1
|
Song Y, Zhao J, Liu W, Li W, Sun Z, Cui Y, Zhang H. Exploring the industrial potential of Lactobacillus delbrueckii ssp. bulgaricus by population genomics and genome-wide association study analysis. J Dairy Sci 2021; 104:4044-4055. [PMID: 33663860 DOI: 10.3168/jds.2020-19467] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/10/2020] [Indexed: 01/26/2023]
Abstract
Lactobacillus delbrueckii ssp. bulgaricus is one of the most commonly used starter cultures for yogurt production. However, how its genetic background affects acid production capacity is unclear. This study investigated the industrial potential of L. delbrueckii ssp. bulgaricus using population genomics and GWAS analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced L. delbrueckii ssp. bulgaricus strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation results with sucrose-fortified reconstituted skim milk revealed a significant association between l-lactate dehydrogenase (lldD; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of L. delbrueckii ssp. bulgaricus by identifying potential targets for further research, development, and use of lactic acid bacteria in the dairy industry.
Collapse
Affiliation(s)
- Yuqin Song
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Weicheng Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing 100071, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China; Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China.
| |
Collapse
|
2
|
Hiller NL, Sá-Leão R. Puzzling Over the Pneumococcal Pangenome. Front Microbiol 2018; 9:2580. [PMID: 30425695 PMCID: PMC6218428 DOI: 10.3389/fmicb.2018.02580] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/09/2018] [Indexed: 12/11/2022] Open
Abstract
The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.
Collapse
Affiliation(s)
- N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA, United States
| | - Raquel Sá-Leão
- Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
- Departamento de Biologia Vegetal, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
3
|
Chang B, Morita M, Lee KI, Ohnishi M. Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections. J Clin Microbiol 2018; 56:e01822-17. [PMID: 29444837 PMCID: PMC5925718 DOI: 10.1128/jcm.01822-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/04/2018] [Indexed: 12/22/2022] Open
Abstract
Streptococcus pneumoniae colonizes the nasopharyngeal mucus in healthy individuals and can cause otitis media, pneumonia, and invasive pneumococcal diseases. In this study, we analyzed S. pneumoniae strains that caused 19 pneumonia episodes in long-term inpatients with severe underlying disease in a hospital during a period of 14 months (from January 2014 to February 2015). Serotyping and whole-genome sequencing analyses revealed that 18 of the 19 pneumonia cases were caused by S. pneumoniae strains belonging to 3 genetically distinct groups: clonal complex 9999 (CC9999), sequence type 282 (ST282), and ST166. The CC9999 and ST282 strains appeared to have emerged separately by a capsule switch from the pandemic PMEN 1 strain (Spain23F-ST81). After all the long-term inpatients were inoculated with the 23-valent pneumococcal polysaccharide vaccine, no other nosocomial pneumonia infections occurred until March 2016.
Collapse
Affiliation(s)
- Bin Chang
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ken-Ichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| |
Collapse
|
4
|
Zhi X, Abdullah IT, Gazioglu O, Manzoor I, Shafeeq S, Kuipers OP, Hiller NL, Andrew PW, Yesilkaya H. Rgg-Shp regulators are important for pneumococcal colonization and invasion through their effect on mannose utilization and capsule synthesis. Sci Rep 2018; 8:6369. [PMID: 29686372 PMCID: PMC5913232 DOI: 10.1038/s41598-018-24910-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 04/05/2018] [Indexed: 01/18/2023] Open
Abstract
Microbes communicate with each other by using quorum sensing (QS) systems and modulate their collective 'behavior' for in-host colonization and virulence, biofilm formation, and environmental adaptation. The recent increase in genome data availability reveals the presence of several putative QS sensing circuits in microbial pathogens, but many of these have not been functionally characterized yet, despite their possible utility as drug targets. To increase the repertoire of functionally characterized QS systems in bacteria, we studied Rgg144/Shp144 and Rgg939/Shp939, two putative QS systems in the important human pathogen Streptococcus pneumoniae. We find that both of these QS circuits are induced by short hydrophobic peptides (Shp) upon sensing sugars found in the respiratory tract, such as galactose and mannose. Microarray analyses using cultures grown on mannose and galactose revealed that the expression of a large number of genes is controlled by these QS systems, especially those encoding for essential physiological functions and virulence-related genes such as the capsular locus. Moreover, the array data revealed evidence for cross-talk between these systems. Finally, these Rgg systems play a key role in colonization and virulence, as deletion mutants of these QS systems are attenuated in the mouse models of colonization and pneumonia.
