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Retamar GC, Bustos CP, Guillemi EC, Becú T, Ivanissevich A, Mesplet M, Muñoz AJ. Streptococcus equi subsp. zooepidemicus: High molecular diversity of Argentinian strains isolated from mares with endometritis. Res Vet Sci 2024; 173:105242. [PMID: 38640833 DOI: 10.1016/j.rvsc.2024.105242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/27/2024] [Accepted: 03/24/2024] [Indexed: 04/21/2024]
Abstract
Streptococcus equi subsp. zooepidemicus (S. zooepidemicus) is a mucosal commensal of the lower genital tract in horses and is the most isolated bacterium causing endometritis in mares. The aim of this study was to determine the molecular diversity of S. zooepidemicus obtained from endometritis in mares in Buenos Aires province, Argentina. Thirty isolates obtained from the uterus of mares in 2005 and 2017 were studied. The MLST scheme was applied to identify the Argentinian genotypes and the clonal relationships and patterns of evolutionary descent were identified using the eBURST algorithm - goeBURST. Twenty six different Sequence types (STs) were identified, being only 11 of them previously reported in horses and also, from several host species and tissues. The other 15 STs were reported in Argentinian reproductive strains of mares in our study for the first time. The genotypes obtained from uterus in Argentina were not evenly distributed when all the published S. zooepidemicus STs were analysed, thus, it was not possible to establish that the same lineage circulates in our equine population. The fact that the identified genotypes were also reported in other countries, diverse samples and host species suggest that there is not a host, and an anatomical niche adaptation. Finally, the isolation of the same genotype in the vagina/clitoris and the uterus of the same mare highlights the versatility of S. zooepidemicus and its role as an opportunistic pathogen.
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Affiliation(s)
- Gabriela C Retamar
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina.
| | - Carla P Bustos
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Eliana C Guillemi
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Instituto de Agrobiotecnología y Biología Molecular (IABIMO) INTA-CONICET, Buenos Aires, Argentina
| | | | | | - Maria Mesplet
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina
| | - Alejandra J Muñoz
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Buenos Aires, Argentina
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Takahashi T, Maeda T, Yoshida H, Goto M, Tsuyuki Y, Kim JS. Genetic organization of an M protein trans-acting positive regulator (Mga) orthologue and its adjacent M-like protein (SCM) alleles in Streptococcus canis. BMC Res Notes 2024; 17:138. [PMID: 38750516 PMCID: PMC11097546 DOI: 10.1186/s13104-024-06795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
OBJECTIVE The purpose of this study was to identify the M protein trans-acting positive regulator (Mga) orthologue and its adjacent M-like protein (SCM) alleles in Streptococcus canis. RESULTS Using the 39 SCM allele isolates and polymerase chain reaction-based amplification and sequencing, we obtained the deduced Mga amino acid (AA) sequences. The 22 Mga sequences in whole-genome sequences were obtained by searching the National Collection of Type Cultures 12,191(T) Mga sequence into the database. The percentage identity to the type-strain Mga sequence was examined along with its size. The presence of the Mga-specific motifs was confirmed. Of the 62 strains, we identified 59 Mga sequences with an AA size of 509 (except for four different sizes). Percentage identity ranged from 96.66 to 100% with the confirmed Mga-specific motifs and diverse SCM allele populations. Our findings support the presence of an Mga orthologue and diverse SCM allele populations.
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Affiliation(s)
- Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Takahiro Maeda
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Haruno Yoshida
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Yuzo Tsuyuki
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, Tokyo, Japan
| | - Jae-Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
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Dobrut A, Siemińska I, Sroka-Oleksiak A, Drożdż K, Sobońska J, Mroczkowska U, Brzychczy-Włoch M. Molecular and phenotypic identification of bacterial species isolated from cows with mastitis from three regions of Poland. BMC Vet Res 2024; 20:193. [PMID: 38734661 PMCID: PMC11088075 DOI: 10.1186/s12917-023-03869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/24/2023] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND Bovine mastitis is a widespread disease affecting dairy cattle worldwide and it generates substantial losses for dairy farmers. Mastitis may be caused by bacteria, fungi or algae. The most common species isolated from infected milk are, among others, Streptococcus spp., Escherichia coli, Staphylococcus aureus and non-aureus staphylococci and mammaliicocci. The aim of this paper is to determine the frequency of occurrence of bacterial species in milk samples from cows with mastitis from three regions of Poland: the north-east, the south-west and the south. To this end 203 milk samples taken from cows with a clinical form (CM) of mastitis (n = 100) and healthy animals (n = 103) were examined, which included culture on an appropriate medium followed by molecular detection of E. coli, S. aureus, Streptococcus agalactiae and Streptococcus uberis, as one of the most common species isolated from mastitis milk. RESULTS The results obtained indicated that S. uberis was the most commonly cultivated CM species (38%, n = 38), followed by S. aureus (22%, n = 22), E. coli (21%, n = 21) and S. agalactiae (18%, n = 18). Similar frequencies in molecular methods were obtained for S. uberis (35.1%) and S. aureus (28.0%). The variation of sensitivity of both methods may be responsible for the differences in the E. coli (41.0%, p = 0.002) and S. agalactiae (5.0%, p = 0.004) detection rates. Significant differences in composition of species between three regions of Poland were noted for E. coli incidence (p < 0.001), in both the culture and molecular methods, but data obtained by the PCR method indicated that this species was the least common in north-eastern Poland, while the culture method showed that in north-eastern Poland E. coli was the most common species. Significant differences for the molecular method were also observed for S. uberis (p < 0.001) and S. aureus (p < 0.001). Both species were most common in southern and south-western Poland. CONCLUSIONS The results obtained confirm the need to introduce rapid molecular tests for veterinary diagnostics, as well as providing important epidemiological data, to the best of our knowledge data on Polish cows in selected areas of Poland is lacking.
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Affiliation(s)
- Anna Dobrut
- Department of Molecular Medical Microbiology, Chair of Microbiology, Jagiellonian University Medical College, Krakow, Poland.
| | - Izabela Siemińska
- Institute of Veterinary Sciences, University Center of Veterinary Medicine JU-AU, University of Agriculture in Krakow, Krakow, Poland
| | - Agnieszka Sroka-Oleksiak
- Department of Molecular Medical Microbiology, Chair of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - Kamil Drożdż
- Department of Molecular Medical Microbiology, Chair of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | - Joanna Sobońska
- Department of Molecular Medical Microbiology, Chair of Microbiology, Jagiellonian University Medical College, Krakow, Poland
| | | | - Monika Brzychczy-Włoch
- Department of Molecular Medical Microbiology, Chair of Microbiology, Jagiellonian University Medical College, Krakow, Poland
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Tsuyuki Y, Maeda T, Torii K, Yoshida H, Ikeda N, Yoshida S, Ito M, Goto M, Takahashi T. Antimicrobial resistance patterns of Streptococcus uberis isolates from bovine milk in Chiba prefecture, Japan: association between multidrug resistance and clonal complex 996. J Vet Med Sci 2024; 86:468-473. [PMID: 38569837 DOI: 10.1292/jvms.23-0526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
Streptococcus uberis is one of major pathogens causing bovine mastitis. However, there is poor information on antimicrobial resistance (AMR) among the Japanese isolates. To provide treatment information for the mastitis caused by S. uberis in Japan, we aimed to clarify AMR patterns of the isolates from bovine milk mainly in Chiba. AMR phenotyping/genotyping [blaZ-erm(A)-erm(B)-mef(A)-linB-lnuD-tet(M)-tet(O)-tet(K)-tet(L)-tet(S)] and multilocus sequence typing were performed to analyze relationships between AMR patterns and clonal complexes (CCs). Resistance to tetracycline-, macrolide-, and lincosamide-classes was mainly associated with possession of tet(O), tet(S), erm(B), linB, and lnuD genes. CC996 was significantly associated with multidrug resistance (P<0.0001). These findings will aid Chiba farm animal clinics in treating bovine mastitis.
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Affiliation(s)
- Yuzo Tsuyuki
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, Tokyo, Japan
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
- Matsuoka Research Institute for Science, Tokyo, Japan
| | - Takahiro Maeda
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Kae Torii
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, Tokyo, Japan
| | - Haruno Yoshida
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Noriaki Ikeda
- Division of Clinical Laboratory, Obihiro Clinical Laboratory, Hokkaido, Japan
| | - Saki Yoshida
- Division of Clinical Laboratory, Obihiro Clinical Laboratory, Hokkaido, Japan
| | - Masahiko Ito
- Division of Clinical Laboratory, Sapporo Clinical Laboratory, Hokkaido, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Tokyo, Japan
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Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL. Expanding the flexibility of base editing for high-throughput genetic screens in bacteria. Nucleic Acids Res 2024; 52:4079-4097. [PMID: 38499498 DOI: 10.1093/nar/gkae174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, the limited number of available, efficient target sites hampers their use for high-throughput screening. Here, we make multiple advances to enable flexible base editing as part of high-throughput genetic screening in bacteria. We first co-opt the Streptococcus canis Cas9 that exhibits more flexible protospacer-adjacent motif recognition than the traditional Streptococcus pyogenes Cas9. We then expand beyond introducing premature stop codons by mutating start codons. Next, we derive guide design rules by applying machine learning to an essentiality screen conducted in Escherichia coli. Finally, we rescue poorly edited sites by combining base editing with Cas9-induced cleavage of unedited cells, thereby enriching for intended edits. The efficiency of this dual system was validated through a conditional essentiality screen based on growth in minimal media. Overall, expanding the scope of genome-wide knockout screens with base editors could further facilitate the investigation of new gene functions and interactions in bacteria.
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Affiliation(s)
- Sandra Gawlitt
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Scott P Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanying Yu
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
| | - Samuel A Blackman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Lars Barquist
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
| | - Chase L Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), 97080 Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080 Würzburg, Germany
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Xie O, Zachreson C, Tonkin-Hill G, Price DJ, Lacey JA, Morris JM, McDonald MI, Bowen AC, Giffard PM, Currie BJ, Carapetis JR, Holt DC, Bentley SD, Davies MR, Tong SYC. Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange. Nat Commun 2024; 15:3477. [PMID: 38658529 PMCID: PMC11043366 DOI: 10.1038/s41467-024-47816-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Streptococcus dysgalactiae subspecies equisimilis (SDSE) and Streptococcus pyogenes share skin and throat niches with extensive genomic homology and horizontal gene transfer (HGT) possibly underlying shared disease phenotypes. It is unknown if cross-species transmission interaction occurs. Here, we conduct a genomic analysis of a longitudinal household survey in remote Australian First Nations communities for patterns of cross-species transmission interaction and HGT. Collected from 4547 person-consultations, we analyse 294 SDSE and 315 S. pyogenes genomes. We find SDSE and S. pyogenes transmission intersects extensively among households and show that patterns of co-occurrence and transmission links are consistent with independent transmission without inter-species interference. We identify at least one of three near-identical cross-species mobile genetic elements (MGEs) carrying antimicrobial resistance or streptodornase virulence genes in 55 (19%) SDSE and 23 (7%) S. pyogenes isolates. These findings demonstrate co-circulation of both pathogens and HGT in communities with a high burden of streptococcal disease, supporting a need to integrate SDSE and S. pyogenes surveillance and control efforts.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, VIC, Australia
| | - Cameron Zachreson
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | | | - David J Price
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VIC, Australia
| | - Jake A Lacey
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jacqueline M Morris
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Malcolm I McDonald
- Division of Tropical Health and Medicine, James Cook University, Townsville, QLD, Australia
| | - Asha C Bowen
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Philip M Giffard
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Faculty of Health, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Jonathan R Carapetis
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia and Perth Children's Hospital, Perth, WA, Australia
| | - Deborah C Holt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
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Hyeon JY, Kim J, Chung DH, Helal ZH, Polkowski R, Lee DH, Risatti GR. Genome analysis of Streptococcus spp. isolates from animals in pre-antibiotic era with respect to antibiotic susceptibility and virulence gene profiles. Vet Res 2024; 55:51. [PMID: 38622639 PMCID: PMC11017511 DOI: 10.1186/s13567-024-01302-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
Lyophilized Streptococcus spp. isolates (n = 50) from animal samples submitted to the diagnostic laboratory at the University of Connecticut in the 1940s were revivified to investigate the genetic characteristics using whole-genome sequencing (WGS). The Streptococcus spp. isolates were identified as follows; S. agalactiae (n = 14), S. dysgalactiae subsp. dysgalactiae (n = 10), S. dysgalactiae subsp. equisimils (n = 5), S. uberis (n = 8), S. pyogenes (n = 7), S. equi subsp. zooepidemicus (n = 4), S. oralis (n = 1), and S. pseudoporcinus (n = 1). We identified sequence types (ST) of S. agalactiae, S. dysgalactiae, S. uberis, S. pyogenes, and S. equi subsp. zooepidemicus and reported ten novel sequence types of those species. WGS analysis revealed that none of Streptococcus spp. carried antibiotic resistance genes. However, tetracycline resistance was observed in four out of 15 S. dysgalactiae isolates and in one out of four S. equi subsp. zooepidemicus isolate. This data highlights that antimicrobial resistance is pre-existed in nature before the use of antibiotics. The draft genome sequences of isolates from this study and 426 complete genome sequences of Streptococcus spp. downloaded from BV-BRC and NCBI GenBank database were analyzed for virulence gene profiles and phylogenetic relationships. Different Streptococcus species demonstrated distinct virulence gene profiles, with no time-related variations observed. Phylogenetic analysis revealed high genetic diversity of Streptococcus spp. isolates from the 1940s, and no clear spatio-temporal clustering patterns were observed among Streptococcus spp. analyzed in this study. This study provides an invaluable resource for studying the evolutionary aspects of antibiotic resistance acquisition and virulence in Streptococcus spp.
