm negative isolates belonged to CC22/ST22 (2 isolates), CC8/ST585 (one isolate), and CC8/ST8 (one isolate). Our result revealed that about three-quarters of PVL-positive strains belonged to CC30/ST30. Our data confirmed the presence of MSSA strains among CC30/ST30 and CC22/ST22 isolates. The mupirocin resistant isolates (n = 8) belonged to CC8/ST585-MRSA III/t713 (37.5 %), CC8/ST239-MRSA III/t030 (25 %), CC8/ST8-MRSA IV/t008 (12.5 %), CC8/ST239-MRSA III/t037 (12.5 %), and CC22/ST22-MRSA IV/t790 (12.5 %) lineages. The VRSA strain belonged to the CC8/ST8-MRSA IV/t008 lineage, carrying the vanA determinant. iMLSB phenotypes (n = 14) were distributed across different lineages, including CC30/ST30-MRSA IV/t019 (21.5 %), CC30/ST30-MSSA/t021 (21.5 %), CC22/ST22-MSSA/t005 (14.3 %), CC8/ST239-MRSA III/t030 (14.3 %), CC22/ST22-MSSA/t1869 (7.1 %), CC22/ST22-MRSA IV/t790 (7.1 %), CC8/ST239-MRSA III/t037 (7.1 %), and CC1/ST772-MRSA IV/t10795 (7.1 %). These findings highlight significant genotypic diversity and high biofilm formation among our isolates. The frequent occurrence of the CC/ST30 clone in S. aureus strains isolated from otitis externa reflects the emergence of these lineages as a predominant clone in Iran, posing a significant public health concern.

SaLTy: a novel Staphylococcus aureus Lineage Typer.

Staphylococcus aureus asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 S. aureus was associated with 20 000 deaths in the USA alone. Dividing S. aureus isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus genome sequences when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (n=21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCCmec) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCCmec and the four largest lineages varied in SCCmec over time. Classifying isolates into SaLTy lineages, which were further SCCmec typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of S. aureus genome data. SaLTy will aid the characterisation of S. aureus populations and ongoing surveillance of sub-groups that threaten human health.

The Emergence of Linezolid-Resistant Staphylococcus Epidermidis in the COVID-19 Hospitalized Intubated Patients in North Khorasan, Iran.

The present study aimed to investigate secondary bacterial infections among patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Coagulase-negative Staphylococci can infect immunocompromised patients. Linezolid resistance among Staphylococcus epidermidis is one of the most critical issues. In 2019, 185 SARS-CoV-2-positive patients who were admitted to North Khorasan Province Hospital (Bojnurd, Iran), were investigated. Patients having positive SARS-CoV-2 reverse transcriptase real-time polymerase chain reaction (RT-PCR) test results, who had a history of intubation, mechanical ventilation, and were hospitalized for more than 48 hours were included. After microbiological evaluation of pulmonary samples, taken from intubated patients with clinical manifestation of pneumonia, co-infections were found in 11/185 patients (5.94%) with S. epidermidis, Staphylococcus aureus, and Acinetobacter baumani, respectively. Remarkably, seven out of nine S. epidermidis isolates were linezolid resistant. Selected isolates were characterized using antimicrobial resistance patterns and molecular methods, such as Staphylococcal cassette chromosome mec (SCCmec) typing, and gene detection for ica, methicillin resistance (mecA), vancomycin resistance (vanA), and chloramphenicol-florfenicol resistance (cfr) genes. All of the isolates were resistant to methicillin, and seven isolates were resistant to linezolid. Nine out of 11 isolated belonged to the SCCmec I, while two belonged to the SCCmec IV. It should be noted that all patients had the underlying disease, and six patients had already passed away. The increasing linezolid resistance in bacterial strains becomes a real threat to patients, and monitoring such infections, in conjunction with surveillance and infection prevention programs, is very critical for reducing the number of linezolid-resistant Staphylococcal strains. A preprint of this study was published at https://europepmc.org/article/ppr/ppr417742.

Prevalence, characterization, and implications of methicillin-resistant Staphylococcus aureus (MRSA) in ready-to-eat foods from Delta, Nigeria: a concern for consumer safety

Abstract Ready-to-eat (RTE) foods are susceptible to contamination with methicillin-resistant Staphylococcus aureus (MRSA), presenting significant health risks to consumers. This study aimed to isolate, identify, and characterize MRSA from RTE foods in Delta, Nigeria, and assess their implications for consumer safety. Four hundred RTE food samples were collected from food outlets, and MRSA presence was determined using oxacillin resistance screening agar supplemented with polymyxin B and oxacillin. Polymerase chain reaction confirmed and characterized MRSA isolates for virulence potentials and antimicrobial resistance genes. Out of the 400 samples, 57(14.25%) tested positive for MRSA. The prevalence of virulence genes varied, with Panton-Valentine Leukocidin (pvl) detected in 40.51% of isolates, along with the detection of several staphylococcal enterotoxin genes. Antimicrobial resistance genes, including tetracycline (tetM, 43.04%), erythromycin (ermC, 32.91%), and methicillin (mecA, 100%; mecC, 29.11%) were detected. Staphylococcal cassette chromosome mec (SCCmec) typing revealed diverse profiles, with type V being predominant (32.9%). MRSA isolates exhibited resistance to multiple antibiotics, with 83.54% of them classified as multidrug-resistant. Extracellular virulence factors were common, with strong biofilm producers observed in 69.62% of isolates. These findings underscore the complexity of MRSA contamination in RTE foods, highlighting the need for enhanced surveillance and control measures to safeguard public health.

