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Phillips ZN, Jennison AV, Whitby PW, Stull TL, Staples M, Atack JM. Examination of phase-variable haemoglobin-haptoglobin binding proteins in Non-typeable Haemophilus influenzae reveals a diverse distribution of multiple variants. FEMS Microbiol Lett 2022; 369:6648706. [PMID: 35867873 PMCID: PMC9341677 DOI: 10.1093/femsle/fnac064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/14/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) is a major human pathogen for which there is no globally licensed vaccine. NTHi has a strict growth requirement for iron and encodes several systems to scavenge elemental iron and heme from the host. An effective NTHi vaccine would target conserved, essential surface factors, such as those involved in iron acquisition. Haemoglobin–haptoglobin binding proteins (Hgps) are iron-uptake proteins localized on the outer-membrane of NTHi. If the Hgps are to be included as components of a rationally designed subunit vaccine against NTHi, it is important to understand their prevalence and diversity. Following analysis of all available Hgp sequences, we propose a standardized grouping method for Hgps, and demonstrate increased diversity of these proteins than previously determined. This analysis demonstrated that genes encoding variants HgpB and HgpC are present in all strains examined, and almost 40% of strains had a duplicate, nonidentical hgpB gene. Hgps are also phase-variably expressed; the encoding genes contain a CCAA(n) simple DNA sequence repeat tract, resulting in biphasic ON–OFF switching of expression. Examination of the ON–OFF state of hgpB and hgpC genes in a collection of invasive NTHi isolates demonstrated that 58% of isolates had at least one of hgpB or hgpC expressed (ON). Varying expression of a diverse repertoire of hgp genes would provide strains a method of evading an immune response while maintaining the ability to acquire iron via heme. Structural analysis of Hgps also revealed high sequence variability at the sites predicted to be surface exposed, demonstrating a further mechanism to evade the immune system—through varying the surface, immune-exposed regions of the membrane anchored protein. This information will direct and inform the choice of candidates to include in a vaccine against NTHi.
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Affiliation(s)
- Zachary N Phillips
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Amy V Jennison
- Queensland Department of Health, Public Health Microbiology, Forensic and Scientific Services, Brisbane, Queensland, Australia
| | | | | | - Megan Staples
- Queensland Department of Health, Public Health Microbiology, Forensic and Scientific Services, Brisbane, Queensland, Australia
| | - John M Atack
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.,School of Environment and Science, Griffith University, Gold Coast, Queensland, Australia
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Osman KL, Jefferies JM, Woelk CH, Cleary DW, Clarke SC. The adhesins of non-typeable Haemophilus influenzae. Expert Rev Anti Infect Ther 2018; 16:187-196. [PMID: 29415569 DOI: 10.1080/14787210.2018.1438263] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen of the respiratory tract and the greatest contributor to invasive Haemophilus disease. Additionally, in children, NTHi is responsible for the majority of otitis media (OM) which can lead to chronic infection and hearing loss. In adults, NTHi infection in the lungs is responsible for the onset of acute exacerbations in chronic obstructive pulmonary disease (COPD). Unfortunately, there is currently no vaccine available to protect against NTHi infections. Areas covered: NTHi uses an arsenal of adhesins to colonise the respiratory epithelium. The adhesins also have secondary roles that aid in the virulence of NTHi, including mechanisms that avoid immune clearance, adjust pore size to avoid antimicrobial destruction, form micro-colonies and invoke phase variation for protein mediation. Bacterial adhesins can also be ideal antigens for subunit vaccine design due to surface exposure and immunogenic capabilities. Expert commentary: The host-pathogen interactions of the NTHi adhesins are not fully investigated. The relationship between adhesins and the extracellular matrix (ECM) play a part in the success of NTHi colonisation and virulence by immune evasion, migration and biofilm development. Further research into these immunogenic proteins would further our understanding and enable a basis for better combatting NTHi disease.
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Affiliation(s)
- Karen L Osman
- a Faulty of Medicine , University of Southampton , Southampton , UK
| | | | - Christopher H Woelk
- a Faulty of Medicine , University of Southampton , Southampton , UK.,b Merck Exploratory Science Center , Merck Research Laboratories , Cambridge , MA , USA
| | - David W Cleary
- a Faulty of Medicine , University of Southampton , Southampton , UK.,c Faculty of Medicine and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK.,d NIHR Southampton Biomedical Research Centre , University Hospital Southampton Foundation NHS Trust , Southampton SO16 6YD , UK
| | - Stuart C Clarke
- a Faulty of Medicine , University of Southampton , Southampton , UK.,c Faculty of Medicine and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK.,d NIHR Southampton Biomedical Research Centre , University Hospital Southampton Foundation NHS Trust , Southampton SO16 6YD , UK.,e Global Health Research Institute , University of Southampton , Southampton SO17 1BJ , UK
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Singh NK, Kunde DA, Tristram SG. Inability of Haemophilus haemolyticus to invade respiratory epithelial cells in vitro. J Med Microbiol 2016; 65:1341-1342. [PMID: 27624822 DOI: 10.1099/jmm.0.000349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Neeraj Kumar Singh
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Dale A Kunde
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Stephen G Tristram
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
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Choby JE, Skaar EP. Heme Synthesis and Acquisition in Bacterial Pathogens. J Mol Biol 2016; 428:3408-28. [PMID: 27019298 PMCID: PMC5125930 DOI: 10.1016/j.jmb.2016.03.018] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 02/06/2023]
Abstract
Bacterial pathogens require the iron-containing cofactor heme to cause disease. Heme is essential to the function of hemoproteins, which are involved in energy generation by the electron transport chain, detoxification of host immune effectors, and other processes. During infection, bacterial pathogens must synthesize heme or acquire heme from the host; however, host heme is sequestered in high-affinity hemoproteins. Pathogens have evolved elaborate strategies to acquire heme from host sources, particularly hemoglobin, and both heme acquisition and synthesis are important for pathogenesis. Paradoxically, excess heme is toxic to bacteria and pathogens must rely on heme detoxification strategies. Heme is a key nutrient in the struggle for survival between host and pathogen, and its study has offered significant insight into the molecular mechanisms of bacterial pathogenesis.
