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Dalmieda J, Hitchcock M, Xu J. High diversity within and low but significant genetic differentiation among geographic and temporal populations of the global Streptococcus pneumoniae. Can J Microbiol 2024; 70:226-237. [PMID: 38422492 DOI: 10.1139/cjm-2023-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Streptococcus pneumoniae is the major cause of invasive pneumococcal disease. However, the global population structure remains largely unexplored. In this study, we investigated the spatial and temporal patterns of genetic variation of S. pneumoniae based on archived multilocus sequence typing data from PubMLST.org. Our analyses demonstrated both shared and unique distributions of sequence types (STs) and allele types among regional populations. Among the 17 915 global STs, 36 representing 15 263 isolates were broadly shared among all six continents, consistent with recent clonal dispersal and expansion of this pathogen. The analysis of molecular variance revealed that >96% genetic variations were found within individual regional populations. However, though low (<4%), statistically significant genetic differentiation among regional populations was observed. Comparisons between non-clone-corrected and clone-corrected datasets showed that localized clonal expansion contributed significantly to the observed genetic differentiations among regions. Temporal analyses of the isolates showed that implementation of pneumococcal conjugate vaccine impacted the distributions of STs, but the effect on population structure was relatively limited. Linkage disequilibrium analyses identified evidence for recombination in all continental populations; however, the inferred recombination was not random. We discussed the limitations and implications of our analyses to the global epidemiology and future vaccine developments for S. pneumoniae.
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Affiliation(s)
- Jezreel Dalmieda
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Megan Hitchcock
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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2
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Yao M, Wang K, Song G, Hu Y, Chen J, Li T, Liang L, Wu J, Xu H, Wang L, Zheng Y, Zhang X, Yin Y, Yao S, Wu K. Transcriptional regulation of TacL-mediated lipoteichoic acids biosynthesis by ComE during competence impacts pneumococcal transformation. Front Cell Infect Microbiol 2024; 14:1375312. [PMID: 38779562 PMCID: PMC11109429 DOI: 10.3389/fcimb.2024.1375312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
Competence development is essential for bacterial transformation since it enables bacteria to take up free DNA from the surrounding environment. The regulation of teichoic acid biosynthesis is tightly controlled during pneumococcal competence; however, the mechanism governing this regulation and its impact on transformation remains poorly understood. We demonstrated that a defect in lipoteichoic acid ligase (TacL)-mediated lipoteichoic acids (LTAs) biosynthesis was associated with impaired pneumococcal transformation. Using a fragment of tacL regulatory probe as bait in a DNA pulldown assay, we successfully identified several regulatory proteins, including ComE. Electrophoretic mobility shift assays revealed that phosphomimetic ComE, but not wild-type ComE, exhibited specific binding to the probe. DNase I footprinting assays revealed the specific binding sequences encompassing around 30 base pairs located 31 base pairs upstream from the start codon of tacL. Expression of tacL was found to be upregulated in the ΔcomE strain, and the addition of exogenous competence-stimulating peptide repressed the tacL transcription in the wild-type strain but not the ΔcomE mutant, indicating that ComE exerted a negative regulatory effect on the transcription of tacL. Mutation in the JH2 region of tacL upstream regulatory sequence led to increased LTAs abundance and displayed higher transformation efficiency. Collectively, our work identified the regulatory mechanisms that control LTAs biosynthesis during competence and thereby unveiled a repression mechanism underlying pneumococcal transformation.
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Affiliation(s)
- Miao Yao
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Kun Wang
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Guangming Song
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Yumeng Hu
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Jiali Chen
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Tingting Li
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Longying Liang
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Jie Wu
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Hongmei Xu
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Libin Wang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yuqiang Zheng
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Xuemei Zhang
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yibing Yin
- Key Laboratory of Laboratory Medical Diagnostics Designated by the Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Shifei Yao
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
- Scientific Research Center, The First People’s Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China
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3
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Rafiqullah IM, Varghese R, Hellmann KT, Velmurugan A, Neeravi A, Kumar Daniel JL, Vidal JE, Kompithra RZ, Verghese VP, Veeraraghavan B, Robinson DA. Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India. Microb Genom 2024; 10:001191. [PMID: 38315173 PMCID: PMC10926699 DOI: 10.1099/mgen.0.001191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.
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Affiliation(s)
- Iftekhar M. Rafiqullah
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - K. Taylor Hellmann
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Aravind Velmurugan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | | | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rajeev Z. Kompithra
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Valsan P. Verghese
- Department of Child Health, Christian Medical College and Hospital, Vellore, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - D. Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS, USA
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS, USA
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Chen YY, Chi H, Liao WC, Li SW, Yang YC, Lin HC, Chang HP, Pan YJ, Chiang RL, Hsieh YC. Genomic analysis of penicillin-binding proteins and recombination events in an emerging amoxicillin- and meropenem-resistant PMEN3 (Spain 9V-3, ST156) variant in Taiwan and comparison with global descendants of this lineage. Microbiol Spectr 2023; 11:e0184023. [PMID: 37930013 PMCID: PMC10715136 DOI: 10.1128/spectrum.01840-23] [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: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
From 2008 to 2020, the Taiwan National Notifiable Disease Surveillance System database demonstrated that the incidence of non-vaccine serotype 23A invasive pneumococcal disease (IPD) approximately doubled. In this study, 276 non-repetitive pneumococcal clinical isolates were collected from two medical centers in Taiwan between 2019 and 2021. Of these 267 pneumococci, 60 were serotype 23A. Among them, 50 (83%) of serotype 23A isolates belonged to the sequence type (ST) 166 variant of the Spain9V-3 clone. Pneumococcal 23A-ST166 isolates were collected to assess their evolutionary relationships using whole-genome sequencing. All 23A-ST166 isolates were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299, the newly identified PBP2x-299 in Taiwan. Transformation of the pbp1a, pbp2b, and pbp2x alleles into the β-lactam-susceptible R6 strain revealed that PBP2x-299 and PBP2b-11 increased the MIC of ceftriaxone and meropenem by 16-fold, respectively. Prediction analysis of recombination sites in PMEN3 descendants (23A-ST166 in Taiwan, 35B-ST156 in the United States, and 11A-ST838/ST6521 in Europe) showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displayed an evolutionary capacity for global dissemination and persistence, increasing IPD incidence, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases, and contributing to high antibiotic resistance. A clonal shift with a highly β-lactam-resistant non-vaccine serotype 23A, from ST338 to ST166, increased in Taiwan. ST166 is a single-locus variant of the Spain9V-3 clone, which is also called the PMEN3 lineage. All 23A-ST166 isolates, in this study, were resistant to amoxicillin and meropenem, and 96% harbored a novel combination of penicillin-binding proteins (PBPs) (1a:2b:2x):15:11:299. PBP2x-299 and PBP2b-11 contributed to the increasing MIC of ceftriaxone and meropenem, respectively. Prediction analysis of recombination sites in PMEN3 descendants showed that adaptive evolution involved repeated, selectively favored convergent recombination in the capsular polysaccharide synthesis region, PBPs, murM, and folP genome sites. In the late 13-valent pneumococcal conjugate vaccine era, PMEN3 continuously displays the evolutionary capacity for dissemination, leading to an offset in the decrease of pneumococcal conjugate vaccine serotype-related diseases and contributing to high antibiotic resistance.
