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Gutiérrez-Martín CB. Detection of Macrolide and/or Tetracycline Genetic Resistance Determinants by PCR. Methods Mol Biol 2024; 2815:73-78. [PMID: 38884911 DOI: 10.1007/978-1-0716-3898-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Globally, the main molecular trials being developed to study the genetic determinants responsible for conferring resistance to bacterial organisms are amplification-based methods, hybridization-based methods, and sequence-based methods. In the specific case of Streptococcus suis, polymerase chain reaction is the only test tuned up until now for detecting resistant clinical isolates to macrolides and/or tetracyclines, the two main groups of antibiotics being ineffective against this human and animal pathogen.
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Zhang J, Yang Y, Sun H, Luo X, Cui X, Miao Q, He D, Zhao J, Yan F, Pan Y, Zhai Y, Hu G. Prevalence of the optrA gene among Streptococcus suis isolates from diseased pigs and identification of a novel integrative conjugative element ICESsu988S. Res Microbiol 2023; 174:104078. [PMID: 37149078 DOI: 10.1016/j.resmic.2023.104078] [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: 12/10/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Aim of this study was to investigate the prevalence and genetic environment of the oxazolidinone resistance gene optrA in Streptococcus suis (S. suis) isolates from diseased pigs in China. A total of 178 S. suis isolates were screened for the optrA gene by PCR. The phenotypes and genotypes of optrA-positive isolates were investigated by antimicrobial susceptibility testing, core genome Multilocus Sequence Typing (cgMLST), capsular serotypes determination and whole-genome sequencing (WGS). Fifty-one (28.7%) S. suis isolates were positive for optrA. Phylogenetic analysis indicated that the spread of the optrA among S. suis isolates was primarily due to horizontal transfer. Analysis of S. suis serotypes from diseased pigs revealed substantial diversity. The genetic environment of optrA was complex and diverse and could be divided into 12 different types. Interestingly, we identified a novel integrative and conjugative element ICESsu988S, carrying optrA and erm(T) genes. This is to the best of our knowledge the first report of the optrA and erm(T) co-located on an ICE in S. suis. Our results showed a high prevalence of optrA gene in S. suis isolates in China. Further research is needed to evaluate the importance of ICEs, as they horizontally propagate important clinical resistance genes.
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Affiliation(s)
- Junkai Zhang
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yingying Yang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China.
| | - Huarun Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
| | - Xingwei Luo
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Xiaodie Cui
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Qingqing Miao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Dandan He
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Jinfeng Zhao
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Fengbin Yan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yushan Pan
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Yajun Zhai
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Gongzheng Hu
- Department of Pharmacology and Toxicology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
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Wang J, Qi K, Bai X, Wu Z, Kang W, Liang P, Zheng H, Xu J. Characterization of integrative and conjugative elements carrying antibiotic resistance genes of Streptococcus suis isolated in China. Front Microbiol 2022; 13:1074844. [PMID: 36620002 PMCID: PMC9815147 DOI: 10.3389/fmicb.2022.1074844] [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: 10/20/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus suis, an emerging zoonotic pathogen, is important reservoirs of antibiotic resistance genes that play critical roles in the horizontal transfer of corresponding resistances. In the present study, 656 antibiotic resistance (AR) genes were detected in 154 of 155 genomes of S. suis strains isolated from the nasopharynx of slaughtered pigs and the lungs of diseased pigs in China. The AR genes were clustered into 11 categories, consisting of tetracycline, macrolides, lincosamide, streptogramin, aminoglycoside, trimethoprim, amphenicols, nucleoside, quinupristin/dalfopristin, glycopeptide, and oxazolidinones resistance genes. In order to investigate the transmission patterns of the AR genes, AR genes-associated the mobile genetic elements (MGEs) were extracted and investigated. Twenty ICEs, one defective ICE, one tandem ICE, and ten prophages were found, which mainly carried tetracycline, macrolides/lincosamides/streptogramin (MLS), and aminoglycosides resistance genes. Three types of DNA cargo with AR genes were integrated into specific sites of ICEs: integrative mobilizable elements (IMEs), cis-IMEs (CIMEs), and transposon Tn916. Obvious differences in AR gene categories were found among the three cargo types. IMEs mainly harbored tetracycline and MLS resistance genes. CIMEs mainly carried aminoglycoside resistance genes, while transposon Tn916 carried only the tet (M) gene. Nearly all AR genes in ICEs were carried by IMEs and CIMEs. IMEs were prevalent and were also detected in additional 29 S. suis genomes. The horizontal transfer of IMEs and CIMEs may play critical role in ICE evolution and AR gene transmission in the S. suis population. Our findings provide novel insights into the transmission patterns of AR genes and the evolutionary mechanisms of ICEs in S. suis.
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Affiliation(s)
- Jianping Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kexin Qi
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zongfu Wu
- OIE Reference Lab for Swine Streptococcosis, MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Weiming Kang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Pujun Liang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China,*Correspondence: Han Zheng, ✉
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Li J, Shen Y, Zuo J, Gao S, Wang H, Wang Y, Yi L, Hou X, Wang Y. Inhibitory Effect of Monoterpenoid Glycosides Extracts from Peony Seed Meal on Streptococcus suis LuxS/AI-2 Quorum Sensing System and Biofilm. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16024. [PMID: 36498098 PMCID: PMC9740070 DOI: 10.3390/ijerph192316024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Streptococcus suis LuxS/AI-2 quorum sensing system regulates biofilm formation, resulting in increased pathogenicity and drug resistance, and diminished efficacy of antibiotic treatment. The remaining peony seed cake after oil extraction is rich in monoterpenoid glycosides, which can inhibit the formation of bacterial biofilm. In this study, we investigated the effect of seven major monocomponents (suffruticosol A, suffruticosol B, suffruticosol C, paeonifloin, albiflorin, trans-ε-viniferin, gnetin H) of peony seed meal on minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of S. suis. The results showed that the MICs of the seven single components were all greater than 200 μg/mL, with no significant bacteriostatic and bactericidal advantages. Crystal violet staining and scanning electron microscope observation showed that the seven single components had a certain inhibitory effect on the biofilm formation ability of S. suis at sub-MIC concentration. Among them, the ability of paeoniflorin to inhibit biofilm was significantly higher than that of the other six single components. AI-2 signaling molecules were detected by bioreporter strain Vibrio harvey BB170. The detection results of AI-2 signal molecules found that at 1/2 MIC concentration, paeoniflorin significantly inhibited the production of S. suis AI-2 signal, and the inhibitory effect was better than that of the other six single components. In addition, molecular docking analysis revealed that paeoniflorin had a significant binding activity with LuxS protein compared with the other six single components. The present study provides evidence that paeoniflorin plays a key role in the regulation of the inhibition of S. suis LuxS/AI-2 system and biofilm formation in peony seed meal.
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Affiliation(s)
- Jinpeng Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yamin Shen
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Jing Zuo
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Shuji Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Haikun Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Yuxin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
| | - Li Yi
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
- College of Life Science, Luoyang Normal University, Luoyang 471000, China
| | - Xiaogai Hou
- College of Agriculture/College of Tree Peony, Henan University of Science and Technology, Luoyang 471000, China
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471000, China
- Key Laboratory of Molecular Pathogen and Immunology of Animal of Luoyang, Luoyang 471000, China
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Uruén C, García C, Fraile L, Tommassen J, Arenas J. How Streptococcus suis escapes antibiotic treatments. Vet Res 2022; 53:91. [DOI: 10.1186/s13567-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractStreptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.
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Excision and integration of unconventional circularizable structures involving the erm(B) gene in enterococci. Vet Microbiol 2022; 273:109542. [PMID: 35969915 DOI: 10.1016/j.vetmic.2022.109542] [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: 01/22/2022] [Revised: 08/04/2022] [Accepted: 08/07/2022] [Indexed: 11/22/2022]
Abstract
Traditionally, insertion sequences (ISs) play a major role in disseminating antimicrobial resistance genes (ARGs) in bacteria through transposition and translocation, forming regions that contain multiple ARGs flanked by single or multiple copies of IS. In addition, unconventional circularizable structures (UCSs), lacking recombinase genes but being surrounded by directly repeated sequences (DRs) of various sizes which do not contain transposase genes, were reported to be involved in the dissemination of ARGs. In this study, a novel UCS was identified on plasmid pE508-2 in E. faecalis E508, which carried a 24,411 bp multiresistance gene cluster, consisting of the resistance genes aphA3, lnu(B), lsa(E), spw, aac(A)-aph(D), lnu(B), dfrG, and two copies of aadE flanked by copies of erm(B). PCR assays revealed that three types of UCSs with lengths of 7235, 16,437, and 23,673 bp were formed, each of which contained the respective resistance genes and one copy of erm(B). Using erm(B)-negative and -positive strains, we demonstrated that erm(B)-carrying UCSs failed to transfer into an erm(B)-negative strain, but could integrate into an erm(B)-positive strain in a new site adjacent to a pre-existing erm(B) gene by natural transformation. Database searches revealed that erm(B)-flanked multiresistance gene regions, which might be able to form the respective UCSs, are present among various bacteria from different sources in various countries. In summary, this study experimentally demonstrated the excision and integration of UCS involving structures that include erm(B). The widespread presence of these UCSs in various Gram-positive bacteria highlights its role in the dissemination of ARGs among bacterial pathogens.