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Affiliation(s)
- Jacob E Choby
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA; Tennessee Valley Healthcare System, U.S. Department of Veterans Affairs, Nashville, TN, USA.
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Shahini Shams Abadi M, Siadat SD, Vaziri F, Davari M, Fateh A, Pourazar S, Abdolrahimi F, Ghazanfari M. Distribution and Diversity of hmw1A Among Invasive Nontypeable Haemophilus influenzae Isolates in Iran. Avicenna J Med Biotechnol 2016; 8:99-102. [PMID: 27141269 PMCID: PMC4842248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND The pathogenesis of nontypeable Haemophilus influenzae (NTHi) begins with adhesion to the rhinopharyngeal mucosa. Almost 38-80% of NTHi clinical isolates produce proteins that belong to the High Molecular Weight (HMW) family of adhesins, which are believed to facilitate colonization. METHODS In the present study, the prevalence of hmwA, which encodes the HMW adhesin, was determined for a collection of 32 NTHi isolates. Restriction Fragment Length Polymorphism (RFLP) was performed to advance our understanding of hmwA binding sequence diversity. RESULTS The results demonstrated that hmwA was detected in 61% of NTHi isolates. According to RFLP, isolates were divided into three groups. CONCLUSION Based on these observations, it is hypothesized that some strains of nontypeable Haemophilus influenzae infect some specific areas more than other parts.
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Affiliation(s)
| | - Seyed Davar Siadat
- Corresponding author: Seyed Davar Siadat, Ph.D., Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran, Tel: +98 21 66953311, E-mail:
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Stevens MRE, Luo TL, Vornhagen J, Jakubovics NS, Gilsdorf JR, Marrs CF, Møretrø T, Rickard AH. Coaggregation occurs between microorganisms isolated from different environments. FEMS Microbiol Ecol 2015; 91:fiv123. [DOI: 10.1093/femsec/fiv123] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2015] [Indexed: 11/12/2022] Open
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Gilsdorf JR. What the pediatrician should know about non-typeable Haemophilus influenzae. J Infect 2015; 71 Suppl 1:S10-4. [PMID: 25917803 DOI: 10.1016/j.jinf.2015.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2015] [Indexed: 11/25/2022]
Abstract
Non-typeable Haemophilus influenzae (NTHi) live exclusively in the pharynges of humans and are increasingly recognized as pathogens that cause both localized infections of the respiratory tract (middle ear spaces, sinuses, and bronchi) and systemic infections such as bacteraemia and pneumonia. Only one vaccine antigen of NTHi, Protein D, has been extensively studied in humans and its efficacy in preventing NTHi otitis media is modest. Recent genetic analyses reveal that NTHi are closely related to Haemophilus haemolyticus (Hh), previously thought to be a non-pathogenic commensal of the pharynx. This review discusses the differences between the pathogenic potential of encapsulated and non-typeable Hi. In addition, information on the lifestyles and bacterial characteristics of NTHi and Hh as they pertain to their pathogenic capacities and the value of the Haemophilus taxonomy to clinicians are presented. Further, the epidemiology and mechanisms of NTHi antibiotic resistance, which include production of β-lactamase and alterations of penicillin-binding protein 3, are reviewed, as are the challenges of vaccine antigen discovery in NTHi.
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Affiliation(s)
- Janet R Gilsdorf
- D5101 Medical Professional Building SPC 5718, Ann Arbor, MI 48109-5718, United States.
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Comparative Profile of Heme Acquisition Genes in Disease-Causing and Colonizing Nontypeable Haemophilus influenzae and Haemophilus haemolyticus. J Clin Microbiol 2015; 53:2132-7. [PMID: 25903577 DOI: 10.1128/jcm.00345-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/16/2015] [Indexed: 02/07/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHI) are Gram-negative bacteria that colonize the human pharynx and can cause respiratory tract infections, such as acute otitis media (AOM). Since NTHI require iron from their hosts for aerobic growth, the heme acquisition genes may play a significant role in avoiding host nutritional immunity and determining virulence. Therefore, we employed a hybridization-based technique to compare the prevalence of five heme acquisition genes (hxuA, hxuB, hxuC, hemR, and hup) between 514 middle ear strains from children with AOM and 235 throat strains from healthy children. We also investigated their prevalences in 148 Haemophilus haemolyticus strains, a closely related species that colonizes the human pharynx and is considered to be nonpathogenic. Four out of five genes (hxuA, hxuB, hxuC, and hemR) were significantly more prevalent in the middle ear strains (96%, 100%, 100%, and 97%, respectively) than in throat strains (80%, 92%, 93%, and 85%, respectively) of NTHI, suggesting that strains possessing these genes have a virulence advantage over those lacking them. All five genes were dramatically more prevalent in NTHI strains than in H. haemolyticus, with 91% versus 9% hxuA, 98% versus 11% hxuB, 98% versus 11% hxuC, 93% versus 20% hemR, and 97% versus 34% hup, supporting their potential role in virulence and highlighting their possibility to serve as biomarkers to distinguish H. influenzae from H. haemolyticus. In summary, this study demonstrates that heme acquisition genes are more prevalent in disease-causing NTHI strains isolated from the middle ear than in colonizing NTHI strains and H. haemolyticus isolated from the pharynx.
