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Di Cesare A, Sathicq MB, Sbaffi T, Sabatino R, Manca D, Breider F, Coudret S, Pinnell LJ, Turner JW, Corno G. Parity in bacterial communities and resistomes: Microplastic and natural organic particles in the Tyrrhenian Sea. MARINE POLLUTION BULLETIN 2024; 203:116495. [PMID: 38759465 DOI: 10.1016/j.marpolbul.2024.116495] [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: 09/28/2023] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/19/2024]
Abstract
Petroleum-based microplastic particles (MPs) are carriers of antimicrobial resistance genes (ARGs) in aquatic environments, influencing the selection and spread of antimicrobial resistance. This research characterized MP and natural organic particle (NOP) bacterial communities and resistomes in the Tyrrhenian Sea, a region impacted by plastic pollution and climate change. MP and NOP bacterial communities were similar but different from the free-living planktonic communities. Likewise, MP and NOP ARG abundances were similar but different (higher) from the planktonic communities. MP and NOP metagenome-assembled genomes contained ARGs associated with mobile genetic elements and exhibited co-occurrence with metal resistance genes. Overall, these findings show that MPs and NOPs harbor potential pathogenic and antimicrobial resistant bacteria, which can aid in the spread of antimicrobial resistance. Further, petroleum-based MPs do not represent novel ecological niches for allochthonous bacteria; rather, they synergize with NOPs, collectively facilitating the spread of antimicrobial resistance in marine ecosystems.
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Affiliation(s)
- Andrea Di Cesare
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Maria Belen Sathicq
- Instituto de Limnología "Dr. Raúl A. Ringuelet" (ILPLA) CONICET-UNLP, Bv. 120 y 62 n1437, La Plata, Buenos Aires, Argentina
| | - Tomasa Sbaffi
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Raffaella Sabatino
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Dario Manca
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy
| | - Florian Breider
- Ecole Polytechnique Fédérale de Lausanne EPFL, Central Environmental Laboratory, IIE, ENAC, Station 2, CH-1015 Lausanne, Switzerland
| | - Sylvain Coudret
- Ecole Polytechnique Fédérale de Lausanne EPFL, Central Environmental Laboratory, IIE, ENAC, Station 2, CH-1015 Lausanne, Switzerland
| | - Lee J Pinnell
- Veterinary Education, Research, and Outreach Program, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, Canyon, TX, USA
| | - Jeffrey W Turner
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, USA
| | - Gianluca Corno
- National Research Council of Italy - Water Research Institute (CNR-IRSA) Molecular Ecology Group (MEG), Verbania, Italy.
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Floris I, Vannuccini A, Ligotti C, Musolino N, Romano A, Viani A, Bianchi DM, Robetto S, Decastelli L. Detection and Characterization of Zoonotic Pathogens in Game Meat Hunted in Northwestern Italy. Animals (Basel) 2024; 14:562. [PMID: 38396530 PMCID: PMC10886018 DOI: 10.3390/ani14040562] [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: 12/15/2023] [Revised: 01/10/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Wildlife can represent a reservoir of zoonotic pathogens and a public health problem. In the present study, we investigated the spread of zoonotic pathogens (Salmonella spp., Yersinia enterocolitica, Listeria monocytogenes, Shiga-toxin-producing Escherichia coli (STEC), and hepatitis E virus (HEV)) considering the presence of virulence and antibiotic resistance genes in game meat from animals hunted in northwest Italy. During two hunting seasons (2020 to 2022), samples of liver and/or muscle tissue were collected from chamois (n = 48), roe deer (n = 26), deer (n = 39), and wild boar (n = 35). Conventional microbiology and biomolecular methods were used for the detection, isolation, and characterization of the investigated pathogens. Two L. monocytogenes serotype IIa strains were isolated from wild boar liver; both presented fosfomycin resistance gene and a total of 22 virulence genes were detected and specified in the text. Eight Y. enterocolitica biotype 1A strains were isolated from chamois (2), wild boar (5), and deer (1) liver samples; all showed streptogramin and beta-lactam resistance genes; the virulence genes found were myfA (8/8 strains), ymoA (8/8), invA (8/8), ystB (8/8), and ail (4/8). Our data underscore the potential role of wildlife as a carrier of zoonotic and antibiotic-resistant pathogens in northwest Italy and a food safety risk for game meat consumers.
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Affiliation(s)
- Irene Floris
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
| | - Andrea Vannuccini
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
- Posto di Controllo Frontaliero (PCF), Ponte Caracciolo MONTITAL, 16126 Genova, Italy
| | - Carmela Ligotti
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
| | - Noemi Musolino
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
| | - Angelo Romano
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
| | - Annalisa Viani
- National Reference Centre for Wild Animals Diseases (CeRMAS), SC Valle d’Aosta, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), 11020 Aosta, Italy; (A.V.); (S.R.)
| | - Daniela Manila Bianchi
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
| | - Serena Robetto
- National Reference Centre for Wild Animals Diseases (CeRMAS), SC Valle d’Aosta, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), 11020 Aosta, Italy; (A.V.); (S.R.)
- SS Patologie della Fauna Selvatica, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), 11020 Aosta, Italy
| | - Lucia Decastelli
- SC Sicurezza e Qualità degli Alimenti, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZSPLV), Via Bologna 148, 10154 Turin, Italy; (I.F.); (A.V.); (N.M.); (A.R.); (D.M.B.); (L.D.)
