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Liu H, Zheng L, Fan H, Pang J. Genomic analysis of antibiotic resistance genes and mobile genetic elements in eight strains of nontyphoid Salmonella. mSystems 2024:e0058624. [PMID: 39158311 DOI: 10.1128/msystems.00586-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/12/2024] [Indexed: 08/20/2024] Open
Abstract
Nontyphoidal Salmonella (NTS) is the main etiological agent of human nontyphoidal salmonellosis. The aim of this study was to analyze the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance (AMR) genes from eight strains of NTS detected in Zhenjiang City, Jiangsu Province, China. Fecal samples from outpatients with food-borne diarrhea were collected in 2022. The NTS isolates were identified, and their susceptibility was tested with the Vitek 2 Compact system. The genomes of the NTS isolates were sequenced with the Illumina NovaSeq platform and Oxford Nanopore Technologies platform. The AMR genes and mobile genetic elements (MGEs) were predicted with the relevant open access resources. Eight strains of NTS were isolated from 153 specimens, and Salmonella Typhimurium ST19 was the most prevalent serotype. The AMR gene with the highest detection rate was AAC(6')-Iaa (10.5%) followed by TEM-1 (7.9%), sul2 (6.6%), and tet(A) (5.3%). Eleven MGEs carrying 34 AMR genes were identified on the chromosomes of 3 of the 8 NTS, including 3 resistance islands, 6 composite transposons (Tns), and 2 integrons. Eighteen plasmids carrying 40 AMR genes were detected in the 8 NTS strains, including 6 mobilizable plasmids, 3 conjugative plasmids, and 9 nontransferable plasmids, 7 of which carried 10 composite Tns and 3 integrons. This study provided a theoretical basis, from a genetic perspective, for the prevention and control of NTS resistance in Zhenjiang City. IMPORTANCE Human nontyphoidal salmonellosis is one of the common causes of bacterial food-borne illnesses, with significant social and economic impacts, especially those caused by invasive multidrug-resistant nontyphoidal Salmonella, which entails high morbidity and mortality. Antimicrobial resistance is mainly mediated by drug resistance genes, and mobile genetic elements play key roles in the capture, accumulation, and dissemination of antimicrobial resistance genes. Therefore, it is necessary to study the epidemiological characteristics and horizontal transfer mechanisms of antimicrobial resistance genes of nontyphoidal Salmonella to prevent the spread of multidrug-resistant nontyphoidal Salmonella.
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Affiliation(s)
- Haibing Liu
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Lijie Zheng
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Huimin Fan
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ji Pang
- Department of Clinical Laboratory, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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Belay WY, Getachew M, Tegegne BA, Teffera ZH, Dagne A, Zeleke TK, Abebe RB, Gedif AA, Fenta A, Yirdaw G, Tilahun A, Aschale Y. Mechanism of antibacterial resistance, strategies and next-generation antimicrobials to contain antimicrobial resistance: a review. Front Pharmacol 2024; 15:1444781. [PMID: 39221153 PMCID: PMC11362070 DOI: 10.3389/fphar.2024.1444781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Antibacterial drug resistance poses a significant challenge to modern healthcare systems, threatening our ability to effectively treat bacterial infections. This review aims to provide a comprehensive overview of the types and mechanisms of antibacterial drug resistance. To achieve this aim, a thorough literature search was conducted to identify key studies and reviews on antibacterial resistance mechanisms, strategies and next-generation antimicrobials to contain antimicrobial resistance. In this review, types of resistance and major mechanisms of antibacterial resistance with examples including target site modifications, decreased influx, increased efflux pumps, and enzymatic inactivation of antibacterials has been discussed. Moreover, biofilm formation, and horizontal gene transfer methods has also been included. Furthermore, measures (interventions) taken to control antimicrobial resistance and next-generation antimicrobials have been discussed in detail. Overall, this review provides valuable insights into the diverse mechanisms employed by bacteria to resist the effects of antibacterial drugs, with the aim of informing future research and guiding antimicrobial stewardship efforts.
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Affiliation(s)
- Wubetu Yihunie Belay
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Melese Getachew
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Bantayehu Addis Tegegne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Zigale Hibstu Teffera
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Dagne
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Tirsit Ketsela Zeleke
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Rahel Belete Abebe
- Department of clinical pharmacy, College of medicine and health sciences, University of Gondar, Gondar, Ethiopia
| | - Abebaw Abie Gedif
- Department of Pharmacy, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Abebe Fenta
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Getasew Yirdaw
- Department of environmental health science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Adane Tilahun
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Yibeltal Aschale
- Department of Medical Laboratory Science, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
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Intuy R, Supa-Amornkul S, Jaemsai B, Ruangchai W, Wiriyarat W, Chaturongakul S, Palittapongarnpim P. A novel variant in Salmonella genomic island 1 of multidrug-resistant Salmonella enterica serovar Kentucky ST198. Microbiol Spectr 2024; 12:e0399423. [PMID: 38687075 PMCID: PMC11237444 DOI: 10.1128/spectrum.03994-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Salmonella enterica serovar Kentucky ST198 is a major health threat due to its resistance to ciprofloxacin and several other drugs, including third-generation cephalosporins. Many drug-resistant genes have been identified in the Salmonella genomic island 1 variant K (SGI1-K). In this study, we investigated the antimicrobial resistance (AMR) profile and genotypic relatedness of two isolates of ciprofloxacin-resistant (CIPR) S. Kentucky ST198 from poultry in Northeastern Thailand. We successfully assembled the complete genomes of both isolates, namely SSSE-01 and SSSE-03, using hybrid de novo assembly of both short- and long-read sequence data. The complete genomes revealed their highly similar genomic structures and a novel variant of SGI1-K underlying multidrug-resistant (MDR) patterns, including the presence of blaTEM-1b, which confers resistance to beta-lactams, including cephalosporins and lnu(F) which confers resistance to lincomycin and other lincosamides. In addition, the chromosomal mutations in the quinolone resistance-determining region (QRDR) were found at positions 83 (Ser83Phe) and 87 (Asp87Asn) of GyrA and at positions 57 (Thr57Ser) and 80 (Ser80Ile) of ParC suggesting high resistance to ciprofloxacin. We also compared SSSE-01 and SSSE-03 with publicly available complete genome data and revealed significant variations in SGI1-K genetic structures and variable relationships to antibiotic resistance. In comparison to the other isolates, SGI1-K of SSSE-01 and SSSE-03 had a relatively large deletion in the backbone, spanning from S011 (traG∆) to S027 (resG), and the inversion of the IS26-S044∆-yidY segment. Their MDR region was characterized by the inversion of a large segment, including the mer operon and the relocation of IntI1 and several resistance genes downstream of the IS26-S044∆-yidY segment. These structural changes were likely mediated by the recombination of IS26. The findings broaden our understanding of the possible evolution pathway of SGI1-K in fostering drug resistance, which may provide opportunities to control these MDR strains.IMPORTANCEThe emergence of ciprofloxacin-resistant (CIPR) Salmonella Kentucky ST198 globally has raised significant concerns. This study focuses on two poultry isolates from Thailand, revealing a distinct Salmonella genomic island 1 variant K (SGI1-K) genetic structure. Remarkably, multiple antibiotic resistance genes (ARGs) were identified within the SGI1-K as well as other locations in the chromosome, but not in plasmids. Comparing the SGI1-K genetic structures among global and even within-country isolates unveiled substantial variations. Intriguingly, certain isolates lacked ARGs within the SGI1-K, while others had ARGs relocated outside. The presence of chromosomal extended-spectrum β-lactamase (ESBL) genes and lincosamide resistance, lnu(F), gene, could potentially inform the choices of the treatment of CIPRS. Kentucky ST198 infections in humans. This study highlights the importance of understanding the diverse genetic structures of SGI1-K and emphasizes the role of animals and humans in the emergence of antimicrobial resistance.
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Affiliation(s)
- Rattanaporn Intuy
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sirirak Supa-Amornkul
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Bharkbhoom Jaemsai
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wuthiwat Ruangchai
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Witthawat Wiriyarat
- Department of Pre-Clinical and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Bangkok, Thailand
| | - Soraya Chaturongakul
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Molecular Medical Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Bangkok, Thailand
| | - Prasit Palittapongarnpim
- Professor Pornchai Matangkasombut Center for Microbial Genomics (CENMIG), Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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Ali S, Aslam MA, Kanwar R, Mehmood Z, Arshad MI, Hussain S. Phage-antibiotic synergism against Salmonella typhi isolated from stool samples of typhoid patients. Ir J Med Sci 2024; 193:1377-1384. [PMID: 38158479 DOI: 10.1007/s11845-023-03599-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Typhoid fever is a fatal disease in humans that is caused by Salmonella typhi. S. typhi infections need immediate antibiotic therapy, and their extensive use has led to multidrug-resistant (MDR) pathogens. The use of bacteriophages is becoming a new way to treat these resistant bacteria. This research was directed to bacteriophage isolation against S. typhi and to determine phage-antibiotic synergism. AIMS To isolate bacteriophages targeting S. typhi, the causative agent of typhoid fever, and investigate their potential synergistic effects when combined with antibiotics. STUDY DESIGN A cross-sectional study. METHODS The Widal test was positive; twenty diarrheal stool samples were taken, and for confirmation of S. typhi, different biochemical tests were performed. The disc-diffusion technique was used to determine antimicrobial resistance, and the double agar overlay method was used for bacteriophage isolation from sewage water against S. typhi. To test antibiotic-phage synergism, the S. typhi bacteria was treated by phages together with varying antibiotic concentrations. RESULTS Eleven samples were positive for S. typhi with black colonies on SS-agar. These were catalase and MR positive with alkali butt on TSI. Clear plaques were observed after the agar overlay. Isolated phages were stable at various pH and temperature levels. Synergism was observed on agar plate. The zone was enlarged when phages were combined with bacterial lawn culture and ciprofloxacin disk. Bacterial growth inhibition had a significant p-value of 0.03 in titration plates, with the phage-ciprofloxacin combination being more effective than the phage and antibiotic alone. CONCLUSION The study highlights the synergistic effects of isolated bacteriophages with antibiotics, which are not only effective against S. typhi infection but also decrease antibiotic resistance.
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Affiliation(s)
- Saqib Ali
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Aamir Aslam
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Rabia Kanwar
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Zain Mehmood
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Imran Arshad
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad, 38000, Pakistan
| | - Sarfaraz Hussain
- School of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255049, Shandong, People's Republic of China.
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
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Murányi G, Szabó M, Acsai K, Kiss J. Two birds with one stone: SGI1 can stabilize itself and expel the IncC helper by hijacking the plasmid parABS system. Nucleic Acids Res 2024; 52:2498-2518. [PMID: 38300764 PMCID: PMC10954446 DOI: 10.1093/nar/gkae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
The SGI1 family integrative mobilizable elements, which are efficient agents in distribution of multidrug resistance in Gammaproteobacteria, have a complex, parasitic relationship with their IncC conjugative helper plasmids. Besides exploiting the transfer apparatus, SGI1 also hijacks IncC plasmid control mechanisms to time its own excision, replication and expression of self-encoded T4SS components, which provides advantages for SGI1 over its helpers in conjugal transfer and stable maintenance. Furthermore, SGI1 destabilizes its helpers in an unknown, replication-dependent way when they are concomitantly present in the same host. Here we report how SGI1 exploits the helper plasmid partitioning system to displace the plasmid and simultaneously increase its own stability. We show that SGI1 carries two copies of sequences mimicking the parS sites of IncC plasmids. These parS-like elements bind the ParB protein encoded by the plasmid and increase SGI1 stability by utilizing the parABS system of the plasmid for its own partitioning, through which SGI1 also destabilizes the helper plasmid. Furthermore, SGI1 expresses a small protein, Sci, which significantly strengthens this plasmid-destabilizing effect, as well as SGI1 maintenance. The plasmid-induced replication of SGI1 results in an increased copy-number of parS-like sequences and Sci expression leading to strong incompatibility with the helper plasmid.