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Hinz R, Zautner AE, Hagen RM, Frickmann H. Difficult identification of Haemophilus influenzae, a typical cause of upper respiratory tract infections, in the microbiological diagnostic routine. Eur J Microbiol Immunol (Bp) 2015; 5:62-7. [PMID: 25883794 PMCID: PMC4397848 DOI: 10.1556/eujmi-d-14-00033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022] Open
Abstract
Haemophilus influenzae is a key pathogen of upper respiratory tract infections. Its reliable discrimination from nonpathogenic Haemophilus spp. is necessary because merely colonizing bacteria are frequent at primarily unsterile sites. Due to close phylogenetic relationship, it is not easy to discriminate H. influenzae from the colonizer Haemophilus haemolyticus. The frequency of H. haemolyticus isolations depends on factors like sampling site, patient condition, and geographic region. Biochemical discrimination has been shown to be nonreliable. Multiplex PCR including marker genes like sodC, fucK, and hpd or sequencing of the 16S rRNA gene, the P6 gene, or multilocus-sequence-typing is more promising. For the diagnostic routine, such techniques are too expensive and laborious. If available, matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry is a routine-compatible option and should be used in the first line. However, the used database should contain well-defined reference spectra, and the spectral difference between H. influenzae and H. haemolyticus is small. Fluorescence in-situ hybridization is an option for less well-equipped laboratories, but the available protocol will not lead to conclusive results in all instances. It can be used as a second line approach. Occasional ambiguous results have to be resolved by alternative molecular methods like 16S rRNA gene sequencing.
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10
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LaCross NC, Marrs CF, Gilsdorf JR. Otitis media associated polymorphisms in the hemin receptor HemR of nontypeable Haemophilus influenzae. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2014; 26:47-57. [PMID: 24820341 PMCID: PMC4499511 DOI: 10.1016/j.meegid.2014.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 04/15/2014] [Accepted: 05/02/2014] [Indexed: 02/01/2023]
Abstract
Nontypeable Haemophilus influenzae (NTHi) colonize the human pharynx asymptomatically, and are also an important cause of otitis media (OM). Previous studies have demonstrated that some genes are more prevalent in OM-causing NTHi strains than in commensal strains, suggesting a role in virulence. These studies, however, are unable to investigate the possible associations between gene polymorphisms and disease. This study examined amino acid polymorphisms and sequence diversity in a potential virulence gene, the hemin receptor hemR, from a previously characterized NTHi strain collection containing both commensal and OM organisms to identify possible associations between the polymorphisms and otitis media. The full open reading frame of hemR was sequenced from a total of 146 NTHi isolates, yielding a total of 47 unique HemR amino acid sequences. The predicted structure of HemR showed substantial similarity to a class of monomeric TonB dependent, ligand-gated channels involved in iron acquisition in other gram negative bacteria. Fifteen amino acid polymorphisms were significantly more prevalent at the 90% confidence level among commensal compared to OM isolates. Upon controlling for the confounding effect of population structure, over half of the polymorphism-otitis media relationships lost statistical significance, emphasizing the importance of assessing the effect of population structure in association studies. The seven polymorphisms that retained significance were dispersed throughout the protein in various functional and structural domains, including the signal peptide, N-terminal plug domain, and intra- and extracellular loops. The alternate amino acid of only one of these seven polymorphisms was more common among OM isolates, demonstrating a strong trend toward the consensus sequence among disease causing NTHi. We hypothesize that variability at these positions in HemR may result in a reduced ability to acquire iron, rendering NTHi with such versions of the gene less fit for survival in the middle ear environment.
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Affiliation(s)
- Nathan C LaCross
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.
| | - Carl F Marrs
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Janet R Gilsdorf
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Puig C, Marti S, Fleites A, Trabazo R, Calatayud L, Liñares J, Ardanuy C. Oropharyngeal colonization by nontypeable Haemophilus influenzae among healthy children attending day care centers. Microb Drug Resist 2014; 20:450-5. [PMID: 24716536 DOI: 10.1089/mdr.2013.0186] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Haemophilus influenzae colonizes the upper respiratory tract and can spread causing otitis and sinusitis. This work aimed to study the oropharyngeal carriage rate in healthy <5-year-old children attending day care centers in Oviedo, Spain in two consecutive years (January to March 2004-2005). The carriage rate was 42% (400/960) and highly variable among centers (range, 12% to 83%). Isolates were mainly identified as nontypeable H. influenzae (NTHi, 99%). Epidemiologically, 127 different genotypes were identified by PFGE with a minimum of two genotypes per center. One hundred fourteen children (12%) were included in both studies and none of them harbored the same strain over a period of time. The isolates only showed resistance to cotrimoxazol and ampicillin, presenting a shift in the level of ampicillin reduced susceptibility, showing a predominance of PBP3 mutations in 2004 and a predominance of β-lactamase production in 2005. This study proved the great genetic variability of NTHi isolates that present similar genotypic patterns in both years with no long-term carriage of the same strain.
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Affiliation(s)
- Carmen Puig
- 1 Microbiology Department, Hospital Universitari de Bellvitge, University of Barcelona , IDIBELL, Barcelona, Spain
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Nørskov-Lauritsen N. Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev 2014; 27:214-40. [PMID: 24696434 PMCID: PMC3993099 DOI: 10.1128/cmr.00103-13] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.
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Su YC, Resman F, Hörhold F, Riesbeck K. Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f. BMC Genomics 2014; 15:38. [PMID: 24438474 PMCID: PMC3928620 DOI: 10.1186/1471-2164-15-38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif. RESULTS The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi. CONCLUSIONS The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.
