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Díaz-Jiménez D, García-Meniño I, Fernández J, García V, Mora A. Chicken and turkey meat: Consumer exposure to multidrug-resistant Enterobacteriaceae including mcr-carriers, uropathogenic E. coli and high-risk lineages such as ST131. Int J Food Microbiol 2020; 331:108750. [PMID: 32559710 DOI: 10.1016/j.ijfoodmicro.2020.108750] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/10/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
For the first time, this study evaluates consumer exposure via poultry meat to Enterobacteriaceae with capacity to develop severe extraintestinal infections by either bacterial virulence and/or antibiotic resistance traits. The characterization of 256 isolates and the assessment of five parameters, showed that 96 of 100 poultry meat samples from supermarkets of northwest Spain posed ≥ one potential risk: i) 96% carried Enterobacteriaceae resistant to antimicrobials of categories A (64% to monobactams) or B (95% to cephalosporins 3rd and 4rd- generation, quinolones and/or polymixins) of the new categorization of EMA. ii) More than one extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae species were recovered from 28% of poultry meat. iii) High-risk lineages of E. coli, including multidrug-resistant ST131-H22, were present in 62% of samples. iv) E. coli recovered from 25% of samples conformed the ExPEC status. v) E. coli from 17% of samples satisfied the UPEC status. Of note, the recovery from different samples of two E. coli CC10-A (CH11-54) carrying mcr-1.1-bearing IncX4 plasmids, and four E. coli CC10-A (eae-beta1) of the hybrid pathotype aEPEC/ExPEC. (ESBL)-producing K. pneumoniae were isolated from 27% of samples. In summary, poultry meat microbiota is a source of genetically diverse Enterobacteriaceae, resistant to relevant antimicrobials and potentially pathogenic for consumers.
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Affiliation(s)
- Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA). Instituto de Investigación del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain.; Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology, University of Copenhagen, København, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain..
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Rodrigues GL, Panzenhagen P, Ferrari RG, Paschoalin VMF, Conte-Junior CA. Antimicrobial Resistance in Nontyphoidal Salmonella Isolates from Human and Swine Sources in Brazil: A Systematic Review of the Past Three Decades. Microb Drug Resist 2020; 26:1260-1270. [PMID: 32412862 DOI: 10.1089/mdr.2019.0475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Salmonella is the leading cause of foodborne illnesses worldwide. The widespread use of antimicrobials as prophylactic, therapeutic, and growth promoters in both livestock and human medicine has resulted in selective pressure regarding antimicrobial-resistant (AMR) bacteria. This systematic review summarizes phenotypic antimicrobial resistance profiles in Salmonella isolates from human and swine sources between 1990 and 2018 in Brazil. The 20 studies that matched the eligibility criteria-isolates from pigs and humans from Brazil, between 1990 and 2016, containing information on the number of Salmonella isolates, and applying the disk diffusion susceptibility method-were included. During the assessed period, Salmonella strains isolated from swine sources displayed the highest resistance rates for tetracycline (20.3%) and sulfonamides (17.4%). In contrast, human isolates displayed the highest resistance rates against ampicillin (19.8%) and tetracycline (17%). Salmonella Typhimurium was the most frequent AMR isolate from both swine and human sources, corresponding to 67% of all isolates. From 2001 to 2005, tetracycline and ampicillin were the top antimicrobial resistance compounds, and the most frequently detected in swine and human sources, respectively. A total of 63 and 58 multiple drug resistance profiles were identified in swine and human isolates, respectively. Antimicrobial resistance has decreased throughout the 1990-2016 period, except for gentamicin and nalidixic acid in swine and human isolates, respectively. The results indicate that Salmonella isolated from human and swine display resistance against clinically important antimicrobials, indicating that swine are possibly one of the main vectors for spreading human salmonellosis in Brazil.
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Affiliation(s)
- Grazielle Lima Rodrigues
- Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Center for Food Analysis, Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, Brazil
| | - Pedro Panzenhagen
- Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Center for Food Analysis, Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, Brazil
| | - Rafaela Gomes Ferrari
- Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Center for Food Analysis, Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, Brazil
| | | | - Carlos Adam Conte-Junior
- Institute of Chemistry, Federal University of Rio de Janeiro, Cidade Universitária, Rio de Janeiro, Brazil.,Center for Food Analysis, Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, Brazil.,Faculty of Veterinary Medicine, Analytical and Molecular Laboratory Center, Fluminense Federal University, Niterói, Brazil.,National Institute of Health Quality Control, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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53
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Díaz-Jiménez D, García-Meniño I, Herrera A, García V, López-Beceiro AM, Alonso MP, Blanco J, Mora A. Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples. Antibiotics (Basel) 2020; 9:antibiotics9040192. [PMID: 32316613 PMCID: PMC7235894 DOI: 10.3390/antibiotics9040192] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/20/2022] Open
Abstract
Different surveillance studies (2005–2015) in northwest Spain revealed the presence of eae-positive isolates of Escherichia coli O153:H10 in meat for human consumption, poultry farm, wildlife and human diarrheagenic samples. The aim of this study was to explore the genetic and genomic relatedness between human and animal/meat isolates, as well as the mechanism of its persistence. We also wanted to know whether it was a geographically restricted lineage, or whether it was also reported elsewhere. Conventional typing showed that 32 isolates were O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1. Amongst these, 21 were CTX-M-32 or SHV-12 producers. The PFGE XbaI-macrorestriction comparison showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like plasmids. The core genome investigation based on the cgMLST scheme from EnteroBase proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of the clonal group O153:H10-A-ST10 (CH11-54) is circulating in our region within different hosts, including wildlife. It seems implicated in human diarrhea via meat transmission, and in the spreading of ESBL genes (mainly of CTX-M-32 type). We found genomic evidence of a related hybrid aEPEC/ExPEC in at least one other country.
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Affiliation(s)
- Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago, Spain
| | - Alexandra Herrera
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago, Spain
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Ana María López-Beceiro
- Departamento de Anatomía, Produción Animal e Ciencias Clínicas Veterinarias, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - María Pilar Alonso
- Unidade de Microbioloxía, Hospital Universitario Lucus Augusti (HULA), 27003 Lugo, Spain;
| | - Jorge Blanco
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain; (D.D.-J.); (I.G.-M.); (A.H.); (V.G.); (J.B.)
