1
|
Adam HJ, Karlowsky JA, Baxter MR, Schellenberg J, Golden AR, Martin I, Demczuk W, Mulvey MR, Zhanel GG. Analysis of MDR in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i17-i25. [PMID: 37130586 DOI: 10.1093/jac/dkad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To investigate the levels of MDR in the predominant serotypes of invasive Streptococcus pneumoniae isolated in Canada over a 10 year period. METHODS All isolates were serotyped and had antimicrobial susceptibility testing performed, in accordance with CLSI guidelines (M07-11 Ed., 2018). Complete susceptibility profiles were available for 13 712 isolates. MDR was defined as resistance to three or more classes of antimicrobial agents (penicillin MIC ≥2 mg/L defined as resistant). Serotypes were determined by Quellung reaction. RESULTS In total, 14 138 invasive isolates of S. pneumoniae were tested in the SAVE study (S. pneumoniae Serotyping and Antimicrobial Susceptibility: Assessment for Vaccine Efficacy in Canada), a collaboration between the Canadian Antimicrobial Resistance Alliance and Public Health Agency of Canada-National Microbiology Laboratory. The rate of MDR S. pneumoniae in SAVE was 6.6% (902/13 712). Annual rates of MDR S. pneumoniae decreased between 2011 and 2015 (8.5% to 5.7%) and increased between 2016 and 2020 (3.9% to 9.4%). Serotypes 19A and 15A were the most common serotypes demonstrating MDR (25.4% and 23.5% of the MDR isolates, respectively); however, the serotype diversity index increased from 0.7 in 2011 to 0.9 in 2020 with a statistically significant linear increasing trend (P < 0.001). In 2020, MDR isolates were frequently serotypes 4 and 12F in addition to serotypes 15A and 19A. In 2020, 27.3%, 45.5%, 50.5%, 65.7% and 68.7% of invasive MDR S. pneumoniae were serotypes included in the PCV10, PCV13, PCV15, PCV20 and PPSV23 vaccines, respectively. CONCLUSIONS Although current vaccine coverage of MDR S. pneumoniae in Canada is high, the increasing diversity of serotypes observed among the MDR isolates highlights the ability of S. pneumoniae to rapidly evolve.
Collapse
Affiliation(s)
- Heather J Adam
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| |
Collapse
|
2
|
Golden AR, Adam HJ, Karlowsky JA, Baxter M, Schellenberg J, Martin I, Demczuk W, Minion J, Van Caeseele P, Kus JV, McGeer A, Lefebvre B, Smadi H, Haldane D, Yu Y, Mead K, Mulvey MR, Zhanel GG. Genomic investigation of the most common Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-2020. J Antimicrob Chemother 2023; 78:i26-i36. [PMID: 37130587 DOI: 10.1093/jac/dkad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
OBJECTIVES To investigate the lineages and genomic antimicrobial resistance (AMR) determinants of the 10 most common pneumococcal serotypes identified in Canada during the five most recent years of the SAVE study, in the context of the 10-year post-PCV13 period in Canada. METHODS The 10 most common invasive Streptococcus pneumoniae serotypes collected by the SAVE study from 2016 to 2020 were 3, 22F, 9N, 8, 4, 12F, 19A, 33F, 23A and 15A. A random sample comprising ∼5% of each of these serotypes collected during each year of the full SAVE study (2011-2020) were selected for whole-genome sequencing (WGS) using the Illumina NextSeq platform. Phylogenomic analysis was performed using the SNVPhyl pipeline. WGS data were used to identify virulence genes of interest, sequence types, global pneumococcal sequence clusters (GPSC) and AMR determinants. RESULTS Of the 10 serotypes analysed in this study, six increased significantly in prevalence from 2011 to 2020: 3, 4, 8, 9N, 23A and 33F (P ≤ 0.0201). Serotypes 12F and 15A remained stable in prevalence over time, while serotype 19A decreased in prevalence (P < 0.0001). The investigated serotypes represented four of the most prevalent international lineages causing non-vaccine serotype pneumococcal disease in the PCV13 era: GPSC3 (serotypes 8/33F), GPSC19 (22F), GPSC5 (23A) and GPSC26 (12F). Of these lineages, GPSC5 isolates were found to consistently possess the most AMR determinants. Commonly collected vaccine serotypes 3 and 4 were associated with GPSC12 and GPSC27, respectively. However, a more recently collected lineage of serotype 4 (GPSC192) was highly clonal and possessed AMR determinants. CONCLUSIONS Continued genomic surveillance of S. pneumoniae in Canada is essential to monitor for the appearance of new and evolving lineages, including antimicrobial-resistant GPSC5 and GPSC162.
Collapse
Affiliation(s)
- Alyssa R Golden
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Heather J Adam
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - James A Karlowsky
- Clinical Microbiology, Shared Health, MS673-820 Sherbrook Street, Winnipeg, Manitoba, R3A 1R9, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - John Schellenberg
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Jessica Minion
- Roy Romanow Provincial Laboratory, Saskatchewan Health Authority, 5 Research Drive, Regina, Saskatchewan, S4S 0A4, Canada
| | - Paul Van Caeseele
- Cadham Provincial Laboratory, Shared Health, 750 William Avenue, Winnipeg, Manitoba, R3E 3J7, Canada
| | - Julianne V Kus
- Public Health Ontario Laboratory, 661 University Avenue, Toronto, Ontario, M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle-6th Floor, Toronto, Ontario, M5S 1A8, Canada
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital. 600 University Avenue-Suite 171, Toronto, Ontario, M5G 1X5, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, 20045 Ch Ste-Marie, Ste-Anne-de-Bellevue, Québec, H9X 3R5, Canada
| | - Hanan Smadi
- Epidemiology and Surveillance Branch, New Brunswick Department of Health, 520 King Street, Fredericton, New Brunswick, E3B 5G8, Canada
| | - David Haldane
- Department of Pathology and Laboratory Medicine, Queen Elizabeth II Health Science Centre, 1276 South Park Street, Halifax, Nova Scotia, B3H 2Y9, Canada
| | - Yang Yu
- Newfoundland and Labrador Public Health Laboratory, Dr. Leonard A. Miller Centre-Suite 1, 100 Forest Road, St. John's, Newfoundland and Labrador, A1A 1E3, Canada
| | - Kristen Mead
- Provincial Laboratory Services, Queen Elizabeth Hospital, 60 Riverside Drive, Charlottetown, Prince Edward Island, C1A 8T5, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Room 543-745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada
| |
Collapse
|
3
|
Brennan AA, Harrington A, Guo M, Renshaw CP, Tillett RL, Miura P, Tal-Gan Y. Investigating the Streptococcus sinensis competence regulon through a combination of transcriptome analysis and phenotypic evaluation. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36282148 DOI: 10.1099/mic.0.001256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Streptococcus sinensis is a recently identified member of the Mitis group of streptococci. This species has been associated with infective endocarditis; however its mechanisms of pathogenesis and virulence are not fully understood. This study aimed to investigate the influence of the competence-stimulating peptide (CSP) and the competence regulon quorum-sensing circuitry (ComABCDE) on subsequent gene transcription and expression, as well as resultant phenotypes. In this study we confirmed the native CSP identity, ascertained when endogenous CSP was produced and completed a transcriptome-wide analysis of all genes following CSP exposure. RNA sequencing analysis revealed the upregulation of genes known to be associated with competence, biofilm formation and virulence. As such, a variety of phenotypic assays were utilized to assess the correlation between increased mRNA expression and potential phenotype response, ultimately gaining insight into the effects of CSP on both gene expression and developed phenotypes. The results indicated that the addition of exogenous CSP aided in competence development and successful transformation, yielding an average transformation efficiency comparable to that of other Mitis group streptococci. Additional studies are needed to further delineate the effects of CSP exposure on biofilm formation and virulence. Overall, this study provides novel information regarding S. sinensis and provides a substantial foundation on which this species and its role in disease pathogenesis can be further investigated.
Collapse
Affiliation(s)
- Alec A Brennan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Anthony Harrington
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Mingzhe Guo
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Clay P Renshaw
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Richard L Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| | - Yftah Tal-Gan
- Department of Chemistry, University of Nevada, Reno, 1664 North Virginia Street, Reno, Nevada 89557, USA
| |
Collapse
|
4
|
Golden A, Griffith A, Demczuk W, Lefebvre B, McGeer A, Tyrrell G, Zhanel G, Kus J, Hoang L, Minion J, Van Caeseele P, Smadi H, Haldane D, Zahariadis G, Mead K, Steven L, Strudwick L, Li A, Mulvey M, Martin I. Invasive pneumococcal disease surveillance in Canada, 2020. CANADA COMMUNICABLE DISEASE REPORT = RELEVE DES MALADIES TRANSMISSIBLES AU CANADA 2022; 48:396-406. [PMID: 38124782 PMCID: PMC10732480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Background Invasive pneumococcal disease (IPD), which is caused by Streptococcus pneumoniae, has been a nationally notifiable disease in Canada since 2000. The use of conjugate vaccines has markedly decreased the incidence of IPD in Canada; however, the distribution of serotypes has shifted in favour of non-vaccine types. This report summarizes the demographics, serotypes and antimicrobial resistance of IPD infections in Canada in 2020. Methods The Public Health Agency of Canada's National Microbiology Laboratory (Winnipeg, Manitoba) collaborates with provincial and territorial public health laboratories to conduct national surveillance of IPD. A total of 2,108 IPD isolates were reported in 2020. Serotyping was performed by Quellung reaction and antimicrobial susceptibilities were determined in collaboration with the University of Manitoba/Canadian Antimicrobial Resistance Alliance. Population-based IPD incidence rates were obtained through the Canadian Notifiable Disease Surveillance System. Results Overall incidence of IPD in Canada decreased significantly from 11.5 (95% confidence interval [CI]: 10.1-13.1) to 6.0 (95% CI: 5.0-7.2), and from 10.0 (95% CI: 9.7-10.3) to 5.9 (95% CI: 5.7-6.2) cases per 100,000 from 2019 to 2020; in those younger than five years and those five years and older, respectively. The most common serotypes overall were 4 (11.2%, n=237), 3 (10.9%, n=229) and 8 (7.2%, n=151). From 2016 to 2020, serotypes with increasing trends (p<0.05) included 4 (6.4%-11.2%), 3 (9.5%-10.9%), 8 (5.2%-7.2%) and 12F (3.6%-5.7%). The overall prevalence of PCV13 serotypes increased over the same period (30.3%-34.9%, p<0.05). Antimicrobial resistance rates in 2020 included 23.0% clarithromycin and 9.9% penicillin (IV meningitis breakpoints). Multidrug-resistant IPD has significantly increased since 2016 (4.2%-9.5%, p<0.05). Conclusion Though the incidence of IPD decreased in 2020 in comparison to previous years across all age groups, disease due to PCV13 serotypes 3 and 4, as well as non-PCV13 serotypes such as 8 and 12F, increased in prevalence. Continued surveillance of IPD is imperative to monitor shifts in serotype distribution and antimicrobial resistance.