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Affiliation(s)
- Gábor Murányi
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
| | - Mónika Szabó
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
| | - Károly Acsai
- Ceva Animal Health, Ceva-Phylaxia, Budapest, H1107 Hungary
| | - János Kiss
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, H2100 Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Gödöllő, H2100 Hungary
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Peng H, Wu H, Gu W, Lu Y, Qin H, You Y, Zhou D, Wang D, Sun L, Zhou C, Zheng Y. Exploring the Application Potential of Aquaculture Sewage Treatment of Pseudomonas chengduensis Strain WD211 Based on Its Complete Genome. Genes (Basel) 2023; 14:2107. [PMID: 38136929 PMCID: PMC10743257 DOI: 10.3390/genes14122107] [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: 10/08/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Pseudomonas chengduensis is a new species of Pseudomonas discovered in 2014, and currently, there is a scarcity of research on this bacterium. The P. chengduensis strain WD211 was isolated from a fish pond. This study investigated the purification capability and environmental adaptability of strain WD211 in wastewater and described the basic features and functional genes of its complete genome. According to the results, the sewage treated with strain WD211 showed a decrease in concentration of 18.12% in total nitrogen, 89.39% in NH4+, 62.16% in NO3-, 79.97% in total phosphorus, and 71.41% in COD after 24 h. Strain WD211 is able to survive in a pH range of 6-11. It shows resistance to 7% sodium chloride and different types of antibiotics. Genomic analysis showed that strain WD211 may remove nitrogen and phosphorus through the metabolic pathway of nitrogen assimilation and phosphorus accumulation, and that it can promote organic decomposition through oxygenase. Strain WD211 possesses genes for producing betaine, trehalose, and sodium ion transport, which provide it with salt tolerance. It also has genes for antibiotic efflux and multiple oxidases, which give it antibiotic resistance. This study contributes to the understanding of the sewage treatment ability and potential applications of P. chengduensis.
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Affiliation(s)
- Huanlong Peng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Hangtao Wu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Wenjie Gu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming 525000, China
| | - Yusheng Lu
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Hongjie Qin
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yi You
- Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Donglai Zhou
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510610, China
| | - Dan Wang
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Lili Sun
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Changmin Zhou
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
| | - Yanling Zheng
- Institute of Agricultural Resources and Environment, Guangdong Academy of Agricultural Sciences, Key Laboratory of Plant Nutrition and Fertilizer in South Region, Ministry of Agriculture, Key Laboratory of Nutrient Cycling and Farmland Conservation of Guangdong Province, Guangzhou 510640, China
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Vázquez X, García-Fierro R, Fernández J, Bances M, Herrero-Fresno A, Olsen JE, Rodicio R, Ladero V, García V, Rodicio MR. Incidence and Genomic Background of Antibiotic Resistance in Food-Borne and Clinical Isolates of Salmonella enterica Serovar Derby from Spain. Antibiotics (Basel) 2023; 12:1204. [PMID: 37508300 PMCID: PMC10376468 DOI: 10.3390/antibiotics12071204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Salmonella enterica serovar Derby (S. Derby) ranks fifth among nontyphoidal Salmonella serovars causing human infections in the European Union. S. Derby isolates (36) collected between 2006 and 2018 in a Spanish region (Asturias) from human clinical samples (20) as well as from pig carcasses, pork- or pork and beef-derived products, or wild boar (16) were phenotypically characterized with regard to resistance, and 22 (12 derived from humans and 10 from food-related samples) were also subjected to whole genome sequence analysis. The sequenced isolates belonged to ST40, a common S. Derby sequence type, and were positive for SPI-23, a Salmonella pathogenicity island involved in adherence and invasion of the porcine jejune enterocytes. Isolates were either susceptible (30.6%), or resistant to one or more of the 19 antibiotics tested for (69.4%). Resistances to tetracycline [tet(A), tet(B) and tet(C)], streptomycin (aadA2), sulfonamides (sul1), nalidixic acid [gyrA (Asp87 to Asn)] and ampicillin (blaTEM-1-like) were detected, with frequencies ranging from 8.3% to 66.7%, and were higher in clinical than in food-borne isolates. The fosA7.3 gene was present in all sequenced isolates. The most common phenotype was that conferred by the tet(A), aadA2 and sul1 genes, located within identical or closely related variants of Salmonella Genomic Island 1 (SGI1), where mercury resistance genes were also present. Diverse IncI1-I(α) plasmids belonging to distinct STs provided antibiotic [blaTEM-1, tet(A) and/or tet(B)] and heavy metal resistance genes (copper and silver), while small pSC101-like plasmids carried tet(C). Regardless of their location, most resistance genes were associated with genetic elements involved in DNA mobility, including a class one integron, multiple insertion sequences and several intact or truncated transposons. By phylogenetic analysis, the isolates were distributed into two distinct clades, both including food-borne and clinical isolates. One of these clades included all SGI1-like positive isolates, which were found in both kinds of samples throughout the entire period of study. Although the frequency of S. Derby in Asturias was very low (0.5% and 3.1% of the total clinical and food isolates of S. enterica recovered along the period of study), it still represents a burden to human health linked to transmission across the food chain. The information generated in the present study can support further epidemiological surveillance aimed to control this zoonotic pathogen.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
| | - Raquel García-Fierro
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 30627 Madrid, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública, Dirección General de Salud Pública, Consejería de Salud del Principado de Asturias, 33011 Oviedo, Spain
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
- Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (IAPA), 33011 Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - M Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Ambrose SJ, Hall RM. Effect of the S008-sgaCD operon on IncC plasmid stability in the presence of SGI1-K or absence of an SGI1 variant. Plasmid 2023; 127:102698. [PMID: 37516393 DOI: 10.1016/j.plasmid.2023.102698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
An IncC or IncA plasmid is needed to enable transfer of SGI1 type integrative mobilisable elements but an IncC plasmid does not stably co-exist with SGI1. However, the plasmid is stably maintained with SGI1-K, a natural SGI1 deletion variant that lacks the sgaDC genes (S007 and S006) and the upstream open reading frame (S008) found in the SGI1 backbone. Here, the effect of the sgaDC genes and S008 on the stability of an IncC plasmid in an Escherichia coli strain with or without SGI1-K was examined. Co-transcription of the S008 open reading frame with the downstream sgaDC genes was established. When a strain containing SGI1-K complemented with a pK18 plasmid that included S008-sgaDC or sgaDC expressed from the constitutive pUC promoter was grown without antibiotic selection, the resident IncC plasmid was rapidly lost but loss was slower when S008 was present. In contrast, SGI1-K and the S008-sgaDC or sgaDC plasmid were quite stably maintained for >100 generations. However, the high copy number plasmids carrying the SGI1-derived S008-sgaDC or sgaDC genes constitutively expressed could not be introduced into an E. coli strain carrying the IncC plasmid but without SGI1-K. Using equivalent plasmids with S008-sgaDC or sgaDC genes controlled by an arabinose-inducible promoter, under inducing conditions the IncC plasmid was stable but the plasmid containing the SGI1-derived genes was rapidly lost. This unexpected observation indicates that there are multiple interactions between the IncC plasmid and SGI1 in which the transcriptional activator genes sgaDC play a role. These interactions will require further investigation.
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Affiliation(s)
- Stephanie J Ambrose
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
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Uzairue LI, Shittu OB, Ojo OE, Obuotor TM, Olanipekun G, Ajose T, Arogbonlo R, Medugu N, Ebruke B, Obaro SK. Antimicrobial resistance and virulence genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. SAGE Open Med 2023; 11:20503121231175322. [PMID: 37223673 PMCID: PMC10201152 DOI: 10.1177/20503121231175322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Objectives Bacteremia due to invasive Salmonella enterica has been reported earlier in children in Nigeria. This study aimed to detect the virulence and antibiotic resistance genes of invasive Salmonella enterica from children with bacteremia in north-central Nigeria. Method From June 2015 to June 2018, 4163 blood cultures yielded 83 Salmonella isolates. This is a secondary cross-sectional analysis of the Salmonella isolates. The Salmonella enterica were isolated and identified using standard bacteriology protocol. Biochemical identifications of the Salmonella enterica were made by Phoenix MD 50 identification system. Further identification and confirmation were done with polyvalent antisera O and invA gene. Antimicrobial susceptibility testing was done following clinical and laboratory standard institute guidelines. Resistant genes and virulence genes were determined using a real-time polymerase chain reaction. Result Salmonella typhi 51 (61.4%) was the most prevalent serovar, followed by Salmonella species 13 (15.7%), choleraesuis 8 (9.6%), enteritidis 6 (7.2%), and typhimurium 5 (6.1%). Fifty-one (61.4%) of 83 Salmonella enterica were typhoidal, while 32 (38.6%) were not. Sixty-five (78.3%) of the 83 Salmonella enterica isolates were resistant to ampicillin and trimethoprim-sulfamethoxazole, followed by chloramphenicol 39 (46.7%), tetracycline 41 (41.4%), piperacillin 33 (33.9%), amoxicillin-clavulanate, and streptomycin 21 (25.3%), while cephalothin was 19 (22.9%). Thirty-nine (46.9%) of the 83 Salmonella enterica isolates were multi-drug resistant, and none were extensive drug resistant or pan-drug resistant. A blaTEM 42 (50.6%), floR 32 (38.6%), qnrA 24 (28.9%), tetB 20 (20.1%), tetA 10 (10.0%), and tetG 5 (6.0%) were the antibiotic resistance genes detected. There were perfect agreement between phenotypic and genotypic detection of antimicrobial resistance in tetracycline, ciprofloxacin, and chloramphenicol, while beta-lactam showed κ = 0.60 agreement. All of the Salmonella enterica isolates had the virulence genes invA, sopB, mgtC, and sip4D, while 33 (39.8%), 45 (51.8%), and 2 (2.4%) had ssaQ, spvC, and ljsGI-1, respectively. Conclusion Our findings showed multi-drug resistant Salmonella enterica in children with bacteremia in northern Nigeria. In addition, significant virulence and antimicrobial resistance genes were found in invasive Salmonella enterica in northern Nigeria. Thus, our study emphasizes the need to monitor antimicrobial resistance in Salmonella enterica from invasive sources in Nigeria and supports antibiotic prudence.
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Affiliation(s)
- Leonard I Uzairue
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Medical Laboratory
Sciences, Federal University Oye Ekiti, Ekiti State, Nigeria
| | - Olufunke B Shittu
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Olufemi E Ojo
- Department of Veterinary Microbiology
and Parasitology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Tolulope M Obuotor
- Department of Microbiology, Federal
University of Agriculture, Abeokuta, Ogun State, Nigeria
| | - Grace Olanipekun
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Theresa Ajose
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Ronke Arogbonlo
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Nubwa Medugu
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Department of Microbiology and
Parasitology, National Hospital, Abuja, FCT, Nigeria
| | - Bernard Ebruke
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
| | - Stephen K Obaro
- International Foundation Against
Infectious Disease in Nigeria, Abuja, Nigeria
- Pediatric Infectious Division, the
University of Nebraska Medical Center, Omaha, NE, USA
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Rabha M, Das D, Konwar T, Acharjee S, Sarmah BK. Whole genome sequencing of a novel Bacillus thuringiensis isolated from Assam soil. BMC Microbiol 2023; 23:91. [PMID: 37003972 PMCID: PMC10064770 DOI: 10.1186/s12866-023-02821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Bacillus thuringiensis (Bt) is a gram-positive ubiquitous saprophytic bacterium that produces proteins (Crystal protein, Vegetative insecticidal protein, and Secreted insecticidal protein) toxic to insects during its growth cycle. In the present study, the whole genome of a locally isolated B. thuringiensis strain BA04 was sequenced to explore the genetic makeup and to identify the genes responsible to produce insecticidal proteins including the virulence factors. The strain was isolated from the soil sample of the Kaziranga National Park, Assam, North-Eastern part of India (Latitude: 26°34'39.11''N and Longitude: 93°10'16.04''E). RESULTS The whole genome sequencing (WGS) of the BA04 strain revealed that it has a circular genome of size 6,113,005 bp with four numbers of plasmids. A total of 6,111 genes including two novel crystal protein-encoding genes (MH753362.1 and MH753363.1) were identified. The BLASTn analysis of MH753362.1 showed 84% similarities (maximum identity) with Cry1Ia (KJ710646.1) gene, whereas MH753363.1 exhibited 66% identity with Insecticidal Crystal Protein (ICP)-6 gene (KM053257.1). At the protein level, MH753362.1 and MH753363.1 shared 79% identity with Cry1Ia (AIW52613.1) and 40% identity with Insecticidal Crystal Protein (ICP)-6 (AJW76687.1) respectively. Three-dimensional structures of these two novel protein sequences revealed that MH753362.1 have 48% structural similarity with Cry8ea1 protein, whereas MH753363.1 showed only 20% structural similarity with Cry4Aa protein. Apart from these insecticidal genes, the strain was also found to contain virulence and virulence-associated factors including the antibiotic resistance genes and Clustered regularly interspaced short palindromic repeat (CRISPR) sequences. CONCLUSION This is the first report on the whole genome sequence of Bt strain BA04 isolated from Assam, a North-Eastern state of India. The WGS of strain BA04 unveils the presence of two novel types of insecticidal crystal protein-encoding genes which can be used for the development of insect-resistant transgenic crops. Additionally, the strain could be used for the formulations of effective biopesticides. The WGS provides the fastest and cheapest platform for a better understanding of the genetic makeup of a strain and helps to explore the role of virulence genes in pathogenicity against the insect host.
