Novel SCCmec type XIII (9A) identified in an ST152 methicillin-resistant Staphylococcus aureus

The role of Staphylococcus aureus in cystic fibrosis pathogenesis and clinico-microbiological interactions

Cystic fibrosis (CF) is a progressive and inherited disease that affects approximately 70000 individuals all over the world annually. A mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene serves as its defining feature. Bacterial infections have a significant impact on the occurrence and development of CF. In this manuscript, we discuss the role and virulence factors of Staphylococcus aureus as an important human pathogen with the ability to induce respiratory tract infections. Recent studies have reported S. aureus as the first isolated bacteria in CF patients. Methicillin-resistant Staphylococcus aureus (MRSA) pathogens are approximately resistant to all β-lactams. CF patients are colonized by MRSA expressing various virulence factors including toxins, and Staphylococcal Cassette Chromosome mec (SCCmec) types, and have the potential for biofilm formation. Therefore, variations in clinical outcomes will be manifested. SCCmec type II has been reported in CF patients more than in other SCCmec types from different countries. The small-colony variants (SCVs) as specific morphologic subtypes of S. aureus with slow growth and unusual properties can also contribute to persistent and difficult-to-treat infections in CF patients. The pathophysiology of SCVs is complicated and not fully understood. Patients with cystic fibrosis should be aware of the intrinsic risk factors for complex S. aureus infections, including recurring infections, physiological issues, or coinfection with P. aeruginosa.

Investigation of SCCmec Types using the Real Time PCR Method in Cefoxitin-Resistant Staphylococcus aureus Isolates

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen that can cause many community and hospital-acquired infections. This study was conducted to investigate the SCCmec gene types responsible for methicillin resistance in MRSA isolates isolated from hospitalised patients.

MATERIAL AND METHODS

MRSA isolates isolated from samples sent from various clinics to Gaziantep University Hospital Microbiology Laboratory between March 2021-January 2022 were included in the study. Bacteria were identified using by VITEK 2 automated system. Cefoxitin (FOX) resistance was determined by the disc diffusion method according to EUCAST standards. Cefoxitin resistance was confirmed by the Penicillin Binding Protein 2' latex agglutination test. Types of mecA, mecC, coa, nuc, Panton Valentin Leukocidin (PVL), ccrC2, class A mec, SCCmec types in isolates detected as MRSA were investigated by real-time PCR.

RESULTS

In this study, 116 isolates meeting the study criteria were examined. By detecting the nuc and coa genes in all isolates by PCR, the phenotypic identification of S.aureus was confirmed. While the mecA gene was detected in all MRSA isolates, no mecC gene was detected in any isolates. Detected SCCmec types were as follows; SCCmec Type 1 (2.6%), Type II (28.4%), Type III (12.9%), Type IVa (11.2%), Type IVb (3.4%), Type IVc (3.4%), Type IVg (12.1%), Type V (0.9%), Type VII (4.3%), Type VIII (18.1%), Type IX (0.9%), Type XII (1.7%). On the other hand, SCCmec Type VI, X, XI and XIII were not found in any isolate. It was determined that four of the MRSA isolates (3.4%) carried the PVL gene that two (50%) of these were found in SCCmec Type VIII.

CONCLUSION

Monitoring of FOX resistance is an effective and safe method for determination of MRSA isolates. The change in the mec gene causes resistance, which should be monitored regularly with molecular methods. Our study is the first study in Turkey.

Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA

Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a global presence in healthcare facilities as well as community settings. The resistance of MRSA to beta-lactam antibiotics can be attributed to a mobile genetic element called the staphylococcal cassette chromosome mec (SCCmec), ranging from 23 to 68 kilobase pairs in length. The mec gene complex contained in SCCmec allows MRSA to survive in the presence of penicillin and other beta-lactam antibiotics. We demonstrate that optical mapping (OM) is able to identify the bacterium as S. aureus, followed by an investigation of the presence of kilobase pair range SCCmec elements by examining the associated OM-generated barcode patterns. By employing OM as an alternative to traditional DNA sequencing, we showcase its potential for the detection of complex genetic elements such as SCCmec in MRSA. This approach holds promise for enhancing our understanding of antibiotic resistance mechanisms and facilitating the development of targeted interventions against MRSA infections.

Current types of staphylococcal cassette chromosome mec (SCCmec) in clinically relevant coagulase-negative staphylococcal (CoNS) species

Coagulase-negative staphylococci (CoNS) colonize human skin and mucosal membranes, which is why they are considered harmless commensal bacteria. Two species, Staphylococcus epidermidis and Staphylococcus haemolyticus belong to the group of CoNS species and are most frequently isolated from nosocomial infections, including device-associated healthcare-associated infections (DA-HAIs) and local or systemic body-related infections (FBRIs). Methicillin resistance, initially described in Staphylococcus aureus, has also been reported in CoNS species. It is mediated by the mecA gene within the staphylococcal cassette chromosome (SCCmec). SCCmec typing, primarily using PCR-based methods, has been employed as a molecular epidemiological tool. However, the introduction of whole genome sequencing (WGS) and next-generation sequencing (NGS) has enabled the identification and verification of new SCCmec types. This review describes the current distribution of SCCmec types, subtypes, and variants among CoNS species, including S. epidermidis, S. haemolyticus, and S. capitis. The literature review focuses on recent research articles from the past decade that discuss new combinations of SCCmec in coagulase-negative Staphylococcus. The high genetic diversity and gaps in CoNS SCCmec annotation rules underscore the need for an efficient typing system. Typing SCCmec cassettes in CoNS strains is crucial to continuously updating databases and developing a unified classification system.

Methicillin-Resistant Staphylococcusaureus Strains Isolated from Burned Patients in a Tunisian Hospital: Molecular Typing, Virulence Genes, and Antimicrobial Resistance

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major causes of a variety of infections in hospitals and the community. Their spread poses a serious public health problem worldwide. Nevertheless, in Tunisia and other African countries, very little molecular typing data on MRSA strains is currently available. In our study, a total of 64 MRSA isolates were isolated from clinical samples collected from burned patients hospitalized in the Traumatology and Burns Center of Ben Arous in Tunisia. The identification of the collection was based on conventional methods (phenotypic and molecular characterization). The characterization of the genetic support for methicillin resistance was performed by amplification of the mecA gene by polymerase chain reaction (PCR), which revealed that 78.12% of S. aureus harbors the gene. The resistance of all the collection to different antibiotic families was studied. Indeed, the analysis of strain antibiotic susceptibility confirmed their multi-resistant phenotype, with high resistance to ciprofloxacin, gentamicin, penicillin, erythromycin, and tetracycline. The resistance to the last three antibiotics was conferred by the blaZ gene (73.43%), the erm(C) gene (1.56%), the msr(A) gene (6.25%), and tet(M) gene (7.81%), respectively. The clonal diversity of these strains was studied by molecular typing of the accessory gene regulator (agr) system, characterization of the SCCmec type, and spa-typing. The results revealed the prevalence of agr types II and III groups, the SCCmec type III and II cassettes, and the dominance of spa type t233. The characterization of the eight enterotoxins genes, the Panton-Valentine leukocidin and the toxic shock syndrome toxin, was determined by PCR. The percentage of virulence genes detected was for enterotoxins (55%), tst (71.88%), leukocidin E/D (79.69%), and pvl (1.56%) factors. Furthermore, our results revealed that the majority of the strains harbor IEC complex genes (94%) with different types. Our findings highlighted the emergence of MRSA strains with a wide variety of toxins, leukocidin associated with resistance genes, and specific genetic determinants, which could constitute a risk of their spread in hospitals and the environment and complicate infection treatment.

