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Tanaka E, Hirai Y, Wajima T, Ishida Y, Kawamura Y, Nakaminami H. High-Level Quinolone-Resistant Haemophilus haemolyticus in Pediatric Patient with No History of Quinolone Exposure. Emerg Infect Dis 2022; 28:104-110. [PMID: 34932443 PMCID: PMC8714209 DOI: 10.3201/eid2801.210248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The prevalence of antimicrobial resistance among Haemophilus spp. is a critical concern, but high-level quinolone-resistant strains had not been isolated from children. We isolated high-level quinolone-resistant H. haemolyticus from the suction sputum of a 9-year-old patient. The patient had received home medical care with mechanical ventilation for 2 years and had not been exposed to any quinolones for >3 years. The H. haemolyticus strain we isolated, 2019-19, shared biochemical features with H. influenzae. However, whole-genome analysis found this strain was closer to H. haemolyticus. Phylogenetic and mass spectrometry analyses indicated that strain 2019-19 was in the same cluster as H. haemolyticus. Comparison of quinolone resistance-determining regions showed strain 2019-19 possessed various amino acid substitutions, including those associated with quinolone resistance. This report highlights the existence of high-level quinolone-resistant Haemophilus species that have been isolated from both adults and children.
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Discriminative Potential of the Vitek MS In Vitro Diagnostic Device Regarding Haemophilus influenzae and Haemophilus haemolyticus. J Clin Microbiol 2020; 58:JCM.00278-20. [PMID: 32404483 DOI: 10.1128/jcm.00278-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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Nontypeable Haemophilus influenzae Invasive Blood Isolates Are Mainly Phosphorylcholine Negative and Show Decreased Complement-Mediated Killing That Is Associated with Lower Binding of IgM and CRP in Comparison to Colonizing Isolates from the Oropharynx. Infect Immun 2019; 87:IAI.00604-18. [PMID: 30455196 DOI: 10.1128/iai.00604-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/09/2018] [Indexed: 11/20/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) bacteria express various molecules that contribute to their virulence. The presence of phosphocholine (PCho) on NTHi lipooligosaccharide increases adhesion to epithelial cells and is an advantage for the bacterium, enabling nasopharyngeal colonization, as measured in humans and animal models. However, when PCho is expressed on the lipooligosaccharide, it is also recognized by the acute-phase protein C-reactive protein (CRP) and PCho-specific antibodies, both of which are potent initiators of the classical pathway of complement activation. In this study, we show that blood isolates, which are exposed to CRP and PCho-specific antibodies in the bloodstream, have a higher survival in serum than oropharyngeal isolates, which was associated with a decreased presence of PCho. PCholow strains showed decreased IgM, CRP, and complement C3 deposition, which was associated with increased survival in human serum. Consistent with the case for the PCholow strains, removal of PCho expression by licA gene deletion decreased IgM, CRP, and complement C3 deposition, which increased survival in human serum. Complement-mediated killing of PChohigh strains was mainly dependent on binding of IgM to the bacterial surface. These data support the hypothesis that a PCholow phenotype was selected in blood during invasive disease, which increased resistance to serum killing, mainly due to lowered IgM and CRP binding to the bacterial surface.
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Osman KL, Jefferies JMC, Woelk CH, Devos N, Pascal TG, Mortier MC, Devaster JM, Wilkinson TMA, Cleary DW, Clarke SC. Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species. Sci Rep 2018; 8:14734. [PMID: 30282975 PMCID: PMC6170463 DOI: 10.1038/s41598-018-32973-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 02/04/2023] Open
Abstract
H. haemolyticus is often misidentified as NTHi due to their close phylogenetic relationship. Differentiating between the two is important for correct identification and appropriate treatment of infective organism and to ensure any role of H. haemolyticus in disease is not being overlooked. Speciation however is not completely reliable by culture and PCR methods due to the loss of haemolysis by H. haemolyticus and the heterogeneity of NTHi. Haemophilus isolates from COPD as part of the AERIS study (ClinicalTrials - NCT01360398) were speciated by analysing sequence data for the presence of molecular markers. Further investigation into the genomic relationship was carried out using average nucleotide identity and phylogeny of allelic and genome alignments. Only 6.3% were identified as H. haemolyticus. Multiple in silico methods were able to distinguish H. haemolyticus from NTHi. However, no single gene target was found to be 100% accurate. A group of omp2 negative NTHi were observed to be phylogenetically divergent from H. haemolyticus and remaining NTHi. The presence of an atypical group from a geographically and disease limited set of isolates supports the theory that the heterogeneity of NTHi may provide a genetic continuum between NTHi and H. haemolyticus.
