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

Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes

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 bla_TEM-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.

A study of various factors affecting satellitism tests of Haemophilus influenzae and Haemophilus parainfluenzae using Staphylococcus aureus as the source of NAD

Many factors affecting satellitism tests are unclear, and it is difficult to avoid misidentification, even if the medium is properly selected. We investigated the factors causing false-positive results for Haemophilus influenzae and false-negative results for Haemophilus parainfluenzae in the satellitism tests using Staphylococcus aureus as the source of nicotinamide adenine dinucleotide (NAD). H. influenzae (four reference strains and 47 clinical isolates), H. parainfluenzae (two reference strains and 67 clinical isolates), four different media, and two strains of S. aureus revived on two different media were used in this study. The type of medium used to revive S. aureus was the most common factor causing false-positive results for H. influenzae, followed by different strains of S. aureus and the type of medium used for the experiment. The production of false-negative results for H. parainfluenzae was only related to the medium used in the experiment. To improve the accuracy of the tests in routine laboratories, using S. aureus as the source of NAD, tryptic soy agar, and S. aureus (ATCC 25923) revived on nutrient agar should be adopted.

Clinical characteristics of bacteremia caused by Haemophilus and Aggregatibacter species and antimicrobial susceptibilities of the isolates

BACKGROUND/PURPOSE

This study aimed to investigate the clinical characteristics and outcomes of bacteremia caused by Haemophilus and Aggregatibacter species in patients who were treated at a medical center between 2006 and 2018.

METHODS

Haemophilus and Aggregatibacter isolates were identified up to the species level using Bruker Biotyper MALDI-TOF analysis and ancillary 16S rRNA gene sequencing analysis (in case of ambiguity). Clinical characteristics and outcomes of patients with bacteremia caused by these organisms were evaluated.

RESULTS

Sixty-five Haemophilus and Aggregatibacter species isolates causing bacteremia were identified from nonduplicated patients, including 51 (78.5%) Haemophilus influenzae, 6 (9.2%) Haemophilus parainfluenzae, 1 (1.5%) Haemophilus haemolyticus, 3 (4.6%) A. aphrophilus, and 4 (6.2%) A. segnis. Hospital mortality was observed in 18 (28.1%) of 64 patients with bacteremia caused by Haemophilus (n = 57) and Aggregatibacter species (n = 7). The majority of patients with bacteremia had community-acquired disease with low severity. The average Sequential Organ Failure Assessment (SOFA) score was low (4.4 ± 4.7). But, a higher SOFA score (adjusted odds ratio 2.5, 95% confidence interval 1.22-5.12; P = 0.01) was an independent factor predicting poor 7-day clinical outcomes in patients with community-acquired H. influenzae bacteremia (n = 39).

CONCLUSIONS

The overall hospital mortality of 28.1% was observed among patients with bacteremia due to Haemophilus and Aggregatibacter species. A higher SOFA score was and independent predictor of poor 7-day clinical outcomes in patients with community-acquired H. influenzae bacteremia.

Learning from -omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives

Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of -omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae-host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.

Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing

MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'

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.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Applications in Bacteriology: brazilian contributions

Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

The role of bacteria in chronic rhinosinusitis (CRS) is still not well understood. Whole microbiome analysis adds new aspects to our current understanding that is mainly based on isolated bacteria. It is still unclear how the results of microbiome analysis and the classical culture based approaches interrelate. To address this, middle meatus swabs and tissue samples were obtained during sinus surgery in 5 patients with CRS with nasal polyps (CRSwNP), 5 patients with diffuse CRS without nasal polyps (CRSsNP), 5 patients with unilateral purulent maxillary CRS (upm CRS) and 3 patients with healthy sinus mucosa. Swabs were cultured, and associated bacteria were identified. Additionally, parts of each tissue sample also underwent culture approaches, and in parallel DNA was extracted for 16S rRNA gene amplicon-based microbiome analysis. From tissue samples 4.2 ± 1.2 distinct species per patient were cultured, from swabs 5.4 ± 1.6. The most frequently cultured species from the swabs were Propionibacterium acnes, Staphylococcus epidermidis, Corynebacterium spp. and Staphylococcus aureus. The 16S-RNA gene analysis revealed no clear differentiation of the bacterial community of healthy compared to CRS samples of unilateral purulent maxillary CRS and CRSwNP. However, the bacterial community of CRSsNP differed significantly from the healthy controls. In the CRSsNP samples Flavobacterium, Pseudomonas, Pedobacter, Porphyromonas, Stenotrophomonas, and Brevundimonas were significantly enriched compared to the healthy controls. Species isolated from culture did not generally correspond with the most abundant genera in microbiome analysis. Only Fusobacteria, Parvimonas, and Prevotella found in 2 unilateral purulent maxillary CRS samples by the cultivation dependent approach were also found in the cultivation independent approach in high abundance, suggesting a classic infectious pathogenesis of odontogenic origin in these two specific cases. Alterations of the bacterial community might be a more crucial factor for the development of CRSsNP compared to CRSwNP. Further studies are needed to investigate the relation between bacterial community characteristics and the development of CRSsNP.

Phenotypic diversity of Haemophilus influenzae and Haemophilus parainfluenzae isolates depending on origin and health condition

Background. Haemophili are common human microbiota representatives. The aim of our study was to investigate a diversity of Haemophilus spp. isolates selected from clinical specimens on the basis of biochemical characteristics, biotypes distribution, protein profiles and antimicrobial resistance. Results. A total of 893/1025 (87%) of haemophili isolates were identified: 260/1025 (25%) as H. influenzae and 633/1025 (62%) as H. parainfluenzae. Moreover, a group of 107/1025 (10%) isolates without species identification (with e.g. abnormal numerical profile) was described as Haemophilus spp. Within the H. influenzae isolates, biotypes II and III were in a great majority (92/893; 10%, each), whereas among H. parainfluenzae, the most commonly occurring was biotype I and II (301/893, 34% and 178/893, 20%, respectively). A similar prevalence of biotypes was obtained regardless of the patient’s age or health condition or the type of specimen. A production of beta-lactamases was shown in 46/893 (5%) haemophili, both H. influenzae (13/46, 28%) and H. parainfluenzae (33/46, 72%) isolates. On the basis of haemophili biochemical characteristics, the cluster analysis using the UPGMA method demonstrated a high degree of phenotypic similarity due to a small distances between isolates taken from both unhealthy children and adults. Conclusion. Based on biochemical characteristics, about 90% of haemophili clinical isolates representing human-specific respiratory microbiota were positively identified as H. influenzae and H. parainfluenzae. The same differences in biotypes and antimicrobial resistance among isolates selected from healthy people or from patients with chronic and recurrent diseases were detected.

Nontypeable Haemophilus influenzae and chronic obstructive pulmonary disease: a review for clinicians

Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality worldwide. In the lower airways of COPD patients, bacterial infection is a common phenomenon and Haemophilus influenzae is the most commonly identified bacteria. Haemophilus influenzae is divided into typeable and nontypeable (NTHi) strains based on the presence or absence of a polysaccharide capsule. While NTHi is a common commensal in the human nasopharynx, it is associated with considerable inflammation when it is present in the lower airways of COPD patients, resulting in morbidity due to worsening symptoms and increased frequency of COPD exacerbations. Treatment of lower airway NTHi infection with antibiotics, though successful in the short term, does not offer long-term protection against reinfection, nor does it change the course of the disease. Hence, there has been much interest in the development of an effective NTHi vaccine. This review will summarize the current literature concerning the role of NTHi infections in COPD patients and the consequences of using prophylactic antibiotics in patients with COPD. There is particular focus on the rationale, findings of clinical studies and possible future directions of NTHi vaccines in patients with COPD.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Human Lung Fibroblasts Present Bacterial Antigens to Autologous Lung Th Cells

