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Chowdhury AR, Mukherjee D, Chatterjee R, Chakravortty D. Defying the odds: Determinants of the antimicrobial response of Salmonella Typhi and their interplay. Mol Microbiol 2024; 121:213-229. [PMID: 38071466 DOI: 10.1111/mmi.15209] [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: 07/31/2023] [Revised: 11/12/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
Salmonella Typhi, the invasive serovar of S. enterica subspecies enterica, causes typhoid fever in healthy human hosts. The emergence of antibiotic-resistant strains has consistently challenged the successful treatment of typhoid fever with conventional antibiotics. Antimicrobial resistance (AMR) in Salmonella is acquired either by mutations in the genomic DNA or by acquiring extrachromosomal DNA via horizontal gene transfer. In addition, Salmonella can form a subpopulation of antibiotic persistent (AP) cells that can survive at high concentrations of antibiotics. These have reduced the effectiveness of the first and second lines of antibiotics used to treat Salmonella infection. The recurrent and chronic carriage of S. Typhi in human hosts further complicates the treatment process, as a remarkable shift in the immune response from pro-inflammatory Th1 to anti-inflammatory Th2 is observed. Recent studies have also highlighted the overlap between AP, persistent infection (PI) and AMR. These incidents have revealed several areas of research. In this review, we have put forward a timeline for the evolution of antibiotic resistance in Salmonella and discussed the different mechanisms of the same availed by the pathogen at the genotypic and phenotypic levels. Further, we have presented a detailed discussion on Salmonella antibiotic persistence (AP), PI, the host and bacterial virulence factors that can influence PI, and how both AP and PI can lead to AMR.
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Affiliation(s)
- Atish Roy Chowdhury
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Debapriya Mukherjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Ritika Chatterjee
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India
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Ali MS, Song HJ, Moon BY, Kim SJ, Kang HY, Moon DC, Lee YH, Kwon DH, Yoon SS, Lim SK. Antibiotic Resistance Profiles and Molecular Characteristics of blaCMY-2-Carrying Salmonella enterica Serovar Albany Isolated from Chickens During 2013-2020 in South Korea. Foodborne Pathog Dis 2023; 20:492-501. [PMID: 37699238 DOI: 10.1089/fpd.2023.0034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
The production of β-lactamase by nontyphoidal Salmonella has become a public health issue throughout the world. In this study, we aimed to investigate the antimicrobial resistance profiles and molecular characteristics of β-lactamase-producing Salmonella enterica serovar Albany isolates. A total of 434 Salmonella Albany were obtained from feces and carcasses of healthy and diseased food-producing animals [cattle (n = 2), pigs (n = 3), chickens (n = 391), and ducks (n = 38)] during 2013-2020. Among the 434 Salmonella Albany isolates, 3.7% showed resistance to cefoxitin, and all the cefoxitin-resistant isolates were obtained from chickens. Moreover, Salmonella Albany isolates demonstrated high resistance to nalidixic acid (99.3%), trimethoprim/sulfamethoxazole (97.9%), ampicillin (86.6%), chloramphenicol (86.6%), and tetracycline (85.7%), as well as higher rates of multidrug resistance were detected in cefoxitin-resistant isolates compared to cefoxitin-susceptible isolates. All cefoxitin-resistant isolates harbored CMY-2-type β-lactamase and belonged to seven different pulsotypes, with type IV-b (43.75%) and IV-a (25%) making up the majority. In addition, genes encoding cefoxitin resistant of all blaCMY-2-harboring Salmonella Albany isolates were horizontally transmitted to a recipient Escherichia coli J53 by conjugation. Furthermore, 93.75% (15/16) of conjugative plasmids harboring blaCMY-2 genes belong to ST12/CC12-IncI1. Genetic characteristics of transmitted blaCMY-2 genes were associated with ISEcp1, which can play an essential role in the effective mobilization and expression of these genes. Salmonella Albany containing blaCMY-2 in chickens can potentially be transferred to humans. Therefore, it is necessary to restrict antibiotic use and conduct continuous monitoring and analysis of resistant bacteria in the poultry industry.
