Detection of staphylococcal cassette chromosome mec type XI carrying highly divergent mecA, mecI, mecR1, blaZ, and ccr genes in human clinical isolates of clonal complex 130 methicillin-resistant Staphylococcus aureus

A Comparative Analysis of MRSA: Epidemiology and Antibiotic Resistance in Greece and Romania

This study provides a comparative analysis of 243 Methicillin-resistant Staphylococcus aureus (MRSA) isolated strains from Greece and Romania, focusing on their epidemiology and antibiotic resistance patterns. Laboratory procedures included phenotypic and automated identification methods, susceptibility testing, DNA isolation, and PCR for detecting antibiotic resistance genes (MecA, SCCmec). Our study results show significant regional differences. In both regions, males have higher MRSA infection rates than females, but the percentages vary. Greece has a higher incidence of MRSA in younger age groups compared to Romania. The majority of MRSA infections occur in inpatient settings in both countries, highlighting the necessity for enhanced infection control measures. Antibiotic resistance profiles reveal higher resistance to several antibiotics in Greece compared to Romania. A molecular analysis shows a widespread distribution of antibiotic resistance genes among MRSA isolates in Greece. These results highlight the necessity for accomplished preventive strategies and optimized treatment protocols.

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.

The zoonotic pathogen Wohlfahrtiimonas chitiniclastica - current findings from a clinical and genomic perspective

The zoonotic pathogen Wohlfahrtiimonas chitiniclastica can cause several diseases in humans, including sepsis and bacteremia. Although the pathogenesis is not fully understood, the bacterium is thought to enter traumatic skin lesions via fly larvae, resulting in severe myiasis and/or wound contamination. Infections are typically associated with, but not limited to, infestation of an open wound by fly larvae, poor sanitary conditions, cardiovascular disease, substance abuse, and osteomyelitis. W. chitiniclastica is generally sensitive to a broad spectrum of antibiotics with the exception of fosfomycin. However, increasing drug resistance has been observed and its development should be monitored with caution. In this review, we summarize the currently available knowledge and evaluate it from both a clinical and a genomic perspective.

Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non-aureus Staphylococci and Mammaliicocci

Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.

Genomic Analysis of a Community-Acquired Methicillin-Resistant Staphylococcus aureus Sequence Type 1 Associated with Caprine Mastitis

This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling

CONTEXT

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation.

METHODS

AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package.

RESULTS

The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

Comparative Study of Linezolid and Vancomycin Regimens in One-Stage Surgery for Treating Limb Traumatic Osteomyelitis Caused by Methicillin-Resistant Staphylococcus aureus

To compare the clinical outcomes of linezolid and vancomycin regimens combined with one-stage surgery in treating traumatic osteomyelitis of the limbs caused by methicillin-resistant Staphylococcus aureus (MRSA) infection. A retrospective study was performed to analyze patients with traumatic osteomyelitis of the limbs attributable to MRSA infection. All of these patients received one-stage surgery to debride their wounds, with subsequent implantation of a vancomycin-loaded calcium sulfate artificial bone. Patients received either intravenous linezolid (study group) or vancomycin (control group) during the perioperative period. The postoperative inflammatory markers, renal function, duration of drainage catheter placement, duration of antibiotic administration, length of hospital stay, adverse events, and recurrence of osteomyelitis in these two groups were compared. The study group had a shorter duration of antibiotic administration and length of hospital stay (p < 0.05). There was a significant difference in the incidences of adverse events between the two groups (5.88% and 17.65% in the study and control groups, respectively, p < 0.05). There was no recurrence in either group during the three-year follow-up period. As of year, five after the surgery, one patient in the control group had a recurrence of osteomyelitis. The linezolid regimen should be preferred to the vancomycin regimen in patients with traumatic osteomyelitis of the extremities caused by MRSA infection because the linezolid regimen showed fewer adverse events, shorter periods of antibiotic use, and shorter hospital stay. However, both treatment regimens achieved satisfactory outcomes and warranted further investigations.

Emergence of livestock-associated Mammaliicoccus sciuri ST71 co-harbouring mecA and mecC genes in Brazil

The discovery and tracking of antimicrobial resistance genes are essential for understanding the evolution of bacterial resistance and restraining its dispersion. Mammaliicoccus sciuri (formerly Staphylococcus sciuri) is the most probable evolutionary repository of the mecA gene, that later disseminated to S. aureus. In this study, we describe the first double mecA/mecC homologue-positive non-aureus staphylococci and mammaliicocci (NASM) from the American continent, also representing the first report of mecC-positive NASM in Brazil. Two clonally related methicillin-resistant M. sciuri strains co-carrying mecA and mecC genes were isolated from the teat skin swab and milk sample collected from an ewe's left udder half. Both M. sciuri strains belonged to the sequence type (ST) 71. Besides mecA and mecC genes, the M. sciuri strains carried broad resistomes for clinically important antimicrobial agents, including β-lactams, tetracyclines, lincosamide, streptogramin, streptomycin, and aminoglycosides. Virulome analysis showed the presence of the clumping factor B (clfB), ATP-dependent protease ClpP (ClpP) and serine-aspartate repeat proteins (sdrC and sdrE) virulence-associated genes. Phylogenomic analysis revealed that these M. sciuri strains are part of a globally disseminated branch, associated with farm and companion animals and even with food. Our findings suggest that M. sciuri is likely to emerge as a pathogen of global interest, carrying a broad repertoire of antimicrobial resistance genes with a remarkable co-presence of mecA and mecC genes. Finally, we strongly encourage to monitor M. sciuri under the One Health umbrella since this bacterial species is spreading at the human-animal-environment interface.

Characterisation of a Staphylococcus aureus Isolate Carrying Phage-Borne Enterotoxin E from a European Badger (Meles meles)

Staphylococcus (S.) aureus colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of S. aureus usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors. Here, we describe a strain of S. aureus isolated from a European badger (Meles meles). For molecular characterisation, DNA microarray-based technology was combined with various next-generation sequencing (NGS) methods. Bacteriophages from this isolate were induced with Mitomycin C and characterized in detail by transmission electron microscopy (TEM) and NGS. The S. aureus isolate belonged to ST425 and had a novel spa repeat sequence (t20845). It did not carry any resistance genes. The uncommon enterotoxin gene see was detected in one of its three temperate bacteriophages. It was possible to demonstrate the induction of all three prophages, although only one of them was expected to be capable of excision based on its carriage of the excisionase gene xis. All three bacteriophages belonged to the family Siphoviridae. Minor differences in size and shape of their heads were noted in TEM images. The results highlight the ability of S. aureus to colonize or infect different host species successfully, which can be attributed to a variety of virulence factors on mobile genetic elements, such as bacteriophages. As shown in the strain described herein, temperate bacteriophages not only contribute to the fitness of their staphylococcal host by transferring virulence factors, but also increase mobility among themselves by sharing genes for excision and mobilization with other prophages.

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.

