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Willems E, Hamerlinck H, Messiaen AS, Schelstraete P, Van Braeckel E, Vande Weygaerde Y, Verhasselt B, Boelens J, Vandendriessche S. Expansion of MALDI-TOF MS database as a strategy for identification of Haemophilus species other than H. influenzae. Acta Clin Belg 2024:1-7. [PMID: 39101268 DOI: 10.1080/17843286.2024.2386216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024]
Abstract
OBJECTIVES This study aimed to evaluate an expanded matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF MS) database for the identification of Haemophilus species other than H. influenzae (Hi). METHODS A total of 144 Haemophilus species, cultured from respiratory samples from people (living) with cystic fibrosis, were identified with MALDI-TOF MS and 16S rRNA sequencing. Of these, 99 Haemophilus strains showed >99% similarity with the best matching strain in the National Center for Biotechnology Information (NCBI) database and were assigned to a single Haemophilus subspecies using both MALDI-TOF MS and 16S rRNA sequencing. The MS profiles of a subset of strains (n = 58/99) were added to the Bruker MALDI-TOF MS database. Subsequently, 270 different strains that were analyzed previously in a routine setting were re-analyzed. RESULTS 16S rRNA sequencing reliably identified 99/144 Haemophilus strains (>99% similarity). H. haemolyticus 16S rRNA identification was suboptimal since only 3/21 H. haemolyticus strains attained a similarity of >99% with H. haemolyticus 16S rRNA sequence in the NCBI database. Expansion of the MALDI-TOF MS database improved the number of reliable identifications only moderately for H. haemolyticus, H. influenzae and H. paraphrohaemolyticus (<10%). By contrast, improved identification was more outspoken for H. parahaemolyticus, H. parainfluenzae, H. sputorum and H. pittmaniae (>85%). CONCLUSION 16S rRNA sequencing is a valuable method for the identification of Haemophilus sp. other than Hi. Expansion of the MALDI-TOF MS database, based on 16S rRNA sequencing results, increased the proportion of reliable identifications and in this study resulted in an increase of 10% of Haemophilus sp. other than Hi strain identifications.
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Affiliation(s)
- Eva Willems
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Hannelore Hamerlinck
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Petra Schelstraete
- Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Eva Van Braeckel
- Respiratory Infection and Defense Lab (RIDL), Department of Internal Medicine and Paediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Bruno Verhasselt
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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Ruiz Del Pino M, Rosales-Castillo A, Hidalgo-Tenorio C, Expósito-Ruiz M, Navarro-Marí JM, Gutiérrez-Fernández J. [Isolation of Haemophilus no ducreyi in samples from the genital tract of men: Its clinical relationship]. Rev Int Androl 2023; 21:100374. [PMID: 37413940 DOI: 10.1016/j.androl.2023.100374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 07/08/2023]
Abstract
INTRODUCTION With the advancement of microbiological methods, the isolation of less typical pathogens in cases of urethral and rectal infection is more frequent, apart from the classic etiological agents. One of them is formed by species of Haemophilus no ducreyi (HND). The objective of this work is to describe frequency, susceptibility to antibiotics, and clinical features of HDN urethritis and proctitis in adult males. PATIENTS AND METHODS This is an observational retrospective descriptive study of the results obtained by the Microbiology laboratory of the Virgen de las Nieves University Hospital on the isolates of HND in genital and rectal samples from males between 2016 and 2019. RESULTS HND was isolated in 135 (7%) of the genital infection episodes diagnosed in men. H. parainfluenzae was the most commonly isolated (34/45; 75.6%). The most frequent symptoms in men with proctitis were rectal tenesmus (31.6%) and lymphadenopathy (10.5%); in those with urethritis, dysuria (71.6%), urethral suppuration (46.7%) and gland lesions (27%), so differentiating it from infections caused by other genitopathogens is difficult. 43% of patients were HIV positive. Antibiotic resistance rates for H. parainfluenzae were high to quinolons, ampicillin, tetracycline and macrolides. CONCLUSION HND species should be considered as possible etiologic agents in episodes of urethral and rectal infection in men, especially in cases with negative screening tests for agents that cause sexually transmitted infections (STIs). Its microbiological identification is essential for the establishment of an effective targeted treatment.
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Affiliation(s)
- Marta Ruiz Del Pino
- Departamento de Microbiología, Hospital Universitario Virgen de las Nieves-IBS, Granada, España
| | - Antonio Rosales-Castillo
- Servicio de Medicina Interna, Hospital Universitario Virgen de las Nieves-IBS, Granada, España; Departamento de Microbiología, Facultad de Medicina, Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada-IBS, Granada, España.
| | - Carmen Hidalgo-Tenorio
- Unidad de Enfermedades Infecciosas, Hospital Universitario Virgen de las Nieves-IBS, Granada, España
| | - Manuela Expósito-Ruiz
- Departamento de Bioestadística de FIBAO, Hospital Universitario Virgen de las Nieves-IBS, Granada, España
| | - José María Navarro-Marí
- Departamento de Microbiología, Facultad de Medicina, Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada-IBS, Granada, España
| | - José Gutiérrez-Fernández
- Departamento de Microbiología, Hospital Universitario Virgen de las Nieves-IBS, Granada, España; Departamento de Microbiología, Facultad de Medicina, Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada-IBS, Granada, España
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Ruiz Del Pino M, Rosales-Castillo A, Navarro-Marí JM, Gutiérrez-Fernández J. Clinical significance of isolation of Haemophilus no ducreyi in genital samples. Systematic review. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2023; 41:468-484. [PMID: 36443187 DOI: 10.1016/j.eimce.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/16/2022] [Accepted: 02/24/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION AND OBJECTIVES Currently, the microbiological diagnosis of genital infections is carried out with molecular methods, which allow the detection of less frequent etiological agents but with potential pathogenic importance, such as Haemophilus spp. The objective of this review is to analyse and highlight the clinical importance of the isolation of Haemophilus spp. in genital and rectal infections, excluding Haemophilus ducreyi. MATERIAL AND METHODS A systematic review was carried out based on an exhaustive search of the publications included in the MEDLINE database up to August 5, 2021, on the presence of Haemophilus spp. in genital and rectal infections, excluding H. ducreyi. RESULTS After reviewing what was described in the literature, Haemophilus spp. (excluding H. ducreyi: HSNOD) was detected in 2397 episodes of genital infection, the most frequently isolated species being H. influenzae and H. parainfluenzae. Most of the episodes (87,6%) are constituted by single isolation. There is a slight predominance in women (48,3%) where it can cause vaginitis, salpingitis, endometritis or complications during pregnancy. In men, the clinical picture usually corresponds to urethritis. Most of the samples correspond to vaginal and urethral exudates, with a minority representation at the rectal level (2.3%). CONCLUSION HSNOD plays a relevant pathogenic role in episodes of genital infection, so microbiological diagnostic protocols must include methods that allow their detection, as well as include them in the etiological spectrum of this type of clinical picture.
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Affiliation(s)
- Marta Ruiz Del Pino
- Departamento de Microbiología, Facultad de Medicina, Universidad de Granada-ibs, Granada, Spain
| | - Antonio Rosales-Castillo
- Servicio de Medicina Interna, Hospital Universitario Virgen de las Nieves-ibs, Granada, Spain; Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada, Granada, Spain.
| | - José María Navarro-Marí
- Departamento de Microbiología, Hospital Universitario Virgen de las Nieves-ibs, Granada, Spain; Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada, Granada, Spain
| | - José Gutiérrez-Fernández
- Departamento de Microbiología, Facultad de Medicina, Universidad de Granada-ibs, Granada, Spain; Programa de Doctorado en Medicina Clínica y Salud Pública, Universidad de Granada, Granada, Spain
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Chen X, Zhang H, Feng J, Zhang L, Zheng M, Luo H, Zhuo H, Xu N, Zhang X, Chen C, Qu P, Li Y. Comparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis. Microbiol Spectr 2023; 11:e0477222. [PMID: 37382545 PMCID: PMC10434262 DOI: 10.1128/spectrum.04772-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/10/2023] [Indexed: 06/30/2023] Open
Abstract
Haemophilus seminalis is a newly proposed species that is phylogenetically related to Haemophilus haemolyticus. The distribution of H. seminalis in the human population, its genomic diversity, and its pathogenic potential are still unclear. This study reports the finding of our comparative genomic analyses of four newly isolated Haemophilus strains (SZY H8, SZY H35, SZY H36, and SZY H68) from human sputum specimens (Guangzhou, China) along with the publicly available genomes of other phylogenetically related Haemophilus species. Based on pairwise comparisons of the 16S rRNA gene sequences, the four isolates showed <98.65% sequence identity to the type strains of all known Haemophilus species but were identified as belonging to H. seminalis, based on comparable phenotypic and genotypic features. Additionally, the four isolates showed high genome-genome relatedness indices (>95% ANI values) with 17 strains that were previously identified as either "Haemophilus intermedius" or hemin (X-factor)-independent H. haemolyticus and therefore required a more detailed classification study. Phylogenetically, these isolates, along with the two previously described H. seminalis isolates (a total of 23 isolates), shared a highly homologous lineage that is distinct from the clades of the main H. haemolyticus and Haemophilus influenzae strains. These isolates present an open pangenome with multiple virulence genes. Notably, all 23 isolates have a functional heme biosynthesis pathway that is similar to that of Haemophilus parainfluenzae. The phenotype of hemin (X-factor) independence and the analysis of the ispD, pepG, and moeA genes can be used to distinguish these isolates from H. haemolyticus and H. influenzae. Based on the above findings, we propose a reclassification for all "H. intermedius" and two H. haemolyticus isolates belonging to H. seminalis with an emended description of H. seminalis. This study provides a more accurate identification of Haemophilus isolates for use in the clinical laboratory and a better understanding of the clinical significance and genetic diversity in human environments. IMPORTANCE As a versatile opportunistic pathogen, the accurate identification of Haemophilus species is a challenge in clinical practice. In this study, we characterized the phenotypic and genotypic features of four H. seminalis strains that were isolated from human sputum specimens and propose the "H. intermedius" and hemin (X-factor)-independent H. haemolyticus isolates as belonging to H. seminalis. The prediction of virulence-related genes indicates that H. seminalis isolates carry several virulence genes that are likely to play an important role in its pathogenicity. In addition, we depict that the genes ispD, pepG, and moeA can be used as biomarkers for distinguishing H. seminalis from H. haemolyticus and H. influenzae. Our findings provide some insights into the identification, epidemiology, genetic diversity, pathogenic potential, and antimicrobial resistance of the newly proposed H. seminalis.