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Affiliation(s)
- Md Sekendar Ali
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Bo-Youn Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hee Young Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Yeon-Hee Lee
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong-Hyeon Kwon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
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Sauget M, Atchon AK, Valot B, Garch FE, de Jong A, Moyaert H, Hocquet D. Genome analysis of third-generation cephalosporin-resistant Escherichia coli and Salmonella species recovered from healthy and diseased food-producing animals in Europe. PLoS One 2023; 18:e0289829. [PMID: 37883425 PMCID: PMC10602299 DOI: 10.1371/journal.pone.0289829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/26/2023] [Indexed: 10/28/2023] Open
Abstract
The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.
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Affiliation(s)
- Marlène Sauget
- Service D’hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
| | - Alban K. Atchon
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Benoît Valot
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
| | - Farid El Garch
- Vétoquinol SA, Global Drug Development Center, Lure, France
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
| | - Anno de Jong
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
| | - Hilde Moyaert
- EASSA and VetPath Study Group, CEESA, Brussels, Belgium
- Zoetis Belgium SA, Veterinary Medicine Research and Development, Zaventem, Belgium
| | - Didier Hocquet
- Service D’hygiène Hospitalière, Centre Hospitalier Universitaire, Besançon, France
- Bioinformatique et Big Data au Service de la Santé, UFR Santé, Université de Bourgogne Franche-Comté, Besançon, France
- UMR 6249 CNRS Chrono-Environnement, Université de Bourgogne Franche-Comté, Besançon, France
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Vilela FP, Dos Prazeres Rodrigues D, Allard MW, Falcão JP. Genomic analyses of drug-resistant Salmonella enterica serovar Heidelberg strains isolated from meat and related sources between 2013 and 2017 in the south region of Brazil. Curr Genet 2023; 69:141-152. [PMID: 36920496 DOI: 10.1007/s00294-023-01264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023]
Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is a zoonotic, ubiquitous, and worldwide-distributed pathogen, responsible for gastroenteritis in humans caused by the consumption of contaminated food. In this study, 11 S. Heidelberg strains isolated from chicken and bovine meat, drag swab, and animal feed between 2013 and 2017 in states of the southern region of Brazil were characterized by whole-genome sequencing (WGS) analyses. Antimicrobial resistance against 18 antimicrobials was determined by disk-diffusion and ciprofloxacin's minimum inhibitory concentration by Etest®. The search for resistance and virulence genes, plasmids, Salmonella Pathogenicity Islands (SPIs) plus multi-locus sequence typing (MLST), and single-nucleotide polymorphisms (SNPs) analyses was conducted using WGS data. All strains harbored resistance genes fosA7, aac(6')-Iaa, sul2, tet(A), blaCMY-2, mdsA, and mdsB, and point mutations in gyrA and parC. All strains showed a phenotypic multidrug-resistant profile, with resistant or intermediate resistant profiles against 14 antimicrobials tested. Plasmids ColpVC, IncC, IncX1, and IncI1-I(Alpha) were detected. Virulence genes related to adherence, macrophage induction, magnesium uptake, regulation, and type III secretion systems plus 10 SPIs were detected. All strains were assigned to ST15 and belonged to two SNP clusters showing high similarity to isolates from the United Kingdom, Chile, Germany, the Netherlands, China, South Africa, and South Korea. In conclusion, the presence of multidrug-resistant S. Heidelberg strains in Brazil showing a global genomic relationship may alert for the necessity of stronger surveillance measures by food safety and public health authorities to limit its spread to humans and animals through foods.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/n, Bloco S-Sala 41, Ribeirão Preto, SP, 14040-903, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Juliana Pfrimer Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, Av. do Café, s/n, Bloco S-Sala 41, Ribeirão Preto, SP, 14040-903, Brazil.
