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Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A. Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species. Open Biol 2018; 7:rsob.170074. [PMID: 28931649 PMCID: PMC5627049 DOI: 10.1098/rsob.170074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member, Streptococcus pneumoniae Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (n = 101) and from carriage (n = 103), and on non-typeable pneumococci from asymptomatic individuals (n = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for S. pneumoniae, targeting cpsA, lytA, piaB, ply, Spn9802, zmpC and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of lytA and piaB were 100% specific for S. pneumoniae, whereas assays targeting cpsA, ply, Spn9802, zmpC and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.
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Affiliation(s)
- Anne L Wyllie
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Sandra Bovenkerk
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands
| | - Jody van Engelsdorp Gastelaars
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Bart Ferwerda
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Diederik van de Beek
- Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Krzysztof Trzciński
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands.,The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, the Netherlands
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Alvarado M, Martín-Galiano AJ, Ferrándiz MJ, Zaballos Á, de la Campa AG. Upregulation of the PatAB Transporter Confers Fluoroquinolone Resistance to Streptococcus pseudopneumoniae. Front Microbiol 2017; 8:2074. [PMID: 29123510 PMCID: PMC5662624 DOI: 10.3389/fmicb.2017.02074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/10/2017] [Indexed: 11/27/2022] Open
Abstract
We characterized the mechanism of fluoroquinolone-resistance in two isolates of Streptococcus pseudopneumoniae having fluoroquinolone-efflux as unique mechanism of resistance. Whole genome sequencing and genetic transformation experiments were performed together with phenotypic determinations of the efflux mechanism. The PatAB pump was identified as responsible for efflux of ciprofloxacin (MIC of 4 μg/ml), ethidium bromide (MICs of 8-16 μg/ml) and acriflavine (MICs of 4-8 μg/ml) in both isolates. These MICs were at least 8-fold lower in the presence of the efflux inhibitor reserpine. Complete genome sequencing indicated that the sequence located between the promoter of the patAB operon and the initiation codon of patA, which putatively forms an RNA stem-loop structure, may be responsible for the efflux phenotype. RT-qPCR determinations performed on RNAs of cultures treated or not treated with subinhibitory ciprofloxacin concentrations were performed. While no significant changes were observed in wild-type Streptococcus pneumoniae R6 strain, increases in transcription were detected in the ciprofloxacin-efflux transformants obtained with DNA from efflux-positive isolates, in the ranges of 1.4 to 3.4-fold (patA) and 2.1 to 2.9-fold (patB). Ciprofloxacin-induction was related with a lower predicted free energy for the stem-loop structure in the RNA of S. pseudopneumoniae isolates (-13.81 and -8.58) than for R6 (-15.32 kcal/mol), which may ease transcription. The presence of these regulatory variations in commensal S. pseudopneumoniae isolates, and the possibility of its transfer to Streptococcus pneumoniae by genetic transformation, could increase fluoroquinolone resistance in this important pathogen.
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Affiliation(s)
- María Alvarado
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - María J. Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Ángel Zaballos
- Unidad de Genómica, Instituto de Salud Carlos III, Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- Presidencia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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López E, Domenech A, Ferrándiz MJ, Frias MJ, Ardanuy C, Ramirez M, García E, Liñares J, de la Campa AG. Induction of prophages by fluoroquinolones in Streptococcus pneumoniae: implications for emergence of resistance in genetically-related clones. PLoS One 2014; 9:e94358. [PMID: 24718595 PMCID: PMC3981806 DOI: 10.1371/journal.pone.0094358] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 03/13/2014] [Indexed: 11/29/2022] Open
Abstract
Antibiotic resistance in Streptococcus pneumoniae has increased worldwide by the spread of a few clones. Fluoroquinolone resistance occurs mainly by alteration of their intracellular targets, the type II DNA topoisomerases, which is acquired either by point mutation or by recombination. Increase in fluoroquinolone-resistance may depend on the balance between antibiotic consumption and the cost that resistance imposes to bacterial fitness. In addition, pneumococcal prophages could play an important role. Prophage induction by fluoroquinolones was confirmed in 4 clinical isolates by using Southern blot hybridization. Clinical isolates (105 fluoroquinolone-resistant and 160 fluoroquinolone-susceptible) were tested for lysogeny by using a PCR assay and functional prophage carriage was studied by mitomycin C induction. Fluoroquinolone-resistant strains harbored fewer inducible prophages (17/43) than fluoroquinolone-susceptible strains (49/70) (P = 0.0018). In addition, isolates of clones associated with fluoroquinolone resistance [CC156 (3/25); CC63 (2/20), and CC81 (1/19)], had lower frequency of functional prophages than isolates of clones with low incidence of fluoroquinolone resistance [CC30 (4/21), CC230 (5/20), CC62 (9/21), and CC180 (21/30)]. Likewise, persistent strains from patients with chronic respiratory diseases subjected to fluoroquinolone treatment had a low frequency of inducible prophages (1/11). Development of ciprofloxacin resistance was tested with two isogenic strains, one lysogenic and the other non-lysogenic: emergence of resistance was only observed in the non-lysogenic strain. These results are compatible with the lysis of lysogenic isolates receiving fluoroquinolones before the development of resistance and explain the inverse relation between presence of inducible prophages and fluoroquinolone-resistance.