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago, Spain
- Correspondence: ; Tel.: +34-982822110
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Egorova SA, Kaftyreva LA, Pomazanov VV. [Current trends in the development of resistance to clinically significant antibiotics in Salmonella (review of literature).]. Klin Lab Diagn 2020; 65:308-315. [PMID: 32298548 DOI: 10.18821/0869-2084-2020-65-5-308-315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 11/17/2022]
Abstract
Salmonella is one of the leading bacterial pathogens of acute diarrhea as well as foodborne outbreaks. Salmonellosis can occur as gastroenteritis with the development of complications and generalization of infection, also the extra intestinal diseases that require antibiotic therapy are often registered. Currently, the effectiveness of many antibiotics is reduced due to the development of resistance in Salmonella. National Salmonella surveillance systems monitor Salmonella resistance to «critically important for medicine» antibiotics (extended-spectrum cephalosporins and fluoroquinolones), as well as multidrug resistance. Quinoloneresistant Salmonella is considered as a high-priority resitant pathogen by the World Health Organization. The article describes the current situation on salmonellosis in the world. Foreign and Russian current data about the leading Salmonella serotypes in different regions of the world are presented. The prevalence of clinically significant resistance depending of the Salmonella serotypes in countries with state monitoring systems is shown. The authors described the leading molecular resistance mechanisms (chromosomal and plasmid mediated) and showed their prevalence in different Salmonella serotypes. The article gives the information about Salmonella successful international multidrug resistant clones with specific resistance phenotypes and genotypes. The authors describe the molecular methods for detection of resistance mechanisms, and show the necessity and significance of antimicrobial susceptibility monitoring in the epidemiological Salmonella surveillance.
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Affiliation(s)
- S A Egorova
- Saint-Petersburg Pasteur Institute, 197101, Saint-Petersburg, Russia
| | - L A Kaftyreva
- Saint-Petersburg Pasteur Institute, 197101, Saint-Petersburg, Russia.,State Educational Institution of the Higher Professional Education «North-Western state medical University n.a. I.I. Mechnikov» of the Ministry of Health of the Russian Federation, 191015, Saint-Petersburg, Russia
| | - V V Pomazanov
- State University of Humanities and Technology, 142611, Orekhovo-Zuyevo, Moscow region
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Alba P, Leekitcharoenphon P, Carfora V, Amoruso R, Cordaro G, Di Matteo P, Ianzano A, Iurescia M, Diaconu EL, Study Group EEAN, Pedersen SK, Guerra B, Hendriksen RS, Franco A, Battisti A. Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid. Microb Genom 2020; 6. [PMID: 32271142 PMCID: PMC7371121 DOI: 10.1099/mgen.0.000365] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Salmonella Infantis is one of the five serovars most frequently causing human salmonellosis in Europe, mainly associated with poultry. A clone harbouring a conjugative plasmid of emerging S. Infantis (pESI)-like megaplasmid, carrying multidrug resistant (MDR) and extended-spectrum beta-lactamases (ESBL) genes, has spread in the Italian broiler chicken industry also causing human illness. This work is aimed at elucidating the molecular epidemiology of S. Infantis and pESI-like in Europe using whole-genome sequencing and bioinformatics analysis, and to investigate the genetic relatedness of S. Infantis clones and pESI-like from animals, meat, feed and humans provided by institutions of nine European countries. Two genotyping approaches were used: chromosome or plasmid SNP-based analysis and the minimum spanning tree (MST) algorithm based on core-genome multilocus sequence typing (cgMLST). The European S. Infantis population appeared heterogeneous, with different genetic clusters defined at core-genome level. However, pESI-like variants present in 64.1 % of the isolates were more genetically homogeneous and capable of infecting different clonal lineages in most of the countries. Two different pESI-like with ESBL genes (n=82) were observed: blaCTX-M-1-positive in European isolates and blaCTX-M-65-positive in American isolates (study outgroup). Both variants had toxin-antitoxin systems, resistance genes towards tetracyclines, trimethoprim, sulphonamides and aminoglycosides, heavy metals (merA) and disinfectants (qacEΔ). Worryingly, 66 % of the total isolates studied presented different gyrA chromosomal point mutations associated with (fluoro)quinolone resistance (MIC range 0.125–0.5 mg/L), while 18 % displayed transferable macrolide resistance mediated by mph, mef and erm(B) genes. Proper intervention strategies are needed to prevent further dissemination/transmission of MDR S. Infantis and pESI-like along the food chain in Europe.
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Affiliation(s)
- Patricia Alba
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Pimlapas Leekitcharoenphon
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Virginia Carfora
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Roberta Amoruso
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Gessica Cordaro
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Paola Di Matteo
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Angela Ianzano
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Manuela Iurescia
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Elena L Diaconu
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | | | - Susanne K Pedersen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Rene S Hendriksen
- European Union Reference Laboratory for Antimicrobial-Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Alessia Franco
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
| | - Antonio Battisti
- Department of General Diagnostics, National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", Rome, Italy
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56
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Nagy T, Szmolka A, Wilk T, Kiss J, Szabó M, Pászti J, Nagy B, Olasz F. Comparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis. Front Microbiol 2020; 11:539. [PMID: 32318036 PMCID: PMC7147451 DOI: 10.3389/fmicb.2020.00539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION The emergence and spread of new strains of zoonotic bacteria, such as multidrug resistant (MDR) Salmonella Infantis, represent a growing health risk for humans in and outside Europe due to foodborne infections of poultry meat origin. OBJECTIVES In order to understand genome relations of S. Infantis strains from Hungary and from different geographic regions, we performed a comprehensive genome analysis of nine Hungarian and 67 globally selected strains of S. Infantis and 26 Salmonella strains representing 13 non-Infantis serovars. RESULTS Analyses of whole-, and accessory genomes, showed that almost all S. Infantis strains were separated from the non-Infantis serovars. S. Infantis strains from Hungary formed subclusters based on their time of isolation. In whole genome sequence analysis, the Swiss strains of S. Infantis were closely related to each other and clustered together with subclusters of strains from Hungary, Japan, Italy, United States, and Israel. The accessory genome analysis revealed that the Swiss strains were distinct from most of the strains investigated, including the Hungarian ones. Analysis of the cloud genes offered the most detailed insight into the genetic distance and relationship of S. Infantis strains confirming that the Swiss and Hungarian strains belonged to different lineages. As expected, core genome analysis provided the least discriminatory power for analysis of S. Infantis. Genomic sequences of nine strains from Brazil, Israel, Mexico, Nigeria, and Senegal (deposited as S. Infantis) proved to be outliers from the S. Infantis clade. They were predicted to be Salmonella Rissen, Salmonella Ouakarm, Salmonella Kentucky, Salmonella Thompson, and Salmonella enterica subsp. diarizonae. CONCLUSION Accessory genome of S. Infantis showed the highest diversity suggesting a faster evolution than that of the whole genomes contributing to the emergence of multiple genetic variants of S. Infantis worldwide. Accordingly, in spite of the comprehensive analysis of several genomic characteristics, no epidemiologic links between these S. Infantis strains from different countries could be established. It is also concluded that several strains originally designated as S. Infantis need in databanks reclassification.