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Yu R, Chen Z, Li D, Schwarz S, Wang X, Du XD. Studies on the Transmission of a Tigecycline Resistance-Mediating tet(A) Gene Variant from Enterobacter hormaechei via a Two-Step Recombination Process. Microbiol Spectr 2022; 10:e0049622. [PMID: 35579466 PMCID: PMC9241890 DOI: 10.1128/spectrum.00496-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/27/2022] [Indexed: 12/13/2022] Open
Abstract
To investigate the contribution of a tet(A) variant to tigecycline resistance in Enterobacter hormaechei and the recombination events that occurred during transmission of this variant. MICs were determined by broth microdilution. E. hormaechei G17 was characterized by PCR, transfer assay, S1-PFGE, Southern blot hybridization, and WGS analysis. A tet(A) variant conferring resistance to tigecycline was present in E. hormaechei G17. This strain harbored two resistance plasmids (pG17-1, 264,084 bp and pG17-2, 68,610 bp) and its E. coli transformant Tm-G17TGC one resistance plasmid (pTm-G17, 93,013 bp). The comparative analysis of pG17-1, pG17-2, and pTm-G17 showed that a tet(A) variant-carrying multiresistance gene cluster (~23 kb) originating from pG17-1 had integrated into pG17-2, forming the novel plasmid pTm-G17. In a first step, this multiresistance gene cluster was excised from pG17-1 by recombination of homologous sequences, including △TnAs1 at both termini, thereby generating an unconventional circularizable structure (UCS). In a second step, this UCS integrated into pG17-2 via recombination between homologous sequences, including IS26 present on both, the UCS and pG17-2, thereby giving rise to the new plasmid pTm-G17. In summary, a tet(A) variant conferring resistance to tigecycline was reported in E. hormaechei. Transfer of a tet(A) variant-carrying multiresistance gene cluster between plasmids occurred in a two-step recombination process, in which homologous sequences, including either △TnAs1 or IS26, were involved. IMPORTANCE Tigecycline is an important last-resort broad spectrum antimicrobial agent. This study describes the two-step recombination processes resulting in the transfer of the tet(A) variant gene between different plasmids in E. hormaechei, which depicts the role of recombination processes in the generation of UCSs and new plasmids, both carrying a tet(A) variant conferring resistance to tigecycline. Such processes enhance the dissemination of resistance genes, which is of particular relevance for resistance genes, such as the tet(A) variant. The presence and transmission of a tet(A) variant in E. hormaechei will compromise the efficacy of tigecycline treatment for E. hormaechei associated infection.
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Affiliation(s)
- Runhao Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Zheng Chen
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Danyang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Xinwei Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, People’s Republic of China
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Estrada AA, Gottschalk M, Gebhart CJ, Marthaler DG. Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates. Vet Res 2022; 53:23. [PMID: 35303917 PMCID: PMC8932342 DOI: 10.1186/s13567-022-01039-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/17/2022] [Indexed: 11/10/2022] Open
Abstract
Streptococcus suis is a significant economic and welfare concern in the swine industry. Pan-genome analysis provides an in-silico approach for the discovery of genes involved in pathogenesis in bacterial pathogens. In this study, we performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulence-associated genes (VAGs) of S. suis. Using chi-square tests and LASSO regression models, three accessory pan-genes corresponding to S. suis strain P1/7 markers SSU_RS09525, SSU_RS09155, and SSU_RS03100 (>95% identity) were identified as having a significant association with the pathogenic pathotype. The proposed novel SSU_RS09525 + /SSU_RS09155 + /SSU_RS03100 + genotype identified 96% of the pathogenic pathotype strains, suggesting a novel genotyping scheme for predicting the pathogenicity of S. suis isolates in North America. In addition, mobile genetic elements carrying antimicrobial resistance genes (ARGs) and VAGs were identified but did not appear to play a major role in the spread of ARGs and VAGs.
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Affiliation(s)
- April A Estrada
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Connie J Gebhart
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Dechêne-Tempier M, Marois-Créhan C, Libante V, Jouy E, Leblond-Bourget N, Payot S. Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis. Microorganisms 2021; 9:microorganisms9081765. [PMID: 34442843 PMCID: PMC8401462 DOI: 10.3390/microorganisms9081765] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | - Virginie Libante
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
| | - Eric Jouy
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, F-22440 Ploufragan, France; (M.D.-T.); (C.M.-C.); (E.J.)
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France; (V.L.); (N.L.-B.)
- Correspondence:
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11
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Chen L, Huang J, Huang X, He Y, Sun J, Dai X, Wang X, Shafiq M, Wang L. Horizontal Transfer of Different erm(B)-Carrying Mobile Elements Among Streptococcus suis Strains With Different Serotypes. Front Microbiol 2021; 12:628740. [PMID: 33841355 PMCID: PMC8032901 DOI: 10.3389/fmicb.2021.628740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 11/24/2022] Open
Abstract
Macrolide-resistant Streptococcus suis is highly prevalent worldwide. The acquisition of the erm(B) gene mediated by mobile genetic elements (MGEs) in particular integrative and conjugative elements (ICEs) is recognized as the main reason for the rapid spread of macrolide-resistant streptococcal strains. However, knowledge about different erm(B)-carrying elements responsible for the widespread of macrolide resistance and their transferability in S. suis remains poorly understood. In the present study, two erm(B)- and tet(O)-harboring putative ICEs, designated as ICESsuYSB17_rplL and ICESsuYSJ15_rplL, and a novel erm(B)- and aadE-spw-like-carrying genomic island (GI), named GISsuJHJ17_rpsI, were identified to be excised from the chromosome and transferred among S. suis strains with different serotypes. ICESsuYSB17_rplL and ICESsuYSJ15_rplL were integrated downstream the rplL gene, a conserve locus of the ICESa2603 family. GISsuJHJ17_rpsI, with no genes belonging to the conjugation module, was integrated into the site of rpsI. All transconjugants did not exhibit obvious fitness cost by growth curve and competition assays when compared with the recipient. The results demonstrate that different erm(B)-carrying elements were presented and highlight the role of these elements in the dissemination of macrolide resistance in S. suis.
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Affiliation(s)
- Li Chen
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Huang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Yuping He
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Junjie Sun
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xingyang Dai
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Wang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Shafiq
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Yi S, Huang J, Hu X, Chen L, Dai X, Sun J, Liu P, Wang X, Wen J, Wang L. Nonconservative integration and diversity of a new family of integrative and conjugative elements associated with antibiotic resistance in zoonotic pathogen Streptococcus suis. Vet Microbiol 2021; 254:109009. [PMID: 33640677 DOI: 10.1016/j.vetmic.2021.109009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/02/2021] [Indexed: 11/24/2022]
Abstract
Macrolide and tetracycline resistance in streptococci is mainly caused by acquisition of integrative and conjugative elements (ICEs) of the ICESa2603 family carrying erm(B) and tet(O). But the characteristics about the transferability and physiological consequences of ICEs with triplet serine integrases are still rare. This study tested the transferability of ICESsuYZDH1_SSU0877, a novel erm(B)- and tet(O)-carrying ICESa2603 family-like ICE with triplet serine integrases, and evaluated the physiological consequences after ICE transferred and integrated into recipient. The prevalence of ICESsuYZDH1-like ICEs in S. suis was analyzed based on 1334 genomic sequences available in GenBank and examined in 330 clinical isolates in China. Nonconservative transfer was observed by integrating of ICESsuYZDH1 into SSU1797 gene besides the primary SSU0877 site. Imperfect direct repeats of 2-/4-nt (5'-TC-3'/5'-TCCC-3') and (5'-GC-3'/5'-TCCC-3') were observed at SSU0877 and SSU1797 sites, respectively. The transconjugant suffered a weak fitness cost with stunted growth and less competition with recipient strain. Successive passages indicate the ICESsuYZDH1 could be persist and endued stable resistant phenotype. Comprehensive analysis of the ICESsuYZDH1-like ICEs from both public genome database and our clinical isolates revealed the widespread and diversity of the ICEs by integration at the sites of SSU0877, SSU0468, SSU1262, and SSU1797. The ICESsuYZDH1-like ICEs could stably co-exist within the host chromosome at more than one attachment sites, which is probably mediated by the triplet serine integrases. Nonconservative integration and diversity of the ICESsuYZDH1 family of ICEs might have contributed to the evolution of ICEs and the dissemination of macrolide and tetracycline resistance in S. suis.
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Affiliation(s)
- Sida Yi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyu Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Wang S, Zhang D, Jiang C, He H, Cui C, Duan W, Hu S, Wang J, Cai X. Strain Characterization of Streptococcus suis Serotypes 28 and 31, Which Harbor the Resistance Genes optrA and ant(6)-Ia. Pathogens 2021; 10:pathogens10020213. [PMID: 33669225 PMCID: PMC7919788 DOI: 10.3390/pathogens10020213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 11/16/2022] Open
Abstract
Streptococcus suis causes disease in pigs and is implicated increasingly in human disease worldwide. Although most clinical cases are associated with serotype 2, infections by other serotypes have sometimes been reported. Here, we sequenced the genome of a multidrug-resistant S. suis serotype 28 (strain 11313) and a multidrug-resistant S. suis serotype 31 (strain 11LB5). Strain 11313 was apathogenic in mouse infection models, whereas strain 11LB5 displayed ganglion demyelination, meningeal thickening, congestion, mononuclear cell infiltration, massive proliferation of cortical glial cells, and bacteria (>104 CFU/g) in the spinal cord and ganglia in mice. Furthermore, immunohistochemistry found that the heavily infiltrated glial cells were astrocytes. Strain 11313 harbored the resistance genes ant(6)-Ia, erm(B), optrA, tet(l), tet(o), and strain 11LB5 harbored the resistance genes ant(6)-Ia, erm(B), tet(40), tet(o/w/32/o), aac(6′)-aph(2″). Mouse studies showed that strain 11LB5 exhibited a similar virulence to serotype 2 strain 700794, highlighting the need for surveillance of the other serotype S. suis isolates, in addition to serotype 2, in farms. This is the first report of the aminoglycoside resistance gene ant(6)-Ia in S. suis from animals. This suggests that S. suis might serve as an antibiotic resistance reservoir, which spreads the resistance gene ant(6)-Ia or optrA to other streptococcal pathogens on farms.
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Affiliation(s)
- Shujie Wang
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
- Correspondence: (S.W.); (X.C.)
| | - Defu Zhang
- College of Food Science and Technology, Bohai University, Jinzhou 121013, China;
| | - Chenggang Jiang
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
| | - Haijuan He
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
- Institute of Animal Husbandry, Heilongjiang Academy of Agriculture Sciences, Harbin 150086, China
| | - Chenchen Cui
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
| | - Weitong Duan
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
| | - Shouping Hu
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
| | - Jun Wang
- Beijing General Station of Animal Husbandry, Beijing 100029, China;
| | - Xuehui Cai
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China; (C.J.); (H.H.); (C.C.); (W.D.); (S.H.)
