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Fang Z, Xu M, Shen S, Sun W, Yu Q, Wu Q, Xiang L, Weng Q. Prediction and characterization of prophages of Stenotrophomonas maltophilia reveals a remarkable phylogenetic diversity of prophages. Sci Rep 2023; 13:22941. [PMID: 38135742 PMCID: PMC10746704 DOI: 10.1038/s41598-023-50449-x] [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: 04/27/2023] [Accepted: 12/20/2023] [Indexed: 12/24/2023] Open
Abstract
Prophages, which enables bacterial hosts to acquire novel traits, and increase genetic variation and evolutionary innovation, are considered to be one of the greatest drivers of bacterial diversity and evolution. Stenotrophomonas maltophilia is widely distributed and one of the most important multidrug resistant bacteria in hospitals. However, the distribution and genetic diversity of S. maltophilia prophages have not been elucidated. In this study, putative prophages were predicted in S. maltophilia genomes by using virus prediction tools, and the genetic diversity and phylogeny of S. maltophilia and the prophages they harbor were further analyzed. A total of 356 prophage regions were predicted from 88 S. maltophilia genomes. Among them, 144 were intact prophages, but 77.09% of the intact prophages did not match any known phage sequences in the public database. The number of prophage carried by S. maltophilia is related to its host habitat and is an important factor affecting the size of the host genome, but it is not related to the genetic diversity of the prophage. The prediction of auxiliary genes encoded by prophage showed that antibiotic resistance genes was not predicted for any of the prophages except for one questionable prophage, while 53 virulence genes and 169 carbohydrate active enzymes were predicted from 11.24 and 44.1% prophages, respectively. Most of the prophages (72.29%) mediated horizontal gene transfer of S. maltophilia genome, but only involved in 6.25% of the horizontal gene transfer events. In addition, CRISPR prediction indicated 97.75% S. maltophilia strains contained the CRISPR-Cas system containing 818 spacer sequences. However, these spacer sequences did not match any known S. maltophilia phages, and only a few S. maltophilia prophages. Comparative genomic analysis revealed a highly conserved and syntenic organization with genomic rearrangement between the prophages and the known related S. maltophilia phages. Our results indicate a high prevalence and genetic diversity of prophages in the genome of S. maltophilia, as well as the presence of a large number of uncharacterized phages. It provides an important complement to understanding the diversity and biological characteristics of phages, as well as the interactions and evolution between bacteria and phages.
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Affiliation(s)
- Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Shan Shen
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Weiwei Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qing Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China
| | - Lan Xiang
- Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, People's Republic of China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, 550025, Guizhou, People's Republic of China.
- Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, People's Republic of China.
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Teixeira IM, de Moraes Assumpção Y, Paletta ACC, Aguiar L, Guimarães L, da Silva IT, Côrtes MF, Botelho AMN, Jaeger LH, Ferreira RF, de Oliveira Ferreira E, Penna B. Investigation of antimicrobial susceptibility and genetic diversity among Staphylococcus pseudintermedius isolated from dogs in Rio de Janeiro. Sci Rep 2023; 13:20219. [PMID: 37980395 PMCID: PMC10657392 DOI: 10.1038/s41598-023-47549-z] [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: 01/16/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023] Open
Abstract
Staphylococcus pseudintermedius is an opportunistic pathogen causing a variety of infections that are difficult to treat, especially because of the development of antimicrobial resistance. It has a clonal distribution around the world. To have a better understanding of the MRSP population, we search the presence of MRSP in colonized or infected dogs. Samples from 99 dogs with infections and 35 from asymptomatic dogs were collected. Isolates were identified by mass spectrometry and Multiplex-PCR. The mecA gene was confirmed by conventional PCR. MRSP strains were analyzed by whole-genome sequencing. 75 S. pseudintermedius were identified, most from infection cases. The species were isolated from 70 out of the 135 dogs. Penicillin and Trimethoprim/Sulfamethoxazole presented higher resistance rates. Forty-seven strains were classified as multi-drug resistant (MDR), and were more isolated from dogs with infection (P < 0.05). Eighteen samples were classified as MRSP, representing 24.0% of the population. Six of 16 MRSP sequenced samples belonged to the world spread clone ST71; others belonged to unknown clones. Most samples carried the SCCmec type IIIA. Twenty-one different genetic resistance determinants were found among MRPS strains. MRSP is circulating among infected and colonized dogs in Rio de Janeiro, Brazil.
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Affiliation(s)
- Izabel Mello Teixeira
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Yasmim de Moraes Assumpção
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Ana Clara Cabral Paletta
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Louise Aguiar
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Luciana Guimarães
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Isabella Thomaz da Silva
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Marina F Côrtes
- Laboratório de Investigação Médica, Instituto de Medicina Tropical, USP, São Paulo, Brazil
| | - Ana Maria Nunes Botelho
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil
| | - Lauren Hubert Jaeger
- Laboratório de Células-Tronco e Parasitologia Molecular, Departamento de Ciências Farmacêuticas, UFJF, Juiz de Fora, Brazil
| | | | - Eliane de Oliveira Ferreira
- Laboratório de Biologia de Anaeróbios, Departamento Microbiologia Médica, IMPPG, UFRJ, Rio de Janeiro, Brazil
| | - Bruno Penna
- Laboratório de Cocos Gram Positivos, Departamento de Microbiologia e Parasitologia, UFF, Rio de Janeiro, Brazil.