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Affiliation(s)
- Mihir Rabha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Silkworm Pathology Section, Central Sericultural Research and Training Institute, Central Silk Board, Ministry of Textile, Govt of India, Berhampore, West Bengal, 7421 01, India
| | - Debajit Das
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Department of Biotechnology-Northeast Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat-13, Assam, India
| | - Trishna Konwar
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Department of Biotechnology-Northeast Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat-13, Assam, India
| | - Sumita Acharjee
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India.
- Department of Biotechnology-Northeast Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat-13, Assam, India.
| | - Bidyut Kumar Sarmah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India.
- Department of Biotechnology-Northeast Centre for Agricultural Biotechnology (DBT-NECAB), Assam Agricultural University, Jorhat-13, Assam, India.
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11
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Association of ISVsa3 with Multidrug Resistance in Salmonella enterica Isolates from Cattle (Bos taurus). Microorganisms 2023; 11:microorganisms11030631. [PMID: 36985205 PMCID: PMC10051122 DOI: 10.3390/microorganisms11030631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Salmonella enterica is, globally, an important cause of human illness with beef being a significant attributable source. In the human patient, systemic Salmonella infection requires antibiotic therapy, and when strains are multidrug resistant (MDR), no effective treatment may be available. MDR in bacteria is often associated with the presence of mobile genetic elements (MGE) that mediate horizontal spread of antimicrobial resistance (AMR) genes. In this study, we sought to determine the potential relationship of MDR in bovine Salmonella isolates with MGE. The present study involved 111 bovine Salmonella isolates obtained collectively from specimens derived from healthy cattle or their environments at Midwestern U.S. feedyards (2000–2001, n = 19), or specimens from sick cattle submitted to the Nebraska Veterinary Diagnostic Center (2010–2020, n = 92). Phenotypically, 33/111 isolates (29.7%) were MDR (resistant to ≥3 drug classes). Based on whole-genome sequencing (WGS; n = 41) and PCR (n = 111), a MDR phenotype was strongly associated (OR = 186; p < 0.0001) with carriage of ISVsa3, an IS91-like Family transposase. In all 41 isolates analyzed by WGS ((31 MDR and 10 non-MDR (resistant to 0–2 antibiotic classes)), MDR genes were associated with carriage of ISVsa3, most often on an IncC type plasmid carrying blaCMY-2. The typical arrangement was floR, tet(A), aph(6)-Id, aph(3″)-Ib, and sul2 flanked by ISVsa3. These results suggest that AMR genes in MDR S. enterica isolates of cattle are frequently associated with ISVsa3 and carried on IncC plasmids. Further research is needed to better understand the role of ISVsa3 in dissemination of MDR Salmonella strains.
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12
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Jiang Y, Wang ZY, Li QC, Lu MJ, Wu H, Mei CY, Shen PC, Jiao X, Wang J. Characterization of Extensively Drug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 Isolates from Chicken Meat Products in Xuancheng, China. Microbiol Spectr 2023; 11:e0321922. [PMID: 36847509 PMCID: PMC10100706 DOI: 10.1128/spectrum.03219-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
The purpose of this study was to characterize extensively drug-resistant Salmonella enterica serovar Kentucky sequence type 198 (ST198) isolates from chicken meat products. Ten S. Kentucky strains obtained from chicken meat products in Xuancheng, China, carried 12 to 17 resistance genes, such as blaCTX-M-55, rmtB, tet(A), floR, and fosA3, combined with mutations within gyrA (S83F and D87N) and parC (S80I), resulting in resistance to numerous antimicrobial agents, including the clinically important antibiotics cephalosporin, ciprofloxacin, tigecycline, and fosfomycin. These S. Kentucky isolates shared a close phylogenetic relationship (21 to 36 single-nucleotide polymorphisms [SNPs]) and showed close genetic relatedness to two human clinical isolates from China. Three S. Kentucky strains were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology. All antimicrobial resistance genes were located on their chromosomes and clustered in one multiresistance region (MRR) and Salmonella genomic island (SGI) SGI1-K. The MRRs in three S. Kentucky strains were bounded by IS26 at both ends and were inserted downstream of the bcfABCDEFG cluster with 8-bp direct repeats. The MRRs were related to those of IncHI2 plasmids but differed by insertions, deletions, and rearrangements of multiple segments involving resistance genes and plasmid backbones. This finding suggests that the MRR fragment possibly originates from IncHI2 plasmids. Four SGI1-K variants with slight differences were identified in 10 S. Kentucky strains. Mobile elements, particularly IS26, play an essential role in forming distinct MRRs and SGI1-K structures. In conclusion, the emergence of extensively drug-resistant S. Kentucky ST198 strains containing numerous chromosomally located resistance genes is alarming and needs continued surveillance. IMPORTANCE Salmonella spp. are important foodborne pathogens, and multidrug-resistant (MDR) Salmonella strains have become a serious threat to clinical therapy. MDR S. Kentucky ST198 strains have been increasingly reported from various sources and have become a global risk. In this study, we described extensively drug-resistant S. Kentucky ST198 strains from chicken meat products from a city in China. Numerous resistance genes are clustered in the chromosomes of S. Kentucky ST198 strains, possibly acquired with the help of mobile elements. This would facilitate the spread of numerous resistance genes as intrinsic chromosomal genes within this global epidemic clone, with the potential to capture more resistance genes. The emergence and dissemination of extensively drug-resistant S. Kentucky ST198 pose a severe clinical and public health threat; therefore, continuous surveillance is warranted.
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Affiliation(s)
- Yue Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Zhen-Yu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Qiu-Chun Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Meng-Jun Lu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Han Wu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Cai-Yue Mei
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Peng-Cheng Shen
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jing Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
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13
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Cao G, Zhao S, Kuang D, Hsu CH, Yin L, Luo Y, Chen Z, Xu X, Strain E, McDermott P, Allard M, Brown E, Meng J, Zheng J. Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans. Sci Rep 2023; 13:1331. [PMID: 36693882 PMCID: PMC9873609 DOI: 10.1038/s41598-022-24150-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/10/2022] [Indexed: 01/25/2023] Open
Abstract
Multidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I-IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3')-IIa, blaCTX-M-55, and blaTEM-1B, whereas blaTEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.
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Affiliation(s)
- Guojie Cao
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA.
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Dai Kuang
- Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Lanlan Yin
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Yan Luo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety & Security Systems, Department of Nutrition and Food Science, University of Maryland, College Park, MD, USA
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Errol Strain
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Patrick McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, Laurel, MD, 20708, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety & Security Systems, Department of Nutrition and Food Science, University of Maryland, College Park, MD, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, 20740, USA.
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14
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Ambrose SJ, Hall RM. Can SGI1 family integrative mobilizable elements overcome entry exclusion exerted by IncA and IncC plasmids on IncC plasmids? Plasmid 2022; 123-124:102654. [DOI: 10.1016/j.plasmid.2022.102654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/28/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
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15
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Zhang G, Cui Q, Li J, Guo R, Leclercq SO, Du L, Tang N, Song Y, Wang C, Zhao F, Feng J. The integrase of genomic island GIsul2 mediates the mobilization of GIsul2 and ISCR-related element CR2-sul2 unit through site-specific recombination. Front Microbiol 2022; 13:905865. [PMID: 35979485 PMCID: PMC9376610 DOI: 10.3389/fmicb.2022.905865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
In the worldwide health threat posed by antibiotic-resistant bacterial pathogens, mobile genetic elements (MGEs) play a critical role in favoring the dissemination of resistance genes. Among them, the genomic island GIsul2 and the ISCR-related element CR2-sul2 unit are believed to participate in this dissemination. However, the mobility of the two elements has not yet been demonstrated. Here, we found that the GIsul2 and CR2-sul2 units can excise from the host chromosomal attachment site (attB) in Shigella flexneri. Through establishing a two-plasmid mobilization system composed of a donor plasmid bearing the GIsul2 and a trap plasmid harboring the attB in recA-deficient Escherichia coli, we reveal that the integrase of GIsul2 can perform the excision and integration of GIsul2 and CR2-sul2 unit by site-specific recombination between att core sites. Furthermore, we demonstrate that the integrase and the att sites are required for mobility through knockout experiments. Our findings provide the first experimental characterization of the mobility of GIsul2 and CR2-sul2 units mediated by integrase. They also suggest a potential and unappreciated role of the GIsul2 integrase family in the dissemination of CR2-sul2 units carrying various resistance determinants in between.
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Affiliation(s)
- Gang Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qinna Cui
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jianjuan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ruiliang Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | | | - Lifeng Du
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Na Tang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yuqin Song
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chao Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Jie Feng
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16
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Lin CS, Lu TL, Chen YA, Yu HY, Wu CY, Yang WY. Safety of bivalent live attenuated Salmonella vaccine and its protection against bacterial shedding and tissue invasion in layers challenged with Salmonella. Poult Sci 2022; 101:101943. [PMID: 35679678 PMCID: PMC9189190 DOI: 10.1016/j.psj.2022.101943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Nontyphoidal Salmonella infection was one of the predominant foodborne illnesses in humans. The medical burden and antimicrobial resistance of salmonellosis gained importance in public health and requested the poultry industry to seek effective measures to control the disease. The objective of this study was to evaluate the safety and effectiveness of a commercial bivalent live attenuated vaccine (AviPro Salmonella DUO) in specific-pathogen-free (SPF) chickens and field layers. It explored its safety and efficacy against medically important strains, Salmonella Enteritidis (SE) and S. Typhimurium (ST). The results demonstrated that ten vaccine doses in SPF chickens and regular doses in commercial layers showed desirable safety without affecting chicken health. Vaccinated layers demonstrated lower flock mortality and higher egg production performance than the unvaccinated layers during the raising and egg production periods. Additionally, no visceral colonization and egg contaminations were detected. Cloacal shedding of vaccine strains was noted, but the colonization of Salmonella disappeared within four weeks of the last vaccination. Regarding vaccine efficacy, one dose significantly reduced Salmonella cloacal shedding (P = 0.037 for SE and P = 0.027 for ST) and viable cell counts (P = 0.003 for SE and ST) on day 7 post the challenges. Significantly low Salmonella loads of cloacal samples on day 14 after the challenges were also determined in the vaccinated group (P = 0.006 for SE; P = 0.041 for ST). Triple immunizations effectively prevented layers from the cloacal shedding on either day 7 or day 14 post Salmonella challenges. Total viable counts of SE and ST in tissues of vaccinated layers were also reduced on day 14 after the challenges (P = 0.026 for SE; P = 0.002 for ST). To conclude, one dose of vaccine exhibited inhibitory effects on Salmonella shedding and tissue invasions in young layers. Following the regimen of triple vaccinations, Salmonella shedding was completely inhibited, and tissue invasions were significantly reduced. Incorporating this vaccine into a comprehensive Salmonella control program is promising to protect layers from the risks of contaminating the flocks and egg products.
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Affiliation(s)
- Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan; Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan
| | - Tsung-Lin Lu
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan; Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan
| | - Yi-An Chen
- Elanco (Taiwan) Animal Health Co., Ltd. 9F, Taipei City, 105, Taiwan
| | - Hsin-Yi Yu
- Elanco (Taiwan) Animal Health Co., Ltd. 9F, Taipei City, 105, Taiwan
| | - Chiu-Yi Wu
- Elanco (Taiwan) Animal Health Co., Ltd. 9F, Taipei City, 105, Taiwan
| | - Wen-Yuan Yang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan; Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei City, 106, Taiwan.