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Siddi G, Piras F, Meloni MP, Gymoese P, Torpdahl M, Fredriksson-Ahomaa M, Migoni M, Cabras D, Cuccu M, De Santis EPL, Scarano C. Hunted Wild Boars in Sardinia: Prevalence, Antimicrobial Resistance and Genomic Analysis of Salmonella and Yersinia enterocolitica. Foods 2023; 13:65. [PMID: 38201093 PMCID: PMC10778173 DOI: 10.3390/foods13010065] [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: 11/22/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
The objective of this investigation was to evaluate Salmonella and Yersinia enterocolitica prevalence in wild boars hunted in Sardinia and further characterize the isolates and analyse antimicrobial resistance (AMR) patterns. In order to assess slaughtering hygiene, an evaluation of carcasses microbial contamination was also carried out. Between 2020 and 2022, samples were collected from 66 wild boars hunted during two hunting seasons from the area of two provinces in northern and central Sardinia (Italy). Samples collected included colon content samples, mesenteric lymph nodes samples and carcass surface samples. Salmonella and Y. enterocolitica detection was conducted on each sample; also, on carcass surface samples, total aerobic mesophilic count and Enterobacteriaceae count were evaluated. On Salmonella and Y. enterocolitica isolates, antimicrobial susceptibility was tested and whole genome sequencing was applied. Salmonella was identified in the colon content samples of 3/66 (4.5%) wild boars; isolates were S. enterica subs. salamae, S. ser. elomrane and S. enterica subs. enterica. Y. enterocolitica was detected from 20/66 (30.3%) wild boars: in 18/66 (27.3%) colon contents, in 3/66 (4.5%) mesenteric lymph nodes and in 3/49 (6.1%) carcass surface samples. In all, 24 Y. enterocolitica isolates were analysed and 20 different sequence types were detected, with the most common being ST860. Regarding AMR, no resistance was detected in Salmonella isolates, while expected resistance towards β-lactams (blaA gene) and streptogramin (vatF gene) was observed in Y. enterocolitica isolates (91.7% and 4.2%, respectively). The low presence of AMR is probably due to the low anthropic impact in the wild areas. Regarding the surface contamination of carcasses, values (mean ± standard deviation log10 CFU/cm2) were 2.46 ± 0.97 for ACC and 1.07 ± 1.18 for Enterobacteriaceae. The results of our study confirm that wild boars can serve as reservoirs and spreaders of Salmonella and Y. enterocolitica; the finding of Y. enterocolitica presence on carcass surface highlights how meat may become superficially contaminated, especially considering that contamination is linked to the conditions related to the hunting, handling and processing of game animals.
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Affiliation(s)
- Giuliana Siddi
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Francesca Piras
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Maria Pina Meloni
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Pernille Gymoese
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (P.G.); (M.T.)
| | - Mia Torpdahl
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (P.G.); (M.T.)
| | - Maria Fredriksson-Ahomaa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, FI-00014 Helsinki, Finland;
| | - Mattia Migoni
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Daniela Cabras
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Mario Cuccu
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Enrico Pietro Luigi De Santis
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
| | - Christian Scarano
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100 Sassari, Italy; (G.S.); (M.P.M.); (M.M.); (D.C.); (M.C.); (E.P.L.D.S.); (C.S.)
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Huang S, Li Y, Hong C, Jin Y, Li S, Xu X, Xia Y, Zhang L, Lou Y, Guan W. Whole-genome sequencing-based analysis of antimicrobial resistance, virulence factors, and genetic diversity in Yersinia isolated in Wenzhou, China 2020. Mol Phylogenet Evol 2023; 188:107903. [PMID: 37574177 DOI: 10.1016/j.ympev.2023.107903] [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: 03/30/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
Yersinia spp. vary significantly in their ability to cause diseases that threaten public health. Their pathogenicity is frequently associated with increasing antimicrobial resistance (AMR) and various virulence factors. The aim of the study was to investigate the AMR genes, virulence factors, and genetic diversity of Yersinia strains isolated from meats and fish in Wenzhou in 2020 by using whole-genome sequencing (WGS). A total of 50 isolates were collected. The phylogenetic relationships among the Yersinia species were also analyzed using multilocus sequence typing (MLST), core genome multi-locus sequence typing (cgMLST), and single nucleotide polymorphism (SNP) analysis. According to the results, all the strains could be classified into five species, with most isolated from beef, followed by poultry, pork, and fish. AMR genes were identified in 23 strains. And the qnrD1 genes were all located in the Col3M plasmid. Virulence genes, such as yaxA, ystB, pla, and yplA, were also found in the 15 Y. enterocolitica strains. And this study also found the presence of icm/dot type IVB-related genes in one Yersinia massiliensis isolate. MLST analysis identified 43 sequence types (STs), 19 of which were newly detected in Yersinia. Moreover, cgMLST analysis revealed that no dense genotype clusters were formed (cgMLST 5341, 5344, 5346-5350, 5353-5390). Instead, the strains appeared to be dispersed over large distances, except when multiple isolates shared the same ST. Isolates Y4 and Y26 were closely related to strains originating from South Korea and Denmark. This study showed considerable diversity in Yersinia spp. isolated from local areas (Wenzhou City). The data generated in our study may enrich the molecular traceability database of Yersinia and provide a basis for the development of more effective antipathogen control strategies.