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Fernandes SA, Tavechio AT, Ghilardi ÂCR, Almeida EAD, Silva JMLD, Camargo CH, Tiba-Casas MR. Salmonella enterica serotypes from human and nonhuman sources in Sao Paulo State, Brazil, 2004-2020. Rev Inst Med Trop Sao Paulo 2022; 64:e66. [PMID: 36197427 PMCID: PMC9528755 DOI: 10.1590/s1678-9946202264066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022] Open
Abstract
Salmonellosis ranks among the most frequently reported zoonosis worldwide and is often associated with foodborne outbreaks. Since the 1950s, the distribution of Salmonella serotypes in Sao Paulo State, Brazil, has been documented and periodically reported. In this study, we updated the data on the distribution of Salmonella serotypes received in our reference laboratory, isolated from human infections and nonhuman sources, from 2004 to 2020. In that period, a total of 9,014 Salmonella isolates were analyzed, of which 3,553 (39.4%) were recovered from human samples, mainly of stool (65%) and blood (25.6%), and 5,461 (60.6%) were isolated from nonhuman origins, such as animals (47.2%), food (27.7%) and animal environments (18.6%). In human isolates, a total of 104 serotypes were identified and the most frequent ones were Enteritidis, Typhimurium, S . I. 4,[5],12:i:-, Dublin and Typhi. A consistent reduction of the Enteritidis proportion was observed over the years. Among the 156 serotypes identified in isolates with nonhuman origins, Enteritidis, Mbandaka, Typhimurium, Agona and Anatum were ranked as the top five Salmonella serotypes; in more recent years, S . Heidelberg has increased in frequency. Although with different proportions, the top 10 prevalent serotypes were identified in both human and nonhuman origins, underscoring the role of animals, food products and environment as reservoirs of Salmonella with potential to cause human salmonellosis.
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. Genomic characterization and antimicrobial resistance profiles of Salmonella enterica serovar Infantis isolated from food, humans and veterinary-related sources in Brazil. J Appl Microbiol 2021; 132:3327-3342. [PMID: 34958707 DOI: 10.1111/jam.15430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 01/07/2023]
Abstract
AIMS To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil. METHODS AND RESULTS Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3″-Ib; aph(6)-Id), β-lactams (blaTEM-1 ; blaCTX-M-8 ; blaCMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids. CONCLUSIONS The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Ribeirão Preto, SP, Brazil
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Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:85/2/e00031-20. [PMID: 33910982 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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Comparative Genomic Analysis of Third-Generation-Cephalosporin-Resistant Escherichia coli Harboring the bla CMY-2-Positive IncI1 Group, IncB/O/K/Z, and IncC Plasmids Isolated from Healthy Broilers in Japan. Antimicrob Agents Chemother 2020; 64:AAC.02385-19. [PMID: 32366721 DOI: 10.1128/aac.02385-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
The off-label use of third-generation cephalosporins (3GCs) during in ovo vaccination or vaccination of newly hatched chicks has been a common practice worldwide. CMY-2-producing Escherichia coli strains have been disseminated in broiler chicken production. The objective of this study was to determine the epidemiological linkage of bla CMY-2-positive plasmids among broilers both within and outside Japan, because the grandparent stock and parent stock were imported into Japan. We examined the whole-genome sequences of 132 3GC-resistant E. coli isolates collected from healthy broilers during 2002 to 2014. The predominant 3GC resistance gene was bla CMY-2, which was detected in the plasmids of 87 (65.9%) isolates. The main plasmid replicon types were IncI1-Iγ (n = 21; 24.1%), IncI (n = 12; 13.8%), IncB/O/K/Z (n = 28; 32.2%), and IncC (n = 22; 25.3%). Those plasmids were subjected to gene clustering, network analyses, and plasmid multilocus sequence typing (pMLST). The chromosomal DNA of isolates was subjected to MLST and single-nucleotide variant (SNV)-based phylogenetic analysis. MLST and SNV-based phylogenetic analysis revealed high diversity of E. coli isolates. The sequence type 429 (ST429) cluster harboring bla CMY-2-positive IncB/O/K/Z was closely related to isolates from broilers in Germany harboring bla CMY-2-positive IncB/O/K/Z. pST55-IncI, pST12-IncI1-Iγ, and pST3-IncC were prevalent in western Japan. pST12-IncI1-Iγ and pST3-IncC were closely related to plasmids detected in E. coli isolates from chickens in North America, whereas 26 IncB/O/K/Z types were related to those in Europe. These data will be useful to reveal the whole picture of transmission of CMY-2-producing bacteria inside and outside Japan.