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Affiliation(s)
- Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan
- Department of Pediatrics, MacKay Children’s Hospital and MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wei-Chao Liao
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Yu-Ching Yang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Ho-Chen Lin
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Hsiao-Pei Chang
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Ruei-Lin Chiang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan
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5
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Lobb B, Lee MC, McElheny CL, Doi Y, Yahner K, Hoberman A, Martin JM, Hirota JA, Doxey AC, Shaikh N. Genomic classification and antimicrobial resistance profiling of Streptococcus pneumoniae and Haemophilus influenza isolates associated with paediatric otitis media and upper respiratory infection. BMC Infect Dis 2023; 23:596. [PMID: 37700242 PMCID: PMC10498559 DOI: 10.1186/s12879-023-08560-x] [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: 04/23/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Acute otitis media (AOM) is the most common childhood bacterial infectious disease requiring antimicrobial therapy. Most cases of AOM are caused by translocation of Streptococcus pneumoniae or Haemophilus influenzae from the nasopharynx to the middle ear during an upper respiratory tract infection (URI). Ongoing genomic surveillance of these pathogens is important for vaccine design and tracking of emerging variants, as well as for monitoring patterns of antibiotic resistance to inform treatment strategies and stewardship.In this work, we examined the ability of a genomics-based workflow to determine microbiological and clinically relevant information from cultured bacterial isolates obtained from patients with AOM or an URI. We performed whole genome sequencing (WGS) and analysis of 148 bacterial isolates cultured from the nasopharynx (N = 124, 94 AOM and 30 URI) and ear (N = 24, all AOM) of 101 children aged 6-35 months presenting with AOM or an URI. We then performed WGS-based sequence typing and antimicrobial resistance profiling of each strain and compared results to those obtained from traditional microbiological phenotyping.WGS of clinical isolates resulted in 71 S. pneumoniae genomes and 76 H. influenzae genomes. Multilocus sequencing typing (MSLT) identified 33 sequence types for S. pneumoniae and 19 predicted serotypes including the most frequent serotypes 35B and 3. Genome analysis predicted 30% of S. pneumoniae isolates to have complete or intermediate penicillin resistance. AMR predictions for S. pneumoniae isolates had strong agreement with clinical susceptibility testing results for beta-lactam and non beta-lactam antibiotics, with a mean sensitivity of 93% (86-100%) and a mean specificity of 98% (94-100%). MLST identified 29 H. influenzae sequence types. Genome analysis identified beta-lactamase genes in 30% of H. influenzae strains, which was 100% in agreement with clinical beta-lactamase testing. We also identified a divergent highly antibiotic-resistant strain of S. pneumoniae, and found its closest sequenced strains, also isolated from nasopharyngeal samples from over 15 years ago.Ultimately, our work provides the groundwork for clinical WGS-based workflows to aid in detection and analysis of H. influenzae and S. pneumoniae isolates.
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Affiliation(s)
- Briallen Lobb
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Matthew C Lee
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, USA
| | - Christi L McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kristin Yahner
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, USA
| | - Alejandro Hoberman
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, USA
| | - Judith M Martin
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, USA
| | - Jeremy A Hirota
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Firestone Institute for Respiratory Health, St. Joseph's Hospital, Hamilton, ON, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew C Doxey
- Department of Biology and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
| | - Nader Shaikh
- University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of UPMC, Division of General Academic Pediatrics, Pittsburgh, USA.
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Orami T, Aho C, Ford RL, Pomat WS, Greenhill A, Kirkham LA, Masiria G, Nivio B, Britton KJ, Jacoby P, Richmond PC, van den Biggelaar AHJ, Lehmann D. Pneumococcal carriage, serotype distribution, and antimicrobial susceptibility in Papua New Guinean children vaccinated with PCV10 or PCV13 in a head-to-head trial. Vaccine 2023; 41:5392-5399. [PMID: 37479616 DOI: 10.1016/j.vaccine.2023.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Children in Papua New Guinea (PNG) are at high risk of pneumococcal infections. We investigated pneumococcal carriage rates, serotype distribution, and antimicrobial susceptibility in PNG children after vaccination with 10-valent or 13-valent pneumococcal conjugate vaccines (PCV10; PCV13). METHODS Infants (N = 262) were randomized to receive 3 doses of PCV10 or PCV13 at 1-2-3 months of age, followed by pneumococcal polysaccharide vaccination (PPV) or no PPV at 9 months of age. Nasopharyngeal swabs (NPS) collected at ages 1, 4, 9, 10, 23 and 24 months were cultured using standard bacteriological procedures. Morphologically distinct Streptococcus pneumoniae colonies were serotyped by the Quellung reaction. Antimicrobial susceptibility was determined by Kirby-Bauer disc diffusion and minimum inhibitory concentration (MIC). RESULTS S. pneumoniae was isolated from 883/1063 NPS collected at 1-23 months of age, including 820 serotypeable (64 different serotypes) and 144 non-serotypeable isolates. At age 23 months, 93.6% (95%CI 86.6-97.6%) of PCV10 recipients and 88.6% (95%CI 80.1-94.4%) of PCV13 recipients were pneumococcal carriers, with higher carriage of PCV10 serotypes by PCV10 recipients (19.8%, 95%CI 12.2-29.5) than PCV13 recipients (9.3%, 95%CI 4.1-17.3) (p = 0.049). There were no other statistically significant differences between PCV10 and PCV13 recipients and children receiving PPV or no PPV. Nearly half (45.6%) of carried pneumococci were non-susceptible to penicillin based on the meningitis breakpoint (MIC ≥ 0.12 µg/mL), but resistance was rare (1.1%) using the non-meningitis cut-off (MIC ≥ 8 µg/mL). Non-susceptibility to trimethoprim-sulfamethoxazole (SXT) was common: 23.2% of isolates showed intermediate resistance (MIC 1/19-2/38 µg/mL) and 16.9% full resistance (MIC ≥ 4/76 µg/mL). PCV serotypes 14 and 19A were commonly non-susceptible to both penicillin (14, 97%; 19A, 70%) and SXT (14, 97%; 19A, 87%). CONCLUSION Even after PCV10 or PCV13 vaccination, children living in a high-risk setting such as PNG continue to experience high levels of pneumococcal colonization, including carriage of highly antimicrobial-resistant PCV serotypes. The study is registered with ClinicalTrials.gov (CTN NCT01619462).
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Affiliation(s)
- Tilda Orami
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Celestine Aho
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Rebecca L Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - William S Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Andrew Greenhill
- School of Science, Psychology and Sport, Federation University, Churchill, Australia
| | - Lea-Ann Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Geraldine Masiria
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Birunu Nivio
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Kathryn J Britton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia; Discipline of Paediatrics, School of Medicine, University of Western Australia, Perth, Australia
| | - Peter Jacoby
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia; Discipline of Paediatrics, School of Medicine, University of Western Australia, Perth, Australia
| | - Anita H J van den Biggelaar
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Deborah Lehmann
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia.
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7
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York A, Huynh E, Mbodj S, Yolda-Carr D, Hislop MS, Echlin H, Rosch JW, Weinberger DM, Wyllie AL. Magnetic bead-based separation of pneumococcal serotypes. CELL REPORTS METHODS 2023; 3:100410. [PMID: 36936076 PMCID: PMC10014298 DOI: 10.1016/j.crmeth.2023.100410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 11/18/2022] [Accepted: 01/26/2023] [Indexed: 02/23/2023]
Abstract
The separation of pneumococcal serotypes from a complex polymicrobial mixture may be required for different applications. For instance, a minority strain could be present at a low frequency in a clinical sample, making it difficult to identify and isolate by traditional culture-based methods. We therefore developed an assay to separate mixed pneumococcal samples using serotype-specific antiserum and a magnetic bead-based separation method. Using qPCR and colony counting methods, we first show that serotypes (12F, 23F, 3, 14, 19A, and 15A) present at ∼0.1% of a dual serotype mixture can be enriched to between 10% and 90% of the final sample. We demonstrate two applications for this method: extraction of known pneumococcal serotypes from saliva samples and efficient purification of capsule switch variants from experimental transformation experiments. This method may have further laboratory or clinical applications when the selection of specific serotypes is required.