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Affiliation(s)
- Shaojie Huang
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Yi Li
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Chengji Hong
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yafang Jin
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Shengkai Li
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Xuelian Xu
- Yuhang Center for Disease Control and Prevention, Yuhang, China.
| | - Yanmei Xia
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Leyi Zhang
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China.
| | - Yongliang Lou
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Wanchun Guan
- Wenzhou Key Laboratory of Sanitary Microbiology, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
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Characterisation of Yersinia enterocolitica strains isolated from wildlife in the northwestern Italian Alps. J Vet Res 2022; 66:141-149. [PMID: 35892105 PMCID: PMC9281523 DOI: 10.2478/jvetres-2022-0021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 04/05/2022] [Indexed: 11/20/2022] Open
Abstract
Introduction Yersiniosis is a zoonosis causing gastroenteritis, diarrhoea, and occasionally reactive arthritis and septicaemia. Cases are often linked to meat consumption and the most common aetiological agent is the Gram-negative bacilliform Yersinia enterocolitica bacterium. The occurrence of Yersinia spp. among wild animals has mostly been studied in wild boar, but it has seldom been in other species. Material and Methods A total of 1,868 faecal samples from animals found dead or hunted were collected between 2015 and 2018 in the Valle d’Aosta region of the northwestern Italian Alps. Alpine ibex faecal samples were collected during a health monitoring program in 2018. Bacteria were isolated via PCR and confirmed as Y. enterocolitica biochemically. Strain antimicrobial susceptibility was tested by Kirby–Bauer disc diffusion, and the presence of virulence factors and antimicrobial resistance genes was investigated using whole-genome sequencing. Results Yersinia enterocolitica strains of biotype 1A were detected in six faecal samples from red deer (0.93%), roe deer (0.49%) and red foxes (0.7%). Strains found in beech martens (3.57%) and Alpine ibex (2.77%) belonged to biotypes 1B and 5, respectively and harboured the pYPTS01 plasmid that had only been detected in Y. pseudotuberculosis PB1/+. All the isolates were resistant to ampicillin and erythromycin. Conclusion The biovar 1A strains exhibited different virulence factors and behaved like non-pathogenic commensals. The strain from an Alpine ibex also harboured the self-transmissible pYE854 plasmid that can mobilise itself and the pYPTS01 plasmid to other strains. The beech marten could be considered a sentinel animal for Y. enterocolitica. Phenotypic resistance may account for the ability of all the strains to resist β-lactams.
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Comparative genomics and antibiotic resistance of Yersinia enterocolitica obtained from a pork production chain and human clinical cases in Brazil. Food Res Int 2022; 152:110917. [DOI: 10.1016/j.foodres.2021.110917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022]
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Terentjeva M, Ķibilds J, Meistere I, Gradovska S, Alksne L, Streikiša M, Ošmjana J, Valciņa O. Virulence Determinants and Genetic Diversity of Yersinia Species Isolated from Retail Meat. Pathogens 2021; 11:37. [PMID: 35055985 PMCID: PMC8778217 DOI: 10.3390/pathogens11010037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 11/16/2022] Open
Abstract
Yersinia enterocolitica is an important foodborne pathogen, and the determination of its virulence factors and genetic diversity within the food chain could help understand the epidemiology of yersiniosis. The aim of the present study was to detect the prevalence, and characterize the virulence determinants and genetic diversity, of Yersinia species isolated from meat. A total of 330 samples of retailed beef (n = 150) and pork (n = 180) in Latvia were investigated with culture and molecular methods. Whole genome sequencing (WGS) was applied for the detection of virulence and genetic diversity. The antimicrobial resistance of pathogenic Y. enterocolitica isolates was detected in accordance with EUCAST. Yersinia species were isolated from 24% (79/330) of meats, and the prevalence of Y. enterocolitica in pork (24%, 44/180) was significantly higher (p < 0.05) than in beef (13%, 19/150). Y. enterocolitica pathogenic bioserovars 2/O:9 and 4/O:3 were isolated from pork samples (3%, 6/180). Only resistance to ampicillin was confirmed in Y. enterocolitica 4/O:3 and 2/O:9 isolates, but not in other antimicrobials. Major virulence determinants, including ail, inv, virF, ystA and myfA, were confirmed with WGS in Y. enterocolitica 2/O:9 and 4/O:3. MLST typing revealed 15 STs (sequence types) of Y. enterocolitica with ST12 and ST18, which were associated with pathogenic bioserovars. For Y. enterocolitica 1A, Y. kristensenii, Y. intermedia and Y. frederiksenii, novel STs were registered (ST680-688). The presence of virulence genes and genetic characteristics of certain Y. enterocolitica STs confirm the common knowledge that pork could be an important source of pathogenic Yersinia.
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Affiliation(s)
- Margarita Terentjeva
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, LV-3004 Jelgava, Latvia
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Juris Ķibilds
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Irēna Meistere
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Silva Gradovska
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Laura Alksne
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Madara Streikiša
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Jevgēnija Ošmjana
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
| | - Olga Valciņa
- Institute of Food Safety, Animal Health and Environment BIOR, LV-1076 Riga, Latvia; (J.Ķ.); (I.M.); (S.G.); (L.A.); (M.S.); (J.O.); (O.V.)