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Affiliation(s)
- Ji-Yeon Hyeon
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
| | - Junwon Kim
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - David H Chung
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Zeinab H Helal
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Robert Polkowski
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea.
| | - Guillermo R Risatti
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
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Wu R, Nahm M, Yang J, Bush CA, Wu H. Identification and genetic engineering of pneumococcal capsule-like polysaccharides in commensal oral streptococci. Microbiol Spectr 2024; 12:e0188523. [PMID: 38488366 PMCID: PMC10986556 DOI: 10.1128/spectrum.01885-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/28/2023] [Indexed: 04/06/2024] Open
Abstract
Capsular polysaccharides (CPS) in Streptococcus pneumoniae are pivotal for bacterial virulence and present extensive diversity. While oral streptococci show pronounced antigenicity toward pneumococcal capsule-specific sera, insights into evolution of capsule diversity remain limited. This study reports a pneumococcal CPS-like genetic locus in Streptococcus parasanguinis, a predominant oral Streptococcus. The discovered locus comprises 15 genes, mirroring high similarity to those from the Wzy-dependent CPS locus of S. pneumoniae. Notably, S. parasanguinis elicited a reaction with pneumococcal 19B antiserum. Through nuclear magnetic resonance analysis, we ascertained that its CPS structure matches the chemical composition of the pneumococcal 19B capsule. By introducing the glucosyltransferase gene cps19cS from a pneumococcal serotype 19C, we successfully transformed S. parasanguinis antigenicity from 19B to 19C. Furthermore, substituting serotype-specific genes, cpsI and cpsJ, with their counterparts from pneumococcal serotype 19A and 19F enabled S. parasanguinis to generate 19A- and 19F-specific CPS, respectively. These findings underscore that S. parasanguinis harbors a versatile 19B-like CPS adaptable to other serotypes. Remarkably, after deleting the locus's initial gene, cpsE, responsible for sugar transfer, we noted halted CPS production, elongated bacterial chains, and diminished biofilm formation. A similar phenotype emerged with the removal of the distinct gene cpsZ, which encodes a putative autolysin. These data highlight the importance of S. parasanguinis CPS for biofilm formation and propose a potential shared ancestry of its CPS locus with S. pneumoniae. IMPORTANCE Diverse capsules from Streptococcus pneumoniae are vital for bacterial virulence and pathogenesis. Oral streptococci show strong responses to a wide range of pneumococcal capsule-specific sera. Yet, the evolution of this capsule diversity in relation to microbe-host interactions remains underexplored. Our research delves into the connection between commensal oral streptococcal and pneumococcal capsules, highlighting the potential for gene transfer and evolution of various capsule types. Understanding the genetic and evolutionary factors that drive capsule diversity in S. pneumoniae and its related oral species is essential for the development of effective pneumococcal vaccines. The present findings provide fresh perspectives on the cross-reactivity between commensal streptococci and S. pneumoniae, its influence on bacteria-host interactions, and the development of new strategies to manage and prevent pneumococcal illnesses by targeting and modulating commensal streptococci.
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Affiliation(s)
- Ren Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, Alabama, USA
| | - Moon Nahm
- Department of Medicine, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama, USA
| | - Jinghua Yang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - C. Allen Bush
- Department of Chemistry and Biochemistry, University of Maryland at Baltimore, Baltimore, Maryland, USA
| | - Hui Wu
- Department of Pediatric Dentistry, University of Alabama at Birmingham, School of Dentistry, Birmingham, Alabama, USA
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University School of Dentistry, Portland, Oregon, USA
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Lee H, Lee DG, Jo H, Heo YM, Baek C, Kim HB, Park G, Kang S, Lee W, Mun S, Han K. Comparative whole genome analysis of face-derived Streptococcus infantis CX-4 unravels the functions related to skin barrier. Genes Genomics 2024; 46:499-510. [PMID: 38453815 DOI: 10.1007/s13258-024-01495-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/21/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND The skin microbiome is essential in guarding against harmful pathogens and responding to environmental changes by generating substances useful in the cosmetic and pharmaceutical industries. Among these microorganisms, Streptococcus is a bacterial species identified in various isolation sources. In 2021, a strain of Streptococcus infantis, CX-4, was identified from facial skin and found to be linked to skin structure and elasticity. As the skin-derived strain differs from other S. infantis strains, which are usually of oral origin, it emphasizes the significance of bacterial variation by the environment. OBJECTIVE This study aims to explore the unique characteristics of the CX-4 compared to seven oral-derived Streptococcus strains based on the Whole-Genome Sequencing data, focusing on its potential role in skin health and its possible application in cosmetic strategies. METHODS The genome of the CX-4 strain was constructed using PacBio Sequencing, with the assembly performed using the SMRT protocol. Comparative whole-genome analysis was then performed with seven closely related strains, utilizing web-based tools like PATRIC, OrthoVenn3, and EggNOG-mapper, for various analyses, including protein association analysis using STRING. RESULTS Our analysis unveiled a substantial number of Clusters of Orthologous Groups in diverse functional categories in CX-4, among which sphingosine kinase (SphK) emerged as a unique product, exclusively present in the CX-4 strain. SphK is a critical enzyme in the sphingolipid metabolic pathway, generating sphingosine-1-phosphate. The study also brought potential associations with isoprene formation and retinoic acid synthesis, the latter being a metabolite of vitamin A, renowned for its crucial function in promoting skin cell growth, differentiation, and maintaining of skin barrier integrity. These findings collectively suggest the potential of the CX-4 strain in enhancing of skin barrier functionality. CONCLUSION Our research underscores the potential of the skin-derived S. infantis CX-4 strain by revealing unique bacterial compounds and their potential roles on human skin.
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Affiliation(s)
- Haeun Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Dong-Geol Lee
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - HyungWoo Jo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Young Mok Heo
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Chaeyun Baek
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Hye-Been Kim
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Geunhwa Park
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Seunghyun Kang
- R&I Center, COSMAX BTI, Pangyo-ro 255, Bundang-gu, Seongnam, 13486, Republic of Korea
| | - Wooseok Lee
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Seyoung Mun
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea
- Department of Cosmedical and Materials, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyudong Han
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
- Smart Animal Bio Institute, Dankook University, Cheonan, 31116, Republic of Korea.
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10
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Lee CY, Chan CK, Chida M, Miyashita M, Lee YS, Wu HC, Chang YC, Lin WT, Chen YS. Streptococcus taonis sp. nov., a novel bacterial species isolated from a blood culture of a patient. Arch Microbiol 2024; 206:168. [PMID: 38489085 DOI: 10.1007/s00203-024-03884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 03/17/2024]
Abstract
One Gram stain-positive, catalase-negative, α-hemolytic, chain-forming or paired cocci, designated ST22-14T, was isolated from a blood culture of a child with suspected infection. The results of 16S rRNA gene sequences analyses showed that the most closely related species to strain ST22-14T were "Streptococcus vulneris" DM3B3T (99.2%), Streptococcus mitis NCTC 12261T (99.0%), "Streptococcus gwangjuense" ChDC B345T, (99.0%), Streptococcus oralis subsp. dentisani 7747T (99.0%), Streptococcus downii CECT 9732T (99.0%), and Streptococcus infantis ATCC 700779T (98.9%). The genome of strain ST22-14T consists of 2,053,261 bp with a G + C content of 39.4%. Average nucleotide identity values between strain ST22-14T and Streptococcus mitis NCTC 12261T or other five species were from 82.2 to 88.0%. In silico DNA-DNA hybridization of ST22-14T showed an estimated DNA reassociation value of 34.6% with the closest species. The main cellular fatty acids of strain ST22-14T were 16:0, 18:0, 14:0, 18:1ω7c and 18:1ω6c. Based on these results, strain ST22-14T should be classified as a novel species of genus Streptococcus, for which the name Streptococcus taonis sp. nov. is proposed (type strain ST22-14T = NBRC 116002T = BCRC 81402T).
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Affiliation(s)
- Chien-Yu Lee
- Department of Pediatrics, Taoyuan General Hospital, Ministry of Health and Welfare, No.1492, Zhongshan Rd., Taoyuan Dist., Taoyuan City, 330, Taiwan ROC
| | - Chin-Kan Chan
- Department of Pediatrics, Taoyuan General Hospital, Ministry of Health and Welfare, No.1492, Zhongshan Rd., Taoyuan Dist., Taoyuan City, 330, Taiwan ROC
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Momoko Chida
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Hui-Chung Wu
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Yu-Chung Chang
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Wen-Ting Lin
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC
| | - Yi-Sheng Chen
- Department of Biotechnology, Ming Chuan University, No. 5, De-Ming Rd., Guishan Dist., Taoyuan City, 333, Taiwan ROC.
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11
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Romani L, Del Chierico F, Pane S, Ristori MV, Pirona I, Guarrasi V, Cotugno N, Bernardi S, Lancella L, Perno CF, Rossi P, Villani A, Campana A, Palma P, Putignani L. Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection. Microbiol Spectr 2024; 12:e0300923. [PMID: 38289047 PMCID: PMC10913489 DOI: 10.1128/spectrum.03009-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 12/12/2023] [Indexed: 03/06/2024] Open
Abstract
The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (T0), 72 h to 7 days (T1), and at the discharge (T2) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (N = 71) was characterized by reduction of α-diversity compared to CTRLs (N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus, Haemophilus, Staphylococcus, Veillonella, Enterococcus, Neisseria, Moraxella, Enterobacteriaceae, Gemella, Bacillus, and reduced in Faecalibacterium, Akkermansia, Blautia, Bifidobacterium, Ruminococcus, and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus, and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL. IMPORTANCE Since the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.
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Affiliation(s)
- L. Romani
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - F. Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - S. Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - M. V. Ristori
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - I. Pirona
- GenomeUp SRL, Viale Pasteur, Rome, Italy
| | | | - N. Cotugno
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - S. Bernardi
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - L. Lancella
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - C. F. Perno
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - P. Rossi
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - A. Villani
- Pediatric Emergency Department and General Pediatrics, Bambino Gesù Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - A. Campana
- Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - P. Palma
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
| | - L. Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - the CACTUS Study TeamCarducciFrancesca CalòCancriniCaterinaChiurchiùSaradegli AttiMarta CiofiCursiLauraCutreraRenatoD’AmoreCarmenD’ArgenioPatriziaDe IorisMaria A.De LucaMaiaFinocchiAndreaMannoEmma ConcettaMorrocchiElenaPansaPaolaSessaLiberaZangariPaola
- Infectious Disease Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- GenomeUp SRL, Viale Pasteur, Rome, Italy
- Research Unit of Congenital and Perinatal Infections, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Systems Medicine, University of Rome ‘‘Tor Vergata’’, Rome, Italy
- Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Pediatric Emergency Department and General Pediatrics, Bambino Gesù Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
- Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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12
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Whiley D, Jolley K, Blanchard A, Coffey T, Leigh J. A core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen. Microb Genom 2024; 10. [PMID: 38512314 DOI: 10.1099/mgen.0.001225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024] Open
Abstract
Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97 %) isolates used and differentiated the associated sequences into 932 discrete core genome sequence types (cgSTs). Analysis of the phylogenetic relationships of cgSTs revealed no clear clustering of isolates based on metadata such as disease status or year of isolation. Geographical clustering of cgSTs was limited to identification of a UK-centric clade, but cgSTs from UK isolates were also dispersed with those originating from other geographical regions across the entire phylogenetic topology. The cgMLST scheme offers a new tool for the detailed analysis of this globally important pathogen of dairy cattle. Initial analysis has re-emphasized and exemplified the genetically diverse nature of the global population of this opportunistic pathogen.