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Affiliation(s)
- Tibor Nagy
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Ama Szmolka
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
| | - Tímea Wilk
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - János Kiss
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Mónika Szabó
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Judit Pászti
- National Center for Epidemiology, Budapest, Hungary
| | - Béla Nagy
- Centre for Agricultural Research, Institute for Veterinary Medical Research, Budapest, Hungary
| | - Ferenc Olasz
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
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57
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Cohen E, Rahav G, Gal-Mor O. Genome Sequence of an Emerging Salmonella enterica Serovar Infantis and Genomic Comparison with Other S. Infantis Strains. Genome Biol Evol 2020; 12:151-159. [PMID: 32145019 PMCID: PMC7144548 DOI: 10.1093/gbe/evaa048] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Salmonella enterica serovar Infantis (S. Infantis) is one of the dominant serovars of the bacterial pathogen S. enterica. In recent years, the number of human infections caused by S. Infantis has been increasing in many countries, and often the emerging population harbors a unique virulence-resistant megaplasmid called plasmid of emerging S. Infantis (pESI). Here, we report the complete gap-free genome sequence of the S. Infantis Israeli emerging clone and compare its chromosome and pESI sequences with other complete S. Infantis genomes. We show a conserved presence of the Salmonella pathogenicity islands 1-6, 9, 11, 12, and CS54 and a common integration of five bacteriophages in the S. Infantis chromosome. In contrast, we found variable presence of additionally three chromosomally integrated phages and eight modular regions in pESI, which contribute to the genetic and phenotypic diversity (including antimicrobial resistance) of this ubiquitous foodborne pathogen.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Israel
- Department of Clinical Microbiology and Immunology, Tel Aviv University, Israel
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58
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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018. EFSA J 2020; 18:e06007. [PMID: 32874244 PMCID: PMC7448042 DOI: 10.2903/j.efsa.2020.6007] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Data on antimicrobial resistance (AMR) in zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs), jointly analysed by EFSA and ECDC and reported in a yearly EU Summary Report. The annual monitoring of AMR in animals and food within the EU is targeted at selected animal species corresponding to the reporting year. The 2017 monitoring specifically focussed on pigs and calves under 1 year of age, as well as their derived carcases/meat, while the monitoring performed in 2018 specifically focussed on poultry and their derived carcases/meat. Monitoring and reporting of AMR in 2017/2018 included data regarding Salmonella, Campylobacter and indicator Escherichia coli isolates, as well as data obtained from the specific monitoring of ESBL-/AmpC-/carbapenemase-producing E. coli isolates. Additionally, some MSs reported voluntary data on the occurrence of meticillin-resistant Staphylococcus aureus in animals and food, with some countries also providing data on antimicrobial susceptibility. This report provides, for the first time, an overview of the main findings of the 2017/2018 harmonised AMR monitoring in the main food-producing animal populations monitored, in related carcase/meat samples and in humans. Where available, data monitoring obtained from pigs, calves/cattle, broilers, laying hens and turkeys, as well as from carcase/meat samples and humans were combined and compared at the EU level, with particular emphasis on multiple drug resistance, complete susceptibility and combined resistance patterns to critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting presumptive ESBL-/AmpC-/carbapenemase-producing phenotypes. The outcome indicators for AMR in food-producing animals, such as complete susceptibility to the harmonised panel of antimicrobials in E. coli and the prevalence of ESBL-/AmpC-producing E. coli have been also specifically analysed over the period 2014-2018.
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59
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Sánchez-Salazar E, Gudiño ME, Sevillano G, Zurita J, Guerrero-López R, Jaramillo K, Calero-Cáceres W. Antibiotic resistance of Salmonella strains from layer poultry farms in central Ecuador. J Appl Microbiol 2020; 128:1347-1354. [PMID: 31867847 DOI: 10.1111/jam.14562] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/03/2019] [Accepted: 12/17/2019] [Indexed: 11/27/2022]
Abstract
AIMS This study evaluated the antimicrobial resistance of Salmonella enterica strains from layer poultry farms in central Ecuador isolated during 2017. This geographical area is responsible for around 60% of total domestic egg production, yet, as of 2019, no reports had been published on the phenotypic and genotypic antibiotic resistance patterns of Salmonella in the layer poultry farms of this area. METHODS AND RESULTS Thirty-one isolates from layer poultry farms in central Ecuador obtained during 2017 were evaluated. The resistance profiles exhibited considerable differences in serovar and sample origin, grouping into nine clades by phenotype. S. Infantis strains were of the MDR phenotype in 94·4% of isolates. S. Typhimurium strains were of a reduced antimicrobial resistance phenotype and 50% showed resistance to one antimicrobial compound. One of the S. enterica nontyped strains had an MDR profile to 11 of the 20 antibiotics evaluated (eight groups). And the two remaining S. enterica nontyped strains showed resistance to two and three antibiotics respectively. The ESBL phenotype, which is resistant to clinically notable antibiotics such as ceftriaxone, ampicillin and cefepime, was observed only in S. Infantis (15/18). These strains harbour the emerging blaCTX-M-65 gene, and co-harbour tetA and sul1 resistance genes in four strains. Additional β-lactamase genes, carbapenemase-producing genes (blaIMP, blaVIM , blaOXA48 , blaKPC , blaNDM ) and colistin-mobile resistance gene mcr-1 were not detected. CONCLUSIONS The findings highlight the potential role of layer poultry farm environments in central Ecuador as reservoirs of MDR Salmonella strains. SIGNIFICANCE AND IMPACT OF THE STUDY These results suggest the necessity of reinforcing biosecurity practices to reduce the probability of transmission of MDR Salmonella across the food chain.