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Affiliation(s)
- Xiaowei Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hanyun Zhang
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
| | - Junhui Feng
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lei Zhang
- Guangzhou Kingmed Center for Clinical Laboratory, Guangzhou, China
| | - Minling Zheng
- Department of Clinical Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
| | - Haimin Luo
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Huiyan Zhuo
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
| | - Ning Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xuan Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Pinghua Qu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Youqiang Li
- Department of Laboratory Medicine, The Affiliated Hexian Memorial Hospital of Southern Medical University, Guangzhou, China
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Roy D, Kim J, Lee M, Park J. Adverse impacts of Asian dust events on human health and the environment-A probabilistic risk assessment study on particulate matter-bound metals and bacteria in Seoul, South Korea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162637. [PMID: 36889412 DOI: 10.1016/j.scitotenv.2023.162637] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
This study aimed to assess the impact of Asian dust (AD) on the human health and the environment. Particulate matter (PM) and PM-bound trace elements and bacteria were examined to determine the chemical and biological hazards associated with AD days and compared with non-AD days in Seoul. On AD days, the mean PM10 concentration was ∼3.5 times higher than that on non-AD days. Elements generated from the Earth's crust (Al, Fe, and Ca) and anthropogenic sources (Pb, Ni, and Cd) were identified as major contributors to coarse and fine particles, respectively. During AD days, the study area was recognized as "severe" for pollution index and pollution load index levels, and "moderately to heavily polluted" for geoaccumulation index levels. The potential cancer risk (CR) and non-CR were estimated for the dust generated during AD events. On AD days, total CR levels were significant (in 1.08 × 10-5-2.22 × 10-5), which were associated with PM-bound As, Cd, and Ni. In addition, inhalation CR was found to be similar to the incremental lifetime CR levels estimated using the human respiratory tract mass deposition model. In a short exposure duration (14 days), high PM and bacterial mass deposition, significant non-CR levels, and a high presence of potential respiratory infection-causing pathogens (Rothia mucilaginosa) were observed during AD days. Significant non-CR levels were observed for bacterial exposure, despite insignificant levels of PM10-bound elements. Therefore, the substantial ecological risk, CR, and non-CR levels for inhalation exposure to PM-bound bacteria, and the presence of potential respiratory pathogens, indicate that AD events pose a significant risk to both human lung health and the environment. This study provides the first comprehensive examination of significant non-CR levels for bacteria and carcinogenicity of PM-bound metals during AD events.
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Affiliation(s)
- Debananda Roy
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jayun Kim
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Minjoo Lee
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Joonhong Park
- Department of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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Limaye MA, Brubaker S, Randis TM, Ratner AJ. Vaginal carriage of Haemophilus influenzae in a non-pregnant reproductive-age population. BMC Microbiol 2023; 23:141. [PMID: 37208594 PMCID: PMC10197216 DOI: 10.1186/s12866-023-02885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Haemophilus influenzae (Hi) is an emerging cause of early onset neonatal sepsis, but mechanisms of transmission are not well understood. We aimed to determine the prevalence of vaginal carriage of Hi in reproductive age women and to examine behavioral and demographic characteristics associated with its carriage. METHODS We performed a secondary analysis of stored vaginal lavage specimens from a prospective cohort study of nonpregnant reproductive-age women. After extraction of bacterial genomic DNA, samples were tested for the presence of the gene encoding Haemophilus protein d (hpd) by quantitative real-time polymerase chain reaction (PCR) using validated primers and probe. PCR for the V3-V4 region of the 16 S rRNA gene (positive control) assessed sample quality. Samples with cycle threshold (CT) value < 35 were defined as positive. Sanger sequencing confirmed the presence of hpd. Behavioral and demographic characteristics associated with vaginal carriage of Hi were examined. RESULTS 415 samples were available. 315 (75.9%) had sufficient bacterial DNA and were included. 14 (4.4%) were positive for hpd. There were no demographic or behavioral differences between the women with Hi vaginal carriage and those without. There was no difference in history of bacterial vaginosis, vaginal microbiome community state type, or presence of Group B Streptococcus in women with and without vaginal carriage of Hi. CONCLUSION Hi was present in vaginal lavage specimens of 4.4% of this cohort. Hi presence was unrelated to clinical or demographic characteristics, though the relatively small number of positive samples may have limited power to detect such differences.
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Affiliation(s)
- Meghana A Limaye
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, USA.
| | - Sara Brubaker
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, USA
| | - Tara M Randis
- Department of Pediatrics, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Adam J Ratner
- Department of Pediatrics, New York University Grossman School of Medicine, New York, NY, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
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Almas S, Carpenter RE, Singh A, Rowan C, Tamrakar VK, Sharma R. Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential. Adv Respir Med 2023; 91:49-65. [PMID: 36825940 PMCID: PMC9952210 DOI: 10.3390/arm91010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify® Platform (Illumina® Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.
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Affiliation(s)
- Sadia Almas
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
| | - Rob E. Carpenter
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
- Department of Human Resource Development, University of Texas at Tyler, 3900 University Boulevard, Tyler, TX 75799, USA
- Correspondence: ; Tel.: +1-903-530-1700
| | - Anuradha Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
| | - Chase Rowan
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
| | - Vaibhav K. Tamrakar
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
- RetroBioTech LLC, 838 Dalmalley Ln, Coppell, TX 75019, USA
| | - Rahul Sharma
- Department of Research, Advanta Genetics, 10935 CR 159, Tyler, TX 75703, USA
- ICMR-National Institute of Research in Tribal Health, Jabalpur 482003, India
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Ruiz del Pino M, Rosales-Castillo A, Navarro-Marí JM, Gutiérrez-Fernández J. Importancia clínica del aislamiento de Haemophilus spp. (excluyendo H. ducreyi) en muestras genitales. Revisión sistemática. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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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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Haemophilin-Producing Strains of Haemophilus haemolyticus Protect Respiratory Epithelia from NTHi Colonisation and Internalisation. Pathogens 2021; 10:pathogens10010029. [PMID: 33401487 PMCID: PMC7823694 DOI: 10.3390/pathogens10010029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 11/17/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a significant respiratory tract pathogen responsible for infections that collectively pose a substantial health and socioeconomic burden. The clinical course of these infections is largely dictated by NTHi interactions with host respiratory epithelia, and thus, approaches that disrupt colonisation and invasion may have significant therapeutic potential. Survival, successful host–cell interactions, and pathogenesis are reliant on NTHi’s ability to sequester host-derived haem. Previously, we demonstrated the therapeutic potential of exploiting this haem-dependence using a closely related competitor bacterium, Haemophilus haemolyticus (Hh). Hh strains capable of producing the novel haem-binding protein haemophilin (Hpl) possessed potent inhibitory activity by restricting NTHi access to haem in a broth co-culture environment. Here, we extend this work to cell culture models that more closely represent the human respiratory epithelium and show that Hh strains with high levels of hpl expression protect epithelial cell line monolayers against adhesion and invasion by NTHi. Inhibitory activity was dependent on the level of Hpl production, which was stimulated by NTHi challenge and nasopharyngeal cell exposure. Provided these protective benefits translate to in vivo applications, Hpl-producing Hh may have probiotic utility against NTHi infections by inhibiting requisite nasopharyngeal colonisation.