Collapse
Affiliation(s)
- Alyssa Golden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Averil Griffith
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue, QC
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital, Toronto, ON
| | - Gregory Tyrrell
- Provincial Laboratory for Public Health (Microbiology), Edmonton, AB
| | - George Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
| | - Julianne Kus
- Public Health Ontario, Toronto, ON
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON
| | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, BC
| | | | | | - Hanan Smadi
- New Brunswick Department of Health, Fredericton, NB
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, NS
| | | | | | - Laura Steven
- Stanton Territorial Hospital Laboratory, Yellowknife, NT
| | | | - Anita Li
- Centre for Immunization & Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, ON
| | - Michael Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB
| |
Collapse
|
5
|
Gaballa A, Cheng RA, Trmcic A, Kovac J, Kent DJ, Martin NH, Wiedmann M. Development of a database and standardized approach for rpoB sequence-based subtyping and identification of aerobic spore-forming Bacillales. J Microbiol Methods 2021; 191:106350. [PMID: 34710512 DOI: 10.1016/j.mimet.2021.106350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 10/20/2022]
Abstract
Aerobic spore-forming Bacillales are a highly diverse and ubiquitous group that includes organisms that cause foodborne illnesses and food spoilage. Classical microbiological and biochemical identification of members of the order Bacillales represents a challenge due to the diversity of organisms in this group as well as the fact that the phenotypic-based taxonomic assignment of some named species in this group is not consistent with their phylogenomic characteristics. DNA-sequencing-based tools, on the other hand, can be fast and cost-effective, and can provide for a more reliable identification and characterization of Bacillales isolates. In comparison to 16S rDNA, rpoB was shown to better discriminate between Bacillales isolates and to allow for improved taxonomic assignment to the species level. However, the lack of a publicly accessible rpoB database, as well as the lack of standardized protocols for rpoB-based typing and strain identification, is a major challenge. Here, we report (i) the curation of a DNA sequence database for rpoB-based subtype classification of Bacillales isolates; (ii) the development of standardized protocols for generating rpoB sequence data, and a scheme for rpoB-based initial taxonomic identification of Bacillales isolates at the species level; and (iii) the integration of the database in a publicly accessible online platform that allows for the analysis of rpoB sequence data from uncharacterized Bacillales isolates. Specifically, we curated a database of DNA sequences for a 632-nt internal variable region within the rpoB gene from representative Bacillales reference type strains and a large number of isolates that we have previously isolated and characterized through multiple projects. As of May 21, 2021, the rpoB database contained more than 8350 rpoB sequences representing 1902 distinct rpoB allelic types that can be classified into 160 different genera. The database also includes 1129 rpoB sequences for representative Bacillales reference type strains as available on May 21, 2021 in the NCBI database. The rpoB database is integrated into the online Food Microbe Tracker platform (www.foodmicrobetracker.com) and can be queried using the integrated BLAST tool to initially subtype and taxonomically identify aerobic and facultative anaerobic spore-formers. While whole-genome sequencing is increasingly used in bacterial taxonomy, the rpoB sequence-based identification scheme described here provides a valuable tool as it allows for rapid and cost-effective initial isolate characterization, which can help to identify and characterize foodborne pathogens and food spoilage bacteria. In addition, the database and primers described here can also be adopted for metagenomics approaches that include rpoB as a target, improving discriminatory power and identification over what can be achieved using 16S rDNA as a target.
Collapse
Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA.
| | - Rachel A Cheng
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Aljosa Trmcic
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Jasna Kovac
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - David J Kent
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
6
|
Kellner JD, Ricketson LJ, Demczuk WHB, Martin I, Tyrrell GJ, Vanderkooi OG, Mulvey MR. Whole-Genome Analysis of Streptococcus pneumoniae Serotype 4 Causing Outbreak of Invasive Pneumococcal Disease, Alberta, Canada. Emerg Infect Dis 2021; 27:1867-1875. [PMID: 34152965 PMCID: PMC8237880 DOI: 10.3201/eid2707.204403] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
After the introduction of pneumococcal conjugate vaccines for children, invasive pneumococcal disease caused by Streptococcus pneumoniae serotype 4 declined in all ages in Alberta, Canada, but it has reemerged and spread in adults in Calgary, primarily among persons who are experiencing homelessness or who use illicit drugs. We conducted clinical and molecular analyses to examine the cases and isolates. Whole-genome sequencing analysis indicated relatively high genetic variability of serotype 4 isolates. Phylogenetic analysis identified 1 emergent sequence type (ST) 244 lineage primarily associated within Alberta and nationally distributed clades ST205 and ST695. Isolates from 6 subclades of the ST244 lineage clustered regionally, temporally, and by homeless status. In multivariable logistic regression, factors associated with serotype 4 invasive pneumococcal disease were being male, being <65 years of age, experiencing homelessness, having a diagnosis of pneumonia or empyema, or using illicit drugs.
Collapse
|
7
|
da Silva RN, Melo LFDA, Luna Finkler CL. Optimization of the cultivation conditions of Bacillus licheniformis BCLLNF-01 for cellulase production. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 29:e00599. [PMID: 33728263 PMCID: PMC7935710 DOI: 10.1016/j.btre.2021.e00599] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 11/12/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023]
Abstract
The objective of this study was to optimize the production of CMCase by Bacillus licheniformis BCLLNF-01, a strain associated with the mucus of the zoanthid Palythoa caribaeorum (Cnidaria, Anthozoa). Production of total cellulase and CMCase was investigated in the supernatant, intracellular content and wall content. Cultivation was carried out in BLM medium supplemented with 1.5 % (w/v) CMC, 5.5 % (v/v) inoculum, 40 °C, pH 6.5, 500 rpm for 72 h, and the highest activity was recorded in the supernatant. A Rotational Central Composite Design (RCCD) 2³ was used to investigate the influence of the carbon source concentration (CMC-0.5 to 1.5 % w/v), inoculum concentration (1-10 % v/v) and temperature (35-45 °C) on CMCase production. The maximum enzyme activity was achieved for a CMC concentration of 1.5 % w/v at 40 °C, attaining 0.493 IU/mL after 96 h of cultivation.
Collapse
Affiliation(s)
- Raquel Nascimento da Silva
- Federal University of Pernambuco, Academic Center of Vitória, R. Alto do Reservatório, s/n, Bela Vista, Vitória de Santo Antão, PE, 55608-250, Brazil
| | - Liany Figuerêdo de Andrade Melo
- Federal University of Pernambuco, Academic Center of Vitória, R. Alto do Reservatório, s/n, Bela Vista, Vitória de Santo Antão, PE, 55608-250, Brazil
| | - Christine Lamenha Luna Finkler
- Federal University of Pernambuco, Academic Center of Vitória, R. Alto do Reservatório, s/n, Bela Vista, Vitória de Santo Antão, PE, 55608-250, Brazil
| |
Collapse
|
8
|
Qi H, Liu D, Zou Y, Wang N, Tian H, Xiao C. Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. Antonie van Leeuwenhoek 2021; 114:113-127. [PMID: 33387140 PMCID: PMC7878260 DOI: 10.1007/s10482-020-01505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Using the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).
Collapse
Affiliation(s)
- He Qi
- Liaoning University of Traditional Chinese Medicine, Shenyang, People's Republic of China
- Department of Medical technology, Medical Science Institute of Liaoning, Shenyang, People's Republic of China
| | - Defeng Liu
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Yang Zou
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Nan Wang
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Han Tian
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Chunling Xiao
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China.
| |
Collapse
|
9
|
Vagococcus zengguangii sp. nov., isolated from yak faeces. J Microbiol 2020; 59:1-9. [PMID: 33355894 DOI: 10.1007/s12275-021-0406-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Two unknown Gram-stain-positive, catalase- and oxidasenegative, non-motile, and coccus-shaped bacteria, designated MN-17T and MN-09, were isolated from yaks faeces (Bos grunniens) in the Qinghai-Tibet Plateau of China. 16S rRNA gene sequence-based comparative analyses revealed that the two strains were grouped within the genus Vagococcus, displaying the highest similarity with Vagococcus xieshaowenii CGMCC 1.16436T (98.6%) and Vagococcus elongatus CCUG 51432T (96.4%). Both strains grew optimally at 37°C and pH 7.0 in the presence of 0.5% (w/v) NaCl. The complete genome of MN-17T comprises 2,085 putative genes with a total of 2,190,262 bp and an average G + C content of 36.7 mol%. The major fatty acids were C16:0 (31.2%), C14:0 (28.5%), and C18:1ω9c (13.0%); the predominant respiratory quinone was MK-7 (68.8%); the peptidoglycan type was A4α(L-Lys-D-Asp); and the major polar lipid was diphosphatidylglycerol. Together, these supported the affiliation of strain MN-17T to the genus Vagococcus. In silico DNA-DNA hybridization and the average nucleotide identity values between MN-17T and all recognized species in the genus were 21.6-26.1% and 70.7-83.0%, respectively. MN-17T produced acid from D-cellobiose, D-fructose, glycerol, D-glucose, N-acetyl-glucosamine, gentiobiose, D-mannose, D-maltose, D-ribose, D-saccharose, salicin, D-trehalose, and D-xylose. These results distinguished MN-17T and MN-09 from closely related species in Vagococcus. Thus, we propose that strains MN-17T and MN-09 represent a novel species in the genus Vagococcus, with the name Vagococcus zengguangii sp. The type strain is MN-17T (= CGMCC 1.16726T = GDMCC 1.1589T = JCM 33478T).