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Sawhney SS, Vargas RC, Wallace MA, Muenks CE, Lubbers BV, Fritz SA, Burnham CAD, Dantas G. Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms. Nat Commun 2023; 14:7065. [PMID: 37923729 PMCID: PMC10624692 DOI: 10.1038/s41467-023-42694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Staphylococcus pseudintermedius is historically understood as a prevalent commensal and pathogen of dogs, though modern clinical diagnostics reveal an expanded host-range that includes humans. It remains unclear whether differentiation across S. pseudintermedius populations is driven primarily by niche-type or host-species. We sequenced 501 diagnostic and commensal isolates from a hospital, veterinary diagnostic laboratory, and within households in the American Midwest, and performed a comparative genomics investigation contrasting human diagnostic, animal diagnostic, human colonizing, pet colonizing, and household-surface S. pseudintermedius isolates. Though indistinguishable by core and accessory gene architecture, diagnostic isolates harbor more encoded and phenotypic resistance, whereas colonizing and surface isolates harbor similar CRISPR defense systems likely reflective of common household phage exposures. Furthermore, household isolates that persist through anti-staphylococcal decolonization report elevated rates of base-changing mutations in - and parallel evolution of - defense genes, as well as reductions in oxacillin and trimethoprim-sulfamethoxazole susceptibility. Together we report parallel niche-specific bolstering of S. pseudintermedius defense mechanisms through gene acquisition or mutation.
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Affiliation(s)
- Sanjam S Sawhney
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Meghan A Wallace
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol E Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Lubbers
- Department of Clinical Sciences, Kansas State University, Manhattan, KS, USA
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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Srednik ME, Perea CA, Giacoboni GI, Hicks JA, Foxx CL, Harris B, Schlater LK. Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study. Int J Mol Sci 2023; 24:11361. [PMID: 37511121 PMCID: PMC10379401 DOI: 10.3390/ijms241411361] [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: 06/07/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.
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Affiliation(s)
- Mariela E Srednik
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Claudia A Perea
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Gabriela I Giacoboni
- Departamento de Microbiología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata 1427, Argentina
| | - Jessica A Hicks
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Christine L Foxx
- Postdoctoral Research Participation Program, Office of Research in Science and Education, Oak Ridge Associated Universities, Oak Ridge, TN 37831, USA
- Transboundary Disease Analytics, Center for Epidemiology and Animal Health, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, CO 80526, USA
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
| | - Linda K Schlater
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA 50010, USA
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Jiang L, Zhu H, Wei J, Jiang L, Li Y, Li R, Wang Z, Wang M. Enterobacteriaceae genome-wide analysis reveals roles for P1-like phage-plasmids in transmission of mcr-1, tetX4 and other antibiotic resistance genes. Genomics 2023; 115:110572. [PMID: 36746220 DOI: 10.1016/j.ygeno.2023.110572] [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: 09/16/2022] [Revised: 12/23/2022] [Accepted: 02/02/2023] [Indexed: 02/07/2023]
Abstract
P1 -like phage-plasmids (PPs) are important gene vehicles in isolated pathogens. In this study, we conducted genome-wide and cross-species analysis of antimicrobial resistance genes (ARGs) from 35 ARG-positive P1-like PPs. LS-BSR analysis reveal that P1-like PPs had in common 7 highly variable regions and carried 48 different ARG subtypes. The most prevalent gene groups were the colistin resistance gene mcr-1 and a class 1 integron. Analysis of the flanking sequences of mcr-1 indicated an "IS30-mcr-1-ORF-IS30" as the core cluster. In particular, we found an mcr-1- and blaCTX-M-55-coharboring large fusion P1-like PP. Also, tet(X4) was detected and flanking sequences indicated tet(X4)-bearing cluster can formed a larger size fusion plasmid mediated a wider spread via IS26 hotspots. Overall, this study demonstrated that P1-like PPs can not only mobilize a large number of ARGs in variable regions but also form larger hybrid P1-like PPs that would increase their ability to spread antimicrobial resistance.
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Affiliation(s)
- Li Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Heng Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Jingyi Wei
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Lei Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Yan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China; International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou, Jiangsu 225009, China.
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, China; Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Yangzhou 225009, China.