Identification of the novel fosfomycin resistance gene fosSC in Staphylococcus capitis

ObjectivesFosfomycin has regained attention for treating infections caused by methicillin-resistant Staphylococcus aureus and multidrug-resistant coagulase-negative staphylococci. In this research, our objective was to investigate the mechanisms underlying fosfomycin resistance in Staphylococcus capitis. MethodsThe minimum inhibitory concentrations (MICs) of fosfomycin were assessed in 109 clinical S. capitis isolates by the agar dilution method. By cloning the fos-like genes into the shuttle vector, pTSSCm-Pcap, and observing the change in fosfomycin MICs, the gene function was verified. Core genome multilocus sequence typing and comparative genomics analysis were conducted to determine the population characteristics of S. capitis isolates and analyse the genetic environment of the fos-like genes. ResultsWe identified a novel fosfomycin resistance gene, fosSC, on the chromosome in 58 out of 109 (53.2%) S. capitis isolates. The deduced products of the fosSC genes shared 67.15–67.88% amino acid sequence identity with FosB. The RN-pT-fosSC transformants carrying fosSC showed a 512-fold increase in the fosfomycin MICs. The fosSC gene was embedded in a conserved genetic context, but IS431mec was located to the left of the fosSC gene in cluster L due to the insertion of staphylococcal cassette chromosome mec. ConclusionsThe chromosomal fosSC genes in some lineages of S. capitis explained their high-level fosfomycin resistance. Ongoing surveillance is crucial for monitoring the potential threat of horizontal transfer, which could be facilitated by the presence of mobile genetic elements surrounding the fosSC gene.

High prevalence of ST5-SCCmec II-t311 clone of methicillin-resistant Staphylococcus aureus isolated from bloodstream infections in East China

ObjectivesMethicillin-resistant Staphylococcus aureus (MRSA) is a challenging global health threat, resulting in significant morbidity and mortality worldwide. This study aims to determine the molecular characteristics and antimicrobial susceptibility of 263 MRSA isolates in Zhejiang Province, east China.MethodsFrom 2014 to 2019, a total of 263 MRSA isolates from bloodstream infections (BSIs) were collected from 6 hospitals in 4 cities in Zhejiang province, east China. Antimicrobial susceptibility tests were conducted according to the guidelines set forth by the Clinical and Laboratory Standards Institute (CLSI). To characterize and analyze these isolates, multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) typing and virulence genes gene profiles were performed.ResultsThe most predominant clone was ST5-SCCmec II-t311, which accounted for 41.8% (110/263), followed by ST59 (44/263, 16.7%). Compared with non-ST5-II-t311 isolates, ST5-II-t311 isolates were more resistant to erythromycin, tetracycline, levofloxacin, moxifloxacin, and ciprofloxacin, but more susceptible to clindamycin. Moreover, the rates of multidrug resistance were higher in ST5-II-t311 isolates compared to the non-ST5-II-t311 isolates. In comparison to the non-ST5-II-t311 isolates, ST5-II-t311 isolates showed no significant difference in virulence genes detected.ConclusionsMRSA ST5-II-t311 clone has become the most predominant clone in Zhejiang Province, east China and has higher rates of multidrug resistance than other isolates, that should be kept in mind when treating BSI. Moreover, MRSA ST59 clone shows an upward trend and has begun to spread into hospitals. Our findings highlight the importance of epidemiological studies of S. aureus carriage in the eastern region.

Comparative structural analysis of MecA encoded beta-lactam resistance in MRSA

As the level of antibiotic resistance in bacteria rises, the threat of patients facing fatal consequences from a simple cut or infection grows dramatically. One example of an emerging antibiotic-resistant threat is MRSA, methicillin-resistant staphylococcus aureus, which is a growing cause of hospital-acquired pneumonia, skin infections, and even sepsis through cross-contamination in health care settings. However, methicillin resistance like that exploited by MRSA is also highly conserved with that of another species of staphylococcus bacteria, Staphylococcus sciuri which is the ancestral bacterium of S. aureus. S. sciuri is a typically animal-associated bacterium with increasing clinical relevance as the amount of human infections from it has grown. Both these bacteria share the commonality of having the mecA gene that determines methicillin resistance transported through the mobile Staphylococcal cassette chromosome. This study focuses on the relationship between the mecA mobile element in S. sciuri compared to S. aureus and explores the specific role of S. sciuri in the creation of the mecA cassette. Understanding the cassette evolution and similarities and differences between S. sciuri and S. aureus will enable the continued tracking of S. sciuri as an emerging clinical threat. To answer all these questions, BLAST analysis, InterProScan, and additional computational analysis were used to characterize differences in homology, structure, function, and effect on infectivity, robustness of antibiotic resistance, and morbidity. The overall goal of this analysis is to characterize the differences between mecA and methicillin-resistant genes in clinically relevant MRSA as well as environmental samples such as S. sciuri.