Collapse
|
10
|
Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
Collapse
Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| |
Collapse
|
11
|
Kosecka-Strojek M, Wolska M, Żabicka D, Sadowy E, Międzobrodzki J. Identification of Clinically Relevant Streptococcus and Enterococcus Species Based on Biochemical Methods and 16S rRNA, sodA, tuf, rpoB, and recA Gene Sequencing. Pathogens 2020; 9:pathogens9110939. [PMID: 33187333 PMCID: PMC7696602 DOI: 10.3390/pathogens9110939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococci and enterococci are significant opportunistic pathogens in epidemiology and infectious medicine. High genetic and taxonomic similarities and several reclassifications within genera are the most challenging in species identification. The aim of this study was to identify Streptococcus and Enterococcus species using genetic and phenotypic methods and to determine the most discriminatory identification method. Thirty strains recovered from clinical samples representing 15 streptococcal species, five enterococcal species, and four nonstreptococcal species were subjected to bacterial identification by the Vitek® 2 system and Sanger-based sequencing methods targeting the 16S rRNA, sodA, tuf, rpoB, and recA genes. Phenotypic methods allowed the identification of 10 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains (Leuconostoc, Granulicatella, and Globicatella genera). The combination of sequencing methods allowed the identification of 21 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains. The 16S rRNA and rpoB genes had the highest identification potential. Only a combination of several molecular methods was sufficient for unambiguous confirmation of species identity. This study will be useful for comparison of several identification methods, both those used as a first choice in routine microbiology and those used for final confirmation.
Collapse
Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
- Correspondence: ; Tel.: +48-12-664-6365
| | - Mariola Wolska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
| | - Dorota Żabicka
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Ewa Sadowy
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
| |
Collapse
|
12
|
Abstract
Abstract
Platelet transfusion is a topic of common interest for many specialists involved in patient care, from laboratory staff to clinical physicians. Various aspects make this type of transfusion different from those of other blood components. In this review, the challenges in platelet transfusion practice that are relevant for laboratory colleagues will be discussed, highlighting how the biochemical and structural characteristics of these blood elements directly affect their function and consequently the clinical outcome. More than 1,300 platelet concentrates are transfused in Germany every day, and several types are offered by their respective manufacturers. We describe the technological advances in platelet concentrate production, with a focus on how the storage conditions of platelets can be improved. Laboratory quality assessment procedures for a safe transfusion are discussed in detail. For this purpose, we will refer to the Hemotherapy Directives (Richtlinie Hämotherapie) of the German Medical Association.
Collapse
Affiliation(s)
- Gianmatteo Vit
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University , German Red Cross Blood Service Baden-Württemberg - Hessen , Mannheim , Germany
- The Novo Nordisk Foundation Center for Protein Research, Protein Signaling Program , Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen , Denmark
| | - Harald Klüter
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University , German Red Cross Blood Service Baden-Württemberg - Hessen , Mannheim , Germany
| | - Patrick Wuchter
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, Heidelberg University , German Red Cross Blood Service Baden-Württemberg - Hessen , Mannheim , Germany
| |
Collapse
|
13
|
Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
Collapse
|
14
|
Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S-23S rRNA region. Antimicrob Resist Infect Control 2019; 8:178. [PMID: 31788235 PMCID: PMC6858756 DOI: 10.1186/s13756-019-0622-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 10/09/2019] [Indexed: 12/28/2022] Open
Abstract
Background Many members of Streptococcus and Enterococcus genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S-23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial and challenging clinical samples. The introduction of this new method to routine diagnostics is hindered by a lack of the reference sequences for the 16S-23S rRNA region for many bacterial species. The aim of this study was to develop a careful assignment for streptococcal and enterococcal species based on NGS of the 16S-23S rRNA region. Methods Thirty two strains recovered from clinical samples and 19 reference strains representing 42 streptococcal species and nine enterococcal species were subjected to bacterial identification by four Sanger-based sequencing methods targeting the genes encoding (i) 16S rRNA, (ii) sodA, (iii) tuf and (iv) rpoB; and NGS of the 16S-23S rRNA region. Results This study allowed obtainment and deposition of reference sequences of the 16S-23S rRNA region for 15 streptococcal and 3 enterococcal species followed by enrichment for 27 and 6 species, respectively, for which reference sequences were available in the databases. For Streptococcus, NGS of the 16S-23S rRNA region was as discriminative as Sanger sequencing of the tuf and rpoB genes allowing for an unambiguous identification of 93% of analyzed species. For Enterococcus, sodA, tuf and rpoB genes sequencing allowed for identification of all species, while the NGS-based method did not allow for identification of only one enterococcal species. For both genera, the sequence analysis of the 16S rRNA gene was endowed with a low identification potential and was inferior to that of other tested identification methods. Moreover, in case of phylogenetically related species the sequence analysis of only the intergenic spacer region was not sufficient enough to precisely identify Streptococcus strains at the species level. Conclusions Based on the developed reference dataset, clinically relevant streptococcal and enterococcal species can now be reliably identified by 16S-23S rRNA sequences in samples. This study will be useful for introduction of a novel diagnostic tool, NGS of the 16S-23S rRNA region, which undoubtedly is an improvement for reliable culture-independent species identification directly from polymicrobially constituted clinical samples.
Collapse
|
15
|
Rungsirivanich P, Inta A, Tragoolpua Y, Thongwai N. Partial rpoB Gene Sequencing Identification and Probiotic Potential of Floricoccus penangensis ML061-4 Isolated from Assam Tea (Camellia sinensis var. assamica). Sci Rep 2019; 9:16561. [PMID: 31719601 PMCID: PMC6851367 DOI: 10.1038/s41598-019-52979-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/27/2019] [Indexed: 12/22/2022] Open
Abstract
Assam tea or Miang is a local name of Camellia sinensis var. assamica in northern Thailand. By the local wisdom, Assam tea leaves are used as the raw material in tea fermentation to produce “Fermented Miang” consumed by people in northern Thailand and the countries nearby. In this study, twenty-eight bacterial isolates were obtained from Assam tea leaf samples collected from Nan province, Thailand. Bacterial isolates were identified within 6 genera including Bacillus, Floricoccus, Kocuria, Lysinibacillus, Micrococcus and Staphylococcus. Among these, the strain ML061-4 shared 100.0 and 99.4% similarity of 16S rRNA and rpoB gene sequence with F. penangensis JCM 31735T, respectively. This is the first discovery of F. penangensis in Thailand. F. penangensis ML061-4 exhibited probiotic characteristics including lactic acid production (9.19 ± 0.10 mg/ml), antibacterial activities (Escherichia coli ATCC 25922 and E. coli O157:H7 DMST 12743), acid and bile salt tolerance (71.1 and 54.9%, respectively), autoaggregation (97.0%), coaggregation (66.0% with E. coli O157:H7), cell surface hydrophobicity (90.0%), bacterial adhesion (82.9% with Lactobacillus plantarum FM03-1), competitive inhibition (17.8% with E. coli O157:H7) and competitive exclusion (34.9% with E. coli O157:H7). Overall, the data suggested that F. penangensis ML061-4 had a great potential to be a probiotic.
Collapse
Affiliation(s)
- Patthanasak Rungsirivanich
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Graduate School, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Angkhana Inta
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Narumol Thongwai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand.
| |
Collapse
|
16
|
Rosa NM, Agnoletti F, Lollai S, Tola S. Comparison of PCR-RFLP, API® 20 Strep and MALDI-TOF MS for identification of Streptococcus spp. collected from sheep and goat milk samples. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
17
|
Golden AR, Adam HJ, Karlowsky JA, Baxter M, Nichol KA, Martin I, Demczuk W, Van Caeseele P, Gubbay JB, Lefebvre B, Levett PN, Zahariadis G, Haldane D, Gad R, German G, Gilmour MW, Mulvey MR, Hoban DJ, Zhanel GG. Molecular characterization of predominant Streptococcus pneumoniae serotypes causing invasive infections in Canada: the SAVE study, 2011-15. J Antimicrob Chemother 2019; 73:vii20-vii31. [PMID: 29982573 DOI: 10.1093/jac/dky157] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objectives This study characterized the 11 most predominant serotypes of invasive Streptococcus pneumoniae infections collected by the annual SAVE study in Canada, between 2011 and 2015. Methods A subset of the 11 most predominant serotypes (7F, 19A, 22F, 3, 12F, 11A, 9N, 8, 33F, 15A and 6C) collected by the SAVE study was analysed using PFGE and MLST, as well as PCR to identify pilus-encoding genes. WGS analyses were performed on a subset of the above isolates plus a random selection of background strains. Results Of the predominant serotypes analysed, 7F, 33F and 19A were obtained more commonly from children <6 years of age, whereas 15A, 6C, 22F and 11A were more common in adults >65 years of age. Pneumococcal pilus PI-1 was identified in antimicrobial-susceptible serotype 15A (61/212) and <10% of 6C isolates (16/188). PI-2 was found in serotype 7F (683/701) and two-thirds of 11A isolates (162/241). Only serotype 19A-ST320 possessed both pili. Molecular and phylogenetic analyses identified serotypes 19A, 15A, 6C, 9N and 33F as highly diverse, whereas 7F, 22F and 11A demonstrated clonality. Antimicrobial resistance determinants were common within diverse serotypes, and usually similar within a clonal complex. Conclusions Despite successful use of conjugate vaccines, S. pneumoniae remains a highly diverse organism in Canada. Several predominant serotypes, both antimicrobial susceptible and MDR, have demonstrated rapid clonal expansion or an increase in diversity. As S. pneumoniae continues to evolve in Canada, WGS will be a necessary component in the ongoing surveillance of antimicrobial-resistant and expanding clones.
