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Mahroum N, Karaoglan BS, Ulucam ES, Shoenfeld Y. Vaccine-induced strain replacement: theory and real-life implications. Future Microbiol 2024; 19:1017-1026. [PMID: 38913745 PMCID: PMC11318708 DOI: 10.1080/17460913.2024.2345003] [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: 01/27/2024] [Accepted: 04/16/2024] [Indexed: 06/26/2024] Open
Abstract
The value of preventive medicine is superior to treatment with vaccinations occupying high priority. Nevertheless, heavy pressure has started to form in regard to strains not included in vaccines contributing to the changing epidemiology of pathogen subtypes leading to 'vaccine-induced strain replacement'. Among other mechanisms, increasing fitness of nonvaccine strains and metabolic shifts in the subtypes have been described. Classical examples include pneumococcal infections and viral diseases, such as the human papilloma virus. Recently, it has been described in SARS-CoV-2, leading to the emergence of new subtypes, such as Omicron and Delta variants. The phenomenon has also been reported in Mycobacterium tuberculosis, Neisseria meningitidis and rotavirus. This study addresses the concepts, examples and implications of this phenomenon.
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Affiliation(s)
- Naim Mahroum
- International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | | | | | - Yehuda Shoenfeld
- Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat-Gan, Israel
- Reichman University, Herzliya, Israel
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2
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Lyu S, Shi W, Dong F, Xu BP, Liu G, Wang Q, Yao KH, Yang YH. Serotype distribution and antimicrobial resistance of pediatric Streptococcus pneumoniae isolated from inpatients and outpatients at Beijing Children's Hospital. Braz J Infect Dis 2024; 28:103734. [PMID: 38471654 PMCID: PMC11004498 DOI: 10.1016/j.bjid.2024.103734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/06/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Understanding the epidemiology of Streptococcus pneumoniae (S. pneumoniae) isolates is important for pneumonia treatment and prevention. This research aimed to explore the epidemiological characteristics of S. pneumoniae isolated from pediatric inpatients and outpatients during the same period. METHODS S. pneumoniae were isolated from unsterile samples of inpatients and outpatients younger than five years old between March 2013 and February 2014. The serotypes were determined using diagnostic pneumococcal antisera. The resistance of each strain to 13 antibiotics was tested using either the E-test or the disc diffusion method. The Sequence Types (STs) were analyzed via Multilocus Sequence Typing (MLST). RESULTS The dominant serotypes obtained from inpatients were 19F (32.9 %), 19A (20.7 %), 23F (10.7 %), 6A (10.0 %), and 14 (8.6 %), while those from outpatients were 19F (13.6 %), 23F (12.9 %), 6A (10.0 %), 6B (10.0 %), and 19A (7.9 %). The coverage rates of 13-valent Pneumococcal Conjugate Vaccine (PCV) formulations were high in both groups. The nonsusceptibility to penicillin, cefuroxime, imipenem, erythromycin, and trimethoprim-sulfamethoxazole among the inpatient isolates was 7.1 %, 92.8 %, 65.7 %, 100 %, and 85.0 %, respectively, while that among the outpatient isolates was 0.7 %, 50.0 %, 38.6 %, 96.4 %, and 65.7 %, respectively. There were 45 and 81 STs detected from the pneumococci isolated from inpatients and outpatients, respectively. CC271 was common among both inpatients and outpatients (43.6 % and 14.3 %). CONCLUSIONS Pneumococcal vaccine-related serotypes are prevalent among both inpatients and outpatients, especially among inpatients, who exhibit more severe antibiotic resistance. Therefore, universal immunization with PCV13 would decrease the hospitalization rate due to S. pneumoniae and the antibiotic resistance rate of S. pneumoniae.
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Affiliation(s)
- Shuang Lyu
- Capital Medical University, Beijing Friendship Hospital, Pediatrics Department, Beijing, China
| | - Wei Shi
- Capital Medical University, Beijing Children's Hospital, Beijing Pediatric Research Institute, Ministry of Education, National Center for Children's Health, Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Beijing, China
| | - Fang Dong
- Capital Medical University, Beijing Children's Hospital, Clinical Laboratory, Beijing, China
| | - Bao Ping Xu
- Capital Medical University, Beijing Children's Hospital, Respiratory Diseases Department, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Gang Liu
- Capital Medical University, Beijing Children's Hospital, Infectious Diseases Department, Beijing, China
| | - Quan Wang
- Capital Medical University, Beijing Children's Hospital, Intensive Care Unit, Beijing, China
| | - Kai Hu Yao
- Capital Medical University, Beijing Children's Hospital, Beijing Pediatric Research Institute, Ministry of Education, National Center for Children's Health, Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Beijing, China.
| | - Yong Hong Yang
- Capital Medical University, Beijing Children's Hospital, Beijing Pediatric Research Institute, Ministry of Education, National Center for Children's Health, Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Beijing, China.
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André C, Van Camp AG, Ung L, Gilmore MS, Bispo PJM. Characterization of the resistome and predominant genetic lineages of Gram-positive bacteria causing keratitis. Antimicrob Agents Chemother 2024; 68:e0124723. [PMID: 38289077 PMCID: PMC10916405 DOI: 10.1128/aac.01247-23] [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: 09/27/2023] [Accepted: 12/03/2023] [Indexed: 02/04/2024] Open
Abstract
Bacterial keratitis is a vision-threatening infection mainly caused by Gram-positive bacteria (GPB). Antimicrobial therapy is commonly empirical using broad-spectrum agents with efficacy increasingly compromised by the emergence of antimicrobial resistance. We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of GPB causing keratitis and to characterize their antimicrobial resistance patterns. A total of 161 isolates, including Staphylococcus aureus (n = 86), coagulase-negative staphylococci (CoNS; n = 34), Streptococcus spp. (n = 34), and Enterococcus faecalis (n = 7), were included. The population of S. aureus isolates consisted mainly of clonal complex 5 (CC5) (30.2%). Similarly, the population of Staphylococcus epidermidis was homogenous with most of them belonging to CC2 (78.3%). Conversely, the genetic population of Streptococcus pneumoniae was highly diverse. Resistance to first-line antibiotics was common among staphylococci, especially among CC5 S. aureus. Methicillin-resistant S. aureus was commonly resistant to fluoroquinolones and azithromycin (78.6%) and tobramycin (57%). One-third of the CoNS were resistant to fluoroquinolones and 53% to azithromycin. Macrolide resistance was commonly caused by erm genes in S. aureus, mphC and msrA in CoNS, and mefA and msr(D) in streptococci. Aminoglycoside resistance in staphylococci was mainly associated with genes commonly found in mobile genetic elements and that encode for nucleotidyltransferases like ant(4')-Ib and ant(9)-Ia. Fluroquinolone-resistant staphylococci carried from 1 to 4 quinolone resistance-determining region mutations, mainly in the gyrA and parC genes. We found that GPB causing keratitis are associated with strains commonly resistant to first-line topical therapies, especially staphylococcal isolates that are frequently multidrug-resistant and associated with major hospital-adapted epidemic lineages.
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Affiliation(s)
- Camille André
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew G. Van Camp
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael S. Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Paulo J. M. Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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Yi Q, Li L, Wang H, Zhu C, Chen Y, Yang L, Zheng Y, Yang Y, Bao Y. A clade of Streptococcus pneumoniae clonal complex 320 with increased tolerance to β-lactam antibiotics in a Chinese metropolitan city. J Glob Antimicrob Resist 2024; 36:379-388. [PMID: 38307252 DOI: 10.1016/j.jgar.2024.01.016] [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: 09/19/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
OBJECTIVES We characterized the population structure and features of clinical Streptococcus pneumoniae isolates associated with invasive pneumococcal disease (IPD) from 2009 to 2017 in a Chinese metropolitan city using a whole-genome sequencing approach. METHODS Seventy-nine pneumococcal strains, including 60 serogroup-19 strains from children enduring IPD from a paediatric hospital in Shenzhen, were subjected to whole-genome sequencing. Population structure was characterized through phylogenetic analysis, sequence typing, serotyping, virulence factor, and antimicrobial drug resistance (AMR) gene profiling, combining the publicly available related WGS data. Clinical demography and antibiotic susceptibility profiles were compared among different populations to emphasize the higher-risk populations. Genetic regions associated with AMR gene mobilization were identified through comparative genomics. RESULTS These IPD strains mainly belonged to clonal complex 320 (CC320) and were composed of serotypes 19A and 19F. In addition to sporadic possible importation-related isolates (ST320), we identified an independent clade, CC320_SZpop (ST271), that predominantly circulated in Shenzhen and possibly expanded its range. Clinical features and antibiotic susceptibility analysis revealed that CC320_SZpop might manifest much higher pathogenicity and tolerance to β-lactams. Specific virulence factors in Shenzhen isolates of CC320_SZpop were identified. Furthermore, an ca. 40 kb hotspot genomic region enduring frequent recombination was identified, possibly associated with the divergence of S. pneumoniae strains. CONCLUSION A novel pneumococcal clade, CC320_SZpop, circulating in Shenzhen and other regions in China, possibly under expansion, was found and deserves more study and surveillance. Our study also emphasizes the importance of continuous genomic surveillance of clinical S. pneumoniae isolates, especially IPD isolates.
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Affiliation(s)
- Qiuwei Yi
- Shenzhen Children's Hospital, Guangdong, China
| | - Liqiang Li
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Guangdong Provincial Clinical Research Center for Infectious Diseases (Tuberculosis), Shenzhen Clinical Research Center for Tuberculosis, Shenzhen, China; Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, China.
| | - Heping Wang
- Shenzhen Children's Hospital, Guangdong, China
| | | | | | - Liang Yang
- Southern University of Science of and Technology, Guangdong, China
| | | | | | - Yanmin Bao
- Shenzhen Children's Hospital, Guangdong, China.
