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Sabença C, Romero-Rivera M, Barbero-Herranz R, Sargo R, Sousa L, Silva F, Lopes F, Abrantes AC, Vieira-Pinto M, Torres C, Igrejas G, Del Campo R, Poeta P. Molecular Characterization of Multidrug-Resistant Escherichia coli from Fecal Samples of Wild Animals. Vet Sci 2024; 11:469. [PMID: 39453061 DOI: 10.3390/vetsci11100469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/23/2024] [Accepted: 09/30/2024] [Indexed: 10/26/2024] Open
Abstract
Antimicrobial resistance (AMR) surveillance in fecal Escherichia coli isolates from wildlife is crucial for monitoring the spread of this microorganism in the environment and for developing effective AMR control strategies. Wildlife can act as carriers of AMR bacteria and spread them to other wildlife, domestic animals, and humans; thus, they have public health implications. A total of 128 Escherichia coli isolates were obtained from 66 of 217 fecal samples obtained from different wild animals using media without antibiotic supplementation. Antibiograms were performed for 17 antibiotics to determine the phenotypic resistance profile in these isolates. Extended-spectrum β-lactamase (ESBL) production was tested using the double-disc synergy test, and 29 E. coli strains were selected for whole genome sequencing. In total, 22.1% of the wild animals tested carried multidrug-resistant E. coli isolates, and 0.93% (2/217) of these wild animals carried E. coli isolates with ESBL-encoding genes (blaCTX-M-65, blaCTX-M-55, and blaEC-1982). The E. coli isolates showed the highest resistance rates to ampicillin and were fully susceptible to amikacin, meropenem, ertapenem, and imipenem. Multiple resistance and virulence genes were detected, as well as different plasmids. The relatively high frequency of multidrug-resistant E. coli isolates in wildlife, with some of them being ESBL producers, raises some concern regarding the potential transmission of antibiotic-resistant bacteria among these animals. Gaining insights into antibiotic resistance patterns in wildlife can be vital in shaping conservation initiatives and developing effective strategies for responsible antibiotic use.
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Affiliation(s)
- Carolina Sabença
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
| | - Mario Romero-Rivera
- Department of Microbiology, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Raquel Barbero-Herranz
- Department of Microbiology, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Roberto Sargo
- CRAS-Center for the Recovery of Wild Animals, Veterinary Hospital, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Luís Sousa
- CRAS-Center for the Recovery of Wild Animals, Veterinary Hospital, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Filipe Silva
- CRAS-Center for the Recovery of Wild Animals, Veterinary Hospital, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Filipa Lopes
- LxCRAS-Centro de Recuperação de Animais Silvestres de Lisboa, 1500-068 Lisboa, Portugal
| | - Ana Carolina Abrantes
- CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Madalena Vieira-Pinto
- CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
| | - Rosa Del Campo
- Department of Microbiology, University Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28040 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Spain
| | - Patrícia Poeta
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
- CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000-801 Vila Real, Portugal
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Garcês A, Pires I. European Wild Carnivores and Antibiotic Resistant Bacteria: A Review. Antibiotics (Basel) 2023; 12:1725. [PMID: 38136759 PMCID: PMC10740848 DOI: 10.3390/antibiotics12121725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/05/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is a global concern that affects not only human health but also the health of wildlife and the environment. Wildlife can serve as reservoirs for antibiotic-resistant bacteria, and antibiotics in veterinary medicine and agriculture can contribute to the development of resistance in these populations. Several European carnivore species, such as wolves, foxes, otters, and bears, can be exposed to antibiotics by consuming contaminated food, water, or other resources in their habitats. These animals can also be indirectly exposed to antibiotics through interactions with domestic animals and human activities in their environment. Antibiotic resistance in wildlife can harm ecosystem health and also impact human health indirectly through various pathways, including zoonotic disease transmission. Moreover, the spread of resistant bacteria in wildlife can complicate conservation efforts, as it can threaten already endangered species. This review aims to describe the presence of antibiotic-resistant bacteria in wild carnivores in Europe.
