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Zhang X, Huang X, Zheng P, Liu E, Bai S, Chen S, Pang Y, Xiao X, Yang H, Guo J. Changes in oral, skin, and gut microbiota in children with atopic dermatitis: a case-control study. Front Microbiol 2024; 15:1442126. [PMID: 39211320 PMCID: PMC11358084 DOI: 10.3389/fmicb.2024.1442126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction Atopic dermatitis (AD) is a common clinical recurrent atopic disease in dermatology, most seen in children and adolescents. In recent years, AD has been found to be closely associated with microbial communities. Methods To explore the synergistic effects between colonizing bacteria from different sites and AD, we comparatively analyzed the skin, oral, and gut microbiota of children with AD (50 individuals) and healthy children (50 individuals) by 16S rRNA gene sequencing. Twenty samples were also randomly selected from both groups for metabolic and macrogenomic sequencing. Results The results of our sequencing study showed reduced microbiota diversity in the oral, skin, and gut of children with AD (P < 0.05). Metabolomics analysis showed that serotonergic synapse, arachidonic acid metabolism, and steroid biosynthesis were downregulated at all three loci in the oral, skin, and gut of children with AD (P < 0.05). Macrogenomic sequencing analysis showed that KEGG functional pathways of the three site flora were involved in oxidative phosphorylation, ubiquitin-mediated proteolysis, mRNA surveillance pathway, ribosome biogenesis in eukaryotes, proteasome, basal transcription factors, peroxisome, MAPK signaling pathway, mitophagy, fatty acid elongation, and so on (P < 0.05). Discussion The combined microbial, metabolic, and macrogenetic analyses identified key bacteria, metabolites, and pathogenic pathways that may be associated with AD development. We provides a more comprehensive and in-depth understanding of the role of the microbiota at different sites in AD patients, pointing to new directions for future diagnosis, treatment and prognosis.
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Affiliation(s)
- Xueer Zhang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaomin Huang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pai Zheng
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - E. Liu
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sixian Bai
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuoyu Chen
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yaobin Pang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinyu Xiao
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huifang Yang
- Department of Dermatology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jing Guo
- Department of Dermatology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Sodagari HR, Agrawal I, Yudhanto S, Varga C. Longitudinal analysis of differences and similarities in antimicrobial resistance among commensal Escherichia coli isolated from market swine and sows at slaughter in the United States of America, 2013-2019. Int J Food Microbiol 2023; 407:110388. [PMID: 37699314 DOI: 10.1016/j.ijfoodmicro.2023.110388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/14/2023]
Abstract
The emergence of antimicrobial resistance in swine enteric bacteria poses a significant public health challenge. Our study evaluated publicly available data collected by the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) between 2013 and 2019 at slaughter plants across the United States of America, focusing on commensal E. coli isolated from swine cecal contents originating from two distinct swine production systems: market hogs (n = 2090) and sows (n = 1147). In both production types, the highest pairwise correlations were detected among β-lactam antimicrobials, including resistance to amoxicillin-clavulanic acid, ceftriaxone, and cefoxitin, suggesting a co-selection for resistance. Compared to 2013, an increase in the rate of E. coli isolates that were resistant to β-lactam antimicrobials was higher in 2017, 2018, and 2019, and this increase was more pronounced in isolates obtained from market hogs. Differences in antimicrobial resistance between these two distinct swine production systems warrant production-type focused mitigation efforts.
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Affiliation(s)
- Hamid Reza Sodagari
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
| | - Isha Agrawal
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
| | - Setyo Yudhanto
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA.