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Affiliation(s)
- Elena López
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Arnau Domenech
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - María-José Ferrándiz
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Maria João Frias
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carmen Ardanuy
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - Mario Ramirez
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ernesto García
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Centro de Investigaciones Biológicas, CSIC (Consejo Superior de Investigaciones Científicas), Madrid, Spain
| | - Josefina Liñares
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Microbiology Department, Hospital Universitari de Bellvitge-IDIBELL- Barcelona University, Barcelona, Spain
| | - Adela G. de la Campa
- Centro Nacional de Microbiología, ISCIII (Instituto de Salud Carlos III), Majadahonda, Madrid, Spain
- Ciber de Enfermedades Respiratorias, ISCIII, Madrid, Spain
- Presidencia, CSIC, Madrid, Spain
- * E-mail:
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Rolo D, S. Simões A, Domenech A, Fenoll A, Liñares J, de Lencastre H, Ardanuy C, Sá-Leão R. Disease isolates of Streptococcus pseudopneumoniae and non-typeable S. pneumoniae presumptively identified as atypical S. pneumoniae in Spain. PLoS One 2013; 8:e57047. [PMID: 23437306 PMCID: PMC3578818 DOI: 10.1371/journal.pone.0057047] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/16/2013] [Indexed: 11/27/2022] Open
Abstract
We aimed to obtain insights on the nature of a collection of isolates presumptively identified as atypical Streptococcus pneumoniae recovered from invasive and non-invasive infections in Spain. One-hundred and thirty-two isolates were characterized by: optochin susceptibility in ambient and CO2-enriched atmosphere; bile solubility; PCR-based assays targeting pneumococcal genes lytA, ply, pspA, cpsA, Spn9802, aliB-like ORF2, and a specific 16S rRNA region; multilocus sequence analysis; and antimicrobial susceptibility. By multilocus sequence analysis, 61 isolates were S. pseudopneumoniae, 34 were pneumococci, 13 were S. mitis, and 24 remained unclassified as non-pneumococci. Among S. pseudopneumoniae isolates, 51 (83.6%) were collected from respiratory tract samples; eight isolates were obtained from sterile sources. High frequency of non-susceptibility to penicillin (60.7%) and erythromycin (42.6%) was found. Only 50.8% of the S. pseudopneumoniae isolates displayed the typical optochin phenotype originally described for this species. None harbored the cpsA gene or the pneumococcal typical lytA restriction fragment length polymorphism. The Spn9802 and the specific 16S rRNA regions were detected among the majority of the S. pseudopneumoniae isolates (n = 59 and n = 49, respectively). The ply and pspA genes were rarely found. A high genetic diversity was found and 59 profiles were identified. Among the S. pneumoniae, 23 were capsulated and 11 were non-typeable. Three non-typeable isolates, associated to international non-capsulated lineages, were recovered from invasive disease sources. In conclusion, half of the atypical pneumococcal clinical isolates were, in fact, S. pseudopneumoniae and one-fourth were other streptococci. We identified S. pseudopneumoniae and non-typeable pneumococci as cause of disease in Spain including invasive disease.
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Affiliation(s)
- Dora Rolo
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexandra S. Simões
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Arnau Domenech
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Asunción Fenoll
- National Center for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Liñares
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Microbiology, The Rockefeller University, New York, New York, United States of America
| | - Carmen Ardanuy
- Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, Microbiology Department, Universistat de Barcelona, Barcelona, Spain
- Centro de investigación en red de enfermedades respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Sá-Leão
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail:
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