Comparative review of the nasal carriage and genetic characteristics of Staphylococcus aureus in healthy livestock: Insight into zoonotic and anthroponotic clones

Given the central role of livestock in understanding the genomic epidemiology of S. aureus, the present study systematically reviewed and synthesized data on the nasal S. aureus carriage, resistance patterns to critical antimicrobial agents, virulence factors and genetic lineages among healthy livestock. Bibliographical databases were searched for published studies from May 2003 to May 2022 on nasal S. aureus carriage, their phenotypic and genetic characteristics among healthy pigs (A), sheep and goats (B), cattle (C), poultry (D), camels (E) and buffaloes (F). Special focus was given to the prevalence of nasal MRSA, MRSA-CC398, MRSA-CC9, mecC-MRSA, MSSA-CC398, and resistance to linezolid (LZD^R), chloramphenicol (CLO^R) and tetracycline (TET^R) in S. aureus isolates. Of the 5492 studies identified, 146 comprised groups A(83)/B(18)/C(33)/D(4)/E(5)/F(3), and were found eligible. The overall pooled nasal prevalence of MRSA in healthy livestock was 13.8% (95% CI: 13.5-14.1) among a pooled 48,154 livestock population. Specifically, the pooled prevalence in groups A to F were: 16.0% (95% CI: 15.6-16.4), 3.7% (95% CI: 2.9-4.6), 13.6% (95% CI: 12.8-14.4), 5.8% (95% CI: 5.1-6.5), 7.1% (95% CI: 6.1-10.7), and 2.8% (95% CI: 1.5-4.8), respectively. These values varied considerably by continent. Varied pooled prevalences of CC398 lineage with respect to MRSA isolates were obtained, with the highest from pigs and cattle (>70%). Moreover, other classical animal-adapted MRSA as well as MSSA-CC398-t1928 were reported. TET^R-MSSA was lowest in cattle (18.9%) and highest in pigs (80.7%). LZD^R-S. aureus was reported in 8 studies (mediated by optrA and cfr), mainly in pigs (n = 4), while CLO^R-S. aureus was reported in 32 studies. The virulence genes luk-S/F-PV, tst, etd, sea, see were sparsely reported, and only in non-CC398-MRSA lineages. Certain S. aureus clones and critical AMR appeared to have predominance in some livestock, as in the case of pigs that are high nasal carriers of MRSA-CC398 and -CC9, and MSSA-CC398. These findings highlight the need for adequate prevention against the transmission of zoonotic S. aureus lineages to humans.

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

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

Antibiotic Adjuvants: A Versatile Approach to Combat Antibiotic Resistance

The problem of antibiotic resistance is on the rise, with multidrug-resistant strains emerging even to the last resort antibiotics. The drug discovery process is often stalled by stringent cut-offs required for effective drug design. In such a scenario, it is prudent to delve into the varying mechanisms of resistance to existing antibiotics and target them to improve antibiotic efficacy. Nonantibiotic compounds called antibiotic adjuvants which target bacterial resistance can be used in combination with obsolete drugs for an improved therapeutic regime. The field of "antibiotic adjuvants" has gained significant traction in recent years where mechanisms other than β-lactamase inhibition have been explored. This review discusses the multitude of acquired and inherent resistance mechanisms employed by bacteria to resist antibiotic action. The major focus of this review is how to target these resistance mechanisms by the use of antibiotic adjuvants. Different types of direct acting and indirect resistance breakers are discussed including enzyme inhibitors, efflux pump inhibitors, inhibitors of teichoic acid synthesis, and other cellular processes. The multifaceted class of membrane-targeting compounds with poly pharmacological effects and the potential of host immune-modulating compounds have also been reviewed. We conclude with providing insights about the existing challenges preventing clinical translation of different classes of adjuvants, especially membrane-perturbing compounds, and a framework about the possible directions which can be pursued to fill this gap. Antibiotic-adjuvant combinatorial therapy indeed has immense potential to be used as an upcoming orthogonal strategy to conventional antibiotic discovery.

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021

Antimicrobial resistance (AMR) data on zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs) and reporting countries, jointly analysed by EFSA and ECDC and presented in a yearly EU Summary Report. This report provides an overview of the main findings of the 2020-2021 harmonised AMR monitoring in Salmonella spp., Campylobacter jejuni and C. coli in humans and food-producing animals (broilers, laying hens and turkeys, fattening pigs and bovines under 1 year of age) and relevant meat thereof. For animals and meat thereof, indicator E. coli data on the occurrence of AMR and presumptive Extended spectrum β-lactamases (ESBL)-/AmpC β-lactamases (AmpC)-/carbapenemases (CP)-producers, as well as the occurrence of methicillin-resistant Staphylococcus aureus are also analysed. In 2021, MSs submitted for the first time AMR data on E. coli isolates from meat sampled at border control posts. Where available, monitoring data from humans, food-producing animals and meat thereof were combined and compared at the EU level, with emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to selected and critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting ESBL-/AmpC-/carbapenemase phenotypes. Resistance was frequently found to commonly used antimicrobials in Salmonella spp. and Campylobacter isolates from humans and animals. Combined resistance to critically important antimicrobials was mainly observed at low levels except in some Salmonella serotypes and in C. coli in some countries. The reporting of a number of CP-producing E. coli isolates (harbouring bla _OXA-48, bla _OXA-181, and bla _NDM-5 genes) in pigs, bovines and meat thereof by a limited number of MSs (4) in 2021, requests a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC- producers) showed that encouraging progress have been registered in reducing AMR in food-producing animals in several EU MSs over the last years.

Genomic Evidence for Direct Transmission of mecC-MRSA between a Horse and Its Veterinarian

Methicillin-resistant Staphylococcus aureus bearing the mecC gene (mecC-MRSA) has been reported from animals and humans in recent years. This study describes the first mecC-MRSA isolates of human and equine origin in Hungary (two isolates from horses and one from a veterinarian, who treated one of the infected horses, but was asymptomatic). MRSA isolates were identified by cultivation and PCR detection of the species-specific spa gene and mecA/mecC methicillin resistance genes. The isolates were characterized by antibiotic susceptibility testing, MLST, spa, SCCmec typing, PFGE and whole genome sequencing (WGS). All three isolates belonged to the ST130-t843-SCCmec XI genotype, and carried the mecC and blaZ genes. Apart from beta-lactam drugs, they were sensitive to all tested antibiotics. The isolates of the infected horse and its veterinarian had the same PFGE pulsotype and showed only slight differences with WGS. Hence, this is the first description of direct transmission of a mecC-carrying MRSA between a horse and its veterinarian. The emergence of mecC in the country highlights the importance of the appropriate diagnostics in MRSA identification.

Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis

BACKGROUND

The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory.

METHODS

Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement.

RESULTS

There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates.

CONCLUSIONS

Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.