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Affiliation(s)
- Karen L Osman
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK
| | - Johanna M C Jefferies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA, USA
| | | | | | | | | | - Tom M A Wilkinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, University of Southampton, Southampton, United Kingdom
| | - David W Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Stuart C Clarke
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK. .,NIHR Biomedical Research Centre, University of Southampton, Southampton, United Kingdom. .,Wessex Investigational Sciences Hub, University of Southampton, Southampton, United Kingdom. .,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom. .,Global Health Research Institute, University of Southampton, Southampton, United Kingdom.
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Takeuchi N, Segawa S, Ishiwada N, Ohkusu M, Tsuchida S, Satoh M, Matsushita K, Nomura F. Capsular serotyping of Haemophilus influenzae by using matrix-associated laser desorption ionization-time of flight mass spectrometry. J Infect Chemother 2018. [PMID: 29534849 DOI: 10.1016/j.jiac.2018.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Haemophilus influenzae is a major pathogenic bacteria causing invasive disease, which is classified into six capsular serotypes (a-f) and non-typeable (NT) strains. Capsular serotyping of H. influenzae is traditionally determined by serological methods and more recently by PCR methods. However, these methods are time-consuming and expensive. In the present study, matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was evaluated as an alternative method for capsular serotyping of H. influenzae clinical strains. We created an in-house database of all six serotypes and NT H. influenzae strains using the main spectrum creation standard method set to the default parameters in MADI-TOF MS. We evaluated the performance of the in-house database using 79 clinical strains already identified by PCR and 58 prospectively collected clinical strains. Measurements were performed using the Bruker MALDI BioTyper system. The peak list was matched against the reference library using the integrated pattern algorithm of the software. The best-matched spectrum was considered the serotyping result. All 137 test strains were correctly identified as H. influenzae using MALDI-TOF MS. The sensitivity and specificity for identification for type b, type e, and type f capsular serotypes and NT H. influenzae using MALDI-TOF MS were 100%/94.3%, 94.7%/97.9%, 97.4%/97.9%, and 85.5%/99.2%, respectively. Our findings indicate that MALDI-TOF MS is a useful alternative method for capsular serotyping of H. influenzae strains. This method is faster and more cost-effective than traditional methods and will therefore be useful for routine applications in clinical laboratories.
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Affiliation(s)
- Noriko Takeuchi
- Department of Infectious Diseases, Medical Mycology Research Center, Japan
| | - Shunsuke Segawa
- Division of Laboratory Medicine and Clinical Genetics, Japan
| | - Naruhiko Ishiwada
- Department of Infectious Diseases, Medical Mycology Research Center, Japan.
| | - Misako Ohkusu
- Department of Infectious Diseases, Medical Mycology Research Center, Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | - Mamoru Satoh
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
| | | | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, Chiba, Japan
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Lützen L, Olesen B, Voldstedlund M, Christensen JJ, Moser C, Knudsen JD, Fuursted K, Hartmeyer GN, Chen M, Søndergaard TS, Rosenvinge FS, Dzajic E, Schønheyder HC, Nørskov-Lauritsen N. Incidence of HACEK bacteraemia in Denmark: A 6-year population-based study. Int J Infect Dis 2018; 68:83-87. [PMID: 29408674 DOI: 10.1016/j.ijid.2018.01.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 01/22/2018] [Accepted: 01/24/2018] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES Bacteria with common microbiological and clinical characteristics are often recognized as a particular group. The acronym HACEK stands for five fastidious genera associated with infective endocarditis (Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella). Data on the epidemiology of HACEK are sparse. This article reports a 6-year nationwide study of HACEK bacteraemia in Denmark. METHODS Cases of HACEK bacteraemia occurring during the years 2010-2015 were retrieved from the national Danish microbiology database, covering an average surveillance population of 5.6 million per year. RESULTS A total of 147 cases of HACEK bacteraemia were identified, corresponding to an annual incidence of 0.44 per 100000 population. The annual incidence for males was 0.56 per 100000 and for females was 0.31 per 100000. The median age was 56 years (range 0-97 years), with variation among the genera. One hundred and forty-three isolates were identified to the species level and six to the genus level: Haemophilus spp, n=55; Aggregatibacter spp, n=37; Cardiobacterium spp, n=9; Eikenella corrodens n=21; and Kingella spp, n=27. CONCLUSIONS This is the first study on the incidence of HACEK bacteraemia in a large surveillance population and may inspire further studies on the HACEK group. Haemophilus spp other than Haemophilus influenzae accounted for most cases of HACEK bacteraemia in Denmark, with Aggregatibacter spp in second place.