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Thongratsakul S, Amavisit P, Poolkhet C. Antimicrobial Resistance in Poultry Farming: A Look Back at Environmental Escherichia coli Isolated from Poultry Farms during the Growing and Resting Periods. Vet Med Int 2023; 2023:8354235. [PMID: 38058657 PMCID: PMC10697774 DOI: 10.1155/2023/8354235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
During the production cycle of poultry farms, pathogens may remain in the next cycle of rearing young chickens. This study was conducted at three industrial chicken farms (A, B, and C) in central Thailand. Results showed that the percentages of E. coli during the resting period in farms A, B, and C were 28.6, 53.8, and 7.8, respectively, and those during the growing period were 45, 68.8, and 75. The most common resistant patterns during the resting period in all farms were AML-AMP-SXT and AML-AMP-DO-SXT, and those during the growing period were AML-AMP and AML-AMP-SXT. The locations of blaTEM-positive E. coli isolates from the inside houses (inside buildings) of all farms included cloacal swabs, floors, water nipples, pan feeders, and husks, whereas that from the outside environment included boots, wastewater, soil, and water from cooling pads and tanks. Our results indicate that the percentage of antimicrobial resistance (AMR) and its pattern depend on the husbandry period and the strictness of biosecurity. Moreover, our findings derived from samples gathered from broiler farms between 2013 and 2015 align with those of the current studies, highlighting persistent trends in E. coli resistance to various antimicrobial agents. Therefore, enhancing biosecurity measures throughout both the resting and growing periods is crucial, with a specific focus on managing raw materials, bedding, breeding equipment, and staff hygiene to reduce the transmission of antimicrobial resistance in poultry farms.
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Affiliation(s)
- Sukanya Thongratsakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Patamabhorn Amavisit
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok 10900, Thailand
| | - Chaithep Poolkhet
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
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4
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Carramaschi IN, de C Queiroz MM, da Mota FF, Zahner V. First Identification of bla NDM-1 Producing Escherichia coli ST 9499 Isolated from Musca domestica in the Urban Center of Rio de Janeiro, Brazil. Curr Microbiol 2023; 80:278. [PMID: 37436443 DOI: 10.1007/s00284-023-03393-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
The present study presents phenotypic and molecular characterization of a multidrug-resistant strain of Escherichia coli (Lemef26), belonging to sequence type ST9499 carrying a blaNDM-1 carbapenem resistance gene. The bacterium was isolated from a specimen of Musca domestica, collected in proximity to a hospital in Rio de Janeiro City, Brazil. The strain was identified as E. coli by matrix-assisted laser desorption-ionization time of flight mass spectrometry (Maldi-TOF-MS) and via genotypic analysis (Whole-Genome Sequencing-WGS), followed by phylogenetic analysis, antibiotic resistance profiling (using phenotypic and genotypic methods) and virulence genotyping. Interestingly, the blaNDM-1 was the only resistance determinant detected using a panel of common resistance genes, as evaluated by PCR. In contrast, WGS detected genes conferring resistance to aminoglycosides, fluoroquinolones, quinolones, trimethoprim, beta-lactams, chloramphenicol, macrolides, sulfonamide, tetracycline, lincosamide and streptogramin B. Conjugation experiments demonstrated the transfer of carbapenem resistance, via acquisition of the blaNDM-1 sequence, to a sensitive receptor strain of E. coli, indicating that blaNDM-1 is located on a conjugative plasmid (most likely of the IncA/C incompatibility group, in association with the transposon Tn3000). Phylogenetic analyses placed Lemef26 within a clade of strains exhibiting allelic and environment diversity, with the greatest level of relatedness recorded with a strain isolated from a human source suggesting a possible anthropogenic origin. Analysis of the virulome revealed the presence of fimbrial and pilus genes, including a CFA/I fimbriae (cfaABCDE), common pilus (ecpABCDER), laminin-bind fimbrae (elfADG), hemorrhagic pilus (hcpABC) and fimbrial adherence determinants (stjC) indicates the ability of strain Lemef26 to colonize animal hosts. To the best of our knowledge, this study represents the first report of blaNDM-1 carbapenemase gene in an E. coli strain isolated from M. domestica. In concordance with the findings of previous studies on the carriage of MDR bacteria by flies, the data presented herein provide support to the idea that flies may represent a convenient means (as sentinel animals) for the monitoring of environmental contamination with multidrug-resistant bacteria.
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Affiliation(s)
- Isabel N Carramaschi
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
| | - Margareth M de C Queiroz
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil
| | - Viviane Zahner
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil.
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5
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Duarte ASR, Marques AR, Andersen VD, Korsgaard HB, Mordhorst H, Møller FD, Petersen TN, Vigre H, Hald T, Aarestrup FM. Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018. Euro Surveill 2023; 28:2200678. [PMID: 37199989 PMCID: PMC10197494 DOI: 10.2807/1560-7917.es.2023.28.20.2200678] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023] Open
Abstract
BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.