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Affiliation(s)
- Andreia Garcês
- Exotic and Wildlife Service from the Veterinary Hospital University of Trás-os-Montes and Alto Douro, Quinta dos Prados, 4500-801 Vila Real, Portugal
- Centre for Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, UTAD, Quinta de Prados, 5000-801 Vila Real, Portugal
| | - Isabel Pires
- Center of Animal and Veterinary Science CECAV University of Trás-os-Montes and Alto Douro, Quinta dos Prados, 4500-801 Vila Real, Portugal;
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Dias D, Fonseca C, Mendo S, Caetano T. First characterization of the faecal resistome of eurasian otter (Lutra lutra), a sentinel species for aquatic environments. CHEMOSPHERE 2022; 309:136644. [PMID: 36181859 DOI: 10.1016/j.chemosphere.2022.136644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 09/17/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Antimicrobial resistance (AMR) is a global health concern. Nowadays, antibiotic resistance genes (ARGs) are considered emerging pollutants. This study followed the One Health framework, in which AMR surveillance in the environment, including in wild animals, is advisable to mitigate this problem. Here we investigated AMR associated with Eurasian otter, a semi-aquatic mammal considered an indicator of freshwater health. To do so, otter's faecal resistome was characterized by a high-throughput qPCR array. This technique has a high-capacity of ARGs profiling. Additionally, we have assessed the antimicrobial susceptibility of two indicator bacteria, E. coli and Enterococcus spp, isolated from otter spraints and interpreted the results according to clinical and epidemiological cut-offs (ECOFFs).
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Carlos Fonseca
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Sónia Mendo
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
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Dias D, Hipólito D, Figueiredo A, Fonseca C, Caetano T, Mendo S. Unravelling the Diversity and Abundance of the Red Fox (Vulpes vulpes) Faecal Resistome and the Phenotypic Antibiotic Susceptibility of Indicator Bacteria. Animals (Basel) 2022; 12:ani12192572. [PMID: 36230313 PMCID: PMC9558537 DOI: 10.3390/ani12192572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/05/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Antimicrobial resistance was considered one of the major concerns of the twenty-first century by the World Health Organization in 2014. A holistic approach known as “One Health” recognizes the connections and interdependence between the health of people, domestic and wild animals, plants, and the ecosystem. The red fox is the most widespread wild canid in Europe that adapts easily and is distributed in natural environments and urban and peri-urban areas due to its increasing abundance. Foxes are reservoirs and disseminators of antibiotic resistance and zoonotic agents. They interact with watercourses, soils and livestock, and although they have no gastronomic interest, they are a game species, highlighting the potential risk of contamination between them and the hunters. Our main goal was to characterize antibiotic resistance in red foxes. Several clinically relevant antibiotic resistance genes were identified, as well as multidrug-resistant bacteria. Abstract The WHO considers that antimicrobial resistance (AMR) is among the ten greatest global public health risks of the 21st century. The expansion of human populations and anthropogenically related activities, accompanied by the fragmentation of natural habitats, has resulted in increased human–wildlife interaction. Natural ecosystems are therefore subjected to anthropogenic inputs, which affect the resistome of wild animals. Thus, urgent multisectoral action is needed to achieve the Sustainable Development Goals following the One Health approach. The present work falls within the scope of this approach and aims to characterize the AMR of the faecal microbiome of the red fox (Vulpes vulpes), an opportunistic and generalist synanthropic species whose abundance has been increasing in urban and peri-urban areas. A high number of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were screened and quantified using a high-throughput qPCR approach, and the antimicrobial susceptibility of cultivable E. coli and Enterococcus spp. were assessed interpreted with both ECOFFs and clinical breakpoints. The most abundant ARGs detected confer resistance to trimethoprim and tetracyclines, although the first were absent in one of the locations studied. Several ARGs considered to be threats to human health were identified in high relative abundances (blaTEM, ermB, aadA, tetM, tetW, tetL, drfA1 and drfA17), especially in the geographical area with greater anthropogenic influence. Although at a low percentage, resistant and multidrug-resistant (MDR) E. coli and Enterococcus spp. were isolated, including one MDR E. coli showing resistance to 12 antimicrobials from 6 different classes.