Phenotyping of Methicillin-Resistant Staphylococcus aureus Using a Ratiometric Sensor Array

Chemical tools capable of classifying multidrug-resistant bacteria (superbugs) can facilitate early-stage disease diagnosis and help guide precision therapy. Here, we report a sensor array that permits the facile phenotyping of methicillin-resistant Staphylococcus aureus (MRSA), a clinically common superbug. The array consists of a panel of eight separate ratiometric fluorescent probes that provide characteristic vibration-induced emission (VIE) profiles. These probes bear a pair of quaternary ammonium salts in different substitution positions around a known VIEgen core. The differences in the substituents result in varying interactions with the negatively charged cell walls of bacteria. This, in turn, dictates the molecular conformation of the probes and affects their blue-to-red fluorescence intensity ratios (ratiometric changes). Within the sensor array, the differences in the ratiometric changes for the probes result in "fingerprints" for MRSA of different genotypes. This allows them to be identified using principal component analysis (PCA) without the need for cell lysis and nucleic acid isolation. The results obtained with the present sensor array agree well with those obtained using polymerase chain reaction (PCR) analysis.

Phenotypic and Genotypic Characterization of Methicillin Resistance in Staphylococci Isolated from an Egyptian University Hospital

Methicillin-resistant in Staphylococci is a serious public health issue. It is mostly encoded by the mecA gene. The mecC gene is a new mecA analog responsible for resistance to methicillin in some Staphylococcal clinical isolates. This mecC gene is still underestimated in Egypt. The aim of the current study was to detect mecA and mecC genes in clinical Staphylococci isolates from a tertiary care university hospital in Egypt compared to the different phenotypic methods. A total of 118 Staphylococcus aureus (S. aureus) and 43 coagulase-negative Staphylococci (CoNS) were identified from various hospital-acquired infections. Methicillin resistance was identified genotypically using the PCR technique and phenotypically using the cefoxitin disc diffusion test, oxacillin broth microdilution and the VITEK2 system in all Staphylococcal isolates. The mecA gene was detected in 82.2% of S. aureus and 95.3% of CoNS isolates, while all of the isolates tested negative for the mecC gene. Interestingly, 30.2% of CoNS isolates showed the unique character of inducible oxacillin resistance, being mecA-positive but oxacillin-susceptible (OS-CoNS). The dual use of genotypic and phenotypic methods is highly recommended to avoid missing any genetically divergent strains.

Invited review: Antimicrobial resistance in bovine mastitis pathogens: A review of genetic determinants and prevalence of resistance in European countries

Antimicrobial resistance is an urgent and growing problem worldwide, both for human and animal health. In the animal health sector actions have been taken as concerns grow regarding the development and spread of antimicrobial resistance. Mastitis is the most common infection in dairy cattle. We aimed to summarize the genetic determinants found in staphylococci, streptococci, and Enterobacteriaceae isolated from mastitic milk samples and provide a comparison of percentage resistance to a variety of antimicrobials in European countries.

Review of pork and pork products as a source for transmission of methicillin-resistant Staphylococcus aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic bacterium that can cause infection in animals and humans. Recently, MRSA from food-producing or farm animals has been identified as livestock-associated MRSA (LA-MRSA). The spread of LA-MRSA is particularly found in pork and pork products because LA-MRSA has been widely known to infect pigs. The most common type of LA-MRSA identified in pork and pork products is the clonal complex LA-MRSA 398 (LA-MRSA CC398). The MRSA strains on the surface of pork carcasses can be spread during the handling and processing of pork and pork products through human hands, cutting tools, and any surface that comes into direct contact with pork. Food infection is the main risk of MRSA in pork and pork products consumed by humans. Antibiotics to treat food infection cases due to MRSA infection include vancomycin and tigecycline. The spread of MRSA in pork and pork products is preventable by appropriately cooking and cooling the pork and pork products at temperatures above 60°C and below 5°C, respectively. It is also necessary to take other preventive measures, such as having a clean meat processing area and disinfecting the equipment used for processing pork and pork products. This review aimed to explain epidemiology, transmission, risk factors, diagnosis, public health consequences, treatment of food poisoning, and preventing the spread of MRSA in pork and pork products.

Genotypic characterization of mecA gene and antibiogram profile of coagulase-negative staphylococci in subclinical mastitic cows

Background and Aim:

Coagulase-negative staphylococci (CNS) are becoming the major cause of clinical and subclinical bovine mastitis around the world. This study aims to estimate the prevalence, antibiogram, and frequency of the methicillin-resistant (MR) (mecA) gene in CNS collected from cows with subclinical mastitis

Materials and Methods:

Thirty-four milk samples were collected from 20 cows. Fifteen subclinical mastitis samples (~44.12%) were identified as CNS isolates. The Vitek2 compact system method was employed for the identification of the species. Furthermore, antibiotic sensitivity tests were performed against 10 different antibiotics for CNS strains. The mecA gene from isolated CNS was detected by conventional polymerase chain reaction (PCR).

Results:

Staphylococcus haemolyticus was the most predominant isolated species with an incidence of 33.3% (5/15 isolates), followed by 26.7% for Staphylococcus sciuri and Staphylococcus vitamins (4/15 isolates), and 13.3% for Staphylococcus vitulinus (2/15 isolates), respectively. The highest resistance rates were determined to be 40% (6/15 isolates) against penicillin and oxacillin (OX), 33.3% (5/15 isolates) against clindamycin, 13% (2/15 isolates) against chloramphenicol, amoxicillin, and erythromycin, and 5% (1/15 isolates) against ciprofloxacin, respectively. The results revealed that the isolates were resistant to one or more antimicrobial agents, with five isolates displaying multiple antimicrobial resistance. Furthermore, the results exhibit that all CNS isolates had the mecA gene at 310 bp with a 100% frequency. Moreover, for detecting MR isolates, there are significant discrepancies between phenotypic and genotypic approaches, and only 6/15 CNS isolates phenotypically demonstrated OX resistance.

Conclusion:

The results emphasize the necessity of frequent monitoring of phenotypic and genotypic profiles of CNS isolates to ensure effective control measures and the prevention of multidrug resistance strain evolution.

Molecular Mechanisms of Drug Resistance in Staphylococcus aureus

This paper discusses the mechanisms of S. aureus drug resistance including: (1) introduction. (2) resistance to beta-lactam antibiotics, with particular emphasis on the mec genes found in the Staphylococcaceae family, the structure and occurrence of SCCmec cassettes, as well as differences in the presence of some virulence genes and its expression in major epidemiological types and clones of HA-MRSA, CA-MRSA, and LA-MRSA strains. Other mechanisms of resistance to beta-lactam antibiotics will also be discussed, such as mutations in the gdpP gene, BORSA or MODSA phenotypes, as well as resistance to ceftobiprole and ceftaroline. (3) Resistance to glycopeptides (VRSA, VISA, hVISA strains, vancomycin tolerance). (4) Resistance to oxazolidinones (mutational and enzymatic resistance to linezolid). (5) Resistance to MLS-B (macrolides, lincosamides, ketolides, and streptogramin B). (6) Aminoglycosides and spectinomicin, including resistance genes, their regulation and localization (plasmids, transposons, class I integrons, SCCmec), and types and spectrum of enzymes that inactivate aminoglycosides. (7). Fluoroquinolones (8) Tetracyclines, including the mechanisms of active protection of the drug target site and active efflux of the drug from the bacterial cell. (9) Mupirocin. (10) Fusidic acid. (11) Daptomycin. (12) Resistance to other antibiotics and chemioterapeutics (e.g., streptogramins A, quinupristin/dalfopristin, chloramphenicol, rifampicin, fosfomycin, trimethoprim) (13) Molecular epidemiology of MRSA.

Staphylococcal Cassette Chromosome mec Typing and Multilocus Variable Number Tandem Repeat Analysis of Methicillin Resistant Staphylococcus aureus Clinical Isolates with Vancomycin Creep Phenomenon

Background

The association of treatment failure and mortality with vancomycin minimum inhibitory concentration creep (MIC) is a matter of serious concern in patients with severe methicillin resistant Staphylococcus aureus (MRSA) infections. The purpose of the study was to identify and characterize staphylococcal cassette chromosome mec (SCCmec) and clonal types of MRSA strains, exhibiting the vancomycin MIC creep phenomenon.