Lung fibroblasts are key structural cells that reside in the submucosa where they are in contact with large numbers of CD4⁺ Th cells. During severe viral infection and chronic inflammation, the submucosa is susceptible to bacterial invasion by lung microbiota such as nontypeable Haemophilus influenzae (NTHi). Given their proximity in tissue, we hypothesized that human lung fibroblasts play an important role in modulating Th cell responses to NTHi. We demonstrate that fibroblasts express the critical CD4⁺ T cell Ag-presentation molecule HLA-DR within the human lung, and that this expression can be recapitulated in vitro in response to IFN-γ. Furthermore, we observed that cultured lung fibroblasts could internalize live NTHi. Although unable to express CD80 and CD86 in response to stimulation, fibroblasts expressed the costimulatory molecules 4-1BBL, OX-40L, and CD70, all of which are related to memory T cell activation and maintenance. CD4⁺ T cells isolated from the lung were predominantly (mean 97.5%) CD45RO⁺ memory cells. Finally, cultured fibroblasts activated IFN-γ and IL-17A cytokine production by autologous, NTHi-specific lung CD4⁺ T cells, and cytokine production was inhibited by a HLA-DR blocking Ab. These results indicate a novel role for human lung fibroblasts in contributing to responses against bacterial infection through activation of bacteria-specific CD4⁺ T cells.

Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation

OBJECTIVE

To investigate the potential roles of PBPs, efflux pumps and slow drug influx for imipenem heteroresistance in nontypeable Haemophilus influenzae (NTHi).

METHODS

Fifty-nine NTHi clinical isolates examined in this study were collected at Geneva University Hospitals between 2009 and 2014. Alterations in PBPs were investigated by gene sequencing. To evaluate the affinities of the PBPs to imipenem, steady-state concentration-response experiments were carried out using imipenem in a competition assay with Bocillin-FL. The effect of the carbonyl cyanide m-chlorophenylhydrazone (CCCP) on imipenem susceptibility was assessed using broth dilution and viable cell counting. Using whole-genome sequencing, we explored the potential roles of outer membrane protein P2 (OmpP2), LytM proteins and the dcw gene cluster in imipenem heteroresistance.

RESULTS

All 46 imipenem-heteroresistant isolates (IMI^hR) harboured amino acid substitutions in the ftsI gene, which encodes PBP3, corresponding to 25 different mutation patterns that varied from the ftsI gene mutation patterns found in imipenem-susceptible isolates. Among all PBPs, the highest affinity to imipenem was documented for PBP3 (IC₅₀, 0.004 μg/mL). Different amino acid substitutions and insertions were noted in OmpP2, suggesting a relationship with imipenem heteroresistance. The IMI^hR isolates were affected by CCCP differently and displayed a higher percentage of killing by imipenem in CCCP-treated cells at concentrations ranging between 0.5 and 8 μg/mL.

CONCLUSIONS

The present study provides robust evidence indicating that in combination with the altered PBP3, the slowed drug influx and its enhanced efflux due to the loss of regulation led to the development of imipenem heteroresistance in NTHi.

Comparative Genomic Analysis of Haemophilus haemolyticus and Nontypeable Haemophilus influenzae and a New Testing Scheme for Their Discrimination

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.

Utilizing Moist or Dry Swabs for the Sampling of Nasal MRSA Carriers? An In Vivo and In Vitro Study

This study investigates the quantitative bacterial recovery of Methicillin-resistant Staphylococcus aureus (MRSA) in nasal screenings by utilizing dry or moistened swabs within an in vivo and an in vitro experimental setting. 135 nasal MRSA carriers were each swabbed in one nostril with a dry and in the other one with a moistened rayon swab. Quantitative bacterial recovery was measured by standard viable count techniques. Furthermore, an anatomically correct artificial nose model was inoculated with a numerically defined suspension of MRSA and swabbed with dry and moistened rayon, polyurethane-foam and nylon-flocked swabs to test these different settings and swab-materials under identical laboratory conditions. In vivo, quantities of MRSA per nostril in carriers varied between <10¹ and >10⁷ colony forming units, with a median of 2.15x10⁴ CFU. However, no statistically significant differences could be detected for the recovery of MRSA quantities when swabbing nasal carriers with moist or dry rayon swabs. In vitro testing confirmed the in vivo data for swabs with rayon, polyurethane and nylon-flocked tips, since pre-moistening of swabs did not significantly affect the quantities of retrieved bacteria. Therefore, pre-moistening of swabs prior to nasal MRSA sampling provides no advantage in terms of recovering greater bacterial quantities and therefore can be omitted. In addition, this situation can be mimicked in an in vitro model, thereby providing a useful basis for future in vitro testings of new swab types or target organisms for screening approaches.