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11
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Harris TM, Price EP, Sarovich DS, Nørskov-Lauritsen N, Beissbarth J, Chang AB, Smith-Vaughan HC. Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of ' Haemophilus intermedius'. Microb Genom 2020; 6. [PMID: 31860436 PMCID: PMC7067038 DOI: 10.1099/mgen.0.000303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The heterogeneous and highly recombinogenic genus Haemophilus comprises several species, some of which are pathogenic to humans. All share an absolute requirement for blood-derived factors during growth. Certain species, such as the pathogen Haemophilus influenzae and the commensal Haemophilus haemolyticus, are thought to require both haemin (X-factor) and nicotinamide adenine dinucleotide (NAD, V-factor), whereas others, such as the informally classified 'Haemophilus intermedius subsp. intermedius', and Haemophilus parainfluenzae, only require V-factor. These differing growth requirements are commonly used for species differentiation, although a number of studies are now revealing issues with this approach. Here, we perform large-scale phylogenomics of 240 Haemophilus spp. genomes, including five 'H. intermedius' genomes generated in the current study, to reveal that strains of the 'H. intermedius' group are in fact haemin-independent H. haemolyticus (hiHh). Closer examination of these hiHh strains revealed that they encode an intact haemin biosynthesis pathway, unlike haemin-dependent H. haemolyticus and H. influenzae, which lack most haemin biosynthesis genes. Our results suggest that the common ancestor of modern-day H. haemolyticus and H. influenzae lost key haemin biosynthesis loci, likely as a consequence of specialized adaptation to otorhinolaryngeal and respiratory niches during their divergence from H. parainfluenzae. Genetic similarity analysis demonstrated that the haemin biosynthesis loci acquired in the hiHh lineage were likely laterally transferred from a H. parainfluenzae ancestor, and that this event probably occurred only once in hiHh. This study further challenges the validity of phenotypic methods for differentiating among Haemophilus species, and highlights the need for whole-genome sequencing for accurate characterization of species within this taxonomically challenging genus.
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Affiliation(s)
- Tegan M Harris
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | | | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Anne B Chang
- Department of Respiratory and Sleep Medicine, Queensland Children's Hospital, Brisbane, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Heidi C Smith-Vaughan
- School of Medicine, Griffith University, Gold Coast, QLD, Australia.,Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
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12
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Weber S, Kabelitz M, Kabelitz N, Schoenborn V. Haemophilus haemolyticus: an atypical pathogen of septic arthritis of the knee joint. J Surg Case Rep 2020; 2020:rjaa318. [PMID: 32968477 PMCID: PMC7497065 DOI: 10.1093/jscr/rjaa318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 11/14/2022] Open
Abstract
Septic knee arthritis is a common disease, mostly due to bacterial infections. We describe a rare case of Haemophilus haemolyticus causing unilateral septic arthritis of a native knee. The affected patient presented with persistent severe knee pain after repeated intra-articular injections. Patient history included knee arthroscopy and a known rheumatoid arthritis treated by steroids. Since conservative treatment was ineffective and infection could not be excluded, diagnostic arthroscopy was performed. Synovial fluid and biopsies verified the uncommon microorganism and antibiotic therapy was initiated. Clinical findings and blood results showed rapid improvement. The patient was discharged in a good condition after 6 weeks. A review of the current literature describes only one joint infection with H. haemolyticus as underlying cause. In immunocompromised patients with septic knee arthritis also atypical pathogens must be considered. Nevertheless, the established treatment algorithm with arthroscopy and anti-infective therapy seems to be effective leading to satisfactory results.
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Affiliation(s)
- Sabrina Weber
- Department of Orthopaedic Surgery, Kantonsspital Graubünden, Chur, Switzerland
| | - Method Kabelitz
- Department of Orthopaedic Surgery, Spitalregion Rheintal, Werdenberg, Switzerland
| | - Nina Kabelitz
- Department of Orthopaedic Surgery, Kantonsspital Graubünden, Chur, Switzerland
| | - Veit Schoenborn
- Department of Orthopaedic Surgery, Kantonsspital Graubünden, Chur, Switzerland
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13
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Hoang VT, Dao TL, Ly TDA, Belhouchat K, Larbi Chaht K, Yezli S, Alotaibi B, Raoult D, Parola P, Pommier de Santi V, Fournier PE, Gautret P. Dynamics and genetic diversity of Haemophilus influenzae carriage among French pilgrims during the 2018 Hajj: A prospective cohort survey. Travel Med Infect Dis 2020; 38:101883. [PMID: 32956850 DOI: 10.1016/j.tmaid.2020.101883] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 07/01/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND To investigate the genetic diversity of Haemophilus influenzae positive samples among French pilgrims attending the 2018 Hajj pilgrimage. METHOD After screening by qPCR, multilocus sequence typing was performed for all H. influenzae-positive samples. The following housekeeping genes were amplified and assigned: adk, atpG, frdB, fucK, mdh, pgi and recA. RESULTS 121 pilgrims were included. H. influenzae was positive in 35.5% pre-Hajj samples, 12.4% at day five post-arrival, 15.7% at day 12 post-arrival, and 43.0% post-Hajj. Of the 129 positive swabs for H. influenzae, only one sample at D12 was negative for all seven genes amplified by standard PCR. The adk, atpG, frdB, mdh, pgi, recA and fucK genes were positive in 123, 107, 122, 70, 127, 118 and 69 samples, respectively. One sequence of atpG and two of recA genes were not possible to assign. None of the sequences of fucK gene was successfully obtained. Consequently, a complete sequence type characterisation was not possible. Of the 128 obtained strains, 111 had distinct patterns of alleles. CONCLUSION H. influenzae genotypes acquired were completely different from those present at pre-Hajj. We observed a great biodiversity and a lack of clonality of H. influenzae among French pilgrims during the 2018 Hajj. Further studies aiming at studying the genome of Hajj-acquired H. influenzae isolates are needed to define the clinical burden of H. influenzae infection during Hajj and to evaluate the potential interest of vaccination in Hajj pilgrims.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Thi-Loi Dao
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Khadidja Belhouchat
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Kamel Larbi Chaht
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Saber Yezli
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Badriah Alotaibi
- The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Vincent Pommier de Santi
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; French Military Center for Epidemiology and Public Health Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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14
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Antibody Binding and Complement-Mediated Killing of Invasive Haemophilus influenzae Isolates from Spain, Portugal, and the Netherlands. Infect Immun 2020; 88:IAI.00454-20. [PMID: 32719154 DOI: 10.1128/iai.00454-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Haemophilus influenzae is a Gram-negative bacterium that can be classified into typeable (types a through f) and nontypeable (NTHi) groups. This opportunistic pathogen asymptomatically colonizes the mucosal epithelium of the upper respiratory tract, from where it spreads to other neighboring regions, potentially leading to disease. Infection with NTHi can cause otitis media, sinusitis, conjunctivitis, exacerbations of chronic obstructive pulmonary disease, and pneumonia, but it is increasingly causing invasive disease, including bacteremia and meningitis. Invasive NTHi strains are more resistant to complement-mediated killing. However, the mechanisms of complement resistance have never been studied in large numbers of invasive NTHi strains. In this study, we determined the relationship between binding of IgG or IgM and the bacterial survival in normal human serum for 267 invasive H. influenzae strains from Spain, Portugal, and the Netherlands, of which the majority (200 [75%]) were NTHi. NTHi bacteria opsonized with high levels of IgM had the lowest survival in human serum. IgM binding to the bacterial surface, but not IgG binding, was shown to be associated with complement-mediated killing of NTHi strains. We conclude that evasion of IgM binding by NTHi strains increases survival in blood, thereby potentially contributing to their ability to cause severe invasive diseases.
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15
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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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16
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Tchatchouang S, Nzouankeu A, Hong E, Terrade A, Denizon M, Deghmane AE, Ndiang SMT, Pefura-Yone EW, Penlap Beng V, Njouom R, Fonkoua MC, Taha MK. Analysis of Haemophilus species in patients with respiratory tract infections in Yaoundé, Cameroon. Int J Infect Dis 2020; 100:12-20. [PMID: 32827751 DOI: 10.1016/j.ijid.2020.08.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES To identifyHaemophilus species and characterize antimicrobial susceptibility of isolates from patients with respiratory tract infections (RTIs) in Cameroon. METHODS Isolates (n = 95) were from patients with RTIs obtained from two Hospitals in Yaoundé, Cameroon. Isolates were identified by biochemical assay, PCR-based method, MALDI-TOF and whole genome sequencing. Antibiotic minimum inhibitory concentrations were determined by E-test. RESULTS H. influenzae was the most prevalent species varying from 76.8% to 84.2% according to different methods. The isolates were mainly nontypable (n = 70, 96%). Three isolates of H. influenzae were capsulated (b, e and f). The isolates were genetically diverse and 40 unique sequence types were identified including 11 new ones. Resistance to ampicillin was observed among 55.3% (52/94) and 9% (14/52) produced TEM-1 β-lactamase. PBP3 mutations occurred in 57.7% of ampicillin resistant isolates (30/52). Eleven isolates were chloramphenicol resistant with 80% producing chloramphenicol acetyltransferase (8/10). Four Haemophilus isolates were rifampicin resistant with two mutations in rpoB gene. Five isolates were ciprofloxacin resistant and harbored mutations in the quinolone resistance determining regions of gyrA and parC genes. CONCLUSION H. influenzae isolates are highly diverse and show high levels of antibiotic resistance. H. influenzae serotype b is still circulating in the post-vaccination era.
