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Izda V, Schlupp L, Prinz E, Dyson G, Barrett M, Dunn CM, Nguyen E, Sturdy C, Jeffries MA. Murine cartilage microbial DNA deposition occurs rapidly following the introduction of a gut microbiome and changes with obesity, aging, and knee osteoarthritis. GeroScience 2024; 46:2317-2341. [PMID: 37946009 PMCID: PMC10828335 DOI: 10.1007/s11357-023-01004-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Cartilage microbial DNA patterns have been recently characterized in osteoarthritis (OA). The objectives of this study were to evaluate the gut origins of cartilage microbial DNA, to characterize cartilage microbial changes with age, obesity, and OA in mice, and correlate these to gut microbiome changes. We used 16S rRNA sequencing performed longitudinally on articular knee cartilage from germ-free (GF) mice following oral microbiome inoculation and cartilage and cecal samples from young and old wild-type mice with/without high-fat diet-induced obesity (HFD) and with/without OA induced by destabilization of the medial meniscus (DMM) to evaluate gut and cartilage microbiota. Microbial diversity was assessed, groups compared, and functional metagenomic profiles reconstructed. Findings were confirmed in an independent cohort by clade-specific qPCR. We found that cartilage microbial patterns developed at 48 h and later timepoints following oral microbiome inoculation of GF mice. Alpha diversity was increased in SPF mouse cartilage samples with age (P = 0.013), HFD (P = 5.6E-4), and OA (P = 0.029) but decreased in cecal samples with age (P = 0.014) and HFD (P = 1.5E-9). Numerous clades were altered with aging, HFD, and OA, including increases in Verrucomicrobia in both cartilage and cecal samples. Functional analysis suggested changes in dihydroorotase, glutamate-5-semialdehyde dehydrogenase, glutamate-5-kinase, and phosphoribosylamine-glycine ligase, in both cecum and cartilage, with aging, HFD, and OA. In conclusion, cartilage microbial DNA patterns develop rapidly after the introduction of a gut microbiome and change in concert with the gut microbiome during aging, HFD, and OA in mice. DMM-induced OA causes shifts in both cartilage and cecal microbiome patterns independent of other factors.
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Affiliation(s)
- Vladislav Izda
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
- Icahn School of Medicine, Mt. Sinai, New York, NY, USA
| | - Leoni Schlupp
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Emmaline Prinz
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Gabby Dyson
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Montana Barrett
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Christopher M Dunn
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
- Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Emily Nguyen
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Cassandra Sturdy
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA
| | - Matlock A Jeffries
- Oklahoma Medical Research Foundation, Arthritis & Clinical Immunology Program, 825 NE 13th Street, Laboratory MC400, Oklahoma City, OK, 73104, USA.
- Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- VA Medical Center, Oklahoma City, OK, USA.
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Cornejo CF, Soken LJ, Salgado PA, Gliosca LA, Squassi AF. Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants. Int J Clin Pediatr Dent 2023; 16:68-73. [PMID: 37020757 PMCID: PMC10067995 DOI: 10.5005/jp-journals-10005-2489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Aim To determine the presence of Streptococcus mutans (S. mutans) and Streptococcus sobrinus (S. sobrinus) and their association with extrinsic and intrinsic variables in 6-18-month-old infants. Methods This was an analytical, cross-sectional study of 65 6-18-month-old infants who visited the Centers for Early Childhood in Buenos Aires City. Three groups were established according to the presence of teeth-group I (GI)-edentulous infants, group II (GII)-infants with 1-8 teeth, and group III (GIII)-infants with 9-16 teeth. Data on the variables, diet, use of artificial teats, and oral hygiene were gathered using a self-administered questionnaire. An oral examination was performed according to the International Caries Detection and Assessment System (ICDAS II) criterion. A saliva sample was taken by aspiration with a sterile plastic syringe. Cariogenic Streptococci (CS) were counted using the adherence test in modified gold broth (AT-MGB). Molecular detection and quantification were performed by quantitative polymerase chain reaction (qPCR) (gtfB, gtfT, and tuf). Results A total of 12% of infants received oral hygiene, 38% used bottles, 30% used pacifiers, and 55% had sugar intake. S. sobrinus and S. mutans were detected in 57.1 and 28.6% of the children with caries, respectively. Groups I, II, and III had CS counts of log 2, 3.4, and 3.7, respectively. S. sobrinus was detected in 26.7% of GI, 52.9% of GII, and 85.7% of GIII, while S. mutans was detected in 13.3%, 35.3%, and 57.7%, respectively. Conclusion The prevalence of S. sobrinus was higher than S. mutans in all groups. The presence of CS was significantly associated with sugar intake. No association was found between S. mutans and S. sobrinus and the presence of caries, hygiene habits, or use of artificial teats. Clinical Significance This study supports the role of diet in developing a cariogenic biofilm in children under 2 years of age. How to cite this article Cornejo CF, Soken LJ, Salgado PA, et al. Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants. Int J Clin Pediatr Dent 2023;16(1):68-73.
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Affiliation(s)
- Celina F Cornejo
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Odontología Preventiva y Comunitaria, Instituto de Investigaciones en Salud Publica, Buenos Aires, Argentina
| | - Luciana J Soken
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Microbiología y Parasitología, Laboratorio de Diagnostico Microbiológico y Molecular, Buenos Aires, Argentina
| | - Pablo A Salgado
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Odontología Preventiva y Comunitaria, Instituto de Investigaciones en Salud Publica, Buenos Aires, Argentina
| | - Laura A Gliosca
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Microbiología y Parasitología, Laboratorio de Diagnostico Microbiológico y Molecular, Buenos Aires, Argentina
| | - Aldo F Squassi
- Universidad de Buenos Aires, Facultad de Odontología, Cátedra de Odontología Preventiva y Comunitaria, Instituto de Investigaciones en Salud Publica, Buenos Aires, Argentina
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Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022; 13:761873. [PMID: 35464955 PMCID: PMC9020828 DOI: 10.3389/fmicb.2022.761873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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Affiliation(s)
- Claudie Lamoureux
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Laure Surgers
- GHU AP-HP Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Vincent Fihman
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France
| | - Guillaume Gricourt
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Melissa N'Debi
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Camille Gomart
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Guilhem Royer
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Nathalie Launay
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jeanne-Marie Le Glaunec
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Charlotte Wemmert
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Giulia La Martire
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Geoffrey Rossi
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jean-Michel Pawlotsky
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Christophe Rodriguez
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France.,NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Paul-Louis Woerther
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France.,Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
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Parasana DK, Javia BB, Fefar DT, Barad DB, Ghodasara SN. Detection of virulence associated genes in Streptococcus agalactiae isolated from bovine mastitis. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:275-279. [PMID: 36425607 PMCID: PMC9681976 DOI: 10.22099/ijvr.2022.43305.6311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/05/2022] [Accepted: 07/30/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mastitis is one of the most expensive diseases in the dairy industry. It causes heavy monetary losses by decreasing milk production and treatment cost. Streptococcus agalactiae, the cause of contagious bovine mastitis, possesses various virulence factors that contribute to pathogenicity. AIMS The main aim of the study was to evaluate the distribution of virulence genes of S. agalactiae. METHODS In the current work, 98 Streptococcus species were isolated from 320 milk samples, collected from Veterinary Clinical Complex, Junagadh. Out of the isolates, 42 S. agalactiae isolates were used for virulence genes detection. RESULTS All Streptococcus spp. were confirmed at genus level by targeting tuf gene, and S. agalactiae was identified at species level by targeting 16S rRNA gene. For virulence gene detection, scpB, cfb, and cylE genes were targeted. Of 42 S. agalactiae isolates, 15, 16, and 10 isolates possessed scpB, cfb, and cylE genes, respectively. CONCLUSION This study aids us to know virulence characteristics and mechanisms responsible for the development of new strains in mastitis epidemiology in response to prevention and control strategies.
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Affiliation(s)
- D. K. Parasana
- MVSc Student in Veterinary Microbiology, Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Junagadh, India
| | - B. B. Javia
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Junagadh, India
| | - D. T. Fefar
- Department of Veterinary Pathology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Junagadh, India
| | - D. B. Barad
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Junagadh, India
| | - S. N. Ghodasara
- Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, Kamdhenu University, Junagadh, India
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5
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Abdelbary MMH, Wilms G, Conrads G. A New Species-Specific Typing Method for Salivarius Group Streptococci Based on the Dephospho-Coenzyme A Kinase ( coaE) Gene Sequencing. Front Cell Infect Microbiol 2021; 11:685657. [PMID: 34422679 PMCID: PMC8378900 DOI: 10.3389/fcimb.2021.685657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Viridans streptococci are a group of α-hemolytic streptococcal species. They are mainly commensals, most abundant in the mouth supporting oral health. But they also include important human pathogens such as Streptococcus pneumoniae. Identification and molecular typing of viridans group streptococci are challenging, especially for members of the salivarius group. In this study, we developed a single-locus molecular typing method that is able to differentiate among the highly phylogenetically related members of the salivarius group (S. salivarius, S. vestibularis and S. thermophilus) and might support differentiation in other groups as well. This typing approach is based on the amplification and sequence analysis of the housekeeping gene dephospho-coenzyme A kinase (coaE), a gene with unrecognized taxonomic potential to date. Here, we analysed coaE gene sequences of 154 publicly available genomes and of 30 salivarius group isolates of our own collection that together belong to 20 different gram-positive bacterial (sub) species. Our results revealed that the coaE phylogeny distinguished between streptococcal and non-streptococcal genomes and that coaE gene sequences were species-specific. In contrast to MALDI-TOF MS performance, the coaE typing was able to precisely identify the phylogenetically very closely related members of the salivarius group.