Collapse
Affiliation(s)
- Alyssa R Golden
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Heather J Adam
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie Baxter
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | - Kimberly A Nichol
- Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Irene Martin
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Walter Demczuk
- National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Paul Van Caeseele
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Cadham Provincial Laboratory, 750 William Avenue, Winnipeg, Manitoba R3E 3J7, Canada
| | - Jonathan B Gubbay
- Public Health Ontario, 661 University Avenue, Toronto, Ontario M5G 1M1, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, 20045 Ch Ste-Marie, Ste-Anne-de-Bellevue, Québec H9X 3R5, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, 5 Research Drive, Regina, Saskatchewan S4S 0A4, Canada
| | - George Zahariadis
- Newfoundland and Labrador Public Health Laboratory, Dr. Leonard A. Miller Centre - Suite 1, 100 Forest Road, St John's, Newfoundland and Labrador A1A 1E3, Canada
| | - David Haldane
- Queen Elizabeth II Health Science Centre, 5805 South Street, Halifax, Nova Scotia B3H 1V8, Canada
| | - Rita Gad
- New Brunswick Department of Health, 520 King Street, Fredericton, New Brunswick E3B 5G8, Canada
| | - Gregory German
- Health PEI, 16 Garfield Street, Charlottetown, Prince Edward Island C1A 7N8, Canada
| | - Matthew W Gilmour
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,National Microbiology Laboratory - Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba R3E 3R2, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada.,Clinical Microbiology - Health Sciences Centre, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, 727 McDermot Avenue, Winnipeg, Manitoba R3E 3P5, Canada
| | | |
Collapse
|
18
|
Shewmaker PL, Whitney AM, Gulvik CA, Humrighouse BW, Gartin J, Moura H, Barr JR, Moore ERB, Karlsson R, Pinto TCA, Teixeira LM. Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound. Int J Syst Evol Microbiol 2019; 69:2268-2276. [PMID: 31125302 DOI: 10.1099/ijsem.0.003459] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %). A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.
Collapse
Affiliation(s)
- Patricia L Shewmaker
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Anne M Whitney
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Christopher A Gulvik
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Ben W Humrighouse
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Jarrett Gartin
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Hercules Moura
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
| | - Edward R B Moore
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Culture Collection University of Gothenburg (CCUG), Gothenburg, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden
| | - Roger Karlsson
- Department of Clinical Microbiology, Sahlgrenska University Hospital, SE-41346 Region Västra Götaland, Sweden.,Department of Infectious Disease, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg SE-41346, Sweden.,Nanoxis Consulting AB, SE-40016 Gothenburg, Sweden
| | - Tatiana C A Pinto
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucia M Teixeira
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
19
|
Liu H, Chen X, Hu X, Niu H, Tian R, Wang H, Pang H, Jiang L, Qiu B, Chen X, Zhang Y, Ma Y, Tang S, Li H, Feng S, Zhang S, Zhang C. Alterations in the gut microbiome and metabolism with coronary artery disease severity. MICROBIOME 2019; 7:68. [PMID: 31027508 PMCID: PMC6486680 DOI: 10.1186/s40168-019-0683-9] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/09/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Coronary artery disease (CAD) is associated with gut microbiota alterations in different populations. Gut microbe-derived metabolites have been proposed as markers of major adverse cardiac events. However, the relationship between the gut microbiome and the different stages of CAD pathophysiology remains to be established by a systematic study. RESULTS Based on multi-omic analyses (sequencing of the V3-V4 regions of the 16S rRNA gene and metabolomics) of 161 CAD patients and 40 healthy controls, we found that the composition of both the gut microbiota and metabolites changed significantly with CAD severity. We identified 29 metabolite modules that were separately classified as being positively or negatively correlated with CAD phenotypes, and the bacterial co-abundance group (CAG) with characteristic changes at different stages of CAD was represented by Roseburia, Klebsiella, Clostridium IV and Ruminococcaceae. The result revealed that certain bacteria might affect atherosclerosis by modulating the metabolic pathways of the host, such as taurine, sphingolipid and ceramide, and benzene metabolism. Moreover, a disease classifier based on differential levels of microbes and metabolites was constructed to discriminate cases from controls and was even able to distinguish stable coronary artery disease from acute coronary syndrome accurately. CONCLUSION Overall, the composition and functions of the gut microbial community differed from healthy controls to diverse coronary artery disease subtypes. Our study identified the relationships between the features of the gut microbiota and circulating metabolites, providing a new direction for future studies aiming to understand the host-gut microbiota interplay in atherosclerotic pathogenesis.
Collapse
Affiliation(s)
- Honghong Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Xi Chen
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaomin Hu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Haitao Niu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Ran Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Hui Wang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Haiyu Pang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Lingjuan Jiang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Bintao Qiu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Xiuting Chen
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Yiyangzi Ma
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Si Tang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Hanyu Li
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Siqin Feng
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Science, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
20
|
Hung WW, Chen YH, Tseng SP, Jao YT, Teng LJ, Hung WC. Using groEL as the target for identification of Enterococcus faecium clades and 7 clinically relevant Enterococcus species. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 52:255-264. [PMID: 30473144 DOI: 10.1016/j.jmii.2018.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND/PURPOSE Accurate identification is important for effective treatment because Enterococcus species have talents to cope with various antibiotics either by intrinsic resistance or by acquisition of mobile genetic elements. The groEL gene is a permissive target in identification of bacteria. We aimed to develop simple assays based on groEL for identification of enterococci. RESULTS We continued our previous work and determined groEL gene sequences of Enterococcus species isolated from clinical specimens. Phylogenetic analysis based on groEL revealed that each strain clustered well with their reference strains (bootstrap value 100%), in which Enterococcusfaecium and Enterococcusgallinarum could be split into two clades. The divergence of E. faecium was coincident with hospital-associated clade, known as clade A, and community-associated clade, known as clade B. A PCR-restriction fragment length polymorphism (PCR-RFLP) assay was therefore designed to differentiate the two E. faecium clades, based on the specific RsaI cutting sites present in the two clades. To differentiate 7 clinical relevant Enterococcus species, the multiplex PCR assay was designed to identify Enterococcusavium, Enterococcuscasseliflavus, Enterococcusfaecalis, E. faecium, E. gallinarum, Enterococcushirae and Enterococcusraffinosus. Specificity was tested with other Enterococcus species including Enterococcuscecorum, Enterococcusdurans and Enterococcusmundtii. None of these bacterial species generated products of similar size to those of the seven Enterococcus species. CONCLUSION The simple PCR-RFLP and multiplex PCR assays on the basis of groEL gene provided an alternative way to identify Enterococcus species.
Collapse
Affiliation(s)
- Wei-Wen Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Ting Jao
- Infection Control Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| |
Collapse
|
21
|
Aydın F, Güneş V, Çakır Bayram L, Abay S, Karakaya E, Varol K, Ekinci G, Gümüşsoy KS, Müştak HK, Diker KS. Neonatal calf meningitis associated with Streptococcus gallolyticus subsp. gallolyticus. Folia Microbiol (Praha) 2018; 64:223-229. [DOI: 10.1007/s12223-018-0649-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
|
22
|
Adam HJ, Golden AR, Karlowsky JA, Baxter MR, Nichol KA, Martin I, Demczuk W, Mulvey MR, Gilmour MW, Hoban DJ, Zhanel GG. Analysis of multidrug resistance in the predominant Streptococcus pneumoniae serotypes in Canada: the SAVE study, 2011–15. J Antimicrob Chemother 2018; 73:vii12-vii19. [DOI: 10.1093/jac/dky158] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Heather J Adam
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Alyssa R Golden
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - James A Karlowsky
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Melanie R Baxter
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | - Kim A Nichol
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Michael R Mulvey
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Matthew W Gilmour
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington St, Winnipeg, Manitoba R3E 3M4, Canada
| | - Daryl J Hoban
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
- Clinical Microbiology, Diagnostic Services Manitoba, MS673-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada
| | - George G Zhanel
- Department of Medical Microbiology, Max Rady College of Medicine, University of Manitoba, Room 543 - 745 Bannatyne Avenue, Winnipeg, Manitoba R3E 0J9, Canada
| | | |
Collapse
|
23
|
Demczuk WHB, Martin I, Desai S, Griffith A, Caron-Poulin L, Lefebvre B, McGeer A, Tyrrell GJ, Zhanel GG, Gubbay J, Hoang L, Levett PN, Van Caeseele P, Raafat Gad R, Haldane D, Zahariadis G, German G, Daley Bernier J, Strudwick L, Mulvey MR. Serotype distribution of invasive Streptococcus pneumoniae in adults 65 years of age and over after the introduction of childhood 13-valent pneumococcal conjugate vaccination programs in Canada, 2010-2016. Vaccine 2018; 36:4701-4707. [PMID: 29937245 DOI: 10.1016/j.vaccine.2018.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 05/24/2018] [Accepted: 06/06/2018] [Indexed: 01/22/2023]
Abstract
The 13-valent conjugate vaccine (PCV13) was recommended for childhood immunization programs in 2010 in Canada and has decreased the incidence of invasive pneumococcal disease (IPD) in children and changed the epidemiology of IPD in adults. This study investigated the epidemiology of IPD in adults 65 years of age and older in Canada. A total of 7282 invasive S. pneumoniae isolated from adults ≥65 years old were serotyped from 2010 to 2016 and antimicrobial susceptibility was performed on 2527 isolates. Serotyping was performed by Quellung reaction using commercial antisera and antimicrobial susceptibilities were determined by broth microdilution. PCV7 serotypes decreased non-significantly from 2010 to 2016 from 9.1% (n = 96) to 6.7% (n = 72) while the additional six PCV13 serotypes declined significantly from 39.5% (n = 418) to 18.6% (n = 201) (p < 0.05). The 23-valent pneumococcal polysaccharide vaccine (PPV23) and non-vaccine (NVT) serotypes increased from 26.3% (n = 278) to 36.2% (n = 393) (p < 0.05), and from 25.1% (n = 266) to 38.4% (n = 416) (p < 0.05), respectively. There were no significant changes in antimicrobial resistance rates from 2011 to 2016: 24.1% of the IPD from adults ≥65 years were resistant to clarithromycin (n = 609), 10.0% to doxycycline (n = 254), 11.8% to penicillin (n = 299), 5.2% to cefuroxime (n = 131), 6.6% to clindamycin (n = 168), 6.0% to trimethoprim-sulfamethoxazole (n = 152), and 0.5% (n = 12) to ceftriaxone. Although overall incidence of IPD in adults ≥65 years has remained relatively constant from 2010 to 2016, childhood PCV13 vaccination programs have been successful in indirectly reducing IPD caused by PCV13 serotypes in adults through herd immunity effects.