Methods

A total of 3305 S. aureus strains were isolated from various clinical samples of Lahore General Hospital, Lahore, Pakistan. MRSA strains were identified by cefoxitin resistant (≤21mm) followed by mecA and mecC gene genotyping. Vancomycin MIC creep was determined by E-test. Isolates having MIC values >1.5 µg/mL were further subjected for SCCmec typing (I–V and XI) and multiple-locus variable number tandem repeat analysis (MLVA) by amplification of spa, sspA, clfA, clfB, and sdrCDE genes. A dendrogram was created based on the similarity index using bioneumerics software.

Results

About 13.3% (440/3305) isolates were MRSA with 99.3% (437/440) and 0.7% (3/440) carried mecA and mecC genes, respectively. In 120 MRSA isolates, the MIC of vancomycin was >1.5µg/mL. In MRSA isolates with high vancomycin MIC (>1.5µg/mL), the most common SCCmec type was SCCmec III (38.3%), followed by SCCmec IVa (15.8%), SCCmec IIIa (13.3%,), SCCmec IVc (7.5%), SCCmec IVe (5.8%), SCCmec IVd (5.8%), SCCmec IVb (4.2%), SCCmec II (2.5%), SCCmec V (1.7%), SCCmec I (1.7%) and SCCmec XI (1.7%). MLVA revealed 60 genotypic groups of MRSA isolates having a 92% similarity index.

Conclusion

SCCmec III was the most common type in genetically related MRSA isolates showing vancomycin MIC creep. The presence of SCCmec XI may further add burden to infection control measures.

Phenotypic and genotypic detection methods for antimicrobial resistance in ESKAPE pathogens (Review)

Antimicrobial resistance (AMR) represents a growing public health problem worldwide. Infections with such bacteria lead to longer hospitalization times, higher healthcare costs and greater morbidity and mortality. Thus, there is a greater need for rapid detection methods in order to limit their spread. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.) are a series of epidemiologically-important microorganisms of great concern due to their high levels of resistance. This review aimed to update the background information on the ESKAPE pathogens as well as to provide a summary of the numerous phenotypic and molecular methods used to detect their AMR mechanisms. While they are usually linked to hospital acquired infections, AMR is also spreading in the veterinary and the environmental sectors. Yet, the epidemiological loop closes with patients which, when infected with such pathogens, often lack therapeutic options. Thus, it was aimed to give the article a One Health perspective.

Novel SCCmec type XV (7A) and two pseudo-SCCmec variants in foodborne MRSA in China

BACKGROUND

Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 14 types. Novel SCCmec variants have been frequently detected from humans and animals but rarely from food.

OBJECTIVES

To characterize a novel SCCmec type and two SCCmec variants identified from food-associated MRSA in China.

METHODS

Three MRSA (NV_1, NT_611 and NT_8) collected from retail foods in China were subjected to WGS and the SCCmec elements were determined.

RESULTS

The novel SCCmecXV identified in NV_1 carried the mec gene complex class A (mecI-mecR1-mecA-IS431) and the ccr gene complex 7 (ccrA1B6), and a Tn558-mediated phenicol exporter gene fexA was detected in this SCCmecXV cassette. The pseudo-SCCmec elements ΨSCCmecNT_611 and ΨSCCmecNT_8 showed a truncated SCCmec pattern, carrying the class C2 mec gene complex but missing the ccr genes. The ΨSCCmecNT_611 element shared more similarities with those of Staphylococcus haemolyticus (AB478934.1) and carried a heavy metal resistance gene cluster cadD-cadX-arsC-arsB-arsR-copA. The ΨSCCmecNT_8 MRSA exhibited a highly resistant phenotype, showing the absence of a 19.3 kb segment compared with the reference SCCmecXII element (CP019945.1). Notably, a 46 kb region containing multiple transposons encoding antimicrobial or metal resistance genes flanked by IS431 or IS256 was identified ∼30 kb downstream from the mec gene complex in ΨSCCmecNT_8, which might explain such high resistance in MRSA NT_8.

CONCLUSIONS

Our finding of novel and pseudo-SCCmec elements reflected the ongoing intra/interspecies genetic rearrangements in staphylococci. Further study will be needed to investigate the biological significance and prevalence of those SCCmec variants along the food chain.

Current Status of Staphylococcal Cassette Chromosome mec (SCCmec)

Staphylococcal cassette chromosome mec (SCCmec) typing was established in the 2000s and has been employed as a tool for the molecular epidemiology of methicillin-resistant Staphylococcus aureus, as well as the evolution investigation of Staphylococcus species. Molecular cloning and the conventional sequencing of SCCmec have been adopted to verify the presence and structure of a novel SCCmec type, while convenient PCR-based SCCmec identification methods have been used in practical settings for many years. In addition, whole-genome sequencing has been widely used, and various SCCmec and similar structures have been recently identified in various species. The current status of the SCCmec types, SCCmec subtypes, rules for nomenclature, and multiple methods for identifying SCCmec types and subtypes were summarized in this review, according to the perspective of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements.

Phylogenetic Distribution of CRISPR-Cas Systems in Staphylococcus lugdunensis

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) genes (CRISPR-Cas) are present in many bacterial genomes with functions beyond adaptive immunity. We aimed to characterize the CRISPR-Cas system in the pathogenic Gram-positive bacterium Staphylococcus lugdunensis and determine its association with sequence types (STs) determined by multilocus sequence typing (MLST) and oxacillin susceptibility. Primers were designed to detect and sequence types IIIA and IIC CRISPR-Cas in 199 S. lugdunensis isolates. MLST and oxacillin susceptibility tests were also performed on the isolates. We found that 84 S. lugdunensis isolates had type IIIA CRISPR-Cas, while 46 had type IIC. The results showed a strong association between STs and CRISPR-Cas types. The ST1, ST6, ST12, and ST15 isolates had type IIIA CRISPR-Cas systems, and the ST4, ST27, and ST29 isolates had type IIC CRISPR-Cas. Interestingly, of 83 isolates containing type IIIA CRISPR-Cas, 17 (20.5%) were oxacillin-resistant S. lugdunensis (ORSL), and all of these ORSL isolates belonged to ST6 cluster 1. Moreover, spacers 23 and 21 were found in 16 and 17 ORSL isolates, respectively. In contrast, all 46 isolates with type IIC CRISPR-Cas were susceptible to oxacillin. Our results showed that 41.3% of CRISPR-Cas IIIA spacers were homologous to plasmids and 20.2% were homologous to phages. However, in type IIC CRISPR-Cas, 11.8% and 39.9% of spacers showed sequence homology with plasmids and phages, respectively. In conclusion, we found that the distribution and composition of the CRISPR-Cas system in S. lugdunensis was associated with STs and oxacillin susceptibility.

IMPORTANCE CRISPR-Cas systems have been characterized as playing several biological roles in many bacterial genomes. Moreover, CRISPR-Cas systems are useful for epidemiological, diagnostic, and evolutionary studies of pathogenic bacteria. However, the characteristics of CRISPR-Cas systems in Staphylococcus lugdunensis have been rarely reported. In this study, we revealed that type IIIA CRISPR-Cas was dominant in S. lugdunensis isolates, followed by type IIC CRISPR-Cas. Moreover, the composition of CRISPR-Cas spacers was strongly associated with multilocus sequence typing and oxacillin susceptibility of S. lugdunensis. These results advance our understanding of the evolution of CRISPR-Cas systems; however, the biological functions of CRISPR-Cas systems in S. lugdunensis remain to be further characterized.