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Affiliation(s)
- Ana Sofia R Duarte
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Ana Rita Marques
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Vibe D Andersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Helle B Korsgaard
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Hanne Mordhorst
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frederik D Møller
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Thomas N Petersen
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Håkan Vigre
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Tine Hald
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
| | - Frank M Aarestrup
- Technical University of Denmark, National Food Institute, Kemitorvet 204, 2800 Kongens Lyngby, Denmark
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Duangurai T, Rungruengkitkul A, Kong-Ngoen T, Tunyong W, Kosoltanapiwat N, Adisakwattana P, Vanaporn M, Indrawattana N, Pumirat P. Phylogenetic analysis and antibiotic resistance of Escherichia coli isolated from wild and domestic animals at an agricultural land interface area of Salaphra wildlife sanctuary, Thailand. Vet World 2022; 15:2800-2809. [PMID: 36718336 PMCID: PMC9880845 DOI: 10.14202/vetworld.2022.2800-2809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022] Open
Abstract
Background and Aim Domestic and wild animals are important reservoirs for antibiotic-resistant bacteria. This study aimed to isolate Escherichia coli from feces of domestic and wild animals at an agricultural land interface area of Salaphra Wildlife Sanctuary, Thailand, and study the phylogenic characteristics and antibiotic resistance in these isolates. Materials and Methods In this cross-sectional, descriptive study, we randomly collected ground feces from free-ranging wild animals (deer and elephants) and domestic animals (cattle and goats). All fecal samples were inoculated onto MacConkey agar plates, and lactose-fermenting colonies were identified as E. coli. Antibiotic susceptibility of the E. coli isolates was determined using the disc diffusion method. Polymerase chain reaction assays were used to detect antibiotic resistance and virulence genes. Results We obtained 362 E. coli isolates from the collected fecal samples. The E. coli isolates were categorized into four phylogenetic groups according to the virulence genes (chuA, vjaA, and TspE4C2). Phylogenetic Group D was predominant in the deer (41.67%) and elephants (63.29%), whereas phylogenetic Group B1 was predominant in the cattle (62.31%), and phylogenetic Groups A (36.36%) and B2 (33.33%) were predominant in the goats. Antibiotic susceptibility testing revealed that most antibiotic-resistant E. coli were isolated from domestic goats (96.96%). Among the 362 E. coli isolates, 38 (10.5%) were resistant to at least one antibiotic, 21 (5.8%) were resistant to two antibiotics, and 6 (1.66%) were resistant to three or more antibiotics. Ampicillin (AMP) was the most common antibiotic (48.48%) to which the E. coli were resistant, followed by tetracycline (TET) (45.45%) and trimethoprim-sulfamethoxazole (3.03%). One isolate from an elephant was resistant to five antibiotics: AMP, amoxicillin, sulfisoxazole, TET, and ciprofloxacin. Determination of antibiotic resistance genes confirmed that E. coli isolates carried antibiotic resistance genes associated with phenotypic resistance to antibiotics. Most antibiotic-resistant E. coli belonged to phylogenic Groups A and B1, and most non-resistant E. coli belonged to phylogenic Groups B2 and D. Conclusion Monitoring E. coli isolates from wild and domestic animals showed that all four phylogenic groups of E. coli have developed antibiotic resistance and are potential sources of multidrug resistance. High levels of antibiotic resistance have been linked to domestic animals. Our results support strengthening surveillance to monitor the emergence and effects of antibiotic-resistant microorganisms in animals.
