scholarly journals Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children hospital in México City.

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Children Health ◽  
Health Care Unit

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides were included. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLST´s) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). However, half of the S. epidermidis analyzed lacked the icaoperon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug-resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.

scholarly journals Genomic analysis of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated during eight years in a single children hospital in México City.

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Children Health ◽  
Health Care Unit

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study. Resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides were included. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLST´s) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). However, half of the S. epidermidis analyzed lacked the icaoperon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug-resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.

scholarly journals Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children’s Hospital in México City in an eight-years survey

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8068 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I. Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez-Herrada ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Multidrug Resistant ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Beta Lactams ◽  
Antibiotic Resistant ◽  
Transfer Rates ◽  
Health Care Unit

Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children’s health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.

scholarly journals Genomic analysis reveals high virulence and antibiotic resistance amongst phage susceptible Acinetobacter baumannii

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Udomluk Leungtongkam ◽  
Rapee Thummeepak ◽  
Thawatchai Kitti ◽  
Kannipa Tasanapak ◽  
Jintana Wongwigkarn ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Biofilm Formation ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Multidrug Resistant ◽  
Copper Tolerance ◽  
Virulence Determinants ◽  
Genome Sequences ◽  
High Virulence

Abstract In this study, we examined the association between antimicrobial resistance, CRISPR/Cas systems and virulence with phage susceptibility in Acinetobacter baumannii and investigated draft genomes of phage susceptible multidrug resistant A. baumannii strains from Thailand. We investigated 230 A. baumannii strains using 17 lytic A. baumannii phages and the phage susceptibility was 46.5% (107/230). Phage susceptibility was also associated with resistance to numerous antibiotics (p-value < 0.05). We also found association between biofilm formation and the presence of ompA gene among phage susceptible A. baumannii strains (p-value < 0.05). A. baumannii isolates carrying cas5 or combinations of two or three other cas genes, showed a significant increase in phage resistance. Whole-genome sequences of seven phage susceptible A. baumannii isolates revealed that six groups of antibiotic resistance genes were carried by all seven phage susceptible A. baumannii. All strains carried biofilm associated genes and two strains harbored complete prophages, acquired copper tolerance genes, and CRISPR-associated (cas) genes. In conclusion, our data exhibits an association between virulence determinants and biofilm formation among phage susceptible A. baumannii strains. These data help to understand the bacterial co-evolution with phages.

scholarly journals Application of combined genomic and transfer analyses to identify factors mediating regional spread of antibiotic resistant bacterial lineages

2020 ◽  
Author(s):  
Joyce Wang ◽  
Betsy Foxman ◽  
Ali Pirani ◽  
Zena Lapp ◽  
Lona Mody ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Analysis ◽  
Patient Characteristics ◽  
Patient Transfer ◽  
Whole Genome ◽  
Nursing Facilities ◽  
Antibiotic Resistant ◽  
Patient Level ◽  
Healthcare Associated

ABSTRACTBackgroundPatients entering nursing facilities (NFs) are frequently colonized with antibiotic resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission we applied whole-genome sequencing to track the spread of four ARO species across regional NFs and evaluated patient-level characteristics and transfer acute-care hospitals (ACHs) as risk factors for colonization.Methods584 patients from six NFs were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm) and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined using multivariable regression models.ResultsThe majority of ARO isolates across study sites belonged to major healthcare-associated lineages: MRSA (ST5;N=89/117); VREfc (ST6;N=68/75); CipREc (ST131; N=58/64), and VREfm (clade A; N=129/129). While the genomic similarity of strains between NF pairs was associated with overlap in their feeder ACHs (Spearman’s rho=0.44-0.75, p<0.05 for MRSA, VREfc and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status (adjusted odds ratio [aOR]>1 for all four AROs) and recent exposure to glycopeptides (aOR>2 for VREfm, VREfc and MRSA) or 3rd/4th-generation cephalosporins (aOR>2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only one ARO/ACH pair (VREfm/ACH19, aOR=2.48[1.06-5.83]).ConclusionIn this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.SummaryUsing a combination of whole-genome sequencing, patient transfer and clinical data, we discerned the dissemination of four high-priority antibiotic-resistant organisms (ARO) in the regional healthcare network, and epidemiolocal drivers underlying the high ARO importation rate into regional nursing facilities.

scholarly journals Genomic diversity of antibiotic multi-resistant Staphylococcus epidermidis isolated from a tertiary care hospital in México City