Genetic Characterization of Staphylococcus aureus From Subclinical Mastitis Cases in Dairy Cows in Rwanda

Whole-genome sequencing was carried out on 30 Staphylococcus (S.) aureus isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters. The largest cluster contain isolates of sequence type (ST) 152 (n = 6) and the closely related ST1633 (n = 2). These sequence types have previously mainly been encountered in humans. The isolates of the second-largest cluster belong to ST5477 (n = 5),so far exclusively isolated from cows in Rwanda. The third cluster consists of isolates of ST97 (n = 4), which is a well-known bovine-adapted sequence type. These three clusters were all widespread over the country. Isolates of the usually human-adapted sequence types 1 (n = 2) and 5 (n= 1) were found and a single isolate of ST2430, previously found among humans in Africa. Finally, four isolates of novel sequence types were found: ST7108 (n = 2), ST7109 (n = 1), and ST7110 (n = 1). The blaZ penicillin resistance gene was found in 84% of the isolates and was in all cases corroborated by phenotypic resistance determination. Five (20%) of the isolates carried a tetracycline resistance gene, tet(K) or tetM, and three of these five also displayed phenotypic resistance while two isolates carried a tetM-gene but were yet tetracycline susceptible. Seven (28%) isolates carried the dfrG gene conferring resistance to trimethoprim. Four of these isolates indeed were resistant to trimethoprim while three isolates were sensitive. The str gene conferring resistance to aminoglycosides was found in three isolates; however, none of these displayed resistance to gentamycin. Our data revealed a high diversity of the sequence types of S. aureus isolates from cows with subclinical mastitis in Rwanda. Two major clusters of ST97 and ST5477 are likely to be bovine adapted and cause mastitis while the third cluster of ST152 usually have been found in humans and may signify a recent transmission of these types from human to cows, for example from hand milking. The high prevalence of this sequence type among dairy cows may pose zoonotic threat. The sequence types were widely distributed without any geographic correlation. Penicillin resistance, the most common type of resistance with a prevalence over 80%, but also tetracycline and trimethoprim resistance were displayed by several isolates.

Emergence of Methicillin-Resistant Staphylococcus aureus ST239/241 SCCmec-III Mercury in Eastern Algeria

In this paper, we investigate the epidemiology of infections-associated Staphylococcusaureus (S. aureus) from the Medical Intensive Care Unit (MICU) at University Hospital Center of Constantine (UHCC) in Algeria, with a special emphasis on methicillin-resistant strains (MRSA) revealed by cefoxitin disks (30 μg), then confirmed by penicillin-binding protein (PBP2a) agglutination and real-time polymerase chain reaction (RT-PCR) targeting mecA and mecC genes. Staphylococcal Cassette Chromosome mec (SCCmec type), staphylococcal protein A (spa-type), multilocus sequence type (MLST), Panton-Valentine Leucocidin (PVL), and toxic shock syndrome toxin-1 (TSST-1) were further investigated in all isolates, and whole genome sequencing was performed for a selected subset of three hospital-acquired MRSA (HA-MRSA) isolates. A measurement of 80% out of the 50 S. aureus isolates were identified as HA-MRSA harbouring the mecA gene, and 72.5% of them were multidrug resistant (MDR). Twelve STs, four different SCCmec cassettes, fourteen spa types, ten isolates Panton-Valentine Leukocidin (PVL)-positive, and three isolates TSST-1 were identified. Interestingly, there was a high prevalence (n = 29; 72.5%) of a worrisome emerging clone: the HA-MRSA ST239/241 SCCmec-III mercury with PVL negative, resistant to β-lactams, aminoglycosides, quinolones, and tetracyclines. Other clones of HA-MRSA isolates were also identified, including PVL-positive ST80 SCCmec-IV/SCCmec-unknown (22.5%), ST34 SCCmec-V with TSST-1 positive (2.5%), and PVL-negative ST72 SCCmec-II (2.5%). Genome analysis enables us to describe the first detection of both PVL-negative HA-MRSA ST239/241 SCCmec-III mercury carrying ccrC, as well as SCCmec-V cassette, which dramatically changes the epidemiology of S. aureus infections in one of the hospitals in eastern Algeria.

Antimicrobial resistance studies in staphylococci and streptococci isolated from cows with mastitis in Argentina

BACKGROUND

Staphylococcus aureus and Streptococcus agalactiae are the main cause of clinical mastitis in dairy cattle in Argentina, whereas coagulase-negative staphylococci (CNS) and environmental streptococci are the main cause of subclinical mastitis. Bacteria isolated from infected animals show increasing antimicrobial resistance.

OBJECTIVES

This study aims to determine the antimicrobial resistance of staphylococci and streptococci isolated from milk with mastitis, and to genotypically characterize the methicillin-resistant (MR) staphylococci.

METHODS

Isolation was performed on blood agar and identification was based on biochemical reactions. Antimicrobial susceptibility was according to the Clinical and Laboratory Standards Institute guidelines. The antimicrobial resistance genes, SCCmec type and spa type were detected by the polymerase chain reaction method.

RESULTS

We isolated a total of 185 staphylococci and 28 streptococci from 148 milk samples. Among the staphylococcal isolates, 154 were identified as CNS and 31 as S. aureus. Among the 154 CNS, 24.6% (n = 38) were resistant to penicillin, 14.9% (n = 23) to erythromycin, 17.5% (n = 27) to clindamycin, 6.5% (n = 10) to cefoxitin and oxacillin. Among the S. aureus isolates, 16.1% (n = 5) were resistant to penicillin, 3.2% (n = 1) to cefoxitin and oxacillin (MRSA). Six MR isolates (5 CNS and 1 MRSA) were positive to the mecA gene, and presented the SCCmec IVa. The MRSA strain presented the sequence type 83 and the spa type 002. Among the 28 streptococcal isolates, 14.3% (n = 4) were resistant to penicillin, 10.7% (n = 3) to erythromycin and 14.3% (n = 4) to clindamycin.

CONCLUSIONS

The present findings of this study indicate a development of antimicrobial resistance in main bacteria isolated from cows with mastitis in Argentina.

Genomic Investigation of Methicillin-Resistant Staphylococcus aureus ST113 Strains Isolated from Tertiary Care Hospitals in Pakistan

Methicillin-resistant Staphylococcus aureus (MRSA) is a multi-drug resistant and opportunistic pathogen. The emergence of new clones of MRSA in both healthcare settings and the community warrants serious attention and epidemiological surveillance. However, epidemiological data of MRSA isolates from Pakistan are limited. We performed a whole-genome-based comparative analysis of two (P10 and R46) MRSA strains isolated from two provinces of Pakistan to understand the genetic diversity, sequence type (ST), and distribution of virulence and antibiotic-resistance genes. The strains belong to ST113 and harbor the SCCmec type IV encoding mecA gene. Both the strains contain two plasmids, and three and two complete prophage sequences are present in P10 and R46, respectively. The specific antibiotic resistance determinants in P10 include two aminoglycoside-resistance genes, aph(3’)-IIIa and aad(6), a streptothrin-resistance gene sat-4, a tetracycline-resistance gene tet(K), a mupirocin-resistance gene mupA, a point mutation in fusA conferring resistance to fusidic acid, and in strain R46 a specific plasmid associated gene ant(4’)-Ib. The strains harbor many virulence factors common to MRSA. However, no Panton-Valentine leucocidin (lukF-PV/lukS-PV) or toxic shock syndrome toxin (tsst) genes were detected in any of the genomes. The phylogenetic relationship of P10 and R46 with other prevailing MRSA strains suggests that ST113 strains are closely related to ST8 strains and ST113 strains are a single-locus variant of ST8. These findings provide important information concerning the emerging MRSA clone ST113 in Pakistan and the sequenced strains can be used as reference strains for the comparative genomic analysis of other MRSA strains in Pakistan and ST113 strains globally.

Characterizing a novel SCCmec with a composite structure from a clinical strain of Staphylococcus hominis, C34847

Staphylococcal cassette chromosome mec (SCCmec) has predominantly been described in methicillin-resistant Staphylococcus aureus. However, studies have indicated that coagulase-negative staphylococci (CoNS) carry a larger diversity of SCC elements. We characterized a composite SCCmec element carrying an uncharacterized ccr1 and type A mec gene combination, in conjunction with a secondary element bearing ccr4, from a clinical strain of S. hominis. The element's complex structure points to a high degree of recombination occurring in SCCmec in CoNS.