Collapse
Affiliation(s)
- Walter H B Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Shalini Desai
- Vaccine Preventable Diseases Section, Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Averil Griffith
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Laurence Caron-Poulin
- Vaccine Preventable Diseases Section, Surveillance and Epidemiology Division, Centre for Immunization and Respiratory Infectious Diseases, Public Health Agency of Canada, Ottawa, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Ste-Anne-de-Bellevue, Québec, Canada
| | - Allison McGeer
- Toronto Invasive Bacterial Diseases Network (TIBDN), Department of Microbiology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gregory J Tyrrell
- The Provincial Laboratory for Public Health (Microbiology), Edmonton, Alberta, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Linda Hoang
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Paul N Levett
- Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada
| | | | - Rita Raafat Gad
- New Brunswick, Office of the Chief Medical Officer of Health, New Brunswick Department of Health, Fredericton, New Brunswick, Canada
| | - David Haldane
- Queen Elizabeth II Health Science Centre, Halifax, Nova Scotia, Canada
| | - George Zahariadis
- Newfoundland Public Health Laboratory, St. John's, Newfoundland and Labrador, Canada
| | - Gregory German
- Queen Elizabeth Hospital, Charlottetown, Prince Edward Island, Canada
| | | | - Lori Strudwick
- Yukon Communicable Disease Control, Government of Yukon, Whitehorse, Yukon, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| |
Collapse
|
24
|
Niu L, Hu S, Lu S, Lai XH, Yang J, Jin D, Rao L, Lu G, Xu J. Isolation and characterization of Streptococcus respiraculi sp. nov. from Marmota himalayana (Himalayan marmot) respiratory tract. Int J Syst Evol Microbiol 2018; 68:2082-2087. [PMID: 29717973 DOI: 10.1099/ijsem.0.002806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Two bacterial strains were individually isolated from Marmota himalayana respiratory tracts; the animals were from the Tibet-Qinghai Plateau, PR China. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of 16S rRNA gene sequences indicated that the type strain HTS25T shared 98.0, 97.4, 97.2 and 97.1 % similarity with Streptococcus cuniculi, Streptococcus acidominimus, Streptococcus marmotae and Streptococcus himalayensis respectively. Sequence analysis of the sodA and rpoB genes indicated that HTS25T was closely related to S. marmotae (similarities of 94.7 and 91.4 % respectively). Analysis of groEL sequences showed interspecies similarity of 84.8 % between HTS25T and S. himalayensis. A whole-genome phylogenetic tree reconstructed from 81 core genes from the genomes of 17 members of the genus Streptococcus was used to validate that HTS25T forms a distinct subline from other recognized species of the genus Streptococcus. DNA-DNA hybridization of HTS25T showed a maximum estimated DNA reassociation value of 32.1 % to Streptococcus cuniculi CCUG 65085T. On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two isolates be classified as representing a novel species of the genus Streptococcus, named Streptococcus respiraculi sp. nov. The type strain is HTS25T (=DSM 101998T=CGMCC 1.15531T). The genome of Streptococcus respiraculi sp. nov. strain HTS25T (2 067 971 bp) contains 2001 genes with an average DNA G+C content of 42.7 mol%.
Collapse
Affiliation(s)
- Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shoukui Hu
- Peking University shougang hospital, Beijing 100144, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- School of Biology and Food Sciences, Shangqiu Normal University, Shangqiu, Henan 476000, PR China.,Central Laboratory of Ganzhou People's Hospital, Ganzhou, Jiangxi Province 341000, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Langyu Rao
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China
| | - Gang Lu
- Department of Pathogen Biology, School of Basic Medicine and Life Science, Hainan Medical University; Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University); Hainan Medical University-University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou 571199, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
25
|
Shewmaker PL, Whitney AM, Gulvik CA, Lipman NS. Streptococcus azizii sp. nov., isolated from naïve weanling mice. Int J Syst Evol Microbiol 2017; 67:5032-5037. [PMID: 29022542 DOI: 10.1099/ijsem.0.002407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three isolates of a previously reported novel catalase-negative, Gram-stain-positive, coccoid, alpha-haemolytic, Streptococcus species that were associated with meningoencephalitis in naïve weanling mice were further evaluated to confirm their taxonomic status and to determine additional phenotypic and molecular characteristics. Comparative 16S rRNA gene sequence analysis showed nearly identical intra-species sequence similarity (≥99.9 %), and revealed the closest phylogenetically related species, Streptococcus acidominimus and Streptococcuscuniculi, with 97.0 and 97.5 % sequence similarity, respectively. The rpoB, sodA and recN genes were identical for the three isolates and were 87.6, 85.7 and 82.5 % similar to S. acidominimus and 89.7, 86.2 and 80.7 % similar to S. cuniculi, respectively. In silico DNA-DNA hybridization analyses of mouse isolate 12-5202T against S. acidominimus CCUG 27296T and S. cuniculi CCUG 65085T produced estimated values of 26.4 and 25.7 % relatedness, and the calculated average nucleotide identity values were 81.9 and 81.7, respectively. These data confirm the taxonomic status of 12-5202T as a distinct Streptococcus species, and we formally propose the type strain, Streptococcusazizii 12-5202T (=CCUG 69378T=DSM 103678T). The genome of Streptococcus azizii sp. nov. 12-5202T contains 2062 total genes with a size of 2.34 Mbp, and an average G+C content of 42.76 mol%.
Collapse
Affiliation(s)
| | - Anne M Whitney
- Centers for Disease Control and Prevention, Atlanta, Georgia 30329, USA
| | | | - Neil S Lipman
- Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
26
|
Current challenges in the accurate identification of Streptococcus pneumoniae and its serogroups/serotypes in the vaccine era. J Microbiol Methods 2017; 141:48-54. [DOI: 10.1016/j.mimet.2017.07.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/21/2022]
|
27
|
Kmiha S, Aouadhi C, Klibi A, Jouini A, Béjaoui A, Mejri S, Maaroufi A. Seasonal and regional occurrence of heat-resistant spore-forming bacteria in the course of ultra-high temperature milk production in Tunisia. J Dairy Sci 2017; 100:6090-6099. [PMID: 28571988 DOI: 10.3168/jds.2016-11616] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/12/2016] [Indexed: 11/19/2022]
Abstract
Spore-forming bacteria, principally Bacillus species, are important contaminants of milk. Because of their high heat resistance, Bacillus species spores are capable of surviving the heat treatment process of milk and lead to spoilage of the final product. To determine the factors influencing the contamination of milk, spore-forming bacteria occurrence throughout the UHT milk production line during winter, spring, and summer was studied. The obtained results confirm that the total viable rate decreases rapidly throughout the production line of UHT milk showing the efficiency of thermal treatments used. However, the persistent high rate of spore-forming bacteria indicates their high heat resistance, especially in spring and summer. In addition, a significant variation of the quality of raw milk according to the location of the collecting centers was revealed. The molecular identification showed a high degree of diversity of heat-resistant Bacillus species, which are isolated from different milk samples. The distribution of Bacillus species in raw milk, stored milk, bactofuged milk, pasteurized milk, and UHT milk were 28, 10, 16, 13, and 33%, respectively. Six Bacillus spp. including Bacillus licheniformis (52.38%), Bacillus pumilus (9.52%), Bacillus sp. (4.76%), Bacillus sporothermodurans (4.76%), Terribacillus aidingensis (4.76%), and Paenibacillus sp. (4.76%) were identified in different milk samples.
Collapse
Affiliation(s)
- S Kmiha
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia
| | - C Aouadhi
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia.
| | - A Klibi
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia
| | - A Jouini
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia
| | - A Béjaoui
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia
| | - S Mejri
- Laboratory of Animal Resources and Food, National Institute of Agronomy, University of Carthage, Tunis (INAT) Tunisia, 43, Rue Charles Nicole, Cité Mahrajène, Le Belvédère, 1082 Tunis, Tunisia
| | - A Maaroufi
- Laboratory of Epidemiology and Veterinary Microbiology, Group of Bacteriology and Biotechnology, Pasteur Institute of Tunisia (IPT), University of Tunis El Manar (UTM), 2092 Tunis, Tunisia
| |
Collapse
|
28
|
Christ APG, Ramos SR, Cayô R, Gales AC, Hachich EM, Sato MIZ. Characterization of Enterococcus species isolated from marine recreational waters by MALDI-TOF MS and Rapid ID API® 20 Strep system. MARINE POLLUTION BULLETIN 2017; 118:376-381. [PMID: 28318563 DOI: 10.1016/j.marpolbul.2017.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 06/06/2023]
Abstract
MALDI-TOF Mass Spectrometry Biotyping has proven to be a reliable method for identifying bacteria at the species level based on the analysis of the ribosomal proteins mass fingerprint. We evaluate the usefulness of this method to identify Enterococcus species isolated from marine recreational water at Brazilian beaches. A total of 127 Enterococcus spp. isolates were identified to species level by bioMérieux's API® 20 Strep and MALDI-TOF systems. The biochemical test identified 117/127 isolates (92%), whereas MALDI identified 100% of the isolates, with an agreement of 63% between the methods. The 16S rRNA gene sequencing of isolates with discrepant results showed that MALDI-TOF and API® correctly identified 74% and 11% of these isolates, respectively. This discrepancy probably relies on the bias of the API® has to identify clinical isolates. MALDI-TOF proved to be a feasible approach for identifying Enterococcus from environmental matrices increasing the rapidness and accuracy of results.
Collapse
Affiliation(s)
- Ana Paula Guarnieri Christ
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Solange Rodrigues Ramos
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Rodrigo Cayô
- UNIFESP - Universidade Federal de São Paulo, Department of Medicine, ALERTA Laboratory, São Paulo - SP, Brazil
| | - Ana Cristina Gales
- UNIFESP - Universidade Federal de São Paulo, Department of Medicine, ALERTA Laboratory, São Paulo - SP, Brazil
| | - Elayse Maria Hachich
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil
| | - Maria Inês Zanoli Sato
- CETESB - Companhia Ambiental do Estado de São Paulo, Department of Environmental Analysis, São Paulo - SP, Brazil.
| |
Collapse
|
29
|
Members of a new subgroup of Streptococcus anginosus harbor virulence related genes previously observed in Streptococcus pyogenes. Int J Med Microbiol 2017; 307:174-181. [DOI: 10.1016/j.ijmm.2017.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/15/2016] [Accepted: 02/24/2017] [Indexed: 11/22/2022] Open
|
30
|
Niu L, Lu S, Lai XH, Hu S, Chen C, Zhang G, Yang J, Jin D, Wang Y, Lan R, Lu G, Xie Y, Ye C, Xu J. Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2017; 67:256-261. [PMID: 27902227 DOI: 10.1099/ijsem.0.001609] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five Marmota himalayana animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus Streptococcus, being phylogenetically closest to Streptococcus marmotae DSM 101995T (98.4 % similarity). The groEL, sodA and rpoB sequence analysis showed interspecies similarity values between HTS2T and Streptococcus. marmotae DSM 101995T, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus Streptococcus validated that HTS2T forms a distinct subline and exhibits specific phylogenetic affinity with S. marmotae. In silico DNA-DNA hybridization of HTS2T showed an estimated DNA reassociation value of 40.5 % with Streptococcus. marmotae DSM 101995T. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus Streptococcus, Streptococcus himalayensis sp. nov. The type strain is HTS2T (=DSM 101997T=CGMCC 1.15533T). The genome of Streptococcus himalayensis sp. nov. strain HTS2T contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.