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Affiliation(s)
- Lisbeth Lützen
- Department of Clinical Microbiology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark; Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte Hospital, Herlev Ringvej 75, 2730 Herlev, Denmark; Department of Clinical Microbiology, Aalborg University Hospital, Hobrovej 18-22, 9100 Aalborg, Denmark.
| | - Bente Olesen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte Hospital, Herlev Ringvej 75, 2730 Herlev, Denmark.
| | - Marianne Voldstedlund
- Infectious Disease Preparedness, Statens Serum Institut, Artillerivej 5, 2300 København S, Denmark.
| | - Jens J Christensen
- Department of Clinical Microbiology, Slagelse Hospital, Ingemannsvej 18, 4200 Slagelse, Denmark.
| | - Claus Moser
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, 2100 København Ø, Denmark.
| | - Jenny D Knudsen
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre Hospital, Kettegård Alle 30, 2650 Hvidovre, Denmark.
| | - Kurt Fuursted
- Department of Clinical Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, 2300 København S, Denmark.
| | - Gitte N Hartmeyer
- Department of Clinical Microbiology, Odense University Hospital, Søndre Boulevard 29, 5000 Odense, Denmark.
| | - Ming Chen
- Department of Clinical Microbiology, Hospital of Southern Jutland, Sydvang 1, 6400 Sønderborg, Denmark.
| | - Turid S Søndergaard
- Department of Clinical Microbiology, Hospital of Southern Jutland, Sydvang 1, 6400 Sønderborg, Denmark; Department of Microbiology, Hospitalsenheden Midt-Vest, Viborg/Herning, Heibergs Alle 4, 8800 Viborg, Denmark.
| | - Flemming S Rosenvinge
- Department of Clinical Microbiology, Odense University Hospital, Søndre Boulevard 29, 5000 Odense, Denmark; Department of Clinical Microbiology, Sygehus Lillebælt Vejle Sygehus, Beriderbakken 4, 7100 Vejle, Denmark.
| | - Esad Dzajic
- Department of Clinical Microbiology, Sydvestjysk Sygehus Esbjerg, Finsensgade 35, 6700 Esbjerg, Denmark.
| | - Henrik C Schønheyder
- Department of Clinical Microbiology, Aalborg University Hospital, Hobrovej 18-22, 9100 Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Fredrik Bajers Vej 5, 9100 Aalborg, Denmark.
| | - Niels Nørskov-Lauritsen
- Department of Clinical Microbiology, Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200 Aarhus N, Denmark.
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8
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Andrzejczuk S, Kosikowska U, Malm A, Chwiejczak E, Stepien-Pysniak D. Phenotypic diversity of Haemophilus influenzae and Haemophilus parainfluenzae isolates depending on origin and health condition. CURRENT ISSUES IN PHARMACY AND MEDICAL SCIENCES 2017. [DOI: 10.1515/cipms-2017-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Background. Haemophili are common human microbiota representatives. The aim of our study was to investigate a diversity of Haemophilus spp. isolates selected from clinical specimens on the basis of biochemical characteristics, biotypes distribution, protein profiles and antimicrobial resistance. Results. A total of 893/1025 (87%) of haemophili isolates were identified: 260/1025 (25%) as H. influenzae and 633/1025 (62%) as H. parainfluenzae. Moreover, a group of 107/1025 (10%) isolates without species identification (with e.g. abnormal numerical profile) was described as Haemophilus spp. Within the H. influenzae isolates, biotypes II and III were in a great majority (92/893; 10%, each), whereas among H. parainfluenzae, the most commonly occurring was biotype I and II (301/893, 34% and 178/893, 20%, respectively). A similar prevalence of biotypes was obtained regardless of the patient’s age or health condition or the type of specimen. A production of beta-lactamases was shown in 46/893 (5%) haemophili, both H. influenzae (13/46, 28%) and H. parainfluenzae (33/46, 72%) isolates. On the basis of haemophili biochemical characteristics, the cluster analysis using the UPGMA method demonstrated a high degree of phenotypic similarity due to a small distances between isolates taken from both unhealthy children and adults. Conclusion. Based on biochemical characteristics, about 90% of haemophili clinical isolates representing human-specific respiratory microbiota were positively identified as H. influenzae and H. parainfluenzae. The same differences in biotypes and antimicrobial resistance among isolates selected from healthy people or from patients with chronic and recurrent diseases were detected.