2019 ◽  
Author(s):  
Roberto Cabrera-Contreras ◽  
Rosa I Santamaría ◽  
Patricia Bustos ◽  
Irma Martínez-Flores ◽  
Enrique Meléndez ◽  
...  
Keyword(s):  
Mexico City ◽  
Staphylococcus Epidermidis ◽  
Tertiary Care ◽  
Hospital Setting ◽  
Opportunistic Pathogen ◽  
Tertiary Hospital ◽  
Genomic Diversity ◽  
Whole Genome ◽  
Care Hospital ◽  
Worldwide Distribution

Staphylococcus epidermidis is a human commensal and opportunistic pathogen worldwide distributed. To ascertain which pathogenic S. epidermidis clones are circulating in a local tertiary hospital setting, we sequenced the complete genomes of 17 S. epidermidis isolates obtained from neonatal infections at a Hospital Care Unit in México City. Genomic comparisons between S. epidermidis isolates revealed high pairwise whole genome nucleotide identities of about 97% to 99% and essentially a clonal structure. We inferred eight Multilocus Sequence Types (MLST´s), six of them of worldwide distribution, and two showing allelic variants, not in MLST databases. The profile of virulence includes genes involved in biofilm and modulin formation; most of the strains are multi-resistant to methicillin and several other beta-lactams, fluoroquinolones, and macrolides. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more frequent than the mutation rate and affected the whole genome. Therefore, recombination properties shape the population structure of local nosocomial S. epidermidis strains, formed by pathogenic and probably, non-pathogenic clones.

scholarly journals Development of Staphylococcus Enzybiotics: The Ph28 Gene of Staphylococcus epidermidis Phage PH15 Is a Two-Domain Endolysin

Antibiotics ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 148
Author(s):  
Magdy Mohamed Muharram ◽  
Ashraf Tawfik Abulhamd ◽  
Mohammed F. Aldawsari ◽  
Mohamed Hamed Alqarni ◽  
Nikolaos E. Labrou
Keyword(s):  
Staphylococcus Epidermidis ◽  
Multidrug Resistant ◽  
Health Concern ◽  
Resistant Bacteria ◽  
Antibiotic Resistant ◽  
E Coli ◽  
Evolutionary Features ◽  
Ncbi Accession ◽  
Molecular Modelling Studies ◽  
Modelling Studies

Given the worldwide increase in antibiotic resistant bacteria, bacteriophage derived endolysins represent a very promising new alternative class of antibacterials in the fight against infectious diseases. Endolysins are able to degrade the prokaryotic cell wall, and therefore have potential to be exploited for biotechnological and medical purposes. Staphylococcus epidermidis is a Gram-positive multidrug-resistant (MDR) bacterium of human skin. It is a health concern as it is involved in nosocomial infections. Genome-based screening approach of the complete genome of Staphylococcus virus PH15 allowed the identification of an endolysin gene (Ph28; NCBI accession number: YP_950690). Bioinformatics analysis of the Ph28 protein predicted that it is a two-domain enzyme composed by a CHAP (22-112) and MurNAc-LAA (171-349) domain. Phylogenetic analysis and molecular modelling studies revealed the structural and evolutionary features of both domains. The MurNAc-LAA domain was cloned, and expressed in E. coli BL21 (DE3). In turbidity reduction assays, the recombinant enzyme can lyse more efficiently untreated S. epidermidis cells, compared to other Staphylococcus strains, suggesting enhanced specificity for S. epidermidis. These results suggest that the MurNAc-LAA domain from Ph28 endolysin may represent a promising new enzybiotic.

scholarly journals Characterisation of Vibrio Species from Surface and Drinking Water Sources and Assessment of Biocontrol Potentials of Their Bacteriophages

2020 ◽  
Vol 2020 ◽  
pp. 1-15
Author(s):  
Mpho Defney Maje ◽  
Christ Donald Kaptchouang Tchatchouang ◽  
Madira Coutlyne Manganyi ◽  
Justine Fri ◽  
Collins Njie Ateba
Keyword(s):  
Water Samples ◽  
Biofilm Formation ◽  
Tap Water ◽  
Multidrug Resistant ◽  
Biochemical Tests ◽  
Antibiotic Resistant ◽  
North West ◽  
The North ◽  
C 50 ◽  
Species Specific

