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

Native valve endocarditis caused by Corynebacterium striatum without underlying structural heart disease or indwelling cardiovascular medical devices: a case report

BACKGROUND

Corynebacterium striatum (C. striatum) is a gram-positive, anaerobic bacillus found both environmentally and in human skin and nasal mucosa flora. It is reportedly the etiologic agent of community-acquired and nosocomial diseases and is significantly associated with bacteremia and medical endovascular devices. This is the rare case of mitral valve native valve endocarditis (NVE) caused by C. striatum occurring in a young adult without underlying structural heart disease or indwelling cardiovascular medical devices successfully treated with multidisciplinary therapy.

CASE PRESENTATION

The patient was a 28-year-old female with no medical history. She was transferred our hospital due to sudden onset of vertigo and vomit. A computed tomography on day 2 revealed the hydrocephalus due to the cerebellar infarction, and she underwent posterior fossa decompression for cerebellar infarction. An angiography on day 8 revealed a left vertebral artery dissection, which was suspected be the etiology. Afterwards, a sudden fever of 39 degrees developed on day 38. She was diagnosed with aspiration pneumonia and treated with ampicillin/sulbactam but was still febrile at the time of transfer for rehabilitation. Treatment continued with levofloxacin, the patient had no fever decline, and she was readmitted to our hospital. Readmission blood cultures (3/3 sets) revealed C. striatum, and an echocardiogram revealed an 11 mm long mitral valve vegetation, leading to NVE diagnosis. On the sixth illness day, cardiac failure symptoms manifested. Echocardiography revealed mitral valve rupture. She was transferred again on the 11th day of illness, during which time her mitral valve was replaced. C. striatum was detected in the vegetation. Following surgery, she returned to our hospital, and vancomycin administration continued. The patient was discharged after 31 total days of postoperative antimicrobial therapy. The patient experienced no exacerbations thereafter.

CONCLUSIONS

We report the rare case of C. striatum mitral valve NVE in a young adult without structural heart disease or indwelling cardiovascular devices.

CLINICAL TRIAL NUMBER

Not applicable.

Effect of Mn-HA on ARGs and MRGs in nitrogen-culturing sludge

The simultaneous escalation in ARGs (antibiotic resistance genes) and MRGs (metal resistance genes) further complicates the intricate network of factors contributing to the proliferation of microbial resistance. Manganese, which has been reported to affect the resistance of bacteria to antibiotics and metals, plays a vital role in microbial nitrogen metabolism. Moreover, nitrifying and denitrifying populations are potential hosts for ARGs. In this study, manganese was introduced in its prevalent organic chelated form in the environment (Manganese humus chelates, Mn-HA) to a N metabolism sludge to explore the effect of manganese on MRGs and ARGs dissemination. Metagenomics results revealed that manganese availability enhances nitrogen metabolism, while a decrease in ARGs was noted which may be attributed to the inhibition of horizontal gene transfer (HGT), reflected in the reduced integrase -encoded gene int. Population analysis revealed that nitrifier and denitrifier genus harbor MRGs and ARGs, indicating that nitrifier and denitrifier are hosts of MRGs and ARGs. This raises the question of whether the prevalence of ARGs is always increased in metal-contained environments.

Corynebacterium striatum-Induced Native Valve Infective Endocarditis in an Immunocompetent Patient

Corynebacterium striatum is often considered a contaminant in blood cultures due to often being found colonizing skin and mucous membranes. This case displays C. striatum infective endocarditis (IE) identified in an immunocompetent patient on a native valve. Despite treatment with vancomycin, the case was complicated by embolic infarcts to the spleen and left cerebellum along with the development of a perivalvular abscess. This case highlights risk factors for C. striatum infection and exemplifies the importance of recognizing this bacteria species as a possible pathogen causing complicated IE.

Dietary supplementation with Macleaya cordata extract alleviates intestinal injury in broiler chickens challenged with lipopolysaccharide by regulating gut microbiota and plasma metabolites

Introduction

The prevention and mitigation of intestinal immune challenge is crucial for poultry production. This study investigated the effects of dietary Macleaya cordata extract (MCE) supplementation on the prevention of intestinal injury in broiler chickens challenged with lipopolysaccharide (LPS).

Methods

A total of 256 one-day-old male Arbor Acres broilers were randomly divided into 4 treatment groups using a 2×2 factorial design with 2 MCE supplemental levels (0 and 400 mg/kg) and 2 LPS challenge levels (0 and 1 mg/kg body weight). The experiment lasted for 21 d.

Results and discussion

The results showed that MCE supplementation increased the average daily feed intake during days 0-14. MCE supplementation and LPS challenge have an interaction on the average daily gain during days 15-21. MCE supplementation significantly alleviated the decreased average daily gain of broiler chickens induced by LPS. MCE supplementation increased the total antioxidant capacity and the activity of catalase and reduced the level of malondialdehyde in jejunal mucosa. MCE addition elevated the villus height and the ratio of villus height to crypt depth of the ileum. MCE supplementation decreased the mRNA expression of pro-inflammatory cytokines interleukin (IL)-6 and IL-8 in the jejunum. MCE addition mitigated LPS-induced mRNA up-expression of pro-inflammatory factors IL-1β and IL-17 in the jejunum. MCE supplementation increased the abundance of probiotic bacteria (such as Lactobacillus and Blautia) and reduced the abundance of pathogenic bacteria (such as Actinobacteriota, Peptostretococcaceae, and Rhodococcus), leading to alterations in gut microbiota composition. MCE addition altered several metabolic pathways such as Amino acid metabolism, Nucleotide metabolism, Energy metabolism, Carbohydrate metabolism, and Lipid metabolism in broilers. In these pathways, MCE supplementation increased the levels of L-aspartic acid, L-Glutamate, L-serine, etc., and reduced the levels of phosphatidylcholine, phosphatidylethanolamine, thromboxane B2, 13-(S)-HODPE, etc. In conclusion, dietary supplementation of 400 mg/kg MCE effectively improved the growth performance and intestinal function in LPS-challenged broiler chickens, probably due to the modulation of gut microbiota and plasma metabolites.

Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK

Corynebacterium striatum is an emerging nosocomial pathogen. This is the first report showing the presence of three distinct multidrug resistant lineages of C. striatum among patients in a UK hospital. The presence of ErmX, Tet(W), Bla and AmpC proteins, and mutations in gyrA gene are associated with the resistance to clindamycin, doxycycline, penicillin and moxifloxacin, respectively. These strains are equipped with several corynebacterial virulence genes including two SpaDEF-type and a novel pilus gene cluster, which needs further molecular characterisation. This study highlights a need of developing an active surveillance strategy for routine monitoring and preventing potential cross-transmission among susceptible patients.

Practice of standardization of CLSI M45 A3 antimicrobial susceptibility testing of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in Guangdong Province 2017-2021

The concentration of antimicrobial agents in environments like water and food has increased rapidly, which led to a rapid increase in antimicrobial resistance levels in the environment. Monitoring of bacterial resistance levels is considered as a necessary means to control the bacterial resistance. Reference standards are critical for antimicrobial susceptibility testing. CLSI M45 A3 standