Antimicrobial and Antifungal Resistance in Domestic Animals, Synanthropic Species and Wildlife

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 18600

Special Issue Editors


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Guest Editor
Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80137 Naples, Italy
Interests: microbiology; antimicrobial resistance; zoonoses and public health; fungal pathogen; antifungal resistance; synanthropic birds; wildlife; rabbit and poultry
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Special Issue Information

Dear Colleagues,

The phenomenon of antimicrobial resistance (AMR) is one of the major public health problems worldwide, with important clinical and economic implications. Concurrently, invasive fungal infections pose an emerging concern in all continents; in fact, human-infecting pathogenic fungi are evolving resistance to all licensed systemic antifungal drugs, but this is an under-recognized component of AMR.

The mechanisms of resistance of drugs are complex because they depend on several causes, ranging from indiscriminate use, overuse, and misuse of these treatments in human and veterinary medicine, animal husbandry, and agriculture to the spread of infections caused by drug-resistant microorganisms and the increase in resistant strains. The mechanism and aspects of this adaptive process are mirrored across the fungal kingdom, and pathogenic fungi can also acquire resistance through analogous mechanisms.

Across a period of profound global environmental changes and continuous spread of resistance to antibiotic and antifungal drugs, it becomes critical for surveillance and containment of this phenomenon to study and collect data at every level of the ecosystem and particularly on animals, which are often true sentinels, reflecting human activities and their impact on the environment.

This Special Issue aims to investigate and collect information and data about the antimicrobial and antifungal resistance phenomenon in domestic animals, synanthropic species, and wildlife, encouraging study and surveys also in rural areas and small agricultural farms where animals of different species often congregate; here, in particular, the horizontal transmission of pathogens occurs due to interindividual and interspecies contact, including interaction with wild animals, animals often not being subjected to treatment, or inappropriate use of drugs.

Dr. Tamara P. Russo
Dr. Antonio Santaniello
Guest Editors

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Keywords

  • antimicrobial resistance bacteria
  • antifungal resistance
  • antibiotics
  • domestic animals
  • wildlife
  • synanthropic animals
  • farms
  • rural areas

Published Papers (11 papers)

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Editorial

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3 pages, 192 KiB  
Editorial
Tackling Antibiotic and Antifungal Resistance in Domestic Animals, Synanthropic Species, and Wildlife: A Global Health Imperative
by Tamara Pasqualina Russo and Antonio Santaniello
Antibiotics 2023, 12(11), 1632; https://doi.org/10.3390/antibiotics12111632 - 17 Nov 2023
Viewed by 809
Abstract
Antibiotic resistance (ABR) and antifungal resistance (AFR) arise when microorganisms evolve mechanisms to resist pharmacological treatments [...] Full article

Research

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17 pages, 341 KiB  
Article
Short-Term Storage of Rooster Ejaculates: Sperm Quality and Bacterial Profile Differences in Selected Commercial Extenders
by Eva Tvrdá, Michaela Petrovičová, Michal Ďuračka, Filip Benko, Tomáš Slanina, Lucia Galovičová and Miroslava Kačániová
Antibiotics 2023, 12(8), 1284; https://doi.org/10.3390/antibiotics12081284 - 03 Aug 2023
Viewed by 997
Abstract
Bacterial contamination of semen has become an important contributor to the reduced shelf life of insemination doses in the poultry industry, which is why antibiotics (ATBs) are an important component of semen extenders. Due to a global rise in antimicrobial resistance, the aim [...] Read more.
Bacterial contamination of semen has become an important contributor to the reduced shelf life of insemination doses in the poultry industry, which is why antibiotics (ATBs) are an important component of semen extenders. Due to a global rise in antimicrobial resistance, the aim of this study was to assess the efficiency of selected commercially available semen extenders to prevent possible bacterial contamination of rooster ejaculates. Two selected extenders free from or containing 31.2 µg/mL kanamycin (KAN) were used to process semen samples from 63 healthy Lohmann Brown roosters. Phosphate-buffered saline without ATBs was used as a control. The extended samples were stored at 4 °C for 24 h. Sperm motility, viability, mitochondrial activity, DNA integrity and the oxidative profile of each extended sample were assessed following 2 h and 24 h of storage. Furthermore, selective media were used to quantify the bacterial load and specific bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The results indicate that semen extenders enriched with KAN ensured a significantly higher preservation of sperm quality in comparison to their KAN-free counterparts. Bacterial load was significantly decreased in diluents supplemented with ATBs (p ≤ 0.001); however, KAN alone was not effective enough to eradicate all bacteria since several Escherichia coli, Enterococcus faecalis, Enterococcus faecium and Micrococcus luteus were retrieved from samples extended in KAN-supplemented commercial extenders. As such, we may suggest that more focus should be devoted to the selection of an optimal combination and dose of antibiotics for poultry extenders, which should be accompanied by a more frequent bacteriological screening of native as well as extended poultry semen. Full article
8 pages, 292 KiB  
Communication
Molecular Detection of Metronidazole and Tetracycline Resistance Genes in Helicobacter pylori-Like Positive Gastric Samples from Pigs
by Francisco Cortez Nunes, Emily Taillieu, Teresa Letra Mateus, Sílvia Teixeira, Freddy Haesebrouck and Irina Amorim
Antibiotics 2023, 12(5), 906; https://doi.org/10.3390/antibiotics12050906 - 13 May 2023
Cited by 1 | Viewed by 1767
Abstract
Antimicrobial resistance is a major public health concern. The aim of this study was to assess the presence of antibiotic resistance genes, previously reported in Helicobacter pylori, in gastric samples of 36 pigs, in which DNA of H. pylori-like organisms had been [...] Read more.
Antimicrobial resistance is a major public health concern. The aim of this study was to assess the presence of antibiotic resistance genes, previously reported in Helicobacter pylori, in gastric samples of 36 pigs, in which DNA of H. pylori-like organisms had been detected. Based on PCR and sequencing analysis, two samples were positive for the 16S rRNA mutation gene, conferring tetracycline resistance, and one sample was positive for the frxA gene with a single nucleotide polymorphism, conferring metronidazole resistance. All three amplicons showed the highest homology with H. pylori-associated antibiotic resistance gene sequences. These findings indicate that acquired antimicrobial resistance may occur in H. pylori-like organisms associated with pigs. Full article
19 pages, 677 KiB  
Article
The Behavior of Some Bacterial Strains Isolated from Fallow Deer Compared to Antimicrobial Substances in Western Romania
by Emil Tîrziu, Alexandrina V. Bulucea, Kalman Imre, Ileana Nichita, Florin Muselin, Eugenia Dumitrescu, Andreea Tîrziu, Narcisa G. Mederle, Alexandru Moza, Iulia M. Bucur and Romeo T. Cristina
Antibiotics 2023, 12(4), 743; https://doi.org/10.3390/antibiotics12040743 - 12 Apr 2023
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Abstract
(1) Background: The resistance levels of Escherichia coli, Salmonella spp., Pseudomonas spp., Staphylococcus spp., etc., isolated from the nasal cavity and the rectum of Dama dama deer from three hunting grounds in Western Romania were assessed. (2) Methods: The analysis was completed [...] Read more.
(1) Background: The resistance levels of Escherichia coli, Salmonella spp., Pseudomonas spp., Staphylococcus spp., etc., isolated from the nasal cavity and the rectum of Dama dama deer from three hunting grounds in Western Romania were assessed. (2) Methods: The analysis was completed using the diffusimetric method, compliant with CLSI reference standards, and with Vitek-2 (BioMérieux, France), on 240 samples. (3) Results: The results were statistically analyzed (by one-way ANOVA) revealing that in four of the ten E. coli strains isolated from animals, 87.5% (p < 0.001) resistance was found. E. coli strains were resistant to cephalexin (100%); seven strains were resistant to cephalothin and ampicillin; six were resistant to cefquinome and cefoperazone; five were resistant to amoxicillin/clavulanic acid; and four were resistant to ceftiofur. However, E. coli was sensitive to amikacin (100%). The most efficient structures were beta-lactams, amikacin, and imipenem, to which all 47 strains studied (100%) were sensitive, followed by nitrofurantoin, to which 45 strains (95.7%) were sensitive, neomycin, to which 44 strains (93.6%) were sensitive, ceftiofur, to which 43 strains (91.5%) were sensitive, and trimethoprim/sulfamethoxazole and marbofloxacin, to which 42 strains (89.4%) were sensitive. (4) Conclusions: In wild animal populations, where a human presence is frequently reported, including a constant presence of domestic animals, despite the perceived low risk of emerging resistance to antimicrobials, resistance is likely to develop frequently. Full article
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15 pages, 2430 KiB  
Article
Pulmonary Aspergillosis in Humboldt Penguins—Susceptibility Patterns and Molecular Epidemiology of Clinical and Environmental Aspergillus fumigatus Isolates from a Belgian Zoo, 2017–2022
by Hanne Debergh, Pierre Becker, Francis Vercammen, Katrien Lagrou, Roel Haesendonck, Claude Saegerman and Ann Packeu
Antibiotics 2023, 12(3), 584; https://doi.org/10.3390/antibiotics12030584 - 15 Mar 2023
Cited by 4 | Viewed by 1567
Abstract
Aspergillus fumigatus is the main causative agent of avian aspergillosis and results in significant health problems in birds, especially those living in captivity. The fungal contamination by A. fumigatus in the environment of Humboldt penguins (Spheniscus humboldti), located in a Belgian [...] Read more.
Aspergillus fumigatus is the main causative agent of avian aspergillosis and results in significant health problems in birds, especially those living in captivity. The fungal contamination by A. fumigatus in the environment of Humboldt penguins (Spheniscus humboldti), located in a Belgian zoo, was assessed through the analysis of air, water, sand and nest samples during four non-consecutive days in 2021–2022. From these samples, potential azole-resistant A. fumigatus (ARAF) isolates were detected using a selective culture medium. A total of 28 veterinary isolates obtained after necropsy of Humboldt penguins and other avian species from the zoo were also included. All veterinary and suspected ARAF isolates from the environment were characterized for their azole-resistance profile by broth microdilution. Isolates displaying phenotypic resistance against at least one medical azole were systematically screened for mutations in the cyp51A gene. A total of 14 (13.6%) ARAF isolates were identified from the environment (n = 8) and from Humboldt penguins (n = 6). The TR34/L98H mutation was observed in all resistant environmental strains, and in two resistant veterinary strains. To the best of our knowledge, this is the first description of this mutation in A. fumigatus isolates from Humboldt penguins. During the period 2017–2022, pulmonary aspergillosis was confirmed in 51 necropsied penguins, which reflects a death rate due to aspergillosis of 68.0%, mostly affecting adults. Microsatellite polymorphism analysis revealed a high level of diversity among environmental and veterinary A. fumigatus isolates. However, a cluster was observed between one veterinary isolate and six environmental strains, all resistant to medical azoles. In conclusion, the environment of the Humboldt penguins is a potential contamination source of ARAF, making their management even more complex. Full article
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15 pages, 1645 KiB  
Article
Antimicrobial Properties of Bacillus Probiotics as Animal Growth Promoters
by Charlie Tran, Darwin Horyanto, Dragana Stanley, Ian E. Cock, Xiaojing Chen and Yunjiang Feng
Antibiotics 2023, 12(2), 407; https://doi.org/10.3390/antibiotics12020407 - 17 Feb 2023
Cited by 11 | Viewed by 2091 | Correction
Abstract
Antibiotic growth promoters (AGPs) suppress the growth of infectious pathogens. These pathogens negatively impact agricultural production worldwide and often cause health problems if left untreated. Here, we evaluate six Bacillus strains (BPR-11, BPR-12, BPR-13, BPR-14, BPR-16 and BPR-17), which are known for their [...] Read more.
Antibiotic growth promoters (AGPs) suppress the growth of infectious pathogens. These pathogens negatively impact agricultural production worldwide and often cause health problems if left untreated. Here, we evaluate six Bacillus strains (BPR-11, BPR-12, BPR-13, BPR-14, BPR-16 and BPR-17), which are known for their ability to survive harsh environmental conditions, as AGP replacements in animal feed. Four of these Bacillus strains (BPR-11, BPR-14, BPR-16 and BPR-17) showed antimicrobial activity against the pathogenic strains Clostridium perfringens, Escherichia coli and Staphylococcus aureus at 25 μg/mL, with BPR-16 and BPR-17 also able to inhibit Pseudomonas aeruginosa and Salmonella enterica at 100 μg/mL. Further chemical investigation of BPR-17 led to the identification of eight metabolites, namely C16, C15, C14 and C13 surfactin C (1–4), maculosin (5), maculosine 2 (6), genistein (7) and daidzein (8). Purified compounds (1–4) were able to inhibit all the tested pathogens with MIC values ranging from 6.25 to 50 μg/mL. Maculosin (5) and maculosine 2 (6) inhibited C. perfringens, E. coli and S. aureus with an MIC of 25 μg/mL while genistein (7) and daidzein (8) showed no activity. An animal trial involving feeding BPR-11, BPR-16 and BPR-17 to a laboratory poultry model led to an increase in animal growth, and a decrease in feed conversion ratio and mortality. The presence of surfactin C analogues (3–4) in the gut following feeding with probiotics was confirmed using an LC–MS analysis. The investigation of these Bacillus probiotics, their metabolites, their impacts on animal performance indicators and their presence in the gastrointestinal system illustrates that these probiotics are effective alternatives to AGPs. Full article
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22 pages, 3374 KiB  
Article
Seminal Bacterioflora of Two Rooster Lines: Characterization, Antibiotic Resistance Patterns and Possible Impact on Semen Quality
by Eva Tvrdá, Michaela Petrovičová, Filip Benko, Michal Ďuračka, Ján Kováč, Tomáš Slanina, Lucia Galovičová, Jana Žiarovská and Miroslava Kačániová
Antibiotics 2023, 12(2), 336; https://doi.org/10.3390/antibiotics12020336 - 05 Feb 2023
Cited by 4 | Viewed by 2051
Abstract
This study aimed to characterize the bacterial profiles and their association with selected semen quality traits among two chicken breeds. Thirty Lohmann Brown and thirty ROSS 308 roosters were selected for semen quality estimation, including sperm motility, membrane and acrosome integrity, mitochondrial activity, [...] Read more.
This study aimed to characterize the bacterial profiles and their association with selected semen quality traits among two chicken breeds. Thirty Lohmann Brown and thirty ROSS 308 roosters were selected for semen quality estimation, including sperm motility, membrane and acrosome integrity, mitochondrial activity, and DNA fragmentation. The oxidative profile of the semen, including the production of reactive oxygen species (ROS), antioxidant capacity, protein, and lipid oxidation, were assessed as well. Moreover, the levels of pro-inflammatory cytokines, including tumor necrosis factor alpha (TNF-α), interleukins 1 and 6 (IL-1, IL-6) and C-reactive protein, as well as the concentrations of selected antibacterial proteins (cathelicidin, β-defensin and lysozyme) in the seminal plasma were evaluated with the enzyme-linked immunosorbent assay. The prevailing bacterial genera identified by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were Citrobacter spp., Enterococcus spp., Escherichia spp. and Staphylococcus spp. While the bacterial load was significantly higher in the ROSS 308 line (p < 0.05), a higher number of potentially uropathogenic bacteria was found in the Lohmann Brown roosters. Antimicrobial susceptibility tests revealed a substantial resistance of randomly selected bacterial strains, particularly to ampicillin, tetracycline, chloramphenicol, and tobramycin. Furthermore, Lohmann Brown ejaculates containing an increased proportion of Escherichia coli presented with significantly (p < 0.05) elevated levels of TNF-α and IL-6, as well as ROS overproduction and lipid peroxidation. Inversely, significantly (p < 0.05) higher levels of β-defensin and lysozyme were found in the semen collected from the ROSS 308 roosters, which was characterized by a higher quality in comparison to the Lohmann Brown roosters. In conclusion, we emphasize the criticality of bacteriospermia in the poultry industry and highlight the need to include a more complex microbiological screening of semen samples designated for artificial insemination. Full article
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11 pages, 2118 KiB  
Article
Biofilm Formation Ability of ESBL/pAmpC-Producing Escherichia coli Isolated from the Broiler Production Pyramid
by Andrea Laconi, Roberta Tolosi, Ilias Apostolakos and Alessandra Piccirillo
Antibiotics 2023, 12(1), 155; https://doi.org/10.3390/antibiotics12010155 - 11 Jan 2023
Cited by 4 | Viewed by 1753
Abstract
Escherichia coli able to produce extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (pAmpCs) represents a serious threat to public health, since these genes confer resistance to critically important antimicrobials (i.e., third generation cephalosporins) and can be transferred to non-resistant bacteria via plasmids. [...] Read more.
Escherichia coli able to produce extended spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC β-lactamases (pAmpCs) represents a serious threat to public health, since these genes confer resistance to critically important antimicrobials (i.e., third generation cephalosporins) and can be transferred to non-resistant bacteria via plasmids. E. coli are known to be able to form a biofilm, which represents a favorable environment for the exchange of resistance determinants. Here, we assessed the ability of 102 ESBL/pAmpC-producing E. coli isolated from the broiler production pyramid to form a biofilm and to identify genetic factors involved in biofilm formation. All but one of the ESBL/pAmpC-producing E. coli were able to form a biofilm, and this represents a great concern to public health. E. coli belonging to phylogroups D, E, and F, as well as strains harboring the blaCTX-M-type gene, seem to be associated with an increased biofilm capability (p < 0.05). Furthermore, virulence genes involved in adherence and invasion (i.e., csgBAC, csgDEFG, matABCDEF, and sfaX) seem to enhance biofilm formation in E. coli. Efforts should be made to reduce the presence of ESBL/pAmpC- and biofilm-producing E. coli in the broiler production pyramid and, therefore, the risk of dissemination of resistant bacteria and genes. Full article
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11 pages, 534 KiB  
Article
Prevalence and Phenotypic Antimicrobial Resistance among ESKAPE Bacteria and Enterobacterales Strains in Wild Birds
by Tamara Pasqualina Russo, Adriano Minichino, Antonio Gargiulo, Lorena Varriale, Luca Borrelli, Antonino Pace, Antonio Santaniello, Marina Pompameo, Alessandro Fioretti and Ludovico Dipineto
Antibiotics 2022, 11(12), 1825; https://doi.org/10.3390/antibiotics11121825 - 15 Dec 2022
Cited by 8 | Viewed by 2372
Abstract
Antimicrobial resistance (AMR) is a current public health issue globally. To counter this phenomenon and prioritize AMR in the health sector, the World Health Organization (WHO) published a list of bacterial pathogens against which the development of new antimicrobial agents is urgently needed, [...] Read more.
Antimicrobial resistance (AMR) is a current public health issue globally. To counter this phenomenon and prioritize AMR in the health sector, the World Health Organization (WHO) published a list of bacterial pathogens against which the development of new antimicrobial agents is urgently needed, designating the ESKAPE pathogens (i.e., Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) with a ‘priority status’. Moreover, the One Health High Level Expert Panel (OHHLEP) states that human health is closely linked to animal and environmental health, thus promoting a holistic One Health approach in order to be prepared to address possible emerging health threats from the human–animal–environment interface. Wild birds may host and spread pathogens, integrating the epidemiology of infectious diseases. The aim of this study was to examine the role of wild birds as a source of ESKAPE bacteria and other antibiotic-resistant enterobacterales. A total of fifty strains within the ESKAPE group were detected in 40/163 cloacal samples of examined birds (24.5%). Additionally, different strains of enterobacterales were detected in 88/163 cloacal samples (53.9%). Isolated strains exhibited antimicrobial resistance, including towards critically important antibiotics (e.g., third, fourth, fifth generation cephalosporins, fluoroquinolones) for human medicine. Our results confirm that wild birds are potential reservoirs of several pathogens and antimicrobial-resistant bacteria and that they could be involved in the dissemination of those bacteria across different environments, with resulting public health concerns. Full article
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14 pages, 1933 KiB  
Communication
Multidrug-Resistant High-Risk Escherichia coli and Klebsiella pneumoniae Clonal Lineages Occur in Black-Headed Gulls from Two Conservation Islands in Germany
by Jana Brendecke, Timo Homeier-Bachmann, Angela Schmitz Ornés, Sebastian Guenther, Stefan E. Heiden, Michael Schwabe, Elias Eger and Katharina Schaufler
Antibiotics 2022, 11(10), 1357; https://doi.org/10.3390/antibiotics11101357 - 05 Oct 2022
Cited by 4 | Viewed by 2303
Abstract
Multidrug-resistant (MDR) Enterobacterales, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae, not only emerge in healthcare settings but also in other habitats, such as livestock and wildlife. The spread of these pathogens, which often combine resistance with high-level virulence, is [...] Read more.
Multidrug-resistant (MDR) Enterobacterales, including extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae, not only emerge in healthcare settings but also in other habitats, such as livestock and wildlife. The spread of these pathogens, which often combine resistance with high-level virulence, is a growing problem, as infections have become increasingly difficult to treat. Here, we investigated the occurrence of ESBL-producing E. coli and K. pneumoniae in fecal samples from two black-headed gull colonies breeding on two nature conservation islands in Western Pomerania, Germany. In addition to cloacal samples from adult birds (n = 211) and their nestlings (n = 99) during the 2021 breeding season, collective fecal samples (n = 29) were obtained. All samples were screened for ESBL producers, which were then subjected to whole-genome sequencing. We found a total of 12 ESBL-producing E. coli and K. pneumoniae consisting of 11 E. coli and 1 K. pneumoniae, and including the international high-risk E. coli sequence types (ST)131, ST38, and ST58. Eight of the investigated strains had a MDR genotype and carried a large repertoire of virulence-associated genes, including the pap operon, which is important for urinary tract infections. In addition, we identified many genes associated with adherence, biofilm formation, iron uptake, and toxin production. Finally, our analysis revealed the close phylogenetic relationship of ST38 strains with genomes originating from human sources, underlining their zoonotic and pathogenic character. This study highlights the importance of the One Health approach, and thus the interdependence between human and animal health and their surrounding environment. Full article
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Other

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1 pages, 162 KiB  
Correction
Correction: Tran et al. Antimicrobial Properties of Bacillus Probiotics as Animal Growth Promoters. Antibiotics 2023, 12, 407
by Charlie Tran, Darwin Horyanto, Dragana Stanley, Ian E. Cock, Xiaojing Chen and Yunjiang Feng
Antibiotics 2023, 12(9), 1420; https://doi.org/10.3390/antibiotics12091420 - 08 Sep 2023
Viewed by 507
Abstract
In the original publication [...] Full article
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