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Sebola DC, Oguttu JW, Kock MM, Qekwana DN. Hospital-acquired and zoonotic bacteria from a veterinary hospital and their associated antimicrobial-susceptibility profiles: A systematic review. Front Vet Sci 2023; 9:1087052. [PMID: 36699325 PMCID: PMC9868922 DOI: 10.3389/fvets.2022.1087052] [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: 11/01/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Background Hospital-acquired infections (HAIs) are associated with increased mortality, morbidity, and an economic burden due to costs associated with extended hospital stays. Furthermore, most pathogens associated with HAIs in veterinary medicine are zoonotic. This study used published data to identify organisms associated with HAIs and zoonosis in veterinary medicine. Furthermore, the study also investigated the antimicrobial-susceptibility profile of these bacterial organisms. Methods A systematic literature review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Search terms and five electronic databases were used to identify studies published over 20 years (2000-2020). The risk of bias was assessed using the "Strengthening the Reporting of Observational Studies in Epidemiology-Vet" (STROBE-Vet) checklist. Results Out of the identified 628 papers, 27 met the inclusion criteria for this study. Most studies (63%, 17/27) included were either from small animal or companion animal clinics/hospitals, while 5% (4/27) were from large animal clinics/hospitals inclusive of bovine and equine hospitals. Hospital-acquired bacteria were reported from environmental surfaces (33%, 9/27), animal clinical cases (29.6%, 8/27), and fomites such as cell phones, clippers, stethoscopes, and computers (14.8%, 4/27). Staphylococcus spp. was the most (63%; 17/27) reported organism, followed by Escherichia coli (19%; 5/27), Enterococcus spp. (15%, 4/27), Salmonella spp. (15%; 4/27), Acinetobacter baumannii (15%, 4/27), Clostridioides difficile (4%, 1/27), and Pseudomonas aeruginosa (4%; 1/27). Multidrug-resistant (MDR) organisms were reported in 71% (12/17) of studies linked to Methicillin-resistant Staphylococcus aureus (MRSA), Methicillin-resistant Staphylococcus pseudintermedius (MRSP), Enterococcus spp., Salmonella Typhimurium, A. baumannii, and E. coli. The mecA gene was identified in both MRSA and MRSP, the blaCMY-2 gene in E. coli and Salmonella spp., and the vanA gene in E. faecium isolate. Six studies reported organisms from animals with similar clonal lineage to those reported in human isolates. Conclusion Organisms associated with hospital-acquired infections and zoonosis have been reported from clinical cases, environmental surfaces, and items used during patient treatment and care. Staphylococcus species is the most reported organism in cases of HAIs and some isolates shared similar clonal lineage to those reported in humans. Some organisms associated with HAIs exhibit a high level of resistance and contain genes associated with antibiotic resistance.
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Affiliation(s)
- Dikeledi C. Sebola
- Section Veterinary Public Health, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - James W. Oguttu
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Johannesburg, South Africa
| | - Marleen M. Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa,Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
| | - Daniel N. Qekwana
- Section Veterinary Public Health, Department of Paraclinical Sciences, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa,*Correspondence: Daniel N. Qekwana ✉
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Penna B, Silva MB, Botelho AMN, Ferreira FA, Ramundo MS, Silva-Carvalho MC, Rabello RF, Vieira-da-Motta O, Figueiredo AMS. Detection of the international lineage ST71 of methicillin-resistant Staphylococcus pseudintermedius in two cities in Rio de Janeiro State. Braz J Microbiol 2022; 53:2335-2341. [PMID: 36319942 PMCID: PMC9679067 DOI: 10.1007/s42770-022-00852-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/13/2022] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus pseudintermedius is the main coagulase-positive staphylococci associated with canine skin/soft tissue infections (SSTI), otitis externa, and surgical site infections. The international spread of an epidemic and multiresistant lineage of methicillin-resistant Staphylococcus pseudintermedius (MRSP), the so-called European clone-displaying sequence type (ST) 71-requires attention. The first isolation of an MRSP ST71 isolate in South America was reported in Rio de Janeiro city, in 2010; however, a limited number of canine isolates were analyzed. Thus, to have a better panel of the MRSP spread in this city, we were stimulated to continue this study and search for the presence of MRSP in 282 colonized or infected dogs in the city of Rio de Janeiro. Among the MRSP isolates collected (N = 17; 6.1%), the pulsed-field gel electrophoresis (PFGE) patterns were similar to those of European clone. All 17 isolates were classified as ST71 by multilocus sequence typing (MLST). In order to assess whether isolates of MRSP ST71 may have also spread to the Rio de Janeiro state countryside, we collected samples from 124 infected dogs in the city of Campos dos Goytacazes (232 km away from Rio de Janeiro city). Our data showed the presence of ST71 lineage in one isolate among three MRSP detected. S. pseudintermedius was isolated from 40.6% of the clinical samples (N = 165/406). A relatively high incidence of methicillin resistance, detected by a PCR-based method, was found in 12.1% of the S. pseudintermedius recovered from animals (N = 20/165). The resistance profile of these isolates was similar to that described for the international ST71 strains whose genomes are publicly available in the GenBank. The prospect of ST71 isolates being resistant to virtually all antimicrobials used in veterinary medicine is alarming and should be considered a central issue considering that MRSP ST71 spreads over large geographic distances and its transmission from animals to humans.
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Affiliation(s)
- Bruno Penna
- Laboratório de Cocos Gram Positivos, Instituto Biomédico, Universidade Federal Fluminense, Niteroi, Brazil.