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Unoarumhi Y, Davis ML, Rowe LA, Mathis S, Li Z, Chochua S, Li Y, McGee L, Metcalf BJ, Lee JS, Beall B. A novel invasive Streptococcus pyogenes variant sublineage derived through recombinational replacement of the emm12 genomic region. Sci Rep 2023; 13:21510. [PMID: 38057343 PMCID: PMC10700362 DOI: 10.1038/s41598-023-48035-2] [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: 04/01/2023] [Accepted: 11/21/2023] [Indexed: 12/08/2023] Open
Abstract
Group A streptococcal strains potentially acquire new M protein gene types through genetic recombination (emm switching). To detect such variants, we screened 12,596 invasive GAS genomes for strains of differing emm types that shared the same multilocus sequence type (ST). Through this screening we detected a variant consisting of 16 serum opacity factor (SOF)-positive, emm pattern E, emm82 isolates that were ST36, previously only associated with SOF-negative, emm pattern A, emm12. The 16 emm82/ST36 isolates were closely interrelated (pairwise SNP distance of 0-43), and shared the same emm82-containing recombinational fragment. emm82/ST36 isolates carried the sof12 structural gene, however the sof12 indel characteristic of emm12 strains was corrected to confer the SOF-positive phenotype. Five independent emm82/ST36 invasive case isolates comprised two sets of genetically indistinguishable strains. The emm82/ST36 isolates were primarily macrolide resistant (12/16 isolates), displayed at least 4 different core genomic arrangements, and carried 11 different combinations of virulence and resistance determinants. Phylogenetic analysis revealed that emm82/ST36 was within a minor (non-clade 1) portion of ST36 that featured almost all ST36 antibiotic resistance. This work documents emergence of a rapidly diversifying variant that is the first confirmed example of an emm pattern A strain switched to a pattern E strain.
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Affiliation(s)
- Yvette Unoarumhi
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Morgan L Davis
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Lori A Rowe
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Saundra Mathis
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Zhongya Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Sopio Chochua
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Yuan Li
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Benjamin J Metcalf
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Justin S Lee
- Centers for Disease Control and Prevention, Biotechnology Core Facility Branch, National Center for Emerging and Zoonotic Infectious Diseases, Division Scientific Resources, Atlanta, GA, USA
| | - Bernard Beall
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, GA, USA.
- Eagle GLobal Scientific, LLC, Atlanta, GA, USA.
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6
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André C, Lebreton F, Van Tyne D, Cadorette J, Boody R, Gilmore MS, Bispo PJM. Microbiology of Eye Infections at the Massachusetts Eye and Ear: An 8-Year Retrospective Review Combined With Genomic Epidemiology. Am J Ophthalmol 2023; 255:43-56. [PMID: 37343741 PMCID: PMC10592486 DOI: 10.1016/j.ajo.2023.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/28/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
PURPOSE Ocular bacterial infections are important causes of morbidity and vision loss. Early antimicrobial therapy is necessary to save vision, but their efficacy is increasingly compromised by antimicrobial resistance (AMR). We assessed the etiology of ocular bacterial infections seen at Massachusetts Eye and Ear and investigated the molecular epidemiology and AMR profiles of contemporary isolates. DESIGN Laboratory investigation. METHODS We used a combination of phenotypic tests and genome sequencing to identify the predominant lineages of leading ocular pathogens and their AMR profiles. RESULTS A total of 1601 isolates were collected from 2014 to 2021, with Staphylococcus aureus (n = 621), coagulase-negative staphylococci (CoNS) (n = 234), Pseudomonas aeruginosa (n = 213), Enterobacteriaceae (n = 167), and Streptococcus pneumoniae (n = 95) being the most common. Resistance was high among staphylococci, with methicillin resistance (MR) detected in 28% of S aureus and 39.8% of CoNS isolates. Multidrug resistance (MDR) was frequent among MR staphylococci (MRSA 60%, MRCoNS 76.1%). The population of S aureus isolates consisted mainly of 2 clonal complexes (CCs): CC8 (26.1%) and CC5 (24.1%). CC5 strains carried a variety of AMR markers, resulting in high levels of resistance to first-line therapies. Similarly, the population of ocular Staphylococcus epidermidis was homogenous with most belonging to CC2 (85%), which were commonly MDR (48%). Conversely, ocular S pneumoniae, P aeruginosa, and Enterobacteriaceae were often susceptible to first-line therapies and grouped into highly diverse genetic populations. CONCLUSION Our data showed that ocular bacterial infections in our patient population are disproportionately caused by strains that are resistant to clinically relevant antibiotics and are associated with major epidemic genotypes with both community and hospital associations.
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Affiliation(s)
- Camille André
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - François Lebreton
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - Daria Van Tyne
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - James Cadorette
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - Rick Boody
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary
| | - Michael S Gilmore
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary; Department of Microbiology and Immunology (F.L., D.V., M.S.G.), Harvard Medical School, Boston, Massachusetts, USA
| | - Paulo J M Bispo
- From the Department of Ophthalmology (C.A., F.L., D.V., J.C., R.B., M.S.G., P.J.M.B.), Massachusetts Eye and Ear Infirmary.
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Hu T, Sarpong EM, Song Y, Done N, Liu Q, Lemus-Wirtz E, Signorovitch J, Mohanty S, Weiss T. Incidence of non-invasive all-cause pneumonia in children in the United States before and after the introduction of pneumococcal conjugate vaccines: a retrospective claims database analysis. Pneumonia (Nathan) 2023; 15:8. [PMID: 37016411 PMCID: PMC10074783 DOI: 10.1186/s41479-023-00109-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/25/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Pneumonia is the most serious form of acute respiratory infection and Streptococcus pneumoniae is a leading cause of pediatric bacterial pneumonia. Pneumococcal conjugate vaccines were introduced in the United States (US) in 2000 (7-valent [PCV7]) and 2010 (13-valent [PCV13]). This study estimated annual incidence rates (IRs) of all-cause pneumonia (ACP) among US children aged < 18 years before and after the introduction of PCV7 and PCV13. METHODS ACP episodes were identified in the IBM MarketScan Commercial and Medicaid Databases using diagnosis codes. Annual IRs were calculated overall and by inpatient and outpatient settings as the number of episodes per 100,000 person-years (PY) for all children aged < 18 years and by age group (< 2, 2-4, and 5-17 years). National estimates of annual pneumonia IRs were extrapolated using Census Bureau data. Interrupted time series (ITS) analyses were used to assess immediate and gradual changes in monthly pneumonia IRs, adjusting for seasonality. RESULTS In the commercially-insured population, ACP IRs declined between the pre-PCV7 period (1998-1999) and late PCV13 period (2014-2018) from 5,322 to 3,471 episodes per 100,000 PY for children aged < 2 years, from 4,012 to 3,794 episodes per 100,000 PY in children aged 2-4 years but increased slightly from 1,383 to 1,475 episodes per 100,000 PY in children aged 5-17 years. The ITS analyses indicated significant decreases in monthly ACP IRs in the early PCV7 period (2001-2005) among younger children and in the early PCV13 period (2011-2013) among all children. Increases were observed in the late PCV7 period (2006-2009) among all age groups, but were only significant among older children. IRs of inpatient ACP decreased across all age groups, but outpatient pneumonia IRs remained stable during the study timeframe, even increasing slightly in children aged 5-17 years. More prominent declines were observed for Medicaid-insured children across all age groups; however, Medicaid IRs were higher than IRs of commercially-insured children during the entire study timeframe. CONCLUSIONS ACP disease burden remains high in US children of all ages despite overall reductions in incidence rates during 1998-2018 following the introduction of PCV7 and PCV13.
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Affiliation(s)
- Tianyan Hu
- Merck & Co., Inc., 126 East Lincoln Ave., Rahway, NJ, 07065, USA
| | - Eric M Sarpong
- Merck & Co., Inc., 126 East Lincoln Ave., Rahway, NJ, 07065, USA
| | - Yan Song
- Analysis Group, Inc., 111 Huntington Ave, Floor 14, Boston, MA, 02199, USA
| | - Nicolae Done
- Analysis Group, Inc., 111 Huntington Ave, Floor 14, Boston, MA, 02199, USA
| | - Qing Liu
- Analysis Group, Inc., 111 Huntington Ave, Floor 14, Boston, MA, 02199, USA
| | | | - James Signorovitch
- Analysis Group, Inc., 111 Huntington Ave, Floor 14, Boston, MA, 02199, USA
| | - Salini Mohanty
- Merck & Co., Inc., 126 East Lincoln Ave., Rahway, NJ, 07065, USA.
| | - Thomas Weiss
- Merck & Co., Inc., 126 East Lincoln Ave., Rahway, NJ, 07065, USA
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Hawkins PA, Chochua S, Lo SW, Belman S, Antonio M, Kwambana-Adams B, von Gottberg A, du Plessis M, Cornick J, Beall B, Breiman RF, Bentley SD, McGee L. A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction. Microb Genom 2023; 9. [PMID: 37083600 DOI: 10.1099/mgen.0.000998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against Streptococcus pneumoniae has led to serotype replacement by non-vaccine serotypes, including serotype 15A. Clonal complex 63 (CC63) is associated with many serotypes and has been reported in association with 15A after introduction of PCVs. A total of 865 CC63 isolates were included in this study, from the USA (n=391) and a global collection (n=474) from 1998-2019 and 1995-2018, respectively. We analysed the genomic sequences to identify serotypes and penicillin-binding protein (PBP) genes 1A, 2B and 2X, and other resistance determinants, to predict minimum inhibitory concentrations (MICs) against penicillin, erythromycin, clindamycin, co-trimoxazole and tetracycline. We conducted phylogenetic and spatiotemporal analyses to understand the evolutionary history of the 15A-CC63 sub-lineage. Overall, most (89.5 %, n=247) pre-PCV isolates in the CC63 cluster belonged to serotype 14, with 15A representing 6.5 % of isolates. Conversely, serotype 14 isolates represented 28.2 % of post-PCV CC63 isolates (n=618), whilst serotype 15A isolates represented 65.4 %. Dating of the CC63 lineage determined the most recent common ancestor emerged in the 1980s, suggesting the 15A-CC63 sub-lineage emerged from its closest serotype 14 ancestor prior to the development of pneumococcal vaccines. This sub-lineage was predominant in the USA, Israel and China. Multidrug resistance (to three or more drug classes) was widespread among isolates in this sub-lineage. We show that the CC63 lineage is globally distributed and most of the isolates are penicillin non-susceptible, and thus should be monitored.