Collapse
Affiliation(s)
- Lina Niu
- School of Life Science, Shanxi University, Taiyuan 030006, PR China.,Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikoux, PR China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Department of Pediatrics, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Shoukui Hu
- Peking University Shougang Hospital, Beijing 100144, PR China
| | - Cuixia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Gui Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yi Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gang Lu
- Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, School of Tropical and Laboratory Medicine, Hainan Medical University, Haikoux, PR China
| | - Yingping Xie
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
31
|
Doll EV, Scherer S, Wenning M. Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination. Front Microbiol 2017; 8:135. [PMID: 28197147 PMCID: PMC5281617 DOI: 10.3389/fmicb.2017.00135] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/19/2017] [Indexed: 01/28/2023] Open
Abstract
Premature spoilage and varying product quality due to microbial contamination still constitute major problems in the production of microfiltered and pasteurized extended shelf life (ESL) milk. Spoilage-associated bacteria may enter the product either as part of the raw milk microbiota or as recontaminants in the dairy plant. To identify spoilage-inducing bacteria and their routes of entry, we analyzed end products for their predominant microbiota as well as the prevalence and biodiversity of psychrotolerant spores in bulk tank milk. Process analyses were performed to determine the removal of psychrotolerant spores at each production step. To detect transmission and recontamination events, strain typing was conducted with isolates obtained from all process stages. Microbial counts in 287 ESL milk packages at the end of shelf life were highly diverse ranging from <1 to 7.9 log cfu/mL. In total, 15% of samples were spoiled. High G+C Gram-positive bacteria were the most abundant taxonomic group, but were responsible for only 31% of spoilage. In contrast, psychrotolerant spores were isolated from 55% of spoiled packages. In 90% of samples with pure cultures of Bacillus cereus sensu lato and Paenibacillus spp., counts exceeded 6 log cfu/mL. In bulk tank milk, the concentration of psychrotolerant spores was low, accounting for merely 0.5 ± 0.8 MPN/mL. Paenibacillus amylolyticus/xylanexedens was by far the most dominant species in bulk tank milk (48% of all isolates), but was never detected in ESL milk, pointing to efficient removal during manufacturing. Six large-scale process analyses confirmed a high removal rate for psychrotolerant spores (reduction by nearly 4 log-units). B. cereus sensu lato, on the contrary, was frequently found in spoiled end products, but was rarely detected in bulk tank milk. Due to low counts in bulk tank samples and efficient spore removal during production, we suggest that shelf life is influenced only to a minor extent by raw-milk-associated factors. In contrast, recontamination with spores, particularly from the B. cereus complex, seems to occur. To enhance milk quality throughout the entire shelf life, improved plant sanitation and disinfection that target the elimination of spores are necessary.
Collapse
Affiliation(s)
| | | | - Mareike Wenning
- Chair of Microbial Ecology, Institute for Food and Health, Technische Universität MünchenFreising, Germany
| |
Collapse
|
32
|
Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm. J Clin Microbiol 2017; 55:914-922. [PMID: 28053215 DOI: 10.1128/jcm.01990-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcusmitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae, whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper.
Collapse
|
33
|
Ricaboni D, Mailhe M, Lagier JC, Michelle C, Armstrong N, Bittar F, Vitton V, Benezech A, Raoult D, Million M. Noncontiguous finished genome sequence and description of Streptococcus timonensis sp. nov. isolated from the human stomach. New Microbes New Infect 2017; 15:77-88. [PMID: 28050252 PMCID: PMC5192475 DOI: 10.1016/j.nmni.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/26/2016] [Accepted: 11/04/2016] [Indexed: 12/31/2022] Open
Abstract
Strain Marseille-P2915T, a Gram-positive, facultative anaerobic and nonmotile coccus, was isolated from the gastric lavage of a patient with severe anaemia. The 16S rRNA and rpoB gene comparison exhibited a sequence identity of 98.7 and 92.6% with Streptococcus infantis strain JCM 10157T, respectively, collocating it within the 'Streptococcus mitis' group. On the basis of phenotypic and genomic analysis, we propose the validation of the type strain Streptococcus timonensis sp. nov. Marseille-P2915T (= DSM 103349 = CSUR P2915).
Collapse
Affiliation(s)
- D. Ricaboni
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Department of Biomedical and Clinical Sciences, 3rd Division of Clinical Infectious Disease, University of Milan, Luigi Sacco Hospital, Milan, Italy
| | - M. Mailhe
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - N. Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - V. Vitton
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - A. Benezech
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - M. Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| |
Collapse
|
34
|
Martinez BA, Stratton J, Bianchini A. Isolation and genetic identification of spore-forming bacteria associated with concentrated-milk processing in Nebraska. J Dairy Sci 2016; 100:919-932. [PMID: 27988120 DOI: 10.3168/jds.2016-11660] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022]
Abstract
Spore-forming bacteria are heat-resistant microorganisms capable of surviving and germinating in milk after pasteurization. They have been reported to affect the quality of dairy products by the production of enzymes (lipolytic and proteolytic) under low-temperature conditions in fluid milk, and have become a limiting factor for milk powder in reaching some selective markets. The objective of this research was to isolate and identify the population of spore-forming bacteria (psychrotrophic and thermophilic strains) associated with concentrated milk processing in Nebraska. During 2 seasons, in-process milk samples from a commercial plant (raw, pasteurized, and concentrated) were collected and heat-treated (80°C/12 min) to recover only spore-formers. Samples were spread-plated using standard methods agar and incubated at 32°C to enumerate mesophilic spore counts. Heat-treated samples were also stored at 7°C and 55°C to recover spore-formers that had the ability to grow under those temperature conditions. Isolates obtained from incubation or storage conditions were identified using molecular techniques (16S or rpoB sequencing). Based on the identification of the isolates and their relatedness, strains found in raw, pasteurized, and concentrated milk were determined to be similar. Paenibacillus spp. were associated with both raw and concentrated milk. Due to their known ability to cause spoilage under refrigeration, this shows the potential risk associated with the transferring of these problematic organisms into other dairy products. Other Bacillus species found in concentrated milk included Bacillus clausii, Bacillus subtilis, Lysinibacillus sp., Bacillus safensis, Bacillus licheniformis, Bacillus sonorensis, and Brevibacillus sp., with the last 3 organisms being capable of growing at thermophilic temperatures. These strains can also be translocated to other dairy products, such as milk powder, representing a quality problem. The results of this research highlight the importance of understanding spore-formers associated with the processing of condensed milk, which then may allow for specific interventions to be applied to control these microorganisms in this processing chain. To our knowledge, this is the first study evaluating spore-formers associated with concentrated milk in the United States.
Collapse
Affiliation(s)
- Bismarck A Martinez
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588
| | - Jayne Stratton
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588; The Food Processing Center, University of Nebraska-Lincoln, Lincoln 68588
| | - Andreia Bianchini
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln 68588; The Food Processing Center, University of Nebraska-Lincoln, Lincoln 68588.
| |
Collapse
|
35
|
Martín V, Mediano P, Del Campo R, Rodríguez JM, Marín M. Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci. J Hum Lact 2016; 32:NP84-NP94. [PMID: 26261225 DOI: 10.1177/0890334415597901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND The genus Streptococcus is 1 of the dominant bacterial groups in human milk, but the taxonomic identification of some species remains difficult. OBJECTIVE The objective of this study was to investigate the discriminatory ability of different methods to identify streptococcal species in order to perform an assessment of the streptococcal diversity of human milk microbiota as accurately as possible. METHODS The identification of 105 streptococcal strains from human milk was performed by 16S rRNA, tuf, and sodA gene sequencing, phylogenetic analysis, and Matrix Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) mass spectrometry. RESULTS Streptococcus salivarius, Streptococcus mitis, and Streptococcus parasanguinis were the streptococcal dominant species in the human milk microbiota. Sequencing of housekeeping genes allowed the classification of 96.2% (16S rRNA), 84.8% ( sodA), and 88.6% ( tuf) of the isolates. Phylogenetic analysis showed 3 main streptococcal clusters corresponding with the mitis (73 isolates), salivarius (29), mutans (1)-pyogenic (2) groups, but many of the mitis group isolates (36) could not be assigned to any species. The application of the MALDI-TOF Bruker Biotyper system resulted in the identification of 56 isolates (53.33%) at the species level, but it could not discriminate between S pneumoniae and S mitis isolates, in contrast to the Vitek-MS system. CONCLUSION There was a good agreement among the different methods assessed in this study to identify those isolates of the salivarius, mutans, and pyogenic groups, whereas unambiguous discrimination could not be achieved concerning some species of the mitis group ( S mitis, S pneumoniae, S pseudopneumoniae, S oralis).