The aim of this study was to characterise Vibrio species of water samples collected from taps, boreholes, and dams in the North West province, South Africa, and assess biocontrol potentials of their bacteriophages. Fifty-seven putative Vibrio isolates were obtained on thiosulfate-citrate-bile-salt-sucrose agar and identified using biochemical tests and species-specific PCRs. Isolates were further characterised based on the presence of virulence factors, susceptibility to eleven antibiotics, and biofilm formation potentials. Twenty-two (38.60%) isolates were confirmed as Vibrio species, comprising V. harveyi (45.5%, n = 10), V. parahaemolyticus (22.7%, n = 5), V. cholerae (13.6%, n = 3), V. mimicus (9.1%, n = 2), and V. vulnificus (9.1%, n = 2). Three of the six virulent genes screened were positively amplified; four V. parahaemolyticus possessed the tdh (18.18%) and trh (18.18%) genes, while the zot gene was harboured by 3 V. cholerae (13.64%) and one V. mimicus (4.55%) isolate. Isolates revealed high levels of resistance to cephalothin (95.45%), ampicillin (77.27%), and streptomycin (40.91%), while lower resistances (4.55%–27.27%) were recorded for other antimicrobials. Sixteen (72.7%) isolates displayed multiple antibiotic-resistant properties. Cluster analysis of antibiotic resistance revealed a closer relationship between Vibrio isolates from different sampling sites. The Vibrio species displayed biofilm formation potentials at 37°C (63.6, n = 14), 35°C (50%, n = 11), and 25°C (36.4%, n = 8). Two phages isolated in this study (vB_VpM_SA3V and vB_VcM_SA3V) were classified as belonging to the family Myoviridae based on electron microscopy. These were able to lyse multidrug-resistant V. parahaemolyticus and V. cholerae strains. These findings not only indicate the presence of antibiotic-resistant virulent Vibrio species from dam, borehole, and tap water samples that could pose a health risk to humans who either come in contact with or consume water but also present these lytic phages as alternative agents that can be exploited for biological control of these pathogenic strains.

scholarly journals Antibacterial Effects of Phage Lysin LysGH15 on Planktonic Cells and Biofilms of Diverse Staphylococci

2018 ◽  
Vol 84 (15) ◽  
Author(s):  
Yufeng Zhang ◽  
Mengjun Cheng ◽  
Hao Zhang ◽  
Jiaxin Dai ◽  
Zhimin Guo ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Multidrug Resistant ◽  
Planktonic Cells ◽  
Content Type ◽  
Resistant Strains ◽  
Staphylococcus Hominis ◽  
Phage Lysin

ABSTRACT Treatment of infections caused by staphylococci has become more difficult because of the emergence of multidrug-resistant strains as well as biofilm formation. In this study, we observed the ability of the phage lysin LysGH15 to eliminate staphylococcal planktonic cells and biofilms formed by Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis. All these strains were sensitive to LysGH15, showing reductions in bacterial counts of approximately 4 log units within 30 min after treatment with 20 μg/ml of LysGH15, and the MICs ranged from 8 μg/ml to 32 μg/ml. LysGH15 efficiently prevented biofilm formation by the four staphylococcal species at a dose of 50 μg/ml. At a higher dose (100 μg/ml), LysGH15 also showed notable disrupting activity against 24-h and 72-h biofilms formed by S. aureus and coagulase-negative species. In the in vivo experiments, a single intraperitoneal injection of LysGH15 (20 μg/mouse) administered 1 h after the injection of S. epidermidis at double the minimum lethal dose was sufficient to protect the mice. The S. epidermidis cell counts were 4 log units lower in the blood and 3 log units lower in the organs of mice 24 h after treatment with LysGH15 than in the untreated control mice. LysGH15 reduced cytokine levels in the blood and improved pathological changes in the organs. The broad antistaphylococcal activity exerted by LysGH15 on planktonic cells and biofilms makes LysGH15 a valuable treatment option for biofilm-related or non-biofilm-related staphylococcal infections. IMPORTANCE Most staphylococcal species are major causes of health care- and community-associated infections. In particular, Staphylococcus aureus is a common and dangerous pathogen, and Staphylococcus epidermidis is a ubiquitous skin commensal and opportunistic pathogen. Treatment of infections caused by staphylococci has become more difficult because of the emergence of multidrug-resistant strains as well as biofilm formation. In this study, we found that all tested S. aureus, S. epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis strains were sensitive to the phage lysin LysGH15 (MICs ranging from 8 to 32 μg/ml). More importantly, LysGH15 not only prevented biofilm formation by these staphylococci but also disrupted 24-h and 72-h biofilms. Furthermore, the in vivo efficacy of LysGH15 was demonstrated in a mouse model of S. epidermidis bacteremia. Thus, LysGH15 exhibits therapeutic potential for treating biofilm-related or non-biofilm-related infections caused by diverse staphylococci.