Collapse
Affiliation(s)
- Xiangyun Zhi
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Iman Tajer Abdullah
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
- Department of Biology, College of Science, University of Kirkuk, Kirkuk, Iraq
| | - Ozcan Gazioglu
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Irfan Manzoor
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sulman Shafeeq
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Peter W Andrew
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK
| | - Hasan Yesilkaya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, LE1 9HN, UK.
| |
Collapse
|
5
|
Bansal S, Yajjala VK, Bauer C, Sun K. IL-1 Signaling Prevents Alveolar Macrophage Depletion during Influenza and Streptococcus pneumoniae Coinfection. THE JOURNAL OF IMMUNOLOGY 2018; 200:1425-1433. [PMID: 29311363 DOI: 10.4049/jimmunol.1700210] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 12/11/2017] [Indexed: 01/17/2023]
Abstract
Influenza and bacterial coinfection is a significant cause of hospitalization and death in humans during influenza epidemics and pandemics. However, the fundamental protective and pathogenic mechanisms involved in this complex virus-host-bacterium interaction remain incompletely understood. In this study, we have developed mild to lethal influenza and Streptococcus pneumoniae coinfection models for comparative analyses of disease pathogenesis. Specifically, wild-type and IL-1R type 1-deficient (Il1r1-/- ) mice were infected with influenza virus and then superchallenged with noninvasive S. pneumoniae serotype 14 (Spn14) or S. pneumoniae serotype 19A (Spn19A). The coinfections were followed by comparative analyses of inflammatory responses and animal protection. We found that resident alveolar macrophages are efficient in the clearance of both pneumococcal serotypes in the absence of influenza infection; in contrast, they are essential for airway control of Spn14 infection but not Spn19A infection. In agreement, TNF-α and neutrophils play a compensatory protective role in secondary bacterial infection associated with Spn19A; however, the essential requirement for alveolar macrophage-mediated clearance significantly enhances the virulence of Spn14 during postinfluenza pneumococcal infection. Furthermore, we show that, although IL-1 signaling is not required for host defense against pneumococcal infection alone, it is essential for sustaining antibacterial immunity during postinfluenza pneumococcal infection, as evidenced by significantly aggravated bacterial burden and animal mortality in Il1r1-/- mice. Mechanistically, we show that through preventing alveolar macrophage depletion, inflammatory cytokine IL-1 signaling is critically involved in host resistance to influenza and pneumococcal coinfection.
Collapse
Affiliation(s)
- Shruti Bansal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900
| | - Vijaya Kumar Yajjala
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900
| | - Christopher Bauer
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900
| | - Keer Sun
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-5900
| |
Collapse
|
6
|
Gene Acquisition by a Distinct Phyletic Group within Streptococcus pneumoniae Promotes Adhesion to the Ocular Epithelium. mSphere 2017; 2:mSphere00213-17. [PMID: 29085912 PMCID: PMC5656748 DOI: 10.1128/msphere.00213-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus pneumoniae (pneumococcus) displays broad tissue tropism and infects multiple body sites in the human host. However, infections of the conjunctiva are limited to strains within a distinct phyletic group with multilocus sequence types ST448, ST344, ST1186, ST1270, and ST2315. In this study, we sequenced the genomes of six pneumococcal strains isolated from eye infections. The conjunctivitis isolates are grouped in a distinct phyletic group together with a subset of nasopharyngeal isolates. The keratitis (infection of the cornea) and endophthalmitis (infection of the vitreous body) isolates are grouped with the remainder of pneumococcal strains. Phenotypic characterization is consistent with morphological differences associated with the distinct phyletic group. Specifically, isolates from the distinct phyletic group form aggregates in planktonic cultures and chain-like structures in biofilms grown on abiotic surfaces. To begin to investigate the association between genotype and epidemiology, we focused on a predicted surface-exposed adhesin (SspB) encoded exclusively by this distinct phyletic group. Phylogenetic analysis of the gene encoding SspB in the context of a streptococcal species tree suggests that sspB was acquired by lateral gene transfer from Streptococcus suis. Furthermore, an sspB deletion mutant displays decreased adherence to cultured cells from the ocular epithelium compared to the isogenic wild-type and complemented strains. Together these findings suggest that acquisition of genes from outside the species has contributed to pneumococcal tissue tropism by enhancing the ability of a subset of strains to infect the ocular epithelium causing conjunctivitis. IMPORTANCE Changes in the gene content of pathogens can modify their ability to colonize and/or survive in different body sites in the human host. In this study, we investigate a gene acquisition event and its role in the pathogenesis of Streptococccus pneumoniae (pneumococcus). Our findings suggest that the gene encoding the predicted surface protein SspB has been transferred from Streptococcus suis (a distantly related streptococcal species) into a distinct set of pneumococcal strains. This group of strains distinguishes itself from the remainder of pneumococcal strains by extensive differences in genomic composition and by the ability to cause conjunctivitis. We find that the presence of sspB increases adherence of pneumococcus to the ocular epithelium. Thus, our data support the hypothesis that a subset of pneumococcal strains has gained genes from neighboring species that enhance their ability to colonize the epithelium of the eye, thus expanding into a new niche.