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Affiliation(s)
- Sylwia Andrzejczuk
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Urszula Kosikowska
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Edyta Chwiejczak
- Students Scientific Association at the Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki 1, 20-093 Lublin , Poland
| | - Dagmara Stepien-Pysniak
- Department of Veterinary Prevention and Birds Diseases, Institute of Biological Basis of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin , Poland
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10
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van Beek J, Veenhoven RH, Bruin JP, van Boxtel RAJ, de Lange MMA, Meijer A, Sanders EAM, Rots NY, Luytjes W. Influenza-like Illness Incidence Is Not Reduced by Influenza Vaccination in a Cohort of Older Adults, Despite Effectively Reducing Laboratory-Confirmed Influenza Virus Infections. J Infect Dis 2017; 216:415-424. [PMID: 28931240 PMCID: PMC7107403 DOI: 10.1093/infdis/jix268] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/01/2017] [Indexed: 12/05/2022] Open
Abstract
Background Data on the relative contribution of influenza virus and other respiratory pathogens to respiratory infections in community-dwelling older adults (≥60 years) are needed. Methods A prospective observational cohort study was performed in the Netherlands during 2 winters. Nasopharyngeal and oropharyngeal swabs were collected during influenza-like illness (ILI) episodes and from controls. Viruses and bacteria were identified by multiplex ligation–dependent probe amplification assay and conventional bacterial culture. Results The ILI incidence in the consecutive seasons was 7.2% and 11.6%, and influenza virus caused 18.9% and 34.2% of ILI episodes. Potential pathogen were detected in 80% of the ILI events with influenza virus, coronaviruses, rhinoviruses, human metapneumovirus, respiratory syncytial virus, parainfluenza viruses, and Haemophilus influenzae being the most common. Influenza vaccination reduced influenza virus infection by 73% (95% confidence interval [CI], 26%–90%) and 51% (95% CI, 7%–74%) in ILI patients. However, ILI incidence was similar between vaccinated (7.6% and 10.8%) and nonvaccinated (4.2% and 11.4%) participants in 2011–2012 and 2012–2013, respectively (P > .05). Conclusions Influenza virus is a frequent pathogen in older adults with ILI. Vaccination reduces the number of influenza virus infections but not the overall number of ILI episodes: other pathogens fill the gap. We suggest the existence of a pool of individuals with high susceptibility to respiratory infections. Clinical Trials Registration NTR3386.
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Affiliation(s)
- Josine van Beek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | | | - Jacob P Bruin
- Regional Laboratory for Public Health Kennemerland, Haarlem
| | - Renée A J van Boxtel
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Marit M A de Lange
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Adam Meijer
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Elisabeth A M Sanders
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven.,Department of Pedriatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center, Utrecht, The Netherlands
| | - Nynke Y Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
| | - Willem Luytjes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven
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11
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Tamura S, Maeda T, Misawa K, Osa M, Hamamoto T, Yuki A, Imai K, Mikita K, Morichika K, Kawana A, Matsumoto H, Nonoyama S. Development of a highly resolved loop-mediated isothermal amplification method to detect the N526K ftsI mutation of β-lactamase-negative ampicillin-resistant Haemophilus influenzae. J Microbiol Methods 2017; 141:108-114. [PMID: 28807759 DOI: 10.1016/j.mimet.2017.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/24/2023]
Abstract
Rapid and easy detection of sequence polymorphisms, including nucleotide point mutations of bacterial pathogens responsible for amino acid substitutions linked to drug resistance, is essential for the proper use of antimicrobial agents. Here, a detection method using loop-mediated amplification (LAMP) combined with amplification refractory mutation system (ARMS) to accurately distinguish a different single nucleotide in the target sequence was established, named ARMS-SNP LAMP. This procedure is capable of species-specific detection of a nucleotide (1578T) in the ftsI gene on Haemophilus influenzae without amplifying the sequence carrying the point mutations (T1578G/A) in β-lactamase-negative ampicillin resistant (BLNAR) strains. Reactions were performed at 61°C for 45min. Successful target gene amplifications were detected by measuring real-time turbidity using a turbidimeter and visual detection. The assay had a detection limit of 10.0pg of genomic DNA per reaction and showed specificity against 52 types of pathogens, whereas amplifications were completely blocked in even 100.0ng/μL of genomic DNA with point mutations at T1578G and T1578A. The expected ARMS-SNP LAMP products were confirmed through identical melting curves in real-time LAMP procedures. This novel procedure was also used to analyze 57 clinical isolates of H. influenzae. All 25 clinical isolates with the naïve sequence of 1578T gave positive results. In addition, concordant negative results were obtained for 31 of the BLNAR strains with the T1578G mutation and one strain with the T1578A mutation. The ARMS-SNP LAMP method is a simple and rapid method for SNP-genotyping of a clinical isolate as point-of-care testing (POCT) technology. It is suitable for use in both resource-limited situations and well-equipped clinical settings because of its simplicity and convenience.