scholarly journals Effects of Ciprofloxacin on the Dynamics of Biofilm Formation by Staphylococcus Epidermidis Strains Isolated from Implant-Associated Infection

2020 ◽  
Vol 13 (3) ◽  
pp. 241-247
Author(s):  
Irina V. Babushkina ◽  
Irina A. Mamonova ◽  
Vladimir Yu. Ulyanov ◽  
Sergey P. Shpinyak ◽  
Aleksandr S. Bondarenko
Keyword(s):  
Periprosthetic Joint Infection ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Gentian Violet ◽  
Joint Infection ◽  
Multidrug Resistant ◽  
Diagnostic Methods ◽  
Microbial Biofilms ◽  
Large Joint

Introduction. The formation of a microbial biofilm in implant-associated infection after arthroplasty of large joints reduces the informative value of traditional microbiological diagnostic methods and limits the range of effective antimicrobial drugs. When prescribing etiotropic therapy for periprosthetic joint infection, it is necessary to take into account not only the antibacterial effect of the drug, but also its effect on biofilm formation. Ciprofloxacin therapy may be a risk factor for the development of biofilm periprosthetic infection caused by multidrug-resistant staphylococcal strains.The aim of research was to study the effect of sub-inhibiting and therapeutic doses of ciprofloxacin on biofilm formation by Staphylococcus epidermidis strains isolated from implant-associated infection.Materials and methods. The authors studied the effect of various concentrations of ciprofloxacin on 15 strains of St. epidermidis isolated from 83 patients with deep periprosthetic joint infection after primary knee arthroplasty, treated at NIITON SSMU in 2018-2019. The effect of the calculated concentrations of ciprofloxacin on the planktonic culture, forming and preformed biofilms was investigated. Biofilm simulation was performed according to the method described by G.D. Christensen under in vitro conditions with determination of the optical density of alcohol eluates of gentian violet in polystyrene microplates.Results. It was demonstrated that ciprofloxacin in a dose 0.01 g/ml inhibits the growth of planktonic forms by 50% and statistically significantly (p = 0.001) stimulates formation of microbial biofilms as compared to the control without antibiotic addition. Concentration of ciprofloxacin equal 0.03 g/ml inhibits the growth of planktonic forms by 90%, statistically significantly (p = 0.001) stimulates formation of biofilms and activates further increase in the mass of pre-formed microbial biofilms. An increase in the concentration of ciprofloxacin to 0.05 g/ml completely inhibits the growth of planktonic forms and statistically significantly stimulates further growth of preformed biofilms.The use of ciprofloxacin at concentrations equal 1-3 g/ml statistically significantly (p = 0.001) inhibits the formation of microbial biofilms, but does not affect the preformed biofilm.Conclusions. Thus, there has been found a dose-dependent effect of ciprofloxacin towards clinical strains of St. epidermidis: subinhibitory and therapeutic concentrations of the drug have a stimulating effect on the formation and further increase in the mass of the preformed microbial biofilms. This fact must be taken into account when prescribing etiotropic therapy for implant-associated complications following large joint replacements.

scholarly journals Fighting Staphylococcus epidermidis Biofilm-Associated Infections: Can Iron Be the Key to Success?

2021 ◽  
Vol 11 ◽  
Author(s):  
Fernando Oliveira ◽  
Holger Rohde ◽  
Manuel Vilanova ◽  
Nuno Cerca
Keyword(s):  
Iron Metabolism ◽  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Iron Acquisition ◽  
Bacterial Species ◽  
Multidrug Resistant ◽  
Formation Mechanisms ◽  
Bacterial Genes ◽  
Amount Of Knowledge ◽  
Biofilm Development

Staphylococcus epidermidis is one of the most important commensal microorganisms of human skin and mucosae. However, this bacterial species is also the cause of severe infections in immunocompromised patients, specially associated with the utilization of indwelling medical devices, that often serve as a scaffold for biofilm formation. S. epidermidis strains are often multidrug resistant and its association with biofilm formation makes these infections hard to treat. Their remarkable ability to form biofilms is widely regarded as its major pathogenic determinant. Although a significant amount of knowledge on its biofilm formation mechanisms has been achieved, we still do not understand how the species survives when exposed to the host harsh environment during invasion. A previous RNA-seq study highlighted that iron-metabolism associated genes were the most up-regulated bacterial genes upon contact with human blood, which suggested that iron acquisition plays an important role in S. epidermidis biofilm development and escape from the host innate immune system. In this perspective article, we review the available literature on the role of iron metabolism on S. epidermidis pathogenesis and propose that exploiting its dependence on iron could be pursued as a viable therapeutic alternative.

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