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Marcella B Silva
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Laboratório de Sanidade Animal - Setor Doenças Infectocontagiosas, Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Macae, Brazil
| | - Ana M N Botelho
- Laboratório de Cocos Gram Positivos, Instituto Biomédico, Universidade Federal Fluminense, Niteroi, Brazil
| | - Fabienne A Ferreira
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Imunologia E Parasitologia, Universidade Federal de Santa Catarina (UFSC), Florianopolis, Brazil
| | - Mariana S Ramundo
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Departamento de Moléstias Infecciosas E Parasitárias, Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo (IMT-FMUSP), Sao Paulo, Brazil
| | - Maria C Silva-Carvalho
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Renata F Rabello
- Laboratório de Cocos Gram Positivos, Instituto Biomédico, Universidade Federal Fluminense, Niteroi, Brazil
| | - Olney Vieira-da-Motta
- Laboratório de Sanidade Animal - Setor Doenças Infectocontagiosas, Universidade Estadual Do Norte Fluminense Darcy Ribeiro (UENF), Macae, Brazil
| | - Agnes M S Figueiredo
- Laboratório de Biologia Molecular de Bactérias Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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Greenrod STE, Stoycheva M, Elphinstone J, Friman VP. Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex. BMC Genomics 2022; 23:689. [PMID: 36199029 PMCID: PMC9535894 DOI: 10.1186/s12864-022-08909-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents. Results Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria. Conclusions Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08909-7.
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Affiliation(s)
| | | | - John Elphinstone
- Fera Science Ltd, National Agri-Food Innovation Campus, Sand Hutton, York, UK
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9
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Zhou G, Wang M, Wang H, Chen X, Gu Y, Shao Z, Zhang J, Zhang M. Species classification and novel plasmid identifications in Arcobacter cryaerophilus and Arcobacter cryaerophilus-like organisms. Front Microbiol 2022; 13:984450. [PMID: 36212879 PMCID: PMC9535334 DOI: 10.3389/fmicb.2022.984450] [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: 07/02/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
The Arcobacter is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other Epsilonproteobacteria. Arcobacter cryaerophilus (A. cryaerophilus) is a heterogeneous species and little is known about its genomic characterization in China. This study aims to determine the genetic and plasmid features of A. cryaerophilus based on whole-genome sequence (WGS). Average Nucleotide Identity (ANI) and in silico DNA–DNA hybridization (isDDH) were used for the species classification for 90 initially identified A. cryaerophilus strains. One complete genome and 42 draft genomes were obtained by whole genome sequencing. The genomic characteristics were determined using various bioinformatics software. The genomes of the strains examined were estimated to vary from 1.81 to 2.28 Mb in length, with a G + C content of around 27%. ANI and isDDH results indicated that 90 initially identified A. cryaerophilus strains should be reclassified into four new species (ANI > 96% or isDDH > 70%). Two clades (four subclades) were identified among 90 genomes with the phylogenetic analysis. The phylogenetic tree indicated these 90 genomes exhibited a high intra-species genomic diversity. No clustering was assorted with the host or geographic location among these genomes. Aminoglycoside resistance genes, such as aph(2’’)-Ih, AAC(6’)-Ie-APH(2’’)-Ia, aac(6’)-IIa, ant(6), and streptothricin resistance gene SAT-4 were detected in the chromosomes from a third of the Chinese strains. Virulence-related genes were identified in all the sequenced strains. A novel large multiple drug-resistant plasmid (named pCNAC48 with 161,992 bp in length) was identified in strain ICDCAC48. Two antibiotic-resistance islands were found in the plasmid with lengths of 7,950 and 25,137 bp and G + C content of 38.23 and 32.39%, respectively. The drug resistance genes and some transposable elements were cross-distributed among the islands in the plasmid. Antimicrobial susceptibility tests indicated these resistance genes in the plasmid were functional. Plasmid conjugation and curing experiments proved pCNAC48 was stable in strain ICDCAC48. It was the first identified multiple drug resistance plasmid in A. cryaerophilus-like.
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10
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Hatoum-Aslan A. The phages of staphylococci: critical catalysts in health and disease. Trends Microbiol 2021; 29:1117-1129. [PMID: 34030968 PMCID: PMC8578144 DOI: 10.1016/j.tim.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/21/2023]
Abstract
The phages that infect Staphylococcus species are dominant residents of the skin microbiome that play critical roles in health and disease. While temperate phages, which can integrate into the host genome, have the potential to promote staphylococcal pathogenesis, the strictly lytic variety are powerful antimicrobials that are being exploited for therapeutic applications. This article reviews recent insights into the diversity of staphylococcal phages and newly described mechanisms by which they influence host pathogenicity. The latest efforts to harness these viruses to eradicate staphylococcal infections are also highlighted. Decades of research has focused on the temperate phages of Staphylococcus aureus as model systems, thus underscoring the need to broaden basic research efforts to include diverse phages that infect other clinically relevant Staphylococcus species.
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Affiliation(s)
- Asma Hatoum-Aslan
- University of Illinois at Urbana-Champaign, Department of Microbiology, Urbana, IL, 61801, USA.