Overview of the risks of Staphylococcus aureus infections and their control by bacteriophages and bacteriophage-encoded products

Staphylococcus aureus is the leading cause of secondary infections in hospitals and a challenging pathogen in food industries. Decades after it was first reported, β-lactam-resistant S. aureus remains a subject of intense research owing to the ever-increasing issue of drug resistance. S. aureus bacteriophages (phages) or their encoded products are considered an alternative to antibiotics as they have been shown to be effective in treating some S. aureus-associated infections. In this review, we present a concise collection of the literature on the pathogenic potential of S. aureus and examine the prospects of using S. aureus phages and their encoded products as antimicrobials.

Whole-Genome Sequencing and Machine Learning Analysis of Staphylococcus aureus from Multiple Heterogeneous Sources in China Reveals Common Genetic Traits of Antimicrobial Resistance

Staphylococcus aureus is a worldwide leading cause of numerous diseases ranging from food-poisoning to lethal infections. Methicillin-resistant S. aureus (MRSA) has been found capable of acquiring resistance to most antimicrobials. MRSA is ubiquitous and diverse even in terms of antimicrobial resistance (AMR) profiles, posing a challenge for treatment. Here, we present a comprehensive study of S. aureus in China, addressing epidemiology, phylogenetic reconstruction, genomic characterization, and identification of AMR profiles. The study analyzes 673 S. aureus isolates from food as well as from hospitalized and healthy individuals. The isolates have been collected over a 9-year period, between 2010 and 2018, from 27 provinces across China. By whole-genome sequencing, Bayesian divergence analysis, and supervised machine learning, we reconstructed the phylogeny of the isolates and compared them to references from other countries. We identified 72 sequence types (STs), of which, 29 were novel. We found 81 MRSA lineages by multilocus sequence type (MLST), spa, staphylococcal cassette chromosome mec element (SCCmec), and Panton-Valentine leukocidin (PVL) typing. In addition, novel variants of SCCmec type IV hosting extra metal and antimicrobial resistance genes, as well as a new SCCmec type, were found. New Bayesian dating of the split times of major clades showed that ST9, ST59, and ST239 in China and European countries fell in different branches, whereas this pattern was not observed for the ST398 clone. On the contrary, the clonal transmission of ST398 was more intermixed in regard to geographic origin. Finally, we identified genetic determinants of resistance to 10 antimicrobials, discriminating drug-resistant bacteria from susceptible strains in the cohort. Our results reveal the emergence of Chinese MRSA lineages enriched of AMR determinants that share similar genetic traits of antimicrobial resistance across human and food, hinting at a complex scenario of evolving transmission routes. IMPORTANCE Little information is available on the epidemiology and characterization of Staphylococcus aureus in China. The role of food is a cause of major concern: staphylococcal foodborne diseases affect thousands every year, and the presence of resistant Staphylococcus strains on raw retail meat products is well documented. We studied a large heterogeneous data set of S. aureus isolates from many provinces of China, isolated from food as well as from individuals. Our large whole-genome collection represents a unique catalogue that can be easily meta-analyzed and integrated with further studies and adds to the library of S. aureus sequences in the public domain in a currently underrepresented geographical region. The new Bayesian dating of the split times of major drug-resistant enriched clones is relevant in showing that Chinese and European methicillin-resistant S. aureus (MRSA) have evolved differently. Our machine learning approach, across a large number of antibiotics, shows novel determinants underlying resistance and reveals frequent resistant traits in specific clonal complexes, highlighting the importance of particular clonal complexes in China. Our findings substantially expand what is known of the evolution and genetic determinants of resistance in food-associated S. aureus in China and add crucial information for whole-genome sequencing (WGS)-based surveillance of S. aureus.

Antimicrobial, modulatory, and antibiofilm activity of tt-farnesol on bacterial and fungal strains of importance to human health

In this study, we analyzed the antimicrobial, antibiofilm, and modulatory activities of trans-trans-farnesol (tt-farnesol). The minimum inhibitory concentration (MIC) of this sesquiterpene was evaluated against 31 Gram-positive and Gram-negative bacterial strains and 4 species of the genus Candida. Furthermore, we examined its inhibitory action on biofilm production as well as antibiotic modulation. Only Gram-positive species presented susceptibility to tt-farnesol (MIC ranging from 8 µg/mL to 128 µg/mL). No synergistic or antagonistic effects were observed between tt-farnesol (1/4 and 1/8 of MIC) and first-choice antibiotics against multidrug resistant strains. However, the modulatory action of tt-farnesol (1/2 and 1/4 of the MIC) decreased 8 × MIC of non-inhibitory β-lactam antibiotic against a Methicillin-resistant strain. In the antibiofilm assay, tt-farnesol inhibited biofilm formation, especially in Methicillin-resistant Staphylococcus aureus (MRSA) strains, at concentrations ranging from 2 μg/mL to 128 μg/mL. Additionally, in the molecular docking study, the tt-farnesol molecule demonstrated a remarkable binding affinity with important proteins involved in the biofilm production, such as IcaA and Srt proteins. The antimicrobial action of tt-farnesol on Streptococcus pyogenes and Streptococcus agalactiae strains was evaluated for the first time, presenting an MIC of 16 µg/mL for both strains. Our findings reveal the antibacterial, antibiofilm, and modulatory potential of tt-farnesol to aid in the fight against infectious processes.

The SCCmec Types and Antimicrobial Resistance among Methicillin-Resistant Staphylococcus Species Isolated from Dogs with Superficial Pyoderma

This study characterizes clinical methicillin-resistant staphylococcal (MRS) isolates obtained from superficial pyoderma infections in dogs. Our interest was to determine the staphylococcal cassette chromosome mec (SCCmec) type and the antimicrobial susceptibility among MRS isolates from clinical cases. Skin swabs were collected and cultured. Staphylococcus species were identified and characterized with biochemical tests and MALDI-TOF-MS and antimicrobial susceptibility testing by disk diffusion. mecA detection and staphylococcal cassette chromosome mec (SCCmec) typing were achieved by PCR. Of the 65 clinical samples, 56 (86.2%) staphylococcal infections were identified. Twelve (21%) of 56 isolates were MRS infections. All MRS isolates were multidrug resistant. The ccrC and class-C2 mec, which were SCCmec type V, were the most prevalent (66.7%) among the 12 MRS isolates. The predominant SCCmec type V was found in S. aureus, S. intermedius group, S. lentus, S. xylosus, and S. arlettae. Treatment failure is a concern with the emergence of highly resistant MRS in dogs associated with superficial pyoderma. The detection of type V SCCmec MRS has previously been reported among veterinarians and dog owners but not in Northern Thailand. These infections serve as a reminder to improve infection prevention and control measures including reducing environmental contamination and potential zoonotic exposures to MRS. In addition, educational awareness of these risks in small animal hospitals needs to be increased among veterinary hospital staff, clients, and patients.

Novel staphylococcal cassette chromosome mec (SCCmec) type XIV (5A) and a truncated SCCmec element in SCC composite islands carrying speG in ST5 MRSA in Japan

BACKGROUND

Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 13 types. The arginine catabolic mobile element (ACME) is an SCC-like element harbouring an arginine deiminase pathway gene cluster (ACME-arc). ACME type I (ACME I), additionally including a spermidine/spermine-N1-acetyltransferase gene (speG), is considered to have contributed to the rapid spread of the most successful MRSA clone, USA300.

OBJECTIVES

To characterize the SCC composite islands (SCC-CIs) in ST5 MRSA positive for both ACME-arc and speG.

METHODS

Three ST5 MRSA strains (SC640, SC792 and SC955) collected in Hokkaido, Japan were subjected to WGS and the SCC-CIs were determined.