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Affiliation(s)
- Shinsuke Tamura
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Takuya Maeda
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan; Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan; Center for Clinical Infectious Diseases and Research, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama 350-0495, Japan.
| | - Kazuhisa Misawa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Morichika Osa
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Atsushi Yuki
- Department of Laboratory Medicine, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuo Imai
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kei Mikita
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kyoko Morichika
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Pulmonary Medicine, Department of Internal Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
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12
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Rapid Differentiation of Haemophilus influenzae and Haemophilus haemolyticus by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry with ClinProTools Mass Spectrum Analysis. J Clin Microbiol 2017. [PMID: 28637909 DOI: 10.1128/jcm.00267-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Haemophilus influenzae is associated with severe invasive disease, while Haemophilus haemolyticus is considered part of the commensal flora in the human respiratory tract. Although the addition of a custom mass spectrum library into the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system could improve identification of these two species, the establishment of such a custom database is technically complicated and requires a large amount of resources, which most clinical laboratories cannot afford. In this study, we developed a mass spectrum analysis model with 7 mass peak biomarkers for the identification of H. influenzae and H. haemolyticus using the ClinProTools software. We evaluated the diagnostic performance of this model using 408 H. influenzae and H. haemolyticus isolates from clinical respiratory specimens from 363 hospitalized patients and compared the identification results with those obtained with the Bruker IVD MALDI Biotyper. The IVD MALDI Biotyper identified only 86.9% of H. influenzae (311/358) and 98.0% of H. haemolyticus (49/50) clinical isolates to the species level. In comparison, the ClinProTools mass spectrum model could identify 100% of H. influenzae (358/358) and H. haemolyticus (50/50) clinical strains to the species level and significantly improved the species identification rate (McNemar's test, P < 0.0001). In conclusion, the use of ClinProTools demonstrated an alternative way for users lacking special expertise in mass spectrometry to handle closely related bacterial species when the proprietary spectrum library failed. This approach should be useful for the differentiation of other closely related bacterial species.
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Sandalakis V, Goniotakis I, Vranakis I, Chochlakis D, Psaroulaki A. Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives. Expert Rev Proteomics 2017; 14:253-267. [PMID: 28092721 DOI: 10.1080/14789450.2017.1282825] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to 'battle time' in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed. Expert commentary: Mass spectrometry is the future of bacterial identification and creates a new era in modern microbiology. Its incorporation in routine practice seems to be not too far, providing a valuable alternative, especially in terms of time, to conventional techniques. If the technology further advances, quick bacterial identification and probable identification of common antibiotic resistance might guide patient decision-making regarding bacterial infectious diseases in the near future.