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Affiliation(s)
- Daniel Whiley
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Keith Jolley
- Department of Biology, University of Oxford, Oxford, UK
| | - Adam Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Tracey Coffey
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - James Leigh
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
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13
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Choi A, Dong K, Williams E, Pia L, Batagower J, Bending P, Shin I, Peters DI, Kaspar JR. Human saliva modifies growth, biofilm architecture, and competitive behaviors of oral streptococci. mSphere 2024; 9:e0077123. [PMID: 38319113 PMCID: PMC10900908 DOI: 10.1128/msphere.00771-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
The bacteria within supragingival biofilms participate in complex exchanges with other microbes inhabiting the same niche. One example is the mutans group streptococci (Streptococcus mutans), implicated in the development of tooth decay, and other health-associated commensal streptococci species. Previously, our group transcriptomically characterized intermicrobial interactions between S. mutans and several species of oral bacteria. However, these experiments were carried out in a medium without human saliva. To better mimic their natural environment, we first evaluated how inclusion of saliva affected growth and biofilm formation of eight Streptococcus species individually and found saliva to positively benefit growth rates while negatively influencing biofilm biomass accumulation and altering spatial arrangement. These results carried over during evaluation of 29 saliva-derived isolates of various species. Surprisingly, we also found that addition of saliva increased the competitive behaviors of S. mutans in coculture competitions against commensal streptococci that led to increases in biofilm microcolony volumes. Through transcriptomically characterizing mono- and cocultures of S. mutans and Streptococcus oralis with and without saliva, we determined that each species developed a nutritional niche under mixed-species growth, with S. mutans upregulating carbohydrate uptake and utilization pathways while S. oralis upregulated genome features related to peptide uptake and glycan foraging. S. mutans also upregulated genes involved in oxidative stress tolerance, particularly manganese uptake, which we could artificially manipulate by supplementing in manganese leading to an advantage over its opponent. Our report highlights observable changes in microbial behaviors through leveraging environmental- and host-supplied resources over their competitors. IMPORTANCE Dental caries (tooth decay) is the most prevalent disease for both children and adults nationwide. Caries are initiated from demineralization of the enamel due to organic acid production through the metabolic activity of oral bacteria growing in biofilm communities attached to the tooth's surface. Mutans group streptococci are closely associated with caries development and initiation of the cariogenic cycle, which decreases the amount of acid-sensitive, health-associated commensal bacteria while selecting for aciduric and acidogenic species that then further drives the disease process. Defining the exchanges that occur between mutans group streptococci and oral commensals in a condition that closely mimics their natural environment is of critical need toward identifying factors that can influence odontopathogen establishment, persistence, and outgrowth. The goal of our research is to develop strategies, potentially through manipulation of microbial interactions characterized here, that prevent the emergence of mutans group streptococci while keeping the protective flora intact.
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Affiliation(s)
- Allen Choi
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Kevin Dong
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Emily Williams
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Lindsey Pia
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Jordan Batagower
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Paige Bending
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Iris Shin
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Daniel I Peters
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Justin R Kaspar
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
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Xiong X, Chen R, Lai J. Comparative genomics analysis of Streptococcus iniae isolated from Trachinotus ovatus: novel insight into antimicrobial resistance and virulence differentiation. BMC Genomics 2023; 24:775. [PMID: 38097934 PMCID: PMC10720119 DOI: 10.1186/s12864-023-09882-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Streptococcus iniae is an important fish pathogen that cause significant economic losses to the global aquaculture industry every year. Although there have some reports on the genotype of S.iniae and its relationship with virulence, no genome-scale comparative analysis has been performed so far. In our previous work, we characterized 17 isolates of S.iniae from Trachinotus ovatus and divided them into two genotypes using RAPD and rep-PCR methods. Among them, BH15-2 was classified as designated genotype A (in RAPD) and genotype 1 (in rep-PCR), while BH16-24 was classified as genotype B and genotype 2. Herein, we compared the differences in growth, drug resistance, virulence, and genome between BH15-2 and BH16-24. RESULTS The results showed that the growth ability of BH16-24 was significantly faster than that of BH15-2 at the exponential stage. Antimicrobial tests revealed that BH15-2 was susceptible to most of the tested antibiotics except neomycin and gentamycin. In contrast, BH16-24 was resistant to 7 antibiotics including penicillin, sulfasomizole, compound sulfamethoxazole tablets, polymyxin B, spectinomycin, rifampin and ceftazidime. Intraperitoneal challenge of T.ovatus, showed that the LD50 value of BH15-2 was 4.0 × 102 CFU/g, while that of BH16-24 was 1.2 × 105 CFU/g. The genome of S.iniae BH15-2 was 2,175,659 bp with a GC content of 36.80%. Meanwhile, the genome of BH16-24 was 2,153,918 bp with a GC content of 36.83%. Comparative genome analysis indicated that compared with BH15-2, BH16-24 genome had a large-scale genomic inversion fragment, at the location from 502,513 bp to 1,788,813 bp, resulting in many of virulence and resistance genes differentially expression. In addition, there was a 46 kb length, intact phage sequence in BH15-2 genome, which was absent in BH16-24. CONCLUSION Comparative genomic studies of BH15-2 and BH16-24 showed that the main difference is a 1.28 Mbp inversion fragment. The inversion fragment may lead to abnormal expression of drug resistant and virulence genes, which is believed to be the main reason for the multiple resistance and weakened virulence of BH16-24. Our study revealed the potential mechanisms in underlying the differences of multidrug resistance and virulence among different genotypes of S.iniae.
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Affiliation(s)
- Xiangying Xiong
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China.
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China.
| | - Ruifang Chen
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Guangxi Institute of Oceanology Limited Liability Company, Beihai, 536000, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
| | - Junxiang Lai
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Marine Sciences, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
- Beibu Gulf Marine Industry Research Institute, Fangchenggang, 538000, Guangxi, China
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15
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Rosa MN, Vezina B, Marogna G, Canu A, Molotzu MR, Tola S. Streptococcus ruminantium-associated sheep mastitis outbreak detected in Italy is distinct from bovine isolates. Vet Res 2023; 54:118. [PMID: 38087338 PMCID: PMC10717183 DOI: 10.1186/s13567-023-01248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Streptococcus ruminantium is the causative agent of several bovine and ovine diseases, however reports are uncommon and application of whole genome sequencing to identify is rare. We report for the first time, a severe ovine mastitis outbreak caused by S. ruminantium in Italy, 2022. S. ruminantium was isolated from 12 adult lactating ewes with diffuse nodules in the mammary parenchyma and predominantly serous and clotted milk. All outbreak isolates, along with five additional historical Italian isolates (between 2011 and 2017), were genomically characterised and then analysed in the context of all publicly available S. ruminantium genomes. Antimicrobial susceptibility testing was performed to determine the MICs of 16 antibiotics. The results showed that all isolates were susceptible to all antimicrobials tested except kanamycin. Single Nucleotide Variant analysis confirmed this as a clonal outbreak across 10 sheep (≤ 15 SNVs), while the two others were colonised by more distantly related clones (≤ 53 pairwise SNVs), indicating the presence of multiple infecting lineages. The five historical S. ruminantium isolates were comprised of genetically-distant singletons (between 1259 and 5430 pairwise SNVs to 2022 outbreak isolates). Ovine isolates were found to be genetically distinct to bovine isolates, forming monophyletic groups. Bovine isolates were similarly made up of singleton clones in all but two isolates. Taken together, our genomic analysis using all globally available genomes is consistent with general opportunistic pathogenesis of S. ruminantium. We encourage future genomic surveillance efforts to facilitate outbreak detection, as well as improve our understanding of this poorly-understood, multi-host, zoonotic pathogen.
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Affiliation(s)
- Maria Nives Rosa
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University and the Alfred Hospital, Melbourne, VIC, Australia.
| | - Gavino Marogna
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Antonella Canu
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Monica Rosaria Molotzu
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy
| | - Sebastiana Tola
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", 07100, Sassari, Italy.
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16
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Breyer GM, Rocha Jacques da Silva ME, Slaviero M, Albuquerque de Almeida B, Machado Sousa da Silva E, de Queiroz Schmidt VR, Alievi M, Maboni G, Petinatti Pavarini S, Maboni Siqueira F. Genotypic characterization of Streptococcus didelphis causative of fatal infection in white-eared opossums. Lett Appl Microbiol 2023; 76:ovad131. [PMID: 37968138 DOI: 10.1093/lambio/ovad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
Streptococcus didelphis was once reported as related to severe infections in opossums. Thus, we present the first comprehensive whole-genome characterization of clinical S. didelphis strains isolated from white-eared opossums (Didelphis albiventris). Long-read whole-genome sequencing was performed using the MinION platform, which allowed the prediction of several genomic features. We observed that S. didelphis genomes harbor a cluster for streptolysin biosynthesis and a conserved genomic island with genes involved in transcriptional regulation (arlR) and transmembrane transport (bcrA). Antimicrobial resistance genes for several drug classes were found, including beta-lactam, which is the main antimicrobial class used in Streptococcus spp. infections; however, no phenotypical resistance was observed. In addition, we predicted the presence of 33 virulence factors in the analyzed genomes. High phylogenetic similarity was observed between clinical and reference strains, yet no clonality was suggested. We also proposed dnaN, gki, pros, and xpt as housekeeping candidates to be used in S. didelphis sequence typing. This is the first whole-genome characterization of S. didelphis, whose data provide important insights into its pathogenicity.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Maria Eduarda Rocha Jacques da Silva
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Mônica Slaviero
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Bruno Albuquerque de Almeida
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Emanoelly Machado Sousa da Silva
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Victória Regina de Queiroz Schmidt
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Marcelo Alievi
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Grazieli Maboni
- Department of Pathobiology, University of Guelph, 50 Stone Road East, NIG 2W1 - Guelph/ON, Canada
| | - Saulo Petinatti Pavarini
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
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17
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Kampff Z, van Sinderen D, Mahony J. Cell wall polysaccharides of streptococci: A genetic and structural perspective. Biotechnol Adv 2023; 69:108279. [PMID: 37913948 DOI: 10.1016/j.biotechadv.2023.108279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/04/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023]
Abstract
The Streptococcus genus comprises both commensal and pathogenic species. Additionally, Streptococcus thermophilus is exploited in fermented foods and in probiotic preparations. The ecological and metabolic diversity of members of this genus is matched by the complex range of cell wall polysaccharides that they present on their cell surfaces. These glycopolymers facilitate their interactions and environmental adaptation. Here, current knowledge on the genetic and compositional diversity of streptococcal cell wall polysaccharides including rhamnose-glucose polysaccharides, exopolysaccharides and teichoic acids is discussed. Furthermore, the species-specific cell wall polysaccharide combinations and specifically highlighting the presence of rhamnose-glucose polysaccharides in certain species, which are replaced by teichoic acids in other species. This review highlights model pathogenic and non-pathogenic species for which there is considerable information regarding cell wall polysaccharide composition, structure and genetic information. These serve as foundations to predict and focus research efforts in other streptococcal species for which such data currently does not exist.
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Affiliation(s)
- Zoe Kampff
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
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18
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Lee M, Choi YJ, Farooq A, Jeong JB, Jung MY. Granulicatella seriolae sp. nov., a Novel Facultative Anaerobe Isolated from Yellowtail Marine Fish. Curr Microbiol 2023; 81:13. [PMID: 38001383 DOI: 10.1007/s00284-023-03523-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/13/2023] [Indexed: 11/26/2023]
Abstract
A bacterial strain, designated as S8T, was isolated from the gut contents of Seriola quinqueradiata from the coastal sea area of Jeju Island, South Korea. The strain is a Gram-staining positive, non-motile, non-spore-forming, facultative anaerobic coccus. Optimal growth was observed at 30 °C, pH 8.0-9.0, and 0-0.5% w/v NaCl, under anaerobic conditions. The predominant fatty acids were C18:1 ω9c, C16:0, C18:0, and C16:1 ω9c, while quinone was not detected. The genome was 2,224,566 bp long, with a GC content of 38.2%. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain S8T had 96.2% similarity with Granulicatella adiacens ATCC 49175T, its closest known species according to nomenclature. The DNA-DNA hybridization (dDDH), average nucleotide identity, and average amino acid identity values between strain S8T and G. adiacens ATCC 49175T were 25.7%, 85.5%, and 77.2%, respectively, all of which fall below the recommended threshold for species differentiation. Based on genomic, phenotypic, and phylogenetic evidence, we propose that strain S8T should be a novel species within the genus Granulicatella, for with the name Granulicatella seriolae sp. nov. is proposed. The type strain is S8T (KCTC 43438T = JCM 35604T).
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Affiliation(s)
- Myunglip Lee
- Department of Marine Life Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Yun Ji Choi
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Adeel Farooq
- Research Institute for Basic Sciences (RIBS), Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Joon Bum Jeong
- Department of Marine Life Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Program in Advance Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
- Department of Biology Education, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
- Jeju Microbiome Research Center, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
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19
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Su Y, Xu MY, Cui Y, Chen RZ, Xie LX, Zhang JX, Chen YQ, Ding T. Bacterial quorum sensing orchestrates longitudinal interactions to shape microbiota assembly. Microbiome 2023; 11:241. [PMID: 37926838 PMCID: PMC10626739 DOI: 10.1186/s40168-023-01699-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND The mechanism of microbiota assembly is one of the main problems in microbiome research, which is also the primary theoretical basis for precise manipulation of microbial communities. Bacterial quorum sensing (QS), as the most common means for bacteria to exchange information and interactions, is characterized by universality, specificity, and regulatory power, which therefore may influence the assembly processes of human microbiota. However, the regulating role of QS in microbiota assembly is rarely reported. In this study, we developed an optimized in vitro oral biofilm microbiota assembling (OBMA) model to simulate the time-series assembly of oral biofilm microbiota (OBM), by which to excavate the QS network and its regulating power in the process. RESULTS By using the optimized OBMA model, we were able to restore the assembly process of OBM and generate time-series OBM metagenomes of each day. We discovered a total of 2291 QS protein homologues related to 21 QS pathways. Most of these pathways were newly reported and sequentially enriched during OBM assembling. These QS pathways formed a comprehensive longitudinal QS network that included successively enriched QS hubs, such as Streptococcus, Veillonella-Megasphaera group, and Prevotella-Fusobacteria group, for information delivery. Bidirectional cross-talk among the QS hubs was found to play critical role in the directional turnover of microbiota structure, which in turn, influenced the assembly process. Subsequent QS-interfering experiments accurately predicted and experimentally verified the directional shaping power of the longitudinal QS network in the assembly process. As a result, the QS-interfered OBM exhibited delayed and fragile maturity with prolonged membership of Streptococcus and impeded membership of Prevotella and Fusobacterium. CONCLUSION Our results revealed an unprecedented longitudinal QS network during OBM assembly and experimentally verified its power in predicting and manipulating the assembling process. Our work provides a new perspective to uncover underlying mechanism in natural complex microbiota assembling and a theoretical basis for ultimately precisely manipulating human microbiota through intervention in the QS network. Video Abstract.