RESULTS

The SCC-CIs consisted of four (SC640 and SC792) or three (SC955) SCC/SCC-like elements and commonly harboured both an ACME type II' and an SCC encoding speG. These SCC-CIs appear to mimic ACME I in USA300, in that they are equipped with ACME-arc and speG. The SCC-CIs of SC640 and SC792 contained novel SCCmec/SCCmec-like elements at the 3' end, whereas SC955 contained SCCmec type V. The SCCmec of SC792 carried mec complex A and ccrC1, which was determined to be novel and designated as SCCmec type XIV (5A). SC640 harboured an SCCmec-like element derived from SCCmec type XIV. It lacked most of the downstream region of the mec complex, including the left chromosomal attachment site (SCCmec XIV Δkdp/DR-L), and lost its capability for chromosomal excision, suggesting that the mecA gene is immobilized on the chromosome.

CONCLUSIONS

These findings provide evidence for increasing complexity of SCC-CIs.

Correlation of MRSA polymerase chain reaction (PCR) wound swab testing and wound cultures in skin and soft tissue infections

Methicillin-resistant Staphylococcus aureus is a considerable pathogen in the setting of skin and soft tissue infections (SSTIs). MRSA PCR swab testing is widely used in the setting of respiratory tract infections, however little data exists relating to the use of MRSA PCR swab testing in SSTIs. Three thousand, nine hundred and ninety-five patients were included in this retrospective study that aimed to validate the clinical correlation of MRSA PCR wound swab testing in SSTIs through sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) analysis. From this review, MRSA PCR wound swabs were found to have a sensitivity of 97.6% (97.5-98.5), a specificity of 94.9% (94.3-95.7), a PPV of 92.3% (91.4-93.2), and a NPV of 98.4% (98.0-98.8). The study results demonstrate that the MRSA SSTI PCR assays have a high NPV and the potential to be a vital tool in de-escalating antimicrobial therapy associated with SSTIs.

Characterization of staphylococci sampled from diabetic foot ulcer of Jordanian patients

AIMS

The aim of this study was to isolate and characterize staphylococcal isolates from diabetic foot ulcers (DFU) in Jordanian patients.

METHODS AND RESULTS

Selected aerobic pathogens recovered from DFU specimens and patients' nares with a focus on staphylococci were investigated. Antimicrobial susceptibilities and the prevalence of methicillin-resistant staphylococci (MRS) were determined. SCCmec types and toxigenic characteristics were analysed and spa typing was performed for methicillin-resistant Staphylococcus aureus (MRSA) isolates. The relationship between toxigenic characteristics of MRSA and the Wagner ulcer grading system was statistically analysed. A total number of 87 DFU patients were recruited for the study. The DFU cultures were polymicrobial. Members of the genus Staphylococcus were the most common among DFU-associated isolates found in 48·3% (n = 42) of all patients enrolled. Coagulase-negative staphylococci (CoNS) comprised 63·3% of staphylococci isolated from DFUs predominated by Staphylococcus epidermidis in both DFU (7·6%) and nares (39·2%). Staphylococcus aureus was isolated from DFUs and nares in 14·2 and 9·8%, respectively, while 93 and 70% of these isolates were MRSA. Most of MRSA carried SCCmec type IV (76·2%) while SCCmec elements were non-typeable in most methicillin resistant coagulase negative staphylococci (MR-CoNS) (61·9%). The most frequent MRSA spa type was t386 (23·8%). Most MRSA and MR-CoNS exhibited resistance towards aminoglycosides, fluoroquinolones and macrolides and susceptibility towards vancomycin, mupirocin and linezolid. No association was found between the possession of pvl, tst, sea and hlg toxins and Wagner ulcer grading system (P value >0·05).

CONCLUSIONS

This analysis of Jordanian DFU culture demonstrated its polymicrobial nature with predominance of Staphylococcus sp.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is the first of its type to assess the microbiology of DFU among Jordanian patients. The results will help in the appropriate application of antimicrobial chemotherapy in the management of DFU.

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.

Staphylococcus aureus in Agriculture: Lessons in Evolution from a Multispecies Pathogen

Staphylococcus aureus is a formidable bacterial pathogen that is responsible for infections in humans and various species of wild, companion, and agricultural animals. The ability of S. aureus to move between humans and livestock is due to specific characteristics of this bacterium as well as modern agricultural practices. Pathoadaptive clonal lineages of S. aureus have emerged and caused significant economic losses in the agricultural sector. While humans appear to be a primary reservoir for S. aureus, the continued expansion of the livestock industry, globalization, and ubiquitous use of antibiotics has increased the dissemination of pathoadaptive S. aureus in this environment. This review comprehensively summarizes the available literature on the epidemiology, pathophysiology, genomics, antibiotic resistance (ABR), and clinical manifestations of S. aureus infections in domesticated livestock. The availability of S. aureus whole-genome sequence data has provided insight into the mechanisms of host adaptation and host specificity. Several lineages of S. aureus are specifically adapted to a narrow host range on a short evolutionary time scale. However, on a longer evolutionary time scale, host-specific S. aureus has jumped the species barrier between livestock and humans in both directions several times. S. aureus illustrates how close contact between humans and animals in high-density environments can drive evolution. The use of antibiotics in agriculture also drives the emergence of antibiotic-resistant strains, making the possible emergence of human-adapted ABR strains from agricultural practices concerning. Addressing the concerns of ABR S. aureus, without negatively affecting agricultural productivity, is a challenging priority.

Genetic and phenotypic diversity of methicillin-resistant Staphylococcus aureus among Japanese inpatients in the early 1980s

To trace the linkage between Japanese healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) strains in the early 1980s and the 2000s onward, we performed molecular characterizations using mainly whole-genome sequencing. Among the 194 S. aureus strains isolated, 20 mecA-positive MRSA (10.3%), 8 mecA-negative MRSA (4.1%) and 3 mecA-positive methicillin-susceptible S. aureus (MSSA) (1.5%) strains were identified. The most frequent sequence type (ST) was ST30 (n = 11), followed by ST5 (n = 8), ST81 (n = 4), and ST247 (n = 3). Rates of staphylococcal cassette chromosome mec (SCCmec) types I, II, and IV composed 65.2%, 13.0%, and 17.4% of isolates, respectively. Notably, 73.3% of SCCmec type I strains were susceptible to imipenem unlike SCCmec type II strains (0%). ST30-SCCmec I (n = 7) and ST5-SCCmec I (n = 5) predominated, whereas only two strains exhibited imipenem-resistance and were tst-positive ST5-SCCmec II, which is the current Japanese HA-MRSA genotype. All ST30 strains shared the common ancestor strain 55/2053, which caused the global pandemic of Panton-Valentine leukocidin-positive MSSA in Europe and the United States in the 1950s. Conspicuously more heterogeneous, the population of HA-MRSA clones observed in the 1980s, including the ST30-SCCmec I clone, has shifted to the current homogeneous population of imipenem-resistant ST5-SCCmec II clones, probably due to the introduction of new antimicrobials.

An epidemic CC1-MRSA-IV clone yields false-negative test results in molecular MRSA identification assays: a note of caution, Austria, Germany, Ireland, 2020

We investigated why a clinical meticillin-resistant Staphylococcus aureus (MRSA) isolate yielded false-negative results with some commercial PCR tests for MRSA detection. We found that an epidemic European CC1-MRSA-IV clone generally exhibits this behaviour. The failure of the assays was attributable to a large insertion in the orfX/SCCmec integration site. To ensure the reliability of molecular MRSA tests, it is vital to monitor emergence of new SCCmec types and junction sites.

Diversity of SCCmec elements and spa types in South African Staphylococcus aureus mecA-positive blood culture isolates

BACKGROUND

The prevalence of Staphylococcus aureus varies depending on the healthcare facility, region and country. To understand its genetic diversity, transmission, dissemination, epidemiology and evolution in a particular geographical location, it is important to understand the similarities and variations in the population being studied. This can be achieved by using various molecular characterisation techniques. This study aimed to provide detailed molecular characterisation of South African mecA-positive S. aureus blood culture isolates by describing the SCCmec types, spa types and to lesser extent, the sequence types obtained from two consecutive national surveillance studies.