Collapse
|
7
|
Cuevas RA, Eutsey R, Kadam A, West-Roberts JA, Woolford CA, Mitchell AP, Mason KM, Hiller NL. A novel streptococcal cell-cell communication peptide promotes pneumococcal virulence and biofilm formation. Mol Microbiol 2017; 105:554-571. [PMID: 28557053 DOI: 10.1111/mmi.13721] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/29/2022]
Abstract
Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human respiratory track, where it utilizes cell-cell communication systems to coordinate population-level behaviors. We reasoned that secreted peptides that are highly expressed during infection are pivotal for virulence. Thus, we used in silico pattern searches to define a pneumococcal secretome and analyzed the transcriptome of the clinically important PMEN1 lineage to identify which peptide-encoding genes are highly expressed in vivo. In this study, we characterized virulence peptide 1 (vp1), a highly expressed Gly-Gly peptide-encoding gene in chinchilla middle ear effusions. The vp1 gene is widely distributed across pneumococcus as well as encoded in related species. Studies in the chinchilla model of middle ear infection demonstrated that VP1 is a virulence determinant. The vp1 gene is positively regulated by a transcription factor from the Rgg family and its cognate SHP (short hydrophobic peptide). In vitro data indicated that VP1 promotes increased thickness and biomass for biofilms grown on chinchilla middle ear epithelial cells. Furthermore, the wild-type biofilm is restored with the exogenous addition of synthetic VP1. We conclude that VP1 is a novel streptococcal regulatory peptide that controls biofilm development and pneumococcal pathogenesis.
Collapse
Affiliation(s)
- Rolando A Cuevas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rory Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jacob A West-Roberts
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Carol A Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Aaron P Mitchell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kevin M Mason
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, PA 15211, USA
| |
Collapse
|
8
|
Kadam A, Eutsey RA, Rosch J, Miao X, Longwell M, Xu W, Woolford CA, Hillman T, Motib AS, Yesilkaya H, Mitchell AP, Hiller NL. Promiscuous signaling by a regulatory system unique to the pandemic PMEN1 pneumococcal lineage. PLoS Pathog 2017; 13:e1006339. [PMID: 28542565 PMCID: PMC5436883 DOI: 10.1371/journal.ppat.1006339] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/07/2017] [Indexed: 01/03/2023] Open
Abstract
Streptococcus pneumoniae (pneumococcus) is a leading cause of death and disease in children and elderly. Genetic variability among isolates from this species is high. These differences, often the product of gene loss or gene acquisition via horizontal gene transfer, can endow strains with new molecular pathways, diverse phenotypes, and ecological advantages. PMEN1 is a widespread and multidrug-resistant pneumococcal lineage. Using comparative genomics we have determined that a regulator-peptide signal transduction system, TprA2/PhrA2, was acquired by a PMEN1 ancestor and is encoded by the vast majority of strains in this lineage. We show that TprA2 is a negative regulator of a PMEN1-specific gene encoding a lanthionine-containing peptide (lcpA). The activity of TprA2 is modulated by its cognate peptide, PhrA2. Expression of phrA2 is density-dependent and its C-terminus relieves TprA2-mediated inhibition leading to expression of lcpA. In the pneumococcal mouse model with intranasal inoculation, TprA2 had no effect on nasopharyngeal colonization but was associated with decreased lung disease via its control of lcpA levels. Furthermore, the TprA2/PhrA2 system has integrated into the pneumococcal regulatory circuitry, as PhrA2 activates TprA/PhrA, a second regulator-peptide signal transduction system widespread among pneumococci. Extracellular PhrA2 can release TprA-mediated inhibition, activating expression of TprA-repressed genes in both PMEN1 cells as well as another pneumococcal lineage. Acquisition of TprA2/PhrA2 has provided PMEN1 isolates with a mechanism to promote