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Affiliation(s)
- Elizabeth Sánchez-Salazar
- UTA RAM One Health Group, Center for Agricultural Research, Faculty of Agricultural Sciences, Technical University of Ambato (UTA), Ambato, Ecuador
| | - Marco E Gudiño
- Department of Clinical Laboratory Science, Faculty of Medical Sciences, Technical University of Ambato (UTA), Ambato, Ecuador
| | - Gabriela Sevillano
- Department of Biomedical Research, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Jeannete Zurita
- Department of Biomedical Research, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Ricardo Guerrero-López
- UTA RAM One Health Group, Center for Agricultural Research, Faculty of Agricultural Sciences, Technical University of Ambato (UTA), Ambato, Ecuador
| | - Katherine Jaramillo
- National Reference Center for Antimicrobial Resistance (RAM), National Institute of Public Health Research (INSPI), Quito, Ecuador
| | - William Calero-Cáceres
- UTA RAM One Health Group, Center for Agricultural Research, Faculty of Agricultural Sciences, Technical University of Ambato (UTA), Ambato, Ecuador
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Lin L, Zheng Q, Lin J, Yuk HG, Guo L. Immuno- and nucleic acid-based current technique for Salmonella detection in food. Eur Food Res Technol 2020. [DOI: 10.1007/s00217-019-03423-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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61
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Bogomazova AN, Gordeeva VD, Krylova EV, Soltynskaya IV, Davydova EE, Ivanova OE, Komarov AA. Mega-plasmid found worldwide confers multiple antimicrobial resistance in Salmonella Infantis of broiler origin in Russia. Int J Food Microbiol 2019; 319:108497. [PMID: 31927155 DOI: 10.1016/j.ijfoodmicro.2019.108497] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/08/2019] [Accepted: 12/20/2019] [Indexed: 01/06/2023]
Abstract
Plasmids which are the mobile part of the bacterial genome can acquire and carry over genes conferring antimicrobial resistance, thus contributing to rapid adaptation of bacterial community to human-defined environment. In 2014, Israeli scientists have reported a large conjugative mega-plasmid pESI (plasmid for emerging S. Infantis) that provides multiple drug resistance (MDR) of Salmonella Infantis isolated from broilers. Later, very similar pESI-like plasmids have been found in Salmonella isolated from poultry in the United States, Italy, Switzerland, Hungary, and Japan. Here we report detection of pESI-like plasmids in Salmonella Infantis isolated from chicken food products in Russia. Whole genome sequencing of three MDR isolates revealed pESI-like plasmids in all three cases. These plasmids have such typical pESI features as a locus for siderophore yersiniabactin, a cluster of IncI1 conjugative genes, a cluster of type IV pilus genes, and three toxin-antitoxin modules. The pESI-like plasmids carry from two to five resistance genes in each isolate. In total, we observed six antimicrobial resistance genes associated with pESI-like plasmids (aadA1, blaCTX-M-14, dfrA14, sul1, tetA/tetR, tetM). Besides plasmid genes of antimicrobial resistance, all three MDR isolates of S. Infantis harbor a mutation in chromosomal gene gyrA (p.S83Y or p.D87Y) that is associated with resistance to fluoroquinolones. In addition, we performed a comparative bioinformatics meta-analysis of 25 pESI-like plasmids hosted by S. Infantis from the USA, Europe, Latin America, Israel, and Japan. This analysis identified a 173 kB sequence that is common for all pESI-like plasmids and carries virulence operons and toxin-antitoxin modules.
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Affiliation(s)
- Alexandra N Bogomazova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia.
| | - Veronika D Gordeeva
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Ekaterina V Krylova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Irina V Soltynskaya
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Ekaterina E Davydova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Olga E Ivanova
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
| | - Alexander A Komarov
- The Russian State Center for Animal Feed and Drug Standardization and Quality (FGBU "VGNKI"), Zvenigorodskoe shosse 5, Moscow 132022, Russia
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62
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Gymoese P, Kiil K, Torpdahl M, Østerlund MT, Sørensen G, Olsen JE, Nielsen EM, Litrup E. WGS based study of the population structure of Salmonella enterica serovar Infantis. BMC Genomics 2019; 20:870. [PMID: 31730461 PMCID: PMC6858691 DOI: 10.1186/s12864-019-6260-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar. RESULTS We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed. CONCLUSIONS This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage. We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.
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Affiliation(s)
- Pernille Gymoese
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mia Torpdahl
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Mark T. Østerlund
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Gitte Sørensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
| | - Eva M. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
| | - Eva Litrup
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Artillerivej 5 Denmark
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63
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Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, Malorny B. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog 2019; 11:48. [PMID: 31636715 PMCID: PMC6791114 DOI: 10.1186/s13099-019-0330-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.