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Affiliation(s)
- Vassilios Sandalakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Ioannis Goniotakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Iosif Vranakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Dimosthenis Chochlakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Anna Psaroulaki
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
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Cherkaoui A, Diene SM, Renzoni A, Emonet S, Renzi G, François P, Schrenzel J. Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation. Clin Microbiol Infect 2016; 23:118.e9-118.e19. [PMID: 27756711 DOI: 10.1016/j.cmi.2016.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/01/2016] [Accepted: 10/10/2016] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To investigate the potential roles of PBPs, efflux pumps and slow drug influx for imipenem heteroresistance in nontypeable Haemophilus influenzae (NTHi). METHODS Fifty-nine NTHi clinical isolates examined in this study were collected at Geneva University Hospitals between 2009 and 2014. Alterations in PBPs were investigated by gene sequencing. To evaluate the affinities of the PBPs to imipenem, steady-state concentration-response experiments were carried out using imipenem in a competition assay with Bocillin-FL. The effect of the carbonyl cyanide m-chlorophenylhydrazone (CCCP) on imipenem susceptibility was assessed using broth dilution and viable cell counting. Using whole-genome sequencing, we explored the potential roles of outer membrane protein P2 (OmpP2), LytM proteins and the dcw gene cluster in imipenem heteroresistance. RESULTS All 46 imipenem-heteroresistant isolates (IMIhR) harboured amino acid substitutions in the ftsI gene, which encodes PBP3, corresponding to 25 different mutation patterns that varied from the ftsI gene mutation patterns found in imipenem-susceptible isolates. Among all PBPs, the highest affinity to imipenem was documented for PBP3 (IC50, 0.004 μg/mL). Different amino acid substitutions and insertions were noted in OmpP2, suggesting a relationship with imipenem heteroresistance. The IMIhR isolates were affected by CCCP differently and displayed a higher percentage of killing by imipenem in CCCP-treated cells at concentrations ranging between 0.5 and 8 μg/mL. CONCLUSIONS The present study provides robust evidence indicating that in combination with the altered PBP3, the slowed drug influx and its enhanced efflux due to the loss of regulation led to the development of imipenem heteroresistance in NTHi.
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Affiliation(s)
- A Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
| | - S M Diene
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - A Renzoni
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - S Emonet
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - G Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - P François
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - J Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland; Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
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15
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Kostrzewa M, Nagy E. How MALDI-TOF mass spectrometry can aid diagnosis of hard-to-identify pathogenic bacteria. Expert Rev Mol Diagn 2016; 16:509-11. [DOI: 10.1586/14737159.2016.1157019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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16
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Evaluation of the Bruker MALDI Biotyper for Identification of Fastidious Gram-Negative Rods. J Clin Microbiol 2015; 54:543-8. [PMID: 26659214 DOI: 10.1128/jcm.03107-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 11/29/2015] [Indexed: 12/21/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as the Enterobacteriaceae. In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.
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17
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Multicenter Evaluation of the Bruker MALDI Biotyper CA System for the Identification of Clinical Aerobic Gram-Negative Bacterial Isolates. PLoS One 2015; 10:e0141350. [PMID: 26529504 PMCID: PMC4631355 DOI: 10.1371/journal.pone.0141350] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 10/06/2015] [Indexed: 11/19/2022] Open
Abstract
The prompt and accurate identification of bacterial pathogens is fundamental to patient health and outcome. Recent advances in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) have revolutionized bacterial identification in the clinical laboratory, but uniform incorporation of this technology in the U.S. market has been delayed by a lack of FDA-cleared systems. In this study, we conducted a multicenter evaluation of the MALDI Biotyper CA (MBT-CA) System (Bruker Daltonics Inc, Billerica, MA) for the identification of aerobic gram-negative bacteria as part of a 510(k) submission to the FDA. A total of 2,263 aerobic gram negative bacterial isolates were tested representing 23 genera and 61 species. Isolates were collected from various clinical sources and results obtained from the MBT-CA System were compared to DNA sequencing and/or biochemical testing. Isolates that failed to report as a "high confidence species ID" [log(score) ≥2.00] were re-tested using an extraction method. The MBT-CA System identified 96.8% and 3.1% of isolates with either a "high confidence" or a "low confidence" [log(score) value between 1.70 and <2.00] species ID, respectively. Two isolates did not produce acceptable confidence scores after extraction. The MBT-CA System correctly identified 99.8% (2,258/2,263) to genus and 98.2% (2,222/2,263) to species level. These data demonstrate that the MBT-CA System provides accurate results for the identification of aerobic gram-negative bacteria.