- Correspondence: (S.W.); (X.C.)
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Nicholson TL, Waack U, Anderson TK, Bayles DO, Zaia SR, Goertz I, Eppinger M, Hau SJ, Brockmeier SL, Shore SM. Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates. Front Microbiol 2021; 11:620843. [PMID: 33574803 PMCID: PMC7870872 DOI: 10.3389/fmicb.2020.620843] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry. Mechanisms used by S. suis to colonize and cause disease remain unknown and vaccines and/or intervention strategies currently do not exist. Studies addressing virulence mechanisms used by S. suis have been complicated because different isolates can cause a spectrum of disease outcomes ranging from lethal systemic disease to asymptomatic carriage. The objectives of this study were to evaluate the virulence capacity of nine United States S. suis isolates following intranasal challenge in swine and then perform comparative genomic analyses to identify genomic attributes associated with swine-virulent phenotypes. No correlation was found between the capacity to cause disease in swine and the functional characteristics of genome size, serotype, sequence type (ST), or in vitro virulence-associated phenotypes. A search for orthologs found in highly virulent isolates and not found in non-virulent isolates revealed numerous predicted protein coding sequences specific to each category. While none of these predicted protein coding sequences have been previously characterized as potential virulence factors, this analysis does provide a reliable one-to-one assignment of specific genes of interest that could prove useful in future allelic replacement and/or functional genomic studies. Collectively, this report provides a framework for future allelic replacement and/or functional genomic studies investigating genetic characteristics underlying the spectrum of disease outcomes caused by S. suis isolates.
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Affiliation(s)
- Tracy L Nicholson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Ursula Waack
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.,Oak Ridge Institute for Science and Education, United States Department of Energy, Oak Ridge, TN, United States
| | - Tavis K Anderson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Darrell O Bayles
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Sam R Zaia
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Isaiah Goertz
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Samantha J Hau
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.,Oak Ridge Institute for Science and Education, United States Department of Energy, Oak Ridge, TN, United States
| | - Susan L Brockmeier
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Sarah M Shore
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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Du F, Lv X, Duan D, Wang L, Huang J. Characterization of a Linezolid- and Vancomycin-Resistant Streptococcus suis Isolate That Harbors optrA and vanG Operons. Front Microbiol 2019; 10:2026. [PMID: 31551963 PMCID: PMC6746840 DOI: 10.3389/fmicb.2019.02026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022] Open
Abstract
Linezolid and vancomycin are among the last-resort antimicrobial agents in the treatment of multidrug-resistant Gram-positive bacterial infections. Linezolid- and vancomycin-resistant (LVR) Gram-positive bacteria may pose severe threats to public health. In this study, three optrA- and vanG-positive Streptococcus suis strains were isolated from two farms of different cities. There were only 1 and 343 single-nucleotide polymorphisms in coding region (cSNPs) of HCB4 and YSJ7 to YSJ17, respectively. Mobilome analysis revealed the presence of vanG, erm(B), tet(O/W/32/O), and aadE-apt-sat4-aphA3 cluster on an integrative and conjugative element, ICESsuYSJ17, and erm(B), aphA3, aac(6')-aph(2″), catpC194, and optrA on a prophage, ΦSsuYSJ17-3. ICESsuYSJ17 exhibited a mosaic structure and belongs to a highly prevalent and transferable ICESa2603 family of Streptococcus species. ΦSsuYSJ17-3 shared conserved backbone to a transferable prophage Φm46.1. A novel composite transposon, IS1216E-araC-optrA-hp-catpC194-IS1216E, which can be circulated as translocatable unit (TU) by IS1216E, was integrated on ΦSsuYSJ17-3. Vancomycin resistance phenotype and vanG transcription assays revealed that the vanG operon was inducible. The LVR strain YSJ17 exhibited moderate virulence in a zebrafish infection model. To our knowledge, this is the first report of LVR isolate, which is mediated by acquired resistance genes optrA and vanG operons in Gram-positive bacteria. Since S. suis has been recognized as an antimicrobial resistance reservoir in the spread of resistance genes to major streptococcal pathogens, the potential risks of disseminating of optrA and vanG from S. suis to other Streptococcus spp. are worrisome and routine surveillance should be strengthened.
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Affiliation(s)
- Fanshu Du
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xi Lv
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Duan Duan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Sun Y, Veseli IA, Vaillancourt K, Frenette M, Grenier D, Pombert JF. The bacteriocin from the prophylactic candidate Streptococcus suis 90-1330 is widely distributed across S. suis isolates and appears encoded in an integrative and conjugative element. PLoS One 2019; 14:e0216002. [PMID: 31039174 PMCID: PMC6490898 DOI: 10.1371/journal.pone.0216002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/12/2019] [Indexed: 01/09/2023] Open
Abstract
The Gram-positive α-hemolytic Streptococcus suis is a major pathogen in the swine industry and an emerging zoonotic agent that can cause several systemic issues in both pigs and humans. A total of 35 S. suis serotypes (SS) have been identified and genotyped into > 700 sequence types (ST) by multilocus sequence typing (MLST). Eurasian ST1 isolates are the most virulent of all S. suis SS2 strains while North American ST25 and ST28 strains display moderate to low/no virulence phenotypes, respectively. Notably, S. suis 90–1330 is an avirulent Canadian SS2-ST28 isolate producing a lantibiotic bacteriocin with potential prophylactic applications. To investigate the suitability of this strain for such purposes, we sequenced its complete genome using the Illumina and PacBio platforms. The S. suis 90–1330 bacteriocin was found encoded in a locus cargoed in what appears to be an integrative and conjugative element (ICE). This bacteriocin locus was also found to be widely distributed across several streptococcal species and in a few Staphylococcus aureus strains. Because the locus also confers protection from the bacteriocin, the potential prophylactic benefits of using this strain may prove limited due to the spread of the resistance to its effects. Furthermore, the S. suis 90–1330 genome was found to code for genes involved in blood survival, suggesting that strain may not be a benign as previously thought.
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Affiliation(s)
- Yukun Sun
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Iva A. Veseli
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
| | - Katy Vaillancourt
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
| | - Michel Frenette
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole, Fonds de Recherche du Québec–Nature et Technologies, Québec, QC, Canada
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
- Centre de Recherche en Infectiologie Porcine et Avicole, Fonds de Recherche du Québec–Nature et Technologies, Québec, QC, Canada
| | - Jean-François Pombert
- Department of Biology, Illinois Institute of Technology, Chicago, IL, United States of America
- * E-mail:
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Che Y, Xia Y, Liu L, Li AD, Yang Y, Zhang T. Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing. MICROBIOME 2019; 7:44. [PMID: 30898140 PMCID: PMC6429696 DOI: 10.1186/s40168-019-0663-0] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/11/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS In this study, we combined Oxford Nanopore and Illumina metagenomics sequencing to comprehensively uncover the resistome context of influent, activated sludge, and effluent of three WWTPs and simultaneously track the hosts of the ARGs. The results showed that most of the ARGs detected in all compartments of the WWTPs were carried by plasmids. Transposons and integrons also showed higher prevalence on plasmids than on the ARG-carrying chromosome. Notably, integrative and conjugative elements (ICEs) carrying five types of ARGs were detected, and they may play an important role in facilitating the transfer of ARGs, particularly for tetracycline and macrolide-lincosamide-streptogramin (MLS). A broad spectrum of ARGs carried by plasmids (29 subtypes) and ICEs (4 subtypes) was persistent across the WWTPs. Host tracking showed a variety of antibiotic-resistant bacteria in the effluent, suggesting the high potential for their dissemination into receiving environments. Importantly, phenotype-genotype analysis confirmed the significant role of conjugative plasmids in facilitating the survival and persistence of multidrug-resistant bacteria in the WWTPs. At last, the consistency in the quantitative results for major ARGs types revealed by Nanopore and Illumina sequencing platforms demonstrated the feasibility of Nanopore sequencing for resistome quantification. CONCLUSION Overall, these findings substantially expand our current knowledge of resistome in WWTPs, and help establish a baseline analysis framework to study ARGs in the environment.
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Affiliation(s)
- You Che
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yu Xia
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lei Liu
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - An-Dong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yu Yang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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18
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Yongkiettrakul S, Maneerat K, Arechanajan B, Malila Y, Srimanote P, Gottschalk M, Visessanguan W. Antimicrobial susceptibility of Streptococcus suis isolated from diseased pigs, asymptomatic pigs, and human patients in Thailand. BMC Vet Res 2019; 15:5. [PMID: 30606175 PMCID: PMC6318959 DOI: 10.1186/s12917-018-1732-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
Background Prophylaxis and treatment of emerging zoonotic Streptococcus suis infection in agricultural and healthcare settings mainly rely on antibiotics. However, continued use of antibiotics contributing to emergence and widespread of antibiotic resistant S. suis becomes a significant challenge in many endemic countries, including Thailand. Meanwhile, the knowledge of antibiotic susceptibility patterns of bacterial pathogens is required for overcoming the antimicrobial resistance problem, the information of antibiotic susceptibility of S. suis strains isolated in Thailand remains limited. This study aims to assess the susceptibility of Thai-isolated S. suis strains to different antibiotic classes in order to gain an insight into the distribution of antibiotic-resistant patterns of S. suis strains in different regions of Thailand. Results This study revealed the antimicrobial resistance and multidrug resistance of 262 S. suis strains isolated in different regions of Thailand. Susceptibility testing indicated widespread resistance to macrolides and tetracyclines of S. suis strains in the country. Beta-lactam antibiotic drugs (including cefotaxime and ceftiofur), vancomycin, chloramphenicol, as well as florfenicol were potentially the most effective therapeutic drugs for the treatment of S. suis infection in both pigs and humans. High prevalence of intermediate susceptibility of S. suis isolated from asymptomatic pigs for penicillin G, gentamicin, enrofloxacin, and norfloxacin could be the premise of the emergence of S. suis antibiotic resistance. Resistance was also found in S. suis strains isolated from asymptomatic pigs indicating that they could act as reservoirs of antibiotic resistance genes. Conclusions To the best of our knowledge, this is the first report on antimicrobial resistance of a large collection of S. suis strains isolated from pigs and humans in Thailand. It revealed the multidrug resistance of S. suis strains in pigs and humans. The information gained from this study raises an awareness and encourage best practices of appropriate antibiotic drug prescribing and use among human health and agriculture sectors. Electronic supplementary material The online version of this article (10.1186/s12917-018-1732-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suganya Yongkiettrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand.