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Affiliation(s)
- Mohamed M H Abdelbary
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, RWTH Aachen University Hospital, Aachen, Germany
| | - Gerrit Wilms
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, RWTH Aachen University Hospital, Aachen, Germany
| | - Georg Conrads
- Division of Oral Microbiology and Immunology, Department of Operative and Preventive Dentistry and Periodontology, RWTH Aachen University Hospital, Aachen, Germany
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Abd El-Aziz NK, Ammar AM, El Damaty HM, Abd Elkader RA, Saad HA, El-Kazzaz W, Khalifa E. Environmental Streptococcus uberis Associated with Clinical Mastitis in Dairy Cows: Virulence Traits, Antimicrobial and Biocide Resistance, and Epidemiological Typing. Animals (Basel) 2021; 11:1849. [PMID: 34206268 PMCID: PMC8300258 DOI: 10.3390/ani11071849] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Mastitis remains a serious problem for dairy animals. The misappropriation of antimicrobial agents helps accelerate resistance, which poses a serious challenge in controlling environmental S. uberis infection. Here, we study the virulence attributes, antimicrobial and biocide resistance, and epidemiological typing of S. uberis recovered from bovine clinical mastitis in dairy farms of diverse hygienic interventions in Egypt. The overall S. uberis infection rate was 20.59%; all were multidrug-resistant (MDR). The sua gene was the most frequent virulence gene (42.02%), followed by pauA (40.57%), cfu (21.73%), skc (20.28%), and opp (11.59%). The erm(B) gene served as the predominant antimicrobial-resistant gene (75.36%), followed by fexA (52.63%) and tet(M), blaZ, and aac(6')aph(2″) genes (46.38% each). Of note, 79.71%, 78.26%, and 18.84% of S. uberis isolates harbored qacED1, qacC/D, and qacA/B genes, respectively. All analyzed isolates were S. uberis type I by their unique RFLP-PCR pattern. In conclusion, the sustained presence of pauA and sua genes throughout the investigated farms contributes to a better understanding of the bacterium's pathogenicity. Furthermore, MDR coupled with the existence of biocide resistance genes indicates the importance of S. uberis surveillance and the prudent use of antimicrobials in veterinary clinical medicine to avoid the dissemination of antimicrobial resistance.
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Affiliation(s)
- Norhan K Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Ahmed M Ammar
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Hend M El Damaty
- Department of Animal Medicine, Infectious Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt
| | - Rehab A Abd Elkader
- Belbies Veterinary Organization, Ministry of Agriculture, Belbies 44974, Egypt
| | - Hosam A Saad
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Waleed El-Kazzaz
- Molecular Microbiology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
| | - Eman Khalifa
- Department of Microbiology, Faculty of Veterinary Medicine, Matrouh University, Matrouh 51511, Egypt
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Abd El-Aziz NK, Ammar AM, El-Naenaeey ESYM, El Damaty HM, Elazazy AA, Hefny AA, Shaker A, Eldesoukey IE. Antimicrobial and antibiofilm potentials of cinnamon oil and silver nanoparticles against Streptococcus agalactiae isolated from bovine mastitis: new avenues for countering resistance. BMC Vet Res 2021; 17:136. [PMID: 33789637 PMCID: PMC8010958 DOI: 10.1186/s12917-021-02842-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/18/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Streptococcus agalactiae (S. agalactiae) is a contagious pathogen of bovine mastitis. It has financial implications for the dairy cattle industry in certain areas of the world. Since antimicrobial resistance increases in dairy farms, natural antimicrobials from herbal origins and nanoparticles have been given more attention as an alternative therapy. Hence, this study reported the antimicrobial and antibiofilm potentials of cinnamon oil, silver nanoparticles (AgNPs), and their combination against multidrug-resistant (MDR) S. agalactiae recovered from clinical bovine mastitis in Egypt. RESULTS Our findings revealed that 73% (146/200) of the examined milk samples collected from dairy cows with clinical mastitis were infected with Streptococci species. Of these, 9.59% (14/146) were identified as S. agalactiae and categorized as MDR. S. agalactiae isolates expressed four virulence genes (Hyl, cylE, scpB, and lmb) and demonstrated an ability to produce biofilms. Cinnamon oil showed high antimicrobial (MICs ≤0.063 μg /mL) and antibiofilm (MBIC50 = 4 μg/mL) potentials against planktonic and biofilms of S. agalactiae isolates, respectively. However, AgNPs showed reasonable antimicrobial (MICs ≤16 μg/mL) and relatively low antibiofilm (MBIC50 = 64 μg/mL) activities against screened isolates. Synergistic antimicrobial or additive antibiofilm interactions of cinnamon oil combined with AgNPs were reported for the first time. Scanning electron microscope (SEM) analysis revealed that biofilms of S. agalactiae isolates treated with cinnamon oil were more seriously damaged than observed in AgNPs cinnamon oil combination. Moreover, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) showed that cinnamon oil exerted a remarkable down-regulation of pili biosynthesis genes (pilA and pilB) and their regulator (rogB) against S. agalactiae biofilms, meanwhile the AgNPs cinnamon oil combination demonstrated a lower efficacy. CONCLUSIONS This is an in vitro preliminary approach that documented the antibiofilm potential of cinnamon oil and the inhibitory activity of cinnamon oil and its combination with AgNPs against MDR S. agalactiae recovered from clinical mastitis. Further in vivo studies should be carried out in animal models to provide evidence of concept for implementing these alternative candidates in the treatment of dairy farms infected by streptococcal mastitis in the future.
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Affiliation(s)
- Norhan K Abd El-Aziz
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt.
| | - Ahmed M Ammar
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - El-Sayed Y M El-Naenaeey
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, 44511, Egypt
| | - Hend M El Damaty
- Department of Animal Medicine, Infectious Diseases, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, Egypt
| | - Asmaa A Elazazy
- Abou Hamad Veterinary Organizations, Ministry of Agriculture, Abou Hamad, Sharkia, Egypt
| | - Ahmed A Hefny
- Veterinary Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia, Egypt
| | - Asmaa Shaker
- Department of Microbiology, Veterinary Hospital, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Ibrahim E Eldesoukey
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
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8
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Bach LL, Ram A, Ijaz UZ, Evans TJ, Lindström J. A Longitudinal Study of the Human Oropharynx Microbiota Over Time Reveals a Common Core and Significant Variations With Self-Reported Disease. Front Microbiol 2021; 11:573969. [PMID: 33552004 PMCID: PMC7861042 DOI: 10.3389/fmicb.2020.573969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
Our understanding of human microbial communities, in particular in regard to diseases is advancing, yet the basic understanding of the microbiome in healthy subjects over time remains limited. The oropharynx is a key target for colonization by several important human pathogens. To understand how the oropharyngeal microbiome might limit infections, and how intercurrent infections might be associated with its composition, we characterized the oropharyngeal microbiome of 18 healthy adults, sampled weekly over a 40-weeks using culture-independent molecular techniques. We detected nine phyla, 202 genera and 1438 assignments on OTU level, dominated by Firmicutes, Bacteroidetes, and Proteobacteria on phylum level. Individual microbiomes of participants were characterized by levels of high alpha diversity (mean = 204.55 OTUs, sd = 35.64), evenness (19.83, sd = 9.74) and high temporal stability (mean Pearson's correlation between samples of 0.52, sd = 0.060), with greater differences in microbiome community composition between than within individuals. Significant changes in community composition were associated with disease states, suggesting that it is possible to detect specific changes in OTU abundance and community composition during illness. We defined the common core microbiota by varying occurrence and abundance thresholds showing that individual core microbiomes share a substantial number of OTUs across participants, chiefly Streptococci and Veillonella. Our results provide insights into the microbial communities that characterize the healthy human oropharynx, community structure and variability, and provide new approaches to define individual and shared cores. The wider implications of this result include the potential for modeling the general dynamics of oropharynx microbiota both in health and in response to antimicrobial treatments or probiotics.
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Affiliation(s)
- Lydia Luise Bach
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Asha Ram
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, United Kingdom
| | - Thomas J. Evans
- Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Jan Lindström
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
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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.