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18
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Marti S, Puig C, de la Campa AG, Tirado-Velez JM, Tubau F, Domenech A, Calatayud L, Garcia-Somoza D, Ayats J, Liñares J, Ardanuy C. Identification of Haemophilus haemolyticus in clinical samples and characterization of their mechanisms of antimicrobial resistance. J Antimicrob Chemother 2015; 71:80-4. [PMID: 26472767 DOI: 10.1093/jac/dkv307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/28/2015] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES The objectives of this study were to establish the frequency of Haemophilus haemolyticus in clinical samples, to determine the antimicrobial resistance rate and to identify the mechanisms of resistance to β-lactams and quinolones. METHODS An updated database was used to differentiate between MALDI-TOF MS results for Haemophilus influenzae and H. haemolyticus. Antimicrobial susceptibility was studied by microdilution, following EUCAST criteria. The β-lactamase types were identified by PCR analysis of isolates that tested positive for nitrocefin hydrolysis. Mutations in the ftsI gene were identified in isolates with ampicillin MICs ≥0.25 mg/L. Mutations in the quinolone resistance-determining region (QRDR) were identified in isolates with ciprofloxacin MICs ≥0.5 mg/L. RESULTS Overall, we identified 69 H. haemolyticus isolates from 1706 clinical isolates of Haemophilus spp. from respiratory, genital, invasive, and other infection sources. The frequency of H. haemolyticus was low in respiratory samples compared with that of H. influenzae, but in genital-related samples, the frequency was similar to that of H. influenzae. We found low antimicrobial resistance rates among H. haemolyticus isolates, with 8.7% for ampicillin, 8.7% for co-trimoxazole, 7.2% for tetracycline and 4.3% for ciprofloxacin. Mutations in the ftsI gene classified the isolates into four groups, including the newly described Group Hhae IV, which presents mutations in the ftsI gene not identified in H. influenzae and H. haemolyticus type strains. Three ciprofloxacin-resistant H. haemolyticus isolates with mutations affecting GyrA and ParC were identified. CONCLUSIONS The frequency of H. haemolyticus was low, especially in respiratory samples, where H. influenzae is the main pathogen of this genus. Although antimicrobial resistance rates were low, three ciprofloxacin-resistant H. haemolyticus clinical isolates have been identified for the first time.
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Affiliation(s)
- Sara Marti
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Puig
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Adela G de la Campa
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - José Manuel Tirado-Velez
- CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Fe Tubau
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Arnau Domenech
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Calatayud
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Garcia-Somoza
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Ayats
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Josefina Liñares
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ardanuy
- Microbiology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona-IDIBELL, Barcelona, Spain CIBER de Enfermedades Respiratorias (CIBERes), Instituto de Salud Carlos III, Madrid, Spain
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Reddington K, Schwenk S, Tuite N, Platt G, Davar D, Coughlan H, Personne Y, Gant V, Enne VI, Zumla A, Barry T. Comparison of Established Diagnostic Methodologies and a Novel Bacterial smpB Real-Time PCR Assay for Specific Detection of Haemophilus influenzae Isolates Associated with Respiratory Tract Infections. J Clin Microbiol 2015; 53:2854-60. [PMID: 26109443 PMCID: PMC4540933 DOI: 10.1128/jcm.00777-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/17/2015] [Indexed: 11/20/2022] Open
Abstract
Haemophilus influenzae is a significant causative agent of respiratory tract infections (RTI) worldwide. The development of a rapid H. influenzae diagnostic assay that would allow for the implementation of infection control measures and also improve antimicrobial stewardship for patients is required. A number of nucleic acid diagnostics approaches that detect H. influenzae in RTIs have been described in the literature; however, there are reported specificity and sensitivity limitations for these assays. In this study, a novel real-time PCR diagnostic assay targeting the smpB gene was designed to detect all serogroups of H. influenzae. The assay was validated using a panel of well-characterized Haemophilus spp. Subsequently, 44 Haemophilus clinical isolates were collected, and 36 isolates were identified as H. influenzae using a gold standard methodology that combined the results of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fucK diagnostic assay. Using the novel smpB diagnostic assay, 100% concordance was observed with the gold standard, demonstrating a sensitivity of 100% (95% confidence interval [CI], 90.26% to 100.00%) and a specificity of 100% (95% CI, 63.06% to 100.00%) when used on clinical isolates. To demonstrate the clinical utility of the diagnostic assay presented, a panel of lower RTI samples (n = 98) were blindly tested with the gold standard and smpB diagnostic assays. The results generated were concordant for 94/98 samples tested, demonstrating a sensitivity of 90.91% (95% CI, 78.33% to 97.47%) and a specificity of 100% (95% CI, 93.40% to 100.00%) for the novel smpB assay when used directly on respiratory specimens.
