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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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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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3
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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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Biggel M, Horlbog J, Nüesch-Inderbinen M, Chattaway MA, Stephan R. Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland. Microb Genom 2022; 8:mgen000877. [PMID: 36301086 PMCID: PMC9676052 DOI: 10.1099/mgen.0.000877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/15/2022] [Indexed: 07/20/2023] Open
Abstract
Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIPR) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIPR. High- and low-level ciprofloxacin resistance among CIPR isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.
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Affiliation(s)
- Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
| | - Jule Horlbog
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
- National Reference Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
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Vázquez X, Fernández J, Bances M, Lumbreras P, Alkorta M, Hernáez S, Prieto E, de la Iglesia P, de Toro M, Rodicio MR, Rodicio R. Genomic Analysis of Ciprofloxacin-Resistant Salmonella enterica Serovar Kentucky ST198 From Spanish Hospitals. Front Microbiol 2021; 12:720449. [PMID: 34675895 PMCID: PMC8525328 DOI: 10.3389/fmicb.2021.720449] [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: 06/04/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Salmonella enterica serovar Kentucky (S. Kentucky) with sequence type (ST) 198 and highly resistant to ciprofloxacin (ST198-CipR) has emerged as a global MDR clone, posing a threat to public health. In the present study, whole genome sequencing (WGS) was applied to characterize all CipRS. Kentucky detected in five Spanish hospitals during 2009–2018. All CipR isolates (n = 13) were ST198 and carried point mutations in the quinolone resistance-determining regions (QRDRs) of both gyrA (resulting in Ser83Phe and Asp87Gly, Asp87Asn, or Asp87Tyr substitutions in GyrA) and parC (with Thr57Ser and Ser80Ile substitutions in ParC). Resistances to other antibiotics (ampicillin, chloramphenicol, gentamicin, streptomycin, sulfonamides, and tetracycline), mediated by the blaTEM–1B, catA1, aacA5, aadA7, strA, strB, sul1, and tet(A) genes, and arranged in different combinations, were also observed. Analysis of the genetic environment of the latter resistance genes revealed the presence of multiple variants of SGI1 (Salmonella genomic island 1)-K and SGI1-P, where all these resistance genes except catA1 were placed. IS26 elements, found at multiple locations within the SGI1 variants, have probably played a crucial role in their generation. Despite the wide diversity of SGI1-K- and SGI1-P-like structures, phylogenetic analysis revealed a close relationship between isolates from different hospitals, which were separated by a minimum of two and a maximum of 160 single nucleotide polymorphisms. Considering that S. enterica isolates resistant to fluoroquinolones belong to the high priority list of antibiotic-resistant bacteria compiled by the World Health Organization, continuous surveillance of the S. Kentucky ST198-CIPR clone is required.
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Affiliation(s)
- Xenia Vázquez
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Javier Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain.,Research and Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública (LSP) del Principado de Asturias, Dirección General de Salud Pública, Oviedo, Spain
| | - Pilar Lumbreras
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Miriam Alkorta
- Servicio de Microbiología, Hospital Universitario Donostia (HUD)-IIS Biodonostia, San Sebastián, Spain
| | - Silvia Hernáez
- Servicio de Microbiología, Hospital Universitario de Álava (HUA), Vitoria-Gasteiz, Spain
| | - Elizabeth Prieto
- Servicio de Microbiología, Hospital Universitario San Agustín, Avilés, Spain
| | | | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - M Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo (UO), Oviedo, Spain.,Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rosaura Rodicio
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), Oviedo, Spain
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6
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Antimicrobial Resistance and Whole-Genome Characterisation of High-Level Ciprofloxacin-Resistant Salmonella Enterica Serovar Kentucky ST 198 Strains Isolated from Human in Poland. Int J Mol Sci 2021; 22:ijms22179381. [PMID: 34502290 PMCID: PMC8431004 DOI: 10.3390/ijms22179381] [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: 07/12/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Salmonella Kentucky belongs to zoonotic serotypes that demonstrate that the high antimicrobial resistance and multidrug resistance (including fluoroquinolones) is an emerging problem. To the best of our knowledge, clinical S. Kentucky strains isolated in Poland remain undescribed. METHODS Eighteen clinical S. Kentucky strains collected in the years 2018-2019 in Poland were investigated. All the strains were tested for susceptibility to 11 antimicrobials using the disc diffusion and E-test methods. Whole genome sequences were analysed for antimicrobial resistance genes, mutations, the presence and structure of SGI1-K (Salmonella Genomic Island and the genetic relationship of the isolates. RESULTS Sixteen of 18 isolates (88.9%) were assigned as ST198 and were found to be high-level resistant to ampicillin (>256 mg/L) and quinolones (nalidixic acid MIC ≥ 1024 mg/L, ciprofloxacin MIC range 6-16 mg/L). All the 16 strains revealed three mutations in QRDR of GyrA and ParC. The substitutions of Ser83 → Phe and Asp87 → Tyr of the GyrA subunit and Ser80→Ile of the ParC subunit were the most common. One S. Kentucky isolate had qnrS1 in addition to the QRDR mutations. Five of the ST198 strains, grouped in cluster A, had multiple resistant determinants like blaTEM1-B, aac(6')-Iaa, sul1 or tetA, mostly in SGI1 K. Seven strains, grouped in cluster B, had shorter SGI1-K with deletions of many regions and with few resistance genes detected. CONCLUSION The results of this study demonstrated that a significant part of S. Kentucky isolates from humans in Poland belonged to ST198 and were high-level resistant to ampicillin and quinolones.