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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
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10
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Deviaene M, Weigel KM, Wood RC, Luabeya AKK, Jones-Engel L, Hatherill M, Cangelosi GA. Sample adequacy controls for infectious disease diagnosis by oral swabbing. PLoS One 2020; 15:e0241542. [PMID: 33125422 PMCID: PMC7598519 DOI: 10.1371/journal.pone.0241542] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
Oral swabs are emerging as a non-invasive sample type for diagnosing infectious diseases including Ebola, tuberculosis (TB), and COVID-19. To assure proper sample collection, sample adequacy controls (SACs) are needed that detect substances indicative of samples collected within the oral cavity. This study evaluated two candidate SACs for this purpose. One detected representative oral microbiota (Streptococcus species DNA) and the other, human cells (human mitochondrial DNA, mtDNA). Quantitative PCR (qPCR) assays for the two target cell types were applied to buccal swabs (representing samples collected within the oral cavity) and hand swabs (representing improperly collected samples) obtained from 51 healthy U.S. volunteers. Quantification cycle (Cq) cutoffs that maximized Youden’s index were established for each assay. The streptococcal target at a Cq cutoff of ≤34.9 had 99.0% sensitivity and specificity for oral swab samples, whereas human mtDNA perfectly distinguished between hand and mouth swabs with a Cq cutoff of 31.3. The human mtDNA test was then applied to buccal, tongue, and gum swabs that had previously been collected from TB patients and controls in South Africa, along with “air swabs” collected as negative controls (total N = 292 swabs from 71 subjects). Of these swabs, 287/292 (98%) exhibited the expected Cq values. In a paired analysis the three oral sites yielded indistinguishable amounts of human mtDNA, however PurFlockTM swabs collected slightly more human mtDNA than did OmniSwabsTM (p = 0.012). The results indicate that quantification of human mtDNA cannot distinguish swabs collected from different sites within the mouth. However, it can reliably distinguish oral swabs from swabs that were not used orally, which makes it a useful SAC for oral swab-based diagnosis.
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Affiliation(s)
- Meagan Deviaene
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kris M. Weigel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Rachel C. Wood
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Angelique K. K. Luabeya
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Lisa Jones-Engel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Hatherill
- Department of Pathology, South African Tuberculosis Vaccine Initiative (SATVI), Institute of Infectious Disease & Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Gerard A. Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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11
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Alnakip MEA, Rhouma NR, Abd-Elfatah EN, Quintela-Baluja M, Böhme K, Fernández-No I, Bayoumi MA, Abdelhafez MM, Taboada-Rodríguez A, Calo-Mata P, Barros-Velázquez J. Discrimination of major and minor streptococci incriminated in bovine mastitis by MALDI-TOF MS fingerprinting and 16S rRNA gene sequencing. Res Vet Sci 2020; 132:426-438. [PMID: 32777539 DOI: 10.1016/j.rvsc.2020.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/13/2020] [Accepted: 07/30/2020] [Indexed: 02/05/2023]
Abstract
The current work investigated the discriminatory potential of MALDI-TOF MS fingerprinting towards most-relevant major (Streptococcus agalactiae, S. dysgalactiae, S. uberis) and minor (S. canis, S. parauberis, S. salivarius, S. equinus and S. gallolyticus) streptococci involved in bovine mastitis (BM), in comparison to 16S rRNA gene sequencing (GS)-based identification. The MALDI-TOF MS-generated spectral fingerprints were recruited for eliciting a detailed proteomic map that demonstrated clear variability for inter- and intra-species-specific biomarkers. Besides, a phyloproteomic dendrogram was evolved and comparatively analyzed against the phylogenetic one obtained from 16S rRNA GS in order to assess the differentiation of streptococci of bovine origin based on variability of protein fingerprints versus the variation of 16S rRNA gene homology. Results showed that the discrimination of BM-implicated streptococci can be obtained by both approaches; however MALDI-TOF MS was superior, achieving more variability at both intra- and sub-species levels. MALDI-TOF MS spectral analytics revealed that Streptococcus spp. exhibited three genus-specific biomarkers (peaks with m/z values at 2112, 4452 and 5955) and all streptococci exhibited spectral variability at both species and subspecies levels. Remarkably, MALDI-TOF MS fingerprinting was found to be at least as robust as 16S rRNA GS-based identification, allowing much cheaper and faster analysis, and additionally exhibiting high reliability for characterization of BM-implicated streptococci, thus proving to be a powerful tool that can be used independently within dairy diagnostics.
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Affiliation(s)
- Mohamed E A Alnakip
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain; Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Nasreddin R Rhouma
- Department of Biology, Faculty of Science, Misurata University, Libya; Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Eman N Abd-Elfatah
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Inmaculada Fernández-No
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Mohmaed A Bayoumi
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Mostafa M Abdelhafez
- Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Amaury Taboada-Rodríguez
- Food Biotechnology Group, Department of Nutrition and Food Science, Faculty of Veterinary Sciences, Murcia university, Campus Espinardo, 30100 Murcia, Spain
| | - Pillar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - J Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain.
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12
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Sánchez-Jiménez MM, de la Cuesta Zuluaga JJ, Garcia-Montoya GM, Dabral N, Alzate JF, Vemulapalli R, Olivera-Angel M. Diagnosis of human and canine Brucella canis infection: development and evaluation of indirect enzyme-linked immunosorbent assays using recombinant Brucella proteins. Heliyon 2020; 6:e04393. [PMID: 32685723 PMCID: PMC7358725 DOI: 10.1016/j.heliyon.2020.e04393] [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: 03/02/2020] [Revised: 04/02/2020] [Accepted: 07/01/2020] [Indexed: 01/18/2023] Open
Abstract
Brucella canis, a Gram-negative coccobacilli belonging to the genus Brucellae, is a pathogenic bacterium that can produce infections in dogs and humans. Multiple studies have been carried out to develop diagnostic techniques to detect all zoonotic Brucellae. Diagnosis of Brucella canis infection is challenging due to the lack of highly specific and sensitive diagnostic assays. This work was divided in two phases: in the first one, were identified antigenic proteins in B. canis that could potentially be used for serological diagnosis of brucellosis. Human sera positive for canine brucellosis infection was used to recognize immunoreactive proteins that were then identified by performing 2D-GEL and immunoblot assays. These spots were analyzed using MALDI TOF MS and predicted proteins were identified. Of the 35 protein spots analyzed, 14 proteins were identified and subsequently characterized using bioinformatics, two of this were selected for the next phase. In the second phase, we developed and validated an indirect enzyme-linked immunosorbent assays using those recombinant proteins: inosine 5' phosphate dehydrogenase, pyruvate dehydrogenase E1 subunit beta (PdhB) and elongation factor Tu (Tuf). These genes were PCR-amplified from genomic DNA of B. canis strain Oliveri, cloned, and expressed in Escherichia coli. Recombinant proteins were purified by metal affinity chromatography, and used as antigens in indirect ELISA. Serum samples from healthy and B. canis-infected humans and dogs were used to evaluate the performance of indirect ELISAs. Our results suggest that PdhB and Tuf proteins could be used as antigens for serologic detection of B. canis infection in humans, but not in dogs. The use of recombinant antigens in iELISA assays to detect B. canis-specific antibodies in human serum could be a valuable tool to improve diagnosis of human brucellosis caused by B. canis.
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Affiliation(s)
- Miryan Margot Sánchez-Jiménez
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
- Colombian Institute of Tropical Medicine, ICMT - CES University, Medellín, Colombia
| | - Juan Jacobo de la Cuesta Zuluaga
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
| | - Gisela María Garcia-Montoya
- National Center for Genomic Sequencing -CNSG, University of Antioquia, Medellín, Colombia
- Parasitology Group, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Neha Dabral
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States
| | - Juan Fernando Alzate
- National Center for Genomic Sequencing -CNSG, University of Antioquia, Medellín, Colombia
- Parasitology Group, School of Medicine, University of Antioquia, Medellín, Colombia
| | - Ramesh Vemulapalli
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, United States
| | - Martha Olivera-Angel
- Vericel-Biogénesis Group, School of Veterinary Medicine, Faculty of Agricultural Sciences, Universidad of Antioquia, Medellín, Colombia
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13
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Sun Y, Liu H, Shen Y, Huang X, Song F, Ge X, Wang A, Zhang K, Li Y, Li C, Wan Y, Li J. Cas12a-Activated Universal Field-Deployable Detectors for Bacterial Diagnostics. ACS OMEGA 2020; 5:14814-14821. [PMID: 32596619 PMCID: PMC7315577 DOI: 10.1021/acsomega.0c01911] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/22/2020] [Indexed: 05/12/2023]
Abstract
Field-deployable detectors of disease biomarkers provide a simple and fast analysis of clinical specimens. However, most of the existing field-deployable diagnostics have poor sensitivity and are not suitable for the detection of biomarkers with low abundance. Herein, we report a highly sensitive and rapid colorimetric readout paper-based assay for pathogen detection by integrating the unique collateral activity of a Cas12a-activated universal field-deployable detector (CUFD). The collateral effect of Cas12a results in a nonspecific destruction of a fluorophore biotin-labeled ssDNA reporter for the CUFD. This technique can quantify seven different kinds of pathogens in blood samples without any purification procedure, with sensitivity as low as 10 aM for the Shigella dysenteriae DNA. This CUFD technique has significant potential for the detection of pathogenic DNA as well as other types of DNA or RNA targets at the point-of-care application.
