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Listorti V, Guardone L, Piccinini C, Martini I, Ferraris C, Ligotti C, Cristina ML, Pussini N, Pitti M, Razzuoli E. Shiga Toxin-Producing Escherichia coli Isolated from Wild Ruminants in Liguria, North-West Italy. Pathogens 2024; 13:576. [PMID: 39057803 PMCID: PMC11279605 DOI: 10.3390/pathogens13070576] [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: 05/31/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Wildlife may represent an important source of infectious diseases for humans and other wild and domestic animals. Wild ruminants can harbour and transmit Shiga toxin-producing Escherichia coli (STEC) to humans, and some strains even carry important antimicrobial resistance. In this study, 289 livers of wild roe deer, fallow deer, red deer and chamois collected in Liguria, north-west Italy, from 2019 to 2023 were analysed. Overall, 44 STEC strains were isolated from 28 samples. The characterisation of serogroups showed the presence of O104, O113, O145 and O146 serogroups, although for 28 colonies, the serogroup could not be determined. The most prevalent Shiga toxin gene in isolated strains was Stx2, and more specifically the subtype Stx2b. The other retrieved subtypes were Stx1a, Stx1c, Stx1d and Stx2g. The isolated strains generally proved to be susceptible to the tested antimicrobials. However, multi-drug resistances against highly critical antimicrobials were found in one strain isolated from a roe deer. This study highlights the importance of wildlife monitoring in the context of a "One Health" approach.
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Affiliation(s)
- Valeria Listorti
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Lisa Guardone
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
- Department of Veterinary Sciences, University of Pisa, Viale Delle Piagge 2, 56124 Pisa, Italy
| | - Carolina Piccinini
- Department of Health Sciences, University of Genova, 16132 Genova, Italy; (C.P.); (M.L.C.)
| | - Isabella Martini
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Carla Ferraris
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Carmela Ligotti
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Maria Luisa Cristina
- Department of Health Sciences, University of Genova, 16132 Genova, Italy; (C.P.); (M.L.C.)
- Hospital Hygiene, E. O. Galliera Hospital, 16128 Genova, Italy
| | - Nicola Pussini
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Monica Pitti
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
| | - Elisabetta Razzuoli
- Istituto Zooprofilattico Sperimentale of Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Turin, Italy; (I.M.); (C.F.); (C.L.); (N.P.); (M.P.); (E.R.)
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Wu Y, Mao W, Shao J, He X, Bao D, Yue M, Wang J, Shen W, Qiang X, Jia H, He F, Ruan Z. Monitoring the long-term spatiotemporal transmission dynamics and ecological surveillance of multidrug-resistant Salmonella enterica serovar Goldcoast: A multicenter genomic epidemiology study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169116. [PMID: 38065491 DOI: 10.1016/j.scitotenv.2023.169116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
The emergence of multidrug-resistant Salmonella enterica serovar Goldcoast poses a significant threat to the effective treatment and control of salmonellosis within the ecological environment. Here, we conducted a genomic epidemiological study delineate the global dissemination scenarios of the multidrug-resistant S. Goldcoast originated from 11 countries for over 20 years. The population structure and evolutionary history of multidrug-resistant S. Goldcoast was investigated through phylogenomic and long-term spatiotemporal transmission dynamic analysis. ST358 and ST2529 are the predominant lineages of S. Goldcoast. Multidrug-resistant S. Goldcoast strains have mainly been identified in the ST358 lineage from human and the ST2529 lineage from livestock. ST358 S. Goldcoast was estimated to have emerged in the United Kingdom in 1969, and then spread to China, with both countries serve as centers for the global dissemination of the ST358 lineage. After its emergence and subsequent spread in Chinese clinical and environmental samples, occasional instances of this lineage have been reported in Canada, the United Kingdom, and Ireland. Clonal transmission of ST358 and ST2529 S. Goldcoast have occurred not only on an international and intercontinental scale but also among clinical, environmental and livestock samples. These data indicated that international circulation and local transmission of S. Goldcoast have occurred for over a decade. Continued surveillance of multidrug-resistant S. Goldcoast from a global "One Health" perspective is urgently needed to facilitate monitoring the spread of the antimicrobial resistant high-risk clones.
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Affiliation(s)
- Yuye Wu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Weifang Mao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, Shaoxing University Affiliated Hospital, Shaoxing 312000, China
| | - Jiayu Shao
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, The Third People's Hospital of Xiaoshan District, Hangzhou 311251, China
| | - Xianhong He
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Clinical Laboratory, The Third People's Hospital of Xiaoshan District, Hangzhou 311251, China
| | - Danni Bao
- Department of Clinical Laboratory, Sanmen People's Hospital, Taizhou 317199, China
| | - Meina Yue
- Department of Clinical Laboratory, Hangzhou Children's Hospital, Hangzhou 310005, China
| | - Jinyue Wang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Weiwei Shen
- Taizhou Center for Disease Control and Prevention, Taizhou 318000, China
| | - Xinhua Qiang
- Department of Clinical Laboratory, The First People's Hospital of Huzhou, Huzhou 313000, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 314408, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou 310016, China.