Collapse
Affiliation(s)
- Virginia Martín
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Pilar Mediano
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa Del Campo
- 2 Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Juan M Rodríguez
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - María Marín
- 1 Departamento de Nutrición, Bromatología y Tecnología de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
36
|
Niu L, Lu S, Hu S, Jin D, Lai X, Yang J, Chen C, Wang Y, Wang Y, Bai X, Lan R, Lv G, Xie Y, Ye C, Xu J. Streptococcusmarmotae sp. nov., isolated from the respiratory tract of Marmota himalayana. Int J Syst Evol Microbiol 2016; 66:4315-4322. [PMID: 27473166 DOI: 10.1099/ijsem.0.001350] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Five strains of a Gram-stain-positive, catalase-negative, α-haemolytic, coccus-shaped chain-forming organism were isolated separately from the lower respiratory tracts of five animals of Marmota himalayana in the endemic area of plague, the Qinghai-Tibet Plateau, China. Based on their morphological characteristics, biochemical features and molecular phylogenetic studies, the strains were placed as representing a new member of the genus Streptococcus. Comparative 16S rRNA gene sequence studies indicated that strain HTS5T shared 96.5, 96.2 and 96.0 % similarity with Streptococcus gallinaceus CCUG 42692T, Streptococcus parasanguinis ATCC 15912T and Streptococcus suis ATCC 43765T, respectively. Sequence analysis of its rpoB and sodA genes showed that strain HTS5T was most closely related to Streptococcus cuniculi CCUG 65085T with 9.2 and 10.9 % interspecies divergence, respectively. The whole genome phylogenetic tree based on 339 core genes of 65 Streptococcus genomes confirmed that HTS5T belongs to a distinct lineage that is well separated from recognized species of the genus Streptococcus. In silico DNA-DNA hybridization using 65 available genomes from GenBank showed that HTS5T displayed less than 70 % DNA-DNA relatedness with the other 65 species of the genus Streptococcus deposited in the GenBank database. The genome of strain HTS5T (2 322 791 bp) contained 2377 genes and had a G+C content of 41.6 mol%. Therefore, the five strains are considered to represent a novel species of the genus Streptococcus for which the name Streptococcusmarmotae sp. nov. is proposed. The type strain is HTS5T (=DSM 101995T=CGMCC 1.15534T).
Collapse
Affiliation(s)
- Lina Niu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,School of Life Science, Shanxi University, Taiyuan 030006, PR China.,School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xinhe Lai
- Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Inflammation and Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Cuixia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yi Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yiting Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gang Lv
- School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
| | - Yingping Xie
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
37
|
Niu L, Lu S, Hu S, Jin D, Lai X, Yang J, Chen C, Wang Y, Bai X, Lan R, Lv G, Xie Y, Ye C, Xu J. Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2016; 66:4211-4217. [PMID: 27469933 DOI: 10.1099/ijsem.0.001337] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9T and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus. They are most closely related to Streptococcus thoraltensis CIP 105518T based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9T forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis. In silico DNA-DNA hybridization of HTS9T showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518T. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA-DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus), we propose with confidence that strains HTS9T and HTS12 should be classified as representing a novel species of the genus Streptococcus, Streptococcus halotolerans sp. nov. The type strain is HTS9T (=DSM 101996T=CGMCC1.15532T). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.
Collapse
Affiliation(s)
- Lina Niu
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
- School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xinhe Lai
- Institute of Inflammation and Diseases, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
- Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Cuixia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yiting Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Gang Lv
- School of Tropical and Laboratory Medicine, Hainan Medical University, Key Laboratory of Translation Medicine Tropical Diseases (Hainan Medical University), Ministry of Education, Haikou, PR China
| | - Yingping Xie
- School of Life Science, Shanxi University, Taiyuan 030006, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
38
|
Bai X, Xiong Y, Lu S, Jin D, Lai X, Yang J, Niu L, Hu S, Meng X, Pu J, Ye C, Xu J. Streptococcuspantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016; 66:3281-3286. [PMID: 27226124 DOI: 10.1099/ijsem.0.001189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Two bacterial strains were isolated from faecal samples of Tibetan antelopes. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped organisms that were tentatively identified as representing a novel streptococcal species based on their morphological features, biochemical test results and phylogenomic findings. Comparative 16S rRNA gene sequencing studies confirmed that the organisms were members of the genus Streptococcus, but they did not correspond to any recognized species of the genus. The nearest phylogenetic relative of the unknown coccus was Streptococcus ursoris NUM 1615T (93.4 % 16S rRNA gene sequence similarity). Analysis of groEL and rpoB gene sequences of the novel isolates showed interspecies divergence of 27.0 and 22.2 %, respectively, from the type strain of its closest 16S rRNA gene phylogenetic relative, S. ursoris. The complete genome of strain TA 26T has been sequenced. Digital DNA-DNA hybridization studies between strain TA 26T and other species of the genus Streptococcus deposited in the GenBank database showed less than 70 % DNA-DNA relatedness, supporting a novel species status of the strain. On the basis of their genotypic and phenotypic differences from recognized Streptococcus species, the two isolates represent a novel species of the genus Streptococcus, for which the nameStreptococcus pantholopis sp. nov. (type strain TA 26T=CGMCC 1.15667T=DSM 102135T) is proposed.
Collapse
Affiliation(s)
- Xiangning Bai
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Yanwen Xiong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Shan Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xinhe Lai
- Institute of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China.,Institute of Inflammation and Diseases, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, PR China
| | - Jing Yang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Lina Niu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China.,School of Tropical and Laboratory Medicine, Hainan Medical University, Haikou, PR China
| | - Shoukui Hu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Xiangli Meng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Changyun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| | - Jianguo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, China CDC, Beijing, PR China
| |
Collapse
|
39
|
Clinical features and outcome of bone and joint infections with streptococcal involvement: 5-year experience of interregional reference centres in the south of France. New Microbes New Infect 2016; 12:8-17. [PMID: 27222712 PMCID: PMC4872313 DOI: 10.1016/j.nmni.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 01/10/2023] Open
Abstract
Streptococcal bone and joint infections are less common than staphylococcal cases. Few studies have reported the cases with well-identified Streptococcus species. Their clinical features and prognosis are not clearly known to date. Moreover, no treatment regimen has yet been clarified. We reviewed the streptococcal bone and joint infection cases managed in our centres from January 2009 to December 2013. We described the epidemiology, clinical and microbiologic characteristics, treatment approach and outcome. Among the 93 cases, 83% of patients were men with a median age of 60 years, and 90% of patients had comorbidities or risk factors. Bacteraemia occurred in 14% of cases. Serious complications occurred in six patients, including severe sepsis (two cases) and infective endocarditis (two cases). Orthopaedic device infections were observed in 35% of cases, including 17 patients with internal osteosynthesis device infection, 14 with prosthetic joint infection and three with vertebral osteosynthesis device infection. The median time between orthopaedic device implantation and onset of infection was 447 days. Fourteen species of Streptococcus were identified, including 97 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and three isolates using molecular identification. The five most represented species included S. agalactiae (37%), S. dysgalactiae (12%), S. anginosus (11%), S. constellatus (10%) and S. pneumoniae (9%). Streptococci isolates were susceptible to amoxicillin, with the exception of one S. mitis isolate. Remission 1 year after the end of treatment was recorded in 83%. One patient died of infection; eight patients had infections that failed to respond to treatment; and seven patients experienced relapse. Twenty patients (22%) had an unfavourable functional outcome, including 19 amputations and one arthrodesis. Five significant prognostic factors associated with an unfavourable clinical outcome were identified, including peripheral neuropathy (p 0.009), peripheral arterial disease (p 0.019), diabetes mellitus (p 0.031), location in the femur (p 0.0036), location in the foot (p 0.0475), osteitis without an orthopaedic device (p 0.041) and infection caused by S. dysgalactiae (p 0.020). The rate of poor outcomes remains high despite the low number of Streptococcus isolates resistant to antibiotics. Some prognostic factors, such as the presence of S. dysgalactiae, are associated with an unfavourable clinical outcome. Antibiotic regimens of streptococcal bone and joint infections are not standardized and need to be further investigated.
Collapse
|
40
|
Gioia G, Werner B, Nydam DV, Moroni P. Validation of a mycoplasma molecular diagnostic test and distribution of mycoplasma species in bovine milk among New York State dairy farms. J Dairy Sci 2016; 99:4668-4677. [PMID: 27016831 DOI: 10.3168/jds.2015-10724] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/09/2016] [Indexed: 11/19/2022]
Abstract
Mycoplasma mastitis is a contagious and costly disease of dairy cattle that significantly affects animal health and milk productivity. Mycoplasma bovis is the most prevalent and invasive agent of mycoplasma mastitis in dairy cattle, and early detection is critical. Other mycoplasma have been isolated from milk; however, the role and prevalence of these species as mastitis pathogens are poorly understood. Routine screening of milk for mycoplasma by bacteriological culture is an important component of a farm control strategy to minimize a herd mycoplasma outbreak, but phenotypic methods have limited ability to speciate mycoplasma, affecting how farms and practitioners can understand the role and effect of species other than M. bovis in herd health. Fastidious mycoplasma culture can be lengthy and inconclusive, resulting in delayed or false negative reports. We developed and validated a multitarget PCR assay that can in the same day confirm or reject a presumptive positive mycoplasma culture found upon bacteriological testing of clinical specimens, further discriminate between Acholeplasma and Mycoplasma, and identify M. bovis. Coupled with sequence analysis isolates can be further identified as bovine mycoplasma Mycoplasma arginini, Mycoplasma alkalescens, Mycoplasma canadense, Mycoplasma bovirhinis, Mycoplasma bovigenitalium, Mycoplasma californicum, Acholeplasma laidlawii, and Acholeplasma oculi. Assay validation included analysis of 845 mycoplasma representing these species and 30 additional bacterial species obtained from routine milk submissions to the Quality Milk Production Services from New York State farms and veterinary clinics between January 2012 and December 2015. Among 95 herds, we found 8 different Mycoplasma species and 3 different Acholeplasma species, with an overall prevalence of M. bovirhinis of 1%, A. oculi of 2%, M. arginini of 2%, M. californicum of 3%, M. canadense of 10%, M. bovigenitalium of 10%, A. laidlawii of 11%, M. alkalescens of 17%, and M. bovis of 78%. More than one mycoplasma was found in 14% of the herds tested, and both M. bovis and Acholeplasma were found in 6% of the farms. Incorporation of the validated molecular diagnostic assay into routine bacteriological screening as a supportive confirmation and identification tool will lead to an improved assessment of Mycoplasma and Acholeplasma prevalence data, which will facilitate increased knowledge about the role of these mycoplasma in mastitis.
