scholarly journals ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages

2021 ◽  
Vol 14 (4) ◽  
pp. 325
Author(s):  
David Sáez Moreno ◽  
Zehra Visram ◽  
Michele Mutti ◽  
Marcela Restrepo-Córdoba ◽  
Susana Hartmann ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Detection Limit ◽  
Host Range ◽  
Alternative Treatment ◽  
Standard Of Care ◽  
Wild Type ◽  
Rapid Spread ◽  
Pharmaceutical Properties ◽  
Human Infections

Due to the rapid spread of antibiotic resistance, and the difficulties of treating biofilm-associated infections, alternative treatments for S. aureus infections are urgently needed. We tested the lytic activity of several wild type phages against a panel of 110 S. aureus strains (MRSA/MSSA) composed to reflect the prevalence of S. aureus clonal complexes in human infections. The plaquing host ranges (PHR) of the wild type phages were in the range of 51% to 60%. We also measured what we called the kinetic host range (KHR), i.e., the percentage of strains for which growth in suspension was suppressed for 24 h. The KHR of the wild type phages ranged from 2% to 49%, substantially lower than the PHRs. To improve the KHR and other key pharmaceutical properties, we bred the phages by mixing and propagating cocktails on a subset of S. aureus strains. These bred phages, which we termed evolution-squared (ε2) phages, have broader KHRs up to 64% and increased virulence compared to the ancestors. The ε2-phages with the broadest KHR have genomes intercrossed from up to three different ancestors. We composed a cocktail of three ε2-phages with an overall KHR of 92% and PHR of 96% on 110 S. aureus strains and called it PM-399. PM-399 has a lower propensity to resistance formation than the standard of care antibiotics vancomycin, rifampicin, or their combination, and no resistance was observed in laboratory settings (detection limit: 1 cell in 1011). In summary, ε2-phages and, in particular PM-399, are promising candidates for an alternative treatment of S. aureus infections.

scholarly journals Half a century of stable antibiotic resistance in livestock-associated Staphylococcus aureus and its dynamic readaptation to humans

2021 ◽  
Author(s):  
Marta Matuszewska ◽  
Gemma G. R. Murray ◽  
Xiaoliang Ba ◽  
Rhiannon Wood ◽  
Mark A Holmes ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Sccmec Type ◽  
Tetracycline Resistance ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Type Iv ◽  
The Stability ◽  
Type V ◽  
Human Infections

Mobile genetic elements (MGEs) often carry genes that benefit their bacterial hosts. In methicillin-resistant Staphylococcus aureus (MRSA), MGEs have been associated with antibiotic resistance, virulence, and host adaptation. Clonal-complex (CC) 398 is the dominant MRSA in European livestock, and a growing cause of human infections. To understand the risk posed by livestock-associated MRSA to human health, we have used a collection of 1,180 CC398 genomes, sampled from several livestock species and humans, with a broad geographic distribution and spanning 27 years, to reconstruct the dynamics of the MGEs. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably vertically inherited for 57 years. This was followed by the acquisition of a large SCCmec type V element that carries methicillin, tetracycline and heavy metal resistance genes. This has been maintained within livestock-associated CC398 for at least 35 years, with occasional truncations and replacements with other, smaller type IV SCCmec elements. In contrast, a class of prophages that carry a human immune-evasion gene cluster, that are largely absent from livestock-associated CC398, have been repeatedly gained and lost across both human- and livestock-associated CC398. The variable dynamics of these three MGEs means that when livestock-associated MRSA infects humans, re-adaptation to the human host outpaces the loss of antibiotic resistance. Moreover, the stability of both Tn916 and SCCmec suggests that they may persist despite ongoing reductions in antibiotic and zinc oxide use in farming.

scholarly journals Role of persisters and small-colony variants in antibiotic resistance of planktonic and biofilm-associated Staphylococcus aureus: an in vitro study