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Silveira L, Nunes A, Pista Â, Isidro J, Belo Correia C, Saraiva M, Batista R, Castanheira I, Machado J, Gomes JP. Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to Portugal. Microb Drug Resist 2020; 27:87-98. [PMID: 32460607 DOI: 10.1089/mdr.2019.0384] [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: 12/18/2022] Open
Abstract
Salmonella enterica serovars Heidelberg and Minnesota frequently display several genetic mobile elements making them potential spreaders of resistance genes. Here, we phenotypically determined the antibiotic resistance profile and subsequently performed whole-genome sequencing on 36 isolates recovered from samples of fresh poultry meat, within the Portuguese Official Inspection Plan for Imported Foodstuffs. Several isolates of both serovars showed high genetic relatedness either with isolates from raw poultry meat imported to the Netherlands from Brazil or with isolates from samples from the broiler production chain in Brazil. The multidrug-resistant (MDR) character was common to the vast majority (94.4%) of isolates from both serovars, and several isolates carried the plasmid IncA/C2 containing the β-lactamase gene blaCMY-2 and IncX1 containing a type IV secretion system. These results somehow mirror the scenario observed in the Netherlands, showing the introduction, through fresh imported poultry meat in compliance with European legislation, of MDR Salmonella enterica serovars Heidelberg and Minnesota in Europe, with the potential spread of resistance markers. These data suggest the need to revise the hygiene criteria for foodstuffs monitoring before its placement on the market, with the determination of the resistome being an invaluable contribute to limit the dissemination of resistance markers.
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Affiliation(s)
- Leonor Silveira
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Ângela Pista
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
| | - Cristina Belo Correia
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Margarida Saraiva
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Porto, Portugal
| | - Rita Batista
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Isabel Castanheira
- Food Microbiology Laboratory, Reference Unit, Department of Food and Nutrition, National Institute of Health, Lisbon, Portugal
| | - Jorge Machado
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), Lisbon, Portugal
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Souza AIS, Saraiva MMS, Casas MRT, Oliveira GM, Cardozo MV, Benevides VP, Barbosa FO, Freitas Neto OC, Almeida AM, Berchieri A. High occurrence of β-lactamase-producing Salmonella Heidelberg from poultry origin. PLoS One 2020; 15:e0230676. [PMID: 32231395 PMCID: PMC7108700 DOI: 10.1371/journal.pone.0230676] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/05/2020] [Indexed: 11/29/2022] Open
Abstract
Salmonella Heidelberg is commonly reported in foodborne outbreaks around the world, and chickens and poultry products are known as important source of these pathogen. Multidrug-resistant S. Heidelberg strains are disseminated into poultry production chair, which can lead to severe clinical infections in humans and of difficult to treat. This study aimed at evaluating the β-lactam susceptibility and genotypic relatedness of Salmonella Heidelberg at Brazilian poultry production chain. Sixty-two S. Heidelberg strains from poultry production chain (poultry, poultry meat and poultry farm) were used. All strains were evaluated to antimicrobial susceptibility by diffusion disk test, as well as β-lactam resistance genes. Genotypic relatedness was assessed by Pulsed-Field Gel Eletrophoresis, using Xba1 restriction enzyme. Forty-one strains were characterized as multidrug-resistant according to phenotype characterization. The resistance susceptibility revealed 31 distinct profiles, with higher prevalence of streptomycin (61/62), nalidixic acid (50/62), tetracycline (43/62) and β-lactam drugs (37/62). blaCMY-2 was the more frequent β-lactamase gene found (38/62); other resistance genes found were blaCTX-M (2/62), blaSHV (3/62) and blaTEM-1 (38/62). No carbapenemase genes was found. The Pulsed-Field Gel Electrophoresis showed 58 different profiles. Strains with a larger number of antimicrobial resistance were grouped into ten major clusters apart from others. The spread of resistance by ampC continues to rise, thereby turning concern to public health, since the β-lactam antimicrobials are used as a therapeutic treatment in humans.