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Affiliation(s)
- Laura Uelze
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Cécile Jacobs
- Landeslabor Schleswig-Holstein, Max-Eyth-Straße 5, 24537 Neumünster, Germany
| | - István Szabó
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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64
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Zhou M, Li X, Hou W, Wang H, Paoli GC, Shi X. Incidence and Characterization of Salmonella Isolates From Raw Meat Products Sold at Small Markets in Hubei Province, China. Front Microbiol 2019; 10:2265. [PMID: 31636615 PMCID: PMC6787437 DOI: 10.3389/fmicb.2019.02265] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/17/2019] [Indexed: 01/02/2023] Open
Abstract
Salmonella is a leading cause of foodborne disease and is often associated with the consumption of foods of animal origin. In this study, sixty-six Salmonella isolates were obtained from 631 raw meat samples purchased at small retail suppliers in Hubei Province, China. The most prevalent Salmonella serotypes were Thompson (18.2%) and Agona (13.6%). Frequent antimicrobial resistance was observed for the sulfonamides (43.9%), tetracycline (43.9%), and the β-lactams amoxicillin and ampicillin (36.4% for each). Interestingly, a high incidence of resistance to cephazolin was observed in strains of the most common serotype, S. Thompson. Class I integrons were found in 27.3% (18/66) of the isolates and five of these integrons contained different gene cassettes (aacA4C-arr-3-dfr2, dfrA12-aadA21, aadA2, dfrA12-aadA2, dfr17-aadA5). Additional antimicrobial resistance genes, including bla TEM-1, bla CTX-M-65, bla CTX-M-15, qnrB, and qnrS, were also identified among these Salmonella isolates. Results of replicon typing and conjugation experiments revealed that an integron with qnrB and bla CTX-M-15 genes was present on incH12 mobile plasmid in S. Thompson strain. Multilocus sequence typing (MLST) analysis revealed 32 sequence types, indicating that these isolates were phenotypically and genetically diverse, among which ST26 (18.2%) and ST541 (12.1%) were the predominant sequence types. The integrons, along with multiple antimicrobial resistance genes on mobile plasmids, are likely contributors to the dissemination of multidrug resistance in Salmonella.
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Affiliation(s)
- Min Zhou
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Xiaofang Li
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Wenfu Hou
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Hongxun Wang
- School of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - George C Paoli
- Molecular Characterization of Foodborne Pathogens Research Unit, United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center (USDA-ARS-ERRC), USDA-MOST Joint Research Center for Food Safety, Wyndmoor, PA, United States
| | - Xianming Shi
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, MOST-USDA Joint Research Center for Food Safety, Shanghai Jiao Tong University, Shanghai, China
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65
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Antonelli P, Belluco S, Mancin M, Losasso C, Ricci A. Genes conferring resistance to critically important antimicrobials in Salmonella enterica isolated from animals and food: A systematic review of the literature, 2013–2017. Res Vet Sci 2019; 126:59-67. [DOI: 10.1016/j.rvsc.2019.08.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/12/2019] [Accepted: 08/12/2019] [Indexed: 01/03/2023]
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66
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Hahyoungchilella caricis gen. nov., sp. nov., isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia), transfer of Thioclava arenosa Thongphrom et al. 2017 to Pseudothioclava as Pseudothioclava arenosa gen. nov., comb. nov. and proposal of Thioclava electrotropha Chang et al. 2018 as a later heterosynonym of Thioclava sediminum. J Microbiol 2019; 57:1048-1055. [DOI: 10.1007/s12275-019-9260-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 10/25/2022]
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67
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Acar S, Bulut E, Stasiewicz MJ, Soyer Y. Genome analysis of antimicrobial resistance, virulence, and plasmid presence in Turkish Salmonella serovar Infantis isolates. Int J Food Microbiol 2019; 307:108275. [PMID: 31408739 DOI: 10.1016/j.ijfoodmicro.2019.108275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/02/2023]
Abstract
Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolates were found to have a multi-drug resistance profile (kanamycin, streptomycin, nalidixic acid, tetracycline, sulfonamide, and sometimes to ampicillin) and high prevalence (91%) in Turkish poultry in our previous studies. To investigate the mechanism behind multi-drug antimicrobial resistance (AMR) and high prevalence in Turkish poultry, 23 of the isolates were sequenced for comparative genomic analyses including: SNP-based comparison to S. Infantis from other countries, comparison of antimicrobial resistance genes (AMGs) with AMR phenotypes, and plasmid identification and annotation. Whole-genome SNP-based phylogenetic analysis found that all 23 Turkish S. Infantis isolates formed a distinct, well-supported clade, separate from 243 comparison S. Infantis genomes in GenomeTrakr identified as from the US and EU; the isolates most closely related to the cluster of these Turkish isolates were from Israel and Egypt. AMGs identified by bioinformatic analysis, without differentiating chromosomal or plasmid located genes, implied AMR phenotypes with 94% similarity overall to wet lab data, which was performed by phenotypic and conventional PCR methods. Most of the S. Infantis (21/23) isolates had identifiable plasmids, with 76% (16/21) larger than 100 kb and 48% (10/21) larger than 200 kb. A plasmid larger than 200 kb, with the incompatibility type of IncX1, similar to United States S. Infantis plasmid N55391 (99% query coverage and 99% identity overall), which itself is similar to Italian and Hungarian S. Infantis plasmids. Turkish S. Infantis plasmids had different beta-lactam resistance genes (blaTEM-70, blaTEM-148 and blaTEM-198) than the gene blaCTX-M-65 found in S. Infantis plasmids from other countries. This is the first observation of these three genes in S. Infantis isolates. The plasmids larger than 200 kb had two distinct regions of interest: Site 1 and Site 2. Site 1 (around 130 kb) had virulence- and bacteriocin- associated genes such as bacteriocin secretion system and type II toxin-antitoxin system genes (vagC, ccdA, ccdB, mchE, cvaB) and an aminoglycoside resistance gene (str). Site 2 (around 75-110 kb) had the antimicrobial resistance genes (aadA, sulI, tetA, tetR) and mercury (mer) resistance gene on tranposons Tn552 and Tn501. Presence of these AMR and virulence genes suggests they may have a role in the emergence of S. Infantis in poultry and support treating this serotype as a an important human health hazard.
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Affiliation(s)
- Sinem Acar
- Department of Food Engineering, Middle East Technical University, Ankara 06810, Turkey
| | - Ece Bulut
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yeşim Soyer
- Department of Food Engineering, Middle East Technical University, Ankara 06810, Turkey.