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Affiliation(s)
- Diana Dias
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Dário Hipólito
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Biology, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000 Zagreb, Croatia
| | - Ana Figueiredo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Department of Bioscience & CEES, University of Oslo, Blindernvn, 31, 0371 Oslo, Norway
| | - Carlos Fonseca
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- ForestWISE—Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Tânia Caetano
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
| | - Sónia Mendo
- CESAM and Department of Biology, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
- Correspondence: (T.C.); (S.M.)
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Osińska M, Nowakiewicz A, Zięba P, Gnat S, Łagowski D, Trościańczyk A. A rich mosaic of resistance in extended-spectrum β-lactamase-producing Escherichia coli isolated from red foxes (Vulpes vulpes) in Poland as a potential effect of increasing synanthropization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151834. [PMID: 34808162 DOI: 10.1016/j.scitotenv.2021.151834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
In our research, we analyzed the resistance of cephalosporin-resistant E. coli strains to antimicrobial agents. The strains were collected during five years from wild animal species commonly inhabiting Poland. We have identified the type of β-lactamases produced and the multidrug-resistance profile. Most strains (73.8%) had genes encoding ESBL enzymes, mainly CTX-M-1 and TEM. Almost all AmpC-β-lactamase-producing isolates had the blaCMY-2 gene. Almost 70% of the strains tested showed a multi-drug resistance profile. The dominant phenotype was resistance to tetracycline (69.05%), and/or sulfamethoxazole (57.1%). We also found high resistance to quinolones: ciprofloxacin 35.7% and nalidixic acid 52.4%. The phenotypic resistance of the strains was in most cases confirmed by the presence of corresponding genes. Among strains, 26.2% were carriers of plasmid-mediated quinolone resistance genes (PMQR). MLST analysis revealed a large clonal variation of the strains, which was reflected in 28 different sequence types. More than half of the strains (54.7%) were classified into the following sequence complexes: 10, 23, 69, 101, 155, 156, 168, 354, 398, 446, and 648. Only one strain in the studied group was assigned to the ExPEC pathotype and represented sequence type 117. The results of our research have confirmed that isolates obtained from wild animals possess many resistance determinants and sequence types, which are also found in food-producing animals and humans. This reflects the doctrine of "One health", which clearly indicates that human health is inextricably linked with animal health as well as degree of environmental contamination. We conclude that the resistance and virulence profiles of strains isolated from wildlife animals may be a resultant of various sources encountered by animals, creating a rich and varied mosaic of genes, which is very often unpredictable and not reflected in the correlation between the sequence type and the gene profile of resistance or virulence observed in epidemic clones.
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Affiliation(s)
- Marcelina Osińska
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Aneta Nowakiewicz
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Przemysław Zięba
- State Veterinary Laboratory, Droga Męczenników Majdanka 50, 20-325 Lublin, Poland
| | - Sebastian Gnat
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Dominik Łagowski
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
| | - Aleksandra Trościańczyk
- University of Life Sciences, Faculty of Veterinary Medicine, Department of Preclinical Veterinary Sciences, Sub-Department of Veterinary Microbiology, Akademicka 12, 20-033 Lublin, Poland.
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Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use. Appl Environ Microbiol 2022; 88:e0027722. [PMID: 35442082 PMCID: PMC9088250 DOI: 10.1128/aem.00277-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.