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Affiliation(s)
- Paulina A Hawkins
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Martin Antonio
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Anne von Gottberg
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jen Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Barkowsky G, Abt C, Pöhner I, Bieda A, Hammerschmidt S, Jacob A, Kreikemeyer B, Patenge N. Antimicrobial Activity of Peptide-Coupled Antisense Peptide Nucleic Acids in Streptococcus pneumoniae. Microbiol Spectr 2022; 10:e0049722. [PMID: 36321914 PMCID: PMC9784828 DOI: 10.1128/spectrum.00497-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniae is the most common cause of community-acquired pneumonia and is responsible for multiple other infectious diseases, such as meningitis and otitis media, in children. Resistance to penicillins, macrolides, and fluoroquinolones is increasing and, since the introduction of pneumococcal conjugate vaccines (PCVs), vaccine serotypes have been replaced by non-vaccine serotypes. Antisense peptide nucleic acids (PNAs) have been shown to reduce the growth of several pathogenic bacteria in various infection models. PNAs are frequently coupled to cell-penetrating peptides (CPPs) to improve spontaneous cellular PNA uptake. In this study, different CPPs were investigated for their capability to support translocation of antisense PNAs into S. pneumoniae. HIV-1 TAT- and (RXR)4XB-coupled antisense PNAs efficiently reduced the viability of S. pneumoniae strains TIGR4 and D39 in vitro. Two essential genes, gyrA and rpoB, were used as targets for antisense PNAs. Overall, the antimicrobial activity of anti-gyrA PNAs was higher than that of anti-rpoB PNAs. Target gene transcription levels in S. pneumoniae were reduced following antisense PNA treatment. The effect of HIV-1 TAT- and (RXR)4XB-anti-gyrA PNAs on pneumococcal survival was also studied in vivo using an insect infection model. Treatment increased the survival of infected Galleria mellonella larvae. Our results represent a proof of principle and may provide a basis for the development of efficient antisense molecules for treatment of S. pneumoniae infections. IMPORTANCE Streptococcus pneumoniae is the most common cause of community-acquired pneumonia and is responsible for the deaths of up to 2 million children each year. Antibiotic resistance and strain replacement by non-vaccine serotypes are growing problems. For this reason, S. pneumoniae has been added to the WHO "global priority list" of antibiotic-resistant bacteria for which novel antimicrobials are most urgently needed. In this study, we investigated whether CPP-coupled antisense PNAs show antibacterial activity in S. pneumoniae. We demonstrated that HIV-1 TAT- and (RXR)4XB-coupled antisense PNAs were able to kill S. pneumoniae in vitro. The specificity of the antimicrobial effect was verified by reduced target gene transcription levels in S. pneumoniae. Moreover, CPP-antisense PNA treatment increased the survival rate of infected Galleria mellonella larvae in vivo. Based on these results, we believe that efficient antisense PNAs can be developed for the treatment of S. pneumoniae infections.
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Affiliation(s)
- Gina Barkowsky
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Corina Abt
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Irina Pöhner
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Adam Bieda
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute for Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Anette Jacob
- Peps4LS GmbH, Heidelberg, Germany
- Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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10
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Mohanty S, Hu T, Yang G, Khan TK, Owusu-Edusei K, Sukarom I. Health and economic burden associated with 15-valent pneumococcal conjugate vaccine serotypes in Korea and Hong Kong. Hum Vaccin Immunother 2022; 18:2046433. [PMID: 35420975 PMCID: PMC9196648 DOI: 10.1080/21645515.2022.2046433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Use of pneumococcal conjugate vaccines (PCVs) has greatly reduced the incidence of invasive pneumococcal disease (IPD). V114 (VAXNEUVANCE™, Merck Sharp & Dohme Corp. a subsidiary of Merck & Co. Inc. Kenilworth, NJ, USA) is a 15-valent PCV currently approved in adults in the United States, containing the 13 serotypes in licensed PCV13 and 2 additional serotypes (22F and 33F) which are important contributors to residual pneumococcal disease. This study quantified the health and economic burden of IPD attributable to V114 serotypes in hypothetical birth cohorts from Korea and Hong Kong. A Markov model was used to estimate the case numbers and costs of IPD in unvaccinated birth cohorts over 20 years. The model was applied to 3 scenarios in Korea (pre-PCV7, pre-PCV13, and post-PCV13) and to 2 scenarios in Hong Kong (pre-PCV7 and post-PCV13). For Korea, the model predicted 62, 26, and 8 IPD cases attributable to V114 serotypes in the pre-PCV7, pre-PCV13, and post-PCV13 scenarios, respectively. Costs of V114-type IPD fell from $1.691 million pre-PCV7 to $.212 million post-PCV13. For Hong Kong, the model estimated 62 V114-associated IPD cases in the pre-PCV7 scenario and 46 in the post-PCV13 scenario. Costs attributed to all V114 serotypes were $2.322 million and $1.726 million in the pre-PCV7 and post-PCV13 periods, respectively. Vaccine-type serotypes are predicted to cause continuing morbidity and cost in Korea (19A) and Hong Kong (3 and 19A). New pediatric pneumococcal vaccines must continue to protect against serotypes in licensed vaccines to maintain disease reduction, while extending coverage to non-vaccine serotypes.
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Affiliation(s)
- Salini Mohanty
- Center for Observational and Real-World Evidence (CORE), Merck & Co., Inc., Kenilworth, NJ, USA
| | - Tianyan Hu
- Center for Observational and Real-World Evidence (CORE), Merck & Co., Inc., Kenilworth, NJ, USA
| | | | - Tsz K Khan
- Global Medical and Scientific Affairs, MSD, Hong Kong, China
| | - Kwame Owusu-Edusei
- Biostatistics & Research Decision Sciences (BARDS), Merck & Co., Inc., Kenilworth, NJ, USA
| | - Isaya Sukarom
- Center for Observational and Real-World Evidence (CORE), MSD Thailand, Bangkok, Thailand
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11
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Hu T, Song Y, Done N, Liu Q, Sarpong EM, Lemus-Wirtz E, Signorovitch J, Mohanty S, Weiss T. Incidence of invasive pneumococcal disease in children with commercial insurance or Medicaid coverage in the United States before and after the introduction of 7- and 13-valent pneumococcal conjugate vaccines during 1998-2018. BMC Public Health 2022; 22:1677. [PMID: 36064378 PMCID: PMC9442936 DOI: 10.1186/s12889-022-14051-6] [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: 01/11/2022] [Accepted: 08/17/2022] [Indexed: 11/29/2022] Open
Abstract
Background Invasive pneumococcal disease (IPD) is a major cause of pediatric morbidity and mortality. Pneumococcal conjugate vaccines (PCVs) were introduced in the US in 2000 (PCV7) and 2010 (PCV13). This study estimated the annual incidence rates (IRs) and time trends of IPD to quantify the burden of disease in children before and after the introduction of PCV7 and PCV13 in the US. Methods IPD episodes were identified in the IBM MarketScan Commercial and Medicaid Databases using claims with International Classification of Diseases 9/10th Revision, Clinical Modification codes. Annual IRs were calculated as the number of IPD episodes/100,000 person-years (PYs) for children < 18 years and by age group (< 2, 2–4, and 5–17 years). National estimates of annual IPD IRs were extrapolated using Census Bureau data. Interrupted time series (ITS) analyses were conducted to assess immediate and gradual changes in IPD IRs before and after introduction of PCV7 and PCV13. Results In commercially insured children, IPD IRs decreased from 9.4 to 2.8 episodes/100,000 PY between the pre-PCV7 (1998–1999) and late PCV13 period (2014–2018) overall, and from 65.6 to 11.6 episodes/100,000 PY in children < 2 years. In the Medicaid population, IPD IRs decreased from 11.3 to 4.2 episodes/100,000 PY between the early PCV7 (2001–2005) and late PCV13 period overall, and from 42.6 to 12.8 episodes/100,000 PY in children < 2 years. The trends of IRs for meningitis, bacteremia, and bacteremic pneumonia followed the patterns of overall IPD episodes. The ITS analyses indicated significant decreases in the early PCV7 period, increases in the late PCV7 and decreases in the early PCV13 period in commercially insured children overall. However, increases were also observed in the late PCV13 period in children < 2 years. The percentage of cases with underlying risk factors increased in both populations. Conclusions IRs of IPD decreased from 1998 to 2018, following introduction of PCV7 and PCV13, with larger declines during the early PCV7 and early PCV13 periods, and among younger children. However, the residual burden of IPD remains substantial. The impact of future PCVs on IPD IRs will depend on the proportion of vaccine-type serotypes and vaccine effectiveness in children with underlying conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12889-022-14051-6.