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Affiliation(s)
- Ying Su
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ming-Ying Xu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Department of Immunology and Pathogenic Biology, Zhaoqing Medical College, Zhaoqing, 526020, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Run-Zhi Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Li-Xiang Xie
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Jing-Xiang Zhang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Yong-Qiu Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
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20
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Öberg J, Inghammar M, Nilson B. Improved identification of Streptococcus bovis-Streptococcus equinus-complex species and subspecies by MALDI-TOF MS using a novel library. Diagn Microbiol Infect Dis 2023; 107:116045. [PMID: 37598592 DOI: 10.1016/j.diagmicrobio.2023.116045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/06/2023] [Accepted: 07/28/2023] [Indexed: 08/22/2023]
Abstract
OBJECTIVES To develop an in-house matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) library for improved identification of species and subspecies of the Streptococcus bovis/Streptococcus equinus-complex (SBSEC). METHODS A total of 236 SBSEC isolates from blood stream infections and culture collections, determined by whole genome sequencing to subspecies level, were grown in brain heart infusion broth. Mass spectra were collected using the Bruker MALDI Biotyper system after ethanol-formic acid extraction. Main spectral profiles from 117 isolates were used to create the "SBSEC-CMRS library." The remaining 119 spectra were used for evaluation of Bruker MALDI Biotyper (MBT) Compass Library Revision K (2022) and the SBSEC-CMRS library. RESULTS The Bruker library correctly identified species and subspecies in 72 of 119 (61 %) isolates, while the SBSEC-CMRS library identified 116 of 119 (97 %), using a cutoff score of ≥2.0. CONCLUSIONS The SBSEC-CMRS library showed sufficient diagnostic accuracy, and can be implemented in clinical practice for SBSEC species and subspecies identification.
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Affiliation(s)
- Jonas Öberg
- Department of Clinical Sciences Lund, Section for Infection Medicine, Lund University, Lund, Sweden; Department of Infectious Diseases, Helsingborg Hospital, Helsingborg, Sweden.
| | - Malin Inghammar
- Department of Clinical Sciences Lund, Section for Infection Medicine, Lund University, Lund, Sweden
| | - Bo Nilson
- Department of Laboratory Medicine Lund, Section of Medical Microbiology, Lund University, Lund, Sweden; Department of Clinical Microbiology, Infection Control and Prevention, Office for Medical Services, Region Skåne, Lund, Sweden
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21
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Funk A, Jia Q, Janke L, Crawford A, Iverson A, Rosch J, Emmons J, Savage C, Glasgow H, Hayden R, Margolis E, Pisharath H. Isolation and Characterization of a Novel Alpha-Hemolytic Streptococcus spp. from the Oral Cavity and Blood of Septicemic Periparturient Immunodeficient Mice. Comp Med 2023; 73:346-356. [PMID: 38087407 PMCID: PMC10702164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 12/18/2023]
Abstract
MISTRG is an immunodeficient mouse strain that expresses multiple human cytokines that support hematopoietic stem cell maintenance and myelopoiesis. While establishing a breeding colony of MISTRG mice in a dedicated barrier room, 6 cases of death or disease occurred in pregnant or postpartum mice. Clinically, this manifested as hunched posture, dyspnea, and 1 case of emaciation with ataxia. Pathologic analysis of 7 mice revealed multisystemic necrosuppurative inflammation variably affecting the uterus and placenta, joints, meninges, inner and middle ears, kidneys, and small intestine. Bacteria cultured from the blood of septic mice were identified with 89% probability by the Vitek 2 identification system as Streptococcus sanguinus with atypical biochemical parameters; the API 20E/NE system fully differentiated the isolates as a novel Streptococcus species. MALDI Biotyper-based mass spectrometry also indicated that the phenotype represented a novel Streptococcus spp. Sequencing revealed that the full-length 16S rRNA gene identity was below 97% with known Streptococcus species, including the 2 closest species Streptococcus acidominimus and Streptococcus azizii. We propose the name Streptococcus murisepticum spp. nov to our novel isolates. All male mice in this colony remained healthy despite their association with diseased female mice. Overall, 19% of the colony carried the novel Streptococcus in their oral cavity, but it could not be detected in feces. The organism was sensitive to amoxicillin, which was administered via drinking water throughout pregnancy and weaning to establish a colony of pathogen-negative future breeders. The colony remained disease-free and culture-negative for Streptococcus murisepticum spp. nov after treatment with amoxicillin. We suspect that oral colonization of MISTRG mice with the novel Streptococcus species and its associated unique pathology in periparturient mice is potentially the principal cause of loss of this strain at several institutions. Therefore, screening the oral cavity for α-hemolytic streptococci followed by targeted antibiotic treatment may be necessary when establishing MISTRG and allied immunodeficient mouse strains.
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Affiliation(s)
| | | | - Laura Janke
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Ashley Crawford
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | | | - Joseph Emmons
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Heather Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Randall Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Harshan Pisharath
- Animal Resource Center
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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22
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Zheng M, Kang Y, Shen Y, Xu Y, Xu F, Chen Y. Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient. Curr Microbiol 2023; 80:378. [PMID: 37861738 DOI: 10.1007/s00284-023-03460-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/28/2023] [Indexed: 10/21/2023]
Abstract
Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the agents of pathogens. In this study, metagenomic sequencing was conducted to investigate the microbial and antibiotic resistance genes (ARGs) composition in the vitreous (intraocular body fluid) of an endophthalmitis patient, who progressed rapidly and accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome in the vitreous. This strain harbor's the ARGs mainly against beta-lactam, macrolide-lincosamide-streptogramin, and multidrug. Additionally, metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was identified. The Tetra Correlation Search (TCS) analysis uncovered that the closest relative of the Streptococcus sp. v1. nov. was Streptococcus mitis SK321. Pan/core genome analysis for Streptococcus sp. v1. nov. and TCS top 25 hits strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to ATP-binding cassette transport system, which could indicate unique virulence and pathogenic potentials of Streptococcus sp. v1. nov. In addition, a total of 7 virulence factors were identified, and the overwhelming of them were classified into "offensive virulence factors". The high pathogenicity of Streptococcus sp. v1. nov. could be a reason for the patient's rapid disease progression. Our study was first isolated an ocular pathogen with highly virulent based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patient in the future.
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Affiliation(s)
- Meiqin Zheng
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi, People's Republic of China
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yutong Kang
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yangyang Shen
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Yi Xu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| | - Fangyi Xu
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yanjiong Chen
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, Shanxi, People's Republic of China.
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23
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Katsburg M, Brombach J, Hanke D, Aubry E, Lübke-Becker A, Fulde M. New variant strain of Streptococcus canis with Lancefield group C isolated from canine otitis externa. Vet Microbiol 2023; 285:109869. [PMID: 37651790 DOI: 10.1016/j.vetmic.2023.109869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/02/2023]
Abstract
Every basic course in microbiology teaches us, Streptococcus canis always tests positive for Lancefield group G. Surprisingly, we identified a strain of S. canis with Lancefield group C, cultured from a dog with otitis externa after lateral ear canal resection. Whole genome sequencing data and analysis points towards a horizontal gene transfer event between S. canis and S. dysgalactiae. Although these species are closely related, gene transfer in this region of the genome of S. canis has not been described before. The value of technologies as MALDI-TOF MS and sequencing in microbiological diagnostics will grow as more diverse streptococci arise that do not always conform anymore to the classical Lancefield group typing.
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Affiliation(s)
- Miriam Katsburg
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Julian Brombach
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Etienne Aubry
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Consulting Laboratory for beta-haemolytic streptococci in Veterinary Clinics and Practice, Freie Universität Berlin, Robert-von-Ostertag-Str. 7, 14163 Berlin, Germany; Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany.
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Morris ERA, Schroeder ME, Ferro PJ, Waller AS, McGlennon AA, Bustos CP, Gressler LT, Wu J, Lawhon SD, Boyle AG, Lingsweiler S, Paul N, Dimitrov K, Swinford AK, Bordin AI, Cohen ND. Development of a novel real-time PCR multiplex assay for detection of Streptococcus equi subspecies equi and Streptococcus equi subspecies zooepidemicus. Vet Microbiol 2023; 284:109797. [PMID: 37290208 DOI: 10.1016/j.vetmic.2023.109797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/02/2023] [Indexed: 06/10/2023]
Abstract
Strangles is a contagious bacterial disease of horses caused by Streptococcus equi subspecies equi (SEE) that occurs globally. Rapid and accurate identification of infected horses is essential for controlling strangles. Because of limitations of existing PCR assays for SEE, we sought to identify novel primers and probes that enable simultaneous detection and differentiation of infection with SEE and S. equi subsp. zooepidemicus (SEZ). Comparative genomics of U.S. strains of SEE and SEZ (n = 50 each) identified SE00768 from SEE and comB from SEZ as target genes. Primers and probes for real-time PCR (rtPCR) were designed for these genes and then aligned in silico with the genomes of strains of SEE (n = 725) and SEZ (n = 343). Additionally, the sensitivity and specificity relative to microbiologic culture were compared between 85 samples submitted to an accredited veterinary medical diagnostic laboratory. The respective primer and probe sets aligned with 99.7 % (723/725) isolates of SEE and 97.1 % (333/343) of SEZ. Of 85 diagnostic samples, 20 of 21 (95.2 %) SEE and 22 of 23 SEZ (95.6 %) culture-positive samples were positive by rtPCR for SEE and SEZ, respectively. Both SEE (n = 2) and SEZ (n = 3) were identified by rtPCR among 32 culture-negative samples. Results were rtPCR-positive for both SEE and SEZ in 21 of 44 (47.7 %) samples that were culture-positive for SEE or SEZ. The primers and probe sets reported here reliably detect SEE and SEZ from Europe and the U.S., and permit detection of concurrent infection with both subspecies.
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Affiliation(s)
- Ellen Ruth A Morris
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Megan E Schroeder
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Pamela J Ferro
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA.
| | - Andrew S Waller
- Intervacc AB, Hägersten, Sweden; Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Abigail A McGlennon
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, Hatfield, United Kingdom
| | - Carla P Bustos
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Leticia T Gressler
- Laboratório de Microbiologia e Imunologia Veterinária, Medicina Veterinária, Instituto Federal Farroupilha (IFFar), Frederico Westphalen, Rio Grande do Sul, Brazil
| | - Jing Wu
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Sara D Lawhon
- Department of Veterinary Pathobiology, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Ashley G Boyle
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, USA
| | - Sonia Lingsweiler
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Narayan Paul
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Kiril Dimitrov
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Amy K Swinford
- Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, TX, USA
| | - Angela I Bordin
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, School of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA.
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Huang J, Dai X, Wu Z, Hu X, Sun J, Tang Y, Zhang W, Han P, Zhao J, Liu G, Wang X, Mao S, Wang Y, Call DR, Liu J, Wang L. Conjugative transfer of streptococcal prophages harboring antibiotic resistance and virulence genes. ISME J 2023; 17:1467-1481. [PMID: 37369704 PMCID: PMC10432423 DOI: 10.1038/s41396-023-01463-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 06/06/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023]
Abstract
Prophages play important roles in the transduction of various functional traits, including virulence factors, but remain debatable in harboring and transmitting antimicrobial resistance genes (ARGs). Herein we characterize a prevalent family of prophages in Streptococcus, designated SMphages, which harbor twenty-five ARGs that collectively confer resistance to ten antimicrobial classes, including vanG-type vancomycin resistance locus and oxazolidinone resistance gene optrA. SMphages integrate into four chromosome attachment sites by utilizing three types of integration modules and undergo excision in response to phage induction. Moreover, we characterize four subtypes of Alp-related surface proteins within SMphages, the lethal effects of which are extensively validated in cell and animal models. SMphages transfer via high-frequency conjugation that is facilitated by integrative and conjugative elements from either donors or recipients. Our findings explain the widespread of SMphages and the rapid dissemination of ARGs observed in members of the Streptococcus genus.