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11
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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12
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Phumthanakorn N, Schwendener S, Donà V, Chanchaithong P, Perreten V, Prapasarakul N. Genomic insights into methicillin-resistant Staphylococcus pseudintermedius isolates from dogs and humans of the same sequence types reveals diversity in prophages and pathogenicity islands. PLoS One 2021; 16:e0254382. [PMID: 34292970 PMCID: PMC8297860 DOI: 10.1371/journal.pone.0254382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022] Open
Abstract
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important opportunistic pathogenic bacterium of dogs that also occasionally colonize and infect humans. However, whether MRSP can adapt to human hosts is not clear and whole genome sequences of MRSP from humans are still limited. Genomic comparative analyses of 3 couples of isolates from dogs (n = 3) and humans (n = 3) belonging to ST45, ST112, and ST181, the dominant clones in Thailand were conducted to determine the degree of similarities between human and animal MRSP of a same ST. Among eight prophages, three prophages associated with the leucocidins genes (lukF/S-I), φVB88-Pro1, φVB16-Pro1 and φAP20-Pro1, were distributed in the human MRSPs, while their remnants, φAH18-Pro1, were located in the dog MRSPs. A novel composite pathogenicity island, named SpPI-181, containing two integrase genes was identified in the ST181 isolates. The distribution of the integrase genes of the eight prophages and SpPI-181 was also analysed by PCR in 77 additional MRSP isolates belonging to different STs. The PCR screen revealed diversity in prophage carriage, especially in ST45 isolates. Prophage φAK9-Pro1 was only observed in ST112 isolates from dogs and SpPI-181 was found associated with ST181 clonal lineage. Among the 3 couple of isolates, ST45 strains showed the highest number of single nucleotide polymorphisms (SNP) in their core genomes (3,612 SNPs). The genomic diversity of ST45 isolates suggested a high level of adaptation that may lead to different host colonization of successful clones. This finding provided data on the genomic differences of MRSP associated with colonization and adaption to different hosts.
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Affiliation(s)
- Nathita Phumthanakorn
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Department of Pre-clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Sybille Schwendener
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valentina Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Diagnosis and Monitoring of Animal Pathogens Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail: (VP); (NP)
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Diagnosis and Monitoring of Animal Pathogens Research Unit, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (VP); (NP)
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13
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Kitagawa H, Hisatsune J, Ohge H, Kutsuno S, Hara T, Masuda K, Aziz F, Sugai M. Implanted Port Catheter System Infection Caused by Methicillin-resistant Staphylococcus pseudintermedius ST71-SCCmec type III. Intern Med 2021; 60:2337-2340. [PMID: 33583884 PMCID: PMC8355384 DOI: 10.2169/internalmedicine.5579-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylococcus pseudintermedius is commonly associated with skin and soft tissue infections in dogs. However, infections caused by S. pseudintermedius are only rarely reported in humans, and this pathogen is frequently misidentified as S. aureus. We herein report a case of an implanted port catheter system infection caused by methicillin-resistant S. pseudintermedius (MRSP) in a patient with hepatocellular carcinoma. The patient was also a dog owner. S. pseudintermedius was first identified using the Vitek2 system (BioMérieux). Whole-genome sequencing revealed that this MRSP was a sequence type 71-carrying staphylococcal cassette chromosome mec type III (ST71-SCCmec III) isolate.
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Affiliation(s)
- Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Junzo Hisatsune
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - Shoko Kutsuno
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Toshinori Hara
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Japan
| | - Kanako Masuda
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
| | - Fatkhanuddin Aziz
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
- Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Indonesia
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
- Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Japan
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14
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Absence of Host-Specific Genes in Canine and Human Staphylococcus pseudintermedius as Inferred from Comparative Genomics. Antibiotics (Basel) 2021; 10:antibiotics10070854. [PMID: 34356775 PMCID: PMC8300826 DOI: 10.3390/antibiotics10070854] [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: 04/29/2021] [Revised: 06/24/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Abstract
Staphylococcus pseudintermedius is an important pathogen in dogs that occasionally causes infections in humans as an opportunistic pathogen of elderly and immunocompromised people. This study compared the genomic relatedness and antimicrobial resistance genes using genome-wide association study (GWAS) to examine host association of canine and human S. pseudintermedius isolates. Canine (n = 25) and human (n = 32) methicillin-susceptible S. pseudintermedius (MSSP) isolates showed a high level of genetic diversity with an overrepresentation of clonal complex CC241 in human isolates. This clonal complex was associated with carriage of a plasmid containing a bacteriocin with cytotoxic properties, a CRISPR-cas domain and a pRE25-like mobile element containing five antimicrobial resistance genes. Multi-drug resistance (MDR) was predicted in 13 (41%) of human isolates and 14 (56%) of canine isolates. CC241 represented 54% of predicted MDR isolates from humans and 21% of predicted MDR canine isolates. While it had previously been suggested that certain host-specific genes were present the current GWAS analysis did not identify any genes that were significantly associated with human or canine isolates. In conclusion, this is the first genomic study showing that MSSP is genetically diverse in both hosts and that multidrug resistance is important in dog and human-associated S. pseudintermedius isolates.