Screening for Gram-negative bacteria: Impact of preanalytical parameters

Screening recommendations for multidrug-resistant Gram-negative bacteria comprise microbiological analyses from rectal swabs. However, essential specifications of the preanalytic steps of such screenings, i.e. the sampling technique, sampling devices and sampling site, are lacking. For standardized and optimum screening conditions these parameters are indispensable. Here, the optimum parameters were examined irrespective of the antibiotic resistance patterns of the target bacteria in order to establish a general basis for this type of screening. Swabs with rayon, polyurethane-cellular-foam and nylon-flocked tips were tested. Different sampling locations were evaluated, i.e. perianal, intraanal and deep intraanal. Subjects were swabbed and quantities of E. coli, K. pneumoniae, P. aeruginosa and A. baumannii were assessed. Overall prevalences of E. coli, K. pneumoniae, P. aeruginosa, and A. baumannii were 94%, 16%, 12%, and 2%, respectively. Bacterial recovery rates were independent from the sampling-timepoint during hospital stay. Polyurethane-cellular-foam or nylon-flocked swabs recovered significantly more bacteria as compared to rayon swabs. Intraanal swabbing resulted in significantly higher bacterial quantities as compared to perianal swabbing. In contrast, for the detection of A. baumannii, perianal swabbing seems more suitable than intraanal swabbing. Gender-related differences in bacterial recovery could be detected from perianal but not from intraanal swabs.

Haemophilus influenzae biofilm formation in chronic otitis media with effusion

Otitis media with effusion (OME) is a highly prevalent disease in children, but the exact pathogenesis and role of bacteria are still not well understood. This study aimed to investigate the presence of otopathogenic bacteria in the middle ear effusion (MEE) and adenoid of children with chronic OME (COME), and to investigate in vivo whether these bacteria, especially Haemophilus influenzae, are organized as a biofilm in the middle ear fluid. MEE and adenoid samples were collected from 21 patients with COME. Extensive bacterial culturing and genotyping was performed on all middle ear and adenoid samples. Fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) was used to visualize possible biofilm structures for a selection of middle ear effusion samples. 34 MEE samples were collected from 21 patients of which 64.7 % were culture positive for bacteria and 47.0 % were culture positive for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus and/or Streptococcus pneumoniae. All 21 adenoid samples were culture positive for one or more of these four otopathogens. H. influenzae (35.3 %) and S. pneumoniae (76.2 %) were the most frequently cultured bacteria in the MEE and adenoid samples, respectively. The same bacterial species was found in MEE and adenoid for 84.6 % of the patients and in 81.2 % of the cases where the same species was found in more than one site it involved the same bacterial genotype. FISH and CLSM demonstrated the presence of H. influenzae specific biofilm structures in five of the eight culture positive MEEs that were tested, but in none of the two culture negative MEEs. The findings in this study indicate that the adenoid acts as a reservoir for bacteria in MEE and confirms that biofilms, in at least half of the cases consisting of H. influenzae, are indeed present in the MEE of children with COME. Biofilms may thus play a crucial role in the pathogenesis of COME, which is important in the understanding of this disease and the development of potential future treatment options.

Evaluation of the Bruker MALDI Biotyper for Identification of Fastidious Gram-Negative Rods