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Affiliation(s)
- Jinhu Huang
- 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
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yijun Tang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wanqiu Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peizhao Han
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaqi Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangjin Liu
- Key Lab of Animal Bacteriology, Ministry of Agriculture, OIE Reference Lab for Swine Streptococcosis, 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
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Douglas R Call
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA, 99164, USA
| | - Jinxin Liu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, 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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Rothman JA, Riis JL, Hamilton KR, Blair C, Granger DA, Whiteson KL. Oral microbial communities in children, caregivers, and associations with salivary biomeasures and environmental tobacco smoke exposure. mSystems 2023; 8:e0003623. [PMID: 37338237 PMCID: PMC10470043 DOI: 10.1128/msystems.00036-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/19/2023] [Indexed: 06/21/2023] Open
Abstract
Human oral microbial communities are diverse, with implications for oral and systemic health. Oral microbial communities change over time; thus, it is important to understand how healthy versus dysbiotic oral microbiomes differ, especially within and between families. There is also a need to understand how the oral microbiome composition is changed within an individual including by factors such as environmental tobacco smoke (ETS) exposure, metabolic regulation, inflammation, and antioxidant potential. Using archived saliva samples collected from caregivers and children during a 90-month follow-up assessment in a longitudinal study of child development in the context of rural poverty, we used 16S rRNA gene sequencing to determine the salivary microbiome. A total of 724 saliva samples were available, 448 of which were from caregiver/child dyads, an additional 70 from children and 206 from adults. We compared children's and caregivers' oral microbiomes, performed "stomatotype" analyses, and examined microbial relations with concentrations of salivary markers associated with ETS exposure, metabolic regulation, inflammation, and antioxidant potential (i.e., salivary cotinine, adiponectin, C-reactive protein, and uric acid) assayed from the same biospecimens. Our results indicate that children and caregivers share much of their oral microbiome diversity, but there are distinct differences. Microbiomes from intrafamily individuals are more similar than microbiomes from nonfamily individuals, with child/caregiver dyad explaining 52% of overall microbial variation. Notably, children harbor fewer potential pathogens than caregivers, and participants' microbiomes clustered into two groups, with major differences being driven by Streptococcus spp. Differences in salivary microbiome composition associated with ETS exposure, and taxa associated with salivary analytes representing potential associations between antioxidant potential, metabolic regulation, and the oral microbiome. IMPORTANCE The human oral cavity is a multi-environment habitat that harbors a diversity of microorganisms. This oral microbiome is often transmitted between cohabitating individuals, which may associate oral and systemic health within family members. Furthermore, family social ecology plays a significant role in childhood development, which may be associated with lifelong health outcomes. In this study, we collected saliva from children and their caregivers and used 16S rRNA gene sequencing to characterize their oral microbiomes. We also analyzed salivary biomeasures of environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. We show there are differences in individuals' oral microbiomes mainly due to Streptococcus spp. that family members share much of their microbes, and several bacterial taxa associate with the selected salivary biomeasures. Our results suggest there are large-scale oral microbiome patterns, and there are likely relationships between oral microbiomes and the social ecology of families.
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Affiliation(s)
- Jason A. Rothman
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
| | - Jenna L. Riis
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Psychological Science, University of California, Irvine, California, USA
| | - Katrina R. Hamilton
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Clancy Blair
- Department of Population Health, New York University, New York, New York, USA
- Department of Applied Psychology, New York University, New York, New York, USA
| | - Douglas A. Granger
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
- Department of Acute and Chronic Care, Johns Hopkins University School of Nursing, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Salivary Bioscience Laboratory, University of Nebraska, Lincoln, Nebraska, USA
- Department of Psychology, University of Nebraska, Lincoln, Nebraska, USA
| | - Katrine L. Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, USA
- Institute for Interdisciplinary Salivary Bioscience Research, University of California, Irvine, California, USA
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Volokhov DV, Zagorodnyaya TA, Furtak VA, Nattanmai G, Randall L, Jose S, Gao Y, Eisenberg T, Delmonte P, Blom J, Mitchell KK. Streptococcus sciuri sp. nov., Staphylococcus marylandisciuri sp. nov. and Staphylococcus americanisciuri sp. nov., isolated from faeces of eastern grey squirrel ( Sciurus carolinensis). Int J Syst Evol Microbiol 2023; 73. [PMID: 37578899 DOI: 10.1099/ijsem.0.006015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
One novel Streptococcus strain (SQ9-PEAT) and two novel Staphylococcus strains (SQ8-PEAT and GRT3T) were isolated from faeces of a wild eastern grey squirrel. The strains were non-spore-forming, non-motile Gram-positive cocci, facultative anaerobes. The genomes for these strains were sequenced. The 16S rRNA gene and core-genome-based phylogenetic analyses showed that strain SQ9-PEAT was closely related to Streptococcus hyointestinalis, strain SQ8-PEAT to Staphylococcus pettenkoferi and Staphylococcus argensis, and strain GRT3T to Staphylococcus rostri, Staphylococcus muscae and Staphylococcus microti. Average nucleotide identity and pairwise digital DNA-DNA hybridization values calculated for these novel strains compared to type strain genomes of phylogenetically related species within the genera Streptococcus and Staphylococcus clearly revealed that strain SQ9-PEAT represents a novel species of the genus Streptococcus and strains SQ8-PEAT and GRT3T represent two novel species of the genus Staphylococcus. Phenotypical features of these novel type strains differed from the features of the type strains of other phylogenetically related species. MALDI-TOF mass spectrometry supported identification of these novel species. Based on these data, we propose one novel species of the genus Streptococcus, for which the name Streptococcus sciuri sp. nov. with the type strain SQ9-PEAT (=DSM 114656T=CCUG 76426T=NCTC 14727T) is proposed, and two novel species of the genus Staphylococcus, for which the names Staphylococcus marylandisciuri sp. nov. with the type strain SQ8-PEAT (=DSM 114685T=CCUG 76423T=NCTC 14723T) and Staphylococcus americanisciuri sp. nov. with the type strain GRT3T (=DSM 114696T=CCUG 76427T=NCTC 14722T) are proposed. The genome G+C contents are 38.29, 36.49 and 37.26 mol% and complete draft genome sizes are 1 692 266, 2 371 088 and 2 237 001 bp for strains SQ9-PEAT, SQ8-PEAT and GRT3T, respectively.
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Affiliation(s)
- Dmitriy V Volokhov
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tatiana A Zagorodnyaya
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Vyacheslav A Furtak
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Geetha Nattanmai
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Linnell Randall
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Sherly Jose
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Yamei Gao
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Department of Veterinary Medicine, Schubertstrasse 60, 35392 Giessen, Germany
| | - Pierluigi Delmonte
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 5001 Campus Drive, College Park, MD 20740, USA
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Heinrich Buff Ring 58, 35392 Giessen, Germany
| | - Kara K Mitchell
- Bacteriology Laboratory, Wadsworth Center, the New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
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Rued BE, Federle MJ. The ComRS-SigX Pathway Regulates Natural Transformation in Streptococcus ferus. J Bacteriol 2023; 205:e0008923. [PMID: 37195233 PMCID: PMC10294618 DOI: 10.1128/jb.00089-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/27/2023] [Indexed: 05/18/2023] Open
Abstract
The ability to take up and incorporate foreign DNA via natural transformation is a well-known characteristic of some species of Streptococcus, and is a mechanism that rapidly allows for the acquisition of antibacterial resistance. Here, we describe that the understudied species Streptococcus ferus is also capable of natural transformation and uses a system analogous to that identified in Streptococcus mutans. S. mutans natural transformation is under the control of the alternative sigma factor sigX (also known as comX), whose expression is induced by two types of peptide signals: CSP (competence stimulating peptide, encoded by comC) and XIP (sigX-inducing peptide, encoded by comS). These systems induce competence via either the two-component signal-transduction system ComDE or the RRNPP transcriptional regulator ComR, respectively. Protein and nucleotide homology searches identified putative orthologs of comRS and sigX in S. ferus, but not homologs of S. mutans blpRH (also known as comDE). We demonstrate that natural transformation in S. ferus is induced by a small, double-tryptophan containing sigX-inducing peptide (XIP), akin to that of S. mutans, and requires the presence of the comR and sigX orthologs for efficient transformation. Additionally, we find that natural transformation is induced in S. ferus by both the native XIP and the XIP variant of S. mutans, implying that cross talk between the two species is possible. This process has been harnessed to construct gene deletions in S. ferus and provides a method to genetically manipulate this understudied species. IMPORTANCE Natural transformation is the process by which bacteria take up DNA and allows for acquisition of new genetic traits, including those involved in antibiotic resistance. This study demonstrates that the understudied species Streptococcus ferus is capable of natural transformation using a peptide-pheromone system like that previously identified in Streptococcus mutans and provides a framework for future studies concerning this organism.
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Affiliation(s)
- Britta E. Rued
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Michael J. Federle
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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Wei Y, Sturges CI, Palmer KL. Human Serum Supplementation Promotes Streptococcus mitis Growth and Induces Specific Transcriptomic Responses. Microbiol Spectr 2023; 11:e0512922. [PMID: 37014220 PMCID: PMC10269507 DOI: 10.1128/spectrum.05129-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/01/2023] [Indexed: 04/05/2023] Open
Abstract
Streptococcus mitis is a normal member of the human oral microbiota and a leading opportunistic pathogen causing infective endocarditis (IE). Despite the complex interactions between S. mitis and the human host, understanding of S. mitis physiology and its mechanisms of adaptation to host-associated environments is inadequate, especially compared with other IE bacterial pathogens. This study reports the growth-promoting effects of human serum on S. mitis and other pathogenic streptococci, including S. oralis, S. pneumoniae, and S. agalactiae. Using transcriptomic analyses, we identified that, with the addition of human serum, S. mitis downregulates uptake systems for metal ions and sugars, fatty acid biosynthetic genes, and genes involved in stress response and other processes related with growth and replication. S. mitis upregulates uptake systems for amino acids and short peptides in response to human serum. Zinc availability and environmental signals sensed by the induced short peptide binding proteins were not sufficient to confer the growth-promoting effects. More investigation is required to establish the mechanism for growth promotion. Overall, our study contributes to the fundamental understanding of S. mitis physiology under host-associated conditions. IMPORTANCE S. mitis is exposed to human serum components during commensalism in the human mouth and bloodstream pathogenesis. However, the physiological effects of serum components on this bacterium remain unclear. Using transcriptomic analyses, S. mitis biological processes that respond to the presence of human serum were revealed, improving the fundamental understanding of S. mitis physiology in human host conditions.
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Affiliation(s)
- Yahan Wei
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Camille I. Sturges
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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Gopalakrishna KP, Hillebrand GH, Bhavana VH, Elder JL, D'Mello A, Tettelin H, Hooven TA. Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects. Commun Biol 2023; 6:620. [PMID: 37296208 PMCID: PMC10256743 DOI: 10.1038/s42003-023-04994-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Group B Streptococcus (GBS; S. agalactiae) causes chorioamnionitis, neonatal sepsis, and can also cause disease in healthy or immunocompromised adults. GBS possesses a type II-A CRISPR-Cas9 system, which defends against foreign DNA within the bacterial cell. Several recent publications have shown that GBS Cas9 influences genome-wide transcription through a mechanism uncoupled from its function as a specific, RNA-programmable endonuclease. We examine GBS Cas9 effects on genome-wide transcription through generation of several isogenic variants with specific functional defects. We compare whole-genome RNA-seq from Δcas9 GBS with a full-length Cas9 gene deletion; dcas9 defective in its ability to cleave DNA but still able to bind to frequently occurring protospacer adjacent motifs; and scas9 that retains its catalytic domains but is unable to bind protospacer adjacent motifs. Comparing scas9 GBS to the other variants, we identify nonspecific protospacer adjacent motif binding as a driver of genome-wide, Cas9 transcriptional effects in GBS. We also show that Cas9 transcriptional effects from nonspecific scanning tend to influence genes involved in bacterial defense and nucleotide or carbohydrate transport and metabolism. While genome-wide transcription effects are detectable by analysis of next-generation sequencing, they do not result in virulence changes in a mouse model of sepsis. We also demonstrate that catalytically inactive dCas9 expressed from the GBS chromosome can be used with a straightforward, plasmid-based, single guide RNA expression system to suppress transcription of specific GBS genes without potentially confounding off-target effects. We anticipate that this system will be useful for study of nonessential and essential gene roles in GBS physiology and pathogenesis.
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Affiliation(s)
| | - Gideon H Hillebrand
- University of Pittsburgh School of Medicine, Program in Microbiology and Immunology, Pittsburgh, PA, USA
| | - Venkata H Bhavana
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA
| | - Jordan L Elder
- The Cleveland Clinic, Clinical Laboratory Services, Cleveland, OH, USA
| | - Adonis D'Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Thomas A Hooven
- University of Pittsburgh School of Medicine, Department of Pediatrics, Pittsburgh, PA, USA.