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Affiliation(s)
- Andrei I S Souza
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
- Agricultural and Livestock Microbiology Postgraduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Mauro M S Saraiva
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Monique R T Casas
- Nucleus of Enteric Diseases and Infections by Special Pathogens of the Center for Bacteriology of the Adolfo Lutz Institute, São Paulo, São Paulo, Brazil
| | - Gustavo M Oliveira
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Marita V Cardozo
- Department of Veterinary Pathology, Laboratory of Microbiology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Valdinete P Benevides
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
- Agricultural and Livestock Microbiology Postgraduation Program, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Fernanda O Barbosa
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
- Veterinary Medicine Postgraduation Program, School of Agricultural ad Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | | | - Adriana M Almeida
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
| | - Angelo Berchieri
- Department of Veterinary Pathology, Laboratory of Avian Pathology, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, São Paulo, Brazil
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F. Rabello R, R. Bonelli R, A. Penna B, P. Albuquerque J, M. Souza R, M. F. Cerqueira A. Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview. Animals (Basel) 2020; 10:E552. [PMID: 32224900 PMCID: PMC7222418 DOI: 10.3390/ani10040552] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/10/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.
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Affiliation(s)
- Renata F. Rabello
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil (B.A.P.); (J.P.A.)
| | - Raquel R. Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Bruno A. Penna
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil (B.A.P.); (J.P.A.)
| | - Julia P. Albuquerque
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil (B.A.P.); (J.P.A.)
| | - Rossiane M. Souza
- Centro Estadual de Pesquisa em Sanidade Animal, Empresa de Pesquisa Agropecuária do Estado do Rio de Janeiro, Niterói 24120-191, Brazil
| | - Aloysio M. F. Cerqueira
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil (B.A.P.); (J.P.A.)
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Rabello RF, Bonelli RR, Penna BA, Albuquerque JP, Souza RM, Cerqueira AMF. Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview. Animals (Basel) 2020. [PMID: 32224900 DOI: 10.3390/ani1004055210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.