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Affiliation(s)
- Yun Sun
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Hong Liu
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Yuanyuan Shen
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Xingmei Huang
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Fengge Song
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Xiaolin Ge
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Aimin Wang
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Kaixiang Zhang
- School
of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001 P. R. China
| | - Yue Li
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Chaoyang Li
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
| | - Yi Wan
- State
Key Laboratory of Marine Resource Utilization in South China Sea,
Marine College, Key Laboratory of Tropical Biological Resources of
Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, 56 Renmin Road, Haikou 570228, China
- CAS
Key Laboratory of Marine Environmental Corrosion and Bio-fouling,
Institute of Oceanology, Chinese Academy
of Sciences, 7 Nanhai
Road, Qingdao 266071, China
| | - Jinghong Li
- Department
of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry &
Chemical Biology, Tsinghua University, Beijing 100084, China
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14
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UMA A, HARRESH AHM, REBECCA G, PRAVEENRAJ J. Multiple drug resistant Enterococcus spp. causes disease and mortality in Zebra fish (Danio rerio). THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i1.98241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The present report describes the isolation and identification of a multiple drug resistant Enterococcus spp. from diseased zebrafish from a commercial rearing facility in Chennai, Tamil Nadu, India. Zebrafish (Danio rerio) has recently gained great significance as a vertebrate animal model, as its immune system is remarkably similar with that of the humans. However, zebrafish are still susceptible to microbial infection. Gram positive diplococci isolated from kidney was identified as Enterococcus spp. using 16S rRNA gene sequencing analysis. The Enterococcus spp. isolate was either resistant and or intermediately resistant to 14 antibiotics assessed by agar disc diffusion method. This communication is the first report on isolation and confirmation of Enterococcus spp. associated with disease and mortality in zebrafish.
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15
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Koh TH, Binte Abdul Rahman N, Sessions OM. Comparative genomic analysis of Streptococcus dysgalactiae subspecies dysgalactiae, an occasional cause of zoonotic infection. Pathology 2019; 52:262-266. [PMID: 31859005 DOI: 10.1016/j.pathol.2019.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Streptococcus dysgalactiae comprise two subspecies. Typically, S. dysgalactiae subspecies equisimilis (SDSE) are large colony β-haemolytic Group C and Group G streptococci that cause pharyngitis, skin and soft tissue infections in humans. On the other hand, S. dysgalactiae subspecies dysgalactiae (SDSD) are classically described as α-haemolytic Group C streptococci that are animal pathogens. We compared the genome sequences of five S. dysgalactiae isolated from four cases of bacteraemia in women with breast cancer, and one from fish meat. One human isolate was SDSE, all other isolates were SDSD. Zoonotic SDSD infection may be under-recognised because of lack of patient and clinician awareness, and failure to distinguish SDSD from SDSE in the routine lab. The possibility of zoonotic SDSD should be suspected in patients with bacteraemia and ascending cellulitis of the upper limb with a history of handling raw fish and meat.
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Affiliation(s)
- Tse Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore.
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16
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Lugli GA, Mangifesta M, Mancabelli L, Milani C, Turroni F, Viappiani A, van Sinderen D, Ventura M. Compositional assessment of bacterial communities in probiotic supplements by means of metagenomic techniques. Int J Food Microbiol 2019; 294:1-9. [DOI: 10.1016/j.ijfoodmicro.2019.01.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/31/2018] [Accepted: 01/20/2019] [Indexed: 10/27/2022]
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17
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Ho EXP, Cheung CMG, Sim S, Chu CW, Wilm A, Lin CB, Mathur R, Wong D, Chan CM, Bhagarva M, Laude A, Lim TH, Wong TY, Cheng CY, Davila S, Hibberd M. Human pharyngeal microbiota in age-related macular degeneration. PLoS One 2018; 13:e0201768. [PMID: 30089174 PMCID: PMC6082546 DOI: 10.1371/journal.pone.0201768] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/20/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND While the aetiology of age-related macular degeneration (AMD)-a major blinding disease-remains unknown, the disease is strongly associated with variants in the complement factor H (CFH) gene. CFH variants also confer susceptibility to invasive infection with several bacterial colonizers of the nasopharyngeal mucosa. This shared susceptibility locus implicates complement deregulation as a common disease mechanism, and suggests the possibility that microbial interactions with host complement may trigger AMD. In this study, we address this possibility by testing the hypothesis that AMD is associated with specific microbial colonization of the human nasopharynx. RESULTS High-throughput Illumina sequencing of the V3-V6 region of the microbial 16S ribosomal RNA gene was used to comprehensively and accurately describe the human pharyngeal microbiome, at genus level, in 245 AMD patients and 386 controls. Based on mean and differential microbial abundance analyses, we determined an overview of the pharyngeal microbiota, as well as candidate genera (Prevotella and Gemella) suggesting an association towards AMD health and disease conditions. CONCLUSIONS Utilizing an extensive study population from Singapore, our results provided an accurate description of the pharyngeal microbiota profiles in AMD health and disease conditions. Through identification of candidate genera that are different between conditions, we provide preliminary evidence for the existence of microbial triggers for AMD. Ethical approval for this study was obtained through the Singapore Health Clinical Institutional Review Board, reference numbers R799/63/2010 and 2010/585/A.
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Affiliation(s)
| | - Chui Ming Gemmy Cheung
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Shuzhen Sim
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Andreas Wilm
- Genome Institute of Singapore,Singapore, Singapore
| | | | - Ranjana Mathur
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Doric Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Choi Mun Chan
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Mayuri Bhagarva
- Department of Ophthalmology, National University of Singapore and National University Health System, Singapore, Singapore
| | - Augustinus Laude
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tock Han Lim
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore
| | - Tien Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Ching Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Center, Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Sonia Davila
- Genome Institute of Singapore,Singapore, Singapore
| | - Martin Hibberd
- Genome Institute of Singapore,Singapore, Singapore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
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18
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The diagnosis of chronic endometritis in infertile asymptomatic women: a comparative study of histology, microbial cultures, hysteroscopy, and molecular microbiology. Am J Obstet Gynecol 2018; 218:602.e1-602.e16. [PMID: 29477653 DOI: 10.1016/j.ajog.2018.02.012] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/07/2018] [Accepted: 02/15/2018] [Indexed: 11/23/2022]
Abstract
BACKGROUND Chronic endometritis is a persistent inflammation of the endometrial mucosa caused by bacterial pathogens such as Enterobacteriaceae, Enterococcus, Streptococcus, Staphylococcus, Mycoplasma, and Ureaplasma. Although chronic endometritis can be asymptomatic, it is found in up to 40% of infertile patients and is responsible for repeated implantation failure and recurrent miscarriage. Diagnosis of chronic endometritis is based on hysteroscopy of the uterine cavity, endometrial biopsy with plasma cells being identified histologically, while specific treatment is determined based on microbial culture. However, not all microorganisms implicated are easily or readily culturable needing a turnaround time of up to 1 week. OBJECTIVE We sought to develop a molecular diagnostic tool for chronic endometritis based on real-time polymerase chain reaction equivalent to using the 3 classic methods together, overcoming the bias of using any of them alone. STUDY DESIGN Endometrial samples from patients assessed for chronic endometritis (n = 113) using at least 1 or several conventional diagnostic methods namely histology, hysteroscopy, and/or microbial culture, were blindly evaluated by real-time polymerase chain reaction for the presence of 9 chronic endometritis pathogens: Chlamydia trachomatis, Enterococcus, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Mycoplasma hominis, Neisseria gonorrhoeae, Staphylococcus, and Streptococcus. The sensitivity and specificity of the molecular analysis vs the classic diagnostic techniques were compared in the 65 patients assessed by all 3 recognized classic methods. RESULTS The molecular method showed concordant results with histological diagnosis in 30 samples (14 double positive and 16 double negative) with a matching accuracy of 46.15%. Concordance of molecular and hysteroscopic diagnosis was observed in 38 samples (37 double positive and 1 double negative), with an accuracy of 58.46%. When the molecular method was compared to microbial culture, concordance was present in 37 samples (22 double positive and 15 double negative), a matching rate of 56.92%. When cases of potential contamination and/or noncultivable bacteria were considered, the accuracy increased to 66.15%. Of these 65 patients, only 27 patients had consistent histological + hysteroscopic diagnosis, revealing 58.64% of nonconcordant results. Only 13 of 65 patients (20%) had consistent histology + hysteroscopy + microbial culture results. In these cases, the molecular microbiology matched in 10 cases showing a diagnostic accuracy of 76.92%. Interestingly, the molecular microbiology confirmed over half of the isolated pathogens and provided additional detection of nonculturable microorganisms. These results were confirmed by the microbiome assessed by next-generation sequencing. In the endometrial samples with concordant histology + hysteroscopy + microbial culture results, the molecular microbiology diagnosis demonstrates 75% sensitivity, 100% specificity, 100% positive and 25% negative predictive values, and 0% false-positive and 25% false-negative rates. CONCLUSION The molecular microbiology method describe herein is a fast and inexpensive diagnostic tool that allows for the identification of culturable and nonculturable endometrial pathogens associated with chronic endometritis. The results obtained were similar to all 3 classic diagnostic methods together with a degree of concordance of 76.92% providing an opportunity to improve the clinical management of infertile patients with a risk of experiencing this ghost endometrial pathology.