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Durand R, Huguet KT, Rivard N, Carraro N, Rodrigue S, Burrus V. Crucial role of Salmonella genomic island 1 master activator in the parasitism of IncC plasmids. Nucleic Acids Res 2021; 49:7807-7824. [PMID: 33834206 PMCID: PMC8373056 DOI: 10.1093/nar/gkab204] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
IncC conjugative plasmids and the multiple variants of Salmonella Genomic Island 1 (SGI1) are two functionally interacting families of mobile genetic elements commonly associated with multidrug resistance in the Gammaproteobacteria. SGI1 and its siblings are specifically mobilised in trans by IncC conjugative plasmids. Conjugative transfer of IncC plasmids is activated by the plasmid-encoded master activator AcaCD. SGI1 carries five AcaCD-responsive promoters that drive the expression of genes involved in its excision, replication, and mobilisation. SGI1 encodes an AcaCD homologue, the transcriptional activator complex SgaCD (also known as FlhDCSGI1) that seems to recognise and activate the same SGI1 promoters. Here, we investigated the relevance of SgaCD in SGI1's lifecycle. Mating assays revealed the requirement for SgaCD and its IncC-encoded counterpart AcaCD in the mobilisation of SGI1. An integrative approach combining ChIP-exo, Cappable-seq, and RNA-seq confirmed that SgaCD activates each of the 18 AcaCD-responsive promoters driving the expression of the plasmid transfer functions. A comprehensive analysis of the activity of the complete set of AcaCD-responsive promoters of SGI1 and the helper IncC plasmid was performed through reporter assays. qPCR and flow cytometry assays revealed that SgaCD is essential to elicit the excision and replication of SGI1 and destabilise the helper IncC plasmid.
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Affiliation(s)
- Romain Durand
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Kévin T Huguet
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Rivard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Nicolas Carraro
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Vincent Burrus
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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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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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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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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Mahindroo J, Thanh DP, Nguyen TNT, Mohan B, Thakur S, Baker S, Taneja N. Endemic fluoroquinolone-resistant Salmonellaenterica serovar Kentucky ST198 in northern India. Microb Genom 2019; 5. [PMID: 31166889 PMCID: PMC6700665 DOI: 10.1099/mgen.0.000275] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Salmonellaenterica serovar Kentucky is an emergent human pathogen. Human infection with ciprofloxacin-resistant S. enterica Kentucky ST198 has been reported in Europe and North America as a consequence of travel to Asia/the Middle East. This is, to the best of our knowledge, the first study reporting the identification of this epidemic clone in India and South Asia.
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Affiliation(s)
- Jaspreet Mahindroo
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Duy Pham Thanh
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- Oxford University Clinical Research Unit, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Vietnam
| | - Balvinder Mohan
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Siddhartha Thakur
- College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Neelam Taneja
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Haley BJ, Kim SW, Haendiges J, Keller E, Torpey D, Kim A, Crocker K, Myers RA, Van Kessel JAS. Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011-2015). Zoonoses Public Health 2019; 66:382-392. [PMID: 30891945 DOI: 10.1111/zph.12571] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/18/2018] [Accepted: 02/07/2019] [Indexed: 11/27/2022]
Abstract
Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America.