| | - Krissana Maneerat
- College of Alternative Medicine, Chandrakasem Rajabhat University, Bangkok, Thailand
| | - Buppa Arechanajan
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, Thailand
| | - Yuwares Malila
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Potjanee Srimanote
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Pathum Thani, Thailand
| | - Marcello Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC, Canada
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani, 12120, Thailand
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19
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Abstract
The genus Streptococcus includes Gram-positive organisms shaped in cocci and organized in chains. They are commensals, pathogens, and opportunistic pathogens for humans and animals. Most Streptococcus species of veterinary relevance have a specific ecological niche, such as S. uberis, which is almost exclusively an environmental pathogen causing bovine mastitis. In contrast, S. suis can be considered as a true zoonotic pathogen, causing specific diseases in humans after contact with infected animals or derived food products. Finally, Streptococcus species such as S. agalactiae can be sporadically zoonotic, even though they are pathogens of both humans and animals independently. For clarification, a short taxonomical overview will be given here to highlight the diversity of streptococci that infect animals. Several families of antibiotics are used to treat animals for streptococcal infections. First-line treatments are penicillins (alone or in combination with aminoglycosides), macrolides and lincosamides, fluoroquinolones, and tetracyclines. Because of the selecting role of antibiotics, resistance phenotypes have been reported in streptococci isolated from animals worldwide. Globally, the dynamic of resistance acquisition in streptococci is slower than what is experienced in Enterobacteriaceae, probably due to the much more limited horizontal spread of resistance genes. Nonetheless, transposons or integrative and conjugative elements can disseminate resistance determinants among streptococci. Besides providing key elements on the prevalence of resistance in streptococci from animals, this article will also largely consider the mechanisms and molecular epidemiology of the major types of resistance to antimicrobials encountered in the most important streptococcal species in veterinary medicine.
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Huang J, Chen L, Li D, Wang M, Du F, Gao Y, Wu Z, Wang L. Emergence of a vanG-carrying and multidrug resistant ICE in zoonotic pathogen Streptococccus suis. Vet Microbiol 2018; 222:109-113. [PMID: 30080664 DOI: 10.1016/j.vetmic.2018.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/03/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022]
Abstract
Vancomycin resistance occurs frequently in Enterococcus species, but has not yet been reported in Streptococcus suis, a previously neglected, newly emergent zoonotic pathogen. In this study, we tested the vancomycin susceptibility of 256 human and swine S. suis isolates from 2005 to 2016 and analyzed the mechanism of vancomycin resistance. We found that one isolate BSB6 was resistant to vancomycin with the MIC value of 4 mg/L and to another eleven kinds of tested antimicrobial agents. Whole genome sequencing showed that chromosomal gene mutations, and acquired genes in ICESsuBSB6 accounted for the resistance phenotypes. ICESsuBSB6 was ∼83-kb in size and encoded two resistance gene regions, ARGR1 and ARGR2. ARGR1 harbored six resistance genes, namely erm(B), aadE-apt-sat4-aphA3 cluster and tet(O/W/32/O), and showed highes similarity with corresponding sequences of S. suis ICESsu32457 and Enterococcus faecalis plasmid pEF418. ARGR2 encoded a vanG-type resistance operon. The resistance region showed highest similarity to that of E. faecalis BM4518 vanG1, but the regulatory region was more similar to that of S. agalactiae GBS-NM vanG2. Vancomycin resistance in isolate BSB6 was inducible. The study is the first report of vanG-type resistance in zoonotic pathogen S. suis and highlights importance of its surveillance.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Chen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Daiwei Li
- Department of Pharmacy, The Second Hospital of Dalian Medical University, Dalian 116027, China; Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
| | - Mengli Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Fanshu Du
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yi Gao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.
| | - Liping Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome. GENOME ANNOUNCEMENTS 2018; 6:6/20/e00447-18. [PMID: 29773639 PMCID: PMC5958261 DOI: 10.1128/genomea.00447-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptococcus suis is an economically important pathogen in the pig industry and is also an emerging zoonotic agent responsible for severe infections in humans. Here, we report the genome sequence of S. suis strain SsRC-1. Specifically, this strain was a serotype 2 and was isolated from a human fatal case of toxic shock syndrome (TSS) in Italy.
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Zhu DK, Luo HY, Liu MF, Zhao XX, Jia RY, Chen S, Sun KF, Yang Q, Wu Y, Chen XY, Cheng AC, Wang MS. Various Profiles of tet Genes Addition to tet(X) in Riemerella anatipestifer Isolates From Ducks in China. Front Microbiol 2018; 9:585. [PMID: 29636748 PMCID: PMC5880999 DOI: 10.3389/fmicb.2018.00585] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/14/2018] [Indexed: 11/26/2022] Open
Abstract
To investigate tetracycline resistance and resistant genotype in Riemerella anatipestifer, the tetracycline susceptibility of 212 R. anatipestifer isolates from China between 2011 and 2017 was tested. The results showed that 192 of 212 (90.6%) R. anatipestifer isolates exhibited resistance to tetracycline (the MICs ranged from 4 to 256 μg/ml). The results of PCR detection showed that, 170 of 212 (80.2%) R. anatipestifer isolates possessed the tet(X) gene. Other genes, including tet(A), tet(M), tet(Q), tet(O), tet(B), and tet(O/W/32/O), were found at frequencies of 20.8, 4.7, 1.4, 0.9, 0.9, and 0.5%, respectively. However, tet(C), tet(E), tet(G), tet(K), and tet(W) were not detected in any isolate. In these tet gene positive strains, 31 (14.6%), 2 (0.9%), 5 (2.4%), 1 (0.5%), 3 (1.4%) were detected containing tet(A)/tet(X), tet(M)/tet(O), tet(M)/tet(X), tet(O)/tet(X), and tet(Q)/tet(X) simultaneously, respectively. One isolates, R131, unexpectedly contained three tet genes, i.e., tet(M), tet(O), and tet(X). Sequence analysis of the tet gene ORFs cloned from R. anatipestifer isolates confirmed that tet(A), tet(B), tet(M), tet(O), tet(Q) and an unusual mosaic tet gene tet(O/W/32/O) were present in R. anatipestifer. The MIC results of R. anatipestifer ATCC 11845 transconjugants carrying tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes exhibited tetracycline resistance with MIC values ranging from 4 to 64 μg/ml. Additionally, the tet(X) gene could transfer into susceptible strain via natural transformation (transformation frequencies of ~10−6). In conclusion, the tet(A), tet(B), tet(M), tet(O), tet(O/W/32/O), tet(Q), and tet(X) genes were found and conferred tetracycline resistance in R. anatipestifer isolates. Moreover, the tet(X) is the main mechanism of tetracycline resistance in R. anatipestifer isolates. To our knowledge, this is the first report of tet(A), tet(B), tet(M), tet(O), tet(Q), and mosaic gene tet(O/W/32/O) in R. anatipestifer.
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Affiliation(s)
- De-Kang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Hong-Yan Luo
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ma-Feng Liu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xin-Xin Zhao
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ren-Yong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Shun Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Kun-Feng Sun
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Yue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - An-Chun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Ming-Shu Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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Zheng H, Du P, Qiu X, Kerdsin A, Roy D, Bai X, Xu J, Vela AI, Gottschalk M. Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada. Vet Res 2018; 49:1. [PMID: 29316972 PMCID: PMC5759227 DOI: 10.1186/s13567-017-0498-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/07/2017] [Indexed: 11/21/2022] Open
Abstract
Streptococcus suis is one of the most important bacterial pathogens in the porcine industry and also a zoonotic agent. Serotype 9 is becoming one of the most prevalent serotypes within the S. suis population in certain European countries. In the present study, serotype 9 strains isolated from a country where infection due to this serotype is endemic (Spain), were compared to those recovered from Canada, where this serotype is rarely isolated from diseased pigs. For comparison purposes, strains from Brazil and the only strain isolated from a human case, in Thailand, were also incorporated. Firstly, sequence types (STs) were obtained followed by detection of putative virulence factors. Phylogenetic trees were constructed using the non-recombinant single nucleotide polymorphisms from core genomes of tested strains. Most Spanish strains were either ST123 or ST125, whereas Canadian strains were highly heterogeneous. However, the distribution of putative virulence factors was similar in both groups of strains. The fact that ST16 strains harbored more putative virulence genes and shared greater similarity with the genome of human serotype 2 strains suggests that they present a higher zoonotic and virulence potential than those from Canada and Spain. More than 80% of the strains included in this study carried genes associated with resistance to tetracycline, lincosamides and macrolides. Serotype 9 strains may be nearly 400 years old and have evolved in parallel into 2 lineages. The rapid population expansion of dominant lineage 1 occurred within the last 40 years probably due to the rapid development of the porcine industry.
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Affiliation(s)
- Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Pengchen Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaotong Qiu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Bangkok, Sakon Nakhon, Thailand
| | - David Roy
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Ana I Vela
- Departamento de Sanidad Animal, Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Marcelo Gottschalk
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada.