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Affiliation(s)
- Anna York
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Emily Huynh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Sidiya Mbodj
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Maikel S. Hislop
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Life Sciences and Chemistry, Utrecht University of Applied Sciences, 3584 CS Utrecht, the Netherlands
| | - Haley Echlin
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jason W. Rosch
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Daniel M. Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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Frequent Transmission of Streptococcus pneumoniae Serotype 35B and 35D, Clonal Complex 558 Lineage, across Continents and the Formation of Multiple Clades in Japan. Antimicrob Agents Chemother 2023; 67:e0108322. [PMID: 36651739 PMCID: PMC9933736 DOI: 10.1128/aac.01083-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Streptococcus pneumoniae is a common bacterial pathogen that causes infections in children worldwide, even after administration of the pneumococcal conjugate vaccine. S. pneumoniae serotype 35B, especially the clonal complex 558 (CC558) lineage, has emerged globally following implementation of the 13-valent pneumococcal conjugate vaccine. Serotype 35B strains are also associated with multidrug resistance to both β-lactams and non-β-lactam drugs. In addition, a novel serotype, 35D, which is closely related to 35B and differs in polysaccharide structure, was recently reported. However, the genetic relationship among globally disseminating serotype 35B and D (35B/D) strains remains unknown. To investigate the molecular epidemiology of global serotype 35B/D strains, we conducted a genomic analysis of serotype 35B/D strains from various continents, including those from the Japanese national surveillance collection. A total of 87 isolates were identified as serotype 35B/D in the Japanese surveillance collection (n = 1,358). All the isolates were assigned to either CC558 or CC2755. Serotype 35D isolates were interspersed with serotype 35B isolates. Phylogenetic analysis revealed the formation of multiple clusters by the Japanese serotype 35B/D-CC558 isolates among the foreign isolates, which suggested multiple events of introduction of the clone into Japan. The global 35B/D-CC558 strains were found to share specific penicillin-binding protein profiles, pbp1a-4, pbp2b-7, and pbp2x-7, associated with penicillin, cephalosporin, and carbapenem nonsusceptibility. Moreover, 88.5% of the Japanese 35B/D-CC558 and 35B/D-CC2755 isolates were found to harbor the Tn916-like integrative and conjugative elements Tn2009, Tn2010, and Tn6002, associated with multidrug resistance to macrolides and tetracyclines. The results of this study imply that serotype 35B/D-CC558 strains could be frequently transmitted intercontinentally.
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Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, Antonio M, Kwambana-Adams B, Cornick J, Everett DB, Dagan R, Hawkins PA, Beall B, Corso A, Grassi Almeida SC, Ochoa TJ, Obaro S, Shakoor S, Donkor ES, Gladstone RA, Ho PL, Paragi M, Doiphode S, Srifuengfung S, Ford R, Moïsi J, Saha SK, Bigogo G, Sigauque B, Eser ÖK, Elmdaghri N, Titov L, Turner P, Kumar KLR, Kandasamy R, Egorova E, Ip M, Breiman RF, Klugman KP, McGee L, Bentley SD, von Gottberg A, The Global Pneumococcal Sequencing Consortium. A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV. Microb Genom 2022; 8. [PMID: 35384831 PMCID: PMC9453074 DOI: 10.1099/mgen.0.000746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005–2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005–2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.
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Affiliation(s)
- Kedibone M Ndlangisa
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Linda de Gouveia
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.,West Africa Partnerships and Strategies, Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | | | - Dean B Everett
- Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi.,Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK
| | - Ron Dagan
- The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Paulina A Hawkins
- Rollins School Public Health, Emory University, Atlanta, USA.,Centers for Disease Control and Prevention, Atlanta, USA
| | - Bernard Beall
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Alejandra Corso
- Administración Nacional de Laboratorios e Institutos de Salud, Buenos Aires, Argentina
| | | | - Theresa J Ochoa
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Eric S Donkor
- Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana
| | | | - Pak Leung Ho
- Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China
| | - Metka Paragi
- National Laboratory of Health, Environment and Food, Ljubljana, Slovenia
| | | | | | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Betuel Sigauque
- Centro de Investigação em Saúde da Manhiça, Maputo, Moçambique
| | - Özgen Köseoglu Eser
- Hacettepe University Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey
| | - Naima Elmdaghri
- Faculty of Medicine and Pharmacy & Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Leonid Titov
- The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K L Ravi Kumar
- Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India
| | - Rama Kandasamy
- University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Ekaterina Egorova
- G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - Margaret Ip
- Department of Microbiology, Chinese University of Hong Kong, Hong Kong, PR China
| | | | - Keith P Klugman
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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10
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Fuji N, Pichichero M, Ehrlich RL, Mell JC, Ehrlich GD, Kaur R. Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children. Front Cell Infect Microbiol 2021; 11:744742. [PMID: 34765566 PMCID: PMC8577857 DOI: 10.3389/fcimb.2021.744742] [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: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
In our community-based prospective cohort study in young children, we observed a significant increase in pneumococcal serotype 35B nasopharyngeal (NP) commensal colonization during the 2011–2014 timeframe, but these strains were not associated with disease. Beginning in 2015 and continuing through to the present, the serotype 35B virulence changed, and it became the dominant bacteria isolated and associated with pneumococcal acute otitis-media (AOM) in our cohort. We performed comparative analyses of 250 35B isolates obtained from 140 children collected between 2006 and 2019. Changes in prevalence, clonal-complex composition, and antibiotic resistance were analyzed. Seventy-two (29%) of 35B isolates underwent whole-genome sequencing to investigate genomic changes associated with the shift in virulence that resulted in increased rates of 35B-associated AOM disease. 35B strains that were commensals and AOM disease-causing were mainly associated with sequence type (ST) 558. Antibiotic concentrations of β-lactams and ofloxacin necessary to inhibit growth of 35B strains rose significantly (2006–2019) (p<0.005). However, only isolates from the 35B/ST558 showed significant increases in MIC50 of penicillin and ofloxacin between the years 2006–2014 and 2015–2019 (p=0.007 and p<0.0001). One hundred thirty-eight SNPs located in 34 different genes were significantly associated with post-2015 strains. SNPs were found in nrdG (metal binding, 10%); metP and metN (ABC transporter, 9%); corA (Mg2+ transporter, 6%); priA (DNA replication, 5%); and on the enzymic gene ldcB (LD-carboxypeptidase, 3%). Pneumococcal serotype 35B strains was a common NP commensal during 2010–2014. In 2015, a shift in increasing number of AOM cases occurred in young children caused by 35B, that was associated with changes in genetic composition and antibiotic susceptibility.
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Affiliation(s)
- Naoko Fuji
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Michael Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Rachel L Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, and Center for Genomic Sciences, Institute of Molecular Medicine and Infectious Disease, Philadelphia, PA, United States.,Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ravinder Kaur
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
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11
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Du QQ, Shi W, Yu D, Yao KH. Epidemiology of non-vaccine serotypes of Streptococcus pneumoniae before and after universal administration of pneumococcal conjugate vaccines. Hum Vaccin Immunother 2021; 17:5628-5637. [PMID: 34726580 DOI: 10.1080/21645515.2021.1985353] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The universal administration of pneumococcal conjugate vaccines (PCVs) had been demonstrated as an effective way to prevent Streptococcus pneumoniae infection. However, the immunity induced by PCVs protected against the infections caused by vaccine serotypes, which were usually more frequent than non-vaccine serotypes (NVTs). The prevalence and pathogenicity of NVTs after universal vaccination have caused widespread concern. We reviewed the epidemiology of non-PCV13 S. pneumoniae before and after PCV13 introduction, and explored the potential reasons for the spread of NVTs. Emerging and spreading NVTs can be regarded as the focus for future serotype epidemiological survey and vaccine optimization.AbbreviationsIPD: invasive pneumococcal disease PCV: pneumococcal conjugate vaccines VT: vaccine serotypeNVT: non-vaccine serotype.
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Affiliation(s)
- Qian-Qian Du
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, Laboratory of Microbiology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wei Shi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, Laboratory of Microbiology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Dan Yu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, Laboratory of Microbiology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kai-Hu Yao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, Laboratory of Microbiology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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12
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Kalizang'oma A, Chaguza C, Gori A, Davison C, Beleza S, Antonio M, Beall B, Goldblatt D, Kwambana-Adams B, Bentley SD, Heyderman RS. Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis. Microb Genom 2021; 7. [PMID: 34550067 PMCID: PMC8715442 DOI: 10.1099/mgen.0.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus, the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis, Streptococcus oralis and S. pneumoniae. With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis. Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis.
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Affiliation(s)
- Akuzike Kalizang'oma
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Chrispin Chaguza
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK.,Darwin College, University of Cambridge, Silver Street, Cambridge, UK.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Andrea Gori
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | - Charlotte Davison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Martin Antonio
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, World Health Organization, Collaborating Centre for New Vaccines Surveillance, Banjul, Gambia
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Atlanta, GA, USA
| | - David Goldblatt
- University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
| | | | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection & Immunity, University College London, London, UK
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13
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Lo SW, Gladstone RA, van Tonder AJ, Du Plessis M, Cornick JE, Hawkins PA, Madhi SA, Nzenze SA, Kandasamy R, Ravikumar KL, Elmdaghri N, Kwambana-Adams B, Almeida SCG, Skoczynska A, Egorova E, Titov L, Saha SK, Paragi M, Everett DB, Antonio M, Klugman KP, Li Y, Metcalf BJ, Beall B, McGee L, Breiman RF, Bentley SD, von Gottberg A. A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa. J Antimicrob Chemother 2021; 75:512-520. [PMID: 31789384 PMCID: PMC7021099 DOI: 10.1093/jac/dkz477] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. METHODS We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model. RESULTS We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. CONCLUSIONS The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.