Staphylococcus aureus and MRSA in Livestock: Antimicrobial Resistance and Genetic Lineages

Animal production is associated with the frequent use of antimicrobial agents for growth promotion and for the prevention, treatment, and control of animal diseases, thus maintaining animal health and productivity. Staphylococcus aureus, in particular methicillin-resistant S. aureus (MRSA), can cause a variety of infections from superficial skin and soft tissue infections to life-threatening septicaemia. S. aureus represents a serious public health problem in hospital and community settings, as well as an economic and animal welfare problem. Livestock-associated MRSA (LA-MRSA) was first described associated with the sequence (ST) 398 that was grouped within the clonal complex (CC) 398. Initially, LA-MRSA strains were restricted to CC398, but over the years it has become clear that its diversity is much greater and that it is constantly changing, a trend increasingly associated with multidrug resistance. Therefore, in this review, we aimed to describe the main clonal lineages associated with different production animals, such as swine, cattle, rabbits, and poultry, as well as verify the multidrug resistance associated with each animal species and clonal lineage. Overall, S. aureus ST398 still remains the most common clone among livestock and was reported in rabbits, goats, cattle, pigs, and birds, often together with spa-type t011. Nevertheless, a wide diversity of clonal lineages was reported worldwide in livestock.

Genetic Diversity among Methicillin-Resistant Staphylococcus aureus in Malaysia (2002-2020)

1.

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is a common organism seen in both healthcare-associated and community-associated infections worldwide and in Malaysia over the past two decades. The aim of this review is to provide a firsthand documentation of all MRSA strains prevalent in the Malaysian population from 2002 to present and briefly describe the changing patterns. 2.

METHODS

Electronic and manual intensive literature searches were conducted between 2002 and 2020, addressing issues directly related to patients and published in the English language were selected. 3.

RESULTS

The literature search retrieved a total of 2217 articles and abstracts of 27 articles. The search yielded a total of 24 articles on genotyping of MRSA in Malaysia. The study found that MRSA strains were mostly genetically related and resulted in the predominant MRSA clones that caused active infections. Thirty-six different sequence types (ST) were recorded. The highest rates of STs detected were ST239 (52.6%), ST1 (47.4%), and ST22 (42.1%). The majority of studies showed that both SCCmec types III and IV were the most common SCCm type in Malaysia, followed by SCCmec type V (57.9%). 4.

CONCLUSIONS

Both Brazilian (ST 239 IIIA) and Hungarian (ST 239-III) MRSA strains were detected in Malaysia. PFGE remains the best method for comparing MRSA strains. However, whole-genome sequencing has a promising chance to replace PFGE in the future.

MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going

Over the years, molecular typing of methicillin-resistant S. aureus (MRSA) has allowed for the identification of endemic MRSA strains and pathogenic strains. After reaching a peak of predominance in a given geographic region, MRSA strains are usually replaced by a new strain. This process is called clonal replacement and is observed worldwide. The worldwide spread of hospital-associated MRSA (HA-MRSA), community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA) clones over the last few decades has allowed this microorganism to be currently considered a pandemic. In Portugal, most HA-MRSA infections are associated with EMRSA-15 (S22-IV), New York/Japan (ST5-II) and Iberian (ST247-I) clones. Regarding the strains found in the community, many of them are frequently associated with the hospital environment, namely the Pediatric, Brazilian and Iberian clones. On the other hand, a strain that is typically found in animals, MRSA clonal complex (CC) 398, has been described in humans as colonizing and causing infections. The ST398 clone is found across all animal species, particularly in farm animals where the economic impact of LA-MRSA infections can have disastrous consequences for industries. In contrast, the EMRSA-15 clone seems to be more related to companion animals. The objective of this review is to better understand the MRSA epidemiology because it is, undoubtedly, an important public health concern that requires more attention, in order to achieve an effective response in all sectors.

Bactericidal Activity of Sodium Bituminosulfonate against Staphylococcus aureus

Antibiotic resistance is increasing worldwide making it necessary to search for alternative antimicrobials. Sodium bituminosulfonate is a long-known substance, whose antimicrobial inhibitory activity has recently been re-evaluated. However, to the best of our knowledge, the bactericidal mode of action of this substance has not been systematically characterized. The aim of this study was to investigate the in vitro bactericidal activity of sodium bituminosulfonate by determining the minimal bactericidal concentrations (MBC), as well as the rapidity of bactericidal effect by time-kill curves. Clinical isolates of methicillin-susceptible (MSSA, n = 20) and methicillin-resistant (mecA/mecC-MRSA, n = 20) Staphylococcus aureus were used to determine MBC by a broth microdilution method. Sodium bituminosulfonate (Ichthyol^® light) was tested in double-dilution concentration steps ranging from 0.03 g/L to 256 g/L. For time-kill analysis, two reference and two clinical S. aureus strains were tested with different concentrations of sodium bituminosulfonate (1× minimal inhibitory concentration (MIC), 2× MIC, 4× MIC, 16× MIC and 256× MIC). For MSSA isolates, MBC₅₀, MBC₉₀ and the MBC range were 0.5 g/L, 1.0 g/L and 0.125–1.0 g/L; (MBC/MIC ratio)₅₀, (MBC/MIC ratio)₉₀ and the range of the MBC/MIC ratio were 4, 4 and 1–8, respectively. Among MRSA isolates, MBC₅₀, MBC₉₀ and the MBC range amounted to 0.5 g/L, 1.0 g/L and 0.06–1.0 g/L; (MBC/MIC ratio)₅₀, (MBC/MIC ratio)₉₀ and the range of the MBC/MIC ratio were 2, 4 and 1–8, respectively. Time-kill kinetics revealed a bactericidal effect after 30 min for sodium bituminosulfonate concentrations of 16× MIC and 256× MIC. The bactericidal activity against MSSA and MRSA was demonstrated for sodium bituminosulfonate. The killing was very rapid with the initial population reduced by 99.9% after only short incubation with concentrations of 16× MIC and higher.

mecC MRSA in Israel—genomic analysis, prevalence and global perspective

Background

MRSA is a major global healthcare problem. In 2011, a new mec variant designated mecC was described, presenting partial identity at the DNA level, thus undetectable by routine mecA PCR.

Objectives

Until now, no reliable information regarding mecC MRSA prevalence was available in Israel. In this study, to the best of our knowledge, we describe the first case of mecC MRSA in Israel, with focus on genomic analysis and global context.

Methods

The mecC MRSA isolate was analysed by WGS with focus on phylogeny, global contextualization, virulence and resistance genes. The strain was characterized by antibiotic susceptibility testing, spa typing and presence of mecA/C and pvl genes.

Results

An MRSA strain (SA10610), isolated from a urine sample of an 83-year old patient, was found negative for the mecA and pvl genes. The MLST and spa type were ST130 and t1736, respectively. SA10610 presented resistance to oxacillin, penicillin and cefoxitin, and susceptibility to all non-β-lactam agents tested. Phylogenetic comparison with a global dataset of 586 mecC MRSA genomes revealed substantial genomic divergence. The nearest genomic relatives were human and animal isolates from Denmark. A screen of 12 761 S. aureus isolates collected during 2011–18 in Israel indicated this is the only mecC-positive strain.