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Affiliation(s)
- Tianyan Hu
- Merck & Co., Inc., 126 East Lincoln Ave, P.O. Box 2000, Rahway, NJ, 07065, USA
| | - Yan Song
- Analysis Group, Inc., 111 Huntington Avenue 14th Floor, Boston, MA, 02199, USA
| | - Nicolae Done
- Analysis Group, Inc., 111 Huntington Avenue 14th Floor, Boston, MA, 02199, USA
| | - Qing Liu
- Analysis Group, Inc., 111 Huntington Avenue 14th Floor, Boston, MA, 02199, USA
| | - Eric M Sarpong
- Merck & Co., Inc., 126 East Lincoln Ave, P.O. Box 2000, Rahway, NJ, 07065, USA
| | - Esteban Lemus-Wirtz
- Analysis Group, Inc., 111 Huntington Avenue 14th Floor, Boston, MA, 02199, USA
| | - James Signorovitch
- Analysis Group, Inc., 111 Huntington Avenue 14th Floor, Boston, MA, 02199, USA
| | - Salini Mohanty
- Merck & Co., Inc., 126 East Lincoln Ave, P.O. Box 2000, Rahway, NJ, 07065, USA.
| | - Thomas Weiss
- Merck & Co., Inc., 126 East Lincoln Ave, P.O. Box 2000, Rahway, NJ, 07065, USA
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12
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Athanasia X, Nektarios M, Theano G, Anastasia P, Stelmos S, Ioanna M, Andreas E, Vassiliki G, Anastasia AK, Efi S, Fani M, Athina A, Georgia V, Genovefa C, Anastasia P, Theodota L, Athanasios M, Vassiliki S, Evaggelia L, George P, Efthymia P, Elpis M, Emmanuel R, Manolis G, Vana P, Maria T, Tzanakaki G. Pneumococcal meningitis in Greece: A retrospective serotype surveillance study in the post-PCV13 era (2010-2020). Vaccine 2022; 40:5079-5087. [PMID: 35871868 DOI: 10.1016/j.vaccine.2022.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
Abstract
BACKGROUND As Greece is a country which has introduced the 13-valent pneumococcal conjugate vaccine (PCV13) both in the infant and in the adult immunization programs, the aim of the study was to investigate age-specific and serotype-specific trends of pneumococcal meningitis over an 11-year period (2010-2020). MATERIALS AND METHODS Data are reported from pneumococcal meningitis cases [notified to the National Public Health Organization (NPHO)], with clinical samples and bacterial isolates sent for pneumococcal identification and serotyping at the National Meningitis Reference Laboratory (NMRL). Pneumococcal identification was performed directly on clinical samples or bacterial isolates by multiplex PCR (mPCR) assay, while serotyping was carried out by application of the Capsular Sequence Typing (CST) method with the combination of single tube PCR assays. RESULTS A total of 427 pneumococcal meningitis cases were notified to the NPHO between 2010 and 2020. Among those, 405 (94.8%) were microbiologically confirmed, while samples from 273 patients were sent to the NMRL for identification and/or further typing. The annual notification rate peaked at 0.47/100,000 in 2016 and since then has been decreasing. The incidence was highest in infants and in older adults. Pneumococcal serotypes were identified in 260/273 (95.2%) cases, where clinical samples were sent to the NMRL. The most prevalent serotypes (≥5%) were 3, 19A, 23B, 15B/C, 11A/D, 23A, 22F. During the study period there has been a decrease of PCV13 serotypes combined with an increase of non-PCV13 serotypes (p = 0.0045). CONCLUSIONS This is the first study to report serotypes for pneumococcal meningitis across all ages in the post-PCV13 era in Greece. There is a need to enhance surveillance, by close monitoring of the emerging serotypes and the impact of vaccination programs. Higher-valency PCVs may help to improve the coverage of pneumococcal disease.
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Affiliation(s)
- Xirogianni Athanasia
- National Meningitis Reference Laboratory, Dept. of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Marmaras Nektarios
- National Meningitis Reference Laboratory, Dept. of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Georgakopoulou Theano
- Department of Vaccine Preventable Diseases, National Public Health Organization (NPHO), Athens, Greece
| | - Papandreou Anastasia
- National Meningitis Reference Laboratory, Dept. of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Simantirakis Stelmos
- National Meningitis Reference Laboratory, Dept. of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Magaziotou Ioanna
- Department of Vaccine Preventable Diseases, National Public Health Organization (NPHO), Athens, Greece
| | - Eliades Andreas
- Dept. of Paediatric Intensive Care Unit, University Hospital of Patras, Greece
| | - Getsi Vassiliki
- Dept. of Paediatrics, (")Hatzikosta" General Hospital, Ioannina, Greece
| | | | - Staikou Efi
- Dept. of Microbiology, "Pentelis" Children Hospital, Athens, Greece
| | - Markou Fani
- Dept. of Microbiology, Serres General Hopsital, Serres, Greece
| | - Argyrοpoulou Athina
- Dept. of Clinical Microbiology "Evangelismos" General Hospital, Athens, Greece
| | - Vlachaki Georgia
- Dept. of Paediatrics, "Venizeleion" General Hospital, Heraklion, Crete, Greece
| | | | | | | | - Michos Athanasios
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Spoulou Vassiliki
- First Department of Pediatrics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | | | - Panagiotakopoulos George
- Department of Vaccine Preventable Diseases, National Public Health Organization (NPHO), Athens, Greece
| | - Petinaki Efthymia
- Dept. of Microbiology, Dept. of Microbiology, Medical School, University of Thessaly, Larissa, Greece
| | - Mantadakis Elpis
- Dept. of Paediatrics, Faculty of Medicine, Democritus University of Thrace, University General Hospital, Alexandroupolis, Greece
| | - Roilides Emmanuel
- 3rd Dept. of Paediatrics, School of Medicine, Aristotle University, and Hippokration General Hospital, Thessaloniki, Greece
| | - Galanakis Manolis
- Paediatric Infectious Diseases Unit, Heraklion University Hospital, University of Crete, Heraklion, Greece
| | - Papaevangelou Vana
- Third Department of Pediatrics, National and Kapodistrian University of Athens, University General Hospital "ATTIKON", Athens, Greece
| | - Tsolia Maria
- Second Dept. of Pediatrics, Medical School, National and Kapodistrian University of Athens, "A&P Kyriakou" Children's Hospital, Athens, Greece
| | - Georgina Tzanakaki
- National Meningitis Reference Laboratory, Dept. of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece.
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13
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Lewnard JA, Bruxvoort KJ, Fischer H, Hong VX, Grant LR, Jódar L, Gessner BD, Tartof SY. Prevention of Coronavirus Disease 2019 Among Older Adults Receiving Pneumococcal Conjugate Vaccine Suggests Interactions Between Streptococcus pneumoniae and Severe Acute Respiratory Syndrome Coronavirus 2 in the Respiratory Tract. J Infect Dis 2022; 225:1710-1720. [PMID: 33693636 PMCID: PMC7989304 DOI: 10.1093/infdis/jiab128] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/04/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND While secondary pneumococcal pneumonia occurs less commonly after coronavirus disease 2019 (COVID-19) than after other viral infections, it remains unclear whether other interactions occur between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Streptococcus pneumoniae. METHODS We probed potential interactions between these pathogens among adults aged ≥65 years by measuring associations of COVID-19 outcomes with pneumococcal vaccination (13-valent conjugate vaccine [PCV13] and 23-valent pneumococcal polysaccharide vaccine [PPSV23]). We estimated adjusted hazard ratios (aHRs) using Cox proportional hazards models with doubly robust inverse-propensity weighting. We assessed effect modification by antibiotic exposure to further test the biologic plausibility of a causal role for pneumococci. RESULTS Among 531 033 adults, there were 3677 COVID-19 diagnoses, leading to 1075 hospitalizations and 334 fatalities, between 1 March and 22 July 2020. Estimated aHRs for COVID-19 diagnosis, hospitalization, and mortality associated with prior PCV13 receipt were 0.65 (95% confidence interval [CI], .59-.72), 0.68 (95% CI, .57-.83), and 0.68 (95% CI, .49-.95), respectively. Prior PPSV23 receipt was not associated with protection against the 3 outcomes. COVID-19 diagnosis was not associated with prior PCV13 within 90 days following antibiotic receipt, whereas aHR estimates were 0.65 (95% CI, .50-.84) and 0.62 (95% CI, .56-.70) during the risk periods 91-365 days and >365 days, respectively, following antibiotic receipt. CONCLUSIONS Reduced risk of COVID-19 among PCV13 recipients, transiently attenuated by antibiotic exposure, suggests that pneumococci may interact with SARS-CoV-2.
