Microbiological investigation and clinical significance of Corynebacterium spp. in respiratory specimens

The in vitro antimicrobial activity of linezolid against unconventional pathogens

Linezolid is an oxazolidinone antibiotic that is mainly permitted to treat Gram-positive bacterial infections. Recent studies have shown that linezolid also has antibacterial effects on several other bacteria outside the package insert, including Mycobacterium tuberculosis, non-tuberculous mycobacteria (NTM), Nocardia, Corynebacterium, and anaerobes, etc. Interestingly, linezolid also has an in vitro inhibitory effect on fungi. This review focuses on the in vitro antibacterial activity of linezolid against microorganisms outside its antibacterial spectrum. We mainly listed the number of the tested strains, the minimum inhibitory concentration (MIC) range, MIC50, and MIC90 of linezolid against those pathogens outside the package insert. The results showed that among these tested pathogens, linezolid displayed strong inhibitory effects against M. tuberculosis, Nocardia, and Corynebacterium, with an MIC range of ≤2 μg/mL. As for NTM, linezolid exhibited moderate to potent inhibitory effects against the strains of different species with an MIC range of 0.06-128 μg/mL. Moreover, linezolid was reported to have a species-dependent inhibitory effect on anaerobes at a concentration range of 0.003-16 μg/mL. Furthermore, linezolid could enhance azoles and amphotericin B's antifungal activity on Candida synergistically. It is hoped that this analysis can provide data for expanding the application of linezolid, make the off-label drug use have more compelling evidence, and provide clues for the development of new drugs.

Hazard assessment of airborne and foodborne biodegradable polyhydroxyalkanoates microplastics and non-biodegradable polypropylene microplastics

Microplastics (MP) are ubiquitous in the environment, and are toxic to various living organisms. Proper application of biodegradable plastics may alleviate the hazards of conventional non-biodegradable plastics. In the current study, multi-omics analyses were performed to compare the biodegradable polyhydroxyalkanoates (PHA) and non-biodegradable polypropylene (PP) MP for their toxicity on mouse liver and lung. Airborne PHA MP induced nasal microbiome dysbiosis, pulmonary microbiome alteration, pulmonary and serum metabolome disruption, and hepatic transcriptome disturbances, resulting in mild pulmonary toxicity. By contrast, airborne PP MP caused greater alterations in nasal and pulmonary microbiome, pulmonary and serum metabolome, and hepatic transcriptome, resulting in pulmonary and hepatic toxicity. Both foodborne PHA and PP MP caused intestinal microbiome dysbiosis, while foodborne PHA MP caused slighter intestinal and serum metabolome disruption, hepatic transcriptome disturbances and hepatotoxicity (e.g., lower serum aspartate aminotransferase and alanine aminotransferase) compared to foodborne PP MP. Some potential differential biomarkers were determined between PP and PHA MP exposures, i.e., nasal Allobaculum and pulmonary Alloprevotella for airborne PHA; nasal Lactobacillus and pulmonary Acinetobacter for airborne PP; intestinal Faecalibacterium for foodborne PHA; and intestinal unclassified_Erysipelatoclostridiaceae for foodborne PP. The results show that PHA MP can induce less pulmonary and hepatic toxicity compared to PP MP, suggesting PHA is a potential substitution for PP. The findings can benefit the hazard assessment of airborne and foodborne PHA and PP MP.

Efficient Biodegradation of Multiple Aryloxyphenoxypropionate Herbicides by Corynebacterium sp. Z-1 and the Proposed Degradation Mechanism

Esterases are crucial for aryloxyphenoxypropionate herbicide (AOPP) biodegradation. However, the underlying molecular mechanisms of AOPP biodegradation by esterases are poorly understood. In the current work, Corynebacterium sp. Z-1 was isolated and found to degrade multiple AOPPs, including quizalofop-p-ethyl (QPE), haloxyfop-p-methyl (HPM), fenoxaprop-p-ethyl (FPE), cyhalofop-butyl (CYB), and clodinafop-propargyl (CFP). A novel esterase, QfeH, which catalyzes the cleavage of ester bonds in AOPPs to form AOPP acids, was identified from strain Z-1. The catalytic activities of QfeH toward AOPPs decreased in the following order: CFP > FPE > CYB > QPE > HPM. Molecular docking, computational analyses, and site-directed mutagenesis indicated the catalytic mechanisms of QfeH-mediated degradation of different AOPPs. Notably, the key residue S159 is essential for the activity of QfeH. Moreover, V222Y, T227M, T227A, A271R, and M275K mutants, exhibiting 2.9-5.0 times greater activity than QfeH, were constructed. This study facilitates the mechanistic understanding of AOPPs bioremediation by esterases.

Yinhuang buccal tablet alters airway microbiota composition and metabolite profile in healthy humans

ETHNOPHARMACOLOGICAL RELEVANCE

Perturbations in airway microbiota composition and disruption of microbe-metabolite interactions have been observed in respiratory infectious diseases (RIDs). The Yinhuang (YH) buccal tablet, as an ancient Chinese medicinal formula, has been traditionally employed for the management of upper RIDs. However, there is a lack of evidence for the effects of YH buccal tablets on upper respiratory tract microbiota and circulating metabolites.

