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Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Jiménez Vázquez O, Utpatel C, Niemann S, Rupp J, Merker M. Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:13. [PMID: 35139905 PMCID: PMC8830169 DOI: 10.1186/s13073-022-01017-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 01/24/2022] [Indexed: 12/31/2022] Open
Abstract
Background Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01017-x.
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Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
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Chien YC, Huang YT, Liao CH, Chien JY, Hsueh PR. Clinical characteristics of bacteremia caused by Haemophilus and Aggregatibacter species and antimicrobial susceptibilities of the isolates. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 54:1130-1138. [PMID: 33390332 DOI: 10.1016/j.jmii.2020.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND/PURPOSE This study aimed to investigate the clinical characteristics and outcomes of bacteremia caused by Haemophilus and Aggregatibacter species in patients who were treated at a medical center between 2006 and 2018. METHODS Haemophilus and Aggregatibacter isolates were identified up to the species level using Bruker Biotyper MALDI-TOF analysis and ancillary 16S rRNA gene sequencing analysis (in case of ambiguity). Clinical characteristics and outcomes of patients with bacteremia caused by these organisms were evaluated. RESULTS Sixty-five Haemophilus and Aggregatibacter species isolates causing bacteremia were identified from nonduplicated patients, including 51 (78.5%) Haemophilus influenzae, 6 (9.2%) Haemophilus parainfluenzae, 1 (1.5%) Haemophilus haemolyticus, 3 (4.6%) A. aphrophilus, and 4 (6.2%) A. segnis. Hospital mortality was observed in 18 (28.1%) of 64 patients with bacteremia caused by Haemophilus (n = 57) and Aggregatibacter species (n = 7). The majority of patients with bacteremia had community-acquired disease with low severity. The average Sequential Organ Failure Assessment (SOFA) score was low (4.4 ± 4.7). But, a higher SOFA score (adjusted odds ratio 2.5, 95% confidence interval 1.22-5.12; P = 0.01) was an independent factor predicting poor 7-day clinical outcomes in patients with community-acquired H. influenzae bacteremia (n = 39). CONCLUSIONS The overall hospital mortality of 28.1% was observed among patients with bacteremia due to Haemophilus and Aggregatibacter species. A higher SOFA score was and independent predictor of poor 7-day clinical outcomes in patients with community-acquired H. influenzae bacteremia.
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Affiliation(s)
- Ying-Chun Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Tsung Huang
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Division of Infectious Diseases, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Chun-Hsing Liao
- Division of Infectious Diseases, Far Eastern Memorial Hospital, New Taipei City, Taiwan; Department of Medicine, Yang-Ming University, Taipei, Taiwan
| | - Jung-Yien Chien
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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3
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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: 12] [Impact Index Per Article: 2.0] [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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Che Y, Wang L, Wu X, Chen R, Wang C, Zhou L. Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. Open Life Sci 2018; 13:217-226. [PMID: 33817086 PMCID: PMC7874736 DOI: 10.1515/biol-2018-0026] [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: 09/23/2017] [Accepted: 02/27/2018] [Indexed: 12/03/2022] Open
Abstract
Haemophilus parasuis is an important bacterium affecting pigs, causing Glässer’s disease. To further characterize this species, we determined the complete genomic sequence of H. parasuis CL120103, which was isolated from diseased pigs. The strain H. parasuis CL120103 was identified as serovar 2. The size of the largest scaffold is 2,326,318 bp and contains 145 large contigs, with the N50 contig being 20,573 bp in length. The complete genome of H. parasuis CL120103 is 2,305,354 bp in length with 39.97% GC content and contains 2227 protein-coding genes, 19 ribosomal rRNA operons and 60 tRNA genes. Sequence similarity of the genome of H. parasuis CL120103 to the previously sequenced genome of H. parasuis was up to 96% and query cover to 86%. Annotation of the genome of H. parasuis CL120103 identified a number of genes encoding potential virulence factors. These virulence factors are involved in metabolism, adhesion, secretion and LPS biosynthesis. These related genes pave the way to better understand mechanisms underlying metabolic capabilities. The comprehensive genetic and phylogenetic analysis shows that H. parasuis is closely related to Actinobacillus pleuropneumoniae and provides a foundation for future experimental confirmation of the virulence and pathogen-host interactions in H. parasuis.