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Affiliation(s)
- Joseph A Lewnard
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, California, USA
- Center for Computational Biology, College of Engineering, University of California, Berkeley, Berkeley, California, USA
| | - Katia J Bruxvoort
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Heidi Fischer
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Vennis X Hong
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | | | - Luis Jódar
- Pfizer Vaccines, Collegeville, Pennsylvania, USA
| | | | - Sara Y Tartof
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
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14
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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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15
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Yamba Yamba L, Uddén F, Fuursted K, Ahl J, Slotved HC, Riesbeck K. Extensive/Multidrug-Resistant Pneumococci Detected in Clinical Respiratory Tract Samples in Southern Sweden Are Closely Related to International Multidrug-Resistant Lineages. Front Cell Infect Microbiol 2022; 12:824449. [PMID: 35392607 PMCID: PMC8981583 DOI: 10.3389/fcimb.2022.824449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Background/ObjectiveThe frequencies of non-susceptibility against common antibiotics among pneumococci vary greatly across the globe. When compared to other European countries antibiotic resistance against penicillin and macrolides has been uncommon in Sweden in recent years. Multidrug resistance (MDR) is, however, of high importance since relevant treatment options are scarce. The purpose of this study was to characterize the molecular epidemiology, presence of resistance genes and selected virulence genes of extensively drug-resistant (XDR) (n=15) and MDR (n=10) Streptococcus pneumoniae detected in clinical respiratory tract samples isolated from patients in a southern Swedish county 2016-2018. With the aim of relating them to global MDR pneumococci.MethodsWhole genome sequencing (WGS) was performed to determine molecular epidemiology, resistance genes and presence of selected virulence factors. Antimicrobial susceptibility profiles were determined using broth microdilution testing. Further analyses were performed on isolates from the study and from the European nucleotide archive belonging to global pneumococcal sequence cluster (GPSC) 1 (n=86), GPSC9 (n=55) and GPSC10 (n=57). Bacteria were analyzed regarding selected virulence determinants (pilus islet 1, pilus islet 2 and Zinc metalloproteinase C) and resistance genes.ResultsNineteen of 25 isolates were related to dominant global MDR lineages. Seventeen belonged to GPSC1, GPSC9 or GPSC10 with MDR non-PCV serotypes in GPSC9 (serotype 15A and 15C) as well as GPSC10 (serotype 7B, 15B and serogroup 24). Pilus islet-1 and pilus islet-2 were present in most sequence types belonging to GPSC1 and in two isolates within GPSC9 but were not detected in isolates belonging to GPSC10. Zinc metalloproteinase C was well conserved within all analyzed isolates belonging to GPSC9 but were not found in isolates from GPSC1 or GPSC10.ConclusionsAlthough MDR S. pneumoniae is relatively uncommon in Sweden compared to other countries, virulent non-PCV serotypes that are MDR may become an increasing problem, particularly from clusters GPSC9 and GPSC10. Since the incidence of certain serotypes (3, 15A, and 19A) found among our MDR Swedish study isolates are persistent or increasing in invasive pneumococcal disease further surveillance is warranted.
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Affiliation(s)
- Linda Yamba Yamba
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Fabian Uddén
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jonas Ahl
- Infectious Diseases, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Faculty of Medicine, Lund University, Malmö, Sweden
- *Correspondence: Kristian Riesbeck,
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16
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Andre C, Rouhana J, Scarpa de Mello S, Rosa da Cunha G, Van Camp AG, Gilmore MS, Bispo PJ. Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines. Microb Genom 2022; 8:000763. [PMID: 35254235 PMCID: PMC9176286 DOI: 10.1099/mgen.0.000763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus pneumoniae is a leading cause of ocular infections including serious and sight-threatening conditions. The use of pneumococcal conjugate vaccines (PCV) has substantially reduced the incidence of pneumonia and invasive pneumococcal diseases, but has had limited impact on ocular infections. Additionally, widespread vaccine use has resulted in ongoing selective pressure and serotype replacement in carriage and disease. To gain insight into the population structure of pneumococcal isolates causing ocular infections in a post-PCV-13 time period, we investigated the genomic epidemiology of ocular S. pneumoniae isolates (n=45) collected at Massachusetts Eye and Ear between 2014 and 2017. By performing a series of molecular typing methods from draft genomes, we found that the population structure of ocular S. pneumoniae is highly diverse with 27 sequence types (grouped into 18 clonal complexes) and 17 serotypes being identified. Distribution of these lineages diverged according to the site of isolation, with conjunctivitis being commonly caused by isolates grouped in the Epidemic Conjunctivitis Cluster-ECC (60 %), and ST448 (53.3 %) being most frequently identified. Conversely, S. pneumoniae keratitis cases were caused by a highly diverse population of isolates grouping within 15 different clonal complexes. Serotyping inference demonstrated that 95.5 % of the isolates were non-PCV-13 vaccine types. Most of the conjunctivitis isolates (80 %) were unencapsulated, with the remaining belonging to serotypes 15B, 3 and 23B. On the other hand, S. pneumoniae causing keratitis were predominantly encapsulated (95.2 %) with 13 different serotypes identified, mostly being non-vaccine types. Carriage of macrolide resistance genes was common in our ocular S. pneumoniae population (42.2 %), and usually associated with the mefA +msrD genotype (n=15). These genes were located in the Macrolide Efflux Genetic Assembly cassette and were associated with low-level in vitro resistance to 14- and 15-membered macrolides. Less frequently, macrolide-resistant isolates carried an ermB gene (n=4), which was co-located with the tetM gene in a Tn-916-like transposon. Our study demonstrates that the population structure of ocular S. pneumoniae is highly diverse, mainly composed by isolates that escape the PCV-13 vaccine, with patterns of tissue/niche segregation, adaptation and specialization. These findings suggest that the population structure of ocular pneumococcus may be shaped by multiple factors including PCV-13 selective pressure, microbial-related and niche-specific host-associated features.
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Affiliation(s)
- Camille Andre
- Infectious Disease Institute, Boston, MA 02114, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - John Rouhana
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Suelen Scarpa de Mello
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Gabriela Rosa da Cunha
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Present address: Clinical Laboratory, Hospital Ernesto Dornelles, Porto Alegre, Brazil
| | - Andrew G. Van Camp
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
| | - Michael S. Gilmore
- Infectious Disease Institute, Boston, MA 02114, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Paulo J.M. Bispo
- Infectious Disease Institute, Boston, MA 02114, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA
- *Correspondence: Paulo J.M. Bispo,
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17
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Beall B, Chochua S, Li Z, Tran T, Varghese J, McGee L, Li Y, Metcalf B. Invasive pneumococcal disease clusters disproportionally impact persons experiencing homelessness, injecting drug users, and the western United States. J Infect Dis 2022; 226:332-341. [PMID: 35172327 DOI: 10.1093/infdis/jiac058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/14/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Invasive pneumococcal disease (IPD) isolates forming genomic clusters can reflect rapid disease transmission between vulnerable individuals. METHODS We performed whole genome sequencing of 2820 IPD isolates recovered during 2019 through CDC's Active Bacterial Core surveillance (ABCs) to provide strain information (serotypes, resistance, genotypes), and 2778 of these genomes were analyzed to detect highly related genomic clusters. RESULTS Isolates from persons experiencing homelessness (PEH) were more often within genomic clusters than those from persons not experiencing homelessness (PNEH) (105/198, 53.0% vs 592/2551, 23.2%, p<0.001). The 4 western sites accounted for 33.4% (929/2778) of isolates subjected to cluster analysis yet accounted for 48.7% (343/705) of clustering isolates (p<0.001) and 150/198 (75.8%) isolates recovered from PEH (p<0.001). Serotypes most frequent among PEH were (in rank order) 12F, 4, 3, 9N, 8, 20, and 22F, all of which were among the 10 serotypes exhibiting the highest proportions of clustering isolates among all cases. These serotypes accounted for 44.9% (1265/2820) of all IPD cases and are included within available vaccines. CONCLUSIONS We identified serotype-specific and geographic differences in IPD transmission. We show the vulnerability of PEH within different regions to rapidly spreading IPD transmission networks representing several pneumococcal serotypes included in available vaccines.
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Affiliation(s)
- Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention (retired), Eagle Global Scientific, LLC, Atlanta, Georgia, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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18
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Gagetti P, Lo SW, Hawkins PA, Gladstone RA, Regueira M, Faccone D, Sireva-Argentina Group, Klugman KP, Breiman RF, McGee L, Bentley SD, Corso A. Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina. Microb Genom 2021; 7. [PMID: 34586054 PMCID: PMC8715423 DOI: 10.1099/mgen.0.000636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Invasive disease caused by Streptococcus pneumoniae (IPD) is one of the leading causes of morbidity and mortality in young children worldwide. In Argentina, PCV13 was introduced into the childhood immunization programme nationwide in 2012 and PCV7 was available from 2000, but only in the private market. Since 1993 the National IPD Surveillance Programme, consisting of 150 hospitals, has conducted nationwide pneumococcal surveillance in Argentina in children under 6 years of age, as part of the SIREVA II-OPS network. A total of 1713 pneumococcal isolates characterized by serotype (Quellung) and antimicrobial resistance (agar dilution) to ten antibiotics, belonging to three study periods: pre-PCV7 era 1998-1999 (pre-PCV), before the introduction of PCV13 2010-2011 (PCV7) and after the introduction of PCV13 2012-2013 (PCV13), were available for inclusion. Fifty-four serotypes were identified in the entire collection and serotypes 14, 5 and 1 represented 50 % of the isolates. Resistance to penicillin was 34.9 %, cefotaxime 10.6 %, meropenem 4.9 %, cotrimoxazole 45 %, erythromycin 21.5 %, tetracycline 15.4 % and chloramphenicol 0.4 %. All the isolates were susceptible to levofloxacin, rifampin and vancomycin. Of 1713 isolates, 1061 (61.9 %) were non-susceptible to at least one antibiotic and 235(13.7 %) were multidrug resistant. A subset of 413 isolates was randomly selected and whole-genome sequenced as part of Global Pneumococcal Sequencing Project (GPS). The genome data was used to investigate the population structure of S. pneumoniae defining pneumococcal lineages using Global Pneumococcal Sequence Clusters (GPSCs), sequence types (STs) and clonal complexes (CCs), prevalent serotypes and their associated pneumococcal lineages and genomic inference of antimicrobial resistance. The collection showed a great diversity of strains. Among the 413 isolates, 73 known and 36 new STs were identified belonging to 38 CCs and 25 singletons, grouped into 52 GPSCs. Important changes were observed among vaccine types when pre-PCV and PCV13 periods were compared; a significant decrease in serotypes 14, 6B and 19F and a significant increase in 7F and 3. Among non-PCV13 types, serogroup 24 increased from 0 % in pre-PCV to 3.2 % in the PCV13 period. Our analysis showed that 66.1 % (273/413) of the isolates were predicted to be non-susceptible to at least one antibiotic and 11.9 % (49/413) were multidrug resistant. We found an agreement of 100 % when comparing the serotype determined by Quellung and WGS-based serotyping and 98.4 % of agreement in antimicrobial resistance. Continued surveillance of the pneumococcal population is needed to reveal the dynamics of pneumococcal isolates in Argentina in post-PCV13. This article contains data hosted by Microreact.