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Affiliation(s)
- Renata F Rabello
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil
| | - Raquel R Bonelli
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Bruno A Penna
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil
| | - Julia P Albuquerque
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil
| | - Rossiane M Souza
- Centro Estadual de Pesquisa em Sanidade Animal, Empresa de Pesquisa Agropecuária do Estado do Rio de Janeiro, Niterói 24120-191, Brazil
| | - Aloysio M F Cerqueira
- Departamento de Microbiologia e Parasitologia, Universidade Federal Fluminense, Niterói 24210-130, Brazil
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Na SH, Moon DC, Kang HY, Song HJ, Kim SJ, Choi JH, Yoon JW, Yoon SS, Lim SK. Molecular characteristics of extended-spectrum β-lactamase/AmpC-producing Salmonella enterica serovar Virchow isolated from food-producing animals during 2010-2017 in South Korea. Int J Food Microbiol 2020; 322:108572. [PMID: 32169770 DOI: 10.1016/j.ijfoodmicro.2020.108572] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/21/2020] [Accepted: 02/21/2020] [Indexed: 01/30/2023]
Abstract
Global dissemination of non-typhoidal Salmonella producing extended-spectrum β-lactamase (ESBL) is a public-health concern. Recently, the prevalence of Salmonella spp. resistant to third-generation cephalosporins has been increasing in food-producing animals in Korea. In this study, we investigated resistance mechanisms and molecular characteristics of S. Virchow isolates resistant to extended-spectrum cephalosporins (ESCs). We obtained 265 S. Virchow isolates from fecal and carcasses samples of cattle (n = 2), pigs (n = 7), and chickens (n = 256) during 2010-2017, and observed high ESC-resistance (63.8%, 169/265); most of the resistant isolates (96.4%) were obtained from chickens. ESC-resistant S. Virchow isolates (n = 169) showed significantly higher resistance rates to other antimicrobials (especially aminoglycosides and tetracycline, p-value <0.0001), as well as prevalence of multidrug resistance, than did ESC-susceptible S. Virchow isolates (n = 96). All ESC-resistant S. Virchow produced CTX-M-15-type ESBL (n = 147) and/or CMY-2-type AmpC β-lactamase (n = 23). ESC-resistant S. Virchow represented seven pulsotypes, predominantly composed of type II (58.6%) and III (26.0%), detected in 69 farms in 10 provinces, and 33 farms in 7 provinces, respectively. Genes encoding ESC-resistance were horizontally transferred by conjugation to recipient E. coli J53; this was demonstrated in 28.8% (42/146) of blaCTX-M-15-positive isolates and in 50.0% (11/22) of blaCMY-2-positive isolates. All conjugative plasmids carrying blaCTX-M-15 and blaCMY-2 genes belonged to ST2-IncHI2 and ST12/CC12-IncI1, respectively. Genetic features of transferred bla genes were involved with ISEcp1 in both blaCTX-M-15 and blaCMY-2; ISEcp1 plays a critical role in the efficient capture, expression, and mobilization of bla genes. In addition to blaCTX-M-15 genes, resistance markers to aminoglycosides and/or tetracycline were co-transferred to recipient E. coli J53. Our results show a high prevalence of ESBL-producing S. Virchow in chickens and chicken carcasses. Specific blaCTX-M-15 and blaCMY-2-carrying S. Virchow clones and plasmids were predominant in food-producing animals nationwide. Restriction of antimicrobial use and proper biosecurity practices at the farm level should be urgently implemented in the poultry industry.
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Affiliation(s)
- Seok Hyeon Na
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Hee Young Kang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Jang Won Yoon
- College of Veterinary Medicine & Institute Veterinary Science, Kangwon National University, Chuncheon, Gangwon-do 24341, Republic of Korea.
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, 177 Hyeksin 8-ro, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea.