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Pegoraro K, Sereno MJ, Viana C, Martins BTF, Yamatogi RS, Nero LA, Bersot LDS. Pathogenic potential and antibiotic resistance of Yersinia enterocolitica, a foodborne pathogen limited to swine tonsils in a pork production chain from Southern Brazil. Braz J Microbiol 2021; 52:2335-2342. [PMID: 34406639 PMCID: PMC8578270 DOI: 10.1007/s42770-021-00591-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022] Open
Abstract
In this study, we aimed to characterize the distribution of Yersinia enterocolitica in a pork production chain in Brazil, as well as the virulence profile and antibiotic resistance of the obtained isolates. Samples from 10 pig lots obtained from finishing farms (water, feed, and barn floors, n = 30), slaughterhouse (lairage floors, carcasses at four processing steps, tonsils, and mesenteric lymph nodes, n = 610), and processing (end cuts, processing environment, n = 160) were obtained in Paraná state, Brazil, and subjected to Y. enterocolitica detection by ISO 10,273. The obtained isolates were identified based on biochemical and molecular features (16 s rRNA, inv, bioserotyping) and subjected to PCR assays to detect virulence (ail, ystA, ystB, virF, myfA, fepA, fepD, fes, tccC, ymoA, hreP, and sat) and multidrug resistance-related genes (emrD, yfhD, and marC). Also, isolates were subjected to disk diffusion test to characterize their resistance against 17 antibiotics from 11 classes and to pulsed field gel electrophoresis (PFGE) after XbaI macro-restriction. Y. enterocolitica was detected in a single sample (tonsil), and the obtained three isolates were characterized as serotype O:3, harboring ail, ystA, virF, myfA, tccC, ymoA, hreP, emrD, yfhD, and marC, and resistant to all tested antibiotics. The three isolates presented identical macro-restriction profiles by PFGE, also identical to isolates obtained from Minas Gerais, other Brazilian state; one selected isolate was identified as biotype 4. Despite the low occurrence of Y. enterocolitica in the studied pork production, the virulence potential and the antibiotic resistance profiles of the isolates demonstrated their pathogenic potential, and the macro-restriction profiles indicate strains descending from a common subtype in the pork production chain of two Brazilian States.
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Affiliation(s)
- Kadigia Pegoraro
- LACOMA, Laboratório de Inspeção e Controle de Qualidade de Água e Alimentos, Universidade Federal do Paraná, Departamento de Ciências Veterinárias, PR, 85950 000, Palotina, Brazil
| | - Mallu Jagnow Sereno
- LACOMA, Laboratório de Inspeção e Controle de Qualidade de Água e Alimentos, Universidade Federal do Paraná, Departamento de Ciências Veterinárias, PR, 85950 000, Palotina, Brazil
- InsPOA, Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Viçosa, MG, 36570 900, Brazil
| | - Cibeli Viana
- LACOMA, Laboratório de Inspeção e Controle de Qualidade de Água e Alimentos, Universidade Federal do Paraná, Departamento de Ciências Veterinárias, PR, 85950 000, Palotina, Brazil
- InsPOA, Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Viçosa, MG, 36570 900, Brazil
| | - Bruna Torres Furtado Martins
- InsPOA, Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Viçosa, MG, 36570 900, Brazil
| | - Ricardo Seiti Yamatogi
- InsPOA, Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Viçosa, MG, 36570 900, Brazil
| | - Luís Augusto Nero
- InsPOA, Laboratório de Inspeção de Produtos de Origem Animal, Universidade Federal de Viçosa, Departamento de Veterinária, Viçosa, MG, 36570 900, Brazil.
| | - Luciano Dos Santos Bersot
- LACOMA, Laboratório de Inspeção e Controle de Qualidade de Água e Alimentos, Universidade Federal do Paraná, Departamento de Ciências Veterinárias, PR, 85950 000, Palotina, Brazil.
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9
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Karlsson PA, Tano E, Jernberg C, Hickman RA, Guy L, Järhult JD, Wang H. Molecular Characterization of Multidrug-Resistant Yersinia enterocolitica From Foodborne Outbreaks in Sweden. Front Microbiol 2021; 12:664665. [PMID: 34054769 PMCID: PMC8155512 DOI: 10.3389/fmicb.2021.664665] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide. In the spring of 2019, the Swedish Public Health Agency and Statens Serum Institut in Denmark independently identified an outbreak caused by Yersinia enterocolitica 4/O:3 that after sequence comparison turned out to be a cross-border outbreak. A trace-back investigation suggested shipments of fresh prewashed spinach from Italy as a common source for the outbreak. Here, we determined the genome sequences of five Y. enterocolitica clinical isolates during the Swedish outbreak using a combination of Illumina HiSeq short-read and Nanopore Technologies’ MinION long-read whole-genome sequencing. WGS results showed that all clinical strains have a fully assembled chromosome of approximately 4.6 Mbp in size and a 72-kbp virulence plasmid; one of the strains was carrying an additional 5.7-kbp plasmid, pYE-tet. All strains showed a high pathogen probability score (87.5%) with associated genes for virulence, all of which are closely related to an earlier clinical strain Y11 from Germany. In addition, we identified a chromosomally encoded multidrug-resistance cassette carrying resistance genes against chloramphenicol (catA1), streptomycin (aadA1), sulfonamides (sul1), and a mercury resistance module. This chromosomally encoded Tn2670 transposon has previously been reported associated with IncFII plasmids in Enterobacteriaceae: a Shigella flexneri clinical isolate from Japan in 1950s, a Klebsiella pneumoniae outbreak from Australia in 1997, and Salmonella enterica serovar Typhimurium. Interestingly, we identified an additional 5.7-kbp plasmid with tetB (encoding an ABC transporter), Rep, and its own ORI and ORIt sites, sharing high homology with small tetB-Rep plasmids from Pasteurellaceae. This is the first time that Tn2670 and Pasteurellaceae plasmids have been reported in Y. enterocolitica. Taken together, our study showed that the Swedish Y. enterocolitica outbreak strains acquired multi-antibiotic and metal-resistance genes through horizontal gene transfer, suggesting a potential reservoir of intraspecies dissemination of multidrug-resistance genes among foodborne pathogens. This study also highlights the concern of food-chain contamination of prewashed vegetables as a perpetual hazard against public health.