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Affiliation(s)
- Paula Gagetti
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Stephanie W Lo
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Paulina A Hawkins
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Centers for Disease Control and Prevention, Atlanta, USA
| | - Rebecca A Gladstone
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mabel Regueira
- Bacteriology Division. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Diego Faccone
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | | | - Keith P Klugman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA.,Emory Global Health Institute, Atlanta, USA
| | - Lesley McGee
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Stephen D Bentley
- Parasites and Microbes, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alejandra Corso
- Antimicrobial Agents Division. National Reference Laboratory in Antimicrobial Resistance. INEI-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
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19
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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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20
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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21
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Metcalf BJ, Chochua S, Walker H, Tran T, Li Z, Varghese J, Snippes Vagnone PM, Lynfield R, McGee L, Li Y, Pilishvili T, Beall B. Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018. Clin Infect Dis 2021; 72:e948-e956. [PMID: 33150366 DOI: 10.1093/cid/ciaa1680] [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] [Received: 06/21/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the United States during 2018 and examine within-serotype propensities of isolates to form related clusters. METHODS We predicted strain features using whole genome sequencing obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs), which has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for ≥27 isolates. RESULTS Thirteen-valent pneumococcal conjugate vaccine (PCV13) serotypes together with 6C accounted for 23 of 105 (21.9%) of isolates from children aged <5 years and 820 of 2780 (29.5%) isolates from those aged ≥5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780 [14.9%]), 22F (291/2780 [10.5%]), and 9N (191/2780 [6.9%]). Among child IPD isolates, serotypes 15BC (18/105 [17.1%]), 3 (11/105 [10.5%]), and 33F (10/105 [9.5%]) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with the highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, 2 instances of highly related isolate pairs from co-residents were identified. CONCLUSIONS Non-PCV13 serotypes accounted for >70% of IPD in ABCs; however, PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness.
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Affiliation(s)
- Benjamin J Metcalf
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | - Ruth Lynfield
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuan Li
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tamara Pilishvili
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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22
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Structural, Genetic, and Serological Elucidation of Streptococcus pneumoniae Serogroup 24 Serotypes: Discovery of a New Serotype, 24C, with a Variable Capsule Structure. J Clin Microbiol 2021; 59:e0054021. [PMID: 33883183 DOI: 10.1128/jcm.00540-21] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pneumococcal capsules are important in pneumococcal pathogenesis and vaccine development. Although conjugate vaccines have brought about a significant reduction in invasive pneumococcal disease (IPD) caused by vaccine serotypes, the relative serotype prevalence has shifted with the dramatic emergence of serotype 24F in some countries. Here, we describe 14 isolates (13 IPD and 1 non-IPD) expressing a new capsule type, 24C, which resembles 24F but has a novel serological profile. We also describe the antigenic, biochemical, and genetic basis of 24F and 24C and the related serotypes 24A and 24B. Structural studies show that 24B, 24C, and 24F have identical polysaccharide backbones [β-Ribf-(1→4)-α-Rhap-(1→3)-β-GlcpNAc-(1→4)-β-Rhap-(1→4)-β-Glcp] but with different side chains, as follows: 24F has arabinitol-phosphate and 24B has ribitol-phosphate. 24C has a mixture of 24F and 24B repeating units, with the ratio of ribitol to arabinitol being strain dependent. In contrast, the 24A capsule has a backbone without β-Ribf but with arabinitol-phosphate and phosphocholine side chains. These structures indicate that factor-sera 24d and 24e recognize arabinitol and ribitol, respectively, which explains the serology of serogroup 24, including those of 24C. The structures can be genetically described by the bispecificity of wcxG, which is capable of transferring arabinitol or ribitol when arabinitol is limiting. Arabinitol is likely not produced in 24B but is produced in reduced amounts in 24C due to various mutations in abpA or abpB genes. Our findings demonstrate how pneumococci modulate their capsule structure and immunologic properties with small genetic changes, thereby evading host immune responses. Our findings also suggest a potential for new capsule types within serogroup 24.
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Nonpneumococcal Strains Recently Recovered from Carriage Specimens and Expressing Capsular Serotypes Highly Related or Identical to Pneumococcal Serotypes 2, 4, 9A, 13, and 23A. mBio 2021; 12:mBio.01037-21. [PMID: 34006665 PMCID: PMC8262907 DOI: 10.1128/mbio.01037-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The polysaccharide capsule is a key virulence factor of Streptococcus pneumoniae There are numerous epidemiologically important pneumococcal capsular serotypes, and recent findings have demonstrated that several of them are commonly found among nonpathogenic commensal species. Here, we describe 9 nonpneumococcal strains carrying close homologs of pneumococcal capsular biosynthetic (cps) loci that were discovered during recent pneumococcal carriage studies of adults in the United States and Kenya. Two distinct Streptococcus infantis strains cross-reactive with pneumococcal serotype 4 and carrying cps4-like capsular biosynthetic (cps) loci were recovered. Opsonophagocytic killing assays employing rabbit antisera raised against S. infantis US67cps4 revealed serotype 4-specific killing of both pneumococcal and nonpneumococcal strains. An S. infantis strain and two Streptococcus oralis strains, all carrying cps9A-like loci, were cross-reactive with pneumococcal serogroup 9 strains in immunodiffusion assays. Antiserum raised against S. infantis US64cps9A specifically promoted killing of serotype 9A and 9V pneumococcal strains as well as S. oralis serotype 9A strains. Serotype-specific PCR of oropharyngeal specimens from a recent adult carriage study in the United States indicated that such nonpneumococcal strains were much more common in this population than serotype 4 and serogroup 9 pneumococci. We also describe S. oralis and S. infantis strains expressing serotypes identical or highly related to serotypes 2, 13, and 23A. This study has expanded the known overlap of pneumococcal capsular serotypes with related commensal species. The frequent occurrence of nonpneumococcal strains in the upper respiratory tract that share vaccine and nonvaccine capsular serotypes with pneumococci could affect population immunity to circulating pneumococcal strains.IMPORTANCE The distributions and frequencies of individual pneumococcal capsular serotypes among nonpneumococcal strains in the upper respiratory tract are unknown and potentially affect pneumococcal serotype distributions among the population and immunity to circulating pneumococcal strains. Repeated demonstration that these nonpneumococcal strains expressing so-called pneumococcal serotypes are readily recovered from current carriage specimens is likely to be relevant to pneumococcal epidemiology, niche biology, and even to potential strategies of employing commensal live vaccines. Here, we describe multiple distinct nonpneumococcal counterparts for each of the pneumococcal conjugate vaccine (PCV) serotypes 4 and 9V. Additional data from contemporary commensal isolates expressing serotypes 2, 13, and 23A further demonstrate the ubiquity of such strains. Increased focus upon this serological overlap between S. pneumoniae and its close relatives may eventually prove that most, or possibly all, pneumococcal serotypes have counterparts expressed by the common upper respiratory tract commensal species Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis.
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Scherer EM, Beall B, Metcalf B. Serotype-Switch Variant of Multidrug-Resistant Streptococcus pneumoniae Sequence Type 271. Emerg Infect Dis 2021; 27:1689-1692. [PMID: 33915076 PMCID: PMC8153891 DOI: 10.3201/eid2706.203629] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We discovered 3 invasive, multidrug-resistant Streptococcus pneumoniae isolates of vaccine-refractory capsular serotype 3 that recently arose within the successful sequence type 271 complex through a serotype switch recombination event. Mapping genomic recombination sites within the serotype 3/sequence type 271 progeny revealed a 55.9-kb donated fragment that encompassed cps3, pbp1a, and additional virulence factors.
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Ruiz García Y, Nieto Guevara J, Izurieta P, Vojtek I, Ortega-Barría E, Guzman-Holst A. CIRCULATING CLONAL COMPLEXES AND SEQUENCE TYPES OF STREPTOCOCCUS PNEUMONIAE SEROTYPE 19A WORLDWIDE: THE IMPORTANCE OF MULTIDRUG RESISTANCE: A SYSTEMATIC LITERATURE REVIEW. Expert Rev Vaccines 2021; 20:45-57. [PMID: 33507135 DOI: 10.1080/14760584.2021.1873136] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Streptococcus pneumoniae is a major cause of morbidity and mortality, especially amongst young children and the elderly. Childhood implementation of pneumococcal conjugate vaccines (PCVs) significantly reduced the incidence of invasive pneumococcal disease (IPD), while several nonvaccine serotypes remained substantial. Although there is evidence of the impact of higher-valent PCVs on serotype 19A, 19A IPD burden and antibiotic resistance remain a major concern post-vaccination. AREAS COVERED We performed a systematic literature review to analyze the frequency and clonal distribution of serotype 19A isolates in the pre- and post-PCV era worldwide providing a scientific background on the factors that influence multidrug resistance in pneumococcal isolates. EXPERT COMMENTARY Serotype 19A IPD incidence increased in all regions following the introduction of the 7-valent PCV. The higher-valent PCVs have reduced the rates of 19A IPD isolates, but several circulating strains with diverse antibiotic resistance prevailed. Heterogeneous clonal distribution in serotype 19A was observed within countries and regions, irrespective of higher-valent PCV used. An increase of 19A isolates from pre- to post-vaccination periods were associated with frequently occurring serotype switching events and with the prevalence of multidrug resistant strains. Rational antibiotic policies must be implemented to control the emergence of resistance.Plain Language SummaryWhat is the context?Streptococcus pneumoniae is a major cause of pneumococcal diseases especially amongst young children and the elderly. Vaccination with pneumococcal conjugate vaccines has significantly reduced the incidence of invasive pneumococcal disease worldwide. However, the invasive pneumococcal disease remains an important health problem due to the increase of nonvaccine serotypes. Serotype 19A is predominant in many countries worldwide. Factors contributing to its prevalence include serotype replacement, the emergence of clones with multidrug resistance due to antibiotic overuse, and potential bacteria adaptation in response to the vaccine.What is new?We performed a systematic literature review to 1) analyze the incidence and clonal distribution of serotype 19A isolates pre- and post-vaccination worldwide, and to collect data evaluating antimicrobial resistance patterns displayed by the clones of serotype 19A. We found that 1) clonal distribution in serotype 19A was heterogeneous within countries and regions, irrespective of the vaccine used; 2) the diversity of 19A isolates increased after vaccination. It was associated with frequent serotype switching events and with the prevalence of multidrug resistant strains.What is the impact?Implementation of policies to educate on sustainable antibiotic use and infectious prevention measures may help control the emergence of antibiotic resistance. High-quality active surveillance and future molecular epidemiology studies are needed to understand rapid genetic changes.