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Fulham M, McDougall F, Power M, McIntosh RR, Gray R. Carriage of antibiotic resistant bacteria in endangered and declining Australian pinniped pups. PLoS One 2022; 17:e0258978. [PMID: 35089935 PMCID: PMC8797192 DOI: 10.1371/journal.pone.0258978] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
The rapid emergence of antimicrobial resistance (AMR) is a major concern for wildlife and ecosystem health globally. Genetic determinants of AMR have become indicators of anthropogenic pollution due to their greater association with humans and rarer presence in environments less affected by humans. The objective of this study was to determine the distribution and frequency of the class 1 integron, a genetic determinant of AMR, in both the faecal microbiome and in Escherichia coli isolated from neonates of three pinniped species. Australian sea lion (Neophoca cinerea), Australian fur seal (Arctocephalus pusillus doriferus) and long-nosed fur seal (Arctocephalus forsteri) pups from eight breeding colonies along the Southern Australian coast were sampled between 2016-2019. DNA from faecal samples (n = 309) and from E. coli (n = 795) isolated from 884 faecal samples were analysed for class 1 integrons using PCRs targeting the conserved integrase gene (intI) and the gene cassette array. Class 1 integrons were detected in A. p. doriferus and N. cinerea pups sampled at seven of the eight breeding colonies investigated in 4.85% of faecal samples (n = 15) and 4.52% of E. coli isolates (n = 36). Integrons were not detected in any A. forsteri samples. DNA sequencing of the class 1 integron gene cassette array identified diverse genes conferring resistance to four antibiotic classes. The relationship between class 1 integron carriage and the concentration of five trace elements and heavy metals was also investigated, finding no significant association. The results of this study add to the growing evidence of the extent to which antimicrobial resistant bacteria are polluting the marine environment. As AMR determinants are frequently associated with bacterial pathogens, their occurrence suggests that these pinniped species are vulnerable to potential health risks. The implications for individual and population health as a consequence of AMR carriage is a critical component of ongoing health investigations.
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Affiliation(s)
- Mariel Fulham
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Fiona McDougall
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, New South Wales, Australia
| | - Michelle Power
- Department of Biological Sciences, Macquarie University, North Ryde, Sydney, New South Wales, Australia
| | | | - Rachael Gray
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, New South Wales, Australia
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Alonso CA, de Toro M, de la Cruz F, Torres C. Genomic Insights into Drug Resistance and Virulence Platforms, CRISPR-Cas Systems and Phylogeny of Commensal E. coli from Wildlife. Microorganisms 2021; 9:999. [PMID: 34063152 PMCID: PMC8148099 DOI: 10.3390/microorganisms9050999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Commensal bacteria act as important reservoirs of virulence and resistance genes. However, existing data are generally only focused on the analysis of human or human-related bacterial populations. There is a lack of genomic studies regarding commensal bacteria from hosts less exposed to antibiotics and other selective forces due to human activities, such as wildlife. In the present study, the genomes of thirty-eight E. coli strains from the gut of various wild animals were sequenced. The analysis of their accessory genome yielded a better understanding of the role of the mobilome on inter-bacterial dissemination of mosaic virulence and resistance plasmids. The study of the presence and composition of the CRISPR/Cas systems in E. coli from wild animals showed some viral and plasmid sequences among the spacers, as well as the relationship between CRISPR/Cas and E. coli phylogeny. Further, we constructed a single nucleotide polymorphisms-based core tree with E. coli strains from different sources (humans, livestock, food and extraintestinal environments). Bacteria from humans or highly human-influenced settings exhibit similar genetic patterns in CRISPR-Cas systems, plasmids or virulence/resistance genes-carrying modules. These observations, together with the absence of significant genetic changes in their core genome, suggest an ongoing flow of both mobile elements and E. coli lineages between human and natural ecosystems.