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Rehman MA, Hasted TL, Persaud-Lachhman MG, Yin X, Carrillo C, Diarra MS. Genome Analysis and Multiplex PCR Method for the Molecular Detection of Coresistance to Cephalosporins and Fosfomycin in Salmonella enterica Serovar Heidelberg. J Food Prot 2019; 82:1938-1949. [PMID: 31633426 DOI: 10.4315/0362-028x.jfp-19-205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Heidelberg is among the top three Salmonella enterica serovars associated with human foodborne illness in Canada. Traditional culture and antimicrobial susceptibility testing techniques can be time-consuming to identify Salmonella Heidelberg resistant to cephalosporins and fosfomycin. Rapid and accurate detection of such antibiotic-resistant Salmonella Heidelberg isolates is essential to adopt appropriate control measures. In this study, 15 Salmonella Heidelberg strains isolated from feces of Canadian broiler chickens were characterized by whole genome sequencing. Salmonella Heidelberg genomes had an average coverage of greater than 80-fold, an average of 4,761 protein-coding genes, and all belonged to multilocus sequence type ST15. Genome sequences were compared with genomes in the National Center for Biotechnology Information Pathogen Detection database ( www.ncbi.nlm.nih.gov/pathogens/ ), including human outbreak isolates. The Canadian broiler isolates clustered with chicken isolates from the United States and an equine clinical isolate from Ontario, Canada. In agreement with their antimicrobial resistance phenotypes, several chromosomally encoded specific antimicrobial resistance genes including fosA7 and multidrug resistance efflux pump determinants were detected. An AmpC-like β-lactamase gene, blaCMY-2, linked with a quaternary ammonium compound resistance gene, sugE, on a replicon type IncI1 plasmid was detected in all 15 broiler Salmonella Heidelberg isolates. Of the 205,031 published Salmonella genomes screened in silico, 4,954 (2.4%) contained blaCMY-2, 8,143 (4.0%) contained fosA7, and 919 (0.4%) contained both resistance genes. The combination of both resistance genes (fosA7 and blaCMY-2) was detected in 64% of the Heidelberg genomes and in a small proportion of various other serovars. A PCR method was developed to detect Salmonella Heidelberg in pure culture and chicken feces based on specific primers targeting genes conferring fosfomycin (fosA7) and third-generation cephalosporin (blaCMY-2) resistance as well as the Salmonella-specific invA gene and the universal 16S rRNA genes. The PCR assay was specific and sensitive for blaCMY-2 and fosA7 harboring Salmonella Heidelberg. However, some other Salmonella serovars containing these two resistance genes could also be detected by the developed PCR method.
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Affiliation(s)
- Muhammad Attiq Rehman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93, Stone Road West, Guelph, Ontario, Canada N1G 5C9 (ORCID: https://orcid.org/0000-0002-2062-1969 [M.A.R.])
| | - Teri-Lyn Hasted
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93, Stone Road West, Guelph, Ontario, Canada N1G 5C9 (ORCID: https://orcid.org/0000-0002-2062-1969 [M.A.R.])
| | - Marissa G Persaud-Lachhman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93, Stone Road West, Guelph, Ontario, Canada N1G 5C9 (ORCID: https://orcid.org/0000-0002-2062-1969 [M.A.R.])
| | - Xianhua Yin
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93, Stone Road West, Guelph, Ontario, Canada N1G 5C9 (ORCID: https://orcid.org/0000-0002-2062-1969 [M.A.R.])
| | - Catherine Carrillo
- Canadian Food Inspection Agency, 960, Carling Avenue, Building 22, Ottawa, Ontario, Canada K1A 0Y9
| | - Moussa S Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93, Stone Road West, Guelph, Ontario, Canada N1G 5C9 (ORCID: https://orcid.org/0000-0002-2062-1969 [M.A.R.])