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Affiliation(s)
- Stephanie W Lo
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rebecca A Gladstone
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andries J van Tonder
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mignon Du Plessis
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jennifer E Cornick
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,Institute of Infection & Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Paulina A Hawkins
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan A Nzenze
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Rama Kandasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK
| | - K L Ravikumar
- Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Centre, Bangalore, India
| | - Naima Elmdaghri
- Department of Microbiology, Faculty of Medicine and Pharmacy, B.P. 9154, Hassan II University of Casablanca, Casablanca, Morocco.,Bacteriology-Virology and Hospital Hygiene Laboratory, University Hospital Centre Ibn Rochd, Casablanca, Morocco
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Samanta Cristine Grassi Almeida
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil
| | - Anna Skoczynska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Ekaterina Egorova
- Laboratory of Clinical Microbiology and Biotechnology, Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russian Federation
| | - Leonid Titov
- Laboratory of Clinical and Experimental Microbiology, The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus
| | - Samir K Saha
- Department of Microbiology, Dhaka Shishu (Children's) Hospital, Child Health Research Foundation, Dhaka, Bangladesh
| | - Metka Paragi
- Department for Public Health Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Dean B Everett
- Malawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.,University of Edinburgh, The Queens Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Martin Antonio
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Keith P Klugman
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Robert F Breiman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.,Emory Global Health Institute, Emory University, Atlanta, GA 30322, USA
| | - Stephen D Bentley
- Parasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne von Gottberg
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.,School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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Chen YY, Hsieh YC, Gong YN, Liao WC, Li SW, Chang IYF, Lin TL, Huang CT, Chiu CH, Wu TL, Su LH, Li TH, Huang YY. Genomic Insight into the Spread of Meropenem-Resistant Streptococcus pneumoniae Spain 23F-ST81, Taiwan. Emerg Infect Dis 2021; 26:711-720. [PMID: 32186492 PMCID: PMC7101100 DOI: 10.3201/eid2604.190717] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Incidence of invasive pneumococcal disease caused by antimicrobial-resistant Streptococcus pneumoniae types not included in pneumococcal conjugate vaccines has increased, including a penicillin- and meropenem-resistant serotype 15A-ST63 clone in Japan. During 2013-2017, we collected 206 invasive pneumococcal isolates in Taiwan for penicillin and meropenem susceptibility testing. We found serotypes 15B/C-ST83 and 15A-ST63 were the most prevalent penicillin- and meropenem-resistant clones. A transformation study confirmed that penicillin-binding protein (PBP) 2b was the primary meropenem resistance determinant, and PBP1a was essential for high-level resistance. The rate of serotype 15B/C-ST83 increased during the study. All 15B/C-ST83 isolates showed an ermB macrolide resistance genotype. Prediction analysis of recombination sites revealed 12 recombination regions in 15B/C-ST83 compared with the S. pneumoniae Spain23F-ST81 genome. Pneumococcal clones rapidly recombine to acquire survival advantages and undergo local expansion under the selective pressure exerted by vaccines and antimicrobial drugs. The spread of 15B/C-ST83 is alarming for countries with high antimicrobial pressure.
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15
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Reissier S, Cattoir V. Streptogramins for the treatment of infections caused by Gram-positive pathogens. Expert Rev Anti Infect Ther 2020; 19:587-599. [PMID: 33030387 DOI: 10.1080/14787210.2021.1834851] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Streptogramins (pristinamycin and quinupristin-dalfopristin) can be interesting options for the treatment of infections due to Gram-positive cocci, especially multidrug-resistant isolates. AREAS COVERED This review provides an updated overview of structural and activity characteristics, mechanisms of action and resistance, pharmacokinetic/pharmacodynamic, and clinical use of streptogramins. EXPERT OPINION The streptogramin antibiotics act by inhibition of the bacterial protein synthesis. They are composed of two chemically distinct compounds, namely type A and type B streptogramins, which exert a rapid bactericidal activity against a wide range of Gram-positive bacteria (including methicillin-resistant staphylococci and vancomycin-resistant enterococci). Several mechanisms of resistance have been identified in staphylococci and enterococci but the prevalence of streptogramin resistance among clinical isolates remains very low. Even if only a few randomized clinical trials have been conducted, the efficacy of pristinamycin has been largely demonstrated with an extensive use for 50 years in France and some African countries. Despite its effectiveness in the treatment of severe Gram-positive bacterial infections demonstrated in several studies and the low rate of reported resistance, the clinical use of quinupristin-dalfopristin has remained limited, mainly due to its poor tolerance. Altogether, streptogramins (especially pristinamycin) can be considered as potential alternatives for the treatment of Gram-positive infections.
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Affiliation(s)
| | - Vincent Cattoir
- Université De Rennes 1, Unité Inserm U1230, Rennes, France.,Service De Bactériologie-Hygiène Hospitalière, CHU De Rennes, Rennes, France.,Centre National De Référence De La Résistance Aux Antibiotiques (Laboratoire Associé 'Entérocoques'), CHU De Rennes, Rennes, France
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16
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A multiple drug-resistant Streptococcus pneumoniae of serotype 15A occurring from serotype 19A by capsular switching. Vaccine 2020; 38:5114-5118. [DOI: 10.1016/j.vaccine.2020.05.075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/15/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022]
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17
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Plumb ID, Gounder PP, Bruden DJ, Bulkow LR, Rudolph KM, Singleton RJ, Hennessy TW, Bruce MG. Increasing non-susceptibility to antibiotics within carried pneumococcal serotypes — Alaska, 2008–2015. Vaccine 2020; 38:4273-4280. [DOI: 10.1016/j.vaccine.2020.04.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 10/24/2022]
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18
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Development of Next Generation Streptococcus pneumoniae Vaccines Conferring Broad Protection. Vaccines (Basel) 2020; 8:vaccines8010132. [PMID: 32192117 PMCID: PMC7157650 DOI: 10.3390/vaccines8010132] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/22/2020] [Accepted: 02/29/2020] [Indexed: 02/06/2023] Open
Abstract
Streptococcus pneumoniae is a major pathogen causing pneumonia with over 2 million deaths annually, especially in young children and the elderly. To date, at least 98 different pneumococcal capsular serotypes have been identified. Currently, the vaccines for prevention of S. pneumoniae infections are the 23-valent pneumococcal polysaccharide-based vaccine (PPV23) and the pneumococcal conjugate vaccines (PCV10 and PCV13). These vaccines only cover some pneumococcal serotypes and are unable to protect against non-vaccine serotypes and unencapsulated S. pneumoniae. This has led to a rapid increase in antibiotic-resistant non-vaccine serotypes. Hence, there is an urgent need to develop new, effective, and affordable pneumococcal vaccines, which could cover a wide range of serotypes. This review discusses the new approaches to develop effective vaccines with broad serotype coverage as well as recent development of promising pneumococcal vaccines in clinical trials. New vaccine candidates are the inactivated whole-cell vaccine strain (Δpep27ΔcomD mutant) constructed by mutations of specific genes and several protein-based S. pneumoniae vaccines using conserved pneumococcal antigens, such as lipoprotein and surface-exposed protein (PspA). Among the vaccines in Phase 3 clinical trials are the pneumococcal conjugate vaccines, PCV-15 (V114) and 20vPnC. The inactivated whole-cell and several protein-based vaccines are either in Phase 1 or 2 trials. Furthermore, the recent progress of nanoparticles that play important roles as delivery systems and adjuvants to improve the performance, as well as the immunogenicity of the nanovaccines, are reviewed.