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Affiliation(s)
- Carla Andrea Alonso
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain;
- Servicio de Microbiología, Hospital San Pedro, 26006 Logroño, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain;
| | - Fernando de la Cruz
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria-CSIC), 39011 Santander, Spain;
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, 26006 Logroño, Spain;
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ESBL-Producing Escherichia coli Carrying CTX-M Genes Circulating among Livestock, Dogs, and Wild Mammals in Small-Scale Farms of Central Chile. Antibiotics (Basel) 2021; 10:antibiotics10050510. [PMID: 33946277 PMCID: PMC8145412 DOI: 10.3390/antibiotics10050510] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic-resistant bacteria of critical importance for global health such as extended-spectrum beta-lactamases-producing (ESBL)-Escherichia coli have been detected in livestock, dogs, and wildlife worldwide. However, the dynamics of ESBL-E. coli between these animals remains poorly understood, particularly in small-scale farms of low and middle-income countries where contact between species can be frequent. We compared the prevalence of fecal carriage of ESBL-E. coli among 332 livestock (207 cows, 15 pigs, 60 horses, 40 sheep, 6 goats, 4 chickens), 82 dogs, and wildlife including 131 European rabbits, 30 rodents, and 12 Andean foxes sharing territory in peri-urban localities of central Chile. The prevalence was lower in livestock (3.0%) and wildlife (0.5%) compared to dogs (24%). Among 47 ESBL-E. coli isolates recovered, CTX-M-group 1 was the main ESBL genotype identified, followed by CTX-M-groups 2, 9, 8, and 25. ERIC-PCR showed no cluster of E. coli clones by either host species nor locality. To our knowledge, this is the first report of ESBL-E. coli among sheep, cattle, dogs, and rodents of Chile, confirming their fecal carriage among domestic and wild animals in small-scale farms. The high prevalence of ESBL-E. coli in dogs encourages further investigation on their role as potential reservoirs of this bacteria in agricultural settings.
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O'Hagan MJH, Pascual-Linaza AV, Couzens C, Holmes C, Bell C, Spence N, Huey RJ, Murphy JA, Devaney R, Lahuerta-Marin A. Estimation of the Prevalence of Antimicrobial Resistance in Badgers ( Meles meles) and Foxes ( Vulpes vulpes) in Northern Ireland. Front Microbiol 2021; 12:596891. [PMID: 33679630 PMCID: PMC7930819 DOI: 10.3389/fmicb.2021.596891] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistant (AMR) bacteria can be shared between humans and animals, through food, water, and the environment. Wild animals are not only potential reservoirs of AMR, but are also sentinels mirroring the presence of AMR zoonotic bacteria in the environment. In Northern Ireland, little is known about levels of AMR in bacteria in wildlife, thus the current study aimed to estimate the prevalence of AMR bacteria in wildlife using wildlife species from two ongoing surveys as a proxy. Nasopharyngeal swabs and faecal samples from European badgers (Meles meles) (146 faecal samples; 118 nasal samples) and red foxes (Vulpes vulpes) (321 faecal samples; 279 nasal samples) were collected throughout Northern Ireland and were used to survey for the presence of extended spectrum beta lactamase resistant and AmpC-type beta lactamases Escherichia coli (ESBL/AmpC), Salmonella spp. (only in badgers) and methicillin resistant Staphylococcus aureus (MRSA). ESBLs were detected in 13 out of 146 badger faecal samples (8.90%) and 37 out of 321 of fox faecal samples (11.53%), all of them presenting multi-drug resistance (MDR). Fourteen out of 146 (9.59%) badger faecal samples carried Salmonella spp. [S. Agama (n = 9), S. Newport (n = 4) and S. enterica subsp. arizonae (n = 1)]. Overall, AMR was found only in the S. enterica subsp. arizonae isolate (1/14, 7.14%). No MRSA were detected in nasopharyngeal swabs from badgers (n = 118) and foxes (n = 279). This is the first attempt to explore the prevalence of AMR in the two common wildlife species in Northern Ireland. These findings are important as they can be used as a base line for further research exploring the origin of the found resistance. These results should encourage similar surveys where environmental samples are included to bring better understanding of AMR dynamics, and the impact on wildlife, domestic livestock and humans.