commensalism over dissemination and control inter-strain gene regulation. Streptococcus pneumoniae (pneumococcus), an important human pathogen, exhibits a dual lifestyle featuring asymptomatic colonization of the host on the one hand as well as infliction of severe local and systemic disease on the other. In pneumococcal strains, differences in gene possession often lead to varied phenotypic outcomes. Epidemiologically, pandemic strains of the PMEN1 lineage show high prevalence in disease as well as carriage, posing an interesting question on the composition and function of the genomic toolkit that leads to their widespread success. Here, we characterize TprA2/PhrA2 sensory system, a genomic region acquired exclusively by the PMEN1 strains. The system consists of a regulator-peptide pair that was horizontally acquired into PMEN1 along with its regulatory circuitry. The regulatory peptide PhrA2 is receptive to cell density of PMEN1 cells and is an example of elegant communication signaling between bacterial cells. The regulatory influence of PhrA2 extends beyond PMEN1 cells such that it controls genes of a widespread signaling system and virulence regulon in non-PMEN1 strains. This work contributes to the knowledge of peptide-communication signals in pneumococcus and further adds a novel mechanism by which an ecologically successful linage may modify the transcriptomic and functional landscape of a multi-strain pneumococcal community.
Collapse
Affiliation(s)
- Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory A. Eutsey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jason Rosch
- Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Xinyu Miao
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mark Longwell
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania, United States of America
| | - Wenjie Xu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Carol A. Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Todd Hillman
- Pittsburgh Ear Associates, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Anfal Shakir Motib
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom
| | - Hasan Yesilkaya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom
| | - Aaron P. Mitchell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
9
|
Sheppard C, Fry NK, Mushtaq S, Woodford N, Reynolds R, Janes R, Pike R, Hill R, Kimuli M, Staves P, Doumith M, Harrison T, Livermore DM. Rise of multidrug-resistant non-vaccine serotype 15A Streptococcus pneumoniae in the United Kingdom, 2001 to 2014. ACTA ACUST UNITED AC 2017; 21:30423. [PMID: 28006650 PMCID: PMC5291132 DOI: 10.2807/1560-7917.es.2016.21.50.30423] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 08/17/2016] [Indexed: 11/20/2022]
Abstract
Conjugate vaccines have reduced pneumococcal disease in vaccinated children and unvaccinated adults, but non-vaccine serotypes are of concern, particularly if antibiotic resistant. We reviewed Streptococcus pneumoniae collected via: (i) the British Society for Antimicrobial Chemotherapy (BSAC) surveillances from 2001–2014; (ii) Public Health England’s (PHE) invasive isolate surveillance from 2005–2014 and (iii) referral to PHE for resistance investigation from 2005–2014. Serotype 15A increased in all series, with many representatives showing triple resistance to macrolides, tetracyclines and penicillin. 15A was consistently among the 10 most prevalent serotypes from 2011 in PHE and BSAC invasive isolate/bacteraemia surveillance but never previously; 26–33% of these invasive 15A isolates had triple resistance. BSAC respiratory isolates were only serotyped in 2013/14 and 2014/15 (October to September); 15A was most prevalent serotype in both periods, comprising 9–11% of isolates, 38–48% of them with triple resistance. Serotype 15A represented 0–4% of S. pneumoniae referred to PHE for reference investigation annually until 2008 but rose to 29% (2013) and 32% (2014). Almost all multidrug-resistant 15A isolates were sequence type (ST) 63 variants, whereas susceptible 15A isolates were clonally diverse. The rise of serotype 15A suggests that pneumococcal conjugate vaccines will need ongoing adaptation.