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Bonardi S, Pitino R. Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health. Ital J Food Saf 2019; 8:7956. [PMID: 31316921 PMCID: PMC6603432 DOI: 10.4081/ijfs.2019.7956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/09/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, Italy
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69
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Wajid M, Saleemi MK, Sarwar Y, Ali A. Detection and characterization of multidrug-resistant Salmonella enterica serovar Infantis as an emerging threat in poultry farms of Faisalabad, Pakistan. J Appl Microbiol 2019; 127:248-261. [PMID: 30990250 DOI: 10.1111/jam.14282] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/26/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022]
Abstract
AIMS The aim of this study was the molecular identification of Salmonella enterica serovar Infantis (S. Infantis) isolated from poultry samples and their antimicrobial resistance and virulence profiling. METHODS AND RESULTS A total of 149 isolates, belonging to genus Salmonella, originally isolated from 340 suspected poultry post mortem specimens reported by us earlier were preliminary identified as Salmonella by biochemical methods and confirmed by polymerase chain reaction targeting genus-specific gene invA. Targeting serovar-specific gene fragment (fljB) resulted in confirmation of 54 isolates as S. Infantis which were further confirmed by sequencing of 16S RNA and fljB genes. Swimming and swarming motilities were detected in 98·1 and 11·1% isolates respectively. Phenotypic disc diffusion assay against 23 antimicrobial agents showed the highest resistance against pefloxacin (PEF) (94·4%), chloramphenicol (83·3%) and imipenem (77·7%) while 5·3% isolates showed extended-spectrum β-lactamase production. Fifty-nine genes reported for antimicrobial resistance and 12 for conferring virulence were targeted. The most prevalent resistance gene for aminoglycosides was aadA (42·3%), for quinolone resistance determining region parE (62·5%), for penicillin's Int1 (62·9%), for chloramphenicol cat3 (66·1%) and for beta-lactams blaTEM -1 (44·4%). Among efflux pump coding genes, armA showed highest (74·2%) prevalence and for virulence, a high prevalence of SopE (89·2%) showed the zoonotic potential of the isolates. The activity of efflux pumps was detected through Ethidium Bromide-agar method. CONCLUSIONS Poultry could act as reservoirs of multidrug resistance Salmonella. SIGNIFICANCE AND IMPACT OF THE STUDY We firstly report the prevalence and molecular characterization of virulence/drug resistance in S. Infantis from this region and the results may contribute to designing precisely targeted therapy. This study has also highlighted the possible emergence of S. Infantis with zoonotic potential.
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Affiliation(s)
- M Wajid
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - M K Saleemi
- Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Y Sarwar
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - A Ali
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
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70
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Fei X, Yin K, Yin C, Hu Y, Li J, Zhou Z, Tian Y, Geng S, Chen X, Pan Z, Li Q, Jiao X. Analyses of prevalence and molecular typing reveal the spread of antimicrobial-resistant Salmonella infection across two breeder chicken farms. Poult Sci 2019; 97:4374-4383. [PMID: 30016482 DOI: 10.3382/ps/pey305] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/21/2018] [Indexed: 01/22/2023] Open
Abstract
In this study, Salmonella prevalence and antimicrobial resistance were evaluated at various production stages in 2 geographically separated breeder farms (referred to as G and F). Day-old chicks for the breeder flock at farm F were purchased from farm G. A total of 219 Salmonella isolates, all identified as Salmonella enterica subsp. enterica serovar Enteritidis, were recovered from 1,430 samples (sick chicken carcasses and/or dead embryos). The isolation rates at breeder farms G and F were 10.53% (56/532) and 18.15% (163/898), respectively. Resistance to 4-6 antimicrobial agents was the most frequent phenotype during the laying stage at both farms, suggesting that chicks are exposed to higher risk of antimicrobial-resistant Salmonella infection during this stage of the breeding process. Using clustered regularly interspaced short palindromic repeat (CRISPR) typing, 5 CRISPR patterns were identified, out of which one pattern was shared by the 2 farms. In addition, pulsed-field gel electrophoresis (PFGE) typing result indicated that 2 clusters (PF-1 and PF-2) were shared among the 2 breeder farms, suggesting that strains were transmitted from breeder farm G to farm F via the trade of day-old chicks. Our findings suggested that the trade of day-old breeder chicks could be one of the potential Salmonella transmission routes, and antibiotics should be administered with caution during the laying stage.
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Affiliation(s)
- Xiao Fei
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Kequan Yin
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Chao Yin
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Yachen Hu
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Jingwen Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Zihao Zhou
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Yuqi Tian
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Shizhong Geng
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China
| | - Xiang Chen
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Zhiming Pan
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Qiuchun Li
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
| | - Xinan Jiao
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China, Yangzhou University, 225009, China.,Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, 225009, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, 225009, China
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71
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Müller A, Jansen W, Grabowski NT, Kehrenberg C. Characterization of Salmonella enterica serovars recovered from meat products legally and illegally imported into the EU reveals the presence of multiresistant and AmpC-producing isolates. Gut Pathog 2018; 10:40. [PMID: 30258498 PMCID: PMC6151051 DOI: 10.1186/s13099-018-0268-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/15/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Food products of animal origin brought into the EU from third countries, both legally and illegally, can harbor foodborne pathogens such as Salmonella enterica. In this study, we examined five S. enterica isolates recovered either from legally imported chicken meat (n = 3) or from meat products confiscated from air travel passengers arriving in Germany (n = 2). The isolates were serotyped and further characterized by antimicrobial susceptibility testing, PCR-detection and sequencing of genes associated with antimicrobial resistances, and macrorestriction analysis. Transferability of resistance to third-generation cephalosporins was assessed by conjugation experiments and the plasmids tested for their incompatibility groups. RESULTS The three isolates from legal imports were identified as S. Heidelberg or as non-flagellated. All three isolates were identified as AmpC producers carrying bla CMY-2 and as non-susceptible to ciprofloxacin. They were additionally resistant to tetracycline and sulfamethoxazole. The bla CMY-2-carrying plasmids were transferable by conjugation and belonged to incompatibility groups IncI1 or IncA/C. The two isolates from illegally imported meat belonged to the serovars Infantis or Weltevreden. The former was phenotypically resistant to five classes of antimicrobial agents while the S. Weltevreden isolate was fully susceptible to all agents tested. CONCLUSION The results of this study demonstrate that meat products imported from third countries, both legally and illegally, can harbor multiresistant Salmonella enterica. Consequently, these imports could constitute a source for the dissemination of antimicrobial resistant isolates, including those resistant to third-generation cephalosporins and fluoroquinolones.