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Affiliation(s)
| | | | | | - Kristian Riesbeck
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
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Geelen TH, Gaajetaan GR, Wouters EF, Rohde GG, Franssen FM, Grauls GE, Stobberingh EE, Bruggeman CA, Stassen FR. The host immune response contributes to Haemophilus influenzae virulence. Respir Med 2013; 108:144-52. [PMID: 24011804 DOI: 10.1016/j.rmed.2013.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/25/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND There is compelling evidence that infections with non-typeable Haemophilus influenzae (NTHi) are associated with exacerbations in COPD patients. However, NTHi has also been isolated frequently during clinically stable disease. In this study we tested the hypothesis that genetically distinct NTHi isolates obtained from COPD patients differ in virulence which could account for dissimilarities in the final outcome of an infection (stable vs. exacerbation). RESULTS NTHi isolates (n = 32) were obtained from stable COPD patients, or during exacerbations. Genetically divergent NTHi isolates were selected and induction of inflammation was assessed as an indicator of virulence using different in vitro models. Despite marked genomic differences among NTHi isolates, in vitro studies could not distinguish between NTHi isolates based on their inflammatory capacities. Alternatively, when using a whole blood assay results demonstrated marked inter-, but not intra-individual differences in cytokine release between healthy volunteers irrespective of the origin of the NTHi isolate used. CONCLUSION Results suggest that the individual immune reactivity might be an important predictor for the clinical outcome (exacerbation vs. no exacerbation) following NTHi infection.
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Affiliation(s)
- Tanja H Geelen
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
| | - Giel R Gaajetaan
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
| | - Emiel F Wouters
- Department of Respiratory Medicine, NUTRIM, Maastricht University Medical Centre, Maastricht, The Netherlands; Program Development Centre, CIRO+, Horn, The Netherlands.
| | - Gernot G Rohde
- Department of Respiratory Medicine, NUTRIM, Maastricht University Medical Centre, Maastricht, The Netherlands.
| | | | - Gert E Grauls
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
| | - Ellen E Stobberingh
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
| | - Cathrien A Bruggeman
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
| | - Frank R Stassen
- Department of Medical Microbiology, NUTRIM, Maastricht University Medical Centre, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
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Low occurrence of ‘non-haemolytic Haemophilus haemolyticus’ misidentified as Haemophilus influenzae in cystic fibrosis respiratory specimens, and frequent recurrence of persistent H. influenzae clones despite antimicrobial treatment. Int J Med Microbiol 2012. [DOI: 10.1016/j.ijmm.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Zhang L, Xie J, Patel M, Bakhtyar A, Ehrlich GD, Ahmed A, Earl J, Marrs CF, Clemans D, Murphy TF, Gilsdorf JR. Nontypeable Haemophilus influenzae genetic islands associated with chronic pulmonary infection. PLoS One 2012; 7:e44730. [PMID: 22970300 PMCID: PMC3435294 DOI: 10.1371/journal.pone.0044730] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae (Hi) colonizes the human respiratory tract and is an important pathogen associated with chronic obstructive pulmonary disease (COPD). Bacterial factors that interact with the human host may be important in the pathogenesis of COPD. These factors, however, have not been well defined. The overall goal of this study was to identify bacterial genetic elements with increased prevalence among H. influenzae strains isolated from patients with COPD compared to those isolated from the pharynges of healthy individuals. Methodology/Principal Findings Four nontypeable H. influenzae (NTHi) strains, two isolated from the airways of patients with COPD and two from a healthy individual, were subjected to whole genome sequencing using 454 FLX Titanium technology. COPD strain-specific genetic islands greater than 500 bp in size were identified by in silico subtraction. Open reading frames residing within these islands include known Hi virulence genes such as lic2b, hgbA, iga, hmw1 and hmw2, as well as genes encoding urease and other enzymes involving metabolic pathways. The distributions of seven selected genetic islands were assessed among a panel of 421 NTHi strains of both disease and commensal origins using a Library-on-a-Slide high throughput dot blot DNA hybridization procedure. Four of the seven islands screened, containing genes that encode a methyltransferase, a dehydrogenase, a urease synthesis enzyme, and a set of unknown short ORFs, respectively, were more prevalent in COPD strains than in colonizing strains with prevalence ratios ranging from 1.21 to 2.85 (p≤0.0002). Surprisingly, none of these sequences show increased prevalence among NTHi isolated from the airways of patients with cystic fibrosis. Conclusions/Significance Our data suggest that specific bacterial genes, many involved in metabolic functions, are associated with the ability of NTHi strains to survive in the lower airways of patients with COPD.
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Affiliation(s)
- Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America.
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Tristram SG, Franks LR, Harvey GL. Sequences of small blaTEM-encoding plasmids in Haemophilus influenzae and description of variants falsely negative for blaTEM by PCR. J Antimicrob Chemother 2012; 67:2621-5. [PMID: 22782486 DOI: 10.1093/jac/dks264] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To characterize an unidentified β-lactamase and associated genetic background in a bla(TEM) and bla(ROB) PCR-negative Haemophilus influenzae isolate, and characterize small bla(TEM)-encoding plasmids in a collection of H. influenzae. METHODS The unidentified β-lactamase gene was identified by cloning and sequencing the encoding plasmid. Strains with small bla(TEM) plasmids were identified using negative PCR for integrative conjugative elements, but positive bla(TEM) PCR; plasmids from selected isolates were sequenced. PCR for rep and divergent bla(TEM) were evaluated for detecting small plasmids on selected H. influenzae isolates. RESULTS Small plasmids (4.8-5.5 kb) encoding bla(TEM) appear to be associated with remnants of Tn2 on a conserved plasmid core. The unidentified β-lactamase was actually a TEM-1, with negative bla(TEM) PCR associated with a previously unrecognized deletion of bp 1-27 of bla(TEM) (Sutcliffe numbering) associated with a larger deletion within Tn2. This deletion was found in other isolates and may be more common than previously thought. PCR for the conserved rep gene appears useful for screening for small bla(TEM)-encoding plasmids or associated cryptic plasmids in H. influenzae. CONCLUSIONS Small bla(TEM)-encoding plasmids in H. influenzae appear relatively conserved, but require further study to confirm this. PCR associated with the rep gene may be useful for studying these small plasmids. A deletion in part of bla(TEM) in some strains may interfere with some PCRs; therefore, care should be taken with primer selection or design and, preferably, regions within the open reading frame should be targeted.