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19
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Barrett's esophagus is associated with a distinct oral microbiome. Clin Transl Gastroenterol 2018; 9:135. [PMID: 29491399 PMCID: PMC5862155 DOI: 10.1038/s41424-018-0005-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/15/2018] [Indexed: 12/15/2022] Open
Abstract
Objectives The esophageal microbiome is composed of predominantly oral flora and is altered in reflux-related conditions including Barrett’s esophagus (BE). Changes to the esophageal microbiome may be reflected in the oral cavity. Assessing the oral microbiome thus represents a potential non-invasive method to identify patients with BE. Methods Patients with and without BE undergoing upper endoscopy were prospectively enrolled. Demographics, clinical data, medications, and dietary intake were assessed. 16S rRNA gene sequencing was performed on saliva samples collected prior to endoscopy. Taxonomic differences between groups were assessed via linear discriminant analysis effect size (LEfSe). Logit models were used to develop microbiome signatures to distinguish BE from non-BE, assessed by area under the receiver operating curve (AUROC). Results A total of 49 patients were enrolled (control = 17, BE = 32). There was no significant difference in alpha diversity comparing all BE patients vs. controls. At the phylum level, the oral microbiome in BE patients had significantly increased relative abundance of Firmicutes (p = 0.005) and decreased Proteobacteria (p = 0.02). There were numerous taxonomic differences in the oral microbiome between BE and controls. A model including relative abundance of Lautropia, Streptococcus, and a genus in the order Bacteroidales distinguished BE from controls with an AUROC 0.94 (95% CI: 0.85–1.00). The optimal cutoff identified BE patients with 96.9% sensitivity and 88.2% specificity. Conclusions The oral microbiome in BE patients was markedly altered and distinguished BE with relatively high accuracy. The oral microbiome represents a potential screening marker for BE, and validation studies in larger and distinct populations are warranted.
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Salli KM, Gürsoy UK, Söderling EM, Ouwehand AC. Effects of Xylitol and Sucrose Mint Products on Streptococcus mutans Colonization in a Dental Simulator Model. Curr Microbiol 2017; 74:1153-1159. [PMID: 28717846 PMCID: PMC5596035 DOI: 10.1007/s00284-017-1299-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/04/2017] [Indexed: 12/15/2022]
Abstract
Few laboratory methods exist for evaluating the cariogenicity of food ingredients. In this study, a dental simulator was used to determine the effects of commercial sucrose and xylitol mint products on the adherence and planktonic growth of Streptococcus mutans. Solutions (3% w/v) of sucrose, xylitol, sucrose mints, xylitol mints, xylitol with 0.02% peppermint oil (PO), and 0.02% PO alone were used to test the levels of planktonic and adhered S. mutans. A dental simulator with continuous artificial saliva flow, constant temperature, and mixing was used as a test environment and hydroxyapatite (HA) discs were implemented into the model to simulate the tooth surface. Bacterial content was quantified by qPCR. Compared with the artificial saliva alone, sucrose and sucrose mints increased the numbers of HA-attached S. mutans, whereas xylitol decreased them. Similarly, planktonic S. mutans quantities rose with sucrose and declined with xylitol and xylitol mints. Versus sucrose mints, xylitol mints significantly reduced the counts of HA-bound and planktonic S. mutans. Similar results were observed with the main ingredients of both types of mints separately. PO-supplemented artificial saliva did not influence the numbers of S. mutans that attached to HA or planktonic S. mutans compared with artificial saliva control. In our dental simulator model, xylitol reduced the counts of adhering and planktonic S.mutans. The mints behaved similarly as their pure, main ingredients-sucrose or xylitol, respectively. PO, which has been suggested to have antimicrobial properties, did not influence S. mutans colonization.
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Affiliation(s)
- Krista M. Salli
- DuPont Nutrition and Health, Global Health and Nutrition Science, Danisco Sweeteners Oy, 02460 Kantvik, Finland
- Department of Periodontology, Institute of Dentistry, University of Turku, Lemminkäisenkatu 2, 20520 Turku, Finland
| | - Ulvi K. Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Lemminkäisenkatu 2, 20520 Turku, Finland
| | - Eva M. Söderling
- Department of Periodontology, Institute of Dentistry, University of Turku, Lemminkäisenkatu 2, 20520 Turku, Finland
| | - Arthur C. Ouwehand
- DuPont Nutrition and Health, Global Health and Nutrition Science, Danisco Sweeteners Oy, 02460 Kantvik, Finland
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Cosorich I, Dalla-Costa G, Sorini C, Ferrarese R, Messina MJ, Dolpady J, Radice E, Mariani A, Testoni PA, Canducci F, Comi G, Martinelli V, Falcone M. High frequency of intestinal T H17 cells correlates with microbiota alterations and disease activity in multiple sclerosis. SCIENCE ADVANCES 2017; 3:e1700492. [PMID: 28706993 PMCID: PMC5507635 DOI: 10.1126/sciadv.1700492] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/09/2017] [Indexed: 05/17/2023]
Abstract
T helper 17 (TH17) cells are key players in multiple sclerosis (MS), and studies in animal models demonstrated that effector TH17 cells that trigger brain autoimmunity originate in the intestine. We validate in humans the crucial role of the intestinal environment in promoting TH17 cell expansion in MS patients. We found that increased frequency of TH17 cells correlates with high disease activity and with specific alterations of the gut mucosa-associated microbiota in MS patients. By using 16S ribosomal RNA sequencing, we analyzed the microbiota isolated from small intestinal tissues and found that MS patients with high disease activity and increased intestinal TH17 cell frequency showed a higher Firmicutes/Bacteroidetes ratio, increased relative abundance of Streptococcus, and decreased Prevotella strains compared to healthy controls and MS patients with no disease activity. We demonstrated that the intestinal TH17 cell frequency is inversely related to the relative abundance of Prevotella strains in the human small intestine. Our data demonstrate that brain autoimmunity is associated with specific microbiota modifications and excessive TH17 cell expansion in the human intestine.
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Affiliation(s)
- Ilaria Cosorich
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS (Istituto di Ricerca e Cura a carattere Scientifico) San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Gloria Dalla-Costa
- Clinical Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Chiara Sorini
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS (Istituto di Ricerca e Cura a carattere Scientifico) San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Roberto Ferrarese
- Microbiology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Josè Messina
- Clinical Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Jayashree Dolpady
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS (Istituto di Ricerca e Cura a carattere Scientifico) San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Elisa Radice
- Gastroenterology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Alberto Mariani
- Gastroenterology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Pier Alberto Testoni
- Gastroenterology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Filippo Canducci
- Microbiology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giancarlo Comi
- Clinical Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vittorio Martinelli
- Clinical Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Marika Falcone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS (Istituto di Ricerca e Cura a carattere Scientifico) San Raffaele Scientific Institute, 20132 Milan, Italy
- Corresponding author.
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22
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Impact of Organism Identification Method on Central Line-Associated Bloodstream Infection Designation. Infect Control Hosp Epidemiol 2017. [PMID: 28633680 DOI: 10.1017/ice.2017.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Maheux AF, Bouchard S, Bérubé È, Bergeron MG. Comparison of MI, Chromocult ® coliform, and Compass CC chromogenic culture-based methods to detect Escherichia coli and total coliforms in water using 16S rRNA sequencing for colony identification. JOURNAL OF WATER AND HEALTH 2017; 15:353-359. [PMID: 28598339 DOI: 10.2166/wh.2017.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The MI, Chromocult® coliform, and Compass CC chromogenic culture-based methods used to assess water quality by the detection of Escherichia coli and total coliforms were compared in terms of their specificity and sensitivity, using 16S rRNA sequencing for colony identification. A sewage water sample was divided in 2-μL subsamples for testing by all three culture-based methods. All growing colonies were harvested and subjected to 16S rRNA sequencing. Test results showed that all E. coli colonies were correctly identified by all three methods, for a specificity and a sensitivity of 100%. However, for the total coliform detection, the MI agar, Chromocult® coliform agar, and Compass CC agar were specific for only 69.2% (9/13), 47.2% (25/53), and 40.5% (17/42), whereas sensitive for 97.8% (45/46), 97.5% (39/40), and 85.7% (24/28), respectively. Thus, given the low level of specificity of these methods for the detection of total coliforms, confirming the identity of total coliform colonies could help to take public health decisions, in particular for cities connected to a public drinking water distribution system since the growth of few putative total coliform colonies on chromogenic agar is problematic and can lead to unnecessary and costly boiling notices from public health authorities.