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Affiliation(s)
- Maria J H O'Hagan
- Veterinary Epidemiology Unit, Department of Agriculture, Environment and Rural Affairs, Belfast, United Kingdom
| | - Ana V Pascual-Linaza
- Surveillance and Antimicrobial Resistance Branch, Department of Agriculture, Environment and Rural Affairs, Belfast, United Kingdom
| | - Catherine Couzens
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Clare Holmes
- Disease Surveillance and Investigation Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Colin Bell
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Nessie Spence
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Robert J Huey
- Department of Agriculture, Environment and Rural Affairs, Belfast, United Kingdom
| | - Julie A Murphy
- Veterinary Epidemiology Unit, Department of Agriculture, Environment and Rural Affairs, Belfast, United Kingdom
| | - Ryan Devaney
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - Angela Lahuerta-Marin
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
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11
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Devane ML, Moriarty E, Weaver L, Cookson A, Gilpin B. Fecal indicator bacteria from environmental sources; strategies for identification to improve water quality monitoring. WATER RESEARCH 2020; 185:116204. [PMID: 32745743 DOI: 10.1016/j.watres.2020.116204] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 06/11/2023]
Abstract
In tropical to temperate environments, fecal indicator bacteria (FIB), such as enterococci and Escherichia coli, can persist and potentially multiply, far removed from their natural reservoir of the animal gut. FIB isolated from environmental reservoirs such as stream sediments, beach sand and vegetation have been termed "naturalized" FIB. In addition, recent research suggests that the intestines of poikilothermic animals such as fish may be colonized by enterococci and E. coli, and therefore, these animals may contribute to FIB concentrations in the aquatic environment. Naturalized FIB that are derived from fecal inputs into the environment, and subsequently adapted to maintain their population within the non-host environment are termed "naturalized enteric FIB". In contrast, an additional theory suggests that some "naturalized" FIB diverged from enteric FIB many millions of years ago and are now normal inhabitants of the environment where they are referred to as "naturalized non-enteric FIB". In the case of the Escherichia genus, the naturalized non-enteric members are identified as E. coli during routine water quality monitoring. An over-estimation of the health risk could result when these naturalized, non-enteric FIB, (that is, not derived from avian or mammalian fecal contamination), contribute to water quality monitoring results. It has been postulated that these environmental FIB belonging to the genera Escherichia and Enterococcus can be differentiated from enteric FIB by genetic methods because they lack some of the genes required for colonization of the host intestine, and have acquired genes that aid survival in the environment. Advances in molecular tools such as next generation sequencing will aid the identification of genes peculiar or "enriched" in particular habitats to discriminate between enteric and environmental FIB. In this appraisal, we have reviewed the research studying "naturalized" FIB, and discussed the techniques for their differentiation from enteric FIB. This differentiation includes the important distinction between enteric FIB derived from fresh and non-recent fecal inputs, and those truly non-enteric environmental microbes, which are currently identified as FIB during routine water quality monitoring. The inclusion of tools for the identification of naturalized FIB (enteric or environmental) would be a valuable resource for future studies assessing water quality.
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Affiliation(s)
- Megan L Devane
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand.