METHODS

S. aureus blood culture isolates from a national laboratory-based and enhanced surveillance programme were identified and antimicrobial susceptibility testing was performed using automated systems. A real-time PCR assay confirmed the presence of the methicillin-resistance determinant, mecA. Conventional PCR assays were used to identify the SCCmec type and spa type, which was subsequently analysed using the Ridom StaphType™ software. Multilocus sequence typing was performed on selected isolates using conventional methods. MRSA clones were defined by their sequence type (ST), SCCmec type and spa type.

RESULTS

A detailed description of findings is reported in this manuscript. SCCmec type III predominated overall followed by type IV. A total of 71 different spa types and 24 novel spa types were observed. Spa type t037 was the most common and predominated throughout followed by t1257. Isolates were multidrug resistant; isolates belonging to all SCCmec types were resistant to most of the antibiotics with the exception of type I; isolates with spa type t045 showed resistance to all antibiotics except vancomycin. The most diverse SCCmec-spa type complex was composed of the SCCmec type IV element and 53 different spa types.

CONCLUSION

Although ST data was limited, thereby limiting the number of clones that could be identified, the circulating clones were relatively diverse.

Dangerous Pathogens as a Potential Problem for Public Health

Pathogens are various organisms, such as viruses, bacteria, fungi, and protozoa, which can cause severe illnesses to their hosts. Throughout history, pathogens have accompanied human populations and caused various epidemics. One of the most significant outbreaks was the Black Death, which occurred in the 14th century and caused the death of one-third of Europe's population. Pathogens have also been studied for their use as biological warfare agents by the former Soviet Union, Japan, and the USA. Among bacteria and viruses, there are high priority agents that have a significant impact on public health. Bacillus anthracis, Francisella tularensis, Yersinia pestis, Variola virus, Filoviruses (Ebola, Marburg), Arenoviruses (Lassa), and influenza viruses are included in this group of agents. Outbreaks and infections caused by them might result in social disruption and panic, which is why special operations are needed for public health preparedness. Antibiotic-resistant bacteria that significantly impede treatment and recovery of patients are also valid threats. Furthermore, recent events related to the massive spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are an example of how virus-induced diseases cannot be ignored. The impact of outbreaks, such as SARS-CoV-2, have had far-reaching consequences beyond public health. The economic losses due to lockdowns are difficult to estimate, but it would take years to restore countries to pre-outbreak status. For countries affected by the 2019 coronavirus disease (COVID-19), their health systems have been overwhelmed, resulting in an increase in the mortality rate caused by diseases or injuries. Furthermore, outbreaks, such as SARS-CoV-2, will induce serious, wide-ranging (and possibly long-lasting) psychological problems among, not only health workers, but ordinary citizens (this is due to isolation, quarantine, etc.). The aim of this paper is to present the most dangerous pathogens, as well as general characterizations, mechanisms of action, and treatments.

A novel DNA primase-helicase pair encoded by SCCmec elements

Mobile genetic elements (MGEs) are a rich source of new enzymes, and conversely, understanding the activities of MGE-encoded proteins can elucidate MGE function. Here, we biochemically characterize three proteins encoded by a conserved operon carried by the Staphylococcal Cassette Chromosome (SCCmec), an MGE that confers methicillin resistance to Staphylococcus aureus, creating MRSA strains. The first of these proteins, CCPol, is an active A-family DNA polymerase. The middle protein, MP, binds tightly to CCPol and confers upon it the ability to synthesize DNA primers de novo. The CCPol-MP complex is therefore a unique primase-polymerase enzyme unrelated to either known primase family. The third protein, Cch2, is a 3’-to-5’ helicase. Cch2 additionally binds specifically to a dsDNA sequence downstream of its gene that is also a preferred initiation site for priming by CCPol-MP. Taken together, our results suggest that this is a functional replication module for SCCmec.

Silence as a way of niche adaptation: mecC-MRSA with variations in the accessory gene regulator (agr) functionality express kaleidoscopic phenotypes

Functionality of the accessory gene regulator (agr) quorum sensing system is an important factor promoting either acute or chronic infections by the notorious opportunistic human and veterinary pathogen Staphylococcus aureus. Spontaneous alterations of the agr system are known to frequently occur in human healthcare-associated S. aureus lineages. However, data on agr integrity and function are sparse regarding other major clonal lineages. Here we report on the agr system functionality and activity level in mecC-carrying methicillin resistant S. aureus (MRSA) of various animal origins (n = 33) obtained in Europe as well as in closely related human isolates (n = 12). Whole genome analysis assigned all isolates to four clonal complexes (CC) with distinct agr types (CC599 agr I, CC49 agr II, CC130 agr III and CC1943 agr IV). Agr functionality was assessed by a combination of phenotypic assays and proteome analysis. In each CC, isolates with varying agr activity levels were detected, including the presence of completely non-functional variants. Genomic comparison of the agr I-IV encoding regions associated these phenotypic differences with variations in the agrA and agrC genes. The genomic changes were detected independently in divergent lineages, suggesting that agr variation might foster viability and adaptation of emerging MRSA lineages to distinct ecological niches.

First report of a livestock-associated methicillin-resistant Staphylococcus aureus ST126 harbouring the mecC variant in Brazil

Staphylococcus aureus is a versatile and highly adaptable pathogen associated with a wide range of infectious diseases in humans and animals. In the last decades, concern has increased worldwide due to the emergence and spread of methicillin-resistant S. aureus (MRSA) strains shortly after this drug became a therapeutic option. In this study, we report the genomic features of the first mecC-mediated, β-lactam resistant MRSA strain associated with livestock in Brazil and in the American continent. Three clonally related phenotypic MRSA isolates originated from a dairy herd were confirmed by polymerase chain reaction as mecC-harbouring MRSA isolates. Whole-genome sequencing was performed by Illumina Miseq platform. Downstream analyses showed that the strain was identified as the sequence type 126 (ST126) and spa type t605. In silico analysis revealed a mecC homolog gene in the orfX region associated with different penicillin-binding proteins. Moreover, genes encoding for efflux pump systems (arlR, mepR, LmrS, norA and mgrA), and antibiotic inactivation enzymes (blaZ and FosB) were also detected. Virulence analyses revealed that the strain harbours genes encoding for exoenzymes (aur, splA, splB and splE), toxin (hlgA, hlgB, hlgC, lukD and lukE) and enterotoxin (sea). The epidemiologic and genomic information provided by this study will support further epidemiological and evolutionary investigations to understand the origin and dissemination of mecC-MRSA among animals and its impact on public health.

High prevalence of t895 and t9364 spa types of methicillin-resistant Staphylococcus aureus in a tertiary-care hospital in Mexico: different lineages of clonal complex 5

BACKGROUND

Staphylococcus aureus is a leading cause of broad-spectrum infections both in the community and within healthcare settings. Methicillin-resistant Staphylococcus aureus (MRSA) has become a global public health issue. The aim of this study was to examine the clinical and molecular characteristics of Staphylococcus aureus isolates and to define the population structure and distribution of major MRSA clones isolated in a tertiary-care hospital in Mexico.

RESULTS

From April 2017 to April 2018, 191 Staphylococcus aureus isolates were collected. The frequency of MRSA was 26.7%; these strains exhibited resistance to clindamycin (84.3%), erythromycin (86.2%), levofloxacin (80.3%), and ciprofloxacin (86.3%). The majority of MRSA strains harbored the SCCmec type II (76.4%) and t895 (56.8%) and t9364 (11.7%) were the most common spa types in both hospital-associated MRSA and community-associated MRSA isolates. ST5-MRSA-II-t895 (New York /Japan clone) and ST1011-MRSA-II-t9364 (New York /Japan-Mexican Variant clone) were the most frequently identified clones. Furthermore, different lineages of Clonal Complexes 5 (85.4%) and 8 (8.3%) were predominantly identified in this study.

CONCLUSION

Our study provides valuable information about the epidemiology of MRSA in a city of the central region of Mexico, and this is the first report on the association between t895 and t9364 spa types and ST5 and ST1011 lineages, respectively. These findings support the importance of permanent surveillance of MRSA aimed to detect the evolutionary changes of the endemic clones and the emergence of new strains.