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17
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Jovčić B, Malešević M, Kojić M, Galić N, Todorović D, Vidanović D, Velhner M. Genomic Analysis of Multidrug-Resistant Salmonella enterica Serovar Kentucky Isolates from Humans, Turkey, and Food in the Republic of Serbia. Foodborne Pathog Dis 2022; 19:630-636. [PMID: 35749151 DOI: 10.1089/fpd.2022.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Owing to the emerging resistance to antimicrobials in Salmonella Kentucky isolates around the globe, the genomic comparison of all the registered multidrug-resistant Salmonella Kentucky isolates in Serbia (five from humans, one from turkey flock, and one from meat) was done. Most of the isolates were isolated from patients returning from Egypt or Tunisia or originated from imported turkey flock and turkey meat. The comparative analysis of resistance and virulence genes was done. All isolates belonged to sequence type-ST198 and were resistant to ciprofloxacin (Cip). The resistance to Cip was mediated by target mutations of the gyrA and parC genes, which encode topoisomerase I and II, respectively. Multidrug-resistant phenotype to aminoglycosides, β-lactam antibiotics, sulfonamides, and tetracyclines was detected in five isolates. However, none of the isolates was pan-resistant to antimicrobials. The number of single nucleotide polymorphisms between isolates varied from 8 to 43 and phylogenomics revealed the genetic proximity of the human isolate 10475/11 and the turkey meat isolate 5264/14, indicating a possible meat-to-human transfer. All isolates belonged to the main Salmonella Kentucky MDR lineage, carrying the Salmonella genomic island 1 (SGI1-K) subtype. The SGI1-K of Serbian isolates showed mosaicism attributed to rapid intraclonal evolution. Many virulence factors were detected in all the isolates, including SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, and C63PI. Although Salmonella Kentucky has rarely been isolated from humans, food, and animals in Serbia, further surveillance is needed to diminish the risk of the spreading of resistant clones and their meat-to-human transmission.
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Affiliation(s)
- Branko Jovčić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milka Malešević
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milan Kojić
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Nataša Galić
- Institute of Public Health of Serbia, Belgrade, Serbia
| | | | - Dejan Vidanović
- Veterinary Specialized Institute "Kraljevo," Kraljevo, Serbia
| | - Maja Velhner
- Scientific Veterinary Institute "Novi Sad," Novi Sad, Serbia
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18
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Bertelli C, Gray KL, Woods N, Lim AC, Tilley KE, Winsor GL, Hoad GR, Roudgar A, Spencer A, Peltier J, Warren D, Raphenya AR, McArthur AG, Brinkman FSL. Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks. Microb Genom 2022; 8. [PMID: 35584003 PMCID: PMC9465072 DOI: 10.1099/mgen.0.000818] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Outbreaks of virulent and/or drug-resistant bacteria have a significant impact on human health and major economic consequences. Genomic islands (GIs; defined as clusters of genes of probable horizontal origin) are of high interest because they disproportionately encode virulence factors, some antimicrobial-resistance (AMR) genes, and other adaptations of medical or environmental interest. While microbial genome sequencing has become rapid and inexpensive, current computational methods for GI analysis are not amenable for rapid, accurate, user-friendly and scalable comparative analysis of sets of related genomes. To help fill this gap, we have developed IslandCompare, an open-source computational pipeline for GI prediction and comparison across several to hundreds of bacterial genomes. A dynamic and interactive visualization strategy displays a bacterial core-genome phylogeny, with bacterial genomes linearly displayed at the phylogenetic tree leaves. Genomes are overlaid with GI predictions and AMR determinants from the Comprehensive Antibiotic Resistance Database (CARD), and regions of similarity between the genomes are also displayed. GI predictions are performed using Sigi-HMM and IslandPath-DIMOB, the two most precise GI prediction tools based on nucleotide composition biases, as well as a novel blast-based consistency step to improve cross-genome prediction consistency. GIs across genomes sharing sequence similarity are grouped into clusters, further aiding comparative analysis and visualization of acquisition and loss of mobile GIs in specific sub-clades. IslandCompare is an open-source software that is containerized for local use, plus available via a user-friendly, web-based interface to allow direct use by bioinformaticians, biologists and clinicians (at https://islandcompare.ca).
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Institute of Microbiology, Lausanne University Hospital and University of Lausanne, 1011 Lausanne, Switzerland
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nolan Woods
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Adrian C Lim
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Keith E Tilley
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Gemma R Hoad
- Research Computing Group, Simon Fraser University, Burnaby, BC, Canada
| | - Ata Roudgar
- Research Computing Group, Simon Fraser University, Burnaby, BC, Canada
| | - Adam Spencer
- Research Computing Group, Simon Fraser University, Burnaby, BC, Canada
| | - James Peltier
- Research Computing Group, Simon Fraser University, Burnaby, BC, Canada
| | - Derek Warren
- Research Computing Group, Simon Fraser University, Burnaby, BC, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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19
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Siebor E, Neuwirth C. Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species. Front Microbiol 2022; 13:857492. [PMID: 35479618 PMCID: PMC9035990 DOI: 10.3389/fmicb.2022.857492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022] Open
Abstract
The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.
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Affiliation(s)
- Eliane Siebor
- Laboratory of Bacteriology, University Hospital of Dijon, Dijon, France
- UMR-CNRS 6249 Chrono-Environnement, University of Burgundy - Franche-Comté, Besançon, France
| | - Catherine Neuwirth
- Laboratory of Bacteriology, University Hospital of Dijon, Dijon, France
- UMR-CNRS 6249 Chrono-Environnement, University of Burgundy - Franche-Comté, Besançon, France
- *Correspondence: Catherine Neuwirth,
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20
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Brown EW, Bell R, Zhang G, Timme R, Zheng J, Hammack TS, Allard MW. Salmonella Genomics in Public Health and Food Safety. EcoSal Plus 2021; 9:eESP00082020. [PMID: 34125583 PMCID: PMC11163839 DOI: 10.1128/ecosalplus.esp-0008-2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/16/2021] [Indexed: 12/26/2022]
Abstract
The species Salmonella enterica comprises over 2,600 serovars, many of which are known to be intracellular pathogens of mammals, birds, and reptiles. It is now apparent that Salmonella is a highly adapted environmental microbe and can readily persist in a number of environmental niches, including water, soil, and various plant (including produce) species. Much of what is known about the evolution and diversity of nontyphoidal Salmonella serovars (NTS) in the environment is the result of the rise of the genomics era in enteric microbiology. There are over 340,000 Salmonella genomes available in public databases. This extraordinary breadth of genomic diversity now available for the species, coupled with widespread availability and affordability of whole-genome sequencing (WGS) instrumentation, has transformed the way in which we detect, differentiate, and characterize Salmonella enterica strains in a timely way. Not only have WGS data afforded a detailed and global examination of the molecular epidemiological movement of Salmonella from diverse environmental reservoirs into human and animal hosts, but they have also allowed considerable consolidation of the diagnostic effort required to test for various phenotypes important to the characterization of Salmonella. For example, drug resistance, serovar, virulence determinants, and other genome-based attributes can all be discerned using a genome sequence. Finally, genomic analysis, in conjunction with functional and phenotypic approaches, is beginning to provide new insights into the precise adaptive changes that permit persistence of NTS in so many diverse and challenging environmental niches.
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Affiliation(s)
- Eric W. Brown
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Guodong Zhang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Ruth Timme
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Thomas S. Hammack
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Marc W. Allard
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
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21
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Li C, Tyson GH, Hsu CH, Harrison L, Strain E, Tran TT, Tillman GE, Dessai U, McDermott PF, Zhao S. Long-Read Sequencing Reveals Evolution and Acquisition of Antimicrobial Resistance and Virulence Genes in Salmonella enterica. Front Microbiol 2021; 12:777817. [PMID: 34867920 PMCID: PMC8640207 DOI: 10.3389/fmicb.2021.777817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Salmonella enterica is a significant and phylogenetically diverse zoonotic pathogen. To understand its genomic heterogeneity and antimicrobial resistance, we performed long-read sequencing on Salmonella isolated from retail meats and food animals. A collection of 134 multidrug-resistant isolates belonging to 33 serotypes were subjected to PacBio sequencing. One major locus of diversity among these isolates was the presence and orientation of Salmonella pathogenic islands (SPI), which varied across different serotypes but were largely conserved within individual serotypes. We also identified insertion of an IncQ resistance plasmid into the chromosome of fourteen strains of serotype I 4,[5],12:i:- and the Salmonella genomic island 1 (SGI-1) in five serotypes. The presence of various SPIs, SGI-1 and integrated plasmids contributed significantly to the genomic variability and resulted in chromosomal resistance in 55.2% (74/134) of the study isolates. A total of 93.3% (125/134) of isolates carried at least one plasmid, with isolates carrying up to seven plasmids. We closed 233 plasmid sequences of thirteen replicon types, along with twelve hybrid plasmids. Some associations between Salmonella isolate source, serotype, and plasmid type were seen. For instance, IncX plasmids were more common in serotype Kentucky from retail chicken. Plasmids IncC and IncHI had on average more than five antimicrobial resistance genes, whereas in IncX, it was less than one per plasmid. Overall, 60% of multidrug resistance (MDR) strains that carried >3 AMR genes also carried >3 heavy metal resistance genes, raising the possibility of co-selection of antimicrobial resistance in the presence of heavy metals. We also found nine isolates representing four serotypes that carried virulence plasmids with the spv operon. Together, these data demonstrate the power of long-read sequencing to reveal genomic arrangements and integrated plasmids with a high level of resolution for tracking and comparing resistant strains from different sources. Additionally, the findings from this study will help expand the reference set of closed Salmonella genomes that can be used to improve genome assembly from short-read data commonly used in One Health antimicrobial resistance surveillance.
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Affiliation(s)
- Cong Li
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Gregory H Tyson
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Chih-Hao Hsu
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Lucas Harrison
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Errol Strain
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Thu-Thuy Tran
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Glenn E Tillman
- Food Safety and Inspection Service, United States Department of Agriculture, Athens, GA, United States
| | - Uday Dessai
- Food Safety and Inspection Service, United States Department of Agriculture, Washington, DC, United States
| | - Patrick F McDermott
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
| | - Shaohua Zhao
- Center for Veterinary Medicine, United States Food and Drug Administration, Laurel, MD, United States
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22
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Durand R, Deschênes F, Burrus V. Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids. PLoS Genet 2021; 17:e1009669. [PMID: 34415925 PMCID: PMC8409611 DOI: 10.1371/journal.pgen.1009669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/01/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria. All known SGI1 variants integrate at the 3’ end of trmE, a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse integrative elements distantly related to SGI1 in several species of Vibrio, Aeromonas, Salmonella, Pokkaliibacter, and Escherichia. Unlike SGI1, these elements target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC. Although they share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of IMEVchUSA3, a dusA-specific integrative element, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that IMEVchUSA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli. IMEVchUSA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA-specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA-specific elements from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of IMEVchUSA3 disrupts dusA, it provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA, yicC, and trmE gives a fresh perspective on the possible origin of SGI1 and its variants. We identified integrative elements distantly related to Salmonella Genomic Island 1 (SGI1), a key vector of antibiotic resistance genes in Gammaproteobacteria. SGI1 and its variants reside at the 3’ end of trmE, share a large, highly conserved core of genes, and carry a complex integron that confers multidrug resistance phenotypes to their hosts. Unlike members of the SGI1 group, these novel genomic islands target the 5’ end dusA or the 3’ end of yicC, lack multidrug resistance genes, and seem much more diverse. We showed here that, like SGI1, these elements are mobilized by conjugative plasmids of the IncC group. Based on comparative genomics and functional analyses, we propose a hypothetical model of the evolution of SGI1 and its siblings from the progenitor of IncA and IncC conjugative plasmids via an intermediate dusA-specific integrative element through gene losses and gain of alternative integration/excision modules.
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Affiliation(s)
- Romain Durand
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Florence Deschênes
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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23
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Antibiotic Susceptibility Profile and Tetracycline Resistance Genes Detection in Salmonella spp. Strains Isolated from Animals and Food. Antibiotics (Basel) 2021; 10:antibiotics10070809. [PMID: 34356729 PMCID: PMC8300615 DOI: 10.3390/antibiotics10070809] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/28/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
Salmonella spp. is among the leading causes of foodborne infections in humans and a large number of animals. Salmonella spp. is a pathogen involved in the dissemination of antimicrobial resistance because it can accumulate antibiotic resistance genes (ARGs). In this study, the antibiotic resistance profile to 15 antibiotics, belonging to six different classes, of 60 strains of Salmonella spp. collected from pets, farm animals, wildlife, and food in Sicily (Italy) was investigated by the Kirby-Bauer method. Given that almost 33.3% of the Salmonella spp. strains were resistant to tetracycline, Real-Time PCR analysis was applied on all the 60 strains to detect the presence of eight selected tet resistance genes. Besides, the presence of the int1 gene, related to the horizontal gene transfer among bacteria, was also investigated in all the strains by Real-Time PCR analysis. Our data showed that 56% of the isolated strains harbored one or more tet resistance genes and that these strains were most frequently isolated from animals living in close contact with humans. Concerning int1, 17 strains (28.3%) harbored this genetic element and eight of these simultaneously contained tet genes. The results of this study highlight the importance of using a molecular approach to detect resistance genetic determinants, whose spread can increase the diffusion of multidrug-resistant strains. Besides, the study of zoonotic bacteria such as Salmonella spp. which significantly contribute to ARGs dissemination should always follow a One Health approach that considers the health of humans, animals, and the environment to be closely related.