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Florez-Cuadrado D, Ugarte-Ruiz M, Meric G, Quesada A, Porrero MC, Pascoe B, Sáez-Llorente JL, Orozco GL, Domínguez L, Sheppard SK. Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes. Front Microbiol 2017; 8:2240. [PMID: 29187841 PMCID: PMC5695097 DOI: 10.3389/fmicb.2017.02240] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/31/2017] [Indexed: 01/14/2023] Open
Abstract
Pathogens in the genus Campylobacter are the most common cause of food-borne bacterial gastro-enteritis. Campylobacteriosis, caused principally by Campylobacter jejuni and Campylobacter coli, is transmitted to humans by food of animal origin, especially poultry. As for many pathogens, antimicrobial resistance in Campylobacter is increasing at an alarming rate. Erythromycin prescription is the treatment of choice for clinical cases requiring antimicrobial therapy but this is compromised by mobility of the erythromycin resistance gene erm(B) between strains. Here, we evaluate resistance to six antimicrobials in 170 Campylobacter isolates (133 C. coli and 37 C. jejuni) from turkeys. Erythromycin resistant isolates (n = 85; 81 C. coli and 4 C. jejuni) were screened for the presence of the erm(B) gene, that has not previously been identified in isolates from turkeys. The genomes of two positive C. coli isolates were sequenced and in both isolates the erm(B) gene clustered with resistance determinants against aminoglycosides plus tetracycline, including aad9, aadE, aph(2″)-IIIa, aph(3')-IIIa, and tet(O) genes. Comparative genomic analysis identified identical erm(B) sequences among Campylobacter from turkeys, Streptococcus suis from pigs and Enterococcus faecium and Clostridium difficile from humans. This is consistent with multiple horizontal transfer events among different bacterial species colonizing turkeys. This example highlights the potential for dissemination of antimicrobial resistance across bacterial species boundaries which may compromise their effectiveness in antimicrobial therapy.
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Affiliation(s)
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Guillaume Meric
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Alberto Quesada
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Badajoz, Spain
| | - M. C. Porrero
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
| | - Ben Pascoe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Jose L. Sáez-Llorente
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de Sanidad de la Producción Agraria, Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente, Madrid, Spain
| | - Gema L. Orozco
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Dirección General de Sanidad de la Producción Agraria, Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense Madrid, Madrid, Spain
| | - Samuel K. Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae Promotes Adhesion to the Ocular Epithelium. mSphere 2017; 2:mSphere00213-17. [PMID: 29085912 PMCID: PMC5656748 DOI: 10.1128/msphere.00213-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) displays broad tissue tropism and infects multiple body sites in the human host. However, infections of the conjunctiva are limited to strains within a distinct phyletic group with multilocus sequence types ST448, ST344, ST1186, ST1270, and ST2315. In this study, we sequenced the genomes of six pneumococcal strains isolated from eye infections. The conjunctivitis isolates are grouped in a distinct phyletic group together with a subset of nasopharyngeal isolates. The keratitis (infection of the cornea) and endophthalmitis (infection of the vitreous body) isolates are grouped with the remainder of pneumococcal strains. Phenotypic characterization is consistent with morphological differences associated with the distinct phyletic group. Specifically, isolates from the distinct phyletic group form aggregates in planktonic cultures and chain-like structures in biofilms grown on abiotic surfaces. To begin to investigate the association between genotype and epidemiology, we focused on a predicted surface-exposed adhesin (SspB) encoded exclusively by this distinct phyletic group. Phylogenetic analysis of the gene encoding SspB in the context of a streptococcal species tree suggests that sspB was acquired by lateral gene transfer from Streptococcus suis. Furthermore, an sspB deletion mutant displays decreased adherence to cultured cells from the ocular epithelium compared to the isogenic wild-type and complemented strains. Together these findings suggest that acquisition of genes from outside the species has contributed to pneumococcal tissue tropism by enhancing the ability of a subset of strains to infect the ocular epithelium causing conjunctivitis. IMPORTANCE Changes in the gene content of pathogens can modify their ability to colonize and/or survive in different body sites in the human host. In this study, we investigate a gene acquisition event and its role in the pathogenesis of Streptococccus pneumoniae (pneumococcus). Our findings suggest that the gene encoding the predicted surface protein SspB has been transferred from Streptococcus suis (a distantly related streptococcal species) into a distinct set of pneumococcal strains. This group of strains distinguishes itself from the remainder of pneumococcal strains by extensive differences in genomic composition and by the ability to cause conjunctivitis. We find that the presence of sspB increases adherence of pneumococcus to the ocular epithelium. Thus, our data support the hypothesis that a subset of pneumococcal strains has gained genes from neighboring species that enhance their ability to colonize the epithelium of the eye, thus expanding into a new niche.
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Zhou K, Xie L, Han L, Guo X, Wang Y, Sun J. ICE Sag37, a Novel Integrative and Conjugative Element Carrying Antimicrobial Resistance Genes and Potential Virulence Factors in Streptococcus agalactiae. Front Microbiol 2017; 8:1921. [PMID: 29051752 PMCID: PMC5633684 DOI: 10.3389/fmicb.2017.01921] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/21/2017] [Indexed: 11/13/2022] Open
Abstract
ICESag37, a novel integrative and conjugative element carrying multidrug resistance and potential virulence factors, was characterized in a clinical isolate of Streptococcus agalactiae. Two clinical strains of S. agalactiae, Sag37 and Sag158, were isolated from blood samples of new-borns with bacteremia. Sag37 was highly resistant to erythromycin and tetracycline, and susceptible to levofloxacin and penicillin, while Sag158 was resistant to tetracycline and levofloxacin, and susceptible to erythromycin. Transfer experiments were performed and selection was carried out with suitable antibiotic concentrations. Through mating experiments, the erythromycin resistance gene was found to be transferable from Sag37 to Sag158. SmaI-PFGE revealed a new SmaI fragment, confirming the transfer of the fragment containing the erythromycin resistance gene. Whole genome sequencing and sequence analysis revealed a mobile element, ICESag37, which was characterized using several molecular methods and in silico analyses. ICESag37 was excised to generate a covalent circular intermediate, which was transferable to S. agalactiae. Inverse PCR was performed to detect the circular form. A serine family integrase mediated its chromosomal integration into rumA, which is a known hotspot for the integration of streptococcal ICEs. The integration site was confirmed using PCR. ICESag37 carried genes for resistance to multiple antibiotics, including erythromycin [erm(B)], tetracycline [tet(O)], and aminoglycosides [aadE, aphA, and ant(6)]. Potential virulence factors, including a two-component signal transduction system (nisK/nisR), were also observed in ICESag37. S1-PFGE analysis ruled out the existence of plasmids. ICESag37 is the first ICESa2603 family-like element identified in S. agalactiae carrying both resistance and potential virulence determinants. It might act as a vehicle for the dissemination of multidrug resistance and pathogenicity among S. agalactiae.
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Affiliation(s)
- Kaixin Zhou
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lianyan Xie
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaokui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong Wang
- Department of Laboratory Medicine, Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Jingyong Sun
- Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Huang J, Ma J, Shang K, Hu X, Liang Y, Li D, Wu Z, Dai L, Chen L, Wang L. Evolution and Diversity of the Antimicrobial Resistance Associated Mobilome in Streptococcus suis: A Probable Mobile Genetic Elements Reservoir for Other Streptococci. Front Cell Infect Microbiol 2016; 6:118. [PMID: 27774436 PMCID: PMC5053989 DOI: 10.3389/fcimb.2016.00118] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 02/04/2023] Open
Abstract
Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S. suis. Integrative conjugative elements (ICEs), prophages and tandem MGEs were located at different insertion sites, while 86% of the AMR-associated MGEs were inserted at rplL and rum loci. Comprehensive analysis of insertions at rplL and rum loci among four pathogenic Streptococcus species (Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, and S. suis) revealed the existence of different groups of MGEs, including Tn5252, ICESp1108, and TnGBS2 groups ICEs, Φm46.1 group prophage, ICE_ICE and ICE_prophage tandem MGEs. Comparative ICE genomics of ICESa2603 family revealed that module exchange and acquisition/deletion were the main mechanisms in MGEs' expansion and evolution. Furthermore, the observation of tandem MGEs reflected a novel mechanism for MGE diversity. Moreover, an in vitro competition assay showed no visible fitness cost was observed between different MGE-carrying isolates and a conjugation assay revealed the transferability of ICESa2603 family of ICEs. Our statistics further indicated that the prevalence and diversity of MGEs in S. suis is much greater than in other three species which prompted our hypothesis that S. suis is probably a MGEs reservoir for other streptococci. In conclusion, our results showed that acquisition of MGEs confers S. suis not only its capability as a multidrug resistance pathogen, but also represents a paradigm to study the modular evolution and matryoshkas of MGEs.
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Affiliation(s)
- Jinhu Huang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jiale Ma
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Yuan Liang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Daiwei Li
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State UniversityAmes, IA, USA; Department of Pharmacy, The Second Hospital of Dalian Medical UniversityDalian, China
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University Ames, IA, USA
| | - Li Chen
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Liping Wang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism. Antimicrob Agents Chemother 2016; 60:6390-2. [PMID: 27458226 DOI: 10.1128/aac.01157-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Spectinomycin is an aminocyclitol antibiotic used clinically to treat a variety of infections in animals. Here, we characterized drug resistance prevalence in clinical Streptococcus suis isolates and discovered a novel resistance mechanism in which the s5 mutation (Gly26Asp) results in high spectinomycin resistance. Additionally, a novel integrative and conjugative element encompassing a multidrug resistance spw_like-aadE-lnu(B)-lsa(E) cluster and a cadmium resistance operon were identified, suggesting a possible cause for the wide dissemination of spectinomycin resistance in S. suis.
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29
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Morici E, Simoni S, Brenciani A, Giovanetti E, Varaldo PE, Mingoia M. A new mosaic integrative and conjugative element from Streptococcus agalactiae carrying resistance genes for chloramphenicol (catQ) and macrolides [mef(I) and erm(TR)]. J Antimicrob Chemother 2016; 72:64-67. [PMID: 27621174 DOI: 10.1093/jac/dkw367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVES To investigate the genetic basis of catQ-mediated chloramphenicol resistance in Streptococcus agalactiae. METHODS Two clinical strains of catQ-positive chloramphenicol-resistant S. agalactiae (Sag236 and Sag403) were recently isolated, typed (MLST, PFGE pulsotypes, capsular types) and their antibiotic resistances investigated by phenotypic and genotypic approaches. Several molecular methods (PCR mapping, restriction assays, Southern blotting, sequencing and sequence analysis, conjugal transfer assays) were used to determine the genetic context of catQ and characterize a genetic element detected in the isolates. RESULTS Sag236 and Sag403 shared the same ST (ST19), but exhibited a different capsular type (III and V, respectively) and pulsotype. Both harboured the macrolide resistance genes mef(I) and erm(TR) and the tetracycline resistance gene tet(M). Accordingly, they were resistant to chloramphenicol, erythromycin and tetracycline. catQ and mef(I) were associated in an IQ module that was indistinguishable in Sag236 and Sag403. In mating assays, chloramphenicol and erythromycin resistance proved transferable, at low frequency, only from Sag236. Transconjugants carried not only catQ and mef(I), but also erm(TR), suggesting a linkage of the three resistance genes in a mobile element, which, though seemingly non-mobile, was also detected in Sag403. The new element (designated ICESag236, ∼110 kb) results from recombination of two integrative and conjugative elements (ICEs) originally described in different streptococcal species: S. agalactiae ICESagTR7, carrying erm(TR); and Streptococcus pneumoniae ICESpn529IQ, carrying the prototype IQ module. CONCLUSIONS These findings strengthen the notion that widespread streptococcal ICEs may form mosaics that enhance their diversity and spread, broaden their host range and carry new cargo genes.