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Affiliation(s)
- Andrée F Maheux
- AFM Water Consulting, 1249 d'Édimbourg, Québec City, Québec, Canada G3J 1C8 E-mail:
| | - Sébastien Bouchard
- AFM Water Consulting, 1249 d'Édimbourg, Québec City, Québec, Canada G3J 1C8 E-mail:
| | - Ève Bérubé
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City, Québec, Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, Québec, Canada
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Vélez JR, Cameron M, Rodríguez-Lecompte JC, Xia F, Heider LC, Saab M, McClure JT, Sánchez J. Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds. Front Vet Sci 2017; 4:63. [PMID: 28589129 PMCID: PMC5438997 DOI: 10.3389/fvets.2017.00063] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
The objectives of this study are to determine the occurrence of antimicrobial resistance (AMR) genes using whole-genome sequence (WGS) of Streptococcus uberis (S. uberis) and Streptococcus dysgalactiae (S. dysgalactiae) isolates, recovered from dairy cows in the Canadian Maritime Provinces. A secondary objective included the exploration of the association between phenotypic AMR and the genomic characteristics (genome size, guanine–cytosine content, and occurrence of unique gene sequences). Initially, 91 isolates were sequenced, and of these isolates, 89 were assembled. Furthermore, 16 isolates were excluded due to larger than expected genomic sizes (>2.3 bp × 1,000 bp). In the final analysis, 73 were used with complete WGS and minimum inhibitory concentration records, which were part of the previous phenotypic AMR study, representing 18 dairy herds from the Maritime region of Canada (1). A total of 23 unique AMR gene sequences were found in the bacterial genomes, with a mean number of 8.1 (minimum: 5; maximum: 13) per genome. Overall, there were 10 AMR genes [ANT(6), TEM-127, TEM-163, TEM-89, TEM-95, Linb, Lnub, Ermb, Ermc, and TetS] present only in S. uberis genomes and 2 genes unique (EF-TU and TEM-71) to the S. dysgalactiae genomes; 11 AMR genes [APH(3′), TEM-1, TEM-136, TEM-157, TEM-47, TetM, bl2b, gyrA, parE, phoP, and rpoB] were found in both bacterial species. Two-way tabulations showed association between the phenotypic susceptibility to lincosamides and the presence of linB (P = 0.002) and lnuB (P < 0.001) genes and the between the presence of tetM (P = 0.015) and tetS (P = 0.064) genes and phenotypic resistance to tetracyclines only for the S. uberis isolates. The logistic model showed that the odds of resistance (to any of the phenotypically tested antimicrobials) was 4.35 times higher when there were >11 AMR genes present in the genome, compared with <7 AMR genes (P < 0.001). The odds of resistance was lower for S. dysgalactiae than S. uberis (P = 0.031). When the within-herd somatic cell count was >250,000 cells/mL, a trend toward higher odds of resistance compared with the baseline category of <150,000 cells/mL was observed. When the isolate corresponded to a post-mastitis sample, there were lower odds of resistance when compared with non-clinical isolates (P = 0.01). The results of this study showed the strength of associations between phenotypic AMR resistance of both mastitis pathogens and their genotypic resistome and other epidemiological characteristics.
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Affiliation(s)
- Julián Reyes Vélez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Marguerite Cameron
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Juan Carlos Rodríguez-Lecompte
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Fangfang Xia
- Mathematics and Computer Science Division, Argonne National Laboratory, Chicago, IL, USA
| | - Luke C Heider
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Matthew Saab
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - J Trenton McClure
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Javier Sánchez
- Department of Health Management, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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25
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Maheux AF, Bouchard S, Bérubé È, Bergeron MG. Rapid molecular identification of fecal origin-colonies growing on Enterococcus spp.-specific culture methods. JOURNAL OF WATER AND HEALTH 2017; 15:239-250. [PMID: 28362305 DOI: 10.2166/wh.2016.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mEI, Chromocult® enterococci, and m-Enterococcus culture-based methods used to assess water quality by the detection of Enterococcus spp. were first compared in terms of sensitivity using (1) 41 different type strains of Enterococcus spp. and (2) environmental colonies identified by 16S rRNA sequencing. Then, two specific-rtPCR assays targeting Enterococcus spp. and Enterococcus faecalis/faecium were tested for their ability to confirm the identity of putative enterococcal colonies. The mEI, Chromocult® enterococci, and m-Enterococcus methods detected β-glucosidase activity for 28 (68.3%), 32 (78.0%), and 12 (29.3%) of the 41 reference enterococcal strains tested, respectively. Analysis with environmental colonies showed that mEI and Chromocult® enterococci media had false positive rates of 4.3% and 5.0%, respectively. Finally, the two rtPCR assays showed a specificity of 100%. Only two (2/19) colonies of E. faecium isolated from mEI agar were not detected by the Enterococcus faecium rtPCR assay, for a sensitivity of 89.5%. Our results showed that Chromocult® enterococci medium recovered more E. faecalis/faecium cells than the two other methods. Thus, the use of Chromocult® enterococci combined with the Enterococcus faecalis/faecium rtPCR assay showed the best combination to decrease the high false-positive rate obtained when the entire Enterococcus genus is targeted.
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Affiliation(s)
- Andrée F Maheux
- AFM Water Consulting, 1249 d'Édimbourg, Québec City (Québec), Canada G3J 1C8 E-mail:
| | - Sébastien Bouchard
- AFM Water Consulting, 1249 d'Édimbourg, Québec City (Québec), Canada G3J 1C8 E-mail:
| | - Ève Bérubé
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada
| | - Michel G Bergeron
- Centre de recherche en infectiologie de l'Université Laval, Axe Maladies infectieuses et immunitaires, Centre de recherche du CHU de Québec-Université Laval, Québec City (Québec), Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City (Québec), Canada
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26
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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.
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27
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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).
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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
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28
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Lin P, Ding B, Feng C, Yin S, Zhang T, Qi X, Lv H, Guo X, Dong K, Zhu Y, Li Q. Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder. J Affect Disord 2017; 207:300-304. [PMID: 27741466 DOI: 10.1016/j.jad.2016.09.051] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The diagnosis of major depression disorder (MDD) and other mental disorders were depended on some subjective survey scales. There are confirmed relationship between the gut flora and the mental states of MDD patients. METHODS The V3-V4 region of the 16S rRNA gene was extracted from the fecal microbial communities in MDD patients, PCR amplified and sequenced on the Illumina Miseq platform. RESULTS More phylum Firmicutes, less Bacteroidetes, and more genus Prevotella, Klebsiella, Streptococcus and Clostridium XI were found in MDD patients. The changes of the proportion of Prevotella and Klebsiella were consistent with Hamilton depression rating scale. LIMITATIONS The conclusion was limited by small sample sizes and potential uncontrollable influence factors on fecal microbiota. DISCUSSION Prevotella and Klebsiella proportion in fecal microbial communities should be concerned in the diagnosis and therapeutic monitoring of MDD in future.
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Affiliation(s)
- Ping Lin
- Department of Medical Laboratory, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Bingyu Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chunyan Feng
- Department of internal medicine, Zhejiang Medical College, Hangzhou 310053, China
| | - Shuwei Yin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ting Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xin Qi
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huiying Lv
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokui Guo
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ke Dong
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yongzhang Zhu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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29
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Sánchez-Samper E, Gómez-Gallego C, Andreo-Martínez P, Salminen S, Ros G. Mice gut microbiota programming by using the infant food profile. The effect on growth, gut microbiota and the immune system. Food Funct 2017; 8:3758-3768. [DOI: 10.1039/c7fo00819h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Infant food profile on programming of the growth, gut microbiota and immune system of C57BL/6J mice.
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Affiliation(s)
- Elvira Sánchez-Samper
- Research group of Human Nutrition & Food Sciences (NUTBRO)
- Veterinary Faculty
- Regional Campus of International Excellence “Campus Mare Nostrum”
- University of Murcia
- Spain
| | - Carlos Gómez-Gallego
- Research group of Human Nutrition & Food Sciences (NUTBRO)
- Veterinary Faculty
- Regional Campus of International Excellence “Campus Mare Nostrum”
- University of Murcia
- Spain
| | | | | | - Gaspar Ros
- Research group of Human Nutrition & Food Sciences (NUTBRO)
- Veterinary Faculty
- Regional Campus of International Excellence “Campus Mare Nostrum”
- University of Murcia
- Spain
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30
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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).
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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
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31
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Salli K, Forssten S, Lahtinen S, Ouwehand A. Influence of sucrose and xylitol on an early Streptococcus mutans biofilm in a dental simulator. Arch Oral Biol 2016; 70:39-46. [DOI: 10.1016/j.archoralbio.2016.05.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 04/14/2016] [Accepted: 05/30/2016] [Indexed: 12/11/2022]
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Obszańska K, Kern-Zdanowicz I, Kozińska A, Machura K, Stefaniuk E, Hryniewicz W, Sitkiewicz I. Streptococcus anginosus (milleri) Group Strains Isolated in Poland (1996-2012) and their Antibiotic Resistance Patterns. Pol J Microbiol 2016; 65:33-41. [PMID: 27281992 DOI: 10.5604/17331331.1197323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Streptococcus anginosus, Streptococcus intermedius and Streptococcus constellatus form a group of related streptococcal species, namely the Streptococcus Anginosus Group (SAG). The group, previously called "milleri" had been rarely described until 1980/1990 as source of infections. Nowadays SAG bacteria are often described as pathogens causing predominantly purulent infections. The number of infections is highly underestimated, as SAG strains are often classified in the microbiology laboratory as less virulent "viridans streptococci" Epidemiological situation regarding SAG infections in Poland has been unrecognized, therefore we performed a retrospective analysis of strains isolated between 1996 and 2012. Strains suspected of belonging to SAG were re-identified using an automated biochemical approach (Vitek2) and MALDI-TOF MS. We performed first analysis of antibiotic resistance among SAG strains isolated in Poland using automated methods (Vitek2), disk diffusion tests and E-Tests. We also performed PCR detection of resistance determinants in antibiotic resistant strains. Clonal structure of analyzed strains was evaluated with PFGE and MLVF methods. All three species are difficult to distinguish using automated diagnostic methods and the same is true for automated MIC evaluation. Our analysis revealed SAG strains are rarely isolated in Poland, predominantly from purulent infections. All isolates are very diverse on the genomic level as estimated by PFGE and MLVF analyses. All analyzed strains are sensitive to penicillin, a substantial group of strains is resistant to macrolides and the majority of strains are resistant to tetracycline.