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15
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Dragoš A, Andersen AJC, Lozano-Andrade CN, Kempen PJ, Kovács ÁT, Strube ML. Phages carry interbacterial weapons encoded by biosynthetic gene clusters. Curr Biol 2021; 31:3479-3489.e5. [PMID: 34186025 DOI: 10.1016/j.cub.2021.05.046] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 04/16/2021] [Accepted: 05/20/2021] [Indexed: 01/08/2023]
Abstract
Bacteria produce diverse specialized metabolites that mediate ecological interactions and serve as a rich source of industrially relevant natural products. Biosynthetic pathways for these metabolites are encoded by organized groups of genes called biosynthetic gene clusters (BGCs). Understanding the natural function and distribution of BGCs provides insight into the mechanisms through which microorganisms interact and compete. Further, understanding BGCs is extremely important for biocontrol and the mining of new bioactivities. Here, we investigated phage-encoded BGCs (pBGCs), challenging the relationship between phage origin and BGC structure and function. The results demonstrated that pBGCs are rare, and they predominantly reside within temperate phages infecting commensal or pathogenic bacterial hosts. Further, the vast majority of pBGCs were found to encode for bacteriocins. Using the soil- and gut-associated bacterium Bacillus subtilis, we experimentally demonstrated how a temperate phage equips a bacterium with a fully functional BGC, providing a clear competitive fitness advantage over the ancestor. Moreover, we demonstrated a similar transfer of the same phage in prophage form. Finally, using genetic and genomic comparisons, a strong association between pBGC type and phage host range was revealed. These findings suggest that bacteriocins are encoded in temperate phages of a few commensal bacterial genera. In these cases, lysogenic conversion provides an evolutionary benefit to the infected host and, hence, to the phage itself. This study is an important step toward understanding the natural role of bacterial compounds encoded by BGCs, the mechanisms driving their horizontal transfer, and the sometimes mutualistic relationship between bacteria and temperate phages.
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Affiliation(s)
- Anna Dragoš
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark.
| | - Aaron J C Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Carlos N Lozano-Andrade
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, Produktionstorvet bldg. 423, DK-2800 Kgs Lyngby, Denmark; National Center for Nano Fabrication and Characterization, Technical University of Denmark, Fysikvej bldg. 307, DK-2800 Kgs Lyngby, Denmark
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads bldg. 221, DK-2800 Kgs Lyngby, Denmark.
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16
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Small C, Beatty N, El Helou G. Staphylococcus pseudintermedius Bacteremia in a Lung Transplant Recipient Exposed to Domestic Pets. Cureus 2021; 13:e14895. [PMID: 34109083 PMCID: PMC8180354 DOI: 10.7759/cureus.14895] [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] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus pseudintermedius commonly colonizes companion animals, including canines. This microbe is a major opportunistic pathogen responsible for pyogenic and necrotizing skin and soft tissue infection in canines. Infection with S. pseudintermedius is increasingly being recognized in humans, especially in those who are immunocompromised. This microbe is quite similar to Staphylococcus aureus, expressing several analogous virulence factors and a variety of toxins. Furthermore, S. pseudintermedius has variants that display multi-drug resistance comparable to methicillin-resistant S. aureus. We report a 50-year-old female with bilateral lung transplant on immunosuppression who presents with signs of sepsis and pneumonia. Initial blood cultures grew Gram-positive cocci that were not initially identified via molecular diagnostics as Staphylococcus species but were later confirmed as S. pseudintermedius through mass spectrometry. Antimicrobial susceptibility testing demonstrated multi-drug resistance, including methicillin. Despite aggressive medical and antimicrobial treatment, our patients succumbed to the infection. The source of infection likely came from her companion canine at home as no other source could be identified; however, cultures were unable to be obtained from the companion canine. Those who are immunosuppressed, such as with solid organ transplants, should take caution with exposure to companion animals due to the potential for S. pseudintermedius infection.
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Affiliation(s)
- Coulter Small
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
| | - Norman Beatty
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
| | - Guy El Helou
- Division of Infectious Diseases and Global Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, USA
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17
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Bünsow D, Tantawy E, Ostermeier T, Bähre H, Garbe A, Larsen J, Winstel V. Methicillin-resistant Staphylococcus pseudintermedius synthesizes deoxyadenosine to cause persistent infection. Virulence 2021; 12:989-1002. [PMID: 33779509 PMCID: PMC8018352 DOI: 10.1080/21505594.2021.1903691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an emerging zoonotic pathogen of canine origin that causes an array of fatal diseases, including bacteremia and endocarditis. Despite large-scale genome sequencing projects have gained substantial insights into the genomic landscape of MRSP, current knowledge on virulence determinants that contribute to S. pseudintermedius pathogenesis during human or canine infection is very limited. Using a panel of genetically engineered MRSP variants and a mouse abscess model, we here identified the major secreted nuclease of S. pseudintermedius designated NucB and adenosine synthase A (AdsA) as two synergistically acting enzymes required for MRSP pathogenesis. Similar to Staphylococcus aureus, S. pseudintermedius requires nuclease secretion along with the activity of AdsA to degrade mammalian DNA for subsequent biosynthesis of cytotoxic deoxyadenosine. In this manner, S. pseudintermedius selectively kills macrophages during abscess formation thereby antagonizing crucial host immune cell responses. Ultimately, bioinformatics analyses revealed that NucB and AdsA are widespread in the global S. pseudintermedius population. Together, these data suggest that S. pseudintermedius deploys the canonical Nuc/AdsA pathway to persist during invasive disease and may aid in the development of new therapeutic strategies to combat infections caused by MRSP.