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Affiliation(s)
- Serges Tchatchouang
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon; Department of Bacteriology, Centre Pasteur of Cameroon, Yaoundé, Cameroon; Department of Biochemistry, University of Yaoundé, Yaoundé, Cameroon; Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France
| | - Ariane Nzouankeu
- Department of Bacteriology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | - Eva Hong
- Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France
| | - Aude Terrade
- Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France
| | - Mélanie Denizon
- Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France
| | - Ala-Eddine Deghmane
- Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France
| | | | | | | | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, Yaoundé, Cameroon
| | | | - Muhamed-Kheir Taha
- Invasive Bacterial Infections Unit, National Reference Centre for Meningococci and Haemophilus influenzae, Institut Pasteur, Paris, France.
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In Vitro Anti-NTHi Activity of Haemophilin-Producing Strains of Haemophilus haemolyticus. Pathogens 2020; 9:pathogens9040243. [PMID: 32218184 PMCID: PMC7238096 DOI: 10.3390/pathogens9040243] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 12/21/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a leading causative organism of opportunistic respiratory tract infections. However, there are currently no effective vaccination strategies, and existing treatments are compromised by antibiotic resistance. We previously characterized Haemophilus haemolyticus (Hh) strains capable of producing haemophilin (HPL), a heme-binding protein that restricts NTHi growth by limiting its access to an essential growth factor, heme. Thus, these strains may have utility as a probiotic therapy against NTHi infection by limiting colonization, migration and subsequent infection in susceptible individuals. Here, we assess the preliminary feasibility of this approach by direct in vitro competition assays between NTHi and Hh strains with varying capacity to produce HPL. Subsequent changes in NTHi growth rate and fitness, in conjunction with HPL expression analysis, were employed to assess the NTHi-inhibitory capacity of Hh strains. HPL-producing strains of Hh not only outcompeted NTHi during short-term and extended co-culture, but also demonstrated a growth advantage compared with Hh strains unable to produce the protein. Additionally, HPL expression levels during competition correlated with the NTHi-inhibitory phenotype. HPL-producing strains of Hh demonstrate significant probiotic potential against NTHi colonization in the upper respiratory tract, however, further investigations are warranted to demonstrate a range of other characteristics that would support the eventual development of a probiotic.
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18
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Comparative Clinical Evaluation of NeoPlex RB-8 with Seeplex PneumoBacter ACE for Simultaneous Detection of Eight Respiratory Bacterial Pathogens. J Clin Microbiol 2020; 58:JCM.01500-19. [PMID: 31748320 DOI: 10.1128/jcm.01500-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/06/2019] [Indexed: 11/20/2022] Open
Abstract
There are several convenient and accurate molecular assays to detect respiratory bacterial infection. The NeoPlex RB-8 detection kit (NeoPlex RB-8) is a new multiplex real-time PCR assay that simultaneously detects Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, Haemophilus influenzae, Bordetella pertussis, Bordetella parapertussis, and Moraxella catarrhalis in a single test. This study compared the clinical concordance of NeoPlex RB-8 with another method, Seeplex PneumoBacter ACE detection assay (Seeplex PB ACE), which simultaneously detects S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis We tested 2,137 nasopharyngeal swab and sputum specimens using both assays. For discordant Bordetella parapertussis and M. catarrhalis specimens, we also performed bidirectional sequencing. For S. pneumoniae, M. pneumoniae, C. pneumoniae, L. pneumophila, H. influenzae, and B. pertussis, which are detected by both NeoPlex RB-8 and Seeplex PB ACE, the positive and negative agreement between the two assays ranged from 91.7 to 100% (κ = 0.918 to 1). S. pneumoniae and H. influenzae were the most discordant targets and measured with higher sensitivity and specificity by NeoPlex RB-8 than Seeplex PB ACE. For Bordetella parapertussis and M. catarrhalis, which are not detected by Seeplex PB ACE, NeoPlex RB-8 sensitivity and specificity were >99%. Overall, NeoPlex RB-8 was highly comparable to Seeplex PB ACE, but NeoPlex RB-8 was more clinically accurate, with higher throughput and more convenience.
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19
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Identification and Characterization of " Haemophilus quentini" Strains Causing Invasive Disease in Ontario, Canada (2016 to 2018). J Clin Microbiol 2019; 57:JCM.01254-19. [PMID: 31578259 DOI: 10.1128/jcm.01254-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/07/2019] [Indexed: 11/20/2022] Open
Abstract
Haemophilus influenzae is a well-established human pathogen capable of causing a range of respiratory and invasive diseases. Since the 1970s, it has been observed that a nontypeable cryptic genospecies of H. influenzae, most often biotype IV, has been associated with the genitourinary tracts of females and with invasive neonatal infections. This distinct genospecies has been provisionally named "Haemophilus quentini" Here, we report seven cases of invasive H. quentini disease in patients from Ontario, Canada, over a 2-year period. Significantly, while most reports of invasive disease with H. quentini to date have been in neonates, we observed five cases in adults (three in women of childbearing age and two in seniors) as well as two in neonates. Identification of H. quentini is challenging and was not possible for frontline laboratories, requiring work at the reference laboratory level. We describe in detail the biochemical results, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-Tof MS) results, and PCR results with several targets, including the 16S rRNA gene and multilocus sequence typing (MLST) genes, for the seven Ontario H. quentini isolates and several controls. Our data, combined with those of other publications, support the fact that H. quentini is distinct from H. influenzae and Haemophilus haemolyticus This organism is recognized as a pathogen of neonates, but we hypothesize that it may be underrecognized as an important pathogen in adults as well, particularly pregnant women. By sharing the detailed descriptions of these isolates, we hope to enable other laboratories to better identify H. quentini so that the true prevalence of this organism and disease can be explored.
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20
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Wootton DG, Cox MJ, Gloor GB, Litt D, Hoschler K, German E, Court J, Eneje O, Keogan L, Macfarlane L, Wilks S, Diggle PJ, Woodhead M, Moffatt MF, Cookson WOC, Gordon SB. A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease. Sci Rep 2019; 9:2388. [PMID: 30787368 PMCID: PMC6382935 DOI: 10.1038/s41598-018-38090-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/18/2018] [Indexed: 11/08/2022] Open
Abstract
The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.
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Affiliation(s)
- Daniel G Wootton
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
- Department of Respiratory Research, Aintree University Hospital NHS Foundation Trust, Liverpool, UK.
| | - Michael J Cox
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Gregory B Gloor
- Departments of Biochemistry and Applied Mathematics, University of Western Ontario, Ontario, ON, Canada
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katja Hoschler
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Esther German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Joanne Court
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Odiri Eneje
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Lynne Keogan
- Department of Respiratory Research, Aintree University Hospital NHS Foundation Trust, Liverpool, UK
| | - Laura Macfarlane
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sarah Wilks
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Peter J Diggle
- CHICAS, Lancaster University Medical School, Lancaster University, Lancaster, UK
| | - Mark Woodhead
- Department of Respiratory Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Manchester Academic Health Science Centre and Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - William O C Cookson
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Stephen B Gordon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- The Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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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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22
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Misawa K, Tarumoto N, Tamura S, Osa M, Hamamoto T, Yuki A, Kouzaki Y, Imai K, Ronald RL, Yamaguchi T, Murakami T, Maesaki S, Suzuki Y, Kawana A, Maeda T. Single nucleotide polymorphisms in genes encoding penicillin-binding proteins in β-lactamase-negative ampicillin-resistant Haemophilus influenzae in Japan. BMC Res Notes 2018; 11:53. [PMID: 29352811 PMCID: PMC5775570 DOI: 10.1186/s13104-018-3169-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/12/2018] [Indexed: 01/31/2023] Open
Abstract
Objective β-Lactamase-negative ampicillin-resistant Haemophilus influenzae is a common opportunistic pathogen of hospital- and community-acquired infections, harboring multiple single nucleotide polymorphisms in the ftsI gene, which codes for penicillin-binding protein-3. The objectives of this study were to perform comprehensive genetic analyses of whole regions of the penicillin-binding proteins in H. influenzae and to identify additional single nucleotide polymorphisms related to antibiotic resistance, especially to ampicillin and other cephalosporins. Results In this genome analysis of the ftsI gene in 27 strains of H. influenzae, 10 of 23 (43.5%) specimens of group III genotype β-lactamase-negative ampicillin-resistant H. influenzae were paradoxically classified as ampicillin-sensitive phenotypes. Unfortunately, we could not identify any novel mutations that were significantly associated with ampicillin minimum inhibitory concentrations in other regions of the penicillin-binding proteins, and we reconfirmed that susceptibility to β-lactam antibiotics was mainly defined by previously reported SNPs in the ftsI gene. We should also consider detailed changes in expression that lead to antibiotic resistance in the future because the acquisition of resistance to antimicrobials can be predicted by the expression levels of a small number of genes. Electronic supplementary material The online version of this article (10.1186/s13104-018-3169-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kazuhisa Misawa
- Department of Infectious Diseases and Pulmonary Medicine, National Defense Medical College, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Shinsuke Tamura
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Morichika Osa
- Department of Infectious Diseases and Pulmonary Medicine, National Defense Medical College, Saitama, Japan
| | - Takaaki Hamamoto
- Department of Laboratory Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Atsushi Yuki
- Department of Laboratory Medicine, National Defense Medical College Hospital, Saitama, Japan
| | - Yuji Kouzaki
- Department of Infectious Diseases and Pulmonary Medicine, National Defense Medical College, Saitama, Japan
| | - Kazuo Imai
- Department of Infectious Diseases and Pulmonary Medicine, National Defense Medical College, Saitama, Japan
| | - Runtuwene Lucky Ronald
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toshiyuki Yamaguchi
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Akihiko Kawana
- Department of Infectious Diseases and Pulmonary Medicine, National Defense Medical College, Saitama, Japan
| | - Takuya Maeda
- Department of Laboratory Medicine, National Defense Medical College Hospital, Saitama, Japan. .,Department of Microbiology, Saitama Medical University, 38 Morohongo, Moroyama-machi, Iruma-gun, Saitama, 350-0495, Japan.