Rapid Detection of mecA and femA Genes by Loop-Mediated Isothermal Amplification in a Microfluidic System for Discrimination of Different Staphylococcal Species and Prediction of Methicillin Resistance

Staphylococcal infection is one of the most pressing problems in modern medicine due to the increasing antibiotic resistance with the overuse of antibiotics. Conventional methods for identification and antimicrobial susceptibility testing (AST) generally take 3-7 days and require skilled technicians. In this study, a microfluidic device based on loop-mediated isothermal amplification (LAMP) was developed, which could discriminate Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis and predict their methicillin resistance by targeting the mecA and femA genes within 70 min including the hands-on time. Multiplex and real-time detection was achieved in a closed system without aerosol contamination. The limits of detection (LODs) for S. aureus, S. epidermidis, S. hominis, and methicillin-resistant S. aureus (MRSA) were 20 CFU/reaction, while that for S. haemolyticus was 200 CFU/reaction. A total of 102 positive cultures of cerebrospinal fluid (CSF) were also tested, and the results were in good agreement with those from conventional methods. Furthermore, mixed cultures were readily identified by our method. The portable and integrated device is rapid, accurate, and easy to use, which can provide information for prompt institution of proper antimicrobial therapy and has great potential for clinical applications, especially in resource-limited settings.

Evolution and Population Dynamics of Clonal Complex 152 Community-Associated Methicillin-Resistant Staphylococcus aureus

Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s. The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe.IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.

MRSA CC398 recovered from wild boar harboring new SCCmec type IV J3 variant

A methicillin-resistant Staphylococcus aureus CC398 was recovered from a wild female boar (Sus scrofa) in the north of Portugal, in 2013 (Sousa et al. 2017). Whole genome sequencing (WGS) revealed this strain carries a new variant of a mecA-containing staphylococcal chromosomal gene cassette (SCCmec) type IV with an uncommon J3 region. WGS studies can facilitate surveillance and provide more detailed characterization of bacterial clones circulating in the wild, reinforcing the need for a one health perspective to better understand and control antimicrobial resistance.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Epidemiological characteristics of methicillin-resistant Staphylococcus aureus isolates from bloodstream cultures at University Hospital in the Czech Republic

The aim of this study was to trace the dynamic changes of methicillin-resistant Staphylococcus aureus (MRSA) lineages in the local hospital in both the national and international context. We describe genotypic and phenotypic characterization of 62 non-duplicate MRSA isolates collected during 2010-2016 at University Hospital in Hradec Kralove, Czech Republic. The isolates were characterized by multilocus sequence typing (MLST), spa typing, and staphylococcal cassette chromosome mec typing (SCCmec typing). Eight different genotypes were described; ST225-t003-II (32/62, 52%), ST5-t002-II (13/62, 22%), and ST225-t014-II (12/62, 21%) were constantly detected over the 7-year follow-up period. The genotypes ST225-t151-II, ST225-t1282-II, ST225-t1623-II, ST78-t2832-II, and ST225-t8799-II occurred only once in the period reported. The majority of the strains, represented by ST225, belonged to clonal complex 5 (CC5).

Novel strategies for rapid identification and susceptibility testing of MRSA

INTRODUCTION

Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes.

AREAS COVERED

We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence.

EXPERT OPINION

Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.

Antimicrobial Resistance in ESKAPE Pathogens

Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.

Detection of sasX Gene and Distribution of SCCmec Types in Invasive and Non-invasive Coagulase-negative Staphylococci

Background

Coagulase-negative staphylococci, which belong to the normal microbiota of the skin and mucous membranes, are opportunistic pathogens. sasX, a newly described protein, is thought to play an important role in nasal colonization and methicillin-resistant Staphylococcus aureus virulence, and it may be acquired from coagulase-negative staphylococci by horizontal gene transfer. It has been considered that understanding the function of sasX gene may help clarify the relevance of the different adhesion mechanisms in the pathogenesis of infections associated with biofilm.

Aims

To investigate the sasX gene presence, staphylococcal cassette chromosome mec types, and antimicrobial resistance patterns of invasive and noninvasive coagulase-negative staphylococci isolates.

Study Design

Cross-sectional study.

Methods

The study included a total of 180 coagulase-negative staphylococci strains. Non-invasive isolates (n=91) were obtained from the hands of healthy volunteers who do not work at the hospital (n=30), the nasal vestibule of healthy volunteer hospital workers (n=26), and central venous catheter (n=35). Invasive isolates (n=89) were isolated from peripheral blood cultures of inpatients who do not have catheters. All isolates were identified by conventional microbiological methods, automated systems, and, if needed, with matrix-assisted laser desorption/ionization-time of flight. Staphylococcal cassette chromosome mec typing, sasX and mec gene detection, antibiotic susceptibility, and sasX gene sequence analysis were performed.

Results

Peripheral blood, central venous catheter colonization, and nasal vestibule isolates were positive for the sasX gene, whereas hand isolates were negative. sasX gene was present in 17 isolates, and no statistical significance was found between invasive and noninvasive isolates (p=0.173). Sequence analysis of the sasX genes showed high homology to related proteins of Staphylococcus phage SPbeta-like and Staphylococcus epidermidis RP62A. staphylococcal cassette chromosome mec type V was the most prevalent regardless of species. staphylococcal cassette chromosome mec type II was more frequent in invasive isolates and found to be statistically important for invasive and noninvasive S. epidermidis isolates (p=0.029). Staphylococcus haemolyticus isolates had the overall highest resistance rates. Resistance to ciprofloxacin, trimethoprim-sulfamethoxazole, and erythromycin was found to be higher in isolates from catheter and blood culture. Staphylococcus hominis isolates had the highest rate for inducible clindamycin resistance. None of the isolates were resistant to vancomycin, teicoplanin, and linezolid.

Conclusion

The sasX gene is detected in 9.44% of the isolates. There is no statistical difference between the sasX-positive and -negative isolates in terms of antibacterial resistance and the presence of sasX and SCCmec types. Further studies about the role of sasX at virulence in coagulase-negative staphylococci, especially from clinical samples such as tracheal aspirate and abscess isolates, and distribution of staphylococcal cassette chromosome mec types are needed.

Molecular Epidemiology of Staphylococcus aureus Lineages in Wild Animals in Europe: A Review

Staphylococcus aureus is an opportunist pathogen that is responsible for numerous types of infections. S. aureus is known for its ability to easily acquire antibiotic resistance determinants. Methicillin-resistant S. aureus (MRSA) is a leading cause of infections both in humans and animals and is usually associated with a multidrug-resistant profile. MRSA dissemination is increasing due to its capability of establishing new reservoirs and has been found in humans, animals and the environment. Despite the fact that the information on the incidence of MRSA in the environment and, in particular, in wild animals, is scarce, some studies have reported the presence of these strains among wildlife with no direct contact with antibiotics. This shows a possible transmission between species and, consequently, a public health concern. The aim of this review is to better understand the distribution, prevalence and molecular lineages of MRSA in European free-living animals.

Methicillin-resistant Staphylococcus aureus in food and the prevalence in Brazil: a review

Foodborne diseases (FBD) occur worldwide and affect a large part of the population, being a cause of international concern among health authorities. Staphylococcus aureus can be transmitted by contaminated food, and it is one of the pathogens that most cause foodborne outbreaks in Brazil. Currently, this organism's ability in developing resistance to antibiotics is notorious; methicillin-resistant Staphylococcus aureus-MRSA-is known for its resistance to methicillin, oxacillin, and others. MRSA is one of the leading causes of infections, becoming a major threat to human health worldwide due to the numerous toxins that can produce. At first, the transmission of MRSA occurred in clinical environments; but in recent decades, its presence has been reported in the community, outside the hospital environment, including food and food-producing animals around the world. In this review, information about MRSA was gathered to verify MRSA incidence in the world but especially in Brazil in food samples, food handlers, food-producing animals, and food processing environments. The studies show that MRSA is easily found and in certain cases with high frequency, thus representing a potential risk to public health.