- Richard King Mellon Institute for Pediatric Research, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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Cao Y, Chen X, Shu L, Shi L, Wu M, Wang X, Deng K, Wei J, Yan J, Feng G. Analysis of the correlation between BMI and respiratory tract microbiota in acute exacerbation of COPD. Front Cell Infect Microbiol 2023; 13:1161203. [PMID: 37180432 PMCID: PMC10166817 DOI: 10.3389/fcimb.2023.1161203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Objective To investigate the distribution differences in the respiratory tract microbiota of AECOPD patients in different BMI groups and explore its guiding value for treatment. Methods Sputum samples of thirty-eight AECOPD patients were collected. The patients were divided into low, normal and high BMI group. The sputum microbiota was sequenced by 16S rRNA detection technology, and the distribution of sputum microbiota was compared. Rarefaction curve, α-diversity, principal coordinate analysis (PCoA) and measurement of sputum microbiota abundance in each group were performed and analyzed by bioinformatics methods. Results 1. The rarefaction curve in each BMI group reached a plateau. No significant differences were observed in the OTU total number or α-diversity index of microbiota in each group. PCoA showed significant differences in the distance matrix of sputum microbiota between the three groups, which was calculated by the Binary Jaccard and the Bray Curtis algorithm. 2. At the phylum level, most of the microbiota were Proteobacteria, Bacteroidetes Firmicutes, Actinobacteria, and Fusobacteria. At the genus level, most were Streptococcus, Prevotella, Haemophilus, Neisseria and Bacteroides. 3. At the phylum level, the abundance of Proteobacteria in the low group was significantly higher than that in normal and high BMI groups, the abundances of Firmicutes in the low and normal groups were significantly lower than that in high BMI groups. At the genus level, the abundance of Haemophilus in the low group was significantly higher than that in high BMI group, and the abundances of Streptococcus in the low and normal BMI groups were significantly lower than that in the high BMI group. Conclusions 1. The sputum microbiota of AECOPD patients in different BMI groups covered almost all microbiota, and BMI had no significant association with total number of respiratory tract microbiota or α-diversity in AECOPD patients. However, there was a significant difference in the PCoA between different BMI groups. 2. The microbiota structure of AECOPD patients differed in different BMI groups. Gram-negative bacteria (G-) in the respiratory tract of patients predominated in the low BMI group, while gram-positive bacteria (G+) predominated in the high BMI group.
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Affiliation(s)
- Yang Cao
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaolin Chen
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Shi
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mingjing Wu
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xueli Wang
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kaili Deng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wei
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiaxin Yan
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ganzhu Feng
- Department of Respiratory Medicine, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Respiratory Medicine, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Prasad A, Ene A, Jablonska S, Du J, Wolfe AJ, Putonti C. Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains. mSphere 2023; 8:e0068722. [PMID: 36744899 PMCID: PMC10117062 DOI: 10.1128/msphere.00687-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.
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Affiliation(s)
- Ananya Prasad
- School of Biological Sciences, University of California San Diego, San Diego, California, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Sandra Jablonska
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Jingjie Du
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
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Joyce LR, Youngblom MA, Cormaty H, Gartstein E, Barber KE, Akins RL, Pepperell CS, Palmer KL. Comparative Genomics of Streptococcus oralis Identifies Large Scale Homologous Recombination and a Genetic Variant Associated with Infection. mSphere 2022; 7:e0050922. [PMID: 36321824 PMCID: PMC9769543 DOI: 10.1128/msphere.00509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The viridans group streptococci (VGS) are a large consortium of commensal streptococci that colonize the human body. Many species within this group are opportunistic pathogens causing bacteremia and infective endocarditis (IE), yet little is known about why some strains cause invasive disease. Identification of virulence determinants is complicated by the difficulty of distinguishing between the closely related species of this group. Here, we analyzed genomic data from VGS that were isolated from blood cultures in patients with invasive infections and oral swabs of healthy volunteers and then determined the best-performing methods for species identification. Using whole-genome sequence data, we characterized the population structure of a diverse sample of Streptococcus oralis isolates and found evidence of frequent recombination. We used multiple genome-wide association study tools to identify candidate determinants of invasiveness. These tools gave consistent results, leading to the discovery of a single synonymous single nucleotide polymorphism (SNP) that was significantly associated with invasiveness. This SNP was within a previously undescribed gene that was conserved across the majority of VGS species. Using the growth in the presence of human serum and a simulated infective endocarditis vegetation model, we were unable to identify a phenotype for the enriched allele in laboratory assays, suggesting a phenotype may be specific to natural infection. These data highlighted the power of analyzing natural populations for gaining insight into pathogenicity, particularly for organisms with complex population structures like the VGS. IMPORTANCE The viridians group streptococci (VGS) are a large collection of closely related commensal streptococci, with many being opportunistic pathogens causing invasive diseases, such as bacteremia and infective endocarditis. Little is known about virulence determinants in these species, and there is a distinct lack of genomic information available for the VGS. In this study, we collected VGS isolates from invasive infections and healthy volunteers and performed whole-genome sequencing for a suite of downstream analyses. We focused on a diverse sample of Streptococcus oralis genomes and identified high rates of recombination in the population as well as a single genome variant highly enriched in invasive isolates. The variant lies within a previously uncharacterized gene, nrdM, which shared homology with the anaerobic ribonucleoside triphosphate reductase, nrdD, and was highly conserved among VGS. This work increased our knowledge of VGS genomics and indicated that differences in virulence potential among S. oralis isolates were, at least in part, genetically determined.
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Affiliation(s)
- Luke R. Joyce
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Madison A. Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Harshini Cormaty
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Evelyn Gartstein
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Katie E. Barber
- Department of Pharmacy Practice, University of Mississippi School of Pharmacy, University of Mississippi, Jackson, Mississippi, USA
| | | | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kelli L. Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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Ma M, Su J, Wang Y, Wang L, Li Y, Ding G, Ma Z, Peppelenbosch MP. Association of body mass index and intestinal (faecal) Streptococcus in adults in Xining city, China P.R. Benef Microbes 2022; 13:465-472. [PMID: 36264094 DOI: 10.3920/bm2021.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Body mass index (BMI) and gut microbiota show significant interaction, but most studies on the relationship between BMI and gut microbiota have been done in Western countries. Relationships that are also identified in other cultural backgrounds are likely to have functional importance. Hence here we explore gut microbiota in adults living in Xining city (China P.R.) and relate results to subject BMI. Analysis of bacterial 16s rRNA gene was performed on faecal samples from participants with normal-weight (n=24), overweight (n=24), obesity (n=11) and type 2 diabetes (T2D) (n=8). The results show that unweighted but not weighted Unifrac distance was significantly different when gut microbiota composition was compared between the groups. Importantly, the genus Streptococcus was remarkably decreased in both obese subjects and subjects suffering from T2D, as compared to normal-weight subjects. Accordingly, strong association was identified between the genus Streptococcus and BMI and especially Streptococcus salivarius subsp. thermophiles was a major contributor in this respect. As previous studies have shown that Streptococcus salivarius subsp. thermophiles is also negatively associated with obesity in Western cohorts, our results suggest that this species is a potential probiotic for the prevention of obesity and related disorders.
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Affiliation(s)
- M Ma
- Department of endocrinology, the Fifth People's Hospital of Qinghai Province (Qinghai Tumor Hospital), Xining, China P.R
| | - J Su
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Basic Medicine, Medical School, Kunming University of Science and Technology, Kunming, 650500, China P.R
| | - Y Wang
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China P.R
| | - L Wang
- Department of endocrinology, the Fifth People's Hospital of Qinghai Province (Qinghai Tumor Hospital), Xining, China P.R
| | - Y Li
- Department of endocrinology, the Fifth People's Hospital of Qinghai Province (Qinghai Tumor Hospital), Xining, China P.R
| | - G Ding
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China P.R
| | - Z Ma
- China-Malaysia National Joint Laboratory, Biomedical Research Center, Northwest Minzu University, Lanzhou, 730030, China P.R
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, P.O. Box 2040, 3000 CA, Rotterdam, the Netherlands
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McLean AR, Torres-Morales J, Dewhirst FE, Borisy GG, Welch JLM. Site-tropism of streptococci in the oral microbiome. Mol Oral Microbiol 2022; 37:229-243. [PMID: 36073311 PMCID: PMC9691528 DOI: 10.1111/omi.12387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.
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Affiliation(s)
- Anthony R. McLean
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
| | | | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA 02142
- Harvard School of Dental Medicine, Boston, MA 02115
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
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Clara L, David C, Laila S, Virginie R, Marie-Joelle V. Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in S. lividans and S. coelicolor Suggests a Link between Various Stresses and Antibiotic Production. Int J Mol Sci 2022; 23:ijms232314792. [PMID: 36499130 PMCID: PMC9739823 DOI: 10.3390/ijms232314792] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Streptomyces coelicolor and Streptomyces lividans constitute model strains to study the regulation of antibiotics biosynthesis in Streptomyces species since these closely related strains possess the same pathways directing the biosynthesis of various antibiotics but only S. coelicolor produces them. To get a better understanding of the origin of the contrasted abilities of these strains to produce bioactive specialized metabolites, these strains were grown in conditions of phosphate limitation or proficiency and a comparative analysis of their transcriptional/regulatory proteins was carried out. The abundance of the vast majority of the 355 proteins detected greatly differed between these two strains and responded differently to phosphate availability. This study confirmed, consistently with previous studies, that S. coelicolor suffers from nitrogen stress. This stress likely triggers the degradation of the nitrogen-rich peptidoglycan cell wall in order to recycle nitrogen present in its constituents, resulting in cell wall stress. When an altered cell wall is unable to fulfill its osmo-protective function, the bacteria also suffer from osmotic stress. This study thus revealed that these three stresses are intimately linked in S. coelicolor. The aggravation of these stresses leading to an increase of antibiotic biosynthesis, the connection between these stresses, and antibiotic production are discussed.
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Affiliation(s)
- Lejeune Clara
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Cornu David
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Sago Laila
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Redeker Virginie
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Laboratory of Neurodegenerative Diseases, Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA) and Centre National de la Recherche Scientifique (CNRS), Molecular Imaging Center (MIRCen), Institut François Jacob, Université Paris-Saclay, 92260 Fontenay-aux-Roses, France
| | - Virolle Marie-Joelle
- Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, Group “Energetic Metabolism of Streptomyces”, CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
- Correspondence:
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Brito LPDE, Santos DS, Freitas NSADE, Medeiros RSDE, Souza PREDE, Soares MTCV, Porto ALF. In silico evaluation of genomic characteristics of Streptococcus infantarius subsp. infantarius for application in fermentations. AN ACAD BRAS CIENC 2022; 94:e20211447. [PMID: 36417612 DOI: 10.1590/0001-3765202220211447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/25/2022] [Indexed: 06/16/2023] Open
Abstract
This study aims to evaluate the in silico genomic characteristics of Streptococcus infantarius subsp. infantarius, isolated from Coalho cheese from Paraíba, Brazil, with a view to application in lactic fermentations. rRNA sequences from the 16S ribosomal region were used as input to GenBank, in the search for patterns that could reveal a non-pathogenic behavior of S. infantarius subsp. infantarius, comparing mobile genetic elements, antibiotic resistance genes, pan-genome analysis and multi-genome alignment among related species. S. infantarius subsp. infantarius CJ18 was the only complete genome reported by BLAST/NCBI with high similarity and after comparative genetics with complete genomes of Streptococcus agalactiae (SAG153, NJ1606) and Streptococcus thermophilus (ST106, CS18, IDCC2201, APC151) revealed that CJ18 showed a low number of transposases and integrases, infection by phage bacteria of the Streptococcus genus, absence of antibiotic resistance genes and presence of bacteriocin, folate and riboflavin producing genes. The genome alignment revealed that the collinear blocks of S. thermophilus ST106 and S. agalactiae SAG153 have inverted blocks when compared to the CJ18 genome due to gene positioning, insertions and deletions. Therefore, the strains of S. infantarius subsp. infantarius isolated from Coalho cheese from Paraíba showed genomic similarity with CJ18 and the mobility of genes analyzed in silico showed absence of pathogenicity throughout the genome of CJ18, indicating the potential of these strains for the dairy industry.