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24
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Lei CW, Yao TG, Yan J, Li BY, Wang XC, Zhang Y, Gao YF, Wang HN. Identification of Proteus genomic island 2 variants in two clonal Proteus mirabilis isolates with coexistence of a novel genomic resistance island PmGRI1. J Antimicrob Chemother 2021; 75:2503-2507. [PMID: 32516381 DOI: 10.1093/jac/dkaa215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES To characterize the MDR genomic islands (GIs) in Proteus mirabilis isolates. METHODS Two P. mirabilis strains (C55 and C74) of chicken origin were subjected to WGS (HiSeq and PacBio) and the MDR GIs were determined. RESULTS P. mirabilis strains C55 and C74 are clonal strains and harbour different Proteus genomic island 2 (PGI2) variants (PGI2-C55 and PGI2-C74). The MDR region of PGI2-C55 is composed of two class 1 integrons, separated by a region containing seven copies of IS26 and eight resistance genes, including blaCTX-M-3 and fosA3. The region in PGI2-C74 is a complete In4-type class 1 integron, harbouring five gene cassettes (dfrA16, blaCARB-2, aadA2, cmlA1 and aadA1). In addition, C55 and C74 carry an SXT/R391 integrative and conjugative element (ICEPmiJpn1), harbouring blaCMY-2, and a novel 50.46 kb genomic resistance island named PmGRI1-C55. PmGRI1-C55 harbours a tyrosine-type recombinase/integrase that might be responsible for the integration of PmGRI1-C55 at the 3' end of tRNA-Sec. It carries an MDR region derived from Tn2670 that harbours a Tn21 region and carries six resistance genes (catA1, blaTEM-1b, aphA1a, sul2, strA and strB). Blast analysis showed diverse PmGRI1 variants in P. mirabilis and Escherichia coli strains. CONCLUSIONS The finding of the two new PGI2 variants highlights that the homologous recombination between shared components of class 1 integrons and transposition by IS26 promote the diversity of MDR regions in PGI2. PmGRI1 is a new GI that carries various resistance genes identified in P. mirabilis and E. coli.
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Affiliation(s)
- Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Tian-Ge Yao
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Jia Yan
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Bo-Yang Li
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Xue-Chun Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Yu Zhang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Yu-Feng Gao
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, China
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25
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Luo X, Yin Z, Zeng L, Hu L, Jiang X, Jing Y, Chen F, Wang D, Song Y, Yang H, Zhou D. Chromosomal Integration of Huge and Complex bla NDM-Carrying Genetic Elements in Enterobacteriaceae. Front Cell Infect Microbiol 2021; 11:690799. [PMID: 34211858 PMCID: PMC8239412 DOI: 10.3389/fcimb.2021.690799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, a detailed genetic dissection of the huge and complex blaNDM-carrying genetic elements and their related mobile genetic elements was performed in Enterobacteriaceae. An extensive comparison was applied to 12 chromosomal genetic elements, including six sequenced in this study and the other six from GenBank. These 12 genetic elements were divided into five groups: a novel IME Tn6588; two related IMEs Tn6523 (SGI1) and Tn6589; four related ICEs Tn6512 (R391), Tn6575 (ICEPvuChnBC22), Tn6576, and Tn6577; Tn7 and its derivatives Tn6726 and 40.7-kb Tn7-related element; and two related IMEs Tn6591 (GIsul2) and Tn6590. At least 51 resistance genes, involved in resistance to 18 different categories of antibiotics and heavy metals, were found in these 12 genetic elements. Notably, Tn6576 carried another ICE Tn6582. In particular, the six blaNDM-carrying genetic elements Tn6588, Tn6589, Tn6575, Tn6576, Tn6726, and 40.7-kb Tn7-related element contained large accessory multidrug resistance (MDR) regions, each of which had a very complex mosaic structure that comprised intact or residual mobile genetic elements including insertion sequences, unit or composite transposons, integrons, and putative resistance units. Core blaNDM genetic environments manifested as four different Tn125 derivatives and, notably, two or more copies of relevant Tn125 derivatives were found in each of Tn6576, Tn6588, Tn6589, and 40.7-kb Tn7-related element. The huge and complex blaNDM-carrying genetic elements were assembled from complex transposition and homolog recombination. Firstly identified were eight novel mobile elements, including three ICEs Tn6576, Tn6577, and Tn6582, two IMEs, Tn6588 and Tn6589, two composite transposons Tn6580a and Tn6580b, and one integron In1718.
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Affiliation(s)
- Xinhua Luo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lijun Zeng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,The Fifth Medical Center, Chinese Peoples Liberation Army General Hospital, Beijing, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaoyuan Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ying Jing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fangzhou Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital Affiliated With Taizhou University, Taizhou, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Huiying Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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Delgado-Suárez EJ, Palós-Guitérrez T, Ruíz-López FA, Hernández Pérez CF, Ballesteros-Nova NE, Soberanis-Ramos O, Méndez-Medina RD, Allard MW, Rubio-Lozano MS. Genomic surveillance of antimicrobial resistance shows cattle and poultry are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico. PLoS One 2021; 16:e0243681. [PMID: 33951039 PMCID: PMC8099073 DOI: 10.1371/journal.pone.0243681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/15/2021] [Indexed: 12/22/2022] Open
Abstract
Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is a public health concern globally. This study reports the phenotypic and genotypic antimicrobial resistance (AMR) profiles of NTS isolates from bovine lymph nodes (n = 48) and ground beef (n = 29). Furthermore, we compared genotypic AMR data of our isolates with those of publicly available NTS genomes from Mexico (n = 2400). The probability of finding MDR isolates was higher in ground beef than in lymph nodes:χ2 = 12.0, P = 0.0005. The most common resistant phenotypes involved tetracycline (40.3%), carbenicillin (26.0%), amoxicillin-clavulanic acid (20.8%), chloramphenicol (19.5%) and trimethoprim-sulfamethoxazole (16.9%), while more than 55% of the isolates showed decreased susceptibility to ciprofloxacin and 26% were MDR. Conversely, resistance to cephalosporins and carbapenems was infrequent (0-9%). MDR phenotypes were strongly associated with NTS serovar (χ2 = 24.5, P<0.0001), with Typhimurium accounting for 40% of MDR strains. Most of these (9/10), carried Salmonella genomic island 1, which harbors a class-1 integron with multiple AMR genes (aadA2, blaCARB-2, floR, sul1, tetG) that confer a penta-resistant phenotype. MDR phenotypes were also associated with mutations in the ramR gene (χ2 = 17.7, P<0.0001). Among public NTS isolates from Mexico, those from cattle and poultry had the highest proportion of MDR genotypes. Our results suggest that attaining significant improvements in AMR meat safety requires the identification and removal (or treatment) of product harboring MDR NTS, instead of screening for Salmonella spp. or for isolates showing resistance to individual antibiotics. In that sense, massive integration of whole genome sequencing (WGS) technologies in AMR surveillance provides the shortest path to accomplish these goals.
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Affiliation(s)
| | - Tania Palós-Guitérrez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Cindy Fabiola Hernández Pérez
- Centro Nacional de Referencia de Plaguicidas y Contaminantes, Dirección General de Inocuidad Agroalimentaria, Acuícola y Pesquera, Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Estado de México, México
| | | | - Orbelín Soberanis-Ramos
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rubén Danilo Méndez-Medina
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, Maryland, United States of America
| | - María Salud Rubio-Lozano
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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Wang Z, Xu H, Chu C, Tang Y, Li Q, Jiao X. Genomic Identification of Multidrug-Resistant Salmonella Virchow Monophasic Variant Causing Human Septic Arthritis. Pathogens 2021; 10:pathogens10050536. [PMID: 33947106 PMCID: PMC8146543 DOI: 10.3390/pathogens10050536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/25/2021] [Accepted: 04/28/2021] [Indexed: 11/21/2022] Open
Abstract
The monophasic variant of Salmonella Typhimurium has emerged and increased rapidly worldwide during the past two decades. The loss of genes encoding the second-phase flagella and the acquirement of the multi-drug resistance cassette are the main genomic characteristics of the S. Typhimurium monophasic variant. In this study, two Salmonella strains were isolated from the knee effusion and feces of a 4-year-old girl who presented with a case of septic arthritis and fever, respectively. Primary serovar identification did not detect the second-phase flagellar antigens of the strains using the classical slide agglutination test. Whole-genome sequencing analysis was performed to reveal that the replacement of the fljAB operon by a 4.8-kb cassette from E. coli caused the non-expression of phase-2 flagellar antigens of the strains, which were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) by core-genome multi-locus sequence typing (cgMLST). Compared to the 16 published S. Virchow genomes, the two strains shared a unique CRISPR type of VCT12, and showed a close genetic relationship to S. Virchow BCW_2814 and BCW_2815 strains, isolated from Denmark and China, respectively, based on cgMLST and CRISPR typing. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the strains to be multidrug-resistant to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emergence of the multidrug-resistant S. Virchow monophasic variant revealed that whole-genome sequencing and CRISPR typing could be applied to identify the serovaraints of Salmonella enterica strains in the national Salmonella surveillance system.
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Affiliation(s)
- Zhenyu Wang
- 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, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, Gongnong South Road 189, Nantong 226007, China;
| | - Chao Chu
- 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, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
| | - Yuanyue Tang
- 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, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 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, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Correspondence: (Q.L.); (X.J.); Tel.: +86-514-87971136 (Q.L.); +86-514-87971136 (X.J.)
| | - 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, Wenhui East Road 48, Yangzhou 225009, China; (Z.W.); (C.C.); (Y.T.)
- Jiangsu Key Lab of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Wenhui East Road 48, Yangzhou 225009, China
- Correspondence: (Q.L.); (X.J.); Tel.: +86-514-87971136 (Q.L.); +86-514-87971136 (X.J.)
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de Curraize C, Siebor E, Neuwirth C. Genomic islands related to Salmonella genomic island 1; integrative mobilisable elements in trmE mobilised in trans by A/C plasmids. Plasmid 2021; 114:102565. [PMID: 33582118 DOI: 10.1016/j.plasmid.2021.102565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/01/2022]
Abstract
Salmonella genomic island 1 (SGI1), an integrative mobilisable element (IME), was first reported 20 years ago, in the multidrug resistant Salmonella Typhimurium DT104 clone. Since this first report, many variants and relatives have been found in Salmonella enterica and Proteus mirabilis. Thanks to whole genome sequencing, more and more complete sequences of SGI1-related elements (SGI1-REs) have been reported in these last few years among Gammaproteobacteria. Here, the genetic organisation and main features common to SGI1-REs are summarised to help to classify them. Their integrases belong to the tyrosine-recombinase family and target the 3'-end of the trmE gene. They share the same genetic organisation (integrase and excisionase genes, replicase module, SgaCD-like transcriptional activator genes, traN, traG, mpsB/mpsA genes) and they harbour AcaCD binding sites promoting their excision, replication and mobilisation in presence of A/C plasmid. SGI1-REs are mosaic structures suggesting that recombination events occurred between them. Most of them harbour a multiple antibiotic resistance (MAR) region and the plasticity of their MAR region show that SGI1-REs play a key role in antibiotic resistance and might help multiple antibiotic resistant bacteria to adapt to their environment. This might explain the emergence of clones with SGI1-REs.
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Affiliation(s)
- Claire de Curraize
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Eliane Siebor
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
| | - Catherine Neuwirth
- Bacteriology Department, University Hospital Dijon, PBHU, BP 37013, 21070 Dijon Cedex, France; UMR 6249, Chrono-Environnement, PBHU, BP 37013, 21070 Dijon Cedex, France.