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has entered clinical laboratories, facilitating identification of bacteria. Here, we evaluated the MALDI Biotyper (Bruker Daltonics) for the identification of fastidious Gram-negative rods (GNR). Three sample preparation methods, direct colony transfer, direct transfer plus on-target formic acid preparation, and ethanol-formic acid extraction, were analyzed for 151 clinical isolates. Direct colony transfer applied with the manufacturer's interpretation criteria resulted in overall species and genus identification rates of 43.0% and 32.5%, respectively; 23.2% of the isolates were not identified, and two misidentifications (1.3%) were observed. The species identification rates increased to 46.4% and 53.7% for direct transfer plus formic acid preparation and ethanol-formic acid extraction, respectively. In addition, we evaluated score value cutoff alterations. The identification rates hardly increased by reducing the genus cutoff, while reducing the 2.0 species cutoff to 1.9 and to 1.8 increased the identification rates to up to 66.2% without increasing the rate of misidentifications. This study shows that fastidious GNR can reliably be identified using the MALDI Biotyper. However, the identification rates do not reach those of nonfastidious GNR such as the Enterobacteriaceae. In addition, two approaches optimizing the identification of fastidious GNR by the MALDI Biotyper were demonstrated: formic acid-based on-target sample treatment and reductions in cutoff scores to increase the species identification rates.

Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM) Mali

Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM) in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014. Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associated Escherichia coli (EPEC, ETEC, EAEC, and EIEC), enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL) with subsequent repetitive sequence-based PCR (rep-PCR) typing was performed. Clinical information was assessed. Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n = 21), ETEC (n = 19), EAEC (n = 15), Norovirus (n = 10), Shigella spp./EIEC (n = 6), Cryptosporidium parvum (n = 3), Giardia duodenalis (n = 2), Salmonella spp. (n = 1), Astrovirus (n = 1), Rotavirus (n = 1), and Sapovirus (n = 1). ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission. Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens.

Ampicillin-resistant Haemophilus influenzae isolates in Geneva: serotype, antimicrobial susceptibility, and β-lactam resistance mechanisms

The purpose of this study was to analyze the molecular mechanisms of ampicillin-resistant Haemophilus influenzae isolated in Geneva, Switzerland. We investigated the association between specific patterns of amino acid substitutions in penicillin-binding protein 3 (with or without β-lactamase production) and β-lactam susceptibility. Another main focus for this study was to compare the accuracy of disk diffusion and Etest methods to detect resistance to ampicillin and amoxicillin/clavulanic acid. The antibiotic susceptibility to β-lactam antibiotics of 124 H. influenzae isolates was determined by disk diffusion and Etest methods, and interpreted by European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) breakpoints. Alterations in PBP3 were investigated by sequencing the ftsI gene. Of the 124 clinical isolates analyzed, ampicillin resistance was found in 36% (45 out of 124). The rate of resistance to amoxicillin/clavulanic acid was 9% and 0.8%, using EUCAST and CLSI breakpoints respectively. For the 78 β-lactamase negative ampicillin-susceptible (BLNAS) isolates for which the Etest method indicated a high degree of susceptibility (MIC ≤ 1 mg/L), the disk diffusion method revealed resistance to ampicillin and amoxicillin/clavulanic acid in 33 cases (42%). Most common amino acid substitutions were Asn526Lys and Val547Ile, followed by Asp569Ser, Ala502Val, Asp350Asn, Met377Ile, Ile449Val, and Arg517His. The patterns observed were classified into six groups (IIa, IIb, IIc, IId, III-like, and miscellaneous). Continued characterization of both invasive and respiratory H. influenzae isolates is necessary in order to observe changes in the microbiology and epidemiology of this pathogen that could lead to clinical failure when treated by empirical antibiotic therapy.

Nasopharyngeal and Adenoid Colonization by Haemophilus influenzae and Haemophilus parainfluenzae in Children Undergoing Adenoidectomy and the Ability of Bacterial Isolates to Biofilm Production