AIM OF THE STUDY

The aim of this study was to analyze the changes in respiratory microbiota composition and circulating metabolite profile after YH buccal tablets administration.

MATERIALS AND METHODS

Throat swab samples and serum samples were collected from 60 healthy subjects for high-throughput 16S ribosomal RNA gene (16S rRNA) sequencing and non-targeted Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis.

RESULTS

Airway microbial composition changed significantly after YH administration. The abundance of Actinomyces and Prevotella_7 increased, while the abundance of potentially pathogenic Pseudomonas and Corynebacterium decreased. A total of 168 significant HMDB taxonomic metabolites were identified in serum samples, of which lipid metabolites accounted for the largest proportion. Correlation analysis showed that circulatory metabolites were significantly correlated with changes in airway microbiota composition.

CONCLUSIONS

YH buccal tablets can inhibit opportunistic pathogens, increase beneficial microorganisms in the upper respiratory tract, and regulate the body's metabolic pathways. These findings provide insights into the mechanism of action of YH buccal tablets in the treatment and prevention of respiratory diseases.

Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing

BACKGROUND

Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).

RESULTS

We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.

CONCLUSION

Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.

Another tick bites the dust: exploring the association of microbial composition with a broad transmission competence of tick vector species

IMPORTANCE

Some tick species are competent to transmit more than one pathogen while other species are, until now, known to be competent to transmit only one single or any pathogen. Such a difference in vector competence for one or more pathogens might be related to the microbiome, and understanding what differentiates these two groups of ticks could help us control several diseases aiming at the bacteria groups that contribute to such a broad vector competence. Using 16S rRNA from tick species that could be classified into these groups, genera such as Rickettsia and Staphylococcus seemed to be associated with such a broad vector competence. Our results highlight differences in tick species when they are divided based on the number of pathogens they are competent to transmit. These findings are the first step into understanding the relationship between one single tick species and the pathogens it transmits.

Pathogen Profiles in Outpatients with Non-COVID-19 during the 7th Prevalent Period of COVID-19 in Gunma, Japan

The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the 7th prevalent period in Gunma, Japan, using deep sequencing combined with a next-generation sequencer (NGS) and advanced bioinformatics technologies. The study included nasopharyngeal swabs from 40 patients who tested negative for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) using immuno-chromatography and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods. Comprehensive pathogen sequencing was conducted through deep sequencing using NGS. Additionally, short reads obtained from NGS were analyzed for comprehensive pathogen estimation using MePIC (Metagenomic Pathogen Identification Pipeline for Clinical Specimens) and/or VirusTap. The results revealed the presence of various pathogens, including respiratory viruses and bacteria, in the present subjects. Notably, human adenovirus (HAdV) was the most frequently detected virus in 16 of the 40 cases (40.0%), followed by coryneforms, which were the most frequently detected bacteria in 21 of the 40 cases (52.5%). Seasonal human coronaviruses (NL63 type, 229E type, HKU1 type, and OC43 type), human bocaviruses, and human herpesviruses (human herpesvirus types 1-7) were not detected. Moreover, multiple pathogens were detected in 50% of the subjects. These results suggest that various respiratory pathogens may be associated with non-COVID-19 patients during the 7th prevalent period in Gunma Prefecture, Japan. Consequently, for an accurate diagnosis of pathogens causing respiratory infections, detailed pathogen analyses may be necessary. Furthermore, it is possible that various pathogens, excluding SARS-CoV-2, may be linked to fever and/or respiratory infections even during the COVID-19 pandemic.

Distribution of Corynebacterium Species and Comparative Results of Diagnostic Methods for Identifying Corynebacterium in Experimental Mice in Korea

Simple Summary

Experimental mice are the most commonly used laboratory animals for biomedical research and comparative studies. However, microbial infection may alter the mouse phenotype and confound interpretation results. The genus Corynebacterium, Gram-positive diphtheroid rod-shaped bacteria, induces severe diseases, such as hyperkeratosis and pseudotuberculosis, in immunodeficient mice. In this report, we described the population of Corynebacterium spp. isolated from laboratory mice in Korea using different approaches, comparing the accuracy and problems associated with each method. When identified based on molecular methods such as 16S rRNA and rpoB gene sequence analysis, the main Corynebacterium species were C. mastitidis (44.8%), C. bovis (25.5%), C. lowii (21.2%), and C. amycolatum (8.5%). In addition, matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) yielded results that were 77.9% identical to the molecular results, whereas biochemical methods showed only 15.5% identical to molecular identification. Collectively, our findings indicate that the different results may be obtained depending on the method used to identify Corynebacterium isolated from experimental mice, highlighting the importance of selecting an appropriate Corynebacterium identification method in obtaining accurate identification results. This result will help to increase the reliability of Corynebacterium diagnosis result from experimental mice.