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Hu T, Weiss T, Owusu-Edusei K, Petigara T. Health and economic burden associated with 15-valent pneumococcal conjugate vaccine serotypes in children in the United States. J Med Econ 2020; 23:1653-1660. [PMID: 33084447 DOI: 10.1080/13696998.2020.1840216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AIMS V114 is an investigational 15-valent pneumococcal conjugate vaccine (PCV) containing the 13 Streptococcus pneumoniae serotypes in 13-valent PCV (PCV13) plus two additional serotypes. This study quantified the health and economic burden of invasive pneumococcal disease (IPD) and acute otitis media (AOM) caused by V114 types among children in the United States. MATERIALS AND METHODS A Markov model estimated the number of V114-type IPD and AOM cases and costs in a hypothetical, unvaccinated US birth cohort over 20 years. Three time periods were analyzed using time-specific epidemiological data to determine the number of IPD and AOM cases associated with all 15 serotypes in V114. The time periods were: (1) pre-PCV7 (1999); (2) pre-PCV13 (2009); (3) post-PCV13 (2017). Costs were estimated from a societal perspective (2018 US dollars) and discounted at 3%. RESULTS The model estimated 18,983 IPD cases and 5.4 million AOM cases associated with V114 serotypes pre-PCV7, 4,697 IPD cases and 3.0 million AOM cases pre-PCV13, and 948 IPD cases and 0.2 million AOM cases post-PCV13. Total discounted costs associated with V114 serotypes were $1.7 billion pre-PCV7, $730 million pre-PCV13, and $75 million US dollars post-PCV13. LIMITATIONS Post-meningitis sequelae, cases of non-bacteremic pneumonia, and direct non-medical costs were not included. CONCLUSIONS IPD and AOM cases and costs were estimated in a hypothetical US birth cohort followed for 20 years at three time periods. In all three periods, the serotypes targeted by V114 contributed to significant morbidity and costs. New pediatric pneumococcal vaccines must continue to retain serotypes in licensed vaccines to maintain disease reduction while extending coverage to non-vaccine serotypes.
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Affiliation(s)
- Tianyan Hu
- Center for Observational and Real-world Evidence, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Thomas Weiss
- Center for Observational and Real-world Evidence, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Kwame Owusu-Edusei
- Center for Observational and Real-world Evidence, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Tanaz Petigara
- Center for Observational and Real-world Evidence, Merck & Co., Inc., Kenilworth, NJ, USA
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Huang J, Kaur B, Farooqi A, Miah T, McGrath E, Seth D, Secord E, Poowuttikul P. Elevated Glycated Hemoglobin Is Associated with Reduced Antibody Responses to Vaccinations in Children. PEDIATRIC ALLERGY, IMMUNOLOGY, AND PULMONOLOGY 2020; 33:193-198. [PMID: 35921562 PMCID: PMC9353988 DOI: 10.1089/ped.2020.1160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 10/03/2020] [Indexed: 06/15/2023]
Abstract
Background: Childhood obesity is a major health concern, and it is associated with an increased risk of infectious morbidity. Previous studies found a decrease in protective antibody titers in obese adults after hepatitis B, influenza, and tetanus vaccination. Objective: We aimed at determining whether obesity or abnormal hemoglobin A1C (HBA1C) levels are associated with altered antibody responses in children. Methods: Children (8-18 years) who have completed routine childhood immunization were recruited. Serum samples were tested by the enzyme-linked immunosorbent assay method for antibody levels to Diphtheria, Tetanus, Haemophilus influenzae type B (HIB), and Streptococcus pneumoniae, along with serum HBA1C levels. An electronic medical record review on the frequency of emergency visits for infection was conducted. Spearman rank correlation, Fisher-exact, and Pearson's Chi-squared tests were used for statistical analysis. Results: There was an overall negative correlation between body mass index (BMI) percentile and the majority of pneumococcal subtypes, Diphtheria and Tetanus titers, although not statistically significant. There was a statistically significant negative correlation between HBA1C level and the S. pneumoniae serotype P9N (P = 0.037), P4 (P = 0.017), P12 (P = 0.023), P19F (P = 0.050), and HIB (P = 0.001). On average, individuals with elevated HBA1C levels had more frequent emergency room visits for infection (P = 0.029) and more viral infections (P = 0.023) as compared with children with normal HBA1C. Conclusion: Children with higher HBA1C levels were more likely to have lower pneumococcal and HIB titers and increased rates of emergency room visits for infection in a prospective, population-based cohort study. Although not statistically significant, there was an overall negative correlation between BMI percentile and titers for routine childhood vaccines.
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Affiliation(s)
- Jenny Huang
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Bani Kaur
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Ahmad Farooqi
- Children's Research Center of Michigan, Detroit, Michigan, USA
| | - Tayaba Miah
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Eric McGrath
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
- Wayne State University, School of Medicine, Detroit, Michigan, USA
| | - Divya Seth
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
- Wayne State University, School of Medicine, Detroit, Michigan, USA
| | - Elizabeth Secord
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
- Wayne State University, School of Medicine, Detroit, Michigan, USA
| | - Pavadee Poowuttikul
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
- Wayne State University, School of Medicine, Detroit, Michigan, USA
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Beall B, Walker H, Tran T, Li Z, Varghese J, McGee L, Li Y, Metcalf BJ, Gierke R, Mosites E, Chochua S, Pilishvili T. Upsurge of Conjugate Vaccine Serotype 4 Invasive Pneumococcal Disease Clusters Among Adults Experiencing Homelessness in California, Colorado, and New Mexico. J Infect Dis 2020; 223:1241-1249. [PMID: 32798216 DOI: 10.1093/infdis/jiaa501] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/04/2020] [Indexed: 11/14/2022] Open
Abstract
After 7-valent pneumococcal conjugate vaccine introduction in the United States in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults within 3 of 10 Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010-2018, 36% were persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100-300 times higher than in the general population within these 3 areas. Genome sequencing for isolates recovered 2015-2018 (n = 246), revealed that increases in serotype 4 IPD were driven by lineages ST10172, ST244, and ST695. Within each lineage, clusters of near-identical isolates indicated close temporal relatedness. Increases in serotype 4 IPD were limited to Colorado, California, and New Mexico, with highest increases among PEH, who were at increased risk for exposure to and infections caused by these strains.
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Affiliation(s)
- Bernard Beall
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Hollis Walker
- IHRC Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Theresa Tran
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zhongya Li
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jasmine Varghese
- ASRT Inc., Contractor to Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lesley McGee
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuan Li
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin J Metcalf
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ryan Gierke
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Emily Mosites
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sopio Chochua
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tamara Pilishvili
- Respiratory Disease Branch, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Li Y, Rivers J, Mathis S, Li Z, Velusamy S, Nanduri SA, Van Beneden CA, Snippes-Vagnone P, Lynfield R, McGee L, Chochua S, Metcalf BJ, Beall B. Genomic Surveillance of Streptococcus pyogenes Strains Causing Invasive Disease, United States, 2016-2017. Front Microbiol 2020; 11:1547. [PMID: 32849323 PMCID: PMC7396493 DOI: 10.3389/fmicb.2020.01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Streptococcus pyogenes is a major cause of severe, invasive infections in humans. The bacterial pathogen harbors a wide array of virulence factors and exhibits high genomic diversity. Rapid changes of circulating strains in a community are common. Understanding the current prevalence and dynamics of S. pyogenes lineages could inform vaccine development and disease control strategies. METHODS We used whole-genome sequencing (WGS) to characterize all invasive S. pyogenes isolates obtained through the United States Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) in 2016 and 2017. We determined the distribution of strain features, including emm type, antibiotic resistance determinants, and selected virulence factors. Changes in strain feature distribution between years 2016 and 2017 were evaluated. Phylogenetic analysis was used to identify expanding lineages within emm type. RESULTS Seventy-one emm types were identified from 3873 isolates characterized. The emm types targeted by a 30-valent M protein-based vaccine accounted for 3230 (89%) isolates. The relative frequencies of emm types collected during the 2 years were similar. While all isolates were penicillin-susceptible, erythromycin-resistant isolates increased from 273 (16% of 2016 isolates) to 432 (23% of 2017 isolates), mainly driven by increase of the erm-positive emm types 92 and 83. The prevalence of 24 virulence factors, including 11 streptococcal pyrogenic toxins, ranged from 6 to 90%. In each of three emm types (emm 49, 82, and 92), a subgroup of isolates significantly expanded between 2016 and 2017 compared to isolates outside of the subgroup (P-values < 0.0001). Specific genomic sequence changes were associated with these expanded lineages. CONCLUSIONS While the overall population structure of invasive S. pyogenes isolates in the United States remained stable, some lineages, including several that were antibiotic-resistant, increased between 2016 and 2017. Continued genomic surveillance can help monitor and characterize bacterial features associated with emerging strains from invasive infections.