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Chen H, Song J, Zeng X, Chen D, Chen R, Qiu C, Zhou K. National Prevalence of Salmonella enterica Serotype Kentucky ST198 with High-Level Resistance to Ciprofloxacin and Extended-Spectrum Cephalosporins in China, 2013 to 2017. mSystems 2021; 6:e00935-20. [PMID: 33436512 PMCID: PMC7901479 DOI: 10.1128/msystems.00935-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
Salmonella enterica serotype Kentucky is frequently associated with high-level fluoroquinolone resistance and has gained epidemiological importance globally. A retrospective screening was performed to understand the national prevalence of ciprofloxacin-resistant S Kentucky in China. S. enterica strains (n = 15,405) were collected within the frame of two national surveillance networks between 2013 and 2017. Thirty-three S. Kentucky strains were detected in 5 of 10 provinces, and 27 were assigned to sequence type 198 (ST198). The 27 isolates were multidrug resistant, with high-level resistance to ciprofloxacin, and 21 isolates were further resistant to extended-spectrum cephalosporins (ESCs). Phylogenomic analysis classified ST198 isolates into two clades (198.1 and 198.2), and recent occurrences of inter-/intraregion and interhost transmission were identified. Phylogenetic reconstruction with a global collection showed that one subclade of clade 198.2 was clustered with historical strains from Egypt, and the other one was clustered with strains from Southeast Asia. Isolates of clade 198.1 were clustered with strains isolated from North America. The various patterns of mutations detected in quinolone resistance-determining regions of GyrA and ParC are accordant with the phylogenetic structure. These findings indicate that our isolates may have various origins. SGI1 was exclusively detected in isolates of clade 198.2 with a highly mosaic structure, which were mainly identified as SGI1-K derivatives. Plasmid-mediated quinolone resistance genes qnrS1 and aac(6')-Ib-cr were identified in three isolates, and bla CTX-M-9 and bla CTX-M-27 were detected in 20 of 21 ESC-resistant isolates. This is the first report of the genetic and epidemiological characterization for the S Kentucky epidemic clone ST198 in China, warranting the necessity of surveillance for the high-risk clone.IMPORTANCE Ciprofloxacin and extended-spectrum cephalosporins are the choice for treatment of severe nontyphoidal S. enterica infections in adults. S. enterica serotype Kentucky ST198 has gained epidemiological importance globally, because the clone is frequently resistant to both of these high-level-resistance drug groups. The genetic and epidemiological characterization of S. Kentucky has been well studied in Western countries; however, the information is unclear for China. To fill in the gap, we here did a retrospective screening on a large collection in China, and ST198 isolates were systematically analyzed by whole-genome sequencing. Our study revealed that multidrug-resistant ST198 has spread in five provinces, and the occurrences of interregion and cross-host clonal disseminations were detected. Of note, phylogenomic analysis suggests that the Chinese isolates may have emerged with diverse origins, including Egypt, Southeast Asia, and North America. This study warrants the necessity of surveillance for the high-risk clone to prevent its further dissemination in China.
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Affiliation(s)
- Honghu Chen
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jingjie Song
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Xianying Zeng
- Guangxi Provincial Center for Disease Control and Prevention, Nanning, China
| | - Dandan Chen
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Rongchang Chen
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Chen Qiu
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Jinan University, Shenzhen, China
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Zhao S, Li C, Hsu CH, Tyson GH, Strain E, Tate H, Tran TT, Abbott J, McDermott PF. Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals. Genes (Basel) 2020; 11:genes11091025. [PMID: 32883017 PMCID: PMC7564550 DOI: 10.3390/genes11091025] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/02/2022] Open
Abstract
Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.
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van Duijkeren E, Schwarz C, Bouchard D, Catry B, Pomba C, Baptiste KE, Moreno MA, Rantala M, Ružauskas M, Sanders P, Teale C, Wester AL, Ignate K, Kunsagi Z, Jukes H. The use of aminoglycosides in animals within the EU: development of resistance in animals and possible impact on human and animal health: a review. J Antimicrob Chemother 2020; 74:2480-2496. [PMID: 31002332 DOI: 10.1093/jac/dkz161] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Aminoglycosides (AGs) are important antibacterial agents for the treatment of various infections in humans and animals. Following extensive use of AGs in humans, food-producing animals and companion animals, acquired resistance among human and animal pathogens and commensal bacteria has emerged. Acquired resistance occurs through several mechanisms, but enzymatic inactivation of AGs is the most common one. Resistance genes are often located on mobile genetic elements, facilitating their spread between different bacterial species and between animals and humans. AG resistance has been found in many different bacterial species, including those with zoonotic potential such as Salmonella spp., Campylobacter spp. and livestock-associated MRSA. The highest risk is anticipated from transfer of resistant enterococci or coliforms (Escherichia coli) since infections with these pathogens in humans would potentially be treated with AGs. There is evidence that the use of AGs in human and veterinary medicine is associated with the increased prevalence of resistance. The same resistance genes have been found in isolates from humans and animals. Evaluation of risk factors indicates that the probability of transmission of AG resistance from animals to humans through transfer of zoonotic or commensal foodborne bacteria and/or their mobile genetic elements can be regarded as high, although there are no quantitative data on the actual contribution of animals to AG resistance in human pathogens. Responsible use of AGs is of great importance in order to safeguard their clinical efficacy for human and veterinary medicine.
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Affiliation(s)
| | - Christine Schwarz
- Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Damien Bouchard
- French Agency for Food, Environmental, and Occupational Safety, National Agency for Veterinary Medicinal Products, Fougères, France
| | - Boudewijn Catry
- Sciensano, Brussels, Belgium
- Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Constança Pomba
- Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | | | - Miguel A Moreno
- Faculty of Veterinary Medicine, Complutense University, Madrid, Spain
| | - Merja Rantala
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | - Pascal Sanders
- French Agency for Food, Environmental, and Occupational Safety, Fougères Laboratory, Fougères, France
| | | | | | | | | | - Helen Jukes
- Veterinary Medicines Directorate, Addlestone, UK
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Berbers B, Ceyssens PJ, Bogaerts P, Vanneste K, Roosens NHC, Marchal K, De Keersmaecker SCJ. Development of an NGS-Based Workflow for Improved Monitoring of Circulating Plasmids in Support of Risk Assessment of Antimicrobial Resistance Gene Dissemination. Antibiotics (Basel) 2020; 9:E503. [PMID: 32796589 PMCID: PMC7460218 DOI: 10.3390/antibiotics9080503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/07/2020] [Accepted: 08/08/2020] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copy mcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistant Salmonella Kentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
| | | | - Pierre Bogaerts
- National Reference Center for Antimicrobial Resistance in Gram-Negative Bacteria, CHU UCL Namur, 5530 Yvoir, Belgium;
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium; (B.B.); (K.V.); (N.H.C.R.)
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria 0083, South Africa
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Huguet KT, Rivard N, Garneau D, Palanee J, Burrus V. Replication of the Salmonella Genomic Island 1 (SGI1) triggered by helper IncC conjugative plasmids promotes incompatibility and plasmid loss. PLoS Genet 2020; 16:e1008965. [PMID: 32760058 PMCID: PMC7433901 DOI: 10.1371/journal.pgen.1008965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/18/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
The mobilizable resistance island Salmonella genomic island 1 (SGI1) is specifically mobilized by IncA and IncC conjugative plasmids. SGI1, its variants and IncC plasmids propagate multidrug resistance in pathogenic enterobacteria such as Salmonella enterica serovars and Proteus mirabilis. SGI1 modifies and uses the conjugation apparatus encoded by the helper IncC plasmid, thus enhancing its own propagation. Remarkably, although SGI1 needs a coresident IncC plasmid to excise from the chromosome and transfer to a new host, these elements have been reported to be incompatible. Here, the stability of SGI1 and its helper IncC plasmid, each expressing a different fluorescent reporter protein, was monitored using fluorescence-activated cell sorting (FACS). Without selective pressure, 95% of the cells segregated into two subpopulations containing either SGI1 or the helper plasmid. Furthermore, FACS analysis revealed a high level of SGI1-specific fluorescence in IncC+ cells, suggesting that SGI1 undergoes active replication in the presence of the helper plasmid. SGI1 replication was confirmed by quantitative PCR assays, and extraction and restriction of its plasmid form. Deletion of genes involved in SGI1 excision from the chromosome allowed a stable coexistence of SGI1 with its helper plasmid without selective pressure. In addition, deletion of S003 (rep) or of a downstream putative iteron-based origin of replication, while allowing SGI1 excision, abolished its replication, alleviated the incompatibility with the helper plasmid and enabled its cotransfer to a new host. Like SGI1 excision functions, rep expression was found to be controlled by AcaCD, the master activator of IncC plasmid transfer. Transient SGI1 replication seems to be a key feature of the life cycle of this family of genomic islands. Sequence database analysis revealed that SGI1 variants encode either a replication initiator protein with a RepA_C domain, or an alternative replication protein with N-terminal replicase and primase C terminal 1 domains. The Salmonella genomic island 1 (SGI1) and its variants propagate multidrug resistance in several species of human and animal pathogens with the help of IncA and IncC conjugative plasmids that are absolutely required for SGI1 dissemination. These helper plasmids are known to trigger the excision of SGI1 from the chromosome. Here, we found that IncC plasmids also trigger the replication of the excised, circular form of SGI1 by enabling the expression of an SGI1-borne replication initiator gene. In return, high-copy replication of SGI1 interferes with the persistence of the IncC plasmid and prevents its cotransfer into a recipient cell, thereby allowing integration and stabilization of SGI1 into the chromosome of the new host. This finding is important to better understand the complex interactions between SGI1-like elements and their helper plasmids that lead to widespread and highly efficient propagation of multidrug resistance genes to a broad range of human and animal pathogens.
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Affiliation(s)
- Kévin T. Huguet
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Nicolas Rivard
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Daniel Garneau
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jason Palanee
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vincent Burrus
- Département de biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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Siebor E, Neuwirth C. New insights regarding Acinetobacter genomic island-related elements. Int J Antimicrob Agents 2020; 56:106117. [PMID: 32745526 DOI: 10.1016/j.ijantimicag.2020.106117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/30/2022]
Abstract
The objective of this study was to mobilise the Acinetobacter genomic island 1-A (AGI1-A) from Enterobacter hormaechei EclCSP2185 (E. cloacae complex) and to search for the distribution and structure of AGI1-related elements in the NCBI database. AGI1-A was transferred to Escherichia coli. Analysis of the attachment (att) sites could locate the possible recombination crossover in the att sequences at position 10-11 (GG) in the last 18 bp of trmE. In silico detection of AGI backbones in the WGS database identified AGI variants in Salmonella enterica (83 strains), Vibrio cholerae (33), E. hormaechei (12), Acinetobacter baumannii (2), most belonging to prevalent clones (ST40, ST69, ST114 and ST25, respectively), but also in E. coli (1) and Klebsiella pneumoniae (1). Two groups of backbone were identified: one similar to AGI1, the other with a short segment from a Shewanella element upstream of ORF A022. The MDR regions were inserted by transposition at the res site in four different positions ATAGG (A. baumannii), CATAG (S. enterica and V. cholerae), TAGGT (S. enterica and K. pneumoniae) and TGCAC (S. enterica) representing four different lineages. In some V. cholerae, E. hormaechei and E. coli, deletion events occurred that eliminated part of the backbone at the left junction. Analysis of the right junction identified a fifth lineage in V. cholerae and E. hormaechei (CCATA). In conclusion, based on the position of the MDR region, AGI-related elements belonged to five groups of closely related genomic islands (AGI1-AGI5), with differences in backbones that evolved independently over time.
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Affiliation(s)
- Eliane Siebor
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France, and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Catherine Neuwirth
- Laboratory of Bacteriology, University Hospital of Dijon, Plateau technique de Biologie, BP 37013, 21070 Dijon Cedex, France, and UMR 6249, CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France.