Conclusions

A high degree of genetic variability was found between the SA10610 strain and previously sequenced mecC MRSA isolated worldwide. The genomic and phylogenetic analysis suggest that mecC MRSA isolates have evolved independently rather than from a common ancestor.

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.

High prevalence and expression of antiseptic resistance genes among infectious t037/ST239 methicillin-resistant Staphylococcus aureus (MRSA) strains in North Khorasan Province, Iran

OBJECTIVES

Staphylococcus aureus is an important infectious agent and the majority of methicillin-resistant S. aureus (MRSA) infections are of nosocomial origin. To define the level and distribution of antiseptic resistance among infectious S. aureus strains we studied MRSA and methicillin-susceptible S. aureus (MSSA) isolates collected from different infection sites in an assortment of patients.

MATERIALS AND METHODS

S. aureus isolates were investigated for in vitro susceptibility to antiseptic agents and detection of qacA/B, smr, vanA, and mecA genes.

RESULTS

Among the S. aureus isolates we studied, 25 and 41 were MRSA and MSSA, respectively. The mean of minimum inhibitory concentrations (MICs) for benzethonium chloride (BTC) among MRSA was statistically significantly higher than for MSSA (26 µg/ml versus 11.7 µg/ml, P=0.003) while there was no significant difference between MRSA and MSSA for benzalkonium chloride (BKC) and chlorhexidine digluconate (CHG). The qacA/B genes were carried in 68% of the MRSA and 58.2% of MSSA (P=0.601), while smr was carried in 39% of MRSA and 29.3% of MSSA strains (P=1.000). In 15 out of 25 cases, MRSA ST239 with spa types t037, t030, and t7688 was isolated from the infection site with 86.6% of them carrying a resistance gene (qacA/B or qacA/B + smr).

CONCLUSION

The frequent presence of antiseptic resistance genes and a consequently elevated MIC against antiseptics among ST239 MRSA emphasizes the importance of mandatorily monitoring MRSA for effective infection control.

Prevalence of Staphylococcus aureus in wild hedgehogs (Erinaceus europaeus) and first report of mecC-MRSA in Hungary

In 2011 mecC, a new mecA gene homologue, was described in a bovine isolate in the UK. Since then, mecC-positive methicillin-resistant Staphylococcus aureus (mecC-MRSA) has also been found in wild animals. An especially high prevalence of mecC-MRSA has been reported among hedgehogs in Sweden (64%) and Denmark (61%). Based on these findings we aimed to survey the hedgehog population for mecC-MRSA in Hungary. Altogether 200 hedgehogs were screened for Staphylococcus aureus using a culture-based method. The antibiotic susceptibility of the isolates to nine drugs was determined, their genetic relatedness was established by PFGE and spa-typing, and virulence genes were identified by PCR. Whole genome sequencing was performed for the single mecC-MRSA isolate found. Of the 200 animals, 13 were carriers of S. aureus (6.5%). Among these, one isolate was mecA positive and one was mecC positive. The isolates were susceptible to non-beta-lactam antibiotics. Toxin genes were not found, but the majority carried genes responsible for adhesion and biofilm production. The mecC-MRSA isolate was a single-locus variant of ST130, had a new spa type (t19701) and belonged to SCCmec type XI. It carried a recently described, novel exfoliative toxin (etE). This is the first report of mecC-MRSA in Hungary and the first survey of staphylococcus carriage among wild animals in the country. The mecC prevalence was much lower than in Northern European countries and rather similar to other countries in our region. MecC-MRSA could potentially emerge as a novel human pathogen, especially where close contact occurs between humans and animals.

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

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

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2019-2020

Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by the EFSA and the ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2020 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on fattening pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2019-2020 included data regarding Salmonella, Campylobacter and indicator E. coli isolates, as well as data obtained from the specific monitoring of presumptive ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of methicillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides an overview of the main findings of the 2019-2020 harmonised AMR monitoring in the main food-producing animal populations monitored, in carcase/meat samples and in humans. Where available, monitoring data obtained from pigs, calves, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL-/AmpC-/carbapenemase phenotypes. The key outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been specifically analysed over the period 2014-2020.

Impact of the Stringent Stress Response on the Expression of Methicillin Resistance in Staphylococcaceae Strains Carrying mecA, mecA1 and mecC

The acquisition of the resistance determinant mecA by Staphylococcus aureus is of major clinical importance, since it confers a resistant phenotype to virtually the entire large family of structurally diverse β-lactam antibiotics. While the common resistance determinant mecA is essential, the optimal expression of the resistance phenotype also requires additional factors. Previous studies showed that the great majority of clinical isolates of methicillin-resistant S. aureus (MRSA) have a heterogeneous resistant phenotype, and we observed that strains carrying methicillin genetic determinants other than mecA also produce similar heterogeneous phenotypes. All these strains were able to express high and homogeneous levels of oxacillin resistance when sub-inhibitory concentrations of mupirocin, an effector of the stringent stress response, were added to growth media. Our studies show that the gene gmk, involved in guanine metabolism, was one of the first genes to exhibit mutations in homoresistant (H*R) derivatives obtained through serial passages (with increasing concentrations of oxacillin) of the prototype mecC-carrying MRSA strain LGA251. All these observations led us to propose that a common molecular mechanism for the establishment of high and homogeneous oxacillin resistance must be present among isolates carrying different methicillin resistance determinants. In this work, we tested this hypothesis using whole-genome sequencing (WGS) to compare isogenic populations differing only in their degrees of oxacillin resistance and carrying various methicillin genetic determinants

Nocturnal Birds of Prey as Carriers of Staphylococcus aureus and Other Staphylococci: Diversity, Antimicrobial Resistance and Clonal Lineages

Owls are nocturnal predators that inhabit urbanized and farmlands. They are in direct contact with other animals, both livestock and small wild rodents that they mostly feed on. Staphylococci can be both commensal and pathogenic bacteria that are widespread across the various ecological niches. We aimed to isolate staphylococci from owls and to characterize their antimicrobial resistance, virulence factors and genetic lineages. Swab samples were collected from the throat and cloaca of 114 owls admitted to two rehabilitation centers in Portugal. The identification of staphylococci species was performed by MALDI-TOF. Staphylococci antimicrobial resistance and virulence genes were investigated by means of the disk diffusion method and PCR. Staphylococcus aureus isolates were characterized by MLST, agr and spa-typing. Of the tested animals, 66 isolates were recovered, including 10 different species of staphylococci, of which 25 were coagulase-positive (CoPS) and 41 were coagulase-negative (CoNS). Twenty-three S. aureus were isolated, of which one mecC-MRSA was identified. The isolates were mainly resistant to penicillin, aminoglycosides, clindamycin and tetracycline. mecC-MRSA belonged to ST1245 and spa-type t843 and the remaining S. aureus were ascribed to 12 STs and 15 spa types. A high diversity of clonal lineages was identified among the S. aureus isolated from wild owls. Owls feed mainly on small rodents often exposed to waste and anthropogenic sources, which may explain the moderate prevalence of S. aureus in these animals.