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Affiliation(s)
- Leandro P DE Brito
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal de Pernambuco, Centro de Biociências, Av. Professor Moraes Rego, 1235, 50670-901, Recife, PE, Brazil
| | - Dayane S Santos
- Universidade Federal de Pernambuco, Departamento de Genética, Av. Professor Moraes Rego, 1235, 50670-901 Recife, PE, Brazil
| | - Nara Suzy A DE Freitas
- Universidade Federal Rural de Pernambuco, Departamento de Biologia, Rua Dom Manoel de Medeiros, s/n, 52171-900 Recife, PE, Brazil
| | - Rosália S DE Medeiros
- Universidade Federal de Campina Grande, Unidade Acadêmica de Ciências Biológicas, Av. Universitária, s/n, 58708-110 Patos, PB, Brazil
| | - Paulo Roberto E DE Souza
- Universidade Federal Rural de Pernambuco, Departamento de Biologia, Rua Dom Manoel de Medeiros, s/n, 52171-900 Recife, PE, Brazil
| | - Maria Taciana C V Soares
- Universidade Federal Rural de Pernambuco, Departamento de Morfologia e Fisiologia Animal, Rua Dom Manoel de Medeiros, s/n, 52171-900 Recife, PE, Brazil
| | - Ana Lúcia F Porto
- Universidade Federal Rural de Pernambuco, Departamento de Morfologia e Fisiologia Animal, Rua Dom Manoel de Medeiros, s/n, 52171-900 Recife, PE, Brazil
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Li X, Wang Y, Jiang X, Zeng Y, Zhao X, Washio J, Takahashi N, Zhang L. Investigation of drug resistance of caries-related streptococci to antimicrobial peptide GH12. Front Cell Infect Microbiol 2022; 12:991938. [PMID: 36159653 PMCID: PMC9492880 DOI: 10.3389/fcimb.2022.991938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Dental caries is associated with caries-related streptococci and antimicrobial agents have been widely used for caries control, but troubled by antibiotic resistance. This study aimed to investigate the intrinsic and acquired resistance of caries-related streptococci to antimicrobial peptide GH12, which was proven promising for caries control, and preliminarily explore the phenotypic changes and whole genome of stable acquired resistant strains. In this study, susceptibility assays and resistance assays were performed, followed by stability assays of resistance, to evaluate the intrinsic resistance and the potential resistance of caries-related streptococci. Then, the phenotypic changes of the stable acquired resistant strain were explored. The whole genome of the resistant strain was sequenced and analyzed by second-generation and third-generation high-throughput sequencing technologies. Streptococcus gordonii and Streptococcus sanguinis were intrinsically resistant to GH12 compared to cariogenic Streptococcus mutans. Acquired GH12 resistance in one S. sanguinis and four S. mutans clinical strains was transient but stable in one S. mutans strain (COCC33-14). However, acquired resistance to daptomycin (DAP) and chlorhexidine in all strains was stable. Furthermore, the COCC33-14 showed cross-resistance to DAP and delayed growth rates and a lower population. However, no drug-resistant gene mutation was detected in this strain, but 6 new and 5 missing genes were found. Among them, annotation of one new gene (gene 1782|COCC33-14R) is related to the integral component of the membrane, and one missing gene rpsN is associated with the metabolism and growth of bacteria. The results indicate that stable resistant mutants of caries-related streptococci could hardly be selected by exposure to consecutive sublethal GH12, but the risk still existed. Resistance in COCC33-14R is mainly related to changes in the cell envelope.
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Affiliation(s)
- Xinwei Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Stomatology, Chengdu Second People’s Hospital, Chengdu, China
| | - Yufei Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuelian Jiang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuhao Zeng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xinran Zhao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumpei Washio
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Linglin Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Disease, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- *Correspondence: Linglin Zhang,
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Trabelsi I, Soltane R, Nejma MB, Albogami BM, Nour M. Genetic variability of the helix 54 of the 23S rDNA and its use as a molecular target for identification of species within the viridans group streptococci (VGS). Infect Genet Evol 2022; 103:105321. [PMID: 35753621 DOI: 10.1016/j.meegid.2022.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The aim of the present study is to establish a method, based on sequence analysis of the helix 54 of 23S rRNA gene, to identify clinical relevant strains belonging to viridans group streptococci (VGS). A set of 25 randomly selected clinical isolates of alpha-hemolytic streptococci from upper respiratory tract were characterized by the routine phenotypic methods (API 20 Strep test). Molecular characterization was assessed by genotypic analysis of the nucleotide sequence of the helix 54 of 23S rRNA and Intergenic spacer region 16S23S. Partial sequencing of the gdh gene was used on 10 strains of mitis group. Sequence variations of the helix 54 allowed the identification of strains to group level and even to species level for certain strains within sanguinis and anginosus groups. Infact, species identification was ambiguous for some strains belonged to the salivarius group (of VGS16 to VGS20) and the mitis group (of VGS1 to VGS14). These results are almost similar to those obtained by sequencing the 16S23S intergenic region. Thus, we use the gdh gene sequencing for the identification of strains, not recognized, within the mitis group. The results generated herein indicate that no single methodology can be used to provide an accurate identification to the species level of all VGS, although nucleotide sequence analysis of the helix 54 of 23S rRNA gene proved to be a reliable method for the identification of VGS to the group level and even to the species level within sanguinis and anginosus groups.
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Affiliation(s)
- Ines Trabelsi
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia.
| | - Raya Soltane
- Departement of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Departement of Biology, Faculty of sciences, Tunis El Manar University, Tunis 1068, Tunisia.
| | - Mouna Ben Nejma
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
| | - Bander M Albogami
- Taif University, College of Science, Laboratory of Applied and Molecular Microbiology, Saudi Arabia
| | - Mohamed Nour
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
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Estévez A, Marín M, Sánchez-Carrillo C, Machado M, Alcalá L, Pinilla B, Delgado A, González-Ramallo V, Pedraz Á, Martínez-Sellés M, Bouza E, Valerio M, Muñoz P, Game-Hgugm OBO. Abiotrophia spp. and Granulicatella spp. Infective Endocarditis: A Contemporary Perspective. Front Biosci (Elite Ed) 2022; 14:23. [PMID: 36137991 DOI: 10.31083/j.fbe1403023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/06/2022] [Accepted: 07/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Abiotrophia spp. and Granulicatella spp. are Gram-positive cocci, formerly known as nutritionally variant or deficient Streptococcus. Their role as causative agents of infective endocarditis (IE) is numerically uncertain, as well as diagnostic and clinical management of this infection. The aim of our study is to describe the clinical, microbiological, therapeutic, and prognosis of patients with IE caused by these microorganisms in a large microbiology department. METHODS Retrospective analysis of all the patients with Abiotrophia spp. and Granulicatella spp. IE registered in our centre in the period 2004-2021. RESULTS Of the 822 IE in the study period, 10 (1.2%) were caused by Abiotrophia spp. (7) or Granulicatella spp. (3). The species involved were A.defectiva (7), G.adiacens (2) and G.elegans (1). Eight patients were male, their mean age was 46 years and four were younger than 21 years. The most frequent comorbidities were congenital heart disease (4; 40%) and the presence of intracardiac prosthetic material (5; 50%). IE occurred on 5 native valves and 5 prosthetic valve or material. Blood cultures were positive in 8/10 patients, within a mean incubation period of 18.07 hours. In the other two patients, a positive 16SPCR from valve or prosthetic material provided the diagnosis. Surgery for IE was performed in seven patients (70%) and in all cases positive 16S rRNA PCR and sequencing from valve or prosthetic material was demonstrated. Valves and/or prosthetic removed material cultures were positive in four patients. Nine patients received ceftriaxone (4 in monotherapy and 5 in combination with other antibiotics). The mean length of treatment was 6 weeks and IE-associated mortality was 20% at one year follow-up. CONCLUSIONS Abiotrophia spp. or Granulicatella spp. IE were infrequent but not exceptional in our environment and particularly affected patients with congenital heart disease or prosthetic material. Blood cultures and molecular methods allowed the diagnosis. Most of them required surgery and the associated mortality, in spite of a mean age of 46 years, was high.
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Affiliation(s)
- Agustín Estévez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
| | - Marina Machado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
| | - Luís Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
| | - Blanca Pinilla
- Internal Medicine Department, HGUGM, 28007 Madrid, Spain
| | - Antonia Delgado
- Cardiology Department, HGUGM, 28007 Madrid, Spain
- CIBER Enfermedades Cardiovasculares-CIBERCV, 28029 Madrid, Spain
| | | | - Álvaro Pedraz
- Cardiac Surgery Department, HGUGM, 28007 Madrid, Spain
| | - Manuel Martínez-Sellés
- Cardiology Department, HGUGM, 28007 Madrid, Spain
- CIBER Enfermedades Cardiovasculares-CIBERCV, 28029 Madrid, Spain
- Universidad Europea de Madrid, Universidad Complutense de Madrid, 28670-28040 Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Maricela Valerio
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón (HGUGM), 28007 Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, 28007 Madrid, Spain
- Medicine Department, Faculty of Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias-CIBERES (CB06/06/0058), 28029 Madrid, Spain
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Chowdhury ZM, Bhattacharjee A, Ahammad I, Hossain MU, Jaber AA, Rahman A, Dev PC, Salimullah M, Keya CA. Exploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae. PLoS One 2022; 17:e0272945. [PMID: 35980906 PMCID: PMC9387852 DOI: 10.1371/journal.pone.0272945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae (S. pneumoniae), the major etiological agent of community-acquired pneumonia (CAP) contributes significantly to the global burden of infectious diseases which is getting resistant day by day. Nearly 30% of the S. pneumoniae genomes encode hypothetical proteins (HPs), and better understandings of these HPs in virulence and pathogenicity plausibly decipher new treatments. Some of the HPs are present across many Streptococcus species, systematic assessment of these unexplored HPs will disclose prospective drug targets. In this study, through a stringent bioinformatics analysis of the core genome and proteome of S. pneumoniae PCS8235, we identified and analyzed 28 HPs that are common in many Streptococcus species and might have a potential role in the virulence or pathogenesis of the bacteria. Functional annotations of the proteins were conducted based on the physicochemical properties, subcellular localization, virulence prediction, protein-protein interactions, and identification of essential genes, to find potentially druggable proteins among 28 HPs. The majority of the HPs are involved in bacterial transcription and translation. Besides, some of them were homologs of enzymes, binding proteins, transporters, and regulators. Protein-protein interactions revealed HP PCS8235_RS05845 made the highest interactions with other HPs and also has TRP structural motif along with virulent and pathogenic properties indicating it has critical cellular functions and might go under unconventional protein secretions. The second highest interacting protein HP PCS8235_RS02595 interacts with the Regulator of chromosomal segregation (RocS) which participates in chromosome segregation and nucleoid protection in S. pneumoniae. In this interacting network, 54% of protein members have virulent properties and 40% contain pathogenic properties. Among them, most of these proteins circulate in the cytoplasmic area and have hydrophilic properties. Finally, molecular docking and dynamics simulation demonstrated that the antimalarial drug Artenimol can act as a drug repurposing candidate against HP PCS8235_RS 04650 of S. pneumoniae. Hence, the present study could aid in drugs against S. pneumoniae.
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Affiliation(s)
| | | | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Abdullah All Jaber
- Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
| | - Anisur Rahman
- Bioinformatics Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | | | - Md. Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology, Dhaka, Bangladesh
| | - Chaman Ara Keya
- Department of Biochemistry & Microbiology, North South University, Dhaka, Bangladesh
- * E-mail:
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Kumar S, Bansal K, Sethi SK. Reclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis. Arch Microbiol 2022; 204:408. [PMID: 35727397 DOI: 10.1007/s00203-022-02979-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/01/2022]
Abstract
The genus Streptococcus, a member of family Streptococcaceae, is known for its wide range of industrial, clinical and human relevance. Among the species of genus Streptococcus two members, namely Streptococcus koreensis and Streptococcus ilei, were isolated from subgingival dental plaque and human small intestinal fluid, respectively. The 16S rRNA gene sequence similarity of the type strains of these members shows a similarity of 99.87%. In this study, we performed a systematic study to clarify the taxonomic assignment of these two species. Genome similarity assessment based on whole-genome sequence information such as average nucleotide identity using orthoANI and fastANI, digital DNA-DNA hybridization value between S. koreensis and S. ilei were 96.31, 96.60, 86.4 and 97.63, respectively. All these genome similarity values clearly exceeded the species delineation cutoffs. Phylogenetic assessment using 16S rRNA gene and whole-genome information using PhyloPhlAn, which uses around 400 conserved genes across bacterial phyla, provides additional evidence for these members forming a monophyletic clade in the phylogenetic tree. Pan genome analysis suggests a very large core genome (n = 1374) and the presence of no unique gene between the genomes of S. koreensis and S. ilei. Additionally, we found highly syntenic genomes of type strains of these two species. Based on these evidences, we propose S. ilei should be reclassified as a later heterotypic synonym of S. koreensis.
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Affiliation(s)
- Sanjeet Kumar
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India
| | - Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, 160036, India
| | - Santosh Kumar Sethi
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
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Sun Q, Li Z, Wang P, Zhao J, Chen S, Sun M. Unveiling the Pathogenic Bacteria Causing Descending Necrotizing Mediastinitis. Front Cell Infect Microbiol 2022; 12:873161. [PMID: 35755831 PMCID: PMC9215328 DOI: 10.3389/fcimb.2022.873161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high mortality. Here, we performed metagenomic next-generation sequencing (mNGS) using samples from 21 patients with MI and eight patients with DNM. In this study, we found that the species richness of the DNM group was higher than that of the MI group, and the species diversity of the DNM group was higher than that of the MI group, with no statistically significant differences between groups (P > 0.05). LefSE analysis revealed that the main species differing between groups were Bacillus, Lactobacillus, Streptococcaceae, and Streptococcus (S. constellatus and S. anginosus). In addition, the PLS-DA analysis revealed that the dominant groups in the DNM group at the species level were S. constellatus, S. anginosus, Streptococcus intermedius, Prevotella oris, Mogibacterium timidum, and Eubacterium nodatum. Next, we correlated the clinical characteristics of the patients with the relative abundance of the pathogens identified in the LefSe and PLS-DA analyses. The relative abundance of S. anginosus was positively correlated with C-reactive protein (CRP) and calcitoninogen (PCT) but negatively correlated with the percentage of lymphocytes (Lymph%) (P < 0.05). On the other hand, M. timidum was positively correlated with the percentage of neutrophils (Neut%) and glycated hemoglobin (GLU) (P < 0.05), and Parvimonas micra was positively correlated with CRP (P < 0.05).