| | - Elaine Moriarty
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Louise Weaver
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
| | - Adrian Cookson
- AgResearch Ltd., Hopkirk Research Institute, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - Brent Gilpin
- Institute of Environmental Science and Research Ltd., 27 Creyke Rd, Ilam, Christchurch, New Zealand
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12
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Darwich L, Vidal A, Seminati C, Albamonte A, Casado A, López F, Molina-López RA, Migura-Garcia L. High prevalence and diversity of extended-spectrum β-lactamase and emergence of OXA-48 producing Enterobacterales in wildlife in Catalonia. PLoS One 2019; 14:e0210686. [PMID: 31381578 PMCID: PMC6681944 DOI: 10.1371/journal.pone.0210686] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/02/2019] [Indexed: 11/22/2022] Open
Abstract
Most of the studies focused on antimicrobial resistance (AMR) performed in wildlife describe Escherichia coli as the principal indicator of the selective pressure. In the present study, several species of Enterobacterales with a large panel of cephalosporin resistant (CR) genes have been isolated from wildlife in Catalonia. A total of 307 wild animals were examined to determine the prevalence of CR enterobacteria, AMR phenotypes and the presence of common carbapenem and CR genes. The overall prevalence of CR-phenotype was 13% (40/307): 17.3% in wild mammals (18/104) and 11.5% in wild birds (22/191) (p<0.01). Hedgehogs showed the highest prevalence (13.5% of 104) of the mammal specimens, and raptors the highest in bird specimen (7.3% of 191). Although CR E. coli was the most frequently isolated (45%), other CR- Enterobacterales like Klebsiella pneumoniae (20%), Citrobacter freundii (15%), Enterobacter cloacae (5%), Proteus mirabilis (5%), Providencia spp (5%) and Serratia marcescens (2.5%) were also isolated. A high diversity of CR genes was identified among the isolates, with 50% yielding blaCMY-2, 23% blaSHV-12, 20% blaCMY-1 and 18% blaCTX-M-15. Additionally, resistance to carbapenems associated to OXA-48 gene was found. Most of the CR isolates, principally K. pneumoniae and C. freundii, were multi-resistant with co-resistance to fluoroquinolones, tetracycline, sulphonamides and aminoglycosides. This study reports high prevalence of Enterobacterales harbouring a variety of CR genes and OXA-48 mediated-carbapenem resistance, all of them frequently associated to nosocomial human infections, for the first time in wild mammals and wild birds. Implementation of control measures to reduce the impact of anthropogenic pressure in the environment is urgently needed.
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Affiliation(s)
- Laila Darwich
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
| | - Anna Vidal
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Chiara Seminati
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Andreu Albamonte
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Alba Casado
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Ferrán López
- Departament de Sanitat i Anatomia Animal, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Rafael A. Molina-López
- Catalan Wildlife Service, Centre de Fauna Salvatge de Torreferrussa, Santa Perpètua de Mogoda, Barcelona, Spain
| | - Lourdes Migura-Garcia
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus). INFECTION GENETICS AND EVOLUTION 2019; 70:107-113. [PMID: 30798035 DOI: 10.1016/j.meegid.2019.02.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/17/2019] [Accepted: 02/20/2019] [Indexed: 01/10/2023]
Abstract
Increasing reports of antimicrobial resistance in wildlife highlight the significance of a One Health approach to managing resistance. We investigated the prevalence and diversity of class 1 integrons, a genetic determinant of resistance, in grey-headed flying foxes, a large fruit bat species belonging to the order Chiroptera. Class 1 integrons were detected in both wild flying foxes (5.3%) and captive flying foxes (41.2%) housed in wildlife rehabilitation facilities. Genes encoding resistance to aminoglycosides, trimethoprim and beta-lactams, and Qac efflux pumps were detected. Analysis of conserved integron elements and gene cassette arrays indicate the direction of integron transfer is from humans to flying foxes. The detection of two novel gene cassette arrays (5'CS-qacH-aacA34-blaOXA-21-3'CS and 5'CS-qacF-3'CS strongly suggests acquisition of genes from the environmental resistome into class 1 integrons within the flying fox microbiota. The dynamics of class 1 integrons in flying foxes indicates bats have a role in the emergence of novel antibiotic resistance determinants.