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Two New SGI1-LK Variants Found in Proteus mirabilis and Evolution of the SGI1-HKL Group of Salmonella Genomic Islands. mSphere 2020; 5:5/2/e00875-19. [PMID: 32132162 PMCID: PMC7056807 DOI: 10.1128/msphere.00875-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Integrative mobilizable elements belonging to the SGI1-H, -K, and -L Salmonella genomic island 1 (SGI1) variant groups are distinguished by the presence of an alteration in the backbone (IS1359 replaces 2.8 kb of the backbone extending from within traN [S005] to within S009). Members of this SGI1-HKL group have been found in Salmonella enterica serovars and in Proteus mirabilis Two novel variants from this group, designated SGI1-LK1 and SGI1-LK2, were found in the draft genomes of antibiotic-resistant P. mirabilis isolates from two French hospitals. Both variants can be derived from SGI1-PmGUE, a configuration found previously in another P. mirabilis isolate from France. SGI1-LK1 could arise via an IS26-mediated inversion in the complex class 1 integron that duplicated the IS26 element and the target site in IS6100 SGI1-LK1 also has a larger 8.59-kb backbone deletion extending from traN to within S013 and removing traG and traH. However, SGI1-LK1 was mobilized by an IncC plasmid. SGI1-LK2 can be derived from a hypothetical progenitor, SGI1-LK0, that is related to SGI1-PmGUE but lacks the aphA1 gene and one copy of IS26. The integron of SGI1-LK2 could arise via deletion of DNA adjacent to an IS26 and a deletion occurring via homologous recombination between duplicated copies of part of the integron 3'-conserved segment. SGI1-K can also be derived from SGI1-LK0. This would involve an IS26-mediated deletion and an inversion via homologous recombination of a segment between inversely oriented IS26s. Similar events can explain the configuration of the integrons in other SGI1-LK variants.IMPORTANCE Members of the SGI1-HKL subgroup of SGI1-type integrative mobilizable elements have a characteristic alteration in their backbone. They are widely distributed among multiply antibiotic-resistant Salmonella enterica serovars and Proteus mirabilis isolates. The SGI1-K type, found in the globally disseminated multiply antibiotic-resistant Salmonella enterica serovar Kentucky clone ST198 (sequence type 198), and various configurations in the original SGI1-LK group, found in other multiresistant S. enterica serovars and Proteus mirabilis isolates, have complex and highly plastic resistance regions due to the presence of IS26 However, how these complex forms arose and the relationships between them had not been analyzed. Here, a hypothetical progenitor, SGI1-LK0, that can be formed from the simpler SGI1-H is proposed, and the pathways to the formation of new variants, SGI1-LK1 and SGI1-LK2, found in P. mirabilis and other reported configurations via homologous recombination and IS26-mediated events are proposed. This led to a better understanding of the evolution of the SGI1-HKL group.
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Multidrug resistance genes are associated with a 42-kb island TGI1 carrying a complex class 1 integron in Trueperella pyogenes. J Glob Antimicrob Resist 2019; 22:1-4. [PMID: 31857248 DOI: 10.1016/j.jgar.2019.12.008] [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: 07/22/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES This research was conducted to ascertain the context and location of the antibiotic resistance determinants in a multiple antibiotic-resistant Trueperella pyogenes isolate TP1. METHODS The genome was sequenced using PacBio RS II, and the filtered data were assembled using Canu. Sequences were annotated on the basis of those in GenBank, and the genomic island (GI) of the TP1 was predicted by IslandPath-DIMOB. RESULTS TP1 as a multiple antibiotic-resistant isolate was recovered at Jilin Province (China) in 2017 from a dairy cow with pneumonia. TP1 exhibited resistance to aminoglycosides (gentamicin and amikacin), macrolides (erythromycin), lincosamides (clindamycin), sulfonamides (sulfamonomethoxine), tetracyclines (tetracycline and doxycycline) and chloramphenicols (chloramphenicol and florfenicol). An antibiotic resistance gene clustered together with the aadB, aadA1, cmlA5 and cmlA6 resistance genes located on a 7-kilobase (kb) multidrug-resistant (MDR) region, constituting a complex class 1 integron. The MDR region was located at one end of a 42-kb GI, and IS6100Δ1 mediated a genetic rearrangement with the complex class 1 integron-like SGI1 and formed a composite transposon. Furthermore, the tetW gene was located outside the four GIs consistent with tetracycline and doxycycline resistance. The ermD gene positioned in the front end of the 42-kb GI played an important role in mediating acquired erythromycin and clindamycin resistance. CONCLUSIONS Multiple resistance genes are located in a complex class 1 integron within a 42-kb T. pyogenes genomic island (TGI1), leading to TP1 multiple drug resistance. In comparison with SG1 families, TGI1 possesses versatile gene distribution and specific gene context for it upstream and downstream, and it represents a new lineage of genomic resistance islands.
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Lei CW, Zhang Y, Wang XC, Gao YF, Wang HN. Draft genome sequence of a multidrug-resistant Salmonella enterica serotype Kentucky ST198 with chromosomal integration of bla CTX-M-14b isolated from a poultry slaughterhouse in China. J Glob Antimicrob Resist 2019; 20:145-146. [PMID: 31846722 DOI: 10.1016/j.jgar.2019.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/02/2019] [Accepted: 12/07/2019] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterise the draft genome sequence of a multidrug-resistant (MDR) Salmonella enterica serotype Kentucky strain (XJ9S) isolated from a poultry slaughterhouse in China. METHODS The genome was sequenced using an Illumina HiSeq platform and was assembled using SPAdes_3.12.0. The CGE Bacterial Analysis Pipeline was used to identify the sequence type (ST) as well as the presence of antimicrobial resistance genes (ARGs) and plasmids in strain XJ9S. Gaps among contigs that carried MDR Salmonella genomic island 1 (SGI1) fragments were filled in by PCR linkage and sequencing. RESULTS The draft genome of strain XJ9S was assembled into 54 contigs with a total assembly size of 4 785 059 bp. XJ9S belonged to ST198 and harboured five acquired ARGs [blaCTX-M-14b, sul1, tetA(A), aacCA5 and aadA7]. The blaCTX-M-14b gene was located on a 2849-bp ISEcp1-mediated translocatable unit inserted in the chromosome. The other four acquired ARGs were carried by a new variant of SGI1 (SGI1-XJ9S; 38 593 bp) belonging to the SGI1-K group. Moreover, point mutations in the quinolone resistance-determining region (QRDR) were found at positions 83 (Ser83Phe) and 87 (Asp87Gly) of GyrA and at position 80 (Ser80Ile) of ParC. CONCLUSION In this study, a new SGI1 variant (SGI1-XJ9S) was characterised for the first time. The draft genome sequence of S. Kentucky ST198 strain XJ9S isolated from a poultry slaughterhouse provides valuable information for tracing the potential spread of this MDR clone from poultry product processing to consumption, and even to humans.
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Affiliation(s)
- Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Yu Zhang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Xue-Chun Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Yu-Feng Gao
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, Sichuan, China.
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Cohen E, Davidovich M, Rokney A, Valinsky L, Rahav G, Gal-Mor O. Emergence of new variants of antibiotic resistance genomic islands among multidrug-resistant Salmonella enterica in poultry. Environ Microbiol 2019; 22:413-432. [PMID: 31715658 DOI: 10.1111/1462-2920.14858] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/07/2023]
Abstract
Non-typhoidal Salmonella enterica (NTS) are diverse and important bacterial pathogens consisting of more than 2600 different serovars, with varying host-specificity. Here, we characterized the poultry-associated serovars in Israel, analysed their resistome and illuminated the molecular mechanisms underlying common multidrug resistance (MDR) patterns. We show that at least four serovars including Infantis, Muenchen, Newport and Virchow present a strong epidemiological association between their temporal trends in poultry and humans. Worrisomely, 60% from all of the poultry isolates tested (n = 188) were multidrug resistant, mediated by chromosomal SNPs and different mobile genetics elements. A novel streptomycin-azithromycin resistance island and previously uncharacterized versions of the mobilized Salmonella genomic island 1 (SGI1) were identified and characterized in S. Blockley and S. Kentucky isolates respectively. Moreover, we demonstrate that the acquisition of SGI1 does not impose fitness cost during growth under nutrient-limited conditions or in the context of Salmonella infection in the mouse model. Overall, our data emphasize the role of the poultry production as a pool of specific epidemic MDR strains and autonomous genetic elements, which confer resistance to heavy metals and medically relevant antibiotics. These are likely to disseminate to humans via the food chain and fuel the increasing global antibiotic resistance crisis.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Assaf Rokney
- Central Laboratories, Ministry of Health, Jerusalem, Israel
| | - Lea Valinsky
- Central Laboratories, Ministry of Health, Jerusalem, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
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de Curraize C, Siebor E, Neuwirth C, Hall RM. SGI0, a relative of Salmonella genomic islands SGI1 and SGI2, lacking a class 1 integron, found in Proteus mirabilis. Plasmid 2019; 107:102453. [PMID: 31705941 DOI: 10.1016/j.plasmid.2019.102453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/16/2019] [Accepted: 10/25/2019] [Indexed: 01/26/2023]
Abstract
Several groups of integrative mobilizable elements (IMEs) that harbour a class 1 integron carrying antibiotic resistance genes have been found at the 3'-end of the chromosomal trmE gene. Here, a new IME, designated SGI0, was found in trmE in the sequenced and assembled genome of a French clinical, multiply antibiotic resistant Proteus mirabilis strain, Pm1LENAR. SGI0 shares the same gene content as the backbones of SGI1 and SGI2 (overall 97.6% and 97.7% nucleotide identity, respectively) but it lacks a class 1 integron. However, SGI0 is a mosaic made up of segments with >98.5% identity to SGI1 and SGI2 interspersed with segments sharing 74-95% identity indicating that further diverged backbone types exist and that recombination between them is occurring. The structure of SGI1-V, here re-named SGI-V, which lacks two SGI1 (S023 and S024) backbone genes and includes a group of additional genes in the backbone, was re-examined. In regions shared with SGI1, the backbones shared 97.3% overall identity with the differences distributed in patches with various levels of identity. The class 1 integron is also in a slightly different position with the target site duplication AAATT instead of ACTTG for SGI1 and variants, indicating that it was acquired independently. The Pm1LENAR resistance genes are in the chromosome, in Tn7 and an ISEcp1-mobilised segment.
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Affiliation(s)
- Claire de Curraize
- Bacteriology Department, University Hospital Dijon, PTB, BP, 37013, 21070, Dijon Cedex, France; UMR 6249, Chrono-Environnement, PTB, BP 37013, 21070, Dijon Cedex, France; School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.
| | - Eliane Siebor
- Bacteriology Department, University Hospital Dijon, PTB, BP, 37013, 21070, Dijon Cedex, France; UMR 6249, Chrono-Environnement, PTB, BP 37013, 21070, Dijon Cedex, France
| | - Catherine Neuwirth
- Bacteriology Department, University Hospital Dijon, PTB, BP, 37013, 21070, Dijon Cedex, France; UMR 6249, Chrono-Environnement, PTB, BP 37013, 21070, Dijon Cedex, France
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia.
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de Curraize C, Neuwirth C, Bador J, Chapuis A, Amoureux L, Siebor E. Two new Salmonella genomic islands 1 from Proteus mirabilis and description of blaCTX-M-15 on a variant (SGI1-K7). J Antimicrob Chemother 2019; 73:1804-1807. [PMID: 29659873 DOI: 10.1093/jac/dky108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/07/2018] [Indexed: 11/12/2022] Open
Abstract
Objectives To characterize the structure of Salmonella genomic islands 1 (SGI1s) from two clinical Proteus mirabilis isolates: one producing an ESBL and the other a penicillinase. Methods WGS completed by PCR and Sanger sequencing was performed to determine sequences of SGI1s from Pm2CHAMA and Pm37THOMI strains. Results Two new variants of SGI1 named SGI1-Pm2CHAMA (53.6 kb) and SGI1-K7 (55.1 kb) were identified. The backbone of SGI1-Pm2CHAMA shared 99.9% identity with that of SGI1. Its MDR region (26.3 kb) harboured two class 1 integrons (an In2-type integron and an In4-type integron) containing in particular a qacH cassette (encoding a quaternary ammonium compound efflux pump). These two integrons framed a complex region (harbouring among others blaCARB-4) resulting from transposon insertions mediated by IS26 and successive transposition events of ISs (ISAba14 isoform and the new ISPmi2). The second variant (SGI1-K7) had the same backbone as SGI1-K. Its MDR region (29.7 kb) was derived from that of SGI1-K and was generated by three events. The two main events were mediated by IS26: inversion of a large portion of the MDR region of SGI1-K and insertion of a structure previously reported on plasmids carried by prevalent and successful MDR clones of Enterobacteriaceae. This last event led to the insertion of the blaCTX-M-15 gene into SGI1-K7. Conclusions This study confirmed the great plasticity of the MDR region of SGI1 and its potential key role for the dissemination of clinically significant antibiotic resistance among Enterobacteriaceae.