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19
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Yamada N, Nakamoto T, Takei H, Shoji T, Takahashi K, Sato J, Takeuchi N, Ohkusu M, Ishiwada N. Two cases of bacterial meningitis due to meropenem-resistant Streptococcus pneumoniae: A threat of serotype 35B, ST 558 lineage. J Infect Chemother 2020; 26:745-748. [PMID: 32171658 DOI: 10.1016/j.jiac.2020.02.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 02/04/2023]
Abstract
Although the pneumococcal conjugate vaccine (PCV) has decreased the incidence of invasive pneumococcal disease (IPD) in children, cases of IPD caused by non-PCV serotypes have been increasing. Here, we report two cases of bacterial meningitis caused by meropenem-resistant Streptococcus pneumoniae; in both the cases, 13-valent PCV (PCV13) had been administered. The isolated S. pneumoniae strains were non-PCV13 serotype 35B and resistant to penicillin G, cefotaxime, and meropenem. In addition, multilocus sequence typing (MLST) revealed the sequence type (ST) to be 558. In case 1, a 6-month-old girl recovered without sequelae after antibiotic therapy comprising cefotaxime and vancomycin, whereas in case 2, a 9-month-old boy was treated with an empirical treatment comprising ceftriaxone and vancomycin administration. However, maintaining the blood concentration of vancomycin within the effective range was difficult, due to which the antibiotics were changed to panipenem/betamipron. During the treatment, he presented with seizures, which were effectively controlled with antiepileptic drugs. The rate of incidence of penicillin-susceptible IPD has been substantially increasing after the introduction of PCV. However, an upsurge in IPD cases due to multidrug-resistant (MDR) serotype 35B has been reported in countries where PCV13 was introduced before introducing in Japan. Moreover, an increase in the proportion of MDR serotype 35B and decrease in the susceptibility to broad-spectrum antimicrobials, including meropenem, have been reported. Hence, the number of meningitis cases caused by MDR serotype 35B/ST558 may increase in the future.
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Affiliation(s)
- Nami Yamada
- Department of Pediatrics, Mie Prefectural General Medical Center, 5450-132 Oaza-Hinaga, Yokkaichi City, Mie, 510-8561, Japan.
| | - Takato Nakamoto
- Department of Pediatric Infectious Diseases, Shizuoka Children's Hospital, 860 Aoiku-Urushiyama, Shizuoka City, Shizuoka, 420-8660, Japan.
| | - Haruka Takei
- Department of Pediatric Infectious Diseases, Shizuoka Children's Hospital, 860 Aoiku-Urushiyama, Shizuoka City, Shizuoka, 420-8660, Japan.
| | - Takayo Shoji
- Department of Pediatric Infectious Diseases, Shizuoka Children's Hospital, 860 Aoiku-Urushiyama, Shizuoka City, Shizuoka, 420-8660, Japan.
| | - Kaori Takahashi
- Department of Pediatrics, Funabashi Municipal Medical Center, 1-21-1 Kanasugi, Funabashi City, Chiba, 273-8588, Japan.
| | - Junichi Sato
- Department of Pediatrics, Funabashi Municipal Medical Center, 1-21-1 Kanasugi, Funabashi City, Chiba, 273-8588, Japan.
| | - Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8673, Japan.
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20
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Nakano S, Fujisawa T, Ito Y, Chang B, Matsumura Y, Yamamoto M, Suga S, Ohnishi M, Nagao M. Nationwide surveillance of paediatric invasive and non-invasive pneumococcal disease in Japan after the introduction of the 13-valent conjugated vaccine, 2015-2017. Vaccine 2019; 38:1818-1824. [PMID: 31882246 DOI: 10.1016/j.vaccine.2019.12.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 01/28/2023]
Abstract
Streptococcus pneumoniae is still one of the major causes of morbidity and mortality worldwide. In Japan, pneumococcal conjugate vaccine (PCV)7 and PCV13 were licensed in 2010 and 2013, respectively. We conducted a nationwide paediatric invasive pneumococcal disease (IPD) and non-IPD surveillance study in Japan between 2015 and 2017. We collected 498 IPD isolates and 231 non-IPD isolates from a total of 187 medical institutions in Japan. We performed serotyping, antimicrobial susceptibility testing and multi-locus sequencing typing (MLST) for the collected isolates. Among the 498 IPD isolates, the most prevalent serotype was 24F, followed by 12F, 15A and 15B/C. However, 12F increased and 24F significantly decreased during the study period (p < 0.001), resulting in 12F becoming the most prevalent serotype in 2017. Among the IPD isolates, the PCV7 and PCV13 coverage rates were 0.8% and 9.2%, respectively. The most prevalent serotype among the non-IPD isolates was 15A, followed by 35B, 15B/C and 19A. The overall resistance rates to penicillin (PG), cefotaxime (CTX), meropenem (MEM), erythromycin (EM) and levofloxacin (LFX) were 40.5%, 12.2%, 19.4%, 91.8% and 0.5%, respectively. PG, CTX and MEM resistance rates were significantly higher in non-IPD isolates than in IPD isolates (p < 0.001). Serotype 15A-CC63 and serotype 35B-CC558 tended to be multi-drug resistant. In conclusion, the PCV13 coverage rate was significantly lower than that in a previous surveillance study in Japan between 2012 and 2014, and IPD cases attributable to serotype 19A also decreased. We should note the rapid increase in the prevalence of serotype 12F in IPD cases and the spread of the multi-drug resistant serotype 15A-CC63 and 35B-CC558 lineages.
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Affiliation(s)
- Satoshi Nakano
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Takao Fujisawa
- Department of Clinical Research, National Hospital Organization Mie National Hospital, Tsu, Japan
| | - Yutaka Ito
- Department of Respiratory Medicine, Allergy and Rheumatology, Nagoya City University Graduate School of Medical Science, Nagoya, Japan
| | - Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masaki Yamamoto
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shigeru Suga
- Department of Clinical Research, National Hospital Organization Mie National Hospital, Tsu, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
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21
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Dewé TCM, D'Aeth JC, Croucher NJ. Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae. Microb Genom 2019; 5. [PMID: 31609685 PMCID: PMC6861860 DOI: 10.1099/mgen.0.000305] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Penicillin-non-susceptible Streptococcus pneumoniae (PNSP) were first detected in the 1960s, and are now common worldwide, predominantly through the international spread of a limited number of strains. Extant PNSP are characterized by mosaic pbp2x, pbp2b and pbp1a genes generated by interspecies recombinations, with the extent of these alterations determining the range and concentrations of β-lactams to which the genotype is non-susceptible. The complexity of the genetics underlying these phenotypes has been the subject of both molecular microbiology and genome-wide association and epistasis analyses. Such studies can aid our understanding of PNSP evolution and help improve the already highly-performing bioinformatic methods capable of identifying PNSP from genomic surveillance data.
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Affiliation(s)
- Tamsin C M Dewé
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Joshua C D'Aeth
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
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22
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Multistate population and whole genome sequence-based strain surveillance of invasive pneumococci recovered in the USA during 2017. Clin Microbiol Infect 2019; 26:512.e1-512.e10. [PMID: 31536818 DOI: 10.1016/j.cmi.2019.09.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/16/2019] [Accepted: 09/07/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVES We aimed to provide population-based and whole-genome sequence (WGS) -based characterization of invasive pneumococcal disease isolates collected from multistate surveillance in the USA during 2017. METHODS We obtained short-read WGS from 2881 isolates with associated bioinformatics pipeline strain feature predictions. For quality control, capsular serotypes and antimicrobial MICs were also obtained conventionally from 442 isolates. Annotated WGS were provided (inclusive of serotypes, MICs, multilocus sequence types, pilus type(s)) from 2723 isolates. For 158 isolates with suboptimal WGS, antimicrobial MICs were obtained conventionally. RESULTS There were 127 isolates from children <5 years of age and 2754 isolates from those ≥5 years old in 2017. One of 43 different serotypes was predicted for 2877 of the 2881 isolates. Serotypes in the 13-valent conjugate vaccine together with 6C (PCV13+6C) accounted for 816 (28.3%) isolates, with PCV13 serotype 3 being the most common serotype overall. Non-PCV13-6C- serotypes accounted for 2065 (71.7%) isolates, comprising 96 (75.6%) isolates from children < 5 years old and 1969 (61.4%) isolates from those aged ≥5 years. Of 36 different categories of recently emerged serotype-switch variants, three showed marked increases relative to 2015-2016 in that the number from 2017 surpassed the number from 2015-2016 combined. Two of these included antimicrobial-resistant serotype 11A and 35B serotype-switch variants of the ST156 clonal complex. CONCLUSIONS PCV13+6C strains are still identified in 2017 but non-PCV13-type strains impose a considerable burden. This well-annotated year 2017 WGS/strain data set will prove useful for a broad variety of analyses and improved our understanding of invasive pneumococcal disease-causing strains in the post-PCV13 era.