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23
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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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24
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Price EP, Harris TM, Spargo J, Nosworthy E, Beissbarth J, Chang AB, Smith-Vaughan HC, Sarovich DS. Simultaneous identification of Haemophilus influenzae and Haemophilus haemolyticus using real-time PCR. Future Microbiol 2017; 12:585-593. [PMID: 28604066 DOI: 10.2217/fmb-2016-0215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
AIM To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic near-neighbor Haemophilus haemolyticus. MATERIALS & METHODS A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed. RESULTS & DISCUSSION PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT. These two assays were multiplexed with the recently described fucP assay for further differentiation among H. influenzae. CONCLUSION The triplex assay provides rapid, unambiguous, sensitive and highly specific genotyping results for the simultaneous detection of hypD and siaT, including fucose-positive H. influenzae (fucP), in a single PCR.
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Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Tegan M Harris
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jessie Spargo
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | | | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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25
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Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination. J Clin Microbiol 2016; 54:3010-3017. [PMID: 27707939 DOI: 10.1128/jcm.01511-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 09/26/2016] [Indexed: 01/26/2023] Open
Abstract
Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.
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26
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Duplex Quantitative PCR Assay for Detection of Haemophilus influenzae That Distinguishes Fucose- and Protein D-Negative Strains. J Clin Microbiol 2016; 54:2380-3. [PMID: 27335148 DOI: 10.1128/jcm.00982-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022] Open
Abstract
We have developed a specific Haemophilus influenzae quantitative PCR (qPCR) that also identifies fucose-negative and protein D-negative strains. Analysis of 100 H. influenzae isolates, 28 Haemophilus haemolyticus isolates, and 14 other bacterial species revealed 100% sensitivity (95% confidence interval [CI], 96% to 100%) and 100% specificity (95% CI, 92% to 100%) for this assay. The evaluation of 80 clinical specimens demonstrated a strong correlation between semiquantitative culture and the qPCR (P < 0.001).
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Pickering JL, Prosser A, Corscadden KJ, de Gier C, Richmond PC, Zhang G, Thornton RB, Kirkham LAS. Haemophilus haemolyticus Interaction with Host Cells Is Different to Nontypeable Haemophilus influenzae and Prevents NTHi Association with Epithelial Cells. Front Cell Infect Microbiol 2016; 6:50. [PMID: 27242968 PMCID: PMC4860508 DOI: 10.3389/fcimb.2016.00050] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/18/2016] [Indexed: 02/02/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that resides in the upper respiratory tract and contributes to a significant burden of respiratory related diseases in children and adults. Haemophilus haemolyticus is a respiratory tract commensal that can be misidentified as NTHi due to high levels of genetic relatedness. There are reports of invasive disease from H. haemolyticus, which further blurs the species boundary with NTHi. To investigate differences in pathogenicity between these species, we optimized an in vitro epithelial cell model to compare the interaction of 10 H. haemolyticus strains with 4 NTHi and 4 H. influenzae-like haemophili. There was inter- and intra-species variability but overall, H. haemolyticus had reduced capacity to attach to and invade nasopharyngeal and bronchoalveolar epithelial cell lines (D562 and A549) within 3 h when compared with NTHi. H. haemolyticus was cytotoxic to both cell lines at 24 h, whereas NTHi was not. Nasopharyngeal epithelium challenged with some H. haemolyticus strains released high levels of inflammatory mediators IL-6 and IL-8, whereas NTHi did not elicit an inflammatory response despite higher levels of cell association and invasion. Furthermore, peripheral blood mononuclear cells stimulated with H. haemolyticus or NTHi released similar and high levels of IL-6, IL-8, IL-10, IL-1β, and TNFα when compared with unstimulated cells but only NTHi elicited an IFNγ response. Due to the relatedness of H. haemolyticus and NTHi, we hypothesized that H. haemolyticus may compete with NTHi for colonization of the respiratory tract. We observed that in vitro pre-treatment of epithelial cells with H. haemolyticus significantly reduced NTHi attachment, suggesting interference or competition between the two species is possible and warrants further investigation. In conclusion, H. haemolyticus interacts differently with host cells compared to NTHi, with different immunostimulatory and cytotoxic properties. This study provides an in vitro model for further investigation into the pathogenesis of Haemophilus species and the foundation for exploring whether H. haemolyticus can be used to prevent NTHi disease.
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Affiliation(s)
- Janessa L Pickering
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
| | - Amy Prosser
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Karli J Corscadden
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
| | - Camilla de Gier
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia; Department of Paediatrics, Princess Margaret Hospital for ChildrenPerth, WA, Australia
| | - Guicheng Zhang
- School of Public Health, Curtin University Perth, WA, Australia
| | - Ruth B Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
| | - Lea-Ann S Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, The University of Western AustraliaPerth, WA, Australia; School of Paediatrics and Child Health, The University of Western AustraliaPerth, WA, Australia
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28
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Post DMB, Ketterer MR, Coffin JE, Reinders LM, Munson RS, Bair T, Murphy TF, Foster ED, Gibson BW, Apicella MA. Comparative Analyses of the Lipooligosaccharides from Nontypeable Haemophilus influenzae and Haemophilus haemolyticus Show Differences in Sialic Acid and Phosphorylcholine Modifications. Infect Immun 2016; 84:765-74. [PMID: 26729761 PMCID: PMC4771351 DOI: 10.1128/iai.01185-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/28/2015] [Indexed: 11/20/2022] Open
Abstract
Haemophilus haemolyticus and nontypeable Haemophilus influenzae (NTHi) are closely related upper airway commensal bacteria that are difficult to distinguish phenotypically. NTHi causes upper and lower airway tract infections in individuals with compromised airways, while H. haemolyticus rarely causes such infections. The lipooligosaccharide (LOS) is an outer membrane component of both species and plays a role in NTHi pathogenesis. In this study, comparative analyses of the LOS structures and corresponding biosynthesis genes were performed. Mass spectrometric and immunochemical analyses showed that NTHi LOS contained terminal sialic acid more frequently and to a higher extent than H. haemolyticus LOS did. Genomic analyses of 10 strains demonstrated that H. haemolyticus lacked the sialyltransferase genes lic3A and lic3B (9/10) and siaA (10/10), but all strains contained the sialic acid uptake genes siaP and siaT (10/10). However, isothermal titration calorimetry analyses of SiaP from two H. haemolyticus strains showed a 3.4- to 7.3-fold lower affinity for sialic acid compared to that of NTHi SiaP. Additionally, mass spectrometric and immunochemical analyses showed that the LOS from H. haemolyticus contained phosphorylcholine (ChoP) less frequently than the LOS from NTHi strains. These differences observed in the levels of sialic acid and ChoP incorporation in the LOS structures from H. haemolyticus and NTHi may explain some of the differences in their propensities to cause disease.
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Affiliation(s)
| | | | - Jeremy E Coffin
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, USA
| | | | - Robert S Munson
- The Center for Microbial Pathogenesis at the Research Institute at Nationwide Children's Hospital and the Center for Microbial Interface Biology and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Thomas Bair
- Bioinformatics Facility, The University of Iowa, Iowa City, Iowa, USA
| | - Timothy F Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Eric D Foster
- Department of Biostatistics, College of Public Health, The University of Iowa, Iowa City, Iowa, USA
| | - Bradford W Gibson
- Buck Institute for Research on Aging, Novato, California, USA Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Michael A Apicella
- Department of Microbiology, The University of Iowa, Iowa City, Iowa, USA
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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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Complete Deletion of the Fucose Operon in Haemophilus influenzae Is Associated with a Cluster in Multilocus Sequence Analysis-Based Phylogenetic Group II Related to Haemophilus haemolyticus: Implications for Identification and Typing. J Clin Microbiol 2015; 53:3773-8. [PMID: 26378279 DOI: 10.1128/jcm.01969-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 09/09/2015] [Indexed: 11/20/2022] Open
Abstract
Nonhemolytic variants of Haemophilus haemolyticus are difficult to differentiate from Haemophilus influenzae despite a wide difference in pathogenic potential. A previous investigation characterized a challenging set of 60 clinical strains using multiple PCRs for marker genes and described strains that could not be unequivocally identified as either species. We have analyzed the same set of strains by multilocus sequence analysis (MLSA) and near-full-length 16S rRNA gene sequencing. MLSA unambiguously allocated all study strains to either of the two species, while identification by 16S rRNA sequence was inconclusive for three strains. Notably, the two methods yielded conflicting identifications for two strains. Most of the "fuzzy species" strains were identified as H. influenzae that had undergone complete deletion of the fucose operon. Such strains, which are untypeable by the H. influenzae multilocus sequence type (MLST) scheme, have sporadically been reported and predominantly belong to a single branch of H. influenzae MLSA phylogenetic group II. We also found evidence of interspecies recombination between H. influenzae and H. haemolyticus within the 16S rRNA genes. Establishing an accurate method for rapid and inexpensive identification of H. influenzae is important for disease surveillance and treatment.