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Affiliation(s)
- Claire de Curraize
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Catherine Neuwirth
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Julien Bador
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Angélique Chapuis
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Lucie Amoureux
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
| | - Eliane Siebor
- Laboratory of Bacteriology, Dijon University Hospital, Plateau technique de Biologie, BP 37013, 21070 Dijon cedex, France.,UMR 6249 CNRS Chrono-environnement, Université de Bourgogne Franche-Comté, 25000 Besançon, France
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Wang XC, Lei CW, Kang ZZ, Zhang Y, Wang HN. IS 26-Mediated Genetic Rearrangements in Salmonella Genomic Island 1 of Proteus mirabilis. Front Microbiol 2019; 10:2245. [PMID: 31608048 PMCID: PMC6769106 DOI: 10.3389/fmicb.2019.02245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/13/2019] [Indexed: 11/13/2022] Open
Abstract
Salmonella genomic island 1 (SGI1) is an integrative mobilizable element integrated into the chromosome of bacteria, which plays an important role in the dissemination of antimicrobial resistance genes. Lots of SGI1 variants are found mainly in Salmonella enterica and Proteus mirabilis. In this study, a total of 157 S. enterica and 132 P. mirabilis strains were collected from food-producing animals in Sichuan Province of China between December 2016 and November 2017. Detection of the SGI1 integrase gene showed that three S. enterica and five P. mirabilis strains were positive for SGI1, which displayed different multidrug resistance profiles. Five different SGI1 variants, including two novel variants (SGI1-PmBC1123 and SGI1-PmSC1111), were characterized by whole genome sequencing and PCR linkage. In two novel SGI1 variants, IS26-mediated rearrangements resulted in large sequence inversions of the MDR regions extending outside the SGI1 backbone. The sul3-type III class 1 integron (5′CS-sat-psp-aadA2-cmlA1-aadA1-qacH-IS440-sul3) and gene cassettes aac(6′)-Ib-cr-blaOXA–1-catB3-arr-3 are found in SGI1-PmSC1111. Mobilization experiments indicated that three known variants were conjugally mobilized in trans to Escherichia coli with the help of a conjugative IncC plasmid. However, the two novel variants seemed to lose the mobilization, which might result from the sequence inversion of partial SGI1 backbone. The identification of the two novel SGI1 variants in this study suggested that IS26-mediated rearrangements promote the diversity of SGI1.
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Affiliation(s)
- Xue-Chun Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chang-Wei Lei
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhuang-Zhuang Kang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Zhang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Hong-Ning Wang
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Parichehr M, Mohammad K, Abbas D, Mehdi K. Developing a multiplex real-time PCR with a new pre-enrichment to simultaneously detect four foodborne bacteria in milk. Future Microbiol 2019; 14:885-898. [PMID: 31368788 DOI: 10.2217/fmb-2019-0044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The aim of this study is to formulate a new single nonselective pre-enrichment medium (ELSS) that can support the concurrent growth of four major foodborne pathogens containing E. coli O157: H7, L. monocytogenes, S. aureus and S. enterica serovar Entertidis to develop a multiplex TaqMan Real-time PCR (mRT-PCR). Methods: The mRT-PCR with a new pre-enrichment was carried out for simultaneous detection and quantification of these foodborne bacteria. Results: By using mRT-PCR after 16 h pre-enrichment in ELSS, the detection limit of each pathogen was 1 CFU/25 ml contaminated milk, as well as inclusivity and exclusivity reached 100%. Conclusion: The mRT-PCR assay with pre-enrichment step is a fast and reliable technique for detecting single or multiple pathogens in food products.
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Affiliation(s)
- Moezi Parichehr
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Kargar Mohammad
- Department of Microbiology, Jahrom Branch, Islamic Azad University, Jahrom, Iran
| | - Doosti Abbas
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Khoshneviszadeh Mehdi
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, Brinkman FSL. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2019; 45:W30-W35. [PMID: 28472413 PMCID: PMC5570257 DOI: 10.1093/nar/gkx343] [Citation(s) in RCA: 913] [Impact Index Per Article: 182.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/18/2017] [Indexed: 11/14/2022] Open
Abstract
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
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Affiliation(s)
- Claire Bertelli
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Matthew R Laird
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kelly P Williams
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | | | - Britney Y Lau
- Systems Biology Department, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Gemma Hoad
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Geoffrey L Winsor
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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Cummins ML, Roy Chowdhury P, Marenda MS, Browning GF, Djordjevic SP. Salmonella Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate. mSphere 2019; 4:e00169-19. [PMID: 31118300 PMCID: PMC6531882 DOI: 10.1128/msphere.00169-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/05/2019] [Indexed: 12/24/2022] Open
Abstract
Salmonella genomic island 1 (SGI1) is an integrative genetic island first described in Salmonella enterica serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of S. enterica, as well as in Proteus mirabilis, Acinetobacter baumannii, Morganella morganii, and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry blaNDM-1, blaVEB-6, and blaCTX-M15 genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins. Genome sequencing studies of avian pathogenic Escherichia coli (APEC) identified a sequence type 117 (ST117) isolate (AVC96) with genetic features found in SGI1. The complete genome sequence of AVC96 was assembled from a combination of Illumina and single-molecule real-time (SMRT) sequence data. Analysis of the AVC96 chromosome identified a variant of SGI1-B located 18 bp from the 3' end of trmE, also known as the attB site, a known hot spot for the integration of genomic islands. This is the first report of SGI1 in wild-type E. coli The variant, here named SGI1-B-Ec1, was otherwise unremarkable, apart from the identification of ISEc43 in open reading frame (ORF) S023.IMPORTANCE SGI1 and variants of it carry a variety of antimicrobial resistance genes, including those conferring resistance to extended-spectrum β-lactams and carbapenems, and have been found in diverse S. enterica serovars, Acinetobacter baumannii, and other members of the Enterobacteriaceae SGI1 integrates into Gram-negative pathogenic bacteria by targeting a conserved site 18 bp from the 3' end of trmE For the first time, we describe a novel variant of SGI1 in an avian pathogenic Escherichia coli isolate. The presence of SGI1 in E. coli is significant because it represents yet another lateral gene transfer mechanism to enhancing the capacity of E. coli to acquire and propagate antimicrobial resistance and putative virulence genes. This finding underscores the importance of whole-genome sequencing (WGS) to microbial genomic epidemiology, particularly within a One Health context. Further studies are needed to determine how widespread SGI1 and variants of it may be in Australia.
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Affiliation(s)
- Max Laurence Cummins
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Piklu Roy Chowdhury
- The ithree institute, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Marc Serge Marenda
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Glenn Francis Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX. Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microb Genom 2019; 5. [PMID: 31107206 PMCID: PMC6700661 DOI: 10.1099/mgen.0.000269] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.
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Affiliation(s)
- Jane Hawkey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Benoît Doublet
- ISP, Institut National de la Recherche Agronomique, Université François Rabelais de Tours, UMR 1282, Nouzilly, France
| | - Sophie A Granier
- Laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, 94701 Maisons-Alfort, France.,Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), 35306 Fougères, France
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Camille Gomart
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
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Kaushik M, Kumar S, Kapoor RK, Gulati P. Integrons and antibiotic resistance genes in water-borne pathogens: threat detection and risk assessment. J Med Microbiol 2019; 68:679-692. [DOI: 10.1099/jmm.0.000972] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Megha Kaushik
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Sanjay Kumar
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Rajeev Kr. Kapoor
- Enzyme Biotechnology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001, India
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Xiao T, Dai H, Lu B, Li Z, Cai H, Huang Z, Kan B, Wang D. Distribution and characteristics of SGI1/PGI2 genomic island from Proteus strains in China. INFECTION GENETICS AND EVOLUTION 2019; 70:123-130. [PMID: 30825526 DOI: 10.1016/j.meegid.2019.02.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/29/2018] [Accepted: 02/24/2019] [Indexed: 01/12/2023]
Abstract
The emergence of multidrug-resistant Salmonella genomic island 1 (SGI1) and Proteus genomic island (PGI) bearing P. mirabilis present a serious threat to public health. In this study, we screened 288 Proteus isolates recovered from seven provinces in China. Fourteen strains (4.9%) all belonged to P. mirabilis were positive for SGI1/PGI2, including twelve from clinical samples (5.3%) and two from food (3.3%). A Blastn search against GenBank and phylogenetic analyses identified eight different SGI1 variants and one PGI2 variant from the fourteen SGI1/PGI2 variants. All SGI1 variants shared a common backbone and harbored different resistance gene(s), except the sul1 gene at its multidrug-resistant (MDR) region. Among the variants, three novel SGI1 variants, designated as SGI1-PmCA11, SGI1-PmCA14 and SGI1-PmCA46, contained different gene cassettes, which were similar to sequences in plasmids or class 1 integrons of Klebsiella pneumoniae, P. mirabilis, Escherichia coli and Salmonella. Moreover, one novel PGI2, designated as PGI2-PmCA72, had an identical gene cassette to the first class 1 integron from PGI2 (GenBank accession no. MG201402.1) in P. mirabilis, but varied due to missing, replaced, inserted and inverted gene clusters. The four novel SGI1/PGI2 variants contained the cmlA5, dfrA14, blaOXA-10, aadA15, blaOXA-1, catB3 and dfrA16 resistance genes, which have never been reported in SGI1/PGI2 variants. Phenotypically, all fourteen SGI1/PGI2-containing strains showed multidrug resistance. All except four strains were resistant to the first, or the second and/or-third generation cephalosporins. Considering the increasing number and the emergence of new SGI1/PGI2 variants, further surveillance is needed to prevent the spreading of the MDR genomic islands among Proteus isolates from human and food.
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Affiliation(s)
- Tao Xiao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China
| | - Hang Dai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Hongyan Cai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China
| | - Zhenzhou Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Duochun Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China; Center for Human Pathogen Collection, China CDC, Beijing, 102206, China.
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Marques C, Belas A, Aboim C, Trigueiro G, Cavaco-Silva P, Gama LT, Pomba C. Clonal relatedness of Proteus mirabilis strains causing urinary tract infections in companion animals and humans. Vet Microbiol 2019; 228:77-82. [DOI: 10.1016/j.vetmic.2018.10.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/07/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
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Bie L, Fang M, Li Z, Wang M, Xu H. Identification and Characterization of New Resistance-Conferring SGI1s ( Salmonella Genomic Island 1) in Proteus mirabilis. Front Microbiol 2018; 9:3172. [PMID: 30619228 PMCID: PMC6305713 DOI: 10.3389/fmicb.2018.03172] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/07/2018] [Indexed: 12/23/2022] Open
Abstract
Salmonella genomic island 1 (SGI1) is a resistance-conferring chromosomal genomic island that contains an antibiotic resistance gene cluster. The international spread of SGI1-containing strains drew attention to the role of genomic islands in the dissemination of antibiotic resistance genes in Salmonella and other Gram-negative bacteria. In this study, five SGI1 variants conferring multidrug and heavy metal resistance were identified and characterized in Proteus mirabilis strains: SGI1-PmCAU, SGI1-PmABB, SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48. The genetic structures of SGI1-PmCAU and SGI1-PmABB were identical to previously reported SGI1s, while structural analysis showed that SGI1-PmJN16, SGI1-PmJN40, and SGI1-PmJN48 are new SGI1 variants. SGI1-PmJN16 is derived from SGI1-Z with the MDR region containing a new gene cassette array dfrA12-orfF-aadA2-qacEΔ1-sul1-chrA-orf1. SGI1-PmJN40 has an unprecedented structure that contains two right direct repeat sequences separated by a transcriptional regulator-rich DNA fragment, and is predicted to form two different extrachromosomal mobilizable DNA circles for dissemination. SGI1-PmJN48 lacks a common ORF S044, and its right junction region exhibits a unique genetic organization due to the reverse integration of a P. mirabilis chromosomal gene cluster and the insertion of part of a P. mirabilis plasmid, making it the largest known SGI1 to date (189.1 kb). Further mobility functional analysis suggested that these SGIs can be excised from the chromosome for transfer between bacteria, which promotes the horizontal transfer of antibiotic and heavy metal resistance genes. The identification and characterization of the new SGI1 variants in this work suggested the diversity of SGI1 structures and their significant roles in the evolution of bacteria.
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Affiliation(s)
- Luyao Bie
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Meng Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Zhiqiang Li
- Advanced Research Center for Optics, Shandong University, Qingdao, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Sahay S, Shome R, Sankarasubramanian J, Vishnu US, Prajapati A, Natesan K, Shome BR, Rahman H, Rajendhran J. Genome sequence analysis of the Indian strain Mannheimia haemolytica serotype A2 from ovine pneumonic pasteurellosis. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1410-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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