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23
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Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM, Van Oyen H, Robert A. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79. [PMID: 31409417 PMCID: PMC6692930 DOI: 10.1186/s13012-019-0930-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 07/26/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist's perspective. METHODS In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. RESULTS Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. CONCLUSIONS For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist's perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance.
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Affiliation(s)
- Nina Van Goethem
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
| | - Tine Descamps
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Brecht Devleesschauwer
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Nele A. M. Boon
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Department of Public Health and Primary Care, Faculty of Medicine, Ghent University, De Pintelaan 185, 9000 Ghent, Belgium
| | - Annie Robert
- Department of Epidemiology and Biostatistics, Institut de recherche expérimentale et clinique, Faculty of Public Health, Université catholique de Louvain, Clos Chapelle-aux-champs 30, 1200 Woluwe-Saint-Lambert, Belgium
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24
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Varghese R, Neeravi A, Subramanian N, Pavithra B, Kavipriya A, Kumar JL, Girish Kumar CP, Jeyraman Y, Karthik G, Verghese VP, Veeraraghavan B. Clonal similarities and sequence-type diversity of invasive and carriage Streptococcus pneumoniae in India among children under 5 Years. Indian J Med Microbiol 2019; 37:358-362. [PMID: 32003333 DOI: 10.4103/ijmm.ijmm_19_348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Pneumococcal pneumonia is one of the major causes of mortality in children less than 5 years in Asia, especially in India. Available PCVs have less serotype coverage in India compared to western countries. Moreover, the baseline pneumococcal serotype and sequence type data is limited and available data doesn't represent the entire India. With this background we aimed to characterize invasive and carriage isolates of S. pneumoniae from a tertiary care hospital in South India. Materials and Methods A total of 221 S. pneumoniae isolates, invasive (n=138) and carriage (n=83) between the time period of 2012-2018 were included. Isolates was identified and confirmed using standard laboratory protocols. Serotyping was performed by Customized sequential multiplex PCR and MLST as described in www.pubmlst.org. Results The major serotypes were 19F, 6B, 14, 6A and 19A and the sequence types (ST) were ST63, 236 and 230. Predominant STs in invasive was ST 63 whereas in carriage were ST4894 and 1701. High level ST diversity in carriage was observed. Majority of the STs were SLVs or DLVs of previously reported STs or PMEN clones. Phylogenetic analyses of the STs revealed gradual expansion of three PMEN CCs CC320, 63 and 230. Conclusion The vaccine serotypes were the predominant ones found to be associated with IPD, PMEN clones, new STs and antimicrobial resistance. Accordingly, PCV13 is expected to provide invasive serotype coverage of 75% in Indian children less than 5 years. This study provides baseline serotype and sequence type data prior to the introduction of PCV in South India.
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Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Nithya Subramanian
- Department of Paediatrics, Christian Medical College, Chennai, Tamil Nadu, India
| | - B Pavithra
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - A Kavipriya
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jones Lionel Kumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - C P Girish Kumar
- ICMR, National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Yuvraj Jeyraman
- ICMR, National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - G Karthik
- Department of Medicine, Christian Medical College, Vellore, Tamil Nadu, India
| | - Valsan P Verghese
- Department of Paediatrics, Christian Medical College, Chennai, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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25
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Levy C, Varon E, Ouldali N, Béchet S, Bonacorsi S, Cohen R. Changes in Invasive Pneumococcal Disease Spectrum After 13-Valent Pneumococcal Conjugate Vaccine Implementation. Clin Infect Dis 2019; 70:446-454. [DOI: 10.1093/cid/ciz221] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/13/2019] [Indexed: 01/28/2023] Open
Affiliation(s)
- Corinne Levy
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés
- Groupe de Pathologie Infectieuse Pédiatrique, Paris
- Université Paris Est, Institut Mondor de Recherche Biomédicale - Groupe de Recherche Clinique, Groupe d’Etude des Maladies Infectieuses Néonatales et Infantiles, Créteil
- Clinical Research Center, Créteil
| | - Emmanuelle Varon
- National Reference Center for Pneumococci, Centre Hospitalier Intercommunal de Créteil
| | - Naim Ouldali
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés
- Groupe de Pathologie Infectieuse Pédiatrique, Paris
- Unité d’épidémiologie clinique, Assistance Publique–Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Epidémiologie Clinique et Evaluation Economique Appliquée aux Populations Vulnérables Institut National de la Santé et de la Recherche Médicale Unité Mixte de Recherche, Paris
- Urgences pédiatriques, Hôpital Necker Enfants Malades, Université Paris Descartes
| | - Stéphane Béchet
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés
- Université Paris Est, Institut Mondor de Recherche Biomédicale - Groupe de Recherche Clinique, Groupe d’Etude des Maladies Infectieuses Néonatales et Infantiles, Créteil
- Clinical Research Center, Créteil
| | - Stéphane Bonacorsi
- Université Paris Diderot, Sorbonne Paris Citépital Robert-Debré, Paris
- Service de Microbiologie, AP-HP, Hôpital Robert-Debré, Paris
| | - Robert Cohen
- Association Clinique et Thérapeutique Infantile du Val-de-Marne, Saint Maur-des-Fossés
- Groupe de Pathologie Infectieuse Pédiatrique, Paris
- Université Paris Est, Institut Mondor de Recherche Biomédicale - Groupe de Recherche Clinique, Groupe d’Etude des Maladies Infectieuses Néonatales et Infantiles, Créteil
- Clinical Research Center, Créteil
- Unité Court Séjour, Petits nourrissons, Service de Néonatalogie, Centre Hospitalier Intercommunal de Créteil, France
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26
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Chen YY, Wang JT, Lin TL, Gong YN, Li TH, Huang YY, Hsieh YC. Prophage Excision in Streptococcus pneumoniae Serotype 19A ST320 Promote Colonization: Insight Into Its Evolution From the Ancestral Clone Taiwan 19F-14 (ST236). Front Microbiol 2019; 10:205. [PMID: 30800118 PMCID: PMC6375853 DOI: 10.3389/fmicb.2019.00205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae 19A ST320, a multidrug-resistant strain with high disease severity that notoriously spread before the use of expanded pneumococcal conjugate vaccines, was derived from a capsular switching event between an international strain Taiwan 19F-14 (ST236) and a serotype 19A strain. However, the molecular mechanisms underlying the adaptive evolution of 19F ST236 to 19A ST320 are unknown. In this study, we compared 19A ST320 to its ancestral clone, 19F ST236, in terms of adherence to respiratory epithelial cells, whole transcriptome, and ability to colonize a young mouse model. Serotype 19A ST320 showed five-fold higher adherence to A549 cells than serotype 19F ST236. High-throughput mRNA sequencing identified a prophage region located between dnaN and ychF in both strains; however, the genes in this region were expressed at significantly higher levels in 19A ST320 than in 19F ST236. Analysis by polymerase chain reaction (PCR) showed that the prophage is able to spontaneously excise from the chromosome and form a circular episome in 19A ST320, but not in 19F ST236. Deletion of the integrase in the prophage of 19A ST320 decreased spontaneous excision and cell adherence, which were restored by complementation. Competition experiments in mice showed that the integrase mutant was six-fold less competitive than the 19A ST320 parent (competitive index [CI]: 0.16; p = 0.02). The 19A ST320 prophage-deleted strain did not change cell adherence capacity, whereas prophage integration strains (integrase mutant and 19F) had decreased expression of the down-stream ychF gene compared to that of 19A ST320. Further deletion of ychF significantly reduced cell adherence. In conclusions, these findings suggest that spontaneous prophage induction confers a competitive advantage to virulent pneumococci.