Antimicrobial and Biocide Resistance among Feline and Canine Staphylococcus aureus and Staphylococcus pseudintermedius Isolates from Diagnostic Submissions

A total of 114 Staphylococcus isolates from various infections of companion animals, including 43 feline Staphylococcus aureus, 19 canine S. aureus, 11 feline Staphylococcus pseudintermedius and 41 canine S. pseudintermedius were investigated for (i) their susceptibility to 24 antimicrobial agents and three combinations of antimicrobial agents by broth microdilution following CLSI recommendations and (ii) the corresponding resistance genes. In addition, the isolates were tested for their susceptibility to the four biocides benzalkonium chloride, chlorhexidine, polyhexanide and octenidine by a recently developed biocide susceptibility testing protocol. Penicillin resistance via blaZ was the dominant resistance property in all four groups of isolates ranging between 76.7 and 90.9%. About one quarter of the isolates (25.4%) proved to be methicillin-resistant and carried the genes mecA or mecC. Macrolide resistance was the second most prevalent resistance property (27.2%) and all isolates harbored the resistance genes erm(A), erm(B), erm(C), erm(T) or msr(A), alone or in combinations. Fluoroquinolone resistance was detected in 21.1% of all isolates tested, whereas tetracycline resistance via tet(K) and/or tet(M) occurred in 19.3% of the isolates. Resistance to last resort antimicrobial agents in human medicine was seen only in single isolates, if at all. The minimal inhibitory concentrations (MICs) of the four biocides showed unimodal distributions and were very similar for the four groups of staphylococci. Because of the large number of (multi)resistant isolates, antimicrobial susceptibility testing of feline and canine S. aureus and S. pseudintermedius isolates is highly recommended before the start of an antimicrobial chemotherapy. Moreover, no hints towards the development of biocide resistance were detected.

Pet dogs as reservoir of oxacillin and vancomycin-resistant Staphylococcus spp

The aim of this study was to verify the bacterial resistance profile and detect the presence of mecA gene in Staphylococcus spp. isolated from the nasal microbiota of domiciled dogs. For this purpose 100 nasal swabs from 100 domiciled dogs were collected from the central area of the city of Umuarama (PR), along with a questionnaire answered by their owners. After the isolation all Staphylococcus spp. isolates were submitted to the diffusion disc test by the Kirby-Bauer method, and only oxacillin-resistant samples were submitted to the PCR technique to search for the mecA gene and the results were then submitted to statistical analysis to verify possible risk variables. The 100 Staphylococcus spp. and coagulase negative, among which 41 isolates were resistant to oxacillin, no samples were positive for the mecA gene presence, however, 12 resistant to vancomycin were found. It can be concluded that the domiciled dogs are carriers of Staphylococcus spp. multiresistant, being these a possible source of human contamination.

Comparison of the Frequency of Biofilm-Forming Genes (icaABCD) in Methicillin-Resistant S. aureus Strains Isolated from Human and Livestock

Methicillin-resistant Staphylococcus aureus (MRSA) can cause infections in both human and animal groups, which is a serious threat to public health worldwide. Attachment and colonization are the first steps for S. aureus pathogenesis, and biofilm-mediated infections have a significant negative impact on human and animal health. The MRSA can adapt to different environments and give rise to different strains of human and animal MRSA, causing transmissions of the disease between humans and animals. This study aimed to investigate biofilm production in vitro, and the presence of icaABCD genes in MRSA isolates in both human as well as the disease transmission between human and animal strains. In total, 39 human and 35 livestock isolates were evaluated by the Congo Red Agar method. The presence of mecA and icaABCDR genes were assessed by polymerase chain reaction (PCR), and finally, the PCR products were examined by agarose gel electrophoresis. The results showed that the mecA gene frequency in human and animal isolates was 64.1% and 36.1%, respectively, and there was a significant relationship between mecA and icaAD in human isolates. In addition, significant relationships were found between icaA and Rifampicin and also between icaC and Chloramphenicol and Penicillin in human isolates. In animal isolates, there was a significant relationship between mecA and Trimethoprim as well as between icaR and Rifampicin. It was concluded that all operon ica genes were involved in biofilm production, but icaA and icaD genes in MRSA were more closely associated with mecA. Both animal and human strains can be involved in disease transmission, but this conclusion should be made cautiously.

Distribution and Clonal Diversity of Staphylococcus aureus and Other Staphylococci in Surface Waters: Detection of ST425-t742 and ST130-t843 mecC-Positive MRSA Strains

Natural aquatic environments represent one of the most important vehicles of bacterial dissemination. Therefore, we aimed to isolate staphylococci from surface waters and to investigate the presence of antimicrobial resistance genes and virulence factors as well as the genetic lineages of all Staphylococcus aureus isolates. Staphylococci were recovered from water samples collected from 78 surface waters, including rivers, streams, irrigation ditches, dams, lakes, and fountains. The presence of antimicrobial resistance genes and virulence factors was investigated by PCR. Multilocus sequence typing and spa-typing were performed in all S. aureus isolates. From the 78 water samples, 33 S. aureus, one S. pseudintermedius, and 51 coagulase-negative staphylococci (CoNS) were identified. Among the S. aureus isolates, four MRSA were identified, and all harbored the mecC gene. Fourteen S. aureus were susceptible to all antimicrobials tested and the remaining showed resistance to penicillin, erythromycin and/or tetracycline encoded by the blaZ, ermT, msr(A/B), tetL, and vgaA genes. Regarding the clonal lineages, one mecC-MRSA isolate belonged to spa-type t843 and sequence type (ST) 130 and the other three to t742 and ST425. The remaining S. aureus were ascribed 14 spa-types and 17 sequence types. Eleven species of CoNS were isolated: S. sciuri, S. lentus, S. xylosus, S. epidermidis, S. cohnii spp. urealyticus, S. vitulinus, S. caprae, S. carnosus spp. Carnosus, S. equorum, S. simulans, and S. succinus. Thirteen CoNS isolates had a multidrug resistance profile and carried the following genes: mecA, msr(A/B), mph(C), aph(3′)-IIIa, aac(6′)-Ie–aph(2′’)-Ia, dfrA, fusB, cat_pC221, and tetK. A high diversity of staphylococci was isolated from surface waters including mecCMRSA strains and isolates presenting multidrug-resistance profiles. Studies on the prevalence of antibiotic-resistant staphylococci in surface waters are still very scarce but extremely important to estimate the contribution of the aquatic environment in the spread of these bacteria.