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Affiliation(s)
- Stephen G Tristram
- School of Human Life Sciences, University of Tasmania, Launceston, Tasmania, Australia.
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Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 2012; 194:3922-37. [PMID: 22609915 DOI: 10.1128/jb.00056-12] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.
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A clonal group of nontypeable Haemophilus influenzae with two IgA proteases is adapted to infection in chronic obstructive pulmonary disease. PLoS One 2011; 6:e25923. [PMID: 21998721 PMCID: PMC3187821 DOI: 10.1371/journal.pone.0025923] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/13/2011] [Indexed: 11/19/2022] Open
Abstract
Strains of nontypeable Haemophilus influenzae show enormous genetic heterogeneity and display differential virulence potential in different clinical settings. The igaB gene, which encodes a newly identified IgA protease, is more likely to be present in the genome of COPD strains of H. influenzae than in otitis media strains. Analysis of igaB and surrounding sequences in the present study showed that H. influenzae likely acquired igaB from Neisseria meningitidis and that the acquisition was accompanied by a ~20 kb genomic inversion that is present only in strains that have igaB. As part of a long running prospective study of COPD, molecular typing of H. influenzae strains identified a clonally related group of strains, a surprising observation given the genetic heterogeneity that characterizes strains of nontypeable H. influenzae. Analysis of strains by 5 independent methods (polyacrylamide gel electrophoresis, multilocus sequence typing, igaB gene sequences, P2 gene sequences, pulsed field gel electrophoresis) established the clonal relationship among the strains. Analysis of 134 independent strains collected prospectively from a cohort of adults with COPD demonstrated that ~10% belonged to the clonal group. We conclude that a clonally related group of strains of nontypeable H. influenzae that has two IgA1 protease genes (iga and igaB) is adapted for colonization and infection in COPD. This observation has important implications in understanding population dynamics of H. influenzae in human infection and in understanding virulence mechanisms specifically in the setting of COPD.
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Martí-Lliteras P, López-Gómez A, Mauro S, Hood DW, Viadas C, Calatayud L, Morey P, Servin A, Liñares J, Oliver A, Bengoechea JA, Garmendia J. Nontypable Haemophilus influenzae displays a prevalent surface structure molecular pattern in clinical isolates. PLoS One 2011; 6:e21133. [PMID: 21698169 PMCID: PMC3116884 DOI: 10.1371/journal.pone.0021133] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 05/20/2011] [Indexed: 11/22/2022] Open
Abstract
Non-typable Haemophilus influenzae (NTHi) is a Gram negative pathogen that causes acute respiratory infections and is associated with the progression of chronic respiratory diseases. Previous studies have established the existence of a remarkable genetic variability among NTHi strains. In this study we show that, in spite of a high level of genetic heterogeneity, NTHi clinical isolates display a prevalent molecular feature, which could confer fitness during infectious processes. A total of 111 non-isogenic NTHi strains from an identical number of patients, isolated in two distinct geographical locations in the same period of time, were used to analyse nine genes encoding bacterial surface molecules, and revealed the existence of one highly prevalent molecular pattern (lgtF+, lic2A+, lic1D+, lic3A+, lic3B+, siaA−, lic2C+, ompP5+, oapA+) displayed by 94.6% of isolates. Such a genetic profile was associated with a higher bacterial resistance to serum mediated killing and enhanced adherence to human respiratory epithelial cells.
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Affiliation(s)
- Pau Martí-Lliteras
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
| | - Antonio López-Gómez
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
| | - Silvia Mauro
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
| | - Derek W. Hood
- Molecular Infectious Diseases Group, Department of Paediatrics, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, United Kingdom
| | - Cristina Viadas
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
| | - Laura Calatayud
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
- Servicio de Microbiología, Hospital Universitario Bellvitge, Barcelona, Spain
- Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Universidad de Barcelona, Barcelona, Spain
| | - Pau Morey
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
| | - Alain Servin
- INSERM, UMR 756, Signalisation and Physiopathology of Epithelial cells, Paris, France
| | - Josefina Liñares
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
- Servicio de Microbiología, Hospital Universitario Bellvitge, Barcelona, Spain
- Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
- Universidad de Barcelona, Barcelona, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Palma Mallorca, Spain
| | - José Antonio Bengoechea
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
- Consejo Superior de Investigaciones Científicas-CSIC, Madrid, Spain
| | - Junkal Garmendia
- Programa de Infección e Inmunidad, Fundación Caubet-CIMERA, Bunyola, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias-CIBERES, Vitoria, Spain
- Instituto de Agrobiotecnología, CSIC-Universidad Pública de Navarra-Gobierno de Navarra, Mutilva, Spain
- * E-mail:
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McCrea KW, Xie J, Marrs CF, Gilsdorf JR. Prevalence of genetic differences in phosphorylcholine expression between nontypeable Haemophilus influenzae and Haemophilus haemolyticus. BMC Microbiol 2010; 10:286. [PMID: 21073698 PMCID: PMC2992063 DOI: 10.1186/1471-2180-10-286] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 11/12/2010] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Although non-typeable (NT) Haemophilus influenzae and Haemophilus haemolyticus are closely related human commensals, H. haemolyticus is non-pathogenic while NT H. influenzae is an important cause of respiratory tract infections. Phase-variable phosphorylcholine (ChoP) modification of lipooligosaccharide (LOS) is a NT H. influenzae virulence factor that, paradoxically, may also promote complement activation by binding C-reactive protein (CRP). CRP is known to bind more to ChoP positioned distally than proximally in LOS, and the position of ChoP within LOS is dictated by specific licD alleles (designated here as licDI, licDIII, and licDIV) that are present in a lic1 locus. The lic1 locus contains the licA-licD genes, and ChoP-host interactions may also be influenced by a second lic1 locus that allows for dual ChoP substitutions in the same strain, or by the number of licA gene tetranucleotide repeats (5'-CAAT-3') that reflect phase-variation mutation rates. RESULTS Using dot-blot hybridization, 92% of 88 NT H. influenzae and 42.6% of 109 H. haemolyticus strains possessed a lic1 locus. Eight percent of NT H. influenzae and none of the H. haemolyticus strains possessed dual copies of lic1. The licDIII and licDIV gene alleles were distributed similarly (18-22%) among the NT H. influenzae and H. haemolyticus strains while licDI alleles were present in 45.5% of NT H. influenzae but in less than 1% of H. haemolyticus strains (P < .0001). NT H. influenzae had an average of 26.8 tetranucleotide repeats in licA compared to 14.8 repeats in H. haemolyticus (P < .05). In addition, NT H. influenzae strains that possessed a licDIII allele had increased numbers of repeats compared to NT H. influenzae with other licD alleles (P < .05). CONCLUSIONS These data demonstrate that genetic similarities and differences of ChoP expression exist between NT H. influenzae and H. haemolyticus and strengthen the hypothesis that, at the population level, these differences may, in part, provide an advantage in the virulence of NT H. influenzae.