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Affiliation(s)
- Eleonora Morici
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Serena Simoni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
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A fatal case of streptococcal toxic shock syndrome caused by Streptococcus suis carrying tet (40) and tet (O/W/32/O), Italy. J Infect Chemother 2016; 22:774-776. [PMID: 27553071 DOI: 10.1016/j.jiac.2016.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 11/22/2022]
Abstract
We report the first human fatal case of streptococcal toxic shock syndrome (STSS) caused by Streptococcus suis serotype 2 carrying the tetracycline efflux tet (40) gene and the tetracycline ribosomal protection tet (O/W/32/O) gene. The patient was splenectomized. The case was characterized by multi-organ dysfunction and disseminated intravascular coagulopathy, in accordance with the clinical parameters of STSS. More investigations are needed to improve the epidemiology and the pathogenesis of S. suis in human infection.
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Warburton PJ, Amodeo N, Roberts AP. Mosaic tetracycline resistance genes encoding ribosomal protection proteins. J Antimicrob Chemother 2016; 71:3333-3339. [PMID: 27494928 PMCID: PMC5181394 DOI: 10.1093/jac/dkw304] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
First reported in 2003, mosaic tetracycline resistance genes are a subgroup of the genes encoding ribosomal protection proteins (RPPs). They are formed when two or more RPP-encoding genes recombine resulting in a functional chimera. To date, the majority of mosaic genes are derived from sections of three RPP genes, tet(O), tet(W) and tet(32), with others comprising tet(M) and tet(S). In this first review of mosaic genes, we report on their structure, diversity and prevalence, and suggest that these genes may be responsible for an under-reported contribution to tetracycline resistance in bacteria.
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Affiliation(s)
- Philip J Warburton
- School of Biomedical and Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry, School of Biomedical and Healthcare Services, Plymouth, UK
| | - Nina Amodeo
- Department of Biomedical and Forensic Science, Faculty of Science and Technology, Anglia Ruskin University, Cambridge, UK
| | - Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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Tohya M, Watanabe T, Maruyama F, Arai S, Ota A, Athey TBT, Fittipaldi N, Nakagawa I, Sekizaki T. Comparative Genome Analyses of Streptococcus suis Isolates from Endocarditis Demonstrate Persistence of Dual Phenotypic Clones. PLoS One 2016; 11:e0159558. [PMID: 27433935 PMCID: PMC4951133 DOI: 10.1371/journal.pone.0159558] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
Many bacterial species coexist in the same niche as heterogeneous clones with different phenotypes; however, understanding of infectious diseases by polyphenotypic bacteria is still limited. In the present study, encapsulation in isolates of the porcine pathogen Streptococcus suis from persistent endocarditis lesions was examined. Coexistence of both encapsulated and unencapsulated S. suis isolates was found in 26 out of 59 endocarditis samples. The isolates were serotype 2, and belonged to two different sequence types (STs), ST1 and ST28. The genomes of each of the 26 pairs of encapsulated and unencapsulated isolates from the 26 samples were sequenced. The data showed that each pair of isolates had one or more unique nonsynonymous mutations in the cps gene, and the encapsulated and unencapsulated isolates from the same samples were closest to each other. Pairwise comparisons of the sequences of cps genes in 7 pairs of encapsulated and unencapsulated isolates identified insertion/deletions (indels) ranging from one to 104 bp in different cps genes of unencapsulated isolates. Capsule expression was restored in a subset of unencapsulated isolates by complementation in trans with cps expression vectors. Examination of gene content common to isolates indicated that mutation frequency was higher in ST28 pairs than in ST1 pairs. Genes within mobile genetic elements were mutation hot spots among ST28 isolates. Taken all together, our results demonstrate the coexistence of dual phenotype (encapsulated and unencapsulated) bacterial clones and suggest that the dual phenotypes arose independently in each farm by means of spontaneous mutations in cps genes.
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Affiliation(s)
- Mari Tohya
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takayasu Watanabe
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
- * E-mail: (TS); (FM)
| | - Sakura Arai
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Atsushi Ota
- Department of Microbiology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
| | | | - Nahuel Fittipaldi
- Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ichiro Nakagawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail: (TS); (FM)
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ICESpy009, a Conjugative Genetic Element Carrying mef(E) in Streptococcus pyogenes. Antimicrob Agents Chemother 2016; 60:3906-12. [PMID: 27067338 DOI: 10.1128/aac.03082-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/01/2016] [Indexed: 01/19/2023] Open
Abstract
Efflux-mediated macrolide resistance due to mef(E) and mel, carried by the mega element, is common in Streptococcus pneumoniae, for which it was originally characterized, but it is rare in Streptococcus pyogenes In S. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916 family containing tet(M) and conferring erythromycin and tetracycline resistance. In this study, S. pyogenes isolates containing mef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated into hylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated into rplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to both S. pyogenes and S. pneumoniae, showing the first evidence of the transferability of mega from S. pyogenes.
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Athey TBT, Teatero S, Takamatsu D, Wasserscheid J, Dewar K, Gottschalk M, Fittipaldi N. Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains. PLoS One 2016; 11:e0150908. [PMID: 26954687 PMCID: PMC4783015 DOI: 10.1371/journal.pone.0150908] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
Strains of serotype 2 Streptococcus suis are responsible for swine and human infections. Different serotype 2 genetic backgrounds have been defined using multilocus sequence typing (MLST). However, little is known about the genetic diversity within each MLST sequence type (ST). Here, we used whole-genome sequencing to test the hypothesis that S. suis serotype 2 strains of the ST25 lineage are genetically heterogeneous. We evaluated 51 serotype 2 ST25 S. suis strains isolated from diseased pigs and humans in Canada, the United States of America, and Thailand. Whole-genome sequencing revealed numerous large-scale rearrangements in the ST25 genome, compared to the genomes of ST1 and ST28 S. suis strains, which result, among other changes, in disruption of a pilus island locus. We report that recombination and lateral gene transfer contribute to ST25 genetic diversity. Phylogenetic analysis identified two main and distinct Thai and North American clades grouping most strains investigated. These clades also possessed distinct patterns of antimicrobial resistance genes, which correlated with acquisition of different integrative and conjugative elements (ICEs). Some of these ICEs were found to be integrated at a recombination hot spot, previously identified as the site of integration of the 89K pathogenicity island in serotype 2 ST7 S. suis strains. Our results highlight the limitations of MLST for phylogenetic analysis of S. suis, and the importance of lateral gene transfer and recombination as drivers of diversity in this swine pathogen and zoonotic agent.
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Affiliation(s)
| | | | - Daisuke Takamatsu
- Bacterial and Parasitic Diseases Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- The United Graduate School of Veterinary Science, Gifu University, Gifu, Japan
| | - Jessica Wasserscheid
- Department of Human Genetics, McGill University and Génome Québec Innovation Centre, Montreal, QC, Canada
| | - Ken Dewar
- Department of Human Genetics, McGill University and Génome Québec Innovation Centre, Montreal, QC, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, QC, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- * E-mail:
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Roberts MC, Schwarz S. Tetracycline and Phenicol Resistance Genes and Mechanisms: Importance for Agriculture, the Environment, and Humans. JOURNAL OF ENVIRONMENTAL QUALITY 2016; 45:576-592. [PMID: 27065405 DOI: 10.2134/jeq2015.04.0207] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent reports have speculated on the future impact that antibiotic-resistant bacteria will have on food production, human health, and global economics. This review examines microbial resistance to tetracyclines and phenicols, antibiotics that are widely used in global food production. The mechanisms of resistance, mode of spread between agriculturally and human-impacted environments and ecosystems, distribution among bacteria, and the genes most likely to be associated with agricultural and environmental settings are included. Forty-six different tetracycline resistance () genes have been identified in 126 genera, with (M) having the broadest taxonomic distribution among all bacteria and (B) having the broadest coverage among the Gram-negative genera. Phenicol resistance genes are organized into 37 groups and have been identified in 70 bacterial genera. The review provides the latest information on tetracycline and phenicol resistance genes, including their association with mobile genetic elements in bacteria of environmental, medical, and veterinary relevance. Knowing what specific antibiotic-resistance genes (ARGs) are found in specific bacterial species and/or genera is critical when using a selective suite of ARGs for detection or surveillance studies. As detection methods move to molecular techniques, our knowledge about which type of bacteria carry which resistance gene(s) will become more important to ensure that the whole spectrum of bacteria are included in future surveillance studies. This review provides information needed to integrate the biology, taxonomy, and ecology of tetracycline- and phenicol-resistant bacteria and their resistance genes so that informative surveillance strategies can be developed and the correct genes selected.