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31
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Price EP, Sarovich DS, Nosworthy E, Beissbarth J, Marsh RL, Pickering J, Kirkham LAS, Keil AD, Chang AB, Smith-Vaughan HC. Haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen. BMC Genomics 2015; 16:641. [PMID: 26311542 PMCID: PMC4551764 DOI: 10.1186/s12864-015-1857-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. Despite its clinical significance, accurate identification of H. influenzae is a non-trivial endeavour. H. haemolyticus can be misidentified as H. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. On the molecular level, frequent genetic exchange amongst Haemophilus spp. has confounded accurate identification of H. influenzae, leading to both false-positive and false-negative results with existing speciation assays. Results Whole-genome single-nucleotide polymorphism data from 246 closely related global Haemophilus isolates, including 107 Australian isolate genomes generated in this study, were used to construct a whole-genome phylogeny. Based on this phylogeny, H. influenzae could be differentiated from closely related species. Next, a H. influenzae-specific locus, fucP, was identified, and a novel TaqMan real-time PCR assay targeting fucP was designed. PCR specificity screening across a panel of clinically relevant species, coupled with in silico analysis of all species within the order Pasteurellales, demonstrated that the fucP assay was 100 % specific for H. influenzae; all other examined species failed to amplify. Conclusions This study is the first of its kind to use large-scale comparative genomic analysis of Haemophilus spp. to accurately delineate H. influenzae and to identify a species-specific molecular signature for this species. The fucP assay outperforms existing H. influenzae targets, most of which were identified prior to the next-generation genomics era and thus lack validation across a large number of Haemophilus spp. We recommend use of the fucP assay in clinical and research laboratories for the most accurate detection and diagnosis of H. influenzae infection and colonisation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1857-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia. .,Menzies School of Health Research, PO Box 41096, Casuarina, NT, 0811, Australia.
| | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
| | | | | | - Anthony D Keil
- Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children and King Edward Memorial Hospital for Women, Perth, WA, Australia.
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.
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Coughlan H, Reddington K, Tuite N, Boo TW, Cormican M, Barrett L, Smith TJ, Clancy E, Barry T. Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae. Diagn Microbiol Infect Dis 2015; 83:112-6. [PMID: 26166209 DOI: 10.1016/j.diagmicrobio.2015.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/03/2015] [Accepted: 06/07/2015] [Indexed: 11/25/2022]
Abstract
Haemophilus influenzae is recognised as an important human pathogen associated with invasive infections, including bloodstream infection and meningitis. Currently used molecular-based diagnostic assays lack specificity in correctly detecting and identifying H. influenzae. As such, there is a need to develop novel diagnostic assays for the specific identification of H. influenzae. Whole genome comparative analysis was performed to identify putative diagnostic targets, which are unique in nucleotide sequence to H. influenzae. From this analysis, we identified 2H. influenzae putative diagnostic targets, phoB and pstA, for use in real-time PCR diagnostic assays. Real-time PCR diagnostic assays using these targets were designed and optimised to specifically detect and identify all 55H. influenzae strains tested. These novel rapid assays can be applied to the specific detection and identification of H. influenzae for use in epidemiological studies and could also enable improved monitoring of invasive disease caused by these bacteria.
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Affiliation(s)
- Helena Coughlan
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland; Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Teck Wee Boo
- Department of Clinical Microbiology, University College Hospital, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Louise Barrett
- National Centre of Sensor Research, School of Physical Sciences, Biomedical Diagnostics Institute, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Terry J Smith
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland; Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Eoin Clancy
- Biomedical Diagnostics Institute Programme, National Centre for Biomedical Engineering Science, National University of Ireland, Galway, Ireland; Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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Shen H, Zhu B, Wang S, Mo H, Wang J, Li J, Zhang C, Zeng H, Guan L, Shi W, Zhang Y, Ma X. Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens. Front Microbiol 2015; 6:532. [PMID: 26074910 PMCID: PMC4446546 DOI: 10.3389/fmicb.2015.00532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/14/2015] [Indexed: 11/24/2022] Open
Abstract
A large number of viral and bacterial organisms are responsible for community-acquired pneumonia (CAP) which contributes to substantial burden on health management. A new resequencing microarray (RPM-IVDC1) associated with targeted multiplex PCR was recently developed and validated for multiple respiratory viruses detection and discrimination. In this study, we evaluated the capability of RPM-IVDC1 for simultaneous identification of multiple viral and bacterial organisms. The nasopharyngeal aspirates (NPAs) of 110 consecutive CAP patients, aged from 1 month to 96 years old, were collected from five distinct general hospitals in Beijing during 1-year period. The samples were subjected to the RPM-IVDC1 established protocol as compared to a real-time PCR (qRT-PCR), which was used as standard. The results of virus detection were consistent with those previously described. A total of 37 of Streptococcus pneumoniae, 14 of Haemophilus influenzae, 10 of Mycoplasma pneumoniae, two of Klebsiella pneumoniae and one of Moraxella catarrhalis were detected by RPM-IVDC1. The sensitivities and specificities were compared with those of qRT-PCR for S. pneumoniae (100, 100%, respectively), H. influenzae (92.3, 97.9%, respectively), M. pneumoniae (69.2, 99.0%, respectively), K. pneumoniae (100, 100%, respectively), and M. catarrhalis (100, 100%, respectively). Additional 22 of Streptococcus spp., 24 of Haemophilus spp. and 16 of Neisseria spp. were identified. In addition, methicillin-resistant and carbapenemases allele were also found in nine of Staphylococcus spp. and one of K. pneumoniae, respectively. These results demonstrated the capability of RPM-IVDC1 for simultaneous detection of broad-spectrum respiratory pathogens in complex backgrounds and the advantage of accessing to the actual sequences, showing great potential use of epidemic outbreak investigation. The detection results should be carefully interpreted when introducing this technique in the clinical diagnostics.
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Affiliation(s)
- Hongwei Shen
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China ; Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Bingqing Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention Beijing, China
| | - Shulian Wang
- Third Hospital of Beijing Armed Police Corps Laboratory Beijing, China
| | - Haolian Mo
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Ji Wang
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Jin Li
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Chen Zhang
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Huashu Zeng
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Li Guan
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
| | - Weixian Shi
- Beijing Center for Disease Control and Prevention, Institute for Infectious Disease and Endemic Disease Control Beijing, China
| | - Yong Zhang
- Futian District Center for Disease Control and Prevention Shenzhen, China
| | - Xuejun Ma
- Key Laboratory of Medical Virology, Ministry of Health, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention Beijing, China
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AbdulWahab A, Taj-Aldeen SJ, Ibrahim EB, Talaq E, Abu-Madi M, Fotedar R. Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis. Infect Drug Resist 2015; 8:83-8. [PMID: 25995646 PMCID: PMC4425335 DOI: 10.2147/idr.s80341] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Early identification of microbial organisms from respiratory secretions of patients with cystic fibrosis (CF) is important to guide therapeutic decisions. The objective was to compare the accuracy of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) relative to the conventional phenotypic method in identifying common bacterial isolates, including nonfermenting Gram-negative bacteria, in a cohort of patients with CF. METHODS A total of 123 isolates from 50 patients with CF representing 14 bacterial species from respiratory specimens were identified using MALDI-TOF MS in parallel with conventional phenotypic methods. Discrepancies were confirmed by 16S ribosomal RNA (rRNA) gene sequencing in five Gram-negative isolates. RESULTS The MALDI-TOF MS managed to identify 122/123 (99.2%) bacterial isolates to the genus level and 118/123 (95.9%) were identified to the species level. The MALDI-TOF MS results were 100% consistent to the species level with conventional phenotypic identification for isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Haemophilus influenzae, Streptococcus pyogenes, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and other uncommon organisms such as Chryseobacterium gleum and Enterobacter cloacae. The 5/123 (4.6%) isolates misidentified were all Gram-negative bacteria. The isolation of E. cloacae and Haemophilus paraphrohaemolyticus may extend the potentially pathogenic list of organisms isolated from patients with CF. CONCLUSION Although the technique provides an early identification and antimicrobial therapy approach in patients with CF, limitation in the diagnosis of uncommon Gram-negative bacteria may exist.