2009 ◽  
Vol 58 (8) ◽  
pp. 1067-1073 ◽  
Author(s):  
Rachna Singh ◽  
Pallab Ray ◽  
Anindita Das ◽  
Meera Sharma
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Wild Type ◽  
Planktonic Cells ◽  
Intrinsic Resistance ◽  
Persister Cells ◽  
Small Colony Variants ◽  
Small Colony ◽  
Wild Type Parent

The presence of persister cells and small-colony variants (SCVs) has been associated with enhanced antibiotic resistance of many organisms in biofilms. This study investigated whether persisters and/or SCVs contribute to the antibiotic resistance of Staphylococcus aureus biofilms. A detailed dose-dependent killing of biofilms and planktonic cells with five antibiotics (oxacillin, cefotaxime, amikacin, ciprofloxacin and vancomycin) was analysed by treating them with each antibiotic at a concentration of 0–100 μg ml−1 at 37 °C for 48 h. The killing of biofilm cells by all of the antibiotics showed the presence of persister cells – most cells in the population died, leaving a fraction that persisted, even at higher concentrations of the antibiotics. These persisters represented a transient resistant phenotype and reverted to a killing curve resembling that of the wild-type parent upon re-exposure to the antibiotics. SCVs were observed in biofilms only after treatment with ciprofloxacin, and these SCVs were of a transient nature. The treatment of planktonic cells with oxacillin, cefotaxime, ciprofloxacin and vancomycin killed the entire population and no persisters were detected. Transient SCVs, observed in planktonic cells following exposure to these antibiotics, were killed at higher antibiotic concentrations. The treatment of planktonic cells with amikacin yielded a small subpopulation of survivors that included persisters (at numbers significantly lower than for the biofilms) and highly resistant, stable SCVs with an increased biofilm-forming capacity in comparison with the wild-type parent. Thus the high resistance of S. aureus biofilms to multiple unrelated antibiotics is largely dependent on the presence of persister cells. Biofilms harbour a large number of persisters in comparison with planktonic cultures, which either do not harbour persisters or harbour only a small number. SCVs, although not specifically associated with S. aureus biofilms, have an increased biofilm-forming capacity and this may explain the frequent isolation of SCVs from biofilm-associated infections. The intrinsic resistance of these variants may in turn contribute to the enhanced antibiotic resistance of the biofilms thus formed.

scholarly journals Natural Bred ε2-Phages Have an Improved Host Range and Virulence against Uropathogenic Escherichia coli over Their Ancestor Phages

Antibiotics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1337
Author(s):  
Maria Loose ◽  
David Sáez Moreno ◽  
Michele Mutti ◽  
Eva Hitzenhammer ◽  
Zehra Visram ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Host Range ◽  
Phage Therapy ◽  
Uropathogenic Escherichia Coli ◽  
Sequence Type ◽  
Wild Type ◽  
E Coli ◽  
Genetic Sequences ◽  
Tract Infections

Alternative treatments for Escherichia coli infections are urgently needed, and phage therapy is a promising option where antibiotics fail, especially for urinary tract infections (UTI). We used wastewater-isolated phages to test their lytic activity against a panel of 47 E. coli strains reflecting the diversity of strains found in UTI, including sequence type 131, 73 and 69. The plaquing host range (PHR) was between 13 and 63%. In contrast, the kinetic host range (KHR), describing the percentage of strains for which growth in suspension was suppressed for 24 h, was between 0% and 19%, substantially lower than the PHR. To improve the phage host range and their efficacy, we bred the phages by mixing and propagating cocktails on a subset of E. coli strains. The bred phages, which we termed evolution-squared ε2-phages, of a mixture of Myoviridae have KHRs up to 23% broader compared to their ancestors. Furthermore, using constant phage concentrations, Myoviridae ε2-phages suppressed the growth of higher bacterial inocula than their ancestors did. Thus, the ε2-phages were more virulent compared to their ancestors. Analysis of the genetic sequences of the ε2-phages with the broadest host range reveals that they are mosaic intercrossings of 2–3 ancestor phages. The recombination sites are distributed over the whole length of the genome. All ε2-phages are devoid of genes conferring lysogeny, antibiotic resistance, or virulence. Overall, this study shows that ε2-phages are remarkably more suitable than the wild-type phages for phage therapy.