Abstract

The genus Corynebacterium, composed of Gram-positive diphtheroid rod-shaped bacteria, induces severe diseases, such as Corynebacterium-associated hyperkeratosis and pseudotuberculosis, in immunodeficient mice. We isolated and identified a total of 165 strains of Corynebacterium species from experimental mice in Korean laboratories, diagnosed using several methods. When identified based on molecular methods, namely, 16S rRNA and rpoB gene sequence analysis, the main Corynebacterium species isolated in Korean laboratory mice were C. mastitidis (44.8%, n = 74), C. bovis (25.5%, n = 42), C. lowii (21.2%, n = 35), and C. amycolatum (8.5%, n = 14). Diagnoses were also performed using matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and biochemical methods. MALDI-TOF MS yielded results that were 77.9% identical to the molecular identification results, whereas biochemical methods showed only 15.5% identical to molecular identification, partly owing to difficulties in distinguishing among C. mastitidis strains. Collectively, our findings indicate that molecular biological methods are better suited for detecting and identifying Corynebacterium species candidates isolated from mice than biochemical methods. Because of limitations associated with the use of MALDI-TOF MS, more precise results will be obtained by complementing this approach with other methods when used for rapid identification testing.

Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy

Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.

Exudative pharyngitis and Corynebacterium pseudodiphtheriticum: A case report and review of the literature

Corynebacterium pseudodiphtheriticum is an established member of the normal flora of the respiratory tract. This organism is an emerging cause of respiratory tract infection, as well as infection of the skin and skin structures, urinary tract and other sterile sites. The syndrome of C. pseudodiphtheriticum exudative pharyngitis is a diagnostic challenge of particular relevance in recent times as this organism can be confused with Corynebacterium diphtheriae in the clinical setting and in the laboratory. We report a case of exudative pharyngitis, possibly due to C. pseudodiphtheriticum, in a 14-month old, incompletely vaccinated, human immunodeficiency virus (HIV)-positive infant and review the role of this organism in terms of its microbiological profile and identification, disease spectrum and antimicrobial susceptibility pattern.

Clinical characteristics and drug susceptibility patterns of Corynebacterium species in bacteremic patients with hematological disorders

The aim of this study was to clarify the clinical and microbiological characteristics of Corynebacterium bacteremia in hematological patients. We retrospectively reviewed the medical records of patients with Corynebacterium bacteremia from April 2013 to June 2018. The causative Corynebacterium species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Drug susceptibility tests were performed using the broth microdilution method recommended by the Clinical and Laboratory Standards Institute. In total, 147 cases of Corynebacterium bacteremia were identified during the study period. Corynebacterium striatum was the most frequent pathogen. Catheter-related bloodstream infection was diagnosed in 19.7% of all patients, and moderate/severe oral or severe gastrointestinal mucosal impairment was detected in 19.7%. Polymicrobial infection was found in about 20% of cases, with Enterococcus faecium being the most frequent isolate. The overall 30-day mortality was 34.7% (51/147). Multivariate analysis showed that E. faecium co-infection (odds ratio (OR) 9.3; 95% confidence interval (CI) 2.1-40), systemic corticosteroids (OR 3.6; 95% CI 1.4-8.9), other immunosuppressive drugs (OR 0.32; 95% CI 0.13-0.76), and a Pitt bacteremia score ≥4 (OR 12; 95% CI 3.9-40) were significant risk factors for overall 30-day mortality. The drug susceptibility rates for beta-lactam antimicrobial agents were quite low. All isolates were susceptible to glycopeptides and linezolid. However, some C. striatum isolates were resistant to daptomycin. Corynebacterium bacteremia can occur in the presence of several types of mucosal impairment. Our drug susceptibility data indicate that Corynebacterium bacteremia in hematological patients could be treated by glycopeptides or linezolid.

In Silico Prediction and Analysis of Unusual Lantibiotic Resistance Operons in the Genus Corynebacterium

Post-translationally modified, (methyl-)lanthionine-containing peptides are produced by several Gram-positive bacteria. These so-called lantibiotics have potent activity against various bacterial pathogens including multidrug-resistant strains and are thus discussed as alternatives to antibiotics. Several naturally occurring mechanisms of resistance against lantibiotics have been described for bacteria, including cell envelope modifications, ABC-transporters, lipoproteins and peptidases. Corynebacterium species are widespread in nature and comprise important pathogens, commensals as well as environmentally and biotechnologically relevant species. Yet, little is known about lantibiotic biosynthesis and resistance in this genus. Here, we present a comprehensive in silico prediction of lantibiotic resistance traits in this important group of Gram-positive bacteria. Our analyses suggest that enzymes for cell envelope modification, peptidases as well as ABC-transporters involved in peptide resistance are widely distributed in the genus. Based on our predictions, we analyzed the susceptibility of six Corynebacterium species to nisin and found that those without dedicated resistance traits are more susceptible and unable to adapt to higher concentrations. In addition, we were able to identify lantibiotic resistance operons encoding for peptidases, ABC-transporters and two-component systems with an unusual predicted structure that are conserved in the genus Corynebacterium. Heterologous expression shows that these operons indeed confer resistance to the lantibiotic nisin.