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Affiliation(s)
- Atqah AbdulWahab
- Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar ; Department of Pediatrics, Weill Cornell Medical College, Doha, Qatar
| | - Saad J Taj-Aldeen
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Emad Bashir Ibrahim
- Microbiology Division, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Eman Talaq
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Marawan Abu-Madi
- Department of Health Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Rashmi Fotedar
- Biotechnology Center, Ministry of Environment, Doha, Qatar
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Gilsdorf JR. What the pediatrician should know about non-typeable Haemophilus influenzae. J Infect 2015; 71 Suppl 1:S10-4. [PMID: 25917803 DOI: 10.1016/j.jinf.2015.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2015] [Indexed: 11/25/2022]
Abstract
Non-typeable Haemophilus influenzae (NTHi) live exclusively in the pharynges of humans and are increasingly recognized as pathogens that cause both localized infections of the respiratory tract (middle ear spaces, sinuses, and bronchi) and systemic infections such as bacteraemia and pneumonia. Only one vaccine antigen of NTHi, Protein D, has been extensively studied in humans and its efficacy in preventing NTHi otitis media is modest. Recent genetic analyses reveal that NTHi are closely related to Haemophilus haemolyticus (Hh), previously thought to be a non-pathogenic commensal of the pharynx. This review discusses the differences between the pathogenic potential of encapsulated and non-typeable Hi. In addition, information on the lifestyles and bacterial characteristics of NTHi and Hh as they pertain to their pathogenic capacities and the value of the Haemophilus taxonomy to clinicians are presented. Further, the epidemiology and mechanisms of NTHi antibiotic resistance, which include production of β-lactamase and alterations of penicillin-binding protein 3, are reviewed, as are the challenges of vaccine antigen discovery in NTHi.
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Affiliation(s)
- Janet R Gilsdorf
- D5101 Medical Professional Building SPC 5718, Ann Arbor, MI 48109-5718, United States.
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Comparative Profile of Heme Acquisition Genes in Disease-Causing and Colonizing Nontypeable Haemophilus influenzae and Haemophilus haemolyticus. J Clin Microbiol 2015; 53:2132-7. [PMID: 25903577 DOI: 10.1128/jcm.00345-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/16/2015] [Indexed: 02/07/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHI) are Gram-negative bacteria that colonize the human pharynx and can cause respiratory tract infections, such as acute otitis media (AOM). Since NTHI require iron from their hosts for aerobic growth, the heme acquisition genes may play a significant role in avoiding host nutritional immunity and determining virulence. Therefore, we employed a hybridization-based technique to compare the prevalence of five heme acquisition genes (hxuA, hxuB, hxuC, hemR, and hup) between 514 middle ear strains from children with AOM and 235 throat strains from healthy children. We also investigated their prevalences in 148 Haemophilus haemolyticus strains, a closely related species that colonizes the human pharynx and is considered to be nonpathogenic. Four out of five genes (hxuA, hxuB, hxuC, and hemR) were significantly more prevalent in the middle ear strains (96%, 100%, 100%, and 97%, respectively) than in throat strains (80%, 92%, 93%, and 85%, respectively) of NTHI, suggesting that strains possessing these genes have a virulence advantage over those lacking them. All five genes were dramatically more prevalent in NTHI strains than in H. haemolyticus, with 91% versus 9% hxuA, 98% versus 11% hxuB, 98% versus 11% hxuC, 93% versus 20% hemR, and 97% versus 34% hup, supporting their potential role in virulence and highlighting their possibility to serve as biomarkers to distinguish H. influenzae from H. haemolyticus. In summary, this study demonstrates that heme acquisition genes are more prevalent in disease-causing NTHI strains isolated from the middle ear than in colonizing NTHI strains and H. haemolyticus isolated from the pharynx.
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Latham R, Zhang B, Tristram S. Identifying Haemophilus haemolyticus and Haemophilus influenzae by SYBR Green real-time PCR. J Microbiol Methods 2015; 112:67-9. [PMID: 25753676 DOI: 10.1016/j.mimet.2015.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
SYBR Green real time PCR assays for protein D (hpd), fuculose kinase (fucK) and [Cu, Zn]-superoxide dismutase (sodC) were designed for use in an algorithm for the identification of Haemophilus influenzae and H. haemolyticus. When tested on 127 H. influenzae and 60 H. haemolyticus all isolates were identified correctly.
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Affiliation(s)
- Roger Latham
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia.
| | - Bowen Zhang
- School of Health Sciences, University of Tasmania, Launceston, Australia.
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Australia.
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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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Pickering J, Richmond PC, Kirkham LAS. Molecular tools for differentiation of non-typeable Haemophilus influenzae from Haemophilus haemolyticus. Front Microbiol 2014; 5:664. [PMID: 25520712 PMCID: PMC4251515 DOI: 10.3389/fmicb.2014.00664] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/15/2014] [Indexed: 12/18/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus are closely related bacteria that reside in the upper respiratory tract. NTHi is associated with respiratory tract infections that frequently result in antibiotic prescription whilst H. haemolyticus is rarely associated with disease. NTHi and H. haemolyticus can be indistinguishable by traditional culture methods and molecular differentiation has proven difficult. This current review chronologically summarizes the molecular approaches that have been developed for differentiation of NTHi from H. haemolyticus, highlighting the advantages and disadvantages of each target and/or technique. We also provide suggestions for the development of new tools that would be suitable for clinical and research laboratories.
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Affiliation(s)
- Janessa Pickering
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia
| | - Peter C Richmond
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia ; Centre for Vaccine and Infectious Disease Research, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
| | - Lea-Ann S Kirkham
- School of Paediatrics and Child Health, The University of Western Australia Perth, WA, Australia ; Centre for Vaccine and Infectious Disease Research, Telethon Kids Institute, The University of Western Australia Perth, WA, Australia
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Zhang B, Kunde D, Tristram S. Haemophilus haemolyticus is infrequently misidentified as Haemophilus influenzae in diagnostic specimens in Australia. Diagn Microbiol Infect Dis 2014; 80:272-3. [PMID: 25266675 DOI: 10.1016/j.diagmicrobio.2014.08.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/27/2014] [Accepted: 08/31/2014] [Indexed: 11/24/2022]
Abstract
The commensal Haemophilus haemolyticus is difficult to differentiate from the respiratory pathogen Haemophilus influenzae using phenotypic tests. In a study that used molecular tests to retrospectively identify 447 phenotypically identified H. influenzae isolates from diagnostic specimens in Australia, only 7 (1.5%) H. haemolyticus were identified.
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Affiliation(s)
- Bowen Zhang
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Dale Kunde
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Tasmania, Australia.
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Necessity of 16S rRNA gene sequencing for identifying Haemophilus parainfluenzae-like strains associated with opportunistic urinary tract infections. J Med Microbiol 2014; 63:805-811. [DOI: 10.1099/jmm.0.071803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The identification of Haemophilus spp. from urogenital sites can be challenging due to the lack of appropriate media for culturing the organisms and the poor resolution of biochemical methods. By incorporating chocolate agar and 16S rRNA gene sequence analysis in our protocol to identify Haemophilus spp. from urinary specimens, we isolated and characterized 30 genetically homogeneous strains of a cryptic species that is phylogenetically close to, but distinct from, Haemophilus parainfluenzae. Commercial biochemical kits and VITEK 2 could not distinguish between the two species. Over 90 % of the strains were isolated from urine and the urogenital area, made possible with the inclusion of chocolate agar in our urine culture protocol. In contrast, no Haemophilus strains isolated from respiratory specimens were identified as the cryptic genospecies. The cryptic genospecies was associated with urinary tract infections (UTIs) in certain patient populations. Distinct from Haemophilus quentinii that also causes urogenital infection, the cryptic genospecies required V factor (NAD) but not X factor (haemin) to grow. The data indicated that 16S rRNA gene sequencing may be necessary in identifying Haemophilus species and that inaccurate categorization of Haemophilus strains isolated from urogenital specimens based on phenotypic characteristics may prevent accurate diagnosis of UTIs.
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Frickmann H, Podbielski A, Essig A, Schwarz NG, Zautner AE. Difficulties in species identification within the genus Haemophilus - A pilot study addressing a significant problem for routine diagnostics. Eur J Microbiol Immunol (Bp) 2014; 4:99-105. [PMID: 24883195 DOI: 10.1556/eujmi.4.2014.2.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 11/19/2022] Open
Abstract
Diagnostic misidentifications of commensalic Haemophilus haemolyticus as pathogenic Haemophilus influenzae are frequent. This pilot study evaluates whether isolations of H. haemolyticus are frequent enough in Germany to cause a relevant diagnostic problem, considering the fact that even H. influenzae is a mere colonizer in about 30% of isolations. In microbiological laboratories of two hospitals located in Northern and Southern Germany, the distribution of Haemophilus spp. was analyzed during a six-month-period. Site of infection, sex, and age of the patients was taken into consideration. A total of 77 Haemophilus spp. isolates was acquired and discriminated on species level, comprising: 48 H. influenzae, 25 Haemophilus parainfluenzae, 3 H. haemolyticus, and 1 Haemophilus parahaemolyticus. The proportion of H. haemolyticus was calculated to range between 1.2% and 16.2 % within the 95% confidence limits. Commensalic Haemophilus spp. were isolated from oropharynx-associated sites only. H. influenzae, in contrast, was detected in clinically relevant materials like lower respiratory materials and conjunctiva swabs. Altogether, there was a low proportion of clinical H. haemolyticus isolates. Accordingly, the problem of unnecessary antibiotic therapies due to misidentifications of H. haemolyticus as H. influenzae is quantitatively negligible compared with the risk of confusing H. influenzae colonizations with infections.