Haemophili are pathogenic or opportunistic bacteria often colonizing the upper respiratory tract mucosa. The prevalence of Haemophilus influenzae (with serotypes distribution), and H. parainfluenzae in the nasopharynx and/or the adenoid core in children with recurrent pharyngotonsillitis undergoing adenoidectomy was assessed. Haemophili isolates were investigated for their ability to biofilm production.Nasopharyngeal swabs and the adenoid core were collected from 164 children who underwent adenoidectomy (2-5 years old). Bacteria were identified by the standard methods. Serotyping of H. influenzae was performed using polyclonal and monoclonal antisera. Biofilm formation was detected spectrophotometrically using 96-well microplates and 0.1% crystal violet.Ninety seven percent (159/164) children who underwent adenoidectomy were colonized by Haemophilus spp. The adenoid core was colonized in 99.4% (158/159) children, whereas the nasopharynx in 47.2% (75/159) children (P < 0.0001). In 32% (51/159) children only encapsulated (typeable) isolates of H. influenzae were identified, in 22.6% (36/159) children only (nonencapsulated) H. influenzae NTHi (nonencapsulated) isolates were present, whereas 7.5% (12/159) children were colonized by both types. 14.5% (23/159) children were colonized by untypeable (rough) H. influenzae. In 22% (35/159) children H. influenzae serotype d was isolated. Totally, 192 isolates of H. influenzae, 96 isolates of H. parainfluenzae and 14 isolates of other Haemophilus spp. were selected. In 20.1% (32/159) children 2 or 3 phenotypically different isolates of the same species (H. influenzae or H. parainfluenzae) or serotypes (H. influenzae) were identified in 1 child. 67.2% (129/192) isolates of H. influenzae, 56.3% (54/96) isolates of H. parainfluenzae and 85.7% (12/14) isolates of other Haemophilus spp. were positive for biofilm production. Statistically significant differences (P = 0.0029) among H. parainfluenzae biofilm producers and nonproducers in the adenoid core and the nasopharynx were detected.H. influenzae and H. parainfluenzae carriage rate was comparatively higher in the adenoid core than that in the nasopharynx in children undergoing adenoidectomy, suggesting that their involvement in chronic adenoiditis. The growth in the biofilm seems to be an important feature of haemophili colonizing the upper respiratory tract responsible for their persistence.

Discrepancy in MALDI-TOF MS identification of uncommon Gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis

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.

What the pediatrician should know about non-typeable Haemophilus influenzae

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.

Improved microbiological diagnostic due to utilization of a high-throughput homogenizer for routine tissue processing

Tissue specimens are valuable materials for microbiological diagnostics and require swift and accurate processing. Established processing methods are complex, labor intensive, hardly if at all standardizable, and prone to incorporate contaminants. To improve analyses from tissue samples in routine microbiological diagnostics, by facilitating, fastening, and standardizing processing as well as increasing the microbial yield, performance of Precellys 24 high-throughput tissue homogenizer was evaluated. Therefore, tissue samples were artificially inoculated with Staphylococcus aureus, Escherichia coli, and Candida albicans in 3 different ways on the surface and within the material. Microbial yield from homogenized samples was compared to direct plating method. Further, as proof of principle, routine tissue samples from knee and hip endoprosthesis infections were analyzed. The process of tissue homogenization with Precellys 24 homogenizer is easy and fast to perform and allows for a high degree of standardization. Microbial yield after homogenization was significantly higher as compared to conventional plating technique.

Identification of nasal colonization with β-lactamase-producing Enterobacteriaceae in patients, health care workers and students in Madagascar

This study assesses the nasal occurrence of β-lactamase-producing Enterobacteriaceae both in patients in a hospital department of infectious diseases at admission and in healthy Madagascan students and health care workers. Nasal swabs from 681 students, 824 health care workers, and 169 patients were obtained in Antananarivo, Madagascar, and transferred to Germany. Screening for β-lactamase (ESBL, ampC) producing Enterobacteriaceae was performed by cultural and molecular approaches, comprising Brilliance ESBL agar, E-testing, ABCD-testing, and commercial hyplex ESBL and SuperBug ID PCR. Regarding ESBL-positive strains and strains with resistance against at least three out of the four tested bactericidal antibiotic drugs, 0.3% (five out of 1541) of the students and health care workers group showed nasal colonization, whereas colonization was observed in 7.1% (12 out of 169) of the hospitalized patients at admission. No appreciably reduced detection rates after sample storage and intercontinental transport were observed. A considerable proportion of nasal colonization with cephalosporin-resistant Enterobacteriaceae was demonstrated in Madagascan hospital patients at admission, posing a risk of developing future endogenous infections. The nasal colonization of healthy individuals was negligible. Good storage and transport stability of Enterobacteriaceae will allow for future studies even in areas difficult to access.

Difficult identification of Haemophilus influenzae, a typical cause of upper respiratory tract infections, in the microbiological diagnostic routine

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.