Clinical relevance and antimicrobial susceptibility profile of the unknown human pathogen Corynebacterium aurimucosum

Introduction. Even though Corynebacterium aurimucosum has been described in 2002, this species has long been underestimated due to the unreliability of conventional identification methods and only a few cases of infections have been reported.Hypothesis/Gap Statement. Little is known about clinical significance and antimicrobial susceptibility profile of this uncommon species.Aim. To evaluate the clinical relevance of C. aurimucosum and its antimicrobial susceptibility profile.Methodology. All C. aurimucosum isolates, collected from 2010 to 2019 in 10 French university hospitals, were retrospectively included. Demographic, clinical and microbiological data were collected for all cases. Antimicrobial susceptibility testing was performed according to the 2019 EUCAST guidelines.Results. Fifty-seven clinical isolates of C. aurimucosum were collected in 57 patients (median age, 65.8 years; male/female sex ratio, 1.1), mostly from urine (28 %), blood culture (28 %) and bone/synovial fluid (19 %) samples. Of them, 14 cases of infection were confirmed, mainly bone and joint infections (50 %) followed by urinary tract infections (UTIs) (21 %), bacteremia (14 %), skin and soft-tissue infections (14 %). C. aurimucosum was recovered in pure culture in 36 % of cases (UTIs and bacteremia) while mixed cultures were observed for other infections. By testing 52 clinical isolates in vitro, this species appeared to be fully susceptible to linezolid and vancomycin while most isolates (>80 %) were susceptible to amoxicillin (MIC₉₀, 2 µg ml^-1), gentamicin, tetracycline and rifampicin. Both cefotaxime and ciprofloxacin seemed to have a limited activity (ca. 50 % of susceptible strains). The MIC distribution for ciprofloxacin showed a bimodal profile with a population of highly-resistant strains with MICs >2 µg ml^-1. Most isolates (>90 %) were categorized as resistant to penicillin G and clindamycin.Conclusion. C. aurimucosum should be considered as an actual opportunistic pathogen, and treatment with amoxicillin, vancomycin or linezolid should be preferred.

Direct detection of Corynebacterium striatum, Corynebacterium propinquum, and Corynebacterium simulans in sputum samples by high-resolution melt curve analysis

BACKGROUND

Pulmonary infections caused by non-diphtheriae corynebacteria are increasing. However, rapid identification of Corynebacterium species poses a challenge due to the low genetic variation within the genus.

METHODS

Three reference strains and 99 clinical isolates were used in this study. A qPCR followed by high-resolution melting (HRM) targeting ssrA was performed to simultaneously identify C. striatum, C. propinquum and C. simulans. To further evaluate this assay's performance, 88 clinical sputum samples were tested by HRM and the detection results were compared with those of the traditional culture method and multiple cross-displacement amplification (MCDA) assay.

RESULTS

The melting curve produced by a pair of universal primers generated species-specific HRM curve profiles and could distinguish the three target species from other related bacteria. The limit of detection of HRM assay for DNA from the three purified Corynebacterium species was 100 fg. Compared with the culture method, HRM detected 22 additional positive specimens, representing a 23.9% relative increase in detection rate. The HRM assay had 98.4% (95% confidence interval [CI], 90.5-99.9%) sensitivity and 100% (95% CI, 82.8-100%) specificity. Additionally, 95.5% concordance between HRM and MCDA (κ = 0.89 [95% CI, 0.79-0.99]) was noted.

CONCLUSIONS

The HRM assay was a simple, rapid, sensitive, and specific diagnostic tool for detecting C. striatum, C. propinquum, and C. simulans, with the potential to contribute to early diagnosis, epidemiological surveillance, and rapid response to outbreak.

Genomic epidemiology of Corynebacterium striatum from three regions of China: an emerging national nosocomial epidemic

BACKGROUND

Corynebacteritum straitum has been considered as an emerging multi-drug-resistant (MDR) pathogen. Isolation of MDR C. striatum as the only organism from respiratory samples from hospitalized patients is increasing in China.

AIM

To elucidate the genomic epidemiology and evolution of C. striatum in China.

METHODS

A total of 260 isolates from 2016 to 2018 were collected from three hospitals in three regions of China. Antibiotic sensitivity testing was performed on all isolates. Whole-genome sequencing was applied to all isolates to assess their genomic diversity and relationships and detect the presence of antimicrobial resistance genes (ARG) and ARG cassettes.

FINDINGS

Almost all isolates (96.2%, 250/260) showed multi-drug-resistance. Genome sequencing revealed four major lineages with lineage IV emerging as the epidemic lineage. Most of the diversity was developed in the last 6 years. Each hospital has its own predominant clones with potential spread between Hebei and Guangdong hospitals. Genomic analysis further revealed multiple antimicrobial resistance genes.

CONCLUSIONS

Our results suggested that four lineages of C. striatum have spread in parallel across China, causing persistent and extensive transmissions within hospitals. MDR C. striatum infection has become a national epidemic. Antibiotic-driven selection pressure may have played significant roles in forming persistent and predominant clones. Our data provide the basis for surveillance and prevention strategies to control the epidemic caused by MDR C. striatum.