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Affiliation(s)
- Yongliang Che
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Longbai Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Xuemin Wu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Rujing Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Chenyan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
| | - Lunjiang Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
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5
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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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6
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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7
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Forstner C, Rohde G, Rupp J, Schuette H, Ott SR, Hagel S, Harrison N, Thalhammer F, von Baum H, Suttorp N, Welte T, Pletz MW. Community-acquired Haemophilus influenzae pneumonia--New insights from the CAPNETZ study. J Infect 2016; 72:554-63. [PMID: 26940505 DOI: 10.1016/j.jinf.2016.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 02/04/2016] [Accepted: 02/20/2016] [Indexed: 11/17/2022]
Abstract
OBJECTIVES We aimed to identify clinical characteristics and to assess effectiveness of different initial antibiotic regimens in adult patients with community-acquired pneumonia (CAP) caused by Haemophilus influenzae. METHODS Characteristics were compared between patients with H. influenzae monoinfection versus CAP of other and unknown aetiology enrolled by the German prospective cohort study CAPNETZ. Impact of initial antibiotic treatment on "early clinical response" according to FDA criteria and overall clinical cure were analysed. RESULTS H. influenzae was found in 176 out of 2790 patients with pathogen detection (6.3%). Characteristics significantly associated with a H. influenzae CAP (p < 0.017) included purulent sputum, prior pneumococcal vaccination and respiratory co-morbidities. Early clinical response rates on day 4 did not differ between patients receiving any mono- versus combination therapy (85.9% versus 88%), but were numerically higher for regimens including any fluoroquinolone (96.7%) and lower under macrolide monotherapy (70%). Initial CURB-65 score and chronic liver disease were identified as negative predictors for "early clinical response". At day 14, overall clinical cure was 91.9%. CONCLUSIONS H. influenzae was a common CAP pathogen, particularly in patients with previous pneumococcal vaccination and respiratory co-morbidities. Severity of illness and chronic liver disease were associated with a lower rate of "early clinical response".
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Affiliation(s)
- Christina Forstner
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany; Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria.
| | - Gernot Rohde
- Department of Respiratory Medicine, Maastricht University Medical Center (MUMC+), P. Debyelaan 25, 6202 AZ Maastricht, The Netherlands; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Hartwig Schuette
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Sebastian R Ott
- Department of Pulmonary Medicine, University Hospital (Inselspital) and University of Bern, Freiburgstrasse 4, 3010 Bern, Switzerland
| | - Stefan Hagel
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
| | - Nicole Harrison
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Florian Thalhammer
- Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Heike von Baum
- Institute for Medical Microbiology and Hygiene, Ulm University Hospital, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Tobias Welte
- Department of Pulmonary Medicine, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Carl-Neuberg-Strasse 1, 30625 Hannover, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Mathias W Pletz
- Center for Infectious Diseases and Infection Control, Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany; CAPNETZ STIFTUNG, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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8
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Yayan J, Ghebremedhin B, Rasche K. No development of ciprofloxacin resistance in the Haemophilus species associated with pneumonia over a 10-year study. BMC Infect Dis 2015; 15:514. [PMID: 26567094 PMCID: PMC4644324 DOI: 10.1186/s12879-015-1267-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background The widespread overuse of antibiotics promotes the development of antibiotic resistance in bacteria, which can cause severe illness and constitutes a major public health concern. Haemophilus species are a common cause of community- and nosocomial-acquired pneumonia. The antibiotic resistance of these Gram-negative bacteria can be prevented through the reduction of unnecessary antibiotic prescriptions, the correct use of antibiotics, and good hygiene and infection control. This article examines, retrospectively, antibiotic resistance in patients with community- and nosocomial-acquired pneumonia caused by Haemophilus species. Methods The demographic, clinical, and laboratory data of all patients with community- and nosocomial-acquired pneumonia caused by Haemophilus species were collected from the hospital charts at the HELIOS Clinic, Witten/Herdecke University, Wuppertal, Germany, within a study period from 2004 to 2014. Antimicrobial susceptibility testing was performed for the different antibiotics that have been consistently used in the treatment of patients with pneumonia caused by Haemophilus species. Results During the study period of January 1, 2004, to August 12, 2014, 82 patients were identified with community- and nosocomial-acquired pneumonia affected by Haemophilus species. These patients had a mean age of 63.8 ± 15.5 (60 [73.2 %, 95 % CI 63.6 %–82.8 %] males and 22 [26.8 %, 95 % CI 17.2 %–36.4 %] females). Haemophilus species had a high resistance rate to erythromycin (38.3 %), ampicillin (24.4 %), piperacillin (20.8 %), cefuroxime (8.5 %), ampicillin-sulbactam (7.3 %), piperacillin-sulbactam (4.3 %), piperacillin-tazobactam (2.5 %), cefotaxime (2.5 %), and levofloxacin (1.6 %). In contrast, they were not resistant to ciprofloxacin in patients with pneumonia (P = 0.016). Conclusion Haemophilus species were resistant to many of the typically used antibiotics. Resistance toward ciprofloxacin was not detected in patients with pneumonia caused by Haemophilus species.