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Huang J, Liang Y, Guo D, Shang K, Ge L, Kashif J, Wang L. Comparative Genomic Analysis of the ICESa2603 Family ICEs and Spread of erm(B)- and tet(O)-Carrying Transferable 89K-Subtype ICEs in Swine and Bovine Isolates in China. Front Microbiol 2016; 7:55. [PMID: 26870017 PMCID: PMC4735348 DOI: 10.3389/fmicb.2016.00055] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3′-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3′-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host range. Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICESa2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried intICESa2603, indicating that ICESa2603 family is widely distributed across these bacteria. Sequencing and conjugation transfer of a novel sequence type ST303 clinical S. suis isolate HB1011 demonstrated that the 89K-subtype ICESsuHB1011 retained its transferrable function, thereby conferring tetracycline and macrolide resistance.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Yuan Liang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Dawei Guo
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Lin Ge
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jam Kashif
- Department of Veterinary Pharmacology, Sindh Agricultural University Tandojam, Pakistan
| | - Liping Wang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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Use of Antibiotics and Antimicrobial Resistance in Veterinary Medicine as Exemplified by the Swine Pathogen Streptococcus suis. Curr Top Microbiol Immunol 2016; 398:103-121. [PMID: 27738916 DOI: 10.1007/82_2016_506] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Use of antimicrobial agents in veterinary medicine is essential to control infectious diseases, thereby keeping animals healthy and animal products safe for the consumer. On the other hand, development and spread of antimicrobial resistance is of major concern for public health. Streptococcus (S.) suis reflects a typical bacterial pathogen in modern swine production due to its facultative pathogenic nature and wide spread in the pig population. Thus, in the present review we focus on certain current aspects and problems related to antimicrobial use and resistance in S. suis as a paradigm for a bacterial pathogen affecting swine husbandry worldwide. The review includes (i) general aspects of antimicrobial use and resistance in veterinary medicine with emphasis on swine, (ii) genetic resistance mechanisms of S. suis known to contribute to bacterial survival under antibiotic selection pressure, and (iii) possible other factors which may contribute to problems in antimicrobial therapy of S. suis infections, such as bacterial persister cell formation, biofilm production, and co-infections. The latter shows that we hardly understand the complexity of factors affecting the success of antimicrobial treatment of (porcine) infectious diseases and underlines the need for further research in this field.
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Mingoia M, Morici E, Marini E, Brenciani A, Giovanetti E, Varaldo PE. Macrolide resistance gene erm(TR) and erm(TR)-carrying genetic elements in Streptococcus agalactiae: characterization of ICESagTR7, a new composite element containing IMESp2907. J Antimicrob Chemother 2015; 71:593-600. [PMID: 26679245 DOI: 10.1093/jac/dkv408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/03/2015] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The objective of this study was to investigate macrolide-resistant Streptococcus agalactiae isolates harbouring erm(TR), an erm(A) gene subclass, with emphasis on their erm(TR)-carrying genetic elements. Four erm(TR)-carrying elements have been described to date: three closely related (ICE10750-RD.2, Tn1806 and ICESp1108) in Streptococcus pyogenes, Streptococcus pneumoniae and S. pyogenes, respectively; and one completely different (IMESp2907, embedded in ICESp2906 to form ICESp2905) in S. pyogenes. METHODS Seventeen macrolide-resistant erm(TR)-positive S. agalactiae isolates were phenotypically and genotypically characterized. Their erm(TR)-carrying elements were explored by analysing the distinctive recombination genes of known erm(TR)-carrying integrative and conjugative elements (ICEs) and by PCR mapping. The new genetic context and organization of IMESp2907 in S. agalactiae were explored using several experimental procedures and in silico analyses. RESULTS Five isolates harboured ICE10750-RD.2/Tn1806, five isolates harboured ICESp1108 and five isolates bore unknown erm(TR)-carrying elements. The remaining two isolates, exhibiting identical serotypes and pulsotypes, harboured IMESp2907 in a new genetic environment, which was further investigated in one of the two isolates, SagTR7. IMESp2907 was circularizable in S. agalactiae, as described in S. pyogenes. The new IMESp2907 junctions were identified based on its site-specific integration; the att sites were almost identical to those in S. pyogenes. In strain SagTR7, erm(TR)-carrying IMESp2907 was embedded in an erm(TR)-less internal element related to ICE10750-RD.2/Tn1806, which, in turn, was embedded in an ICESde3396-like element. The resulting whole ICE, ICESagTR7 (∼129 kb), was integrated into the chromosome downstream of the rplL gene, and was excisable in circular form and transferable by conjugation. CONCLUSIONS This is the first study exploring erm(TR)-carrying genetic elements in S. agalactiae.
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Affiliation(s)
- Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Morici
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Emanuela Marini
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
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Marini E, Palmieri C, Magi G, Facinelli B. Recombination between Streptococcus suis ICESsu32457 and Streptococcus agalactiae ICESa2603 yields a hybrid ICE transferable to Streptococcus pyogenes. Vet Microbiol 2015; 178:99-104. [DOI: 10.1016/j.vetmic.2015.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/13/2015] [Accepted: 04/17/2015] [Indexed: 10/23/2022]
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40
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Huang J, Shang K, Kashif J, Wang L. Genetic diversity of Streptococcus suis isolated from three pig farms of China obtained by acquiring antibiotic resistance genes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2015; 95:1454-1460. [PMID: 25060787 DOI: 10.1002/jsfa.6841] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 06/30/2014] [Accepted: 07/21/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND Acquiring antibiotic resistance genes may change an organism's genetic characteristics and the effect of antibiotics, resulting in a rapid transmission of microbial pathogens. The objectives of this experiment were to identify the features of Streptococcus suis (S. suis) isolated from three pig farms in China which are geographically isolated. RESULTS Among the isolates, 56.52% were sequence type 7 (ST7), followed by ST1 (26.09%), indicating that ST7 prevails in China, as revealed by multi-locus sequence typing (MLST). Statistical analysis indicated an association between geography, sequence types and antibiotic resistance genotypes. 66.67% of the isolates in Sichuan province presented a (ermB(-) + mefA(-) + tetO(-) + tetM(-)) + ST7 type. The tetM(+) +ST7 type was the most prevalent in Jiangsu province, whereas the strains from Hebei province had a phenotype ermB(+) +tetO(+) +ST1 (63.64%). Pulsed-field gel electrophoresis (PGFE) pattern A2 with 100% similarity reflected the clonal dissemination between Sichuan and Jiangsu provinces. Strains carrying or not carrying antibiotic resistance genes presented different PFGE patterns in Hebei province. CONCLUSION ST7 is widespread in many regions of China and a clonal dissemination occurred between Sichuan and Jiangsu provinces in diseased pigs. However, ST1 strains with macrolide and tetracycline resistance (ermB(+) +tetO(+) +ST1) isolated from a farm in Hebei province demonstrated that the genetic diversity was contributed by horizontal acquiring of ermB and tetO carrying elements.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, P.R. China
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Giovanetti E, Brenciani A, Morroni G, Tiberi E, Pasquaroli S, Mingoia M, Varaldo PE. Transduction of the Streptococcus pyogenes bacteriophage Φm46.1, carrying resistance genes mef(A) and tet(O), to other Streptococcus species. Front Microbiol 2015; 5:746. [PMID: 25620959 PMCID: PMC4288039 DOI: 10.3389/fmicb.2014.00746] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/09/2014] [Indexed: 11/13/2022] Open
Abstract
Φm46.1 – Streptococcus pyogenes bacteriophage carrying mef(A) and tet(O), respectively, encoding resistance to macrolides (M phenotype) and tetracycline – is widespread in S. pyogenes but has not been reported outside this species. Φm46.1 is transferable in vitro among S. pyogenes isolates, but no information is available about its transferability to other Streptococcus species. We thus investigated Φm46.1 for its ability to be transduced in vitro to recipients of different Streptococcus species. Transductants were obtained from recipients of Streptococcus agalactiae, Streptococcus gordonii, and Streptococcus suis. Retransfer was always achieved, and from S. suis to S. pyogenes occurred at a much greater frequency than in the opposite direction. In transductants Φm46.1 retained its functional properties, such as inducibility with mitomycin C, presence both as a prophage and as a free circular form, and transferability. The transductants shared the same Φm46.1 chromosomal integration site as the donor, at the 3′ end of a conserved RNA uracil methyltransferase (rum) gene, which is an integration hotspot for a variety of genetic elements. No transfer occurred to recipients of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus salivarius, even though rum-like genes were also detected in the sequenced genomes of these species. A largely overlapping 18-bp critical sequence, where the site-specific recombination process presumably takes place, was identified in the rum genes of all recipients, including those of the species yielding no transductants. Growth assays to evaluate the fitness cost of Φm46.1 acquisition disclosed a negligible impact on S. pyogenes, S. agalactiae, and S. gordonii transductants and a noticeable fitness advantage in S. suis. The S. suis transductant also displayed marked overexpression of the autolysin-encoding gene atl.
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Affiliation(s)
- Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Erika Tiberi
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Sonia Pasquaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School Ancona, Italy
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McNeilly CL, McMillan DJ. Horizontal gene transfer and recombination in Streptococcus dysgalactiae subsp. equisimilis. Front Microbiol 2014; 5:676. [PMID: 25566202 PMCID: PMC4266089 DOI: 10.3389/fmicb.2014.00676] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 11/19/2014] [Indexed: 11/13/2022] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis (SDSE) is a human pathogen that colonizes the skin or throat, and causes a range of diseases from relatively benign pharyngitis to potentially fatal invasive diseases. While not as virulent as the close relative Streptococcus pyogenes the two share a number of virulence factors and are known to coexist in a human host. Both pre- and post-genomic studies have revealed that horizontal gene transfer (HGT) and recombination occurs between these two organisms and plays a major role in shaping the population structure of SDSE. This review summarizes our current knowledge of HGT and recombination in the evolution of SDSE.
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Affiliation(s)
- Celia L McNeilly
- Bacterial Pathogenesis Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD, Australia
| | - David J McMillan
- Inflammation and Healing Research Cluster, School of Health and Sport Sciences, University of the Sunshine Coast , Maroochydore, QLD, Australia
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Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. Diversification of bacterial genome content through distinct mechanisms over different timescales. Nat Commun 2014; 5:5471. [PMID: 25407023 PMCID: PMC4263131 DOI: 10.1038/ncomms6471] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/03/2014] [Indexed: 12/16/2022] Open
Abstract
Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptococcus pneumoniae lineages are typically characterized by combinations of infrequently transferred stable genomic islands: those moving primarily through transformation, along with integrative and conjugative elements and phage-related chromosomal islands. The only lineage containing extensive unique sequence corresponds to a set of atypical unencapsulated isolates that may represent a distinct species. However, prophage content is highly variable even within lineages, suggesting frequent horizontal transmission that would necessitate rapidly diversifying anti-phage mechanisms to prevent these viruses sweeping through populations. Correspondingly, two loci encoding Type I restriction-modification systems able to change their specificity over short timescales through intragenomic recombination are ubiquitous across the collection. Hence short-term pneumococcal variation is characterized by movement of phage and intragenomic rearrangements, with the slower transfer of stable loci distinguishing lineages. Populations of the pathogenic bacterium Streptococcus pneumoniae consist of distinct co-circulating lineages. Here, the authors show lineages are characterized by particular combinations of stable genomic islands, whereas prophage and restriction-modification systems vary over short timescales.