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Affiliation(s)
- Philip A Karlsson
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Eva Tano
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | | | - Rachel A Hickman
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Lionel Guy
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden.,Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Helen Wang
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, Uppsala, Sweden
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Tekedar HC, Arick MA, Hsu CY, Thrash A, Blom J, Lawrence ML, Abdelhamed H. Identification of Antimicrobial Resistance Determinants in Aeromonas veronii Strain MS-17-88 Recovered From Channel Catfish ( Ictalurus punctatus). Front Cell Infect Microbiol 2020; 10:348. [PMID: 32766165 PMCID: PMC7379393 DOI: 10.3389/fcimb.2020.00348] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Aeromonas veronii is a Gram-negative species ubiquitous in different aquatic environments and capable of causing a variety of diseases to a broad host range. Aeromonas species have the capability to carry and acquire antimicrobial resistance (AMR) elements, and currently multi-drug resistant (MDR) Aeromonas isolates are commonly found across the world. A. veronii strain MS-17-88 is a MDR strain isolated from catfish in the southeastern United States. The present study was undertaken to uncover the mechanism of resistance in MDR A. veronii strain MS-17-88 through the detection of genomic features. To achieve this, genomic DNA was extracted, sequenced, and assembled. The A. veronii strain MS-17-88 genome comprised 5,178,226-bp with 58.6% G+C, and it encoded several AMR elements, including imiS, ampS, mcr-7.1, mcr-3, catB2, catB7, catB1, floR, vat(F), tet(34), tet(35), tet(E), dfrA3, and tetR. The phylogeny and resistance profile of a large collection of A. veronii strains, including MS-17-88, were evaluated. Phylogenetic analysis showed a close relationship between MS-17-88 and strain Ae5 isolated from fish in China and ARB3 strain isolated from pond water in Japan, indicating a common ancestor of these strains. Analysis of phage elements revealed 58 intact, 63 incomplete, and 15 questionable phage elements among the 53 A. veronii genomes. The average phage element number is 2.56 per genome, and strain MS-17-88 is one of two strains having the maximum number of identified prophage elements (6 elements each). The profile of resistance against various antibiotics across the 53 A. veronii genomes revealed the presence of tet(34), mcr-7.1, mcr-3, and dfrA3 in all genomes (100%). By comparison, sul1 and sul2 were detected in 7.5% and 1.8% of A. veronii genomes. Nearly 77% of strains carried tet(E), and 7.5% of strains carried floR. This result suggested a low abundance and prevalence of sulfonamide and florfenicol resistance genes compared with tetracycline resistance among A. veronii strains. Overall, the present study provides insights into the resistance patterns among 53 A. veronii genomes, which can inform therapeutic options for fish affected by A. veronii.
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Affiliation(s)
- Hasan C. Tekedar
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Mark A. Arick
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Adam Thrash
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Jochen Blom
- Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Mark L. Lawrence
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Hossam Abdelhamed
- College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
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11
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 PMCID: PMC6283892 DOI: 10.3389/fmicb.2018.02928] [Citation(s) in RCA: 418] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 11/13/2022] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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12
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Antonelli A, D’Andrea MM, Brenciani A, Galeotti CL, Morroni G, Pollini S, Varaldo PE, Rossolini GM. Characterization of poxtA, a novel phenicol–oxazolidinone–tetracycline resistance gene from an MRSA of clinical origin. J Antimicrob Chemother 2018; 73:1763-1769. [DOI: 10.1093/jac/dky088] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/23/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | - Andrea Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Cesira L Galeotti
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Research Centre, GlaxoSmithKline Vaccines S.r.l, Siena, Italy
| | - Gianluca Morroni
- Infectious Diseases Clinic, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Pietro Emanuele Varaldo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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13
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Peterson E, Kaur P. Antibiotic Resistance Mechanisms in Bacteria: Relationships Between Resistance Determinants of Antibiotic Producers, Environmental Bacteria, and Clinical Pathogens. Front Microbiol 2018; 9:2928. [PMID: 30555448 DOI: 10.3389/fmicb.2018.02928/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/14/2018] [Indexed: 05/20/2023] Open
Abstract
Emergence of antibiotic resistant pathogenic bacteria poses a serious public health challenge worldwide. However, antibiotic resistance genes are not confined to the clinic; instead they are widely prevalent in different bacterial populations in the environment. Therefore, to understand development of antibiotic resistance in pathogens, we need to consider important reservoirs of resistance genes, which may include determinants that confer self-resistance in antibiotic producing soil bacteria and genes encoding intrinsic resistance mechanisms present in all or most non-producer environmental bacteria. While the presence of resistance determinants in soil and environmental bacteria does not pose a threat to human health, their mobilization to new hosts and their expression under different contexts, for example their transfer to plasmids and integrons in pathogenic bacteria, can translate into a problem of huge proportions, as discussed in this review. Selective pressure brought about by human activities further results in enrichment of such determinants in bacterial populations. Thus, there is an urgent need to understand distribution of resistance determinants in bacterial populations, elucidate resistance mechanisms, and determine environmental factors that promote their dissemination. This comprehensive review describes the major known self-resistance mechanisms found in producer soil bacteria of the genus Streptomyces and explores the relationships between resistance determinants found in producer soil bacteria, non-producer environmental bacteria, and clinical isolates. Specific examples highlighting potential pathways by which pathogenic clinical isolates might acquire these resistance determinants from soil and environmental bacteria are also discussed. Overall, this article provides a conceptual framework for understanding the complexity of the problem of emergence of antibiotic resistance in the clinic. Availability of such knowledge will allow researchers to build models for dissemination of resistance genes and for developing interventions to prevent recruitment of additional or novel genes into pathogens.