Collapse
Affiliation(s)
- Carmen Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, London, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health England, London, United Kingdom
| | - Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Rosy Reynolds
- Southmead Hospital, Bristol, United Kingdom.,British Society for Antimicrobial Chemotherapy, Birmingham, United Kingdom
| | | | - Rachel Pike
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Robert Hill
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Maimuna Kimuli
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Peter Staves
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - Timothy Harrison
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom
| | - David M Livermore
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, London, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| |
Collapse
|
10
|
Wen Z, Liu Y, Qu F, Zhang JR. Allelic Variation of the Capsule Promoter Diversifies Encapsulation and Virulence In Streptococcus pneumoniae. Sci Rep 2016; 6:30176. [PMID: 27465908 PMCID: PMC4964562 DOI: 10.1038/srep30176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/28/2016] [Indexed: 02/05/2023] Open
Abstract
The polysaccharide capsule is the major virulence factor of Streptococcus pneumoniae (pneumococcus), a major human pathogen. The sequences in the promoter and coding regions of the capsule gene locus undergo extensive variations through the natural transformation-mediated horizontal gene transfer. The sequence variations in the coding region have led to at least 97 capsular serotypes. However, it remains unclear whether the sequence polymorphisms in the promoter region have any biological significance. In this study, we determined the sequences of the cps promoter region from 225 invasive pneumococcal isolates, and identified modular composition and remarkable inter-strain sequence variations in this region. The strain-to strain variations in the cps promoter are characterized by diversity in sequence and size, mosaic combinations of nucleotide polymorphisms and sequence modules, selective preservation of the sequence combinations, and promiscuous assortments of the sequences between the promoter and coding regions. Isogenic pneumococci carrying allelic variants of the cps promoter displayed significant differences in the transcription of the capsule genes, capsule production, adhesion to host epithelial cells, anti-phagocytosis and virulence in mouse bacteremia model. This study has thus indicated that the sequence polymorphisms in the cps promoter represent a novel mechanism for fine-tuning the level of encapsulation and virulence among S. pneumoniae strains.
Collapse
Affiliation(s)
- Zhensong Wen
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yanni Liu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fen Qu
- The Center of Clinical Diagnosis, 302 Hospital of PLA, Beijing, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China.,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| |
Collapse
|
11
|
Kawaguchiya M, Urushibara N, Kobayashi N. Multidrug Resistance in Non-PCV13 Serotypes of Streptococcus pneumoniae in Northern Japan, 2014. Microb Drug Resist 2016; 23:206-214. [PMID: 27257915 DOI: 10.1089/mdr.2016.0054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Since the implementation of routine PCV13 immunization in Japan, nonvaccine serotypes (NVTs) have been increasing among clinical isolates of Streptococcus pneumoniae. In this study, susceptibility to 18 antibiotics was tested for all the 231 isolates with NVTs, which were collected from children <16 years of age in northern Japan in 2014 (July-November). High resistance rates were observed for macrolides (>90.9%), tetracycline (91.3%), and clindamycin (75.3%), while penicillin (PEN) nonsusceptibility (PNSP; MIC ≥0.12 μg/ml) was detected in 42.9% of the pneumococci [39.4%; PEN-intermediate S. pneumoniae (PISP), 3.5%; PEN-resistant S. pneumoniae (PRSP)]. All serotype 15A isolates were PRSP (MIC, ≥2 μg/ml) or PISP, and PNSP was prevalent in also serotypes 23A (96.9%), 6C (41%), and 35B (33.3%). Overall, 42.0% of the isolates showed multidrug resistance (MDR). Sequence types (STs) determined for 20 PNSP isolates with NVTs were ST63 (15A), STs 242 or 5832 (6C), STs 338 or 5242 (23A), and ST558 (35B). All the PNSP isolates possessed tet(M), and erm(B) or mefA(A/E), and 70% of them were gPRSP having three altered genes pbp1a, pbp2x, and pbp2b. Among alterations in transpeptidase-coding region of penicillin-binding proteins (PBPs), two substitutions of T371S in the STMK motif and TSQF574-577NTGY in PBP1a were common to all PRSP isolates. The present study showed the spread of PNSP in NVTs 15A, 23A, 6C, and 35B, and the emergence of the MDR international clone Sweden15A-ST63 in northern Japan.