Screening agars for MRSA: evaluation of a stepwise diagnostic approach with two different selective agars for the screening for methicillin-resistant Staphylococcus aureus (MRSA)

BACKGROUND

Colonization with methicillin-resistant Staphylococcus aureus (MRSA) poses a hygiene risk that does not spare field hospitals or military medical field camps during military deployments. Diagnostic options for unambiguously identifying MRSA isolates are usually scarce in military environments. In this study, we assessed the stepwise application of two different selective agars for the specific identification of MRSA in screening analyses.

METHODS

Nasal swabs from 1541 volunteers were subjected to thioglycollate broth enrichment and subsequently screened on CHROMagar MRSA selective agar for the identification of MRSA. The MRSA identity of suspicious-looking colonies was confirmed afterwards or excluded by another selective agar, chromID MRSA. All isolates from the selective agars with MRSA-specific colony morphology were identified by biochemical methods and mass spectrometry.

RESULTS

The initial CHROMagar MRSA screening identified suspicious colonies in 36 out of 1541 samples. A total of 25 of these 36 isolates showed MRSA-like growth on chromID agar. Out of these 25 isolates, 24 were confirmed as MRSA, while one isolate was identified as Staphylococcus kloosii. From the 11 strains that did not show suspicious growth on chromID agar, 3 were methicillin-sensitive Staphylococcus aureus (MSSA, with one instance of co-colonization with Corynebacterium spp.), 2 were confirmed as MRSA (with 1 instance of co-colonization with MSSA), 2 were lost during passaging and could not be re-cultured, one could not be identified by the applied approaches, and the remaining 3 strains were identified as Staphylococcus saprophyticus, Staphylococcus hominis (co-colonized with Macrococcus caseolyticus) and Staphylococcus cohnii, respectively.

CONCLUSIONS

The application of the selective agar CHROMagar MRSA alone proved to be too non-specific to allow for a reliable diagnosis of the presence of MRSA. The combined use of two selective agars in a stepwise approach reduced this non-specificity with an acceptably low loss of sensitivity. Accordingly, such a stepwise screening approach might be an option for resource-restricted military medical field camps.

Molecular tools for differentiation of non-typeable Haemophilus influenzae from Haemophilus haemolyticus

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.

Non-typeable Haemophilus influenzae, an under-recognised pathogen

Non-typeable Haemophilus influenzae (NTHi) is a major cause of mucosal infections such as otitis media, sinusitis, conjunctivitis, and exacerbations of chronic obstructive pulmonary disease. In some regions, a strong causal relation links this pathogen with infections of the lower respiratory tract. In the past 20 years, a steady but constant increase has occurred in invasive NTHi worldwide, with perinatal infants, young children, and elderly people most at risk. Individuals with underlying comorbidities are most susceptible and infection is associated with high mortality. β-lactamase production is the predominant mechanism of resistance. However, the emergence and spread of β-lactamase-negative ampicillin-resistant strains in many regions of the world is of substantial concern, potentially necessitating changes to antibiotic treatment guidelines for community-acquired infections of the upper and lower respiratory tract and potentially increasing morbidity associated with invasive NTHi infections. Standardised surveillance protocols and typing methodologies to monitor this emerging pathogen should be implemented. International scientific organisations need to raise the profile of NTHi and to document the pathobiology of this microbe.

Necessity of 16S rRNA gene sequencing for identifying Haemophilus parainfluenzae-like strains associated with opportunistic urinary tract infections

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.

Difficulties in species identification within the genus Haemophilus - A pilot study addressing a significant problem for routine diagnostics

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.

Classification, identification, and clinical significance of Haemophilus and Aggregatibacter species with host specificity for humans

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.

Application of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of the fastidious pediatric pathogens Aggregatibacter, Eikenella, Haemophilus, and Kingella

The accuracy of matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) in the identification of Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, and Kingella (HACEK) species was compared to that of phenotypic methods (Remel RapID and Vitek 2). Overall, Vitek MS correctly identified more isolates, incorrectly identified fewer isolates, and failed to identify fewer isolates than both phenotypic methods.