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Affiliation(s)
- Taksaon Duangurai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Amporn Rungruengkitkul
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thida Kong-Ngoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Witawat Tunyong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nathamon Kosoltanapiwat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand,Corresponding author: Pornpan Pumirat, e-mail: Co-authors: TD: , AR: , TK: , WT: , NK: , PA: , MV: , NI:
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Wongtawan T, Narinthorn R, Sontigun N, Sansamur C, Petcharat Y, Fungwithaya P, Saengsawang P, Blackall PJ, Thomrongsuwannakij T. Characterizing the antimicrobial resistance profile of Escherichia coli found in sport animals (fighting cocks, fighting bulls, and sport horses) and soils from their environment. Vet World 2022; 15:2673-2680. [PMID: 36590125 PMCID: PMC9798048 DOI: 10.14202/vetworld.2022.2673-2680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 10/13/2022] [Indexed: 11/27/2022] Open
Abstract
Background and Aim Antimicrobial resistance (AMR) is a significant threat to global health and development. Inappropriate antimicrobial drug use in animals cause AMR, and most studies focus on livestock because of the widespread use of antimicrobial medicines. There is a lack of studies on sports animals and AMR issues. This study aimed to characterize the AMR profile of E. coli found in sports animals (fighting cocks, fighting bulls, and sport horses) and soils from their environment. Materials and Methods Bacterial isolation and identification were conducted to identify E. coli isolates recovered from fresh feces that were obtained from fighting cocks (n = 32), fighting bulls (n = 57), sport horses (n = 33), and soils from those farms (n = 32) at Nakhon Si Thammarat. Antimicrobial resistance was determined using 15 tested antimicrobial agents - ampicillin (AM), amoxicillin-clavulanic acid, cephalexin (CN), cefalotin (CF), cefoperazone, ceftiofur, cefquinome, gentamicin, neomycin, flumequine (UB), enrofloxacin, marbofloaxacin, polymyxin B, tetracycline (TE), and sulfamethoxazole/trimethoprim (SXT). The virulence genes, AMR genes, and phylogenetic groups were also examined. Five virulence genes, iroN, ompT, hlyF, iss, and iutA, are genes determining the phylogenetic groups, chuA, cjaA, and tspE4C2, were identified. The AMR genes selected for detection were blaTEM and blaSHV for the beta-lactamase group; cml-A for phenicol; dhfrV for trimethoprim; sul1 and sul2 for sulfonamides; tetA, tetB, and tetC for TEs; and qnrA, qnrB, and qnrS for quinolones. Results The E. coli derived from sports animals were resistant at different levels to AM, CF, CN, UB, SXT, and TE. The AMR rate was overall higher in fighting cocks than in other animals, with significantly higher resistance to AM, CF, and TE. The highest AMR was found in fighting cocks, where 62.5% of their isolates were AM resistant. In addition, multidrug resistance was highest in fighting cocks (12.5%). One extended-spectrum beta-lactamase E. coli isolate was found in the soils, but none from animal feces. The phylogenetic analysis showed that most E. coli isolates were in Group B1. The E. coli isolates from fighting cocks had more virulence and AMR genes than other sources. The AMR genes found in 20% or more of the isolates were blaTEM (71.9%), qnrB (25%), qnrS (46.9%), and tetA (56.25%), whereas in the E. coli isolates collected from soils, the only resistance genes found in 20% or more of the isolates were blaTEM (30.8%), and tetA (23.1%). Conclusion Escherichia coli from fighting cock feces had significantly higher resistance to AM, CF, and TE than isolates from other sporting animals. Hence, fighting cocks may be a reservoir of resistant E. coli that can transfer to the environment and other animals and humans in direct contact with the birds or the birds' habitat. Programs for antimicrobial monitoring should also target sports animals and their environment.
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Affiliation(s)
- Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Excellence Centre for Melioidosis and other microorganisms, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Ruethai Narinthorn
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Narin Sontigun
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Excellence Centre for Melioidosis and other microorganisms, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Chalutwan Sansamur
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Yotsapat Petcharat
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Punpichaya Fungwithaya
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Excellence Centre for Melioidosis and other microorganisms, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Phirabhat Saengsawang
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand
| | - Patrick J. Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia 4067, Australia
| | - Thotsapol Thomrongsuwannakij
- Akkhraratchakumari Veterinary College, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Centre for One Health, Walailak University, Thai Buri, Tha Sala, Nakhon Si Thammarat 80160, Thailand,Corresponding author: Thotsapol Thomrongsuwannakij, e-mail: Co-authors: TW: , RN: , NS: , CS: , YP: , PF: , PS: , PJB:
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8
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Hesp A, ter Braak C, van der Goot J, Veldman K, van Schaik G, Mevius D. Antimicrobial resistance clusters in commensal Escherichia coli from livestock. Zoonoses Public Health 2021; 68:194-202. [PMID: 33455079 PMCID: PMC8048968 DOI: 10.1111/zph.12805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/19/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022]
Abstract
To combat antimicrobial resistance (AMR), policymakers need an overview of evolution and trends of AMR in relevant animal reservoirs, and livestock is monitored by susceptibility testing of sentinel organisms such as commensal E. coli. Such monitoring data are often vast and complex and generates a need for outcome indicators that summarize AMR for multiple antimicrobial classes. Model-based clustering is a data-driven approach that can help to objectively summarize AMR in animal reservoirs. In this study, a model-based cluster analysis was carried out on a dataset of minimum inhibitory concentrations (MIC), recoded to binary variables, for 10 antimicrobials of commensal E. coli isolates (N = 12,986) derived from four animal species (broilers, pigs, veal calves and dairy cows) in Dutch AMR monitoring, 2007-2018. This analysis revealed four clusters in commensal E. coli in livestock containing 201 unique resistance combinations. The prevalence of these combinations and clusters differs between animal species. Our results indicate that to monitor different animal populations, more than one indicator for multidrug resistance seems necessary. We show how these clusters summarize multidrug resistance and have potential as monitoring outcome indicators to benchmark and prioritize AMR problems in livestock.