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Affiliation(s)
- Kirk W McCrea
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jingping Xie
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109-0244, USA
- Beacon Analytical Systems Inc., Saco, ME 04072, USA
| | - Carl F Marrs
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109-0244, USA
| | - Janet R Gilsdorf
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
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Prevalence of Haemophilus influenzae type b genetic islands among clinical and commensal H. influenzae and H. haemolyticus isolates. J Clin Microbiol 2010; 48:2565-8. [PMID: 20463164 DOI: 10.1128/jcm.02453-09] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Five genetic islands (HiGI) found in Haemophilus influenzae type b strain Eagan were used as hybridization probes on type b, Haemophilus haemolyticus, and nontypeable H. influenzae (NTHi) isolates. HiGI2 and HiGI7 were significantly more prevalent in NTHi isolates from children with otitis media than in those from the throats of healthy children.
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Hotomi M, Kono M, Togawa A, Arai J, Takei S, Ikeda Y, Ogami M, Murphy TF, Yamanaka N. Haemophilus influenzae and Haemophilus haemolyticus in tonsillar cultures of adults with acute pharyngotonsillitis. Auris Nasus Larynx 2010; 37:594-600. [PMID: 20392581 DOI: 10.1016/j.anl.2010.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 02/06/2010] [Accepted: 02/12/2010] [Indexed: 11/24/2022]
Abstract
OBJECTIVE The aim of this study was to evaluate the clinical implication of Haemophilus haemolyticus, one of the closest relative of Haemophilus influenzae, on acute pharyngotonsillitis. METHODS We applied polymerase chain reaction (PCR) for 16S ribosomal DNA (rDNA) and IgA protease gene (iga) to distinguish H. haemolyticus and H. influenzae. RESULTS Among the 199 Haemophilus spp. isolated from 214 patients with acute pharyngotonsillitis, 52 (24.3%) H. influenzae strains and 23 (10.7%) H. haemolyticus strains were identified by polymerase chain reaction (PCR) for 16S rDNA and IgA protease gene (iga). All H. haemolyticus strains showed hemolysis on horse blood agar and there were no other Haemophilus spp., nonhemolytic H. haemolyticus and H. influenzae variant strains that had absent iga gene. H. hemolyticus showed close genetic relationship with H. influenzae evaluated by pulsed field gel electrophoresis (PFGE). The cases of acute pharyngotonsillitis showing WBC=7000/mm(3) or CRP=8 mg/dl were frequently found among cases with H. influenzae rather than cases with H. haemolyticus. CONCLUSION H. haemolyticus is a pharyngeal commensal that is isolated frequently from adults with acute pharyngotonsillitis.
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Affiliation(s)
- Muneki Hotomi
- Department of Otolaryngology-Head and Neck Surgery, Wakayama Medical University, 811-1 Kimiidera, Wakayama-shi, Wakayama, 640-8501, Japan
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Prevalence of the sodC gene in nontypeable Haemophilus influenzae and Haemophilus haemolyticus by microarray-based hybridization. J Clin Microbiol 2009; 48:714-9. [PMID: 20042621 DOI: 10.1128/jcm.01416-09] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The sodC gene has been reported to be a useful marker for differentiating nontypeable (NT) Haemophilus influenzae from Haemophilus haemolyticus in respiratory-tract samples, but discrepancies exist as to the prevalence of sodC in NT H. influenzae. Therefore, we used a microarray-based, "library-on-a-slide" method to differentiate the species and found that 21 of 169 (12.4%) NT H. influenzae strains and all 110 (100%) H. haemolyticus strains possessed the sodC gene. Multilocus sequence analysis confirmed that the 21 NT H. influenzae strains were H. influenzae and not H. haemolyticus. An inactive sodC gene has been reported in encapsulated H. influenzae strains belonging to phylogenetic division II. Capsule-specific Southern hybridization and PCR and a lack of copper/zinc-cofactored superoxide dismutase (CuZnSOD) expression indicated that 6 of the 21 sodC-containing NT H. influenzae strains in our study were likely capsule-deficient mutants belonging to phylogenetic division II. DNA sequence comparisons of the 21 H. influenzae sodC genes with sodC from H. haemolyticus or encapsulated H. influenzae demonstrated that the sodC genes of the six H. influenzae capsule-deficient mutants were, on average, 99% identical to sodC from encapsulated H. influenzae but only 85% identical to sodC from H. haemolyticus. The sodC genes from 2/15 NT H. influenzae strains were similarly more closely related to sodC from encapsulated strains, while sodC genes from 13 NT H. influenzae strains were almost 95% identical to sodC genes from H. haemolyticus, suggesting the possibility of interspecies recombination in these strains. In summary, this study demonstrates that sodC is not completely absent (9.2%) in true NT H. influenzae strains.