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Affiliation(s)
- Bradd J Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
| | | | - Eric Keller
- Maryland Department of Health, Baltimore, Maryland
| | - David Torpey
- Maryland Department of Health, Baltimore, Maryland
| | | | - Kia Crocker
- Maryland Department of Health, Baltimore, Maryland
| | | | - Jo Ann S Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, Maryland
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Juhas M. Genomic Islands and the Evolution of Multidrug-Resistant Bacteria. HORIZONTAL GENE TRANSFER 2019:143-153. [DOI: 10.1007/978-3-030-21862-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Multidrug Resistance Salmonella Genomic Island 1 in a Morganella morganii subsp. morganii Human Clinical Isolate from France. mSphere 2017; 2:mSphere00118-17. [PMID: 28435889 PMCID: PMC5397566 DOI: 10.1128/msphere.00118-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/01/2017] [Indexed: 01/19/2023] Open
Abstract
Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development. Salmonella genomic island 1 (SGI1) is a multidrug resistance integrative mobilizable element that harbors a great diversity of antimicrobial resistance gene clusters described in numerous Salmonella enterica serovars and also in Proteus mirabilis. A serious threat to public health was revealed in the recent description in P. mirabilis of a SGI1-derivative multidrug resistance island named PGI1 (Proteus genomic island 1) carrying extended-spectrum-β-lactamase (ESBL) and metallo-β-lactamase resistance genes, blaVEB-6 and blaNDM-1, respectively. Here, we report the first description of Salmonella genomic island 1 (SGI1) in a multidrug-resistant clinical Morganella morganii subsp. morganii strain isolated from a patient in France in 2013. Complete-genome sequencing of the strain revealed SGI1 variant SGI1-L carrying resistance genes dfrA15, floR, tetA(G), blaPSE-1 (now referred to as blaCARB-2), and sul1, conferring resistance to trimethoprim, phenicols, tetracyclines, amoxicillin, and sulfonamides, respectively. The SGI1-L variant was integrated into the usual chromosome-specific integration site at the 3′ end of the trmE gene. Beyond Salmonella enterica and Proteus mirabilis, the SGI1 integrative mobilizable element may thus also disseminate its multidrug resistance phenotype in another genus belonging to the Proteae tribe of the family Enterobacteriaceae. IMPORTANCE Since its initial identification in epidemic multidrug-resistant Salmonella enterica serovar Typhimurium DT104 strains, several SGI1 variants, SGI1 lineages, and SGI1-related elements (SGI2, PGI1, and AGI1) have been described in many bacterial genera (Salmonella, Proteus, Morganella, Vibrio, Shewanella, etc.). They constitute a family of multidrug resistance site-specific integrative elements acquired by horizontal gene transfer, SGI1 being the best-characterized element. The horizontal transfer of SGI1/PGI1 elements into other genera is of public health concern, notably with regard to the spread of critically important resistance genes such as ESBL and carbapenemase genes. The identification of SGI1 in Morganella morganii raises the issue of (i) the potential for SGI1 to emerge in other human pathogens and (ii) its bacterial host range. Further surveillance and research are needed to understand the epidemiology, the spread, and the importance of the members of this SGI1 family of integrative elements in contributing to antibiotic resistance development.
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Haley BJ, Kim SW, Pettengill J, Luo Y, Karns JS, Van Kessel JAS. Genomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America. PLoS One 2016; 11:e0161225. [PMID: 27695032 PMCID: PMC5047448 DOI: 10.1371/journal.pone.0161225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/02/2016] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - James Pettengill
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Yan Luo
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, MD, United States of America
| | - Jeffrey S. Karns
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Jo Ann S. Van Kessel
- Environmental Microbial and Food Safety Laboratory, Beltsville Area Research Center, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD, United States of America
- * E-mail:
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Destabilization of IncA and IncC plasmids by SGI1 and SGI2 type Salmonella genomic islands. Plasmid 2016; 87-88:51-57. [DOI: 10.1016/j.plasmid.2016.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 11/24/2022]
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17
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PCR-based typing of IncC plasmids. Plasmid 2016; 87-88:37-42. [DOI: 10.1016/j.plasmid.2016.08.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/19/2016] [Accepted: 08/29/2016] [Indexed: 11/22/2022]
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Two novel Salmonella genomic island 1 variants in Proteus mirabilis isolates from swine farms in China. Antimicrob Agents Chemother 2015; 59:4336-8. [PMID: 25918148 DOI: 10.1128/aac.00120-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/18/2015] [Indexed: 12/24/2022] Open
Abstract
Four different Salmonella genomic island 1 (SGI1) variants, including two novel variants, were characterized in one Salmonella enterica serovar Rissen sequence type ST1917 isolate and three Proteus mirabilis isolates from swine farms in China. One novel variant was derived from SGI1-B with the backbone gene S021 disrupted by a 12.72-kb IS26 composite transposon containing the dfrA17-aadA5 cassettes and macrolide inactivation gene cluster mphA-mrx-mphR. The other one was an integron-free SGI1 and contained a 183-bp truncated S025 next to IS6100 and S044.
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