Infection and colonization by Corynebacterium pseudodiphtheriticum: a 9-year observational study in a university central hospital

Despite constituting part of the human commensal flora, Corynebacterium pseudodiphtheriticum has been recognized as a potentially infectious agent, most frequently in immunocompromised patients or individuals with other morbidity factors, but significant association to comorbid states remains unproven. This study's purpose was to assess clinical significance, risk factors for infection and antimicrobial susceptibility of C. pseudodiphtheriticum isolates. A retrospective observational study was conducted. Relevance of isolation was determined by clinical, laboratory, and imaging criteria. Forty-nine isolates occurred in 47 episodes. Colonization was assumed in 12% and infection in 78%, of which 51% were nosocomial. Patients with infection were older, with male predominance; both age and gender were statistically significant (p < 0.05) between infection and colonization groups. Although dyslipidemia (58%), arterial hypertension (58%), invasive procedures (56%), and chronic lung disease (50%) were prevalent in the infection group, no comorbidity was a significant risk factor for infection compared with colonization. Charlson comorbidity index showed no statistically difference between groups. Mortality rate was 14% in infection. Respiratory samples were the main isolation product; all tested strains were susceptible to amoxicillin/clavulanate and vancomycin. Resistant strains were observed for clindamycin (77%) and erythromycin (48%). C. pseudodiphtheriticum isolation was associated with infection in most cases. Despite the high prevalence of comorbidities and invasive procedures, no factors other than age and gender were significantly associated with infection. Although C. pseudodiphtheriticum may constitute a contaminant or colonizer in clinical samples, positive cultures in patients with signs and symptoms consistent with infection should not be neglected.

Clinical relevance and impact of Corynebacterium isolation in lower respiratory tract of critically ill patients requiring mechanical ventilation

Purpose

Corynebacterium spp. (C. spp.) is commonly considered as a contaminant in respiratory specimens. No study has ever focused on its clinical relevance in the lower respiratory tract of patients admitted to the intensive care unit (ICU) and requiring mechanical ventilation. The aims were to describe the characteristics of ICU patients with a C. spp. positive deep respiratory specimen, to investigate the impact of C. spp. on the occurrence of pneumonia, and to evaluate the outcomes of these pneumonia.

Methods

We retrospectively included all adult patients admitted to ICU in a 1000-bed University Hospital (2007–2017) who had a C. spp. positive lower respiratory tract specimen at a significant quantitative level. We used clinical, radiological, and microbiological criteria to classify the likelihood of such pneumonia.

Results

Among the 31 patients included, acute respiratory failure and postoperative care after major surgery were the main reasons of admission. SAPS II was 47 [34–60]. C. spp. pneumonia was considered as probable, possible and unlikely in 10, 14, and 7 patients, respectively. Fifty-two and 94% of C. spp. strains were sensitive to amoxicillin, and vancomycin/linezolid, respectively. Seventeen patients had a complete course of antibiotic against C. spp. The overall ICU mortality was 58%.

Conclusion

Corynebacterium spp seems to be responsible for authentic pneumonia in mechanically ventilated patients. It should be considered as clinically relevant when predominantly present in respiratory specimen from patients suspected with pneumonia in ICU, and empirically treated.

Antimicrobial Resistance and Molecular Epidemiology of Corynebacterium striatum Isolated in a Tertiary Hospital in Turkey

Although Corynebacterium striatum is part of the human flora, it has recently drawn attention both for its multidrug resistance and its role as an invasive infection/outbreak agent. This cross-sectional study aimed to determine the antimicrobial resistance and clonal relationships among C. striatum strains. In total, 81 C. striatum strains were identified using Phoenix-100^TM (BD, Sparks, MD, USA). The antimicrobial resistance of the strains was determined using the Kirby–Bauer disk diffusion method. Clonal relatedness among the strains was performed via arbitrarily primed polymerase chain reaction (AP-PCR). All 81 C. striatum strains were resistant to penicillin, cefotaxime, ciprofloxacin, and tetracycline, but susceptible to vancomycin and linezolid. The resistance rates to gentamicin, erythromycin, and clindamycin were 34.6%, 79%, and 87.7% respectively. AP-PCR results showed no predominant clone among the C. striatum strains. Corynebacterium striatum is reportedly the cause of an increasing number of invasive infections/outbreaks. Moreover, treatment options are limited. The study showed that vancomycin, linezolid, and gentamicin can be selected for the empirical treatment of C. striatum infections. Although no single-clone outbreak was observed in our hospital, small clonal circulations were observed within some units, indicating cross-contamination. Therefore, a comprehensive infection control program is warranted in future.

Cytokine Levels in the In Vitro Response of T Cells to Planktonic and Biofilm Corynebacterium amycolatum

Unravelling of the interplay between the immune system and non-diphtheria corynebacteria would contribute to understanding their increasing role as medically important microorganisms. We aimed at the analysis of pro- (TNF, IL-1β, IL-6, IL-8, and IL-12p70) and anti-inflammatory (IL-10) cytokines produced by Jurkat T cells in response to planktonic and biofilm Corynebacterium amycolatum. Two reference strains: C. amycolatum ATCC 700207 (R-CA), Staphylococcus aureus ATCC 25923 (R-SA), and ten clinical strains of C. amycolatum (C-CA) were used in the study. Jurkat T cells were stimulated in vitro by the planktonic-conditioned medium (PCM) and biofilm-conditioned medium (BCM) derived from the relevant cultures of the strains tested. The cytokine concentrations were determined in the cell culture supernatants using the flow cytometry. The levels of the cytokines analyzed were lower after stimulation with the BCM when compared to the PCM derived from the cultures of C-CA; statistical significance (p < 0.05) was observed for IL-1β, IL-12 p70, and IL-10. Similarly, planktonic R-CA and R-SA stimulated a higher cytokine production than their biofilm counterparts. The highest levels of pro-inflammatory IL-8, IL-1β, and IL-12p70 were observed after stimulation with planktonic R-SA whereas the strongest stimulation of anti-inflammatory IL-10 was noted for the BCM derived from the mixed culture of both reference species. Our results are indicative of weaker immunostimulatory properties of the biofilm C. amycolatum compared to its planktonic form. It may play a role in the persistence of biofilm-related infections. The extent of the cytokine response can be dependent on the inherent virulence of the infecting microorganism.

Clinical Characteristics and Outcome of Lung Transplant Recipients with Respiratory Isolation of Corynebacterium spp

Although chronic respiratory disease and immunosuppression are risk factors for Corynebacterium species respiratory infection, data are scarce regarding this disease in lung transplantation. Our aim was to describe the clinical characteristics and outcomes of lung transplant recipients (LTR) with respiratory isolation of Corynebacterium spp. This was a retrospective observational study performed at a referral center in Barcelona, Spain (2014 to 2016). We included all LTR in whom Corynebacterium spp. were isolated in at least one good-quality lower respiratory tract specimen. Overall, 24 of 527 (4.6%) LTR at risk during the study period were included. The main epidemiological, clinical, and microbiological data were analyzed. The most frequently isolated species were C. striatum (11/24), C. pseudodiphtheriticum (3/24), and C. amycolatum (3/24). All 19 (76%) patients who underwent bronchoscopy showed abnormalities, mainly mucosal plaques at the bronchial suture and purulent secretions. Clinical cure was achieved in 8/12 (67%) patients who fulfilled the CDC definition of lower respiratory tract infection (LRTI). To assess the clinical relevance of Corynebacterium spp., only patients with monomicrobial isolation (n = 18) were evaluated. LRTI was diagnosed in 9, and a nonsignificant association was found with a significant number of Corynebacterium sp. CFU/ml (7/9 LRTI versus 2/9 non-LRTI, P = 0.057). Persistent infection was associated with metallic bronchial stent implantation (4/4 versus 2/14, P = 0.005). The isolation of Corynebacterium spp. in respiratory specimens of lung transplant recipients may herald a respiratory tract infection or bronchial suture damage. Bronchial stent implantation is a risk factor for the persistence of Corynebacterium species infection.

Contemporary microbiology and identification of Corynebacteria spp. causing infections in human

The Corynebacterium is a genus of bacteria of growing clinical importance. Progress in medicine results in growing population of immunocompromised patients and growing number of infections caused by opportunistic pathogens. A new infections caused by new Corynebacterium species and species previously regarded as commensal micro-organisms have been described. Parallel with changes in Corynebacteria infections, the microbiological laboratory diagnostic possibilities are changing. But identification of this group of bacteria to the species level remains difficult. In the paper, we present various manual, semi-automated and automated assays used in clinical laboratories for Corynebacterium identification, such as API Coryne, RapID CB Plus, BBL Crystal Gram Positive ID System, MICRONAUT-RPO, VITEK 2, BD Phoenix System, Sherlock Microbial ID System, MicroSeq Microbial Identification System, Biolog Microbial Identification Systems, MALDI-TOF MS systems, polymerase chain reaction (PCR)-based and sequencing-based assays. The presented assays are based on various properties, like biochemical tests, specific DNA sequences, composition of cellular fatty acids, protein profiles and have specific limitations.

SIGNIFICANCE AND IMPACT OF THE STUDY

The number of opportunistic infections caused by Corynebacteria is increasing due to increase in number of immunocompromised patients. New Corynebacterium species and new human infections, caused by this group of bacteria, has been described recently. However, identification of Corynebacteria is still a challenge despite application of sophisticated laboratory methods. In the study we present possibilities and limitations of various commercial systems for identification of Corynebacteria.

Multidrug-Resistant Corynebacterium striatum Associated with Increased Use of Parenteral Antimicrobial Drugs

Device-related infections with this pathogen frequently require prolonged parenteral therapy.

Corynebacterium striatum is an emerging multidrug-resistant bacteria. We retrospectively identified 179 isolates in a clinical database. Clinical relevance, in vitro susceptibility, and length of parenteral antimicrobial drug use were obtained from patient records. For patients with hardware- or device-associated infections, those with C. striatum infections were matched with patients infected with coagulase-negative staphylococci for case–control analysis. A total of 87 (71%) of 121 isolates were resistant to all oral antimicrobial drugs tested, including penicillin, tetracycline, clindamycin, erythromycin, and ciprofloxacin. When isolated from hardware or devices, C. striatum was pathogenic in 38 (87%) of 44 cases. Patients with hardware-associated C. striatum infections received parenteral antimicrobial drugs longer than patients with hardware-associated coagulase-negative staphylococci infections (mean ± SD 69 ± 5 days vs. 25 ± 4 days; p<0.001). C. striatum commonly shows resistance to antimicrobial drugs with oral bioavailability and is associated with increased use of parenteral antimicrobial drugs.

When Good Bugs Go Bad: Epidemiology and Antimicrobial Resistance Profiles of Corynebacterium striatum, an Emerging Multidrug-Resistant, Opportunistic Pathogen

Infections with Corynebacterium striatum have been described in the literature over the last 2 decades, with the majority being bacteremia, central line infections, and occasionally, endocarditis. In recent years, the frequency of C. striatum infections appears to be increasing; a factor likely contributing to this is the increased ease and accuracy of the identification of Corynebacterium spp., including C. striatum, from clinical cultures. The objective of this study was to retrospectively characterize C. striatum isolates recovered from specimens submitted as part of routine patient care at a 1,250-bed, tertiary-care academic medical center. Multiple strain types were recovered, as demonstrated by repetitive-sequence-based PCR. Most of the strains of C. striatum characterized were resistant to antimicrobials commonly used to treat Gram-positive organisms, such as penicillin, ceftriaxone, meropenem, clindamycin, and tetracycline. The MIC₅₀ for ceftaroline was >32 μg/ml. Although there are no interpretive criteria for susceptibility with telavancin, it appeared to have potent in vitro efficacy against this species, with MIC₅₀ and MIC₉₀ values of 0.064 and 0.125 μg/ml, respectively. Finally, as previously reported in case studies, we demonstrated rapid in vitro development of daptomycin resistance in 100% of the isolates tested (n = 50), indicating that caution should be exhibited when using daptomycin for the treatment of C. striatum infections. C. striatum is an emerging, multidrug-resistant pathogen that can be associated with a variety of infection types.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for identification of Corynebacterium species

Background

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool that has initiated a revolution in the clinical microbiology laboratory for identification of nosocomial pathogens. The efficacy of MALDI-TOF MS produced by bioMerieux, Marcy l'Etoile, France (VITEK MS) for detecting Corynebacterium remains unknown.

Methods

Corynebacterium isolates were isolated from clinical specimen in a tertial teaching hospital from 2012 to 2013. All strains confirmed by rpoB sequencing were identified by API Coryne (bioMerieux), Phoenix (BD) and VITEK MS, respectively. The coincidence rate was used to evaluate the consistency and accuracy across three methods.

Results

In all, 75 Corynebacterium isolates were collected in this study. The dominant isolates were Corynebacterium striatum (58.7%), Corynebacterium jeikeium (16.0%), Corynebacterium amycolatum (5.3%), Corynebacterium urealyticum (5.3%), Corynebacterium glucuronolyticum (2.7%) and Corynebacterium minutissimum (2.7%). We found that there was no significant difference in the identification of corynebacterium to genus level by MS (100%, 75/75) or Phoenix (93.3%, 70/75) (P=0.058). However, 92.0% (69/75) strains were successfully identified to species by MS while which by Phoenix and API was 78.7% and 65.3% respectively. Compared with gene sequencing, the coincidence rate of identification by MS was significantly higher than Phoenix (P=0.036) and API (P<0.001). Compared with API Coryne (bioMerieux) and Phoenix, VITEK MS shown significant shorter detecting period and less cost.

Conclusions

VITEK MS was a powerful tool, which could be applied in clinical laboratory, improving the diagnosis for Corynebacterium infection.

Metataxonomic and Metagenomic Approaches vs. Culture-Based Techniques for Clinical Pathology

Diagnoses that are both timely and accurate are critically important for patients with life-threatening or drug resistant infections. Technological improvements in High-Throughput Sequencing (HTS) have led to its use in pathogen detection and its application in clinical diagnoses of infectious diseases. The present study compares two HTS methods, 16S rRNA marker gene sequencing (metataxonomics) and whole metagenomic shotgun sequencing (metagenomics), in their respective abilities to match the same diagnosis as traditional culture methods (culture inference) for patients with ventilator associated pneumonia (VAP). The metagenomic analysis was able to produce the same diagnosis as culture methods at the species-level for five of the six samples, while the metataxonomic analysis was only able to produce results with the same species-level identification as culture for two of the six samples. These results indicate that metagenomic analyses have the accuracy needed for a clinical diagnostic tool, but full integration in diagnostic protocols is contingent on technological improvements to decrease turnaround time and lower costs.

Identification of clinically relevant Corynebacterium strains by Api Coryne, MALDI-TOF-mass spectrometry and molecular approaches

We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 97 Corynebacterium clinical in comparison to identification strains by Api Coryne and MALDI-TOF-MS using 16S rRNA gene and hypervariable region of rpoB genes sequencing as a reference method. C. striatum was the predominant species isolated followed by C. amycolatum. There was an agreement between Api Coryne strips and MALDI-TOF-MS identification in 88.65% of cases. MALDI-TOF-MS was unable to differentiate C. aurimucosum from C. minutissimum and C. minutissimum from C. singulare but reliably identify 92 of 97 (94.84%) strains. Two strains remained incompletely identified to the species level by MALDI-TOF-MS and molecular approaches. They belonged to Cellulomonas and Pseudoclavibacter genus. In conclusion, MALDI-TOF-MS is a rapid and reliable method for the identification of Corynebacterium species. However, some limits have been noted and have to be resolved by the application of molecular methods.

Clinical relevance of Corynebacterium pseudodiphtheriticum in lower respiratory tract specimens

BACKGROUND

Corynebacterium pseudodiphtheriticum may be present as commensal flora of the respiratory tract and therefore it may be difficult to assess clinical relevance when it is cultured from lower respiratory tract specimens. Our objective was to determine the clinical relevance of C. pseudodiphtheriticum as a lower respiratory tract pathogen and to define patients at risk of developing lower respiratory tract infections caused by C. pseudodiphtheriticum.

METHODS

We retrospectively identified all lower respiratory tract cultures positive for C. pseudodiphtheriticum over a 10-year period and assessed clinical relevance by predefined criteria.

RESULTS

Clinical relevance was likely or possible in 86% of patients. Pre-existent comorbidity was present in 86% of patients, mostly underlying cardiac or pulmonary disease. All isolates were susceptible to amoxicillin.

CONCLUSION

C. pseudodiphtheriticum should be considered a clinically relevant pathogen when cultured from the lower respiratory tract in symptomatic patients.

Respiratory infection by Corynebacterium striatum: epidemiological and clinical determinants

The increasing prevalence of advanced chronic respiratory disease, with frequent exposure to broad-spectrum antibiotics for repeated and prolonged hospitalizations, favours the emergence of nosocomial respiratory infection by Gram-positive bacteria, such as outbreaks of Corynebacterium striatum. There is little evidence about patterns of respiratory infection, transmission and adaptive ability of this pathogen. Seventy-two C. striatum isolates from 51 advanced respiratory patients, mainly chronic obstructive pulmonary disease, were studied during 38 months. Patients were 74.8 ± 8.6 years old and 81.9% were men, who had required an average of 2.2 hospitalizations and 63.5 days in the hospital in the previous year. Of 49 isolates from 42 patients we were able to identify 12 clones by multilocus sequence analysis (MLSA), nine phenotypic variants and 22 antibiotic susceptibility patterns, and we determined their clinical and epidemiological determinants. MLSA allows identification of the existence of nosocomial outbreaks by transmission of the same or different clones, the persistence of the same clone in the environment or in patient airways for months. The study showed the high variability and adaptive capacity of the isolates, the antibiotic multidrug-resistance in all of them, and their contribution to a high morbidity and mortality (41%) during the study period.

Patient nostril microbial flora: individual-dependency and diversity precluding prediction of Staphylococcus aureus acquisition

The potential role of a patient's resident microbial flora in the risk of acquiring multiresistant bacteria (MRB) during hospitalization is unclear. We investigated this role by cross-sectional study of 103 patients at risk of acquisition of Staphylococcus aureus (SA), resistant (MRSA) or not (MSSA) to methicillin, recruited in four French hospitals. The flora was analysed by an exhaustive culture-based approach combined with molecular and/or mass-spectrometry-based identification, and SA strain typing. Forty-three of the 53 SA-negative patients at entry were followed for up to 52 weeks: 19 (44.2%) remained negative for SA and 24 (55.8%) became positive, including 19 (79%) who acquired an MSSA, four (17%) who acquired an MRSA and one who acquired both (4%). Fifty-one different species were identified among the 103 patients, of which two, Corynebacterium accolens and Staphylococcus haemolyticus (p = 0.02-0.01), were more prevalent in the absence of SA. However, the same number of patients carrying or not these two species acquired an MSSA/MRSA during follow-up, regardless of antibiotic treatment received. Clustering analysis showed that the microbial flora was highly specific to each patient, and not predictive for acquisition of MSSA/MRSA or not. Patient-specific microbial resident flora is not predictive of SA acquisition.

Non-diphtheriae Corynebacterium species: an emerging respiratory pathogen

The purpose of the study was to describe the microbiological and clinical features of ten cases of lower respiratory tract infection due to Corynebacterium striatum, Corynebacterium propinquum and Corynebacterium pseudodiphtheriticum. Respiratory samples were recovered from hospitalised patients who were diagnosed of pneumonia and exacerbations of chronic respiratory infections. The samples were Gram-stained and seeded on conventional bacterial growing media. Bacteria were identified by matrix-assisted linear desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility was tested by the disk diffusion method. All patients presented an acute respiratory onset, most of them in the context of an underlying disease and/or immunosuppression. In all patients, the microscopical examination of Gram-stained respiratory samples showed numerous polymorphonuclear cells and Gram-positive bacilli, suggestive of the Corynebacterium morphotype. A pure culture growth of Corynebacterium was obtained in the majority (72 %) of samples. The conclusions are that non-diphtheriae Corynebacterium species are an emerging cause of respiratory infection among patients with chronic respiratory disease and/or immunosuppression, and cannot always be considered as mere colonisers. The microorganism's predominance in Gram-stained purulent respiratory samples together with abundant growth in the culture is the key for the microbiological diagnosis.