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33
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Tena D, Fernández C, López-Garrido B, Pérez-Balsalobre M, Losa C, Medina-Pascual MJ, Sáez-Nieto JA. Lactational mastitis caused by Streptococcus lactarius. Diagn Microbiol Infect Dis 2016; 85:490-2. [PMID: 27220606 DOI: 10.1016/j.diagmicrobio.2016.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/27/2016] [Accepted: 04/30/2016] [Indexed: 11/25/2022]
Abstract
Human infections caused by Streptococcus lactarius have not been previously reported. In the present report, we describe a lactational mastitis caused by this organism. The infection occurred in a 28-year-old breast-feeding female, with a 10-days history of moderate pain on the right breast. The patient was cured after antibiotic treatment with levofloxacin for 21 days. Our case shows that S. lactarius should be considered as a cause of lactational mastitis. The introduction of molecular microbiology techniques can be extremely useful for knowing the implication of streptococci in lactational mastitis.
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Affiliation(s)
- Daniel Tena
- Section of Microbiology, University Hospital of Guadalajara, Guadalajara, Spain.
| | - Cristina Fernández
- Section of Microbiology, University Hospital of Guadalajara, Guadalajara, Spain
| | | | | | - Cristina Losa
- Section of Microbiology, University Hospital of Guadalajara, Guadalajara, Spain
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Cui B, Smooker PM, Rouch DA, Deighton MA. Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress. Mol Genet Genomics 2016; 291:1795-811. [PMID: 27000656 DOI: 10.1007/s00438-016-1197-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 03/05/2016] [Indexed: 11/28/2022]
Abstract
Accurate and reproducible measurement of gene transcription requires appropriate reference genes, which are stably expressed under different experimental conditions to provide normalization. Staphylococcus capitis is a human pathogen that produces biofilm under stress, such as imposed by antimicrobial agents. In this study, a set of five commonly used staphylococcal reference genes (gyrB, sodA, recA, tuf and rpoB) were systematically evaluated in two clinical isolates of Staphylococcus capitis (S. capitis subspecies urealyticus and capitis, respectively) under erythromycin stress in mid-log and stationary phases. Two public software programs (geNorm and NormFinder) and two manual calculation methods, reference residue normalization (RRN) and relative quantitative (RQ), were applied. The potential reference genes selected by the four algorithms were further validated by comparing the expression of a well-studied biofilm gene (icaA) with phenotypic biofilm formation in S. capitis under four different experimental conditions. The four methods differed considerably in their ability to predict the most suitable reference gene or gene combination for comparing icaA expression under different conditions. Under the conditions used here, the RQ method provided better selection of reference genes than the other three algorithms; however, this finding needs to be confirmed with a larger number of isolates. This study reinforces the need to assess the stability of reference genes for analysis of target gene expression under different conditions and the use of more than one algorithm in such studies. Although this work was conducted using a specific human pathogen, it emphasizes the importance of selecting suitable reference genes for accurate normalization of gene expression more generally.
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Affiliation(s)
- Bintao Cui
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia
| | - Peter M Smooker
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia
| | - Duncan A Rouch
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia
| | - Margaret A Deighton
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, VIC, 3083, Australia.
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35
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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.
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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
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36
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Maal KB, Bouzari M, Zavareh FA. Biotechnological Applications of Two Novel Lytic Bacteriophages of Streptococcus mutans in Tooth Decay Bio-Controlling. ACTA ACUST UNITED AC 2015. [DOI: 10.3923/crb.2015.90.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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37
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Cui B, Smooker PM, Rouch DA, Deighton MA. Effects of erythromycin on the phenotypic and genotypic biofilm expression in two clinical Staphylococcus capitis subspecies and a functional analysis of Ica proteins in S. capitis. J Med Microbiol 2015; 64:591-604. [DOI: 10.1099/jmm.0.000059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bintao Cui
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, 3083 Victoria, Australia
| | - Peter M. Smooker
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, 3083 Victoria, Australia
| | - Duncan A. Rouch
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, 3083 Victoria, Australia
| | - Margaret A. Deighton
- School of Applied Sciences, RMIT University, Plenty Road, Bundoora, 3083 Victoria, Australia
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38
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Caamaño-Antelo S, Fernández-No I, Böhme K, Ezzat-Alnakip M, Quintela-Baluja M, Barros-Velázquez J, Calo-Mata P. Genetic discrimination of foodborne pathogenic and spoilage Bacillus spp. based on three housekeeping genes. Food Microbiol 2015; 46:288-298. [DOI: 10.1016/j.fm.2014.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 08/17/2014] [Indexed: 11/28/2022]
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39
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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.
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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
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40
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Kim DH, Chon JW, Kim H, Kim HS, Choi D, Hwang DG, Seo KH. Detection and Enumeration of Lactic Acid Bacteria, Acetic Acid Bacteria and Yeast in Kefir Grain and Milk Using Quantitative Real-Time PCR. J Food Saf 2014. [DOI: 10.1111/jfs.12153] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Dong-Hyeon Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Jung-Whan Chon
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Hyunsook Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Hong-Seok Kim
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Dasom Choi
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Dae-Geun Hwang
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
| | - Kun-Ho Seo
- KU Center for Food Safety; College of Veterinary Medicine; Konkuk University; Hwayang-dong, Gwangjin-gu Seoul 143-701 Korea
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41
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Satzke C, Turner P, Virolainen-Julkunen A, Adrian PV, Antonio M, Hare KM, Henao-Restrepo AM, Leach AJ, Klugman KP, Porter BD, Sá-Leão R, Scott JA, Nohynek H, O'Brien KL. Standard method for detecting upper respiratory carriage of Streptococcus pneumoniae: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group. Vaccine 2014; 32:165-79. [PMID: 24331112 DOI: 10.1016/j.vaccine.2013.08.062] [Citation(s) in RCA: 328] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 11/29/2022]
Abstract
In 2003 the World Health Organization (WHO) convened a working group and published a set of standard methods for studies measuring nasopharyngeal carriage of Streptococcus pneumoniae (the pneumococcus). The working group recently reconvened under the auspices of the WHO and updated the consensus standard methods. These methods describe the collection, transport and storage of nasopharyngeal samples, as well as provide recommendations for the identification and serotyping of pneumococci using culture and non-culture based approaches. We outline the consensus position of the working group, the evidence supporting this position, areas worthy of future research, and the epidemiological role of carriage studies. Adherence to these methods will reduce variability in the conduct of pneumococcal carriage studies undertaken in the context of pneumococcal vaccine trials, implementation studies, and epidemiology studies more generally so variability in methodology does not confound the interpretation of study findings.
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Affiliation(s)
- Catherine Satzke
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Centre for International Child Health, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, Australia.
| | - Paul Turner
- Microbiology Department, Angkor Hospital for Children, Siem Reap, Kingdom of Cambodia; Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anni Virolainen-Julkunen
- Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare, Helsinki, Finland
| | - Peter V Adrian
- MRC/Wits Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kim M Hare
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | | | - Amanda J Leach
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Respiratory and Meningeal Pathogens Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Barbara D Porter
- Pneumococcal Research, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - J Anthony Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; London School of Hygiene & Tropical Medicine, London, UK
| | - Hanna Nohynek
- Vaccine Programme Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Katherine L O'Brien
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Zhang DF, Zhang QQ, Li AH. Development of a multiplex PCR assay for rapid and simultaneous detection of four genera of fish pathogenic bacteria. Lett Appl Microbiol 2014; 59:471-8. [PMID: 25041355 DOI: 10.1111/lam.12303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/04/2014] [Accepted: 07/01/2014] [Indexed: 10/25/2022]
Abstract
UNLABELLED Species of genus Aeromonas, Vibrio, Edwardsiella and Streptococcus are the most common fish pathogenic bacteria that cause economically devastating losses in aquaculture. A multiplex polymerase chain reaction (mPCR) was developed for the simultaneous detection and differentiation of the four genera of fish pathogenic bacteria. Through the use of genus-specific primers instead of species-specific ones, the current mPCR covered much more target bacterial species compared with previously reported species-specific mPCR methods. The specificity of the four putative genus-specific primers was validated experimentally while used exclusively (uniplex PCR) or combined (mPCR) against bacterial genomic DNA templates of the target bacteria and nontarget bacteria. The PCR amplicons for the following genera were obtained as expected: Aeromonas (875 bp), Vibrio (524 bp), Edwardsiella (302 bp) and Streptococcus (197 bp), and the fragments could be separated clearly on the agarose gel electrophoresis. The mPCR did not produce nonspecific amplification products when used to amplify 21 nontarget species of bacteria. The mPCR detection limits for each target bacterial genera were 50 colony-forming units (CFU) in pure culture and 100 CFU in fish tissue samples. In conclusion, the mPCR assay was proven to be a powerful alternative to the conventional culture-based method, given its rapid, specific, sensitive and reliable detection of target pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY The fish pathogenic bacteria of genus Aeromonas, Vibrio, Edwardsiella and Streptococcus frequently cause severe outbreaks of diseases in cultured fish, and the genus-specific multiplex PCR assay developed in this study can detect the bacteria of the four genera when present in the samples either alone or mixed. The mPCR assay is expected to identify the causative agents more efficiently than uniplex PCR or species-specific multiplex PCR for clinical diagnosis, resulting in the earlier implementation of control measures. This mPCR assay provides a rapid, specific and sensitive tool for the detection or identification of common fish pathogenic bacteria in aquaculture practice.