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Affiliation(s)
- Ayla Hesp
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
- Department of Infectious Diseases and ImmunologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Cajo ter Braak
- BiometrisWageningen University & ResearchWageningenThe Netherlands
| | - Jeanet van der Goot
- Department of Diagnostics and Crisis OrganisationWageningen Bioveterinary ResearchLelystadThe Netherlands
| | - Kees Veldman
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
| | - Gerdien van Schaik
- Royal GDDeventerThe Netherlands
- Department of Farm Animal HealthFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Dik Mevius
- Department of Bacteriology and EpidemiologyWageningen Bioveterinary ResearchLelystadThe Netherlands
- Department of Infectious Diseases and ImmunologyFaculty of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
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Athanasakopoulou Z, Reinicke M, Diezel C, Sofia M, Chatzopoulos DC, Braun SD, Reissig A, Spyrou V, Monecke S, Ehricht R, Tsilipounidaki K, Giannakopoulos A, Petinaki E, Billinis C. Antimicrobial Resistance Genes in ESBL-Producing Escherichia coli Isolates from Animals in Greece. Antibiotics (Basel) 2021; 10:389. [PMID: 33916633 PMCID: PMC8067336 DOI: 10.3390/antibiotics10040389] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 12/13/2022] Open
Abstract
The prevalence of multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The present study aimed to provide an overview of the multidrug resistance phenotype and genotype of ESBL-producing Escherichia coli (E. coli) isolates of livestock and wild bird origin in Greece. Nineteen phenotypically confirmed ESBL-producing E. coli strains isolated from fecal samples of cattle (n = 7), pigs (n = 11) and a Eurasian magpie that presented resistance to at least one class of non β-lactam antibiotics, were selected and genotypically characterized. A DNA-microarray based assay was used, which allows the detection of various genes associated with antimicrobial resistance. All isolates harbored blaCTX-M-1/15, while blaTEM was co-detected in 13 of them. The AmpC gene blaMIR was additionally detected in one strain. Resistance genes were also reported for aminoglycosides in all 19 isolates, for quinolones in 6, for sulfonamides in 17, for trimethoprim in 14, and for macrolides in 8. The intI1 and/or tnpISEcp1 genes, associated with mobile genetic elements, were identified in all but two isolates. This report describes the first detection of multidrug resistance genes among ESBL-producing E. coli strains retrieved from feces of cattle, pigs, and a wild bird in Greece, underlining their dissemination in diverse ecosystems and emphasizing the need for a One-Health approach when addressing the issue of antimicrobial resistance.
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Affiliation(s)
- Zoi Athanasakopoulou
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Martin Reinicke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Celia Diezel
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Marina Sofia
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Dimitris C. Chatzopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Annett Reissig
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Vassiliki Spyrou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece;
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institut fuer Medizinische Mikrobiologie und Hygiene, Medizinische Fakultaet “Carl Gustav Carus”, TU Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (M.R.); (C.D.); (S.D.B.); (A.R.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07737 Jena, Germany
| | | | - Alexios Giannakopoulos
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
| | - Efthymia Petinaki
- Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece; (K.T.); (E.P.)
| | - Charalambos Billinis
- Faculty of Veterinary Science, University of Thessaly, 43100 Karditsa, Greece; (Z.A.); (M.S.); (D.C.C.); (A.G.)
- Faculty of Public and Integrated Health, University of Thessaly, 43100 Karditsa, Greece
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