1
|
Huang J, Xiao J, Wang X, Xue X, Ma Y, Zhang Z, Zheng L, Zafir M, Liu P, Zhao X, Larsen AR, Xue H. Unearthing New ccr Genes and Staphylococcal Cassette Chromosome Elements in Staphylococci Through Genome Mining. J Infect Dis 2024; 230:231-238. [PMID: 39052728 DOI: 10.1093/infdis/jiae044] [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: 08/18/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 01/27/2024] Open
Abstract
Staphylococcal cassette chromosome mec (SCCmec) typing is crucial for investigating methicillin-resistant Staphylococcus aureus (MRSA), relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB, and 3 ccrC) through mining of the National Center for Biotechnology Information (NCBI) database, forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of 5 groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.
Collapse
Affiliation(s)
- Jianguo Huang
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Jinhe Xiao
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Xiaokun Wang
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Xuemei Xue
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Yadong Ma
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Ziqian Zhang
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Liangjun Zheng
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Muhammad Zafir
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Pilong Liu
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| | - Xin Zhao
- Department of Animal Science, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Huping Xue
- College of Animal Science and Technology, Northwest Agricultural and Forestry University, Yangling, Shaanxi, People's Republic of China
| |
Collapse
|
2
|
Juhas M. Multidrug-Resistant Bacteria. BRIEF LESSONS IN MICROBIOLOGY 2023:65-77. [DOI: 10.1007/978-3-031-29544-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
3
|
Juhas M. Gene Transfer. BRIEF LESSONS IN MICROBIOLOGY 2023:51-63. [DOI: 10.1007/978-3-031-29544-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
|
4
|
Comparative Genomic Analysis of a Multidrug-Resistant Staphylococcus hominis ShoR14 Clinical Isolate from Terengganu, Malaysia, Led to the Discovery of Novel Mobile Genetic Elements. Pathogens 2022; 11:pathogens11121406. [PMID: 36558739 PMCID: PMC9782665 DOI: 10.3390/pathogens11121406] [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: 10/29/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus hominis is a coagulase-negative Staphylococcus (CoNS) commensal capable of causing serious systemic infections in humans. The emergence of multidrug-resistant S. hominis strains is of concern but little is known about the characteristics of this organism, particularly from Malaysia. Here, we present the comparative genome analysis of S. hominis ShoR14, a multidrug-resistant, methicillin-resistant blood isolate from Terengganu, Malaysia. Genomic DNA of S. hominis ShoR14 was sequenced on the Illumina platform and assembled using Unicycler v0.4.8. ShoR14 belonged to sequence type (ST) 1 which is the most prevalent ST of the S. hominis subsp. hominis. Comparative genomic analysis with closely related strains in the database with complete genome sequences, led to the discovery of a novel variant of the staphylococcal chromosome cassette mec (SCCmec) type VIII element harboring the mecA methicillin-resistance gene in ShoR14 and its possible carriage of a SCCfus element that encodes the fusidic acid resistance gene (fusC). Up to seven possible ShoR14 plasmid contigs were identified, three of which harbored resistance genes for tetracycline (tetK), chloramphenicol (catA7), macrolides, lincosamides, and streptogramin B (ermC). Additionally, we report the discovery of a novel mercury-resistant transposon, Tn7456, other genomic islands, and prophages which make up the S. hominis mobilome.
Collapse
|
5
|
Cabrera-Contreras R, Santamaría RI, Bustos P, Martínez-Flores I, Meléndez-Herrada E, Morelos-Ramírez R, Barbosa-Amezcua M, González-Covarrubias V, Silva-Herzog E, Soberón X, González V. Genomic diversity of prevalent Staphylococcus epidermidis multidrug-resistant strains isolated from a Children's Hospital in México City in an eight-years survey. PeerJ 2019; 7:e8068. [PMID: 31768302 PMCID: PMC6874853 DOI: 10.7717/peerj.8068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/20/2019] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus epidermidis is a human commensal and pathogen worldwide distributed. In this work, we surveyed for multi-resistant S. epidermidis strains in eight years at a children's health-care unit in México City. Multidrug-resistant S. epidermidis were present in all years of the study, including resistance to methicillin, beta-lactams, fluoroquinolones, and macrolides. To understand the genetic basis of antibiotic resistance and its association with virulence and gene exchange, we sequenced the genomes of 17 S. epidermidis isolates. Whole-genome nucleotide identities between all the pairs of S. epidermidis strains were about 97% to 99%. We inferred a clonal structure and eight Multilocus Sequence Types (MLSTs) in the S. epidermidis sequenced collection. The profile of virulence includes genes involved in biofilm formation and phenol-soluble modulins (PSMs). Half of the S. epidermidis analyzed lacked the ica operon for biofilm formation. Likely, they are commensal S. epidermidis strains but multi-antibiotic resistant. Uneven distribution of insertion sequences, phages, and CRISPR-Cas immunity phage systems suggest frequent horizontal gene transfer. Rates of recombination between S. epidermidis strains were more prevalent than the mutation rate and affected the whole genome. Therefore, the multidrug resistance, independently of the pathogenic traits, might explain the persistence of specific highly adapted S. epidermidis clonal lineages in nosocomial settings.