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Affiliation(s)
- Anja Müller
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Wiebke Jansen
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
- Integrated Veterinary Research Unit, University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Nils Th. Grabowski
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Corinna Kehrenberg
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover Foundation, Bischofsholer Damm 15, 30173 Hannover, Germany
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72
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Carfora V, Alba P, Leekitcharoenphon P, Ballarò D, Cordaro G, Di Matteo P, Donati V, Ianzano A, Iurescia M, Stravino F, Tagliaferri T, Battisti A, Franco A. Colistin Resistance Mediated by mcr-1 in ESBL-Producing, Multidrug Resistant Salmonella Infantis in Broiler Chicken Industry, Italy (2016-2017). Front Microbiol 2018; 9:1880. [PMID: 30174660 PMCID: PMC6108180 DOI: 10.3389/fmicb.2018.01880] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/26/2018] [Indexed: 11/13/2022] Open
Abstract
Colistin-resistance mediated by mobilisable and plasmid-borne mcr genes has emerged worldwide, threatening the efficacy of colistin, a last resort antibiotic increasingly used for treating human invasive infections by multidrug-resistant or extensively drug-resistant Enterobacteriaceae. In this study, we report the first evidence of mcr-1-mediated colistin resistance in four multidrug resistant (MDR) out of 324 Salmonella infantis from the Italian antimicrobial resistance (AMR) monitoring (2001-2017) in broilers and broiler meat. Two were also Extended Spectrum Beta-Lactamases (ESBL)-producing isolates. Characterization by whole genome sequencing (WGS), located mcr-1.1 on an incX4 plasmid. Phylogenetic analysis of these isolates with selected Italian S. Infantis previously isolated from animals, meat and human clinical cases with unknown epidemiological relationship, demonstrated that ESBL-producing, mcr-1-positive isolates belonged to the emerging pESI-like-positive-ESBL-producing clone described in Italy in 2015.
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Affiliation(s)
- Virginia Carfora
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Patricia Alba
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Pimlapas Leekitcharoenphon
- European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Daniele Ballarò
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Gessica Cordaro
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Paola Di Matteo
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Valentina Donati
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Angela Ianzano
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Manuela Iurescia
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Fiorentino Stravino
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Tania Tagliaferri
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Antonio Battisti
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
| | - Alessia Franco
- National Reference Laboratory for Antimicrobial Resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri,” General Diagnostics Department, Rome, Italy
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73
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Abstract
The number of human salmonellosis within the European Union tended to increase since 2013. One of the reasons might be Salmonella Enteritidis rising in laying hens flocks by around 17% in 2015 vs 2014 and by 57% in 2016 vs 2015. The most important sources of food-borne Salmonella outbreaks are still eggs and egg products as well as ready-to-eat foods having a long shelf life. Specific actions are suggested to restart decreasing the number of human salmonellosis: (1) revision of sampling schemes to solve pathogen under detection in both animals and foods; (2) integration of microbiological criteria with fit for purpose performance objectives and food safety objectives; and (3) improvement of epidemiological investigations of human, food, and animal isolates by using whole-genome sequencing in order to effectively track salmonellosis and verify which prevention measures are most effective.
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74
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Eeckhaut V, Haesebrouck F, Ducatelle R, Van Immerseel F. Oral vaccination with a live Salmonella Enteritidis/Typhimurium bivalent vaccine in layers induces cross-protection against caecal and internal organ colonization by a Salmonella Infantis strain. Vet Microbiol 2018; 218:7-12. [PMID: 29685223 DOI: 10.1016/j.vetmic.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/17/2018] [Accepted: 03/17/2018] [Indexed: 01/06/2023]
Abstract
Salmonella is an important zoonotic agent, and poultry products remain one of the main sources of infection for humans. Salmonella Infantis is an emerging serotype in poultry worldwide, reflected by an increased prevalence in poultry flocks, on broiler meat and in human foodborne illness cases. In the current study, the efficacy of oral administration of a live monovalent Salmonella Enteritidis and a live bivalent Salmonella Enteritidis/Typhimurium vaccine, against a Salmonella Enteritidis and Infantis infection, was determined. Oral administration of the live vaccines to day-old chickens caused a decrease in caecal colonization by Salmonella Enteritidis, but not Infantis, at day 7, when challenged at day 2. Vaccination with the bivalent vaccine at day 1 resulted in a decreased spleen colonization by both Salmonella Infantis and Enteritidis. Twice (at day 1 and week 6) and thrice vaccination (at day 1, week 6 and 16) of laying hens with the bivalent vaccine resulted in a decreased caecal colonization by Salmonella Enteritidis and Infantis, and significantly lower oviduct colonization levels by Salmonella Enteritidis. These data show cross-protection against Salmonella Infantis by oral administration of live vaccine strains belonging to other serogroups.