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Affiliation(s)
- Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Nong Gong
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Hsuan Li
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Yu Huang
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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27
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Nakano S, Fujisawa T, Ito Y, Chang B, Matsumura Y, Yamamoto M, Nagao M, Suga S, Ohnishi M, Ichiyama S. Spread of Meropenem-Resistant Streptococcus pneumoniae Serotype 15A-ST63 Clone in Japan, 2012-2014. Emerg Infect Dis 2019; 24:275-283. [PMID: 29350141 PMCID: PMC5782878 DOI: 10.3201/eid2402.171268] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
After the introduction of pneumococcal conjugate vaccines, the incidence of pneumococcal infections due to meropenem-resistant serotype 15A-ST63 strains increased in Japan. By using whole-genome sequencing and comparing sequences with those of clones from the United Kingdom, the United States, and Canada, we clarified the traits of the serotype 15A-ST63 clone. Our analysis revealed that the meropenem-resistant serotype 15A-ST63 strains from Japan originated from meropenem-susceptible strains from Japan. Recombination site prediction analysis showed that the meropenem-resistant strain-specific recombination regions included the pbp1a and pbp2b regions. A detailed analysis of the composition of these genes indicated that resistance seems to be caused by pbp1a recombination. The pbp1a gene in meropenem-resistant isolates was identical to that in multidrug (including meropenem)-resistant serotype 19A-ST320 pneumococci, which have spread in the United States. The global spread of pneumococci of this lineage is noteworthy because serotype 15A is not included in the currently used 13-valent pneumococcal conjugate vaccine.
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Geno KA, Spencer BL, Bae S, Nahm MH. Ficolin-2 binds to serotype 35B pneumococcus as it does to serotypes 11A and 31, and these serotypes cause more infections in older adults than in children. PLoS One 2018; 13:e0209657. [PMID: 30586458 PMCID: PMC6306229 DOI: 10.1371/journal.pone.0209657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
Among 98 serotypes of Streptococcus pneumoniae, only a small subset regularly causes invasive pneumococcal diseases (IPD). We previously demonstrated that serotype 11A binds to ficolin-2 and has low invasiveness in children. Epidemiologic data suggested, however, that serotype 11A IPD afflicts older adults, possibly indicating reduced ficolin-2-mediated immune protection. Therefore, we studied the epidemiology of ficolin-2-bound serotypes. We obtained IPD case data from the United States Centers for Disease Control and Prevention. We studied three prominent ficolin-2-bound serotypes and their acetyltransferase-deficient variants for ficolin-2 binding and ficolin-2-mediated complement deposition with flow-cytometry. We determined the age distributions of these serotypes from the obtained epidemiologic data. We discovered that the serotype 35B capsule is a novel ficolin-2 ligand due to O-acetylation via WciG. Ficolin-2-mediated complement deposition was observed on serotypes 11A and 35B but not serotype 31 or any O-acetyl transferase deficient derivatives of these serotypes. Serotypes 11A, 35B, and 31 cause more IPD among older adults than children. Studies of the three serotypes provide additional evidence for ficolin-2 providing innate immunity against IPD. The skewed age distribution of the three serotypes suggests that older adults have reduced ficolin-2-mediated immunity and are more susceptible to these serotypes.
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Affiliation(s)
- K. Aaron Geno
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brady L. Spencer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Sejong Bae
- Division of Preventive Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Moon H. Nahm
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Beall B, Chochua S, Gertz RE, Li Y, Li Z, McGee L, Metcalf BJ, Ricaldi J, Tran T, Walker H, Pilishvili T. A Population-Based Descriptive Atlas of Invasive Pneumococcal Strains Recovered Within the U.S. During 2015-2016. Front Microbiol 2018; 9:2670. [PMID: 30524382 PMCID: PMC6262371 DOI: 10.3389/fmicb.2018.02670] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/19/2018] [Indexed: 11/17/2022] Open
Abstract
Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010. We used whole genome sequencing (WGS) to predict phenotypic traits (serotypes, antimicrobial phenotypes, and pilus determinants) and determine multilocus genotypes from 5334 isolates (~90% of cases) recovered during 2015–2016 through Active Bacterial Core surveillance. We identified 44 serotypes; 26 accounted for 98% of the isolates. PCV13 serotypes (inclusive of serotype 6C) accounted for 1503 (28.2%) isolates, with serotype 3 most common (657/5334, 12.3%), while serotypes 1 and 5 were undetected. Of 305 isolates from children <5 yrs, 60 (19.7%) were of PCV13 serotypes 19A, 19F, 3, 6B, and 23F (58/60 were 19A, 19F, or 3). We quantitated MLST-based lineages first detected during the post-PCV era (since 2002) that potentially arose through serotype-switching. The 7 predominant emergent post-PCV strain complexes included 23B/CC338, 15BC/CC3280, 19A/CC244, 4/CC439, 15A/CC156, 35B/CC156, and 15BC/CC156. These strains accounted for 332 isolates (6.2% of total) and were more frequently observed in children <5 yrs (17.7%; 54/305). Fifty-seven categories of recently emerged (in the post PCV7 period) putative serotype-switch variants were identified, accounting for 402 isolates. Many of these putative switch variants represented newly emerged resistant strains. Penicillin-nonsusceptibility (MICs > 0.12 μg/ml) was found among 22.4% (1193/5334) isolates, with higher penicillin MICs (2–8 μg/ml) found in 8.0% (425/5334) of isolates that were primarily (372/425, 87.5%) serotypes 35B and 19A. Most (792/1193, 66.4%) penicillin-nonsusceptible isolates were macrolide-resistant, 410 (34.4%) of which were erm gene positive and clindamycin-resistant. The proportion of macrolide-resistant isolates increased with increasing penicillin MICs; even isolates with reduced penicillin susceptibility (MIC = 0.06 μg/ml) were much more likely to be macrolide-resistant than basally penicillin-susceptible isolates (MIC < 0.03 μg/ml). The contribution of recombination to strain diversification was assessed through quantitating 35B/CC558-specific bioinformatic pipeline features among non-CC558 CCs and determining the sizes of gene replacements. Although IPD has decreased greatly and stabilized in the post-PCV13 era, the species continually generates recombinants that adapt to selective pressures exerted by vaccines and antimicrobials. These data serve as a baseline for monitoring future changes within each invasive serotype.
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Affiliation(s)
- Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Robert E Gertz
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Zhongya Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jessica Ricaldi
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Theresa Tran
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Hollis Walker
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tamara Pilishvili
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States
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30
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Erdem G, Singh AK, Brusnahan AJ, Moore AN, Barson WJ, Leber A, Vidal JE, Atici S, King SJ. Pneumococcal colonization among tracheostomy tube dependent children. PLoS One 2018; 13:e0206305. [PMID: 30339709 PMCID: PMC6195293 DOI: 10.1371/journal.pone.0206305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/10/2018] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae colonization is a precursor to pneumococcal disease. Although children with a tracheostomy have an increased risk of pneumococcal pneumonia, the pneumococci colonizing their lower airways remain largely uncharacterized. We sought to compare lower respiratory tract isolates colonizing tracheostomy patients and a convenience sample of isolates from individuals intubated for acute conditions. We collected pneumococcal isolates from the lower respiratory tract of 27 patients with a tracheostomy and 42 patients intubated for acute conditions. We compared the penicillin susceptibility, rates of co-colonization, genetic background, and serotype of isolates colonizing these patient populations. Isolates from both groups showed high genetic diversity. Forty multi-locus sequence types and 20 serotypes were identified. There was no significant difference in serotype distribution, co-colonization rates, vaccine coverage, or non-susceptibility to penicillin among pneumococcal isolates from the two groups. Colonization of the lower airways with non-vaccine serotypes 15B/C, 23B and 35B was noted for the first time in patients with tracheostomies and supports recently observed increases in nasopharyngeal colonization and disease due to these serotypes.