scholarly journals Prevalence of the Enterotoxigenic Staphylococcus Aureus Strains Isolated from Raw Milk and Cheese Produced in North Macedonia

2021 ◽  
Vol 44 (1) ◽  
pp. 71-77
Author(s):  
Marija Ratkova Manovska ◽  
Mirko Prodanov ◽  
Ljupcho Angelovski ◽  
Dean Jankuloski ◽  
Pavle Sekulovski
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Detection Limit ◽  
Scientific Literature ◽  
Foodborne Pathogen ◽  
Food Poisoning ◽  
Raw Milk ◽  
Microbiological Criteria ◽  
Possible Cause ◽  
Raw Cow’S Milk

Abstract Staphylococcus aureus is an important foodborne pathogen due to toxin-related virulence, invasiveness and antibiotic resistance. The ability of S. aureus strains to produce one or more staphylococcal enterotoxins (SEs) in food has been associated with the occurrence of staphylococcal food poisoning (SFP), which is the most common foodborne intoxication worldwide. The study aimed to determine the count of S. aureus strains in samples of raw cow’s milk and various cheeses produced in R. North Macedonia and to detect their ability to produce enterotoxins by passive agglutination SET RPLA (OXOID, UK) and by enzyme-linked fluorescence assay (ELFA) VIDAS SET 2 (Biomerieux, France). A total of 130 S. aureus strains were analyzed. The ability to produce SEs was determined in 17 (13.1%) strains using the SET RPLA detection kit and in 20 (15.4%) strains using the VIDAS SET 2. The study detected enterotoxigenic strains in cheese samples, despite the low count of S. aureus which was below the detection limit according to the Book of rules for microbiological criteria (Off. G. of R.M no 100/2013). Based on these and similar findings, S. aureus must be considered as a possible cause of intoxication, despite the undetected and underreported cases of SFP in the scientific literature.

scholarly journals Species-scale genomic analysis of S. aureus genes influencing phage host range and their relationships to virulence and antibiotic resistance genes

2021 ◽  
Author(s):  
Abraham G. Moller ◽  
Robert A. Petit ◽  
Timothy D. Read
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Host Range ◽  
Resistance Genes ◽  
Phage Therapy ◽  
Genetic Material ◽  
Phage Resistance ◽  
Phage Adsorption ◽  
Immunity Genes ◽  
Core Genes

AbstractPhage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful phage therapy requires knowing both host and phage genetic factors influencing host range for rational cocktail formulation. To further our understanding of host range, we searched 40,000+ public S. aureus genome sequences for previously identified phage resistance genes. We found that phage adsorption targets and genes that block phage assembly were significantly more conserved than genes targeting phage biosynthesis. Core phage resistance genes had similar nucleotide diversity, ratio of non-synonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes in a set of 380 non-redundant S. aureus genomes (each from a different MLST sequence type). Non-core phage resistance genes were significantly less consistent with the core genome phylogeny than all non-core genes in this set. Only superinfection immunity genes correlated with empirically determined temperate phage resistance, accessory genome content, and numbers of accessory antibiotic resistance or virulence genes encoded per strain. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, they are not undergoing positive selection, arms race dynamics. They also suggested genes classified as involved in assembly are least phylogenetically constrained and superinfection immunity genes best predict both empirical phage resistance and levels of phage-mediated HGT.ImportanceStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen that is commonly antibiotic resistant. It causes diverse diseases affecting both the skin and internal organs. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent, such as phage therapy, in which viruses specific to infecting bacteria clear infection. S. aureus phage host range not only determines whether phage therapy will be successful by killing bacteria but also horizontal gene transfer through transduction of host genetic material by phages. In this work, we comprehensively reviewed existing literature to build a list of S. aureus phage resistance genes and searched our database of almost 43,000 S. aureus genomes for these genes to understand their patterns of evolution, finding that prophages’ superinfection immunity correlates best with phage resistance and HGT. These findings improved our understanding of the relationship between known phage resistance genes and phage host range in the species.

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