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Affiliation(s)
- Dorothea Bünsow
- Research Group Pathogenesis of Bacterial Infections; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Eshraq Tantawy
- Research Group Pathogenesis of Bacterial Infections; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Tjorven Ostermeier
- Research Group Pathogenesis of Bacterial Infections; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Annette Garbe
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Jesper Larsen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Volker Winstel
- Research Group Pathogenesis of Bacterial Infections; TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
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18
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Frosini SM, Bond R, McCarthy AJ, Feudi C, Schwarz S, Lindsay JA, Loeffler A. Genes on the Move: In Vitro Transduction of Antimicrobial Resistance Genes between Human and Canine Staphylococcal Pathogens. Microorganisms 2020; 8:E2031. [PMID: 33353175 PMCID: PMC7766859 DOI: 10.3390/microorganisms8122031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 01/09/2023] Open
Abstract
Transmission of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) between people and pets, and their co-carriage, are well-described. Potential exchange of antimicrobial resistance (AMR) genes amongst these staphylococci was investigated in vitro through endogenous bacteriophage-mediated transduction. Bacteriophages were UV-induced from seven donor isolates of canine (MRSP) and human (MRSA) origin, containing tet(M), tet(K), fusB or fusC, and lysates filtered. Twenty-seven tetracycline- and fusidic acid- (FA-) susceptible recipients were used in 122 donor-recipient combinations (22 tetracycline, 100 FA) across 415 assays (115 tetracycline, 300 FA). Bacteriophage lysates were incubated with recipients and presumed transductants quantified on antimicrobial-supplemented agar plates. Tetracycline resistance transduction from MRSP and MRSA to methicillin-susceptible S. pseudintermedius (MSSP) was confirmed by PCR in 15/115 assays. No FA-resistance transfer occurred, confirmed by negative fusB/fusC PCR, but colonies resulting from FA assays had high MICs (≥32 mg/L) and showed mutations in fusA, two at a novel position (F88L), nine at H457[Y/N/L]. Horizontal gene transfer of tetracycline-resistance confirms that resistance genes can be shared between coagulase-positive staphylococci from different hosts. Cross-species AMR transmission highlights the importance of good antimicrobial stewardship across humans and veterinary species to support One Health.
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Affiliation(s)
- Sian Marie Frosini
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Ross Bond
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
| | - Alex J. McCarthy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK;
| | - Claudia Feudi
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14195 Berlin, Germany; (C.F.); (S.S.)
| | - Jodi A. Lindsay
- Institute of Infection and Immunity, St George’s, University of London, Cranmer Terrace, London SW17 0RE, UK;
| | - Anette Loeffler
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK; (R.B.); (A.L.)
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19
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Staphylococcal Protein A ( spa) Locus Is a Hot Spot for Recombination and Horizontal Gene Transfer in Staphylococcus pseudintermedius. mSphere 2020; 5:5/5/e00666-20. [PMID: 33115833 PMCID: PMC7593597 DOI: 10.1128/msphere.00666-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus pseudintermedius is a major canine pathogen but can also occasionally infect humans. Identification of genetic factors contributing to the virulence and clonal success of multidrug-resistant S. pseudintermedius clones is critical for the development of therapeutics against this pathogen. Here, we characterized the genome sequences of a global collection of 622 S. pseudintermedius isolates. We show that all major clones, besides carrying core virulence genes, which are present in all strains, carry one or more lineage-specific genes. Many of these genes have been acquired from other bacterial species through a horizontal gene transfer mechanism. Importantly, we have discovered that the staphylococcal protein A gene (spa), a widely used marker for molecular typing of S. pseudintermedius strains and a potential vaccine candidate antigen, is deleted in 62% of strains. Furthermore, the spa locus in S. pseudintermedius acts as a reservoir to accumulate lineage-associated genes with adaptive functions. Staphylococcus pseudintermedius is a major canine pathogen but also occasionally colonizes and infects humans. Multidrug-resistant methicillin-resistant S. pseudintermedius (MDR MRSP) strains have emerged globally, making treatment and control of this pathogen challenging. Sequence type 71 (ST71), ST68, and ST45 are the most widespread and successful MDR MRSP clones. The potential genetic factors underlying the clonal success of these and other predominant clones remain unknown. Characterization of the pangenome, lineage-associated accessory genes, and genes acquired through horizontal gene transfer from other bacteria is important for identifying such factors. Here, we analyzed genome sequence data from 622 S. pseudintermedius isolates to investigate the evolution of pathogenicity across lineages. We show that the predominant clones carry one or more lineage-associated virulence genes. The gene encoding staphylococcal protein A (SpA), a key virulence factor involved in immune evasion and a potential vaccine antigen, is deleted in 62% of isolates. Most importantly, we have discovered that the spa locus is a hot spot for recombination and horizontal gene transfer in S. pseudintermedius, where genes related to restriction modification, prophage immunity, mercury resistance, and nucleotide and carbohydrate metabolism have been acquired in different lineages. Our study also establishes that ST45 is composed of two distinct sublineages that differ in their accessory gene content and virulence potential. Collectively, this study reports several previously undetected lineage-associated genetic factors that may have a role in the clonal success of the major MDR MRSP clones. These data provide a framework for future experimental studies on S. pseudintermedius pathogenesis and for developing novel therapeutics against this pathogen. IMPORTANCEStaphylococcus pseudintermedius is a major canine pathogen but can also occasionally infect humans. Identification of genetic factors contributing to the virulence and clonal success of multidrug-resistant S. pseudintermedius clones is critical for the development of therapeutics against this pathogen. Here, we characterized the genome sequences of a global collection of 622 S. pseudintermedius isolates. We show that all major clones, besides carrying core virulence genes, which are present in all strains, carry one or more lineage-specific genes. Many of these genes have been acquired from other bacterial species through a horizontal gene transfer mechanism. Importantly, we have discovered that the staphylococcal protein A gene (spa), a widely used marker for molecular typing of S. pseudintermedius strains and a potential vaccine candidate antigen, is deleted in 62% of strains. Furthermore, the spa locus in S. pseudintermedius acts as a reservoir to accumulate lineage-associated genes with adaptive functions.