Methicillin-Resistant Staphylococcus aureus Proteome Response to Antibiotic Stress Provides Insights for New Therapeutic Strategies

Antimicrobial resistance is a global threat, with methicillin-resistant Staphylococcus aureus (MRSA) being one of the most representative drug-resistant pathogens. MRSA spread is increasing due to its ability to establish new reservoirs. To this end, the clonal complex (CC)-130 is an emerging genetic lineage, generally regarded as animal adapted and carrying the mecC gene, and sporadically found in humans. Although the MRSA antibiotic resistance mechanisms have been described, there are limited data on systems-wide omics responses to antibiotic stress, particularly at the proteome level. In this study, a gel-based quantitative proteomics approach was performed to assess the cellular responses of a mecC-harboring CC130 MRSA strain of human origin to subinhibitory doses of cefoxitin. We focused on the global response of MRSA to antibiotic stress and upon this treatment, 53 proteins were significantly differentially expressed. Most of the latter proteins were mapped to having functions in cellular metabolism while some glycolysis-related proteins showed a decreased expression after cefoxitin stress. On the contrary, pyruvate kinase, a potential antimicrobial drug target, was found upregulated. Also, quorum sensing, genetic information processing, and stress response proteins were found upregulated. Low-affinity penicillin-binding protein (mecC-encoded) was found in cefoxitin-treated samples. In conclusion, these new findings on cefoxitin-induced proteome changes provide important insights and molecular leads for innovation in treatment of MRSA specifically, and omics approaches to address antibiotic resistance generally.

Benzylpenicillin-producing Trichophyton erinacei and methicillin resistant Staphylococcus aureus carrying the mecC gene on European hedgehogs - A pilot-study

Background

A high carriage rate of methicillin-resistant Staphylococcus aureus with the mecC gene (mecC-MRSA) has been described among Wild European hedgehogs (Europeaus erineaus). Due to this frequent occurrence, it has been suggested that hedgehogs could be a natural reservoir for mecC-MRSA. However, the reason why hedgehogs carry mecC-MRSA remains unknown, but it has been hypothesized that mecC-MRSA could have evolved on the skin of hedgehogs due to the co-occurrence with antibiotic producing dermatophytes. The aim of this pilot-study was therefore to investigate if hedgehogs in Sweden carry Trichophyton spp. and to provide evidence that these dermatophytes are able to produce penicillin or similar substances. In addition, the study aimed to identify if dermatophytes co-occurred with mecC-MRSA.

Methods

Samples were collected from hedgehogs (Europeaus erineaus) that were euthanized or died of natural causes. All samples were screened for dermatophytes and mecC-MRSA using selective cultivation methods. Suspected isolates were characterized using PCR-based methods, genome sequencing and bioinformatic analyses. Identification of penicillin was performed by ultra-high-performance liquid chromatography-tandem mass spectrometry.

Results

In total 23 hedgehogs were investigated, and it was shown that two carried Trichophyton erinacei producing benzyl-penicillin, and that these hedgehogs also carried mecC-MRSA. The study also showed that 60% of the hedgehogs carried mecC-MRSA.

Conclusion

The pilot-study demonstrated that Trichophyton erinacei, isolated from Swedish hedgehogs, can produce benzylpenicillin and that these benzylpenicillin-producing T. erinacei co-occurred with mecC-MRSA. The study also reconfirmed the high occurrence of mecC-MRSA among hedgehogs.

Pet husbandry as a risk factor for colonization or infection with MDR organisms: a systematic meta-analysis

BACKGROUND

MDR organisms (MDROs) pose a relevant risk for patients in modern healthcare. Although ownership of pet animals is common and owners and pets commonly live in close contact, it is still unclear whether pet ownership may be considered as a risk factor for MDRO acquisition prior to hospitalization.

METHODS

We performed three separate meta-analyses in accordance with the PRISMA guidelines, assessing contact to pets as a risk factor for acquisition of MRSA, VRE and MDR Gram-negatives [namely third-generation cephalosporin-resistant Enterobacterales (3GCRE) and carbapenem-resistant Enterobacterales (CRE)].

RESULTS

We calculated an increased risk of MRSA carriage for dog owners [risk ratio (RR) 2.28, 95% CI 1.47-3.56]. Meta-analysis did not show a significantly higher risk for 3GCRE colonization among owners of different pet species compared with non-pet owners (RR 1.18, 95% CI 0.83-1.68 for pet owners in general, RR 0.88, 95% CI 0.56-1.40 for dog owners, RR 1.16, 95% CI 0.58-2.34 for cat owners, RR 1.34, 95% CI 0.43-4.18 for rodent owners, RR 0.91, 95% CI 0.38-2.18 for bird owners, and RR 2.34, 95% CI 0.33-16.63 for lizard/frog owners). For VRE, there were insufficient data to perform a meta-analysis.

CONCLUSIONS

Our analyses suggest contact to pet animals is a risk factor for MRSA, but not for 3GCRE/CRE acquisition. Evaluation of the underlying literature suggested a possible role of pet animals as: (i) vectors for the transmission of MDROs between livestock and humans; as well as (ii) a reservoir for MDROs. Pets, therefore, may promote transmission and reinfection of humans.

Hedgehogs as a Potential Source of Zoonotic Pathogens-A Review and an Update of Knowledge

Simple Summary

Up to date studies indicate that wild hedgehogs may act as carriers and/or hosts for bacterial, viral, and fungal pathogens with zoonotic potential, posing a significant threat to humans. The same applies to domestic hedgehogs, which are increasingly kept as pets. Considering the potential risk of infection to humans through close contact with hedgehogs or the contaminated environment they inhabit, current data on the prevalence of various zoonotic pathogens in these animals is desirable.

Abstract

Hedgehogs are small insectivorous mammals common across Europe, Asia, and Africa. The increased encroachment of humans into hedgehog habitats has disrupted the human-animal-environment interface. With growing interest in the zoonotic diseases of wildlife species, more studies have been devoted to this subject in the last few years. These papers provide information about known and new emerging diseases. Here we review the current knowledge regarding bacterial, viral, protozoic, and mycotic pathogens with zoonotic potential and assess the importance of hedgehogs as their carriers. Both wild and pet hedgehogs were included in the review. Data from several countries and various hedgehog species were included. The study shows the importance of hedgehogs as carriers of zoonotic diseases and reservoirs of zoonotic pathogens in varied habitats.

Identification of a mecA/mecC-positive MRSA ST1-t127 isolate from a racehorse in Japan

OBJECTIVES

MRSA is a known pathogen that affects horses. We investigated an equine MRSA isolate for potential antimicrobial resistance genes, classified the staphylococcal cassette chromosome mec (SCCmec) and identified the strain-specific dissemination in the horse community based on WGS.

METHODS

WGS, using short-read sequencing, and subsequent long-read sequencing by hybrid assembly, was conducted to obtain a complete genome sequence. Pairwise sequence alignment of relative SCCmec sequences and core-genome phylogenetic analysis were performed to highlight transmission routes of the SCCmec and MRSA strain-specific lineages.

RESULTS

In 2018, we isolated the MRSA JRA307 strain from the pus of a wound on a racehorse and the complete genome sequence suggests that it is a clinically relevant pvl-negative ST1-t127 MRSA that harbours both mecA and mecC on SCCmec-307. SCCmec-307 exhibited marked sequence identity to the previously reported SCCmec-mecC in the Staphylococcus sciuri GVGS2 strain isolated from cattle. The JRA307 mecC gene was classified as a mecC allotype of S. sciuri rather than that of Staphylococcus aureus.