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Detection of cryptic genospecies misidentified as Haemophilus influenzae in routine clinical samples by assessment of marker genes fucK, hap, and sodC. J Clin Microbiol 2009; 47:2590-2. [PMID: 19535530 DOI: 10.1128/jcm.00013-09] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical isolates of Haemophilus influenzae were assessed for the presence of fucK, hap, and sodC by hybridization with gene-specific probes, and isolates diverging from the expected H. influenzae genotype were characterized by phenotype and 16S rRNA gene sequencing. Two of 480 isolates were finally classified as variant strains ("nonhemolytic Haemophilus haemolyticus").
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Abstract
Nontypeable Haemophilus influenzae is a significant pathogen in children, causing otitis media, sinusitis, conjunctivitis, pneumonia, and occasionally invasive infections. H. influenzae type b conjugate vaccines have no effect on infections caused by nontypeable strains because nontypeable strains are nonencapsulated. Approximately, one-third of episodes of otitis media are caused by nontypeable H. influenzae and the bacterium is the most common cause of recurrent otitis media. Recent progress in elucidating molecular mechanisms of pathogenesis, understanding the role of biofilms in otitis media and an increasing understanding of immune responses have potential for development of novel strategies to improve prevention and treatment of otitis media caused by nontypeable H. influenzae. Feasibility of vaccination for prevention of otitis media due to nontypeable H. influenzae was recently demonstrated in a clinical trial with a vaccine that included the surface virulence factor, protein D.
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Delineation of the species Haemophilus influenzae by phenotype, multilocus sequence phylogeny, and detection of marker genes. J Bacteriol 2008; 191:822-31. [PMID: 19060144 DOI: 10.1128/jb.00782-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
To obtain more information on the much-debated definition of prokaryotic species, we investigated the borders of Haemophilus influenzae by comparative analysis of H. influenzae reference strains with closely related bacteria including strains assigned to Haemophilus haemolyticus, cryptic genospecies biotype IV, and the never formally validated species "Haemophilus intermedius". Multilocus sequence phylogeny based on six housekeeping genes separated a cluster encompassing the type and the reference strains of H. influenzae from 31 more distantly related strains. Comparison of 16S rRNA gene sequences supported this delineation but was obscured by a conspicuously high number of polymorphic sites in many of the strains that did not belong to the core group of H. influenzae strains. The division was corroborated by the differential presence of genes encoding H. influenzae adhesion and penetration protein, fuculokinase, and Cu,Zn-superoxide dismutase, whereas immunoglobulin A1 protease activity or the presence of the iga gene was of limited discriminatory value. The existence of porphyrin-synthesizing strains ("H. intermedius") closely related to H. influenzae was confirmed. Several chromosomally encoded hemin biosynthesis genes were identified, and sequence analysis showed these genes to represent an ancestral genotype rather than recent transfers from, e.g., Haemophilus parainfluenzae. Strains previously assigned to H. haemolyticus formed several separate lineages within a distinct but deeply branching cluster, intermingled with strains of "H. intermedius" and cryptic genospecies biotype IV. Although H. influenzae is phenotypically more homogenous than some other Haemophilus species, the genetic diversity and multicluster structure of strains traditionally associated with H. influenzae make it difficult to define the natural borders of that species.
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Sandstedt SA, Zhang L, Patel M, McCrea KW, Qin Z, Marrs CF, Gilsdorf JR. Comparison of laboratory-based and phylogenetic methods to distinguish between Haemophilus influenzae and H. haemolyticus. J Microbiol Methods 2008; 75:369-71. [PMID: 18652852 DOI: 10.1016/j.mimet.2008.06.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 10/21/2022]
Abstract
New methods to distinguish between nontypeable Haemophilus influenzae and nonhemolytic H. haemolyticus were compared. The results of iga variable region hybridization to dotblots and library-on-a-slide microarrays were more similar to a "gold standard" multigenephylogenetic tree than iga-conserved region hybridization or P6 7F3 epitope immunoblots.
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Affiliation(s)
- Sara A Sandstedt
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029, United States.
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Erwin AL, Sandstedt SA, Bonthuis PJ, Geelhood JL, Nelson KL, Unrath WCT, Diggle MA, Theodore MJ, Pleatman CR, Mothershed EA, Sacchi CT, Mayer LW, Gilsdorf JR, Smith AL. Analysis of genetic relatedness of Haemophilus influenzae isolates by multilocus sequence typing. J Bacteriol 2008; 190:1473-83. [PMID: 18065541 PMCID: PMC2238191 DOI: 10.1128/jb.01207-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 11/26/2007] [Indexed: 12/13/2022] Open
Abstract
The gram-negative bacterium Haemophilus influenzae is a human-restricted commensal of the nasopharynx that can also be associated with disease. The majority of H. influenzae respiratory isolates lack the genes for capsule production and are nontypeable (NTHI). Whereas encapsulated strains are known to belong to serotype-specific phylogenetic groups, the structure of the NTHI population has not been previously described. A total of 656 H. influenzae strains, including 322 NTHI strains, have been typed by multilocus sequence typing and found to have 359 sequence types (ST). We performed maximum-parsimony analysis of the 359 sequences and calculated the majority-rule consensus of 4,545 resulting equally most parsimonious trees. Eleven clades were identified, consisting of six or more ST on a branch that was present in 100% of trees. Two additional clades were defined by branches present in 91% and 82% of trees, respectively. Of these 13 clades, 8 consisted predominantly of NTHI strains, three were serotype specific, and 2 contained distinct NTHI-specific and serotype-specific clusters of strains. Sixty percent of NTHI strains have ST within one of the 13 clades, and eBURST analysis identified an additional phylogenetic group that contained 20% of NTHI strains. There was concordant clustering of certain metabolic reactions and putative virulence loci but not of disease source or geographic origin. We conclude that well-defined phylogenetic groups of NTHI strains exist and that these groups differ in genetic content. These observations will provide a framework for further study of the effect of genetic diversity on the interaction of NTHI with the host.