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Affiliation(s)
- Guliz Erdem
- College of Medicine, The Ohio State University, and Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- * E-mail: (SJK); (GE)
| | - Anirudh K. Singh
- Center for Microbial Pathogenesis, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Anthony J. Brusnahan
- Center for Microbial Pathogenesis, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Amber N. Moore
- Center for Microbial Pathogenesis, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - William J. Barson
- College of Medicine, The Ohio State University, and Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Amy Leber
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Jorge E. Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Serkan Atici
- Department of Pediatrics, Marmara University School of Medicine, Istanbul, Turkey
| | - Samantha J. King
- College of Medicine, The Ohio State University, and Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Center for Microbial Pathogenesis, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- * E-mail: (SJK); (GE)
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31
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Yahiaoui RY, Bootsma HJ, den Heijer CDJ, Pluister GN, John Paget W, Spreeuwenberg P, Trzcinski K, Stobberingh EE. Distribution of serotypes and patterns of antimicrobial resistance among commensal Streptococcus pneumoniae in nine European countries. BMC Infect Dis 2018; 18:440. [PMID: 30157780 PMCID: PMC6116386 DOI: 10.1186/s12879-018-3341-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 08/17/2018] [Indexed: 11/26/2022] Open
Abstract
Background Streptococcus pneumoniae is a commensal of the human upper respiratory tract and a major cause of morbidity and mortality worldwide. This paper presents the distribution of serotypes and antimicrobial resistance in commensal S. pneumoniae strains cultured from healthy carriers older than four years of age in nine European countries. Methods Nasal swabs from healthy persons (age between 4 and 107 years old) were obtained by general practitioners from each country from November 2010 to August 2011. Swabs were cultured for S. pneumoniae using a standardized protocol. Antibiotic resistance was determined for isolated S. pneumoniae by broth microdilution. Capsular sequencing typing was used to identify serotypes, followed by serotype-specific PCR assays in case of ambiguous results. Results Thirty-two thousand one hundred sixty-one nasal swabs were collected from which 937 S. pneumoniae were isolated. A large variation in serotype distribution and antimicrobial resistant serotypes across the participating countries was observed. Pneumococcal vaccination was associated with a higher risk of pneumococcal colonization and antimicrobial resistance independently of country and vaccine used, either conjugate vaccine or PPV 23). Conclusions Serotype 11A was the most common in carriage followed by serotypes 23A and 19A. The serotypes showing the highest resistance to penicillin were 14 followed by 19A. Serotype 15A showed the highest proportion of multidrug resistance. Electronic supplementary material The online version of this article (10.1186/s12879-018-3341-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachid Y Yahiaoui
- Maastricht University Medical Centre/CAPHRI, Maastricht, The Netherlands. .,Haga hospital, Department medical microbiology, The Hague, The Netherlands.
| | - Hester J Bootsma
- Centre for Infectious Diseases Research Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Gerlinde N Pluister
- Centre for Infectious Diseases Research Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - W John Paget
- NIVEL, The Netherlands Institute for Health Services Research, Utrecht, The Netherlands.,Department of Primary and Community Care, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Peter Spreeuwenberg
- NIVEL, The Netherlands Institute for Health Services Research, Utrecht, The Netherlands
| | - Krzysztof Trzcinski
- Centre for Infectious Diseases Research Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.,Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Ellen E Stobberingh
- Maastricht University Medical Centre/CAPHRI, Maastricht, The Netherlands.,Centre for Infectious Diseases Research Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Global Distribution of Invasive Serotype 35D Streptococcus pneumoniae Isolates following Introduction of 13-Valent Pneumococcal Conjugate Vaccine. J Clin Microbiol 2018; 56:JCM.00228-18. [PMID: 29720431 PMCID: PMC6018339 DOI: 10.1128/jcm.00228-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/24/2018] [Indexed: 02/08/2023] Open
Abstract
A newly recognized pneumococcal serotype, 35D, which differs from the 35B polysaccharide in structure and serology by not binding to factor serum 35a, was recently reported. The genetic basis for this distinctive serology is due to the presence of an inactivating mutation in wciG, which encodes an O-acetyltransferase responsible for O-acetylation of a galactofuranose. Here, we assessed the genomic data of a worldwide pneumococcal collection to identify serotype 35D isolates and understand their geographical distribution, genetic background, and invasiveness potential. Of 21,980 pneumococcal isolates, 444 were originally typed as serotype 35B by PneumoCaT. Analysis of the wciG gene revealed 23 isolates from carriage (n = 4) and disease (n = 19) with partial or complete loss-of-function mutations, including mutations resulting in premature stop codons (n = 22) and an in-frame mutation (n = 1). These were selected for further analysis. The putative 35D isolates were geographically widespread, and 65.2% (15/23) of them was recovered after the introduction of pneumococcal conjugate vaccine 13 (PCV13). Compared with serotype 35B isolates, putative serotype 35D isolates have higher invasive disease potentials based on odds ratios (OR) (11.58; 95% confidence interval[CI], 1.42 to 94.19 versus 0.61; 95% CI, 0.40 to 0.92) and a higher prevalence of macrolide resistance mediated by mefA (26.1% versus 7.6%; P = 0.009). Using the Quellung reaction, 50% (10/20) of viable isolates were identified as serotype 35D, 25% (5/20) as serotype 35B, and 25% (5/20) as a mixture of 35B/35D. The discrepancy between phenotype and genotype requires further investigation. These findings illustrated a global distribution of an invasive serotype, 35D, among young children post-PCV13 introduction and underlined the invasive potential conferred by the loss of O-acetylation in the pneumococcal capsule.
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A Mechanism of Unidirectional Transformation, Leading to Antibiotic Resistance, Occurs within Nasopharyngeal Pneumococcal Biofilm Consortia. mBio 2018; 9:mBio.00561-18. [PMID: 29764945 PMCID: PMC5954218 DOI: 10.1128/mbio.00561-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Streptococcus pneumoniae acquires genes for resistance to antibiotics such as streptomycin (Str) or trimethoprim (Tmp) by recombination via transformation of DNA released by other pneumococci and closely related species. Using naturally transformable pneumococci, including strain D39 serotype 2 (S2) and TIGR4 (S4), we studied whether pneumococcal nasopharyngeal transformation was symmetrical, asymmetrical, or unidirectional. Incubation of S2Tet and S4Str in a bioreactor simulating the human nasopharynx led to the generation of SpnTet/Str recombinants. Double-resistant pneumococci emerged soon after 4 h postinoculation at a recombination frequency (rF) of 2.5 × 10−4 while peaking after 8 h at a rF of 1.1 × 10−3. Acquisition of antibiotic resistance genes by transformation was confirmed by treatment with DNase I. A high-throughput serotyping method demonstrated that all double-resistant pneumococci belonged to one serotype lineage (S2Tet/Str) and therefore that unidirectional transformation had occurred. Neither heterolysis nor availability of DNA for transformation was a factor for unidirectional transformation given that the density of each strain and extracellular DNA (eDNA) released from both strains were similar. Unidirectional transformation occurred regardless of the antibiotic-resistant gene carried by donors or acquired by recipients and regardless of whether competence-stimulating peptide-receptor cross talk was allowed. Moreover, unidirectional transformation occurred when two donor strains (e.g., S4Str and S19FTmp) were incubated together, leading to S19FStr/Tmp but at a rF 3 orders of magnitude lower (4.9 × 10−6). We finally demonstrated that the mechanism leading to unidirectional transformation was due to inhibition of transformation of the donor by the recipient. Pneumococcal transformation in the human nasopharynx may lead to the acquisition of antibiotic resistance genes or genes encoding new capsular variants. Antibiotics and vaccines are currently putting pressure on a number of strains, leading to an increase in antibiotic resistance and serotype replacement. These pneumococcal strains are also acquiring virulence traits from vaccine types via transformation. In this study, we recapitulated multiple-strain colonization with strains carrying a resistance marker and selected for those acquiring resistance to two or three antibiotics, such as would occur in the human nasopharynx. Strains acquiring dual and triple resistance originated from one progenitor, demonstrating that transformation was unidirectional. Unidirectional transformation was the result of inhibition of transformation of donor strains. Unidirectional transformation has implications for the understanding of acquisition patterns of resistance determinants or capsule-switching events.
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34
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Olarte L, Kaplan SL, Barson WJ, Romero JR, Lin PL, Tan TQ, Hoffman JA, Bradley JS, Givner LB, Mason EO, Hultén KG. Invasive Serotype 35B Pneumococci Including an Expanding Serotype Switch Lineage. Emerg Infect Dis 2018; 24:405. [PMID: 29350161 PMCID: PMC5782886 DOI: 10.3201/eid2402.170982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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35
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Swanson DS, Harrison CJ. Playing "Whack-a-Mole" With Pneumococcal Serotype Eradication. Pediatrics 2017; 140:peds.2017-2034. [PMID: 28978717 DOI: 10.1542/peds.2017-2034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2017] [Indexed: 11/24/2022] Open
Affiliation(s)
- Douglas S Swanson
- Division of Infectious Diseases, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri
| | - Christopher J Harrison
- Division of Infectious Diseases, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri
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36
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Principi N, Esposito S. Development of pneumococcal vaccines over the last 10 years. Expert Opin Biol Ther 2017; 18:7-17. [DOI: 10.1080/14712598.2018.1384462] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nicola Principi
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Susanna Esposito
- Paediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
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