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Abstract
The ancestral strain of Bacillus subtilis NCIB3610 (3610) bears a large, low-copy-number plasmid, called pBS32, that was lost during the domestication of laboratory strain derivatives. Selection against pBS32 may have been because it encodes a potent inhibitor of natural genetic competence (ComI), as laboratory strains were selected for high-frequency transformation. Previous studies have shown that pBS32 and its sibling, pLS32 in Bacillus subtilis subsp. natto, encode a replication initiation protein (RepN), a plasmid partitioning system (AlfAB), a biofilm inhibitor (RapP), and an alternative sigma factor (SigN) that can induce plasmid-mediated cell death in response to DNA damage. Here, we review the literature on pBS32/pLS32, the genes found on it, and their associated phenotypes.
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González-Domínguez MS, Carvajal HD, Calle-Echeverri DA, Chinchilla-Cárdenas D. Molecular Detection and Characterization of the mecA and nuc Genes From Staphylococcus Species ( S. aureus, S. pseudintermedius, and S. schleiferi) Isolated From Dogs Suffering Superficial Pyoderma and Their Antimicrobial Resistance Profiles. Front Vet Sci 2020; 7:376. [PMID: 32793641 PMCID: PMC7390895 DOI: 10.3389/fvets.2020.00376] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Canine superficial pyoderma (CSP) is a bacterial infection secondary to several skin diseases of the dog. Staphylococcus pseudintermedius, which is a commensal bacterium of the dog's skin, is the leading agent found in dogs affected by CSP, which can progress to deep pyoderma. It is also of clinical significance because S. pseudintermedius strains carry antimicrobial resistance genes, mainly the mecA gene. In this descriptive longitudinal study, molecular characterization of bacterial isolates from dogs affected by CSP was performed in addition to phenotyping, antimicrobial profiling, and assessment of resistance carriage status. Fifty dogs (24 females and 26 males) attending the CES University Veterinary Teaching Hospital were included in the study. CSP was confirmed according to clinical signs and cytological examination. Swabs were taken from active skin lesions for bacterial culture, and phenotyping and antimicrobial resistance profiles were assessed using API-Staph phenotyping and the Kirby–Bauer method, respectively. We also performed molecular detection and characterization of the mecA and nuc encoding gene of coagulase-positive Staphylococci. The mecA gene frequency was established by qPCR amplification of a 131bp gene fragment. Data were evaluated by descriptive statistics. Erythema, peeling, pruritus, and alopecia were the predominant symptoms (72, 56, and 46%, respectively). We isolated bacteria compatible with Staphylococcus species from all samples tested. API phenotyping showed 83.1 to 97.8% compatibility with S. pseudintermedius. PCR-genotyping resulted in 15, 3, and 1 isolates positive for S. pseudintermedius, S. aureus, and S. schleiferi, respectively. Isolated strains showed high susceptibility to Imipenem, Ampicillin/Sulbactam, and Rifampicin (100, 94, and 92%, respectively). The highest resistance was against Vancomycin and Trimethoprim/Sulfamethoxazole (98 and 74%, respectively). S. pseudintermedius, S. aureus, and S. schleiferi isolates were cloned and shared 96% sequence homology. Finally, we found 62% carriage status of the mecA gene in isolates of CSP patients, although only 36% of the isolates were methicillin-resistant. Identification of three Staphylococcus species causing CSP, high-level resistance against conventional antimicrobials, and carriage of the mecA gene highlight the importance of performing molecular characterization of bacteria causing dermatological conditions in dogs.
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Affiliation(s)
- María S González-Domínguez
- INCA-CES Research Group, Veterinary Teaching Hospital, Faculty of Veterinary Medicine and Zootechny, CES University, Medellín, Colombia
| | - Hernán D Carvajal
- Instituto Colombiano de Medicina Tropical (ICMT), CES University, Medellín, Colombia
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