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14
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Lucas P, Jouy E, Le Devendec L, de Boisséson C, Perrin-Guyomard A, Jové T, Blanchard Y, Touzain F, Kempf I. Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs. Vet Microbiol 2018; 224:100-106. [DOI: 10.1016/j.vetmic.2018.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 12/29/2022]
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15
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Dolejska M, Papagiannitsis CC. Plasmid-mediated resistance is going wild. Plasmid 2018; 99:99-111. [PMID: 30243983 DOI: 10.1016/j.plasmid.2018.09.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/08/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
Multidrug resistant (MDR) Gram-negative bacteria have been increasingly reported in humans, companion animals and farm animals. The growing trend of plasmid-mediated resistance to antimicrobial classes of critical importance is attributed to the emergence of epidemic plasmids, rapidly disseminating resistance genes among the members of Enterobacteriaceae family. The use of antibiotics to treat humans and animals has had a significant impact on the environment and on wild animals living and feeding in human-influenced habitats. Wildlife can acquire MDR bacteria selected in hospitals, community or livestock from diverse sources, including wastewater, sewage systems, landfills, farm facilities or agriculture fields. Therefore, wild animals are considered indicators of environmental pollution by antibiotic resistant bacteria, but they can also act as reservoirs and vectors spreading antibiotic resistance across the globe. The level of resistance and reported plasmid-mediated resistance mechanisms observed in bacteria of wildlife origin seem to correlate well with the situation described in humans and domestic animals. Additionaly, the identification of epidemic plasmids in samples from different human, animal and wildlife sources underlines the role of horizontal gene transfer in the dissemination of resistance genes. The present review focuses on reports of plasmid-mediated resistance to critically important antimicrobial classes such as broad-spectrum beta-lactams and colistin in Enterobacteriaceae isolates from samples of wildlife origin. The role of plasmids in the dissemination of ESBL-, AmpC- and carbapenemase-encoding genes as well as plasmid-mediated colistin resistance determinants in wildlife are discussed, and their similarities to plasmids previously identified in samples of human clinical or livestock origin are highlighted. Furthermore, we present features of completely sequenced plasmids reported from wildlife Enterobacteriaceae isolates, with special focus on genes that could be associated with the plasticity and stable maintenance of these molecules in antibiotic-free environments.
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Affiliation(s)
- Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic.
| | - Costas C Papagiannitsis
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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16
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Cao B, Luo Q, Fu Y, Du L, Qiu T, Yang X, Chen X, Chen Q, Soares JC, Cho RY, Zhang XY, Qiu H. Predicting individual responses to the electroconvulsive therapy with hippocampal subfield volumes in major depression disorder. Sci Rep 2018; 8:5434. [PMID: 29615675 PMCID: PMC5882798 DOI: 10.1038/s41598-018-23685-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022] Open
Abstract
Electroconvulsive therapy (ECT) is one of the most effective treatments for major depression disorder (MDD). ECT can induce neurogenesis and synaptogenesis in hippocampus, which contains distinct subfields, e.g., the cornu ammonis (CA) subfields, a granule cell layer (GCL), a molecular layer (ML), and the subiculum. It is unclear which subfields are affected by ECT and whether we predict the future treatment response to ECT by using volumetric information of hippocampal subfields at baseline? In this study, 24 patients with severe MDD received the ECT and their structural brain images were acquired with magnetic resonance imaging before and after ECT. A state-of-the-art hippocampal segmentation algorithm from Freesurfer 6.0 was used. We found that ECT induced volume increases in CA subfields, GCL, ML and subiculum. We applied a machine learning algorithm to the hippocampal subfield volumes at baseline and were able to predict the change in depressive symptoms (r = 0.81; within remitters, r = 0.93). Receiver operating characteristic analysis also showed robust prediction of remission with an area under the curve of 0.90. Our findings provide evidence for particular hippocampal subfields having specific roles in the response to ECT. We also provide an analytic approach for generating predictions about clinical outcomes for ECT in MDD.
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Affiliation(s)
- Bo Cao
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, United States
| | - Qinghua Luo
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Yixiao Fu
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Lian Du
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Tian Qiu
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Xiangying Yang
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Xiaolu Chen
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Qibin Chen
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Jair C Soares
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, United States
| | - Raymond Y Cho
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, United States
| | - Xiang Yang Zhang
- Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, United States
| | - Haitang Qiu
- Mental Health Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P. R. China.
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