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Affiliation(s)
- Yuan Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Joy Rivers
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Saundra Mathis
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Zhongya Li
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivasan Velusamy
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Srinivas A. Nanduri
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Chris A. Van Beneden
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | | | - Ruth Lynfield
- Minnesota Department of Health, St Paul, MN, United States
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Sopio Chochua
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Benjamin J. Metcalf
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
| | - Bernard Beall
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, United States Department of Health and Human Services, Atlanta, GA, United States
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Klugman KP, Rodgers GL. Time for a third-generation pneumococcal conjugate vaccine. THE LANCET. INFECTIOUS DISEASES 2020; 21:14-16. [PMID: 32702301 DOI: 10.1016/s1473-3099(20)30513-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Keith P Klugman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA 98119, USA.
| | - Gail L Rodgers
- Pneumonia Program, Bill & Melinda Gates Foundation, Seattle, WA 98119, USA
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Expanded sequential quadriplex real-time polymerase chain reaction (PCR) for identifying pneumococcal serotypes, penicillin susceptibility, and resistance markers. Diagn Microbiol Infect Dis 2020; 97:115037. [PMID: 32265073 DOI: 10.1016/j.diagmicrobio.2020.115037] [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] [Received: 01/10/2020] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 01/23/2023]
Abstract
We expanded our current Centers for Disease Control and Prevention triplexed real-time polymerase chain reaction scheme identifying 11 individual serotypes and 10 serogroups to a quadriplex format identifying 34 individual serotypes and 13 small serogroups, 4 antibiotic resistance determinants, pilus targets, and penicillin susceptibility. Newly developed assays are specific for serotypes/serogroups, are sensitive (10 copies/reaction), and further discriminate larger serogroups into individual serotypes or smaller serogroups.
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Kasher M, Roizin H, Cohen A, Jaber H, Mikhailov S, Rubin C, Doron D, Rahav G, Regev-Yochay G. The impact of PCV7/13 on the distribution of carried pneumococcal serotypes and on pilus prevalence; 14 years of repeated cross-sectional surveillance. Vaccine 2020; 38:3591-3599. [DOI: 10.1016/j.vaccine.2020.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/26/2020] [Accepted: 03/05/2020] [Indexed: 11/24/2022]
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Hjálmarsdóttir MÁ, Haraldsson G, Quirk SJ, Haraldsson Á, Erlendsdóttir H, Kristinsson KG. Reduction of antimicrobial resistant pneumococci seven years after introduction of pneumococcal vaccine in Iceland. PLoS One 2020; 15:e0230332. [PMID: 32182260 PMCID: PMC7077842 DOI: 10.1371/journal.pone.0230332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/26/2020] [Indexed: 11/18/2022] Open
Abstract
Background Penicillin non-susceptible (PNSP) and multi-resistant pneumococci have been prevalent in Iceland since early nineties, mainly causing problems in treatment of acute otitis media. The 10-valent protein conjugated pneumococcal vaccine (PHiD-CV) was introduced into the childhood vaccination program in 2011. The aim of the study was to investigate the changes in antimicrobial susceptibility and serotype distribution of penicillin non-susceptible pneumococci (PNSP) in Iceland 2011–2017. Methods and findings All pneumococcal isolates identified at the Landspítali University Hospital in 2011–2017, excluding isolates from the nasopharynx and throat were studied. Susceptibility testing was done according to the EUCAST guidelines using disk diffusion with chloramphenicol, erythromycin, clindamycin, tetracycline, trimethoprim/sulfamethoxazole and oxacillin for PNSP screening. Penicillin and ceftriaxone minimum inhibitory concentrations (MIC) were measured for oxacillin resistant isolates using the E-test. Serotyping was done using latex agglutination and/or multiplex PCR. The total number of pneumococcal isolates that met the study criteria was 1,706, of which 516 (30.2%) were PNSP, and declining with time. PNSP isolates of PHiD-CV vaccine serotypes (VT) were 362/516 (70.2%) declining with time, 132/143 (92.3%) in 2011 and 17/54 (31.5%) in 2017. PNSP were most commonly of serotype 19F, 317/516 isolates declining with time, 124/143 in 2011 and 15/54 in 2017. Their number decreased in all age groups, but mainly in the youngest children. PNSP isolates of non PHiD-CV vaccine serotypes (NVT) were 154/516, increasing with time, 11/14, in 2011 and 37/54 in 2017. The most common emerging NVTs in 2011 and 2017 were 6C, 1/143 and 10/54 respectively. Conclusions PNSP of VTs have virtually disappeared from children with pneumococcal diseases after the initiation of pneumococcal vaccination in Iceland and a clear herd effect was observed. This was mainly driven by a decrease of PNSP isolates belonging to a serotype 19F multi-resistant lineage. However, emerging multi-resistant NVT isolates are of concern.
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Affiliation(s)
- Martha Á. Hjálmarsdóttir
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Clinical Microbiology, Landspitali University Hospital, Reykjavík, Iceland
- BioMedical Centre of the University of Iceland, Reykjavik, Iceland
- * E-mail:
| | - Gunnsteinn Haraldsson
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Clinical Microbiology, Landspitali University Hospital, Reykjavík, Iceland
- BioMedical Centre of the University of Iceland, Reykjavik, Iceland
| | - Sigríður Júlía Quirk
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Clinical Microbiology, Landspitali University Hospital, Reykjavík, Iceland
- BioMedical Centre of the University of Iceland, Reykjavik, Iceland
| | - Ásgeir Haraldsson
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Children´s Hospital Iceland, Landspitali University Hospital, Reykjavík, Iceland
| | - Helga Erlendsdóttir
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Clinical Microbiology, Landspitali University Hospital, Reykjavík, Iceland
| | - Karl G. Kristinsson
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Department of Clinical Microbiology, Landspitali University Hospital, Reykjavík, Iceland
- BioMedical Centre of the University of Iceland, Reykjavik, Iceland
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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: 38] [Impact Index Per Article: 7.6] [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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Pimenta F, Gertz RE, Park SH, Kim E, Moura I, Milucky J, Rouphael N, Farley MM, Harrison LH, Bennett NM, Bigogo G, Feikin DR, Breiman R, Lessa FC, Whitney CG, Rajam G, Schiffer J, da Gloria Carvalho M, Beall B. Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis Strains With Highly Similar cps5 Loci and Antigenic Relatedness to Serotype 5 Pneumococci. Front Microbiol 2019; 9:3199. [PMID: 30671034 PMCID: PMC6332807 DOI: 10.3389/fmicb.2018.03199] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/10/2018] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pneumoniae is a highly impactful bacterial pathogen on a global scale. The principal pneumococcal virulence factor and target of effective vaccines is its polysaccharide capsule, of which there are many structurally distinct forms. Here, we describe four distinct strains of three Mitis group commensal species (Streptococcus infantis, Streptococcus mitis, and Streptococcus oralis) recovered from upper respiratory tract specimens from adults in Kenya and the United States that were PCR-positive for the pneumococcal serotype 5 specific gene, wzy5. For each of the four strains, the 15 genes comprising the capsular polysaccharide biosynthetic gene cluster (cps5) shared the same order found in serotype 5 pneumococci, and each of the serotype 5-specific genes from the serotype 5 pneumococcal reference strain shared 76-99% sequence identity with the non-pneumococcal counterparts. Double-diffusion experiments demonstrated specific reactivity of the non-pneumococcal strains with pneumococcal serotype 5 typing sera. Antiserum raised against S. mitis strain KE67013 specifically reacted with serotype 5 pneumococci for a positive Quellung reaction and stimulated serotype 5 specific opsonophagocytic killing of pneumococci. Four additional commensal strains, identified using PCR serotyping assays on pharyngeal specimens, revealed loci highly homologous to those of pneumococci of serotypes 12F, 15A, 18C, and 33F. These data, in particular the species and strain diversity shown for serotype 5, highlight the existence of a broad non-pneumococcal species reservoir in the upper respiratory tract for the expression of capsular polysaccharides that are structurally related or identical to those corresponding to epidemiologically significant serotypes. Very little is known about the genetic and antigenic capsular diversity among the vast array of commensal streptococcal strains that represent multiple diverse species. The discovery of serotype 5 strains within three different commensal species suggests that extensive capsular serologic overlap exists between pneumococci and other members of the diverse Mitis group. These findings may have implications for our current understanding of naturally acquired immunity to S. pneumoniae and pneumococcal serotype distributions in different global regions. Further characterization of commensal strains carrying homologs of serotype-specific genes previously thought to be specific for pneumococci of known serotypes may shed light on the evolution of these important loci.
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Affiliation(s)
- Fabiana Pimenta
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Robert E Gertz
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - So Hee Park
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Ellie Kim
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Iaci Moura
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jennifer Milucky
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Nadine Rouphael
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Monica M Farley
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Atlanta Veterans Affairs Medical Center, Atlanta GA, United States
| | - Lee H Harrison
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Nancy M Bennett
- Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States
| | - Godfrey Bigogo
- Kenya Medical Research Institute, Nairobi, Kenya.,International Emerging Infections Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Daniel R Feikin
- Kenya Medical Research Institute, Nairobi, Kenya.,International Emerging Infections Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Robert Breiman
- Kenya Medical Research Institute, Nairobi, Kenya.,International Emerging Infections Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Cynthia G Whitney
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gowrisankar Rajam
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jarad Schiffer
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Maria da Gloria Carvalho
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Bernard Beall
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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