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Affiliation(s)
- Josef Yayan
- Witten/Herdecke University, Witten, Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany.
| | - Beniam Ghebremedhin
- Witten/Herdecke University, Witten, Institute of Medical Laboratory Diagnostics, Center for Clinical and Translational Research, HELIOS Clinic Wuppertal, Wuppertal, Germany.
| | - Kurt Rasche
- Witten/Herdecke University, Witten, Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany.
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9
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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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10
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Kluin PM, Langerak AW, Beverdam-Vincent J, Geurts-Giele WRR, Visser L, Rutgers B, Schuuring E, Van Baarlen J, Lam KH, Seldenrijk K, Kibbelaar RE, de Wit P, Diepstra A, Rosati S, van Noesel MM, Zwaan CM, Hunting JCB, Hoogendoorn M, van der Gaag EJ, van Esser JWJ, de Bont E, Kluin-Nelemans HC, Winter RH, Lo ten Foe JR, van der Zanden AGM. Paediatric nodal marginal zone B-cell lymphadenopathy of the neck: a Haemophilus influenzae
-driven immune disorder? J Pathol 2015; 236:302-14. [DOI: 10.1002/path.4524] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 02/10/2015] [Accepted: 02/23/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Philip M Kluin
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Anton W Langerak
- Department of Immunology, Erasmus MC; University Medical Centre Rotterdam; Rotterdam The Netherlands
| | - Jannetta Beverdam-Vincent
- Microbiology and Infection Control, Zorggroep Twente; Hengelo The Netherlands
- Laboratory for Microbiology; Twente Achterhoek Hengelo The Netherlands
| | | | - Lydia Visser
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Bea Rutgers
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Ed Schuuring
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | | | - King H Lam
- Department of Pathology, Erasmus Medical Centre Rotterdam; EMCR; Rotterdam The Netherlands
| | - Kees Seldenrijk
- Department of Pathology; St Antonius Hospital; Nieuwegein The Netherlands
| | - Robby E Kibbelaar
- Department of Pathology; Pathologie Friesland; Leeuwarden The Netherlands
| | - Peter de Wit
- Department of Pathology; Amphia Hospital; Breda The Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Stefano Rosati
- Department of Pathology and Medical Biology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Max M van Noesel
- Department of Oncology and Hematology; Sophia Children Hospital; Rotterdam The Netherlands
| | - C Michel Zwaan
- Department of Oncology and Hematology; Sophia Children Hospital; Rotterdam The Netherlands
| | - Jarmo CB Hunting
- Department of Internal Medicine; St Antonius Ziekenhuis; Nieuwegein The Netherlands
| | - Mels Hoogendoorn
- Department of Internal Medicine; Medisch Centrum Leeuwarden; The Netherlands
| | | | | | - Eveline de Bont
- Department of Pediatric Oncology & Hematology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Hanneke C Kluin-Nelemans
- Department of Hematology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Rik H Winter
- Department of Medical Microbiology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Jerome R Lo ten Foe
- Department of Medical Microbiology; University Medical Centre Groningen, University of Groningen; Groningen The Netherlands
| | - Adri GM van der Zanden
- Microbiology and Infection Control, Zorggroep Twente; Hengelo The Netherlands
- Laboratory for Microbiology; Twente Achterhoek Hengelo The Netherlands
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11
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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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