Collapse
Affiliation(s)
- Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine , Sapporo, Japan
| |
Collapse
|
12
|
Grau I, Ardanuy C, Cubero M, Benitez MA, Liñares J, Pallares R. Declining mortality from adult pneumococcal infections linked to children's vaccination. J Infect 2016; 72:439-49. [PMID: 26868606 DOI: 10.1016/j.jinf.2016.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 01/14/2016] [Accepted: 01/22/2016] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To determine changes in mortality among adults with invasive pneumococcal disease (IPD) after introducing pneumococcal conjugate vaccines (PCVs) in children. METHODS An active surveillance of adults with culture-proven IPD in Barcelona. Serotype-specific mortality and rates of disease and death were analysed in three periods: baseline (1994-2001), PCV7 (2002-2009) and PCV13 (2010-2013). RESULTS Overall, IPD caused by PCV7 serotypes was associated with increased case fatality rate (24 percent). In patients 18-64 years (baseline vs. PCV7 vs. PCV13 periods), case fatality rate from IPD decreased (22 vs.14 vs. 12 percent), and it was associated with a decline in PCV7 serotypes (3.56 vs. 2.80 vs. 1.49 cases/10(5) person-years) and in PCV7 serotypes-specific death (0.74 vs. 0.53 vs. 0.09 deaths/10(5) person-years). In patients ≥65 years, case fatality rate did not change (24 vs. 22 vs. 24 percent); however, there was a decline in PCV7 serotypes-specific death (4.94 vs. 3.58 vs. 2.45 deaths/10(5) person-years), and an increase in non-PCV serotypes-specific death (2.55 vs. 3.70 vs. 4.09 deaths/10(5) person-years). CONCLUSIONS The use of PCVs for children was associated with a reduction of mortality from IPD in adults 18-64 years, through the indirect effect of herd protection. In older adults, age-related factors could play a role in IPD mortality.
Collapse
Affiliation(s)
- Imma Grau
- Infectious Diseases Department, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, Barcelona, Spain.
| | - Carmen Ardanuy
- Microbiology Department, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, Barcelona, Spain.
| | - Meritxell Cubero
- Microbiology Department, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, Barcelona, Spain.
| | - Miguel A Benitez
- Microbiology Department, Hospital Moises Broggi, Sant Joan Despi, Barcelona, Spain.
| | - Josefina Liñares
- Microbiology Department, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, Barcelona, Spain.
| | - Roman Pallares
- Infectious Diseases Department, Hospital Bellvitge, Ciberes, Idibell, University of Barcelona, Barcelona, Spain.
| |
Collapse
|
13
|
Frazão N, Hermans P, van Selm S, Sá-Leão R, de Lencastre H, Tomasz A, Diavatopoulos D. Ability of Antibiotic-Resistant Nonvaccine-Type Pneumococcal Clones to Cause Otitis Media in an Infant Mouse Model of Pneumococcal-Influenza Virus Coinfection. Microb Drug Resist 2015; 22:97-101. [PMID: 26366835 DOI: 10.1089/mdr.2015.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The introduction of the 7-valent pneumococcal conjugate vaccine in Portugal resulted in reduced carriage in children by vaccine-type strains and an increased carriage of three major antibiotic-resistant clones, ST2191, ST276, and ST63 expressing capsules 6A, 19A, and 15A, respectively. Pneumococcal otitis media (OM), a frequent infection among preschool age children, is often associated with viral coinfection. To evaluate the ability of these three antibiotic-resistant clones to cause disease, we used an infant mouse model of influenza virus pneumococcal coinfection. The 6A and 19A clonal types induced OM, while 15A induced pneumococcal pneumonia and bloodstream infection, suggesting potential for invasive disease.
Collapse
Affiliation(s)
- Nelson Frazão
- 1 Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa , Oeiras, Portugal .,2 Laboratory of Microbiology, The Rockefeller University , New York City, New York
| | - Peter Hermans
- 3 Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center , Nijmegen, the Netherlands .,4 Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Saskia van Selm
- 3 Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center , Nijmegen, the Netherlands .,4 Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center , Nijmegen, the Netherlands
| | - Raquel Sá-Leão
- 5 Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa , Oeiras, Portugal
| | - Hermínia de Lencastre
- 1 Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa , Oeiras, Portugal .,2 Laboratory of Microbiology, The Rockefeller University , New York City, New York
| | - Alexander Tomasz
- 2 Laboratory of Microbiology, The Rockefeller University , New York City, New York
| | - Dimitri Diavatopoulos
- 3 Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center , Nijmegen, the Netherlands .,4 Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Center , Nijmegen, the Netherlands
| |
Collapse
|