Collapse
Affiliation(s)
- Roberto Cabrera-Contreras
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rosa I Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Irma Martínez-Flores
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Meléndez-Herrada
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Rubén Morelos-Ramírez
- Laboratorio de Patogenicidad Bacteriana, Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | | | | | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Ciudad de México, México
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
6
|
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]
|
7
|
Wu Z, Zhang L, Qiao D, Xue H, Zhao X. Functional Analyses of Cassette Chromosome Recombinase C2 (CcrC2) and Its Use in Eliminating Methicillin Resistance by Combining CRISPR-Cas9. ACS Synth Biol 2018; 7:2590-2599. [PMID: 30278126 DOI: 10.1021/acssynbio.8b00261] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Worldwide occurrence of methicillin-resistant Staphylococcus aureus (MRSA) poses enormous challenges for both communities and health care settings. Cassette chromosome recombinases (Ccr) specifically perform excision and acquisition of a staphylococcal cassette chromosome mec (SCC mec) in staphylococci and are responsible for the spread of methicillin resistance. This study explored the roles of CcrC2, a recently discovered Ccr, in the horizontal transfer of SCC mec and developed a potential means to control the spread of methicillin resistance. Knockout of CcrC2 completely aborted the excision of SCC mec, while overexpression of CcrC2 partially removed the SCC mec from the genome and transformed methicillin-resistant Staphylococcus aureus (MRSA) into methicillin-susceptible Staphylococcus aureus (MSSA). Moreover, two nucleotide residues (G5C6) in the direct repeat sequence within an att site were found to be critical for excision and acquisition efficiencies. To block the horizontal transfer of methicillin resistance, a SCC mec killer system was developed by combining the CcrC2-mediated SCC mec excision and the mecA-targeting CRISPR-Cas9 machinery. The SCC mec killer transformed MRSA to MSSA and disrupted the mecA-carrying SCC mec intermediate, thereby eliminating methicillin resistance determinant mecA gene inside a MRSA cell and blocking the horizontal transfer of SCC mec. The SCC mec killer was versatile for efficiently removing multiple types of SCC mec elements. It is envisioned that this approach could offer a new means to control the spread of methicillin resistance.
Collapse
Affiliation(s)
- Zhaowei Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi, People’s Republic of China
| | - Limin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi, People’s Republic of China
| | - Dandan Qiao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi, People’s Republic of China
| | - Huping Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi, People’s Republic of China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 Shaanxi, People’s Republic of China
- Department of Animal Science, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| |
Collapse
|
8
|
Tong C, Wu Z, Zhao X, Xue H. Arginine Catabolic Mobile Elements in Livestock-Associated Methicillin-Resistant Staphylococcal Isolates From Bovine Mastitic Milk in China. Front Microbiol 2018; 9:1031. [PMID: 29867908 PMCID: PMC5964201 DOI: 10.3389/fmicb.2018.01031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/01/2018] [Indexed: 12/19/2022] Open
Abstract
The arginine catabolic mobile element (ACME) facilitates colonization of staphylococci on skin and mucous membranes by improving their tolerances to polyamines and acidic conditions. ACME is inserted in tandem with the SCCmec element and Staphylococcus epidermidis has been proposed to be a reservoir of ACME for other staphylococci. In this study, we investigated the existence of ACME in 146 staphylococcal isolates from mastitic milk and found 21 of them carried ACME. Almost half of the investigated S. epidermidis isolates contained the element. The whole genome of a S. epidermidis strain Y24 with ACME was further sequenced and the ACME-SCCmec composite island was assembled. This composite island is 81.3 kb long and consisted of 77 ORFs including a methicillin resistance gene mecA, a type II’ ACME gene cluster, a virulence gene pls and eight heavy metal tolerance genes. Wide existence of ACME in livestock-associated staphylococci from this study and a potential risk of spreading ACME among different staphylococcal species warrant close monitoring and further studies.
Collapse
Affiliation(s)
- Chao Tong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhaowei Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal Science, McGill University, Montreal, QC, Canada
| | - Huping Xue
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| |
Collapse
|