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Affiliation(s)
- D F Zhang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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43
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França SDA, Braga JFV, Moreira MVL, Silva VCM, Souza EF, Pereira LC, Rezende CMDF, Ecco R. Splendore-Hoeppli phenomenon in a cat with osteomyelitis caused by Streptococcus species. J Feline Med Surg 2014; 16:189-93. [PMID: 23906707 PMCID: PMC11383136 DOI: 10.1177/1098612x13499012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
A 9-month-old male neutered mixed-breed cat had a history of chronic lameness of the right hind limb, which was non-responsive to antibiotic treatment. Hematologic analysis revealed marked neutrophilia and mild monocytosis. Radiography revealed extensive loss of cortical bone, and replacement with irregular and disorganized bone. There was loss of the normal cortico-medullary distinction, and the medullary cavity had an irregular radiodensity suggestive of osteomyelitis. Surgical curettage and antibiotics did not improve the clinical condition, and amputation was performed. Grossly, the skin over the right tibia was ulcerated with a viscous and granular exudate. At histopathology, there was marked diffuse pyogranulomatous dermatitis, myositis, periostitis and osteomyelitis associated with Splendore-Hoeppli phenomenon. In addition, there was marrow osteoproliferation and multifocal cortical loss, reabsorption, fibroplasia and endosteal bone formation. Gram staining revealed myriad slightly elongated Gram-positive bacteria, arranged in pairs or single chains, confirmed by polymerase chain reaction as Streptococcus species.
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Affiliation(s)
- Silvia de Araujo França
- Departamento de Clinica e Cirurgia, Escola de Veterinaria da Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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44
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Camelo-Castillo A, Benítez-Páez A, Belda-Ferre P, Cabrera-Rubio R, Mira A. Streptococcus dentisani sp. nov., a novel member of the mitis group. Int J Syst Evol Microbiol 2014; 64:60-65. [DOI: 10.1099/ijs.0.054098-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic, taxonomic and biochemical studies were performed on two strains of α-haemolytic streptococci that showed them to be clustered with major members of the
Streptococcus mitis
group. These Gram-stain-positive strains were isolated from tooth surfaces of caries-free humans and showed the classical spherical shape of streptococcal species growing in chains. Sequence analysis from concatenated 16S and 23S rRNA gene and sodA genes showed that these strains belonged to the mitis group, but both of them clustered into a new phylogenetic branch. The genomes of these two isolates were sequenced, and whole-genome average nucleotide identity (ANI) demonstrated that these strains significantly differed from any streptococcal species, showing ANI values under 91 % even when compared with the phylogenetically closest species such as
Streptococcus oralis
and
S. mitis
. Biochemically, the two isolates also showed distinct metabolic features relative to closely related species, like α-galactosidase activity. From the results of the present study, the name Streptococcus dentisani sp. nov. is proposed to accommodate these novel strains, which have been deposited in open collections at the Spanish type Culture Collection (CECT) and Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures (DSMZ), being respectively identified as Streptococcus dentisani Str. 7746 ( = CECT 8313 = DSM 27089) and Streptococcus dentisani Str. 7747T ( = CECT 8312T = DSM 27088T).
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Affiliation(s)
- Anny Camelo-Castillo
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Alfonso Benítez-Páez
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Pedro Belda-Ferre
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Raúl Cabrera-Rubio
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
| | - Alex Mira
- Oral Microbiome Laboratory, Genomics & Health Department – Center for Advanced Research in Public Health (CSISP-FISABIO), Valencia, Spain
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URUSHIBARA Y, OHSHIMA T, SATO M, HAYASHI Y, HAYAKAWA T, MAEDA N, OHKUBO C. An analysis of the biofilms adhered to framework alloys using in vitro denture plaque models. Dent Mater J 2014; 33:402-14. [DOI: 10.4012/dmj.2013-325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abdelsalam M, Eissa AE, Chen SC. Genetic diversity of geographically distinct Streptococcus dysgalactiae isolates from fish. J Adv Res 2013; 6:233-8. [PMID: 25750757 PMCID: PMC4348444 DOI: 10.1016/j.jare.2013.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 11/13/2013] [Accepted: 12/05/2013] [Indexed: 11/16/2022] Open
Abstract
Streptococcus dysgalactiae is an emerging pathogen of fish. Clinically, infection is characterized by the development of necrotic lesions at the caudal peduncle of infected fishes. The pathogen has been recently isolated from different fish species in many countries. Twenty S. dysgalactiae isolates collected from Japan, Taiwan, Malaysia and Indonesia were molecularly characterized by biased sinusoidal field gel electrophoresis (BSFGE) using SmaI enzyme, and tuf gene sequencing analysis. DNA sequencing of ten S. dysgalactiae revealed no genetic variation in the tuf amplicons, except for three strains. The restriction patterns of chromosomal DNA measured by BSFGE were differentiated into six distinct types and one subtype among collected strains. To our knowledge, this report gives the first snapshot of S. dysgalactiae isolates collected from different countries that are localized geographically and differed on a multinational level. This genetic unrelatedness among different isolates might suggest a high recombination rate and low genetic stability.
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Affiliation(s)
- M Abdelsalam
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - A E Eissa
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt ; Departments of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Tripoli University, Tripoli, Libya
| | - S-C Chen
- Graduate Institute of Animal Vaccine Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan ; Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Resembling breast milk: influence of polyamine-supplemented formula on neonatal BALB/cOlaHsd mouse microbiota. Br J Nutr 2013; 111:1050-8. [DOI: 10.1017/s0007114513003565] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Infant microbiota is influenced by numerous factors, such as delivery mode, environment, prematurity and diet (breast milk or formula). In addition to its nutritional value, breast milk contains bioactive substances that drive microbial colonisation and support immune system development, which are usually not present in infant formulas. Among these substances, polyamines have been described to be essential for intestinal and immune functions in newborns. However, their effect on the establishment of microbiota remains unclear. Therefore, the aim of the present study was to ascertain whether an infant formula supplemented with polyamines has an impact on microbial colonisation by modifying it to resemble that in breast-fed neonatal BALB/c mice. In a 4 d intervention, a total of sixty pups (14 d old) were randomly assigned to the following groups: (1) breast-fed group; (2) non-enriched infant formula-fed group; (3) three different groups fed an infant formula enriched with increasing concentrations of polyamines (mixture of putrescine, spermidine and spermine), following the proportions found in human milk. Microbial composition in the contents of the oral cavity, stomach and small and large intestines was analysed by quantitative PCR targeted at fourteen bacterial genera and species. Significantly different (P< 0·05) microbial colonisation patterns were observed in the entire gastrointestinal tract of the breast-fed and formula-fed mice. In addition, our findings demonstrate that supplementation of polyamines regulates the amounts of total bacteria,Akkermansia muciniphila,Lactobacillus,Bifidobacterium,Bacteroides–PrevotellaandClostridiumgroups to levels found in the breast-fed group. Such an effect requires further investigation in human infants, as supplementation of an infant formula with polyamines might contribute to healthy gastrointestinal tract development.
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Evaluation of two matrix-assisted laser desorption ionization–time of flight mass spectrometry systems for identification of viridans group streptococci. Eur J Clin Microbiol Infect Dis 2013; 33:779-88. [DOI: 10.1007/s10096-013-2012-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 10/23/2013] [Indexed: 10/26/2022]
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Huang CH, Chang MT, Huang L, Chu WS. Utilization of elongation factor Tu gene (tuf) sequencing and species-specific PCR (SS-PCR) for the molecular identification of Acetobacter species complex. Mol Cell Probes 2013; 28:31-3. [PMID: 23969032 DOI: 10.1016/j.mcp.2013.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/26/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
Abstract
The aim of this study was to use tuf gene as a molecular target for species discrimination in the Acetobacter genus, as well as to develop species-specific PCR method for direct species identification of Acetobacter aceti. The results showed that most Acetobacter species could be clearly distinguished, and the average sequence similarity for the tuf gene (89.5%) among type strains was significantly lower than that of the 16S rRNA gene sequence (98.0%). A pair of species-specific primers were designed and used to specifically identify A. aceti, but none of the other Acetobacter strains. Our data indicate that the phylogenetic relationships of most strains in the Acetobacter genus can be resolved using tuf gene sequencing, and the novel species-specific primer pair could be used to rapidly and accurately identify the species of A. aceti by the PCR based assay.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Road, Hsinchu 30062, Taiwan, ROC
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Wullschleger S, Lacroix C, Bonfoh B, Sissoko-Thiam A, Hugenschmidt S, Romanens E, Baumgartner S, Traoré I, Yaffee M, Jans C, Meile L. Analysis of lactic acid bacteria communities and their seasonal variations in a spontaneously fermented dairy product (Malian fènè) by applying a cultivation/genotype-based binary model. Int Dairy J 2013. [DOI: 10.1016/j.idairyj.2012.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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