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Affiliation(s)
- Nicholas J Croucher
- 1] Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA [2] Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College, London W2 1PG, UK
| | - Paul G Coupland
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Abbie E Stevenson
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Alanna Callendrello
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
| | - Stephen D Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - William P Hanage
- Centre for Communicable Disease Dynamics, Harvard School of Public Health, 677 Huntington Avenue, Boston, Massachusetts 02115, USA
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Conjugative transfer of ICESde3396 between three β-hemolytic streptococcal species. BMC Res Notes 2014; 7:521. [PMID: 25115242 PMCID: PMC4266954 DOI: 10.1186/1756-0500-7-521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/31/2014] [Indexed: 12/02/2022] Open
Abstract
Background Integrative conjugative elements (ICEs) are mobile genetic elements (MGEs) that possess all genes necessary for excision, transfer and integration into recipient genome. They also carry accessory genes that impart new phenotypic features to recipient strains. ICEs therefore play an important role in genomic plasticity and population structure. We previously characterised ICESde3396, the first ICE identified in the β-hemolytic Streptococcus dysgalactiae subsp equisimilis (SDSE) and demonstrated its transfer to single isolates of Streptococcus pyogenes (group A streptococcus, GAS) and Streptococcus agalactiae (group B streptococcus, GBS). While molecular studies found the ICE in multiple SDSE and GBS isolates, it was absent in all GAS isolates examined. Results Here we demonstrate that ICESde3396:km is transferable from SDSE to multiple SDSE, GAS and GBS isolates. However not all strains of these species were successful recipients under the same growth conditions. To address the role that host factors may have in conjugation we also undertook conjugation experiments in the presence of A549 epithelial cells and DMEM. While Horizontal Gene Transfer (HGT) occurred, conjugation efficiencies were no greater than when similar experiments were conducted in DMEM. Additionally transfer to GAS NS235 was successful in the presence of DMEM but not in Todd Hewitt Broth suggesting that nutritional factors may also influence HGT. The GAS and GBS transconjugants produced in this study are also able to act as donors of the ICE. Conclusion We conclude that ICEs are major sources of interspecies HGT between β-hemolytic streptococci, and by introducing accessory genes imparting novel phenotypic characteristics, have the potential to alter the population structure of these species.
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Tn5253 family integrative and conjugative elements carrying mef(I) and catQ determinants in Streptococcus pneumoniae and Streptococcus pyogenes. Antimicrob Agents Chemother 2014; 58:5886-93. [PMID: 25070090 DOI: 10.1128/aac.03638-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The linkage between the macrolide efflux gene mef(I) and the chloramphenicol inactivation gene catQ was first described in Streptococcus pneumoniae (strain Spn529), where the two genes are located in a module designated IQ element. Subsequently, two different defective IQ elements were detected in Streptococcus pyogenes (strains Spy029 and Spy005). The genetic elements carrying the three IQ elements were characterized, and all were found to be Tn5253 family integrative and conjugative elements (ICEs). The ICE from S. pneumoniae (ICESpn529IQ) was sequenced, whereas the ICEs from S. pyogenes (ICESpy029IQ and ICESpy005IQ, the first Tn5253-like ICEs reported in this species) were characterized by PCR mapping, partial sequencing, and restriction analysis. ICESpn529IQ and ICESpy029IQ were found to share the intSp 23FST81 integrase gene and an identical Tn916 fragment, whereas ICESpy005IQ has int5252 and lacks Tn916. All three ICEs were found to lack the linearized pC194 plasmid that is usually associated with Tn5253-like ICEs, and all displayed a single copy of a toxin-antitoxin operon that is typically contained in the direct repeats flanking the excisable pC194 region when this region is present. Two different insertion sites of the IQ elements were detected, one in ICESpn529IQ and ICESpy029IQ, and another in ICESpy005IQ. The chromosomal integration of the three ICEs was site specific, depending on the integrase (intSp 23FST81 or int5252). Only ICESpy005IQ was excised in circular form and transferred by conjugation. By transformation, mef(I) and catQ were cotransferred at a high frequency from S. pyogenes Spy005 and at very low frequencies from S. pneumoniae Spn529 and S. pyogenes Spy029.
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Unconventional circularizable bacterial genetic structures carrying antibiotic resistance determinants. Antimicrob Agents Chemother 2013; 57:2440-1. [PMID: 23580584 DOI: 10.1128/aac.02548-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Characterization of Tn5801.Sag, a variant of Staphylococcus aureus Tn916 family transposon Tn5801 that is widespread in clinical isolates of Streptococcus agalactiae. Antimicrob Agents Chemother 2013; 57:4570-4. [PMID: 23817370 DOI: 10.1128/aac.00521-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tn5801, originally detected in Staphylococcus aureus Mu50, is a Tn916 family element in which a unique int gene (int5801) replaces the int and xis genes in Tn916 (int916 and xis916). Among 62 tet(M)-positive tetracycline-resistant Streptococcus agalactiae isolates, 43 harbored Tn916, whereas 19 harbored a Tn5801-like element (Tn5801.Sag, ∼20.6 kb). Tn5801.Sag was characterized (PCR mapping, partial sequencing, and chromosomal integration) and compared to other Tn5801-like elements. Similar to Tn5801 from S. aureus Mu50, tested in parallel, Tn5801.Sag was unable to undergo circularization and conjugal transfer.
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Palmieri C, Brenciani A, Mingoia M, Giovanetti E, Facinelli B, Varaldo PE. Pitfalls encountered while investigating genetic elements by PCR. Mob Genet Elements 2013; 3:e25255. [PMID: 23956950 PMCID: PMC3742598 DOI: 10.4161/mge.25255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 05/31/2013] [Accepted: 06/03/2013] [Indexed: 01/01/2023] Open
Abstract
The unprecedented wealth of databases that have become available in the era of next-generation sequencing has considerably increased our knowledge of bacterial genetic elements (GEs). At the same time, the advent of single-cell based approaches has brought realization that unsuspected heterogeneity may occur in the bacterial population from a single colony. The increasing use of PCR-based techniques to study new GEs requires careful consideration of the possible different PCR targets associated with different subpopulations if incorrect or incomplete interpretations are to be avoided. In this commentary, confining ourselves to our direct experience, we illustrate some examples of PCR pitfalls that may be encountered while investigating GEs.
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Affiliation(s)
- Claudio Palmieri
- Department of Biomedical Sciences and Public Health, Section of Microbiology; Polytechnic University of Marche; Ancona, Italy
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Novais C, Freitas AR, Silveira E, Baquero F, Peixe L, Roberts AP, Coque TM. A tet(S/M) hybrid from CTn6000 and CTn916 recombination. MICROBIOLOGY-SGM 2012; 158:2710-2711. [PMID: 22968088 DOI: 10.1099/mic.0.062729-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Carla Novais
- REQUIMTE, Faculdade Farmácia, Universidade do Porto, Portugal
| | - Ana R Freitas
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,REQUIMTE, Faculdade Farmácia, Universidade do Porto, Portugal
| | | | - Fernando Baquero
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain.,Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luisa Peixe
- REQUIMTE, Faculdade Farmácia, Universidade do Porto, Portugal
| | - Adam P Roberts
- Division of Microbial Diseases. UCL Eastman Dental Institute. University College London. UK
| | - Teresa M Coque
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain.,Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
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Palmieri C, Magi G, Creti R, Baldassarri L, Imperi M, Gherardi G, Facinelli B. Interspecies mobilization of an ermT-carrying plasmid of Streptococcus dysgalactiae subsp. equisimilis by a coresident ICE of the ICESa2603 family. J Antimicrob Chemother 2012; 68:23-6. [PMID: 22949621 DOI: 10.1093/jac/dks352] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The recently documented presence of almost identical, small, non-self-transmissible, erm(T)-carrying plasmids in clonally unrelated erythromycin-resistant isolates of Streptococcus pyogenes and Streptococcus agalactiae suggests that these plasmids somehow circulate in the streptococcal population. The objective of this study was to characterize the erm(T)-carrying genetic element in a clinical isolate of Streptococcus dysgalactiae subsp. equisimilis (Sde5580) and to provide a possible explanation for the spread of erm(T)-carrying plasmids in streptococci. METHODS The erm(T)-carrying element of Sde5580 was investigated by plasmid analysis, PCR experiments and sequencing. Transfer and retransfer experiments were performed using S. pyogenes, S. agalactiae and Streptococcus suis strains as recipients and by selection in the presence of suitable drug concentrations. Transconjugants were analysed by SmaI-macrorestriction analysis. Genetic studies also included PCR-restriction fragment length polymorphism analysis using HindIII endonuclease. RESULTS Sde5580 contained two mobile genetic elements: a 4950 bp erm(T)-carrying plasmid (p5580) almost identical to the non-self-transmissible erm(T)-carrying plasmids of S. pyogenes and S. agalactiae mentioned above, and an ~63 kb cadC/cadA-carrying integrative and conjugative element (ICESde3396-like) of the ICESa2603 family. p5580 was transferable at high frequency to the recipients of all three species through in trans mobilization by the coresident ICESde3396-like element. p5580 and ICESde3396-like were able to be transferred either separately or together. CONCLUSIONS This is the first evidence of horizontal transfer of an erm(T)-carrying plasmid between streptococci. In trans mobilization by coresident ICEs may be one mechanism for the spread of erm(T)-carrying plasmids in the streptococcal population.
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Affiliation(s)
- Claudio Palmieri
- Dipartimento di Scienze Biomediche e Sanità Pubblica, Sezione Microbiologia, Università Politecnica delle Marche, Ancona, Italy
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