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Affiliation(s)
- Alice L Erwin
- Microbial Pathogens Program, Seattle Biomedical Research Institute, Seattle, Washington, USA.
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Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains. J Clin Microbiol 2007; 46:406-16. [PMID: 18039799 DOI: 10.1128/jcm.01832-07] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Haemophilus influenzae is both a human respiratory pathogen and pharyngeal commensal, while H. haemolyticus, the closest phylogenetic relative of H. influenzae, is arguably a strict pharyngeal commensal. A hemolytic phenotype has historically differentiated H. haemolyticus from H. influenzae, but the recent recognition of significant nonhemolytic H. haemolyticus colonization has decreased this trait's resolvability. Given this and the potential of recombination between the species, we examined the distribution of microbiologic and molecular traits between collections of H. influenzae and H. haemolyticus strains separated within a dendrogram obtained by multilocus sequence analysis (MLSA). All strains hybridizing with a probe to iga, a gene encoding an immunoglobulin A protease of H. influenzae, clustered apart from strains that did not hybridize with the probe. Other traits also segregated significantly along this division, suggesting a separation of the species. Of note, the LOS genes licA, lic2A, and lgtC of H. influenzae were approximately 2, 6, and 54 times, respectively, more prevalent in H. influenzae than in H. haemolyticus. In contrast to species separation, interspecies recombination was evidenced by the inability of single gene sequences to phylogenetically separate the species and by the "fuzzy" distribution of some species-specific traits across the species dividing line. Together, these data support the historically accurate and pragmatic division of these species while recognizing their potential for recombination. Future comparative genomic studies identifying common and distinctive genes could be useful in evaluating their role in the commensal or virulent growth, respectively, of H. influenzae.
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Syed SS, Gilsdorf JR. Prevalence ofhicAB,lav,traA, andhifBCamongHaemophilus influenzaemiddle ear and throat strains. FEMS Microbiol Lett 2007; 274:180-3. [PMID: 17608697 DOI: 10.1111/j.1574-6968.2007.00822.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an important cause of illness among children. To further understand the role of laterally transferred genes in NTHi colonization and otitis media, the prevalence of hicAB, lav, tnaA, and hifBC was determined among 44 middle ear and 35 throat NTHi isolates by dot-blot hybridization.
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Affiliation(s)
- Salma S Syed
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI, USA
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Erwin AL, Smith AL. Nontypeable Haemophilus influenzae: understanding virulence and commensal behavior. Trends Microbiol 2007; 15:355-62. [PMID: 17600718 DOI: 10.1016/j.tim.2007.06.004] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 04/11/2007] [Accepted: 06/13/2007] [Indexed: 11/22/2022]
Abstract
Haemophilus influenzae is genetically diverse and exists as a near-ubiquitous human commensal or as a pathogen. Invasive type b disease has been almost eliminated in developed countries; however, unencapsulated strains - nontypeable H. influenzae (NTHi) - remain important as causes of respiratory infections. Respiratory tract disease occurs when NTHi adhere to or invade respiratory epithelial cells, initiating one or more of several proinflammatory pathways. Biofilm formation explains many of the observations seen in chronic otitis media and chronic bronchitis. However, NTHi biofilms seem to lack a biofilm-specific polysaccharide in the extracellular matrix, a source of controversy regarding their relevance. Successful commensalism requires dampening of the inflammatory response and evasion of host defenses, accomplished in part through phase variation.
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Affiliation(s)
- Alice L Erwin
- Microbial Pathogens Program, Seattle Biomedical Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, WA 98109-5219, USA
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Juliao PC, Marrs CF, Xie J, Gilsdorf JR. Histidine auxotrophy in commensal and disease-causing nontypeable Haemophilus influenzae. J Bacteriol 2007; 189:4994-5001. [PMID: 17496076 PMCID: PMC1951860 DOI: 10.1128/jb.00146-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Histidine biosynthesis is one of the best studied metabolic pathways in bacteria. Although this pathway is thought to be highly conserved within and between bacterial species, a previous study identified a genetic region within the histidine operon (his) of nontypeable strains of Haemophilus influenzae (NTHI) that was more prevalent among otitis media strains than among throat commensal NTHI strains. In the present study, we further characterized this region and showed that genes in the complete his operon (hisG, -D, -C, -NB, -H, -A, -F, and -IE) are >99% conserved among four fully sequenced NTHI strains, are present in the same location in these four genomes, and are situated in the same gene order. Using PCR and dot blot hybridization, we determined that the his operon was significantly more prevalent in otitis media NTHI strains (106/121; 87.7%) than in throat strains (74/137; 54%) (prevalence ratio, 1.62; P<0.0001), suggesting a possible role in middle ear survival and/or acute otitis media. NTHI strains lacking the his operon showed attenuated growth in histidine-restricted media, confirming them as his-negative auxotrophs. Our results suggest that the ability to make histidine is an important factor in bacterial growth and survival in the middle ear, where nutrients such as histidine may be found in limited amounts. Those isolates lacking the histidine pathway were still able to survive well in the throat, which suggests that histidine is readily available in the throat environment.
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Affiliation(s)
- Patricia C Juliao
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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