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Affiliation(s)
- Venessa Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
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75
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2016. EFSA J 2018; 16:e05182. [PMID: 32625816 PMCID: PMC7009656 DOI: 10.2903/j.efsa.2018.5182] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The data on antimicrobial resistance in zoonotic and indicator bacteria in 2016, submitted by 28 EU Member States (MSs), were jointly analysed by the EFSA and ECDC. Resistance in bacterial isolates of zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as in meticillin-resistant Staphylococcus aureus from animals and food were addressed. 'Microbiological' resistance was assessed using epidemiological cut-off (ECOFF) values; for some countries, qualitative data on isolates from humans were interpreted in a way that corresponds closely to ECOFF-defined 'microbiological' resistance. In Salmonella from humans, the occurrence of resistance to ampicillin, sulfonamides and tetracyclines was high, whereas resistance to third-generation cephalosporins was low. In Salmonella and E. coli isolates from broilers, fattening turkeys and their meat, resistance to ampicillin, (fluoro)quinolones, tetracyclines and sulfonamides was frequently high, whereas resistance to third-generation cephalosporins was rare. The occurrence of ESBL-/AmpC producers was low in Salmonella and E. coli from poultry and in Salmonella from humans. The prevalence of ESBL-/AmpC-producing E. coli, assessed in poultry and its meat for the first time, showed marked variations among MSs. Fourteen presumptive carbapenemase-producing E. coli were detected from broilers and its meat in two MSs. Resistance to colistin was observed at low levels in Salmonella and E. coli from poultry and meat thereof and in Salmonella from humans. In Campylobacter from humans, broilers and broiler meat, resistance to ciprofloxacin and tetracyclines was high to extremely high, whereas resistance to erythromycin was low to moderate. Combined resistance to critically important antimicrobials in isolates from both humans and animals was generally uncommon, but very high to extremely high multidrug resistance levels were observed in certain Salmonella serovars. Specific serovars of Salmonella (notably Kentucky) from both humans and animals exhibited high-level resistance to ciprofloxacin, in addition to findings of ESBL.
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76
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Nair DVT, Vazhakkattu Thomas J, Noll S, Porter R, Kollanoor Johny A. Effect of Various Inoculum Levels of Multidrug-Resistant Salmonella enterica Serovar Heidelberg (2011 Ground Turkey Outbreak Isolate) on Cecal Colonization, Dissemination to Internal Organs, and Deposition in Skeletal Muscles of Commercial Turkeys after Experimental Oral Challenge. Front Microbiol 2018; 8:2680. [PMID: 29379476 PMCID: PMC5771268 DOI: 10.3389/fmicb.2017.02680] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/22/2017] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is a major foodborne pathogen colonizing poultry. The pathogen is associated with a significant number of foodborne outbreaks through contaminated poultry meat, including turkeys. Recently, multidrug-resistant (MDR) strains of S. Heidelberg have emerged as a threat to human public health in the United States. The objective of this study was to determine the cecal colonization, dissemination to internal organs, and the potential for skeletal muscle deposition of an MDR S. Heidelberg isolate from the 2011 ground turkey outbreak in the United States after the experimental oral challenge of poults (young turkeys) and adult turkey hens. In the poult study, two separate experiments using day-old, straight-run, commercial hybrid converter poults were randomly assigned to five challenge groups (0, 10∧2, 10∧4, 10∧6, 10∧8 CFU groups; 12 poults/group; N = 60/experiment) and a week after, treatment groups were challenged separately with 0-, 2-, 4-, 6-, and 8- log10 CFU of S. Heidelberg orally. After 14 days post-challenge, the poults were euthanized, and samples were collected to determine MDR S. Heidelberg colonization in the cecum, dissemination to liver and spleen, and deposition in the thigh, drumstick, and breast muscles. A similar experimental design was followed for the adult turkey hens. In two separate experiments, 11-week-old commercial Hybrid Converter turkey hens (4 hens/group; N = 20/experiment) were challenged with MDR S. Heidelberg and on day 16 post-challenge, birds were euthanized and samples were collected to determine Salmonella populations in the samples. The results indicated that, in turkey poults, the recovery of MDR S. Heidelberg was highest in the cecum followed by spleen, liver, thigh, drumstick, and breast. All tested inoculum levels resulted in more than 3.5 log10 CFU/g colonization in the poult cecum. The cecal colonization, dissemination to internal organs, and tissue deposition of MDR S. Heidelberg were high in poults. The pathogen recovery from the cecum of adult turkey hens ranged from 37.5 to 62.5% in the challenge groups. The results signify the importance of controlling MDR S. Heidelberg in turkeys at the farm level to improve the safety of turkey products.
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Affiliation(s)
- Divek V. T. Nair
- Department of Animal Science, University of Minnesota, Saint Paul, MN, United States
| | | | - Sally Noll
- Department of Animal Science, University of Minnesota, Saint Paul, MN, United States
| | - Robert Porter
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Anup Kollanoor Johny
- Department of Animal Science, University of Minnesota, Saint Paul, MN, United States
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77
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The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016. EFSA J 2017; 15:e05077. [PMID: 32625371 PMCID: PMC7009962 DOI: 10.2903/j.efsa.2017.5077] [Citation(s) in RCA: 268] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
This report of the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of the zoonoses monitoring activities carried out in 2016 in 37 European countries (28 Member States (MS) and nine non-MS). Campylobacteriosis was the most commonly reported zoonosis and the increasing European Union (EU) trend for confirmed human cases since 2008 stabilised during 2012-2016. In food, the occurrence of Campylobacter remained high in broiler meat. The decreasing EU trend for confirmed human salmonellosis cases since 2008 ended during 2012-2016, and the proportion of human Salmonella Enteritidis cases increased. Most MS met their Salmonella reduction targets for poultry, except five MS for laying hens. At primary production level, the EU-level flock prevalence of target Salmonella serovars in breeding hens, broilers, breeding and fattening turkeys decreased or stabilised compared with previous years but the EU prevalence of S. Enteritidis in laying hens significantly increased. In foodstuffs, the EU-level Salmonella non-compliance for minced meat and meat preparations from poultry was low. The number of human listeriosis confirmed cases further increased in 2016, despite the fact that Listeria seldom exceeds the EU food safety limit in ready-to-eat foods. The decreasing EU trend for confirmed yersiniosis cases since 2008 stabilised during 2012-2016, and also the number of confirmed Shiga toxin-producing Escherichia coli (STEC) infections in humans was stable. In total, 4,786 food-borne outbreaks, including waterborne outbreaks, were reported. Salmonella was the most commonly detected causative agent - with one out of six outbreaks due to S. Enteritidis - followed by other bacteria, bacterial toxins and viruses. Salmonella in eggs continued to represent the highest risk agent/food combination. The report further summarises trends and sources for bovine tuberculosis, brucellosis, trichinellosis, echinococcosis, toxoplasmosis, rabies, Q fever, West Nile fever and tularaemia.
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