CONCLUSIONS

We demonstrated the complete genome sequence of equine isolate JRA307, which is a clinically relevant MRSA harbouring mecA and mecC on SCCmec-307. The finding of mecC MRSA suggests a possible SCCmec transmission between distinct staphylococcal species. To the best of our knowledge, this is the first report of mecC detection in Japan.

Mass spectrometry and machine learning for the accurate diagnosis of benzylpenicillin and multidrug resistance of Staphylococcus aureus in bovine mastitis

Staphylococcus aureus is a serious human and animal pathogen threat exhibiting extraordinary capacity for acquiring new antibiotic resistance traits in the pathogen population worldwide. The development of fast, affordable and effective diagnostic solutions capable of discriminating between antibiotic-resistant and susceptible S. aureus strains would be of huge benefit for effective disease detection and treatment. Here we develop a diagnostics solution that uses Matrix-Assisted Laser Desorption/Ionisation-Time of Flight Mass Spectrometry (MALDI-TOF) and machine learning, to identify signature profiles of antibiotic resistance to either multidrug or benzylpenicillin in S. aureus isolates. Using ten different supervised learning techniques, we have analysed a set of 82 S. aureus isolates collected from 67 cows diagnosed with bovine mastitis across 24 farms. For the multidrug phenotyping analysis, LDA, linear SVM, RBF SVM, logistic regression, naïve Bayes, MLP neural network and QDA had Cohen's kappa values over 85.00%. For the benzylpenicillin phenotyping analysis, RBF SVM, MLP neural network, naïve Bayes, logistic regression, linear SVM, QDA, LDA, and random forests had Cohen's kappa values over 85.00%. For the benzylpenicillin the diagnostic systems achieved up to (mean result ± standard deviation over 30 runs on the test set): accuracy = 97.54% ± 1.91%, sensitivity = 99.93% ± 0.25%, specificity = 95.04% ± 3.83%, and Cohen's kappa = 95.04% ± 3.83%. Moreover, the diagnostic platform complemented by a protein-protein network and 3D structural protein information framework allowed the identification of five molecular determinants underlying the susceptible and resistant profiles. Four proteins were able to classify multidrug-resistant and susceptible strains with 96.81% ± 0.43% accuracy. Five proteins, including the previous four, were able to classify benzylpenicillin resistant and susceptible strains with 97.54% ± 1.91% accuracy. Our approach may open up new avenues for the development of a fast, affordable and effective day-to-day diagnostic solution, which would offer new opportunities for targeting resistant bacteria.

Antimicrobial Resistance and Genetic Lineages of Staphylococcus aureus from Wild Rodents: First Report of mecC-Positive Methicillin-Resistant S. aureus (MRSA) in Portugal

The frequent carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), by wild animals along with its zoonotic potential poses a public health problem. Furthermore, the repeated detection of the mecA gene homologue, mecC, in wildlife raises the question whether these animals may be a reservoir for mecC-MRSA. Thus, we aimed to isolate S. aureus and MRSA from wild rodents living in port areas and to characterize their antimicrobial resistance and genetic lineages. Mouth and rectal swab samples were recovered from 204 wild rodents. The samples were incubated in BHI broth with 6.5% of NaCl and after 24 h at 37 °C the inoculum was seeded onto Baird-Parker agar, Mannitol Salt agar and ORSAB (supplemented with 2 mg/L of oxacillin) plates. Species identification was confirmed by MALDI-TOF MS. The antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method against 14 antibiotics. The presence of virulence and resistance genes was performed by PCR. The immune evasion cluster (IEC) system was investigated in all S. aureus. All isolates were characterized by MLST, spa- and agr typing. From 204 samples, 38 S. aureus were isolated of which six MRSA were detected. Among the six MRSA isolates, three harbored the mecC gene and the other three, the mecA gene. All mecC-MRSA isolates were ascribed to sequence type (ST) 1945 (which belongs to CC130) and spa-type t1535 whereas the mecA isolates belonged to ST22 and ST36 and spa-types t747 and t018. Twenty-five S. aureus were susceptible to all antibiotics tested. S. aureus isolates were ascribed to 11 MLST and 12 spa-types. S. aureus presents a great diversity of genetic lineages in wild rodents. This is the first report of mecC-MRSA in Portugal.

The Genotype-to-Phenotype Dilemma: How Should Laboratories Approach Discordant Susceptibility Results?

Traditional culture-based methods for identification and antimicrobial susceptibility testing (AST) of bacteria take 2 to 3 days on average. Syndromic molecular diagnostic panels have revolutionized clinical microbiology laboratories as they can simultaneously identify an organism and detect some of the most significant antimicrobial resistance (AMR) genes directly from positive blood culture broth or from various specimen types (e.g., whole blood, cerebrospinal fluid, and respiratory specimens). The presence or absence of an AMR marker associated with a particular organism can be used to predict the phenotypic AST results to more rapidly guide therapy. Numerous studies have shown that genotypic susceptibility predictions by syndromic panels can improve patient outcomes. However, an important limitation of AMR marker detection to predict phenotype is the potential discrepancies that may arise upon performing phenotypic AST of the recovered organism in culture. The focus of this minireview is to address how clinical laboratories should interpret rapid molecular results from commercial platforms in relation to phenotypic AST. Stepwise approaches and solutions are provided to resolve discordant results between genotypic and phenotypic susceptibility results.

Antibiotic resistance in the environment: a critical insight on its occurrence, fate, and eco-toxicity

The overuse, misuse, and underuse of antibiotics tend to increase the antibiotic burden in the environment resulting into the evolution in microbial community to possess resistance that renders antibiotics ineffective against them. The current review recapitulates the present state of knowledge about the occurrence and fate of antibiotics in various environmental matrices. Also, the prevalence of antibiotic-resistant bacteria/antibiotic-resistant genes (ARB/ARGs) in various biological and non-biological systems, eco-toxicity of antibiotics on non-target organisms, and remediation methods for antibiotics and ARB/ARGs removal were critically reviewed. Furthermore, a comparison of various technologies for their efficiency to eliminate antibiotic residues and ARB/ARGs is made. The study identified gaps in the investigation of toxic effects of low concentration of antibiotics and the mixture of multiple antibiotics on non-target organisms. The study of antibiotics' phytotoxicity and toxicity towards sediment and soil-dwelling organisms are also recognized as a knowledge gap. The review also details policies implemented across the globe to fight against antibiotic resistance, and the scarcity of data on lab to land transferred remediation technology was identified. The present study entails a critical review of literature providing guidelines for the articulation of policies for prudent use of antibiotics, limits on the amount of antibiotics in pharmaceutical formulations, and regular surveillance in the Indian context.