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Lin Q, Zhou X, Zhang S, Gao J, Xie M, Tao L, Sun F, Shen C, Hashmi MZ, Su X. Oxidative dehalogenation and mineralization of polychlorinated biphenyls by a resuscitated strain Streptococcus sp. SPC0. Environ Res 2022; 207:112648. [PMID: 34990605 DOI: 10.1016/j.envres.2021.112648] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Most functional microorganisms cannot be cultivated due to entering a viable but non-culturable (VBNC) state, which limits the characterization and application of polychlorinated biphenyl (PCB)-degrading strains. Resuscitating VBNC bacteria could provide huge candidates for obtaining high-efficient PCB degraders. However, limited studies have focused on the ability of resuscitated strains for PCBs degradation. In the present study, whole-genome analysis of a resuscitated strain SPC0, and its performances in degradation of three prevalent PCB congeners (PCBs 18, 52 and 77) were investigated. The results indicate that the strain SPC0 belonged to the genus Streptococcus, possessed the degradation potential for aromatic xenobiotics. The SPC0 could effectively degrade PCBs 18 and 52, but exhibited lower degradation efficiency of PCB 77. Degradation of PCBs 18 and 52 could be fitted well by zero-order model, whereas the fittest model for PCB 77 degradation was pseudo second-order kinetics. The bph genes expression, chloride ions release and degradation metabolites identification, suggest that SPC0 possessed the capability of oxidative dehalogenation and mineralization of PCBs. Interestingly, SPC0 can degrade PCBs via the bph-encoded biphenyl pathway, and further mineralize metabolite dichlorobenzoate via protocatechuate pathway. This study is the first to show that a strain belonging to genus Streptococcus possessed PCB-degrading capability, which uncovered the powerful potential of resuscitated strains for bioremediation of PCB-contaminated sites.
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Affiliation(s)
- Qihua Lin
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Xinru Zhou
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Shusheng Zhang
- The Management Center of Wuyanling National Natural Reserve in Zhejiang, Wenzhou, 325500, China
| | - Junliang Gao
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Mengqi Xie
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Linqin Tao
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Faqian Sun
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | | | - Xiaomei Su
- College of Geography and Environmental Science, Zhejiang Normal University, Jinhua, 321004, China.
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Alsheikh-Hussain AS, Ben Zakour NL, Forde BM, Silayeva O, Barnes AC, Beatson SA. A high-quality reference genome for the fish pathogen Streptococcus iniae. Microb Genom 2022; 8:000777. [PMID: 35229712 PMCID: PMC9176272 DOI: 10.1099/mgen.0.000777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.
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Affiliation(s)
- Areej S. Alsheikh-Hussain
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Nouri L. Ben Zakour
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- The Westmead Institute for Medical Research and the University of Sydney, Sydney, New South Wales, Australia
| | - Brian M. Forde
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Oleksandra Silayeva
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Andrew C. Barnes
- School of Biological Science, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Andrew C. Barnes,
| | - Scott A. Beatson
- School of Chemistry & Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- *Correspondence: Scott A. Beatson,
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Song G, Zhang F, Tian C, Gao X, Zhu X, Fan D, Tian Y. Discovery of potent and versatile CRISPR–Cas9 inhibitors engineered for chemically controllable genome editing. Nucleic Acids Res 2022; 50:2836-2853. [PMID: 35188577 PMCID: PMC8934645 DOI: 10.1093/nar/gkac099] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/28/2022] [Accepted: 02/05/2022] [Indexed: 12/26/2022] Open
Abstract
Abstract
Anti-CRISPR (Acr) proteins are encoded by many mobile genetic elements (MGEs) such as phages and plasmids to combat CRISPR–Cas adaptive immune systems employed by prokaryotes, which provide powerful tools for CRISPR–Cas-based applications. Here, we discovered nine distinct type II-A anti-CRISPR (AcrIIA24–32) families from Streptococcus MGEs and found that most Acrs can potently inhibit type II-A Cas9 orthologs from Streptococcus (SpyCas9, St1Cas9 or St3Cas9) in bacterial and human cells. Among these Acrs, AcrIIA26, AcrIIA27, AcrIIA30 and AcrIIA31 are able to block Cas9 binding to DNA, while AcrIIA24 abrogates DNA cleavage by Cas9. Notably, AcrIIA25.1 and AcrIIA32.1 can inhibit both DNA binding and DNA cleavage activities of SpyCas9, exhibiting unique anti-CRISPR characteristics. Importantly, we developed several chemically inducible anti-CRISPR variants based on AcrIIA25.1 and AcrIIA32.1 by comprising hybrids of Acr protein and the 4-hydroxytamoxifen-responsive intein, which enabled post-translational control of CRISPR–Cas9-mediated genome editing in human cells. Taken together, our work expands the diversity of type II-A anti-CRISPR families and the toolbox of Acr proteins for the chemically inducible control of Cas9-based applications.
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Affiliation(s)
- Guoxu Song
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Zhang
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhong Tian
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Gao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoxiao Zhu
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Dongdong Fan
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tian
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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47
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Kwack KH, Lee JH, Moon JH. Whole genome and RNA sequencing of oral commensal bacterium Streptococcus anginosus subsp. anginosus with vancomycin tolerance. J Microbiol 2022; 60:167-176. [PMID: 34997538 DOI: 10.1007/s12275-022-1425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/24/2022]
Abstract
"Antibiotic tolerance" promotes the rapid subsequent evolution of "antibiotic resistance," however, it is often overlooked because it is difficult to distinguish between tolerant and susceptible organisms. A commensal bacterium S. anginosus subsp. anginosus strain KHUD_S1, isolated from dental biofilm was found to exhibit a high MBC/MIC ratio of 32 against vancomycin. We observed KHUD_S1 cells exposed to vancomycin did not grow but maintained viability. Transmission electron microscope showed KHUD_S1 cells possessed a dense, thick capsule and maintained the cell wall integrity upon vancomycin exposure. To infer the underlying mechanisms of the vancomycin tolerance in KHUD_S1, we performed whole genome sequencing and RNA sequencing. The KHUD_S1 genome carried three genes encoding branching enzymes that can affect peptidoglycan structure through interpeptide bridge formation. Global gene expression profiling revealed that the vancomycin-induced downregulation of carbohydrate and inorganic ion transport/metabolism as well as translation is less prominent in KHUD_S1 than in the vancomycin susceptible strain KHUD_S3. Based on the transcriptional levels of genes related to peptidoglycan synthesis, KHUD_S1 was determined to have a 3D peptidoglycan architecture distinct from KHUD_S3. It was found that, under vancomycin exposure, the peptidoglycan was remodeled through changes in the interpeptide bridge and transpeptidation reactions. Collectively, these features of S. anginosus KHUD_S1, including a dense capsule and differential gene expression in peptidoglycan synthesis, may contribute to vancomycin tolerance. Our results showing the occurrence of vancomycin tolerance amongst oral commensal bacteria highlight the need for considering future strategies for screening of antibiotic tolerance as an effort to reduce antibiotic resistance.
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Affiliation(s)
- Kyu Hwan Kwack
- Department of Dentistry, Graduate School, Kyung Hee University, Seoul, 02447, Republic of Korea
- Present address: Department of Oral Biology, University at Buffalo School of Dental Medicine, Buffalo, New York, 14214, USA
| | - Jae-Hyung Lee
- Department of Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, 02447, Republic of Korea.
| | - Ji-Hoi Moon
- Department of Oral Microbiology, School of Dentistry, Kyung Hee University, Seoul, 02447, Republic of Korea.
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Oftedal TF, Ovchinnikov KV, Hestad KA, Goldbeck O, Porcellato D, Narvhus J, Riedel CU, Kjos M, Diep DB. Ubericin K, a New Pore-Forming Bacteriocin Targeting mannose-PTS. Microbiol Spectr 2021; 9:e0029921. [PMID: 34643411 PMCID: PMC8515946 DOI: 10.1128/spectrum.00299-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Bovine mastitis infection in dairy cattle is a significant economic burden for the dairy industry globally. To reduce the use of antibiotics in treatment of clinical mastitis, new alternative treatment options are needed. Antimicrobial peptides from bacteria, also known as bacteriocins, are potential alternatives for combating mastitis pathogens. In search of novel bacteriocins against mastitis pathogens, we screened samples of Norwegian bovine raw milk and found a Streptococcus uberis strain with potent antimicrobial activity toward Enterococcus, Streptococcus, Listeria, and Lactococcus. Whole-genome sequencing of the strain revealed a multibacteriocin gene cluster encoding one class IIb bacteriocin, two class IId bacteriocins, in addition to a three-component regulatory system and a dedicated ABC transporter. Isolation and purification of the antimicrobial activity from culture supernatants resulted in the detection of a 6.3-kDa mass peak by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, a mass corresponding to the predicted size of one of the class IId bacteriocins. The identification of this bacteriocin, called ubericin K, was further confirmed by in vitro protein synthesis, which showed the same inhibitory spectrum as the purified antimicrobial compound. Ubericin K shows highest sequence similarity to the class IId bacteriocins bovicin 255, lactococcin A, and garvieacin Q. We found that ubericin K uses the sugar transporter mannose phosphotransferase (PTS) as a target receptor. Further, by using the pHlourin sensor system to detect intracellular pH changes due to leakage across the membrane, ubericin K was shown to be a pore former, killing target cells by membrane disruption. IMPORTANCE Bacterial infections in dairy cows are a major burden to farmers worldwide because infected cows require expensive treatments and produce less milk. Today, infected cows are treated with antibiotics, a practice that is becoming less effective due to antibiotic resistance. Compounds other than antibiotics also exist that kill bacteria causing infections in cows; these compounds, known as bacteriocins, are natural products produced by other bacteria in the environment. In this work, we discover a new bacteriocin that we call ubericin K, which kills several species of bacteria known to cause infections in dairy cows. We also use in vitro synthesis as a novel method for rapidly characterizing bacteriocins directly from genomic data, which could be useful for other researchers. We believe that ubericin K and the methods described in this work will aid in the transition away from antibiotics in the dairy industry.
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Affiliation(s)
- Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kai A. Hestad
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, Ulm University, Ulm, Germany
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Judith Narvhus
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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49
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Liu T, Zeng D, Zheng Z, Lin Z, Xue Y, Li T, Xie X, Ma G, Liu YG, Zhu Q. The ScCas9 ++ variant expands the CRISPR toolbox for genome editing in plants. J Integr Plant Biol 2021; 63:1611-1619. [PMID: 34411422 DOI: 10.1111/jipb.13164] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The development of clustered regularly interspaced palindromic repeats (CRISPR)-associated protein (Cas) variants with a broader recognition scope is critical for further improvement of CRISPR/Cas systems. The original Cas9 protein from Streptococcus canis (ScCas9) can recognize simple NNG-protospacer adjacent motif (PAM) targets, and therefore possesses a broader range relative to current CRISPR/Cas systems, but its editing efficiency is low in plants. Evolved ScCas9+ and ScCas9++ variants have been shown to possess higher editing efficiencies in human cells, but their activities in plants are currently unknown. Here, we utilized codon-optimized ScCas9, ScCas9+ and ScCas9++ and a nickase variant ScCas9n++ to systematically investigate genome cleavage activity and cytidine base editing efficiency in rice (Oryza sativa L.). This analysis revealed that ScCas9++ has higher editing efficiency than ScCas9 and ScCas9+ in rice. Furthermore, we fused the evolved cytidine deaminase PmCDA1 with ScCas9n++ to generate a new evoBE4max-type cytidine base editor, termed PevoCDA1-ScCas9n++ . This base editor achieved stable and efficient multiplex-site base editing at NNG-PAM sites with wider editing windows (C- 1 -C17 ) and without target sequence context preference. Multiplex-site base editing of the rice genes OsWx (three targets) and OsEui1 (two targets) achieved simultaneous editing and produced new rice germplasm. Taken together, these results demonstrate that ScCas9++ represents a crucial new tool for improving plant editing.
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Affiliation(s)
- Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zhiye Zheng
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhansheng Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Tie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Genglu Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, 510642, China
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
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50
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Ma G, Kuang Y, Lu Z, Li X, Xu Z, Ren B, Zhou X, Zhou H. CRISPR/Sc ++ -mediated genome editing in rice. J Integr Plant Biol 2021; 63:1606-1610. [PMID: 34427973 DOI: 10.1111/jipb.13166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Streptococcus canis Cas9 (ScCas9) is an RNA-guided endonuclease with NNG protospacer adjacent motif (PAM) specificity whose genome-editing activity in rice is locus-dependent. Here we investigated the performance of a ScCas9 variant named Sc++ at different NNG PAM sites in the rice genome; Sc++ harbors a T1227K mutation and the substitution of a positively charged loop (residues 367-376). Sc++ nuclease achieved broader genome editing compared to the original ScCas9, and its nickase improved targeted base editing in transgenic rice plants. Using the high-efficiency adenine base editor rBE73b, we generated many new OsGS1 alleles suitable for screening of rice germplasm for potential herbicide resistance in the future. The CRISPR/Sc++ system expands the genome-editing toolkit for rice.
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Affiliation(s)
- Guigen Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Yongjie Kuang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Zhenwan Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Xueqi Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Ziyan Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Bin Ren
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Scientific Observing and Experimental Station of Crop Pests in Guilin, Ministry of Agriculture and Rural Affairs, Guilin, 541399, China
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