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Pereira GDN, Seribelli AA, Campioni F, Gomes CN, Tiba-Casas MR, Medeiros MIC, Rodrigues DDP, Falcão JP. High levels of multidrug-resistant isolates of genetically similar Salmonella 1,4, [5],12:I:- from Brazil between 1983 and 2020. J Med Microbiol 2024; 73. [PMID: 38375878 DOI: 10.1099/jmm.0.001792] [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] [Indexed: 02/21/2024] Open
Abstract
Introduction. Salmonella 1,4, [5],12:i:- strains with different antimicrobial resistance profiles have been associated with foodborne disease outbreaks in several countries. In Brazil, S. 1,4, [5],12:i:- was identified as one of the most prevalent serovars in São Paulo State during 2004-2020.Gap Statement. However, few studies have characterized this serovar in Brazil.Aim. This study aimed to determine the antimicrobial resistance profiles of S. 1,4, [5],12:i:- strains isolated from different sources in Southeast Brazil and compare their genetic diversity.Methodology. We analysed 113 S. 1,4, [5],12:i:- strains isolated from humans (n=99), animals (n=7), food (n=5) and the environment (n=2) between 1983 and 2020. Susceptibility testing against 13 antimicrobials was performed using the disc diffusion method for all the strains. Plasmid resistance genes and mutations in the quinolone resistance-determining regions were identified in phenotypically fluoroquinolone-resistant strains. Molecular typing was performed using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) for all strains and multilocus sequence typing (MLST) for 40 selected strains.Results. Of the 113 strains, 54.87 % were resistant to at least one antimicrobial. The highest resistance rates were observed against ampicillin (51.33 %), nalidixic acid (39.82 %) and tetracycline (38.05 %). Additionally, 39 (34.51 %) strains were classified as multidrug-resistant (MDR). Nine fluoroquinolone-resistant strains exhibited the gyrA mutation (Ser96→Tyr96) and contained the qnrB gene. The 113 strains were grouped into two clusters using ERIC-PCR, and most of strains were present in one cluster, with a genetic similarity of ≥80 %. Finally, 40 strains were typed as ST19 using MLST.Conclusion. The prevalence of MDR strains is alarming because antimicrobial treatment against these strains may lead to therapeutic failure. Furthermore, the ERIC-PCR and MLST results suggested that most strains belonged to one main cluster. Thus, a prevalent subtype of Salmonella 1,4, [5],12:i:- strains has probably been circulating among different sources in São Paulo, Brazil, over decades.
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Affiliation(s)
- Giovana do Nascimento Pereira
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
| | - Amanda Aparecida Seribelli
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo (USP), Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Ribeirão Preto, SP, Brazil
| | - Fábio Campioni
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
- Universidade de São Paulo (USP), Instituto de Física de São Carlos, Departamento de Física e Ciência Interdisciplinar, São Carlos, SP, Brazil
| | - Carolina Nogueira Gomes
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
| | | | | | | | - Juliana Pfrimer Falcão
- Universidade de São Paulo (USP), Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Departamento de Análises Clínicas, Toxicológicas e Bromatológicas (DACTB), Ribeirão Preto, SP, Brazil
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Ayoola MB, Das AR, Krishnan BS, Smith DR, Nanduri B, Ramkumar M. Predicting Salmonella MIC and Deciphering Genomic Determinants of Antibiotic Resistance and Susceptibility. Microorganisms 2024; 12:134. [PMID: 38257961 PMCID: PMC10819212 DOI: 10.3390/microorganisms12010134] [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: 11/29/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
Salmonella spp., a leading cause of foodborne illness, is a formidable global menace due to escalating antimicrobial resistance (AMR). The evaluation of minimum inhibitory concentration (MIC) for antimicrobials is critical for characterizing AMR. The current whole genome sequencing (WGS)-based approaches for predicting MIC are hindered by both computational and feature identification constraints. We propose an innovative methodology called the "Genome Feature Extractor Pipeline" that integrates traditional machine learning (random forest, RF) with deep learning models (multilayer perceptron (MLP) and DeepLift) for WGS-based MIC prediction. We used a dataset from the National Antimicrobial Resistance Monitoring System (NARMS), comprising 4500 assembled genomes of nontyphoidal Salmonella, each annotated with MIC metadata for 15 antibiotics. Our pipeline involves the batch downloading of annotated genomes, the determination of feature importance using RF, Gini-index-based selection of crucial 10-mers, and their expansion to 20-mers. This is followed by an MLP network, with four hidden layers of 1024 neurons each, to predict MIC values. Using DeepLift, key 20-mers and associated genes influencing MIC are identified. The 10 most significant 20-mers for each antibiotic are listed, showcasing our ability to discern genomic features affecting Salmonella MIC prediction with enhanced precision. The methodology replaces binary indicators with k-mer counts, offering a more nuanced analysis. The combination of RF and MLP addresses the limitations of the existing WGS approach, providing a robust and efficient method for predicting MIC values in Salmonella that could potentially be applied to other pathogens.
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Affiliation(s)
- Moses B. Ayoola
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - Athish Ram Das
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - B. Santhana Krishnan
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - David R. Smith
- Department of Population Medicine, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA;
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA; (M.B.A.); (A.R.D.); (B.S.K.); (B.N.)
| | - Mahalingam Ramkumar
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS 39762, USA
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