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Affiliation(s)
- Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Stefan Schwenk
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Gareth Platt
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Danesh Davar
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helena Coughlan
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Yoann Personne
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Virve I Enne
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Alimuddin Zumla
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, United Kingdom
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Cherkaoui A, Diene SM, Emonet S, Renzi G, Francois P, Schrenzel J. Ampicillin-resistant Haemophilus influenzae isolates in Geneva: serotype, antimicrobial susceptibility, and β-lactam resistance mechanisms. Eur J Clin Microbiol Infect Dis 2015; 34:1937-45. [PMID: 26187432 DOI: 10.1007/s10096-015-2435-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/22/2015] [Indexed: 01/21/2023]
Abstract
The purpose of this study was to analyze the molecular mechanisms of ampicillin-resistant Haemophilus influenzae isolated in Geneva, Switzerland. We investigated the association between specific patterns of amino acid substitutions in penicillin-binding protein 3 (with or without β-lactamase production) and β-lactam susceptibility. Another main focus for this study was to compare the accuracy of disk diffusion and Etest methods to detect resistance to ampicillin and amoxicillin/clavulanic acid. The antibiotic susceptibility to β-lactam antibiotics of 124 H. influenzae isolates was determined by disk diffusion and Etest methods, and interpreted by European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) breakpoints. Alterations in PBP3 were investigated by sequencing the ftsI gene. Of the 124 clinical isolates analyzed, ampicillin resistance was found in 36% (45 out of 124). The rate of resistance to amoxicillin/clavulanic acid was 9% and 0.8%, using EUCAST and CLSI breakpoints respectively. For the 78 β-lactamase negative ampicillin-susceptible (BLNAS) isolates for which the Etest method indicated a high degree of susceptibility (MIC ≤ 1 mg/L), the disk diffusion method revealed resistance to ampicillin and amoxicillin/clavulanic acid in 33 cases (42%). Most common amino acid substitutions were Asn526Lys and Val547Ile, followed by Asp569Ser, Ala502Val, Asp350Asn, Met377Ile, Ile449Val, and Arg517His. The patterns observed were classified into six groups (IIa, IIb, IIc, IId, III-like, and miscellaneous). Continued characterization of both invasive and respiratory H. influenzae isolates is necessary in order to observe changes in the microbiology and epidemiology of this pathogen that could lead to clinical failure when treated by empirical antibiotic therapy.
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Affiliation(s)
- A Cherkaoui
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.
| | - S M Diene
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - S Emonet
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - G Renzi
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - P Francois
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
| | - J Schrenzel
- Bacteriology Laboratory, Division of Laboratory Medicine, Department of Genetics and Laboratory Medicine, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland.,Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, 4 rue Gabrielle-Perret-Gentil, 1205, Geneva, Switzerland
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Identification of Haemophilus influenzae Type b Isolates by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2015; 53:2215-24. [PMID: 25926500 DOI: 10.1128/jcm.00137-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 04/27/2015] [Indexed: 01/22/2023] Open
Abstract
Haemophilus influenzae type b (Hib) is, in contrast to non-type b H. influenzae, associated with severe invasive disease, such as meningitis and epiglottitis, in small children. To date, accurate H. influenzae capsule typing requires PCR, a time-consuming and cumbersome method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) provides rapid bacterial diagnostics and is increasingly used in clinical microbiology laboratories. Here, MALDI-TOF MS was evaluated as a novel approach to separate Hib from other H. influenzae. PCR-verified Hib and non-Hib reference isolates were selected based on genetic and spectral characteristics. Mass spectra of reference isolates were acquired and used to generate different classification algorithms for Hib/non-Hib differentiation using both ClinProTools and the MALDI Biotyper software. A test series of mass spectra from 33 Hib and 77 non-Hib isolates, all characterized by PCR, was used to evaluate the algorithms. Several algorithms yielded good results, but the two best were a ClinProTools model based on 22 separating peaks and subtyping main spectra (MSPs) using MALDI Biotyper. The ClinProTools model had a sensitivity of 100% and a specificity of 99%, and the results were 98% reproducible using a different MALDI-TOF MS instrument. The Biotyper subtyping MSPs had a sensitivity of 97%, a specificity of 100%, and 93% reproducibility. Our results suggest that it is possible to use MALDI-TOF MS to differentiate Hib from other H. influenzae. This is a promising method for rapidly identifying Hib in unvaccinated populations and for the screening and surveillance of Hib carriage in vaccinated populations.
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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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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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