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Le Floch AS, Cassir N, Hraiech S, Guervilly C, Papazian L, Rolain JM. Haemophilus parahaemolyticus septic shock after aspiration pneumonia, France. Emerg Infect Dis 2014; 19:1694-5. [PMID: 24050515 PMCID: PMC3810756 DOI: 10.3201/eid1910.130608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Nørskov-Lauritsen N. Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans. Clin Microbiol Rev 2014; 27:214-40. [PMID: 24696434 PMCID: PMC3993099 DOI: 10.1128/cmr.00103-13] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The aim of this review is to provide a comprehensive update on the current classification and identification of Haemophilus and Aggregatibacter species with exclusive or predominant host specificity for humans. Haemophilus influenzae and some of the other Haemophilus species are commonly encountered in the clinical microbiology laboratory and demonstrate a wide range of pathogenicity, from life-threatening invasive disease to respiratory infections to a nonpathogenic, commensal lifestyle. New species of Haemophilus have been described (Haemophilus pittmaniae and Haemophilus sputorum), and the new genus Aggregatibacter was created to accommodate some former Haemophilus and Actinobacillus species (Aggregatibacter aphrophilus, Aggregatibacter segnis, and Aggregatibacter actinomycetemcomitans). Aggregatibacter species are now a dominant etiology of infective endocarditis caused by fastidious organisms (HACEK endocarditis), and A. aphrophilus has emerged as an important cause of brain abscesses. Correct identification of Haemophilus and Aggregatibacter species based on phenotypic characterization can be challenging. It has become clear that 15 to 20% of presumptive H. influenzae isolates from the respiratory tracts of healthy individuals do not belong to this species but represent nonhemolytic variants of Haemophilus haemolyticus. Due to the limited pathogenicity of H. haemolyticus, the proportion of misidentified strains may be lower in clinical samples, but even among invasive strains, a misidentification rate of 0.5 to 2% can be found. Several methods have been investigated for differentiation of H. influenzae from its less pathogenic relatives, but a simple method for reliable discrimination is not available. With the implementation of identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry, the more rarely encountered species of Haemophilus and Aggregatibacter will increasingly be identified in clinical microbiology practice. However, identification of some strains will still be problematic, necessitating DNA sequencing of multiple housekeeping gene fragments or full-length 16S rRNA genes.
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A PCR-high-resolution melt assay for rapid differentiation of nontypeable Haemophilus influenzae and Haemophilus haemolyticus. J Clin Microbiol 2013; 52:663-7. [PMID: 24478508 DOI: 10.1128/jcm.02191-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a PCR-high-resolution melt (PCR-HRM) assay to discriminate nontypeable Haemophilus influenzae (NTHi) colonies from Haemophilus haemolyticus. This method is rapid and robust, with 96% sensitivity and 92% specificity compared to the hpd#3 assay. PCR-HRM is ideal for high-throughput screening for NTHi surveillance and clinical trials.
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Eutsey RA, Hiller NL, Earl JP, Janto BA, Dahlgren ME, Ahmed A, Powell E, Schultz MP, Gilsdorf JR, Zhang L, Smith A, Murphy TF, Sethi S, Shen K, Post JC, Hu FZ, Ehrlich GD. Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates. BMC Genomics 2013; 14:484. [PMID: 23865594 PMCID: PMC3723446 DOI: 10.1186/1471-2164-14-484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 07/10/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates. RESULTS We describe and validate a Haemophilus influenzae supragenome hybridization (SGH) array that can be used to characterize the full genic complement of any strain within the species, as well as strains from several highly related species. The array contains 31,307 probes that collectively cover essentially all alleles of the 2890 gene clusters identified from the whole genome sequencing of 24 clinical H. influenzae strains. The finite supragenome model predicts that these data include greater than 85% of all non-rare genes (where rare genes are defined as those present in less than 10% of sequenced strains). The veracity of the array was tested by comparing the whole genome sequences of eight strains with their hybridization data obtained using the supragenome array. The array predictions were correct and reproducible for ~ 98% of the gene content of all of the sequenced strains. This technology was then applied to an investigation of the gene content of 193 geographically and clinically diverse H. influenzae clinical strains. These strains came from multiple locations from five different continents and Papua New Guinea and include isolates from: the middle ears of persons with otitis media and otorrhea; lung aspirates and sputum samples from pneumonia and COPD patients, blood specimens from patients with sepsis; cerebrospinal fluid from patients with meningitis, as well as from pharyngeal specimens from healthy persons. CONCLUSIONS These analyses provided the most comprehensive and detailed genomic/phylogenetic look at this species to date, and identified a subset of highly divergent strains that form a separate lineage within the species. This array provides a cost-effective and high-throughput tool to determine the gene content of any H. influenzae isolate or lineage. Furthermore, the method for probe selection can be applied to any species, given a group of available whole genome sequences.
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Affiliation(s)
- Rory A Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - N Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joshua P Earl
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Benjamin A Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Margaret E Dahlgren
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Matthew P Schultz
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Janet R Gilsdorf
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Arnold Smith
- Center for Childhood Infections, Seattle Children’s Hospital Research Institute, Seattle, WA, USA
| | - Timothy F Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sanjay Sethi
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Kai Shen
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - J Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Fen Z Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Garth D Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
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47
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Abstract
In a world where most emerging and reemerging infectious diseases are zoonotic in nature and our contacts with both domestic and wild animals abound, there is growing awareness of the potential for human acquisition of animal diseases. Like other Pasteurellaceae, Pasteurella species are highly prevalent among animal populations, where they are often found as part of the normal microbiota of the oral, nasopharyngeal, and upper respiratory tracts. Many Pasteurella species are opportunistic pathogens that can cause endemic disease and are associated increasingly with epizootic outbreaks. Zoonotic transmission to humans usually occurs through animal bites or contact with nasal secretions, with P. multocida being the most prevalent isolate observed in human infections. Here we review recent comparative genomics and molecular pathogenesis studies that have advanced our understanding of the multiple virulence mechanisms employed by Pasteurella species to establish acute and chronic infections. We also summarize efforts being explored to enhance our ability to rapidly and accurately identify and distinguish among clinical isolates and to control pasteurellosis by improved development of new vaccines and treatment regimens.
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Affiliation(s)
- Brenda A Wilson
- Department of Microbiology and Host-Microbe Systems Theme of the Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
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48
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Frickmann H, Christner M, Donat M, Berger A, Essig A, Podbielski A, Hagen RM, Poppert S. Rapid discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by fluorescence in situ hybridization (FISH) and two matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry (MALDI-TOF-MS) platforms. PLoS One 2013; 8:e63222. [PMID: 23646201 PMCID: PMC3639997 DOI: 10.1371/journal.pone.0063222] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 04/01/2013] [Indexed: 12/12/2022] Open
Abstract
Background Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH) and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. Methodology A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu) with and without prior formic acid extraction. Principal Findings Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%), 13 uninterpretable results (15%), and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%), 19 uninterpretable results (23%), and 6 misidentifications (7%), using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%), 4 uninterpretable results (5%) and 6 misidentifications (7%). The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients.
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Affiliation(s)
- Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany.
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49
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Abdeldaim GMK, Strålin K, Olcén P, Blomberg J, Mölling P, Herrmann B. Quantitative fucK gene polymerase chain reaction on sputum and nasopharyngeal secretions to detect Haemophilus influenzae pneumonia. Diagn Microbiol Infect Dis 2013; 76:141-6. [PMID: 23541117 DOI: 10.1016/j.diagmicrobio.2013.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 11/26/2022]
Abstract
A quantitative polymerase chain reaction (PCR) for the fucK gene was developed for specific detection of Haemophilus influenzae. The method was tested on sputum and nasopharyngeal aspirate (NPA) from 78 patients with community-acquired pneumonia (CAP). With a reference standard of sputum culture and/or serology against the patient's own nasopharyngeal isolate, H. influenzae etiology was detected in 20 patients. Compared with the reference standard, fucK PCR (using the detection limit 10(5) DNA copies/mL) on sputum and NPA showed a sensitivity of 95.0% (19/20) in both cases, and specificities of 87.9% (51/58) and 89.5% (52/58), respectively. In a receiver operating characteristic curve analysis, sputum fucK PCR was found to be significantly superior to sputum P6 PCR for detection of H. influenzae CAP. NPA fucK PCR was positive in 3 of 54 adult controls without respiratory symptoms. In conclusion, quantitative fucK real-time PCR provides a sensitive and specific identification of H. influenzae in respiratory secretions.
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Affiliation(s)
- Guma M K Abdeldaim
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, S-75185, Uppsala, Sweden
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50
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Zhu B, Xiao D, Zhang H, Zhang Y, Gao Y, Xu L, Lv J, Wang Y, Zhang J, Shao Z. MALDI-TOF MS distinctly differentiates nontypable Haemophilus influenzae from Haemophilus haemolyticus. PLoS One 2013; 8:e56139. [PMID: 23457514 PMCID: PMC3573053 DOI: 10.1371/journal.pone.0056139] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/05/2013] [Indexed: 11/19/2022] Open
Abstract
Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories.
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Affiliation(s)
- Bingqing Zhu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Di Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Huifang Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yongchan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuan Gao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Li Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Jing Lv
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, People’s Republic of China
| | - Yingtong Wang
- Hebei Provincial Center for Disease Control and Prevention, Shijiazhuang, People’s Republic of China
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (ZS); (JZ)
| | - Zhujun Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- * E-mail: (ZS); (JZ)
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