Collapse
Affiliation(s)
- G Gioia
- Quality Milk Production Services, Cornell University, Ithaca, NY 14853
| | - B Werner
- Quality Milk Production Services, Cornell University, Ithaca, NY 14853
| | - D V Nydam
- Quality Milk Production Services, Cornell University, Ithaca, NY 14853
| | - P Moroni
- Quality Milk Production Services, Cornell University, Ithaca, NY 14853; Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, via Celoria 10, 20133 Milan, Italy.
| |
Collapse
|
41
|
Using Nucleic Acid Amplification Techniques in a Syndrome-Oriented Approach: Detection of Respiratory Agents. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
42
|
Vela AI, Mentaberre G, Lavín S, Domínguez L, Fernández-Garayzábal JF. Streptococcus caprae sp. nov., isolated from Iberian ibex (Capra pyrenaica hispanica). Int J Syst Evol Microbiol 2016; 66:196-200. [DOI: 10.1099/ijsem.0.000697] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A. I. Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - G. Mentaberre
- Servei d'Ecopatologia de Fauna Salvatge (SEFAS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, , 08193 Bellaterra, Spain
| | - S. Lavín
- Servei d'Ecopatologia de Fauna Salvatge (SEFAS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, , 08193 Bellaterra, Spain
| | - L. Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - J. F. Fernández-Garayzábal
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| |
Collapse
|
43
|
Lo CI, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Sokhna C, Faye N, Diemé Y, Wade B, Raoult D, Fenollar F. MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa). PLoS One 2015; 10:e0145889. [PMID: 26716681 PMCID: PMC4696746 DOI: 10.1371/journal.pone.0145889] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022] Open
Abstract
Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries.
Collapse
Affiliation(s)
- Cheikh I. Lo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | | | | | | | | | - Oleg Mediannikov
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Ngor Faye
- Université Cheikh Anta Diop, Dakar, Senegal
| | - Yaya Diemé
- Hôpital Principal de Dakar, Dakar, Senegal
| | | | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
| |
Collapse
|
44
|
Kalia VC, Kumar R, Kumar P, Koul S. A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus. Indian J Microbiol 2015; 56:46-58. [PMID: 26843696 DOI: 10.1007/s12088-015-0561-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/13/2015] [Indexed: 12/19/2022] Open
Abstract
The use of rrs (16S rRNA) gene is widely regarded as the "gold standard" for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4-7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.
Collapse
Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| |
Collapse
|
45
|
Vela AI, Casas-Díaz E, Lavín S, Domínguez L, Fernández-Garayzábal JF. Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits. Int J Syst Evol Microbiol 2015; 65:2903-2907. [DOI: 10.1099/ijs.0.000351] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four isolates of an unknown Gram-stain-positive, catalase-negative coccus-shaped organism, isolated from the pharynx of four wild rabbits, were characterized by phenotypic and molecular genetic methods. The micro-organisms were tentatively assigned to the genus Streptococcus based on cellular morphological and biochemical criteria, although the organisms did not appear to correspond to any species with a validly published name. Comparative 16S rRNA gene sequencing confirmed their identification as members of the genus Streptococcus, being most closely related phylogenetically to Streptococcus porcorum 682-03T (96.9 % 16S rRNA gene sequence similarity). Analysis of rpoB and sodA gene sequences showed divergence values between the novel species and S. porcorum 682-03T (the closest phylogenetic relative determined from 16S rRNA gene sequences) of 18.1 and 23.9 %, respectively. The novel bacterial isolate could be distinguished from the type strain of S. porcorum by several biochemical characteristics, such as the production of glycyl-tryptophan arylamidase and α-chymotrypsin, and the non-acidification of different sugars. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be assigned to a novel species of the genus Streptococcus, and named Streptococcus pharyngis sp. nov. The type strain is DICM10-00796BT ( = CECT 8754T = CCUG 66496T).
Collapse
Affiliation(s)
- Ana I. Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
| | - Encarna Casas-Díaz
- Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Santiago Lavín
- Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lucas Domínguez
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| | - Jose F. Fernández-Garayzábal
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, 28040 Madrid, Spain
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040 Madrid, Spain
| |
Collapse
|
46
|
Plumed-Ferrer C, Barberio A, Franklin-Guild R, Werner B, McDonough P, Bennett J, Gioia G, Rota N, Welcome F, Nydam DV, Moroni P. Antimicrobial susceptibilities and random amplified polymorphic DNA-PCR fingerprint characterization of Lactococcus lactis ssp. lactis and Lactococcus garvieae isolated from bovine intramammary infections. J Dairy Sci 2015; 98:6216-25. [PMID: 26142865 DOI: 10.3168/jds.2015-9579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
In total, 181 streptococci-like bacteria isolated from intramammary infections (IMI) were submitted by a veterinary clinic to Quality Milk Production Services (QMPS, Cornell University, Ithaca, NY). The isolates were characterized by sequence analysis, and 46 Lactococcus lactis ssp. lactis and 47 Lactococcus garvieae were tested for susceptibility to 17 antibiotics. No resistant strains were found for β-lactam antibiotics widely used in clinical practice (penicillin, ampicillin, and amoxicillin), and all minimum inhibitory concentrations (MIC) were far from the resistance breakpoints. Eight strains had MIC intermediate to cefazolin. The random amplification of polymorphic DNA (RAPD)-PCR fingerprint patterns showed a slightly higher heterogeneity for Lc. lactis ssp. lactis isolates than for Lc. garvieae isolates.
Collapse
Affiliation(s)
- C Plumed-Ferrer
- Food Biotechnology, Institute of Public Health and Clinical Nutrition, University of Eastern Finland, PO Box 1627, FI-70210 Kuopio, Finland
| | - A Barberio
- Istituto Zooprofilattico Sperimentale delle Venezie, Sez. terr. Vicenza viale Fiume 78, 36100 Vicenza, Italy
| | - R Franklin-Guild
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - B Werner
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - P McDonough
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - J Bennett
- Northern Valley Dairy Production Medicine Center, 900 N Wabasha, Plainview, MN 55964
| | - G Gioia
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - N Rota
- Università degli Studi di Milano, Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, Via Celoria 10, 20133 Milan, Italy
| | - F Welcome
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - D V Nydam
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853
| | - P Moroni
- Cornell University, Animal Health Diagnostic Center, 240 Farrier Road, Ithaca, NY 14853; Università degli Studi di Milano, Dipartimento di Scienze Veterinarie per la Salute, la Produzione Animale e la Sicurezza Alimentare, Via Celoria 10, 20133 Milan, Italy.
| |
Collapse
|
47
|
The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
Collapse
|
48
|
Chen JHK, She KKK, Wong OY, Teng JLL, Yam WC, Lau SKP, Woo PCY, Cheng VCC, Yuen KY. Use of MALDI Biotyper plus ClinProTools mass spectra analysis for correct identification ofStreptococcus pneumoniaeandStreptococcus mitis/oralis. J Clin Pathol 2015; 68:652-6. [DOI: 10.1136/jclinpath-2014-202818] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/22/2015] [Indexed: 12/23/2022]
|
49
|
Angeletti S, Dicuonzo G, Avola A, Crea F, Dedej E, Vailati F, Farina C, De Florio L. Viridans Group Streptococci clinical isolates: MALDI-TOF mass spectrometry versus gene sequence-based identification. PLoS One 2015; 10:e0120502. [PMID: 25781023 PMCID: PMC4362942 DOI: 10.1371/journal.pone.0120502] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/23/2015] [Indexed: 11/29/2022] Open
Abstract
Viridans Group Streptococci (VGS) species-level identification is fundamental for patients management. Matrix-assisted laser desorption ionization—time of flight mass spectrometry (MALDI-TOF MS) has been used for VGS identification but discrimination within the Mitis group resulted difficult. In this study, VGS identifications with two MALDI-TOF instruments, the Biotyper (Bruker) and the VITEK MS (bioMérieux) have been compared to those derived from tuf, soda and rpoB genes sequencing. VGS isolates were clustered and a dendrogram constructed using the Biotyper 3.0 software (Bruker). RpoB gene sequencing resulted the most sensitive and specific molecular method for S. pneumonia identification and was used as reference method. The sensitivity and the specificity of the VITEK MS in S. pneumonia identification were 100%, while the Biotyper resulted less specific (92.4%). In non pneumococcal VGS strains, the group-level correlation between rpoB and the Biotyper was 100%, while the species-level correlation was 61% after database upgrading (than 37% before upgrading). The group-level correlation between rpoB and the VITEK MS was 100%, while the species-level correlation was 36% and increases at 69% if isolates identified as S. mitis/S. oralis are included. The less accurate performance of the VITEK MS in VGS identification within the Mitis group was due to the inability to discriminate between S. mitis and S. oralis. Conversely, the Biotyper, after the release of the upgraded database, was able to discriminate between the two species. In the dendrogram, VGS strains from the same group were grouped into the same cluster and had a good correspondence with the gene-based clustering reported by other authors, thus confirming the validity of the upgraded version of the database. Data from this study demonstrated that MALDI-TOF technique can represent a rapid and cost saving method for VGS identification even within the Mitis group but improvements of spectra database are still recommended.
Collapse
Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
- * E-mail:
| | - Giordano Dicuonzo
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Alessandra Avola
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Francesca Crea
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Etleva Dedej
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| | - Francesca Vailati
- Microbiology Institute, AO ‘Papa Giovanni XXIII’ (formerly AO ‘Ospedali Riuniti’) of Bergamo, Bergamo, Italy
| | - Claudio Farina
- Microbiology Institute, AO ‘Papa Giovanni XXIII’ (formerly AO ‘Ospedali Riuniti’) of Bergamo, Bergamo, Italy
| | - Lucia De Florio
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico of Rome, Rome, Italy
| |
Collapse
|
50
|
Isolation and phylogenetic characterization of Streptococcus halichoeri from a European badger (Meles meles) with pyogranulomatous pleuropneumonia. J Comp Pathol 2015; 152:269-73. [PMID: 25678424 PMCID: PMC7094581 DOI: 10.1016/j.jcpa.2014.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/17/2014] [Accepted: 12/22/2014] [Indexed: 11/23/2022]
Abstract
Clinical and pathological studies in European badgers (Meles meles) are limited. Badgers play a significant role in the epidemiology of bovine tuberculosis (TB) in some countries and an accurate diagnosis is needed for this infection. However, the lesions of bovine TB are similar to those associated with other pathogens, making pathological diagnosis difficult. In the present study, Streptococcus halichoeri was isolated from a European badger with pyogranulomatous pleuropneumonia and suspected of having tuberculosis. TB and other pathogens able to induce similar lesions were ruled out. Comparative 16S rRNA and rpoB gene sequencing studies showed an identity of 99.51% and 98.28%, respectively, with S. halichoeri. This report represents the third description of this bacterium and the first in an animal species other than the grey seal (Halichoerus grypus). It also shows that S. halichoeri can be associated with a pathological process characterized by granulomatous inflammation and resembling tuberculosis.
Collapse
|