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Identification of Primary Antimicrobial Resistance Drivers in Agricultural Nontyphoidal Salmonella enterica Serovars by Using Machine Learning. mSystems 2019; 4:4/4/e00211-19. [PMID: 31387929 PMCID: PMC6687941 DOI: 10.1128/msystems.00211-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) is a leading global cause of bacterial foodborne morbidity and mortality. Our ability to treat severe NTS infections has been impaired by increasing antimicrobial resistance (AMR). To understand and mitigate the global health crisis AMR represents, we need to link the observed resistance phenotypes with their underlying genomic mechanisms. Broiler chickens represent a key reservoir and vector for NTS infections, but isolates from this setting have been characterized in only very low numbers relative to clinical isolates. In this study, we sequenced and assembled 97 genomes encompassing 7 serotypes isolated from broiler chicken in farms in British Columbia between 2005 and 2008. Through application of machine learning (ML) models to predict the observed AMR phenotype from this genomic data, we were able to generate highly (0.92 to 0.99) precise logistic regression models using known AMR gene annotations as features for 7 antibiotics (amoxicillin-clavulanic acid, ampicillin, cefoxitin, ceftiofur, ceftriaxone, streptomycin, and tetracycline). Similarly, we also trained "reference-free" k-mer-based set-covering machine phenotypic prediction models (0.91 to 1.0 precision) for these antibiotics. By combining the inferred k-mers and logistic regression weights, we identified the primary drivers of AMR for the 7 studied antibiotics in these isolates. With our research representing one of the largest studies of a diverse set of NTS isolates from broiler chicken, we can thus confirm that the AmpC-like CMY-2 β-lactamase is a primary driver of β-lactam resistance and that the phosphotransferases APH(6)-Id and APH(3″-Ib) are the principal drivers of streptomycin resistance in this important ecosystem.IMPORTANCE Antimicrobial resistance (AMR) represents an existential threat to the function of modern medicine. Genomics and machine learning methods are being increasingly used to analyze and predict AMR. This type of surveillance is very important to try to reduce the impact of AMR. Machine learning models are typically trained using genomic data, but the aspects of the genomes that they use to make predictions are rarely analyzed. In this work, we showed how, by using different types of machine learning models and performing this analysis, it is possible to identify the key genes underlying AMR in nontyphoidal Salmonella (NTS). NTS is among the leading cause of foodborne illness globally; however, AMR in NTS has not been heavily studied within the food chain itself. Therefore, in this work we performed a broad-scale analysis of the AMR in NTS isolates from commercial chicken farms and identified some priority AMR genes for surveillance.
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van den Berg RR, Dissel S, Rapallini MLBA, van der Weijden CC, Wit B, Heymans R. Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands. PLoS One 2019; 14:e0219795. [PMID: 31329622 PMCID: PMC6645675 DOI: 10.1371/journal.pone.0219795] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023] Open
Abstract
Multidrug-resistant Salmonella enterica serovar Heidelberg isolates are frequently recovered in the Netherlands from poultry meat imported from South America. Our aim was to retrospectively assess the characteristics of the antimicrobial determinants, gene content and the clonal relatedness of 122 unique S. Heidelberg isolates from chicken meat from Brazil (n = 119) and Argentina (n = 3) that were imported between 2010 and 2015. These isolates were subjected to antimicrobial susceptibility testing, PCR and Illumina HiSeq2500 whole genome sequencing. Draft genomes were assembled to assess the gene content, and the phylogenetic relationships between isolates were determined using single nucleotide polymorphisms. Ciprofloxacin-resistance was identified in 98.4% of the isolates and 83.7% isolates showed resistance to the extended-spectrum cephalosporins cefotaxime and ceftazidime (83.6% and 82.8% respectively). Of the latter, 97.1% exhibited an AmpC phenotype and contained blaCMY-2, whereas the remaining three isolates contained an extended spectrum beta-lactamase. Of the 99 extended-spectrum cephalosporins-resistant isolates harboring CMY-2 plasmids, 56.6% contained the incompatibility group I1 replicon. Phylogenetic cluster analysis showed that all isolates from Brazil clustered together, with 49% occurring in clusters larger than 5 isolates that revealed intra-cluster similarities based on geographical location and/or resistance profiles. The remaining isolates were classified in smaller clusters or as singletons, highlighting the large diversity of S. Heidelberg in the poultry chain in Brazil that was revealed by this study. Considering the potential public health risk associated with multidrug-resistant S. Heidelberg in imported poultry, collaborative whole genome sequencing-based surveillance is needed to monitor the spread, pathogenic properties and epidemiological distribution of these isolates.
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Affiliation(s)
- Redmar R. van den Berg
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Serge Dissel
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Michel L. B. A. Rapallini
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Coen C. van der Weijden
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Ben Wit
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
| | - Raymond Heymans
- Netherlands Food and Consumer Product Safety Authority, Consumer and Safety Division, Laboratory Food and Feed Safety, WB Wageningen, the Netherlands
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