Diversity and genetic lineages of environmental staphylococci: a surface water overview

Antimicrobial resistance in the environmental dimension is one of the greatest challenges and emerging threats. The presence of resistant bacteria and resistance genes in the environment, especially in aquatic systems, has been a matter of growing concern in the past decade. Monitoring the presence of antimicrobial resistance species, in this particular case, Staphylococcus spp., in natural water environments could lead to a better understanding of the epidemiology of staphylococci infections. Thus, the investigation of natural waters as a potential reservoir and vehicle for transmission of these bacteria is imperative. Only a few studies have investigated the prevalence, antimicrobial resistance and genetic lineages of staphylococci in natural waters. Those studies reported a high diversity of staphylococci species and lineages in surface waters. Methicillin-resistant S. aureus were relatively prevalent in surface waters and, as expected, often presented a multidrug-resistant profile. There was a high diversity of S. aureus lineages in surface waters. The presence of S. aureus CC8 and CC5 suggests a human origin. Among the coagulase-negative staphylococci, the most frequently found in natural waters was S. warneri and S. epidermidis. These studies are extremely important to estimate the contribution of the aquatic environment in the spread of pathogenic bacteria.

The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019

Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by the EFSA and the ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2018 monitoring specifically focussed on poultry and their derived carcases/meat, while the monitoring performed in 2019 specifically focused on pigs and calves under 1 year of age, as well as their derived carcases/meat. Monitoring and reporting of AMR in 2018/2019 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of presumptive ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides an overview of the main findings of the 2018/2019 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates possessing ESBL-/AmpC-/carbapenemase phenotypes. The outcome indicators for AMR in food-producing animals such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2015-2019.

Genomic Analysis of Staphylococcus aureus of the Lineage CC130, Including mecC-Carrying MRSA and MSSA Isolates Recovered of Animal, Human, and Environmental Origins

Most methicillin resistant Staphylococcus aureus (MRSA) isolates harboring mecC gene belong to clonal complex CC130. This lineage has traditionally been regarded as animal-associated as it lacks the human specific immune evasion cluster (IEC), and has been recovered from a broad range of animal hosts. Nevertheless, sporadic mecC-MRSA human infections have been reported, with evidence of zoonotic transmission in some cases. The objective of this study was to investigate the whole-genome sequences of 18 S. aureus CC130 isolates [13 methicillin-resistant (mecC-MRSA) and five methicillin-susceptible (MSSA)] from different sequences types, obtained from a variety of host species and origins (human, livestock, wild birds and mammals, and water), and from different geographic locations, in order to identify characteristic markers and genomic features. Antibiotic resistance genes found among MRSA-CC130 were those associated with the SSCmecXI element. Most MRSA-CC130 strains carried a similar virulence gene profile. Additionally, six MRSA-CC130 possessed scn-sak and one MSSA-ST130 had lukMF'. The MSSA-ST700 strains were most divergent in their resistance and virulence genes. The pan-genome analysis showed that 29 genes were present solely in MRSA-CC130 (associated with SCCmecXI) and 21 among MSSA-CC130 isolates (associated with phages). The SCCmecXI, PBP3, GdpP, and AcrB were identical at the amino acid level in all strains, but some differences were found in PBP1, PBP2, PBP4, and YjbH proteins. An examination of the host markers showed that the 3' region of the bacteriophage φ3 was nearly identical to the reference sequence. Truncated hlb gene was also found in scn-negative strains (two of them carrying sak-type gene). The dtlB gene of wild rabbit isolates included novel mutations. The vwbp gene was found in the three MSSA-ST700 strains from small ruminants and in one MSSA-ST130 from a red deer; these strains also carried a scn-type gene, different from the human and equine variants. Finally, a phylogenetic analysis showed that the three MSSA-ST700 strains and the two MSSA-ST130 strains cluster separately from the remaining MRSA-CC130 strains with the etD2 gene as marker for the main lineage. The presence of the human IEC cluster in some mecC-MRSA-CC130 strains suggests that these isolates may have had a human origin.

Multicentre study of the burden of multidrug-resistant bacteria in the aetiology of infected diabetic foot ulcers

Background

Infected diabetic foot ulcer (IDFU) is a public health issue and the leading cause of non-traumatic limb amputation. Very few published data on IDFU exist in most West African countries.

Objective

The study investigated the aetiology and antibacterial drug resistance burden of IDFU in tertiary hospitals in Osun state, Nigeria, between July 2016 and April 2017.

Methods

Isolates were cultured from tissue biopsies or aspirates collected from patients with IDFU. Bacterial identification, antibiotic susceptibility testing and phenotypic detection of extended-spectrum beta-lactamase and carbapenemase production were done by established protocols. Specific resistance genes were detected by polymerase chain reaction.

Results

There were 218 microorganisms isolated from 93 IDFUs, comprising 129 (59.2%) Gram-negative bacilli (GNB), 59 (27.1%) Gram-positive cocci and 29 (13.3%) anaerobic bacteria. The top five facultative anaerobic bacteria isolated were: Staphylococcus aureus (34; 15.6%), Escherichia coli (23; 10.6%), Pseudomonas aeruginosa (20; 9.2%), Klebsiella pneumoniae (19; 8.7%) and Citrobacter spp. (19; 8.7%). The most common anaerobes were Bacteroides spp. (7; 3.2%) and Peptostreptococcus anaerobius (6; 2.8%). Seventy-four IDFUs (80%) were infected by multidrug-resistant bacteria, predominantly methicillin-resistant S. aureus and GNB producing extended-spectrum β-lactamases, mainly of the CTX-M variety. Only 4 (3.1%) GNB produced carbapenemases encoded predominantly by bla _VIM. Factors associated with presence of multidrug-resistant bacteria were peripheral neuropathy (adjusted odds ratio [AOR] = 4.05, p = 0.04) and duration of foot infection of more than 1 month (AOR = 7.63, p = 0.02).

Conclusion

Multidrug-resistant facultative anaerobic bacteria are overrepresented as agents of IDFU. A relatively low proportion of the aetiological agents were anaerobic bacteria.

No Detection of Methicillin-Resistant Staphylococcus aureus in Dairy Goats

This short communication addresses the hypothesis that the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is low in dairy goats in Sweden. Methicillin-resistant S. aureus is a widespread zoonotic bacterium of clinical importance in both animals and humans. In Sweden, MRSA is rare among both animals and humans. However, MRSA has been detected in a few goat herds in Sweden with a high within-herd occurrence of mecC-MRSA, but only a limited number of herds were investigated and most of them were not producing milk for human consumption. The prevalence of MRSA among dairy goat herds in Sweden is not known and a cross-sectional prevalence study was therefore conducted. A total of 22 bulk milk samples from the same number of herds, and pooled swabs from nose, mouth, and perineum from 113 goats, were collected during August and September 2019 for bacteriological investigation. After culturing on selective media, suspected isolates were confirmed as S. aureus using MALDI-TOF and subjected to PCR targeting the mecA and mecC genes to confirm MRSA status. No samples were found to be positive for MRSA, and there are therefore no indications of a spread of MRSA in Swedish dairy goat herds.