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Affiliation(s)
- Elizabeth Peterson
- Department of Biology, Georgia State University, Atlanta, GA, United States
| | - Parjit Kaur
- Department of Biology, Georgia State University, Atlanta, GA, United States
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14
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Schwarz S, Shen J, Kadlec K, Wang Y, Brenner Michael G, Feßler AT, Vester B. Lincosamides, Streptogramins, Phenicols, and Pleuromutilins: Mode of Action and Mechanisms of Resistance. Cold Spring Harb Perspect Med 2016; 6:a027037. [PMID: 27549310 PMCID: PMC5088508 DOI: 10.1101/cshperspect.a027037] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Lincosamides, streptogramins, phenicols, and pleuromutilins (LSPPs) represent four structurally different classes of antimicrobial agents that inhibit bacterial protein synthesis by binding to particular sites on the 50S ribosomal subunit of the ribosomes. Members of all four classes are used for different purposes in human and veterinary medicine in various countries worldwide. Bacteria have developed ways and means to escape the inhibitory effects of LSPP antimicrobial agents by enzymatic inactivation, active export, or modification of the target sites of the agents. This review provides a comprehensive overview of the mode of action of LSPP antimicrobial agents as well as of the mutations and resistance genes known to confer resistance to these agents in various bacteria of human and animal origin.
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Affiliation(s)
- Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, P.R. China
| | - Geovana Brenner Michael
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), 31535 Neustadt-Mariensee, Germany
| | - Birte Vester
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
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15
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Ye Q, Wu Q, Hu H, Zhang J, Huang H. Prevalence and characterization of Yersinia enterocolitica isolated from retail foods in China. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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17
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Penders J, Stobberingh EE, Savelkoul PHM, Wolffs PFG. The human microbiome as a reservoir of antimicrobial resistance. Front Microbiol 2013; 4:87. [PMID: 23616784 PMCID: PMC3627978 DOI: 10.3389/fmicb.2013.00087] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/27/2013] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is amongst the most densely populated microbial ecosystem on earth. While the microbiome exerts numerous health beneficial functions, the high density of micro-organisms within this ecosystem also facilitates horizontal transfer of antimicrobial resistance (AMR) genes to potential pathogenic bacteria. Over the past decades antibiotic susceptibility testing of specific indicator bacteria from the microbiome, such as Escherichia coli, has been the method of choice in most studies. These studies have greatly enlarged our understanding on the prevalence and distribution of AMR and associated risk factors. Recent studies using (functional) metagenomics, however, highlighted the unappreciated diversity of AMR genes in the human microbiome and identified genes that had not been described previously. Next to metagenomics, more targeted approaches such as polymerase chain reaction for detection and quantification of AMR genes within a population are promising, in particular for large-scale epidemiological screening. Here we present an overview of the indigenous microbiota as a reservoir of AMR genes, the current knowledge on this “resistome” and the recent and upcoming advances in the molecular diagnostic approaches to unravel this reservoir.
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Affiliation(s)
- John Penders
- Department of Medical Microbiology, Maastricht University Medical Centre+ Maastricht, Netherlands
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18
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Characterization of two newly identified genes, vgaD and vatH, [corrected] conferring resistance to streptogramin A in Enterococcus faecium. Antimicrob Agents Chemother 2010; 54:4744-9. [PMID: 20713681 DOI: 10.1128/aac.00798-09] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized two new streptogramin A resistance genes from quinupristin-dalfopristin-resistant Enterococcus faecium JS79, which was selected from 79 E. faecium isolates lacking known genes encoding streptogramin A acetyltransferase. A 5,650-bp fragment of HindIII-digested plasmid DNA from E. faecium JS79 was cloned and sequenced. The fragment contained two open reading frames carrying resistance genes related to streptogramin A, namely, genes for an acetyltransferase and an ATP efflux pump. The first open reading frame comprised 648 bp encoding 216 amino acids with a predicted left-handed parallel β-helix domain structure; this new gene was designated vatH. [corrected] The second open reading frame consisted of 1,575 bp encoding 525 amino acids with two predicted ATPase binding cassette transporters comprised of Walker A, Walker B, and LSSG motifs; this gene was designated vgaD. vgaD is located 65 bp upstream from vatH, [corrected] was detected together with vatH [corrected] in 12 of 179 quinupristin-dalfopristin-resistant E. faecium isolates, and was located on the same plasmid. Also, the 5.6-kb HindIII-digested fragment which was observed in JS79 was detected in nine vgaD- and vatH-containing [corrected] E. faecium isolates by Southern hybridization. Therefore, it was expected that these two genes were strongly correlated with each other and that they may be composed of a transposon. Importantly, vgaD is the first identified ABC transporter conferring resistance to streptogramin A in E. faecium. Pulsed-field gel electrophoresis patterns and sequence types of vgaD- and vatH-containing [corrected] E. faecium isolates differed for isolates from humans and nonhumans.
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19
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Gillespie JJ, Williams K, Shukla M, Snyder EE, Nordberg EK, Ceraul SM, Dharmanolla C, Rainey D, Soneja J, Shallom JM, Vishnubhat ND, Wattam R, Purkayastha A, Czar M, Crasta O, Setubal JC, Azad AF, Sobral BS. Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life. PLoS One 2008; 3:e2018. [PMID: 19194535 PMCID: PMC2635572 DOI: 10.1371/journal.pone.0002018] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 03/07/2008] [Indexed: 11/19/2022] Open
Abstract
Background Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular α-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs). Methodology/Principal Findings We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (∼1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions. Conclusion/Significance Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets.
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Affiliation(s)
- Joseph J Gillespie
- Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA, USA.
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20
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Roberts MC. Update on macrolide-lincosamide-streptogramin, ketolide, and oxazolidinone resistance genes. FEMS Microbiol Lett 2008; 282:147-59. [PMID: 18399991 DOI: 10.1111/j.1574-6968.2008.01145.x] [Citation(s) in RCA: 256] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
This Minireview summarizes the changes in the field of bacterial resistance to macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone (MLSKO) antibiotics since the nomenclature review in 1999. A total of 66 genes conferring resistance to this group of antibiotics has now been identified and includes 13 new rRNA methylase genes, four ATP-binding transporter genes coding for efflux proteins, and five new inactivating enzymes. During this same time period, 73 new genera carrying known rRNA methylase genes and 87 new genera carrying known efflux and/or inactivating genes have been recognized. The number of bacteria with mutations in the genes for 23S rRNA, L4 and L22 ribosomal proteins, resulting in reduced susceptibility to some members of the group of MLSKO antibiotics has also increased and now includes nine different Gram-positive and 10 different Gram-negative genera. New conjugative transposons carrying different MLSKO genes along with an increased number of antibiotics and/or heavy metal resistance genes have been identified. These mobile elements may play a role in the continued spread of the MLSKO resistance genes into new species, genera, and ecosystems.
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Affiliation(s)
- Marilyn C Roberts
- Department of Environmental & Occupational Health Sciences, School of Public Health and Community Medicine, University of Washington, Seattle, WA, USA.
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21
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D'Costa VM, Griffiths E, Wright GD. Expanding the soil antibiotic resistome: exploring environmental diversity. Curr Opin Microbiol 2007; 10:481-9. [PMID: 17951101 DOI: 10.1016/j.mib.2007.08.009] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 08/20/2007] [Accepted: 08/29/2007] [Indexed: 10/22/2022]
Abstract
Antibiotic resistance has largely been studied in the context of failure of the drugs in clinical settings. There is now growing evidence that bacteria that live in the environment (e.g. the soil) are multi-drug-resistant. Recent functional screens and the growing accumulation of metagenomic databases are revealing an unexpected density of resistance genes in the environment: the antibiotic resistome. This challenges our current understanding of antibiotic resistance and provides both barriers and opportunities for antimicrobial drug discovery.
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Affiliation(s)
- Vanessa M D'Costa
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main St W, Hamilton, Ontario, Canada L8N 3Z5
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Abstract
Over the millennia, microorganisms have evolved evasion strategies to overcome a myriad of chemical and environmental challenges, including antimicrobial drugs. Even before the first clinical use of antibiotics more than 60 years ago, resistant organisms had been isolated. Moreover, the potential problem of the widespread distribution of antibiotic resistant bacteria was recognized by scientists and healthcare specialists from the initial use of these drugs. Why is resistance inevitable and where does it come from? Understanding the molecular diversity that underlies resistance will inform our use of these drugs and guide efforts to develop new efficacious antibiotics.
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Affiliation(s)
- Gerard D Wright
- Antimicrobial Research Centre, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1200 Main Street West Hamilton, Ontario, L8N 3Z5, Canada.
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23
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Cassone M, D'Andrea MM, Iannelli F, Oggioni MR, Rossolini GM, Pozzi G. DNA microarray for detection of macrolide resistance genes. Antimicrob Agents Chemother 2006; 50:2038-41. [PMID: 16723563 PMCID: PMC1479117 DOI: 10.1128/aac.01574-05] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A DNA microarray was developed to detect bacterial genes conferring resistance to macrolides and related antibiotics. A database containing 65 nonredundant genes selected from publicly available DNA sequences was constructed and used to design 100 oligonucleotide probes that could specifically detect and discriminate all 65 genes. Probes were spotted on a glass slide, and the array was reacted with DNA templates extracted from 20 reference strains of eight different bacterial species (Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, Enterococcus faecium, Staphylococcus aureus, Staphylococcus haemolyticus, Escherichia coli, and Bacteroides fragilis) known to harbor 29 different macrolide resistance genes. Hybridization results showed that probes reacted with, and only with, the expected DNA templates and allowed discovery of three unexpected genes, including msr(SA) in B. fragilis, an efflux gene that has not yet been described for gram-negative bacteria.
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Affiliation(s)
- Marco Cassone
- LAMMB, Università di Siena, Policlinico Le Scotte/V Lotto, Italy
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24
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Roberts MC. Resistance to macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone antibiotics. Mol Biotechnol 2005; 28:47-62. [PMID: 15456963 DOI: 10.1385/mb:28:1:47] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Macrolides have enjoyed a resurgence as new derivatives and related compounds have come to market. These newer compounds have become important in the treatment of community-acquired pneumoniae and nontuberculosis-Mycobacterium diseases. In this review, the bacterial mechanisms of resistance to the macrolide, lincosamide, streptogramin, ketolide, and oxazolidinone antibiotics, the distribution of the various acquired genes that confer resistance, as well as mutations that have been identified in clinical and laboratory strains are examined.
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Affiliation(s)
- Marilyn C Roberts
- Department of Pathobiology, Box 357238, School of Public Health and Community Medicine, University of Washington, Seattle, WA 98195, USA.
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de Benito I, Cano ME, Agüero J, Lobo JMG. A polymorphic tandem repeat potentially useful for typing in the chromosome of Yersinia enterocolitica. Microbiology (Reading) 2004; 150:199-204. [PMID: 14702413 DOI: 10.1099/mic.0.26642-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hexanucleotide CCAGCA was found repeated 15 times in tandem on the 5' side of the virginiamycin acetyl transferase gene of Yersinia enterocolitica strain Y56. The corresponding region was analysed by PCR from 54 clinical strains belonging to the same biotype and serotype, and others from this laboratory collection belonging to different biotypes and serotypes. Each strain produced a single amplification product whose size was variable among strains, revealing that the locus was polymorphic. Nucleotide sequence determination of selected PCR products showed that the polymorphism was due to the precise expansion or reduction in the number of hexanucleotide repeats. Analysis of this locus in a few strains showing the same PFGE pattern showed that it was also polymorphic. These results suggest that this method could be valuable to increase the discriminatory power of current Y. enterocolitica typing schemes.
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Affiliation(s)
- Inés de Benito
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Avenida de Valdecilla s/n, 39008-Santander, Spain
| | - María Eliecer Cano
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Avenida de Valdecilla s/n, 39008-Santander, Spain
| | - Jesús Agüero
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Centro Asociado al CIB, CSIC, Cardenal Herrera Oria s/n, 39011, Santander, Spain
- Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Avenida de Valdecilla s/n, 39008-Santander, Spain
| | - Juan M García Lobo
- Departamento de Biología Molecular, Facultad de Medicina, Universidad de Cantabria, Centro Asociado al CIB, CSIC, Cardenal Herrera Oria s/n, 39011, Santander, Spain
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Golubov A, Heesemann J, Rakin A. Uncovering genomic differences in human pathogenic Yersinia enterocolitica. FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY 2003; 38:107-11. [PMID: 13129644 DOI: 10.1016/s0928-8244(03)00182-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To map out genomic differences between highly pathogenic Yersinia enterocolitica WA-314C biogroup 1B, serotype O:8 strain and low-pathogenic Y. enterocolitica Y-108C biogroup 4, serotype O:3 strain we have applied a method of suppression subtractive hybridization (SSH). In total, 428 WA-314-specific and 83 Y-108-specific sequences were uncovered by SSH. Among them were DNA fragments with similarity to known genes from several groups: (1) genes involved in O-antigen biosynthesis, (2) host-specific restriction-modification systems, (3) systems of iron and heme acquisition and storage, (4) flagellar biogenesis genes, (5) putative virulence factors, (6) drug resistance genes, and (7) mobile elements. Mapped out genomic differences may be applied in identification and development of novel therapeutic strategies for the treatment of enteropathogenic Yersinia.
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Affiliation(s)
- Andrey Golubov
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Pettenkofer Str. 9a, 80336 Munich, Germany
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Werner G, Klare I, Witte W. Molecular analysis of streptogramin resistance in enterococci. Int J Med Microbiol 2002; 292:81-94. [PMID: 12195739 DOI: 10.1078/1438-4221-00194] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The new semi-synthetic streptogramin antibiotic combination quinupristin/dalfopristin (Synercid) is a promising alternative for a treatment of infections with multiple resistant gram-positive pathogens, e.g. glycopeptide- and multi-resistant Enterococcus faecium. Streptogramins consist of two unrelated compounds, a streptogramin A and B, which act synergistically when given in combination. Mechanisms conferring resistance against both components are essential for resistance against the combination in E. faecium. In this species resistance to streptogramin A compounds is mediated via related acetyltransferases VatD and VatE. Resistance against streptogramins B is either encoded by the widespread ermB gene cluster conferring resistance to macrolide-lincosamide-streptogramin B antibiotics or via expression of the vgbA gene, which encodes a staphylococcal-type lactonase. E. faecalis is intrinsically resistant to streptogramins. Due to a wide use of streptogramins (virginiamycins S/M) in commercial animal farming a reservoir of streptogramin-resistant E. faecium isolates had already been selected. Determinants for streptogramin resistance are localized on plasmids that can be transferred into an E. faecium recipient both in vitro in filter-matings and in vivo in the digestive tracts of rats. Hybridization and sequencing experiments revealed a linkage of resistance determinants for streptogramins A and B on definite plasmid fragments.
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Affiliation(s)
- Guido Werner
- Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855 Wernigerode, Germany.
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Roberts MC. Resistance to tetracycline, macrolide-lincosamide-streptogramin, trimethoprim, and sulfonamide drug classes. Mol Biotechnol 2002; 20:261-83. [PMID: 11936257 DOI: 10.1385/mb:20:3:261] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The discovery and use of antimicrobial agents in the last 50 yr has been one of medicine's greatest achievements. These agents have reduced morbidity and mortality of humans and animals and have directly contributed to human's increased life span. However, bacteria are becoming increasingly resistant to these agents by mutations, which alter existing bacterial proteins, and/or acquisition of new genes, which provide new proteins. The latter are often associated with mobile elements that can be exchanged quickly across bacterial populations and may carry multiple antibiotic genes for resistance. In some case, virulence factors are also found on these same mobile elements. There is mounting evidence that antimicrobial use in agriculture, both plant and animal, and for environmental purposes does influence the antimicrobial resistant development in bacteria important in humans and in reverse. In this article, we will examine the genes which confer resistance to tetracycline, macrolide-lincosamide-streptogramin (MLS), trimethoprim, and sulfonamide.
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Affiliation(s)
- Marilyn C Roberts
- Department of Pathobiology, School of Public Health and Community Medicine, University of Washington, Seattle 98195, USA.
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Affiliation(s)
- Jesús Oteo
- Servicio de Microbiología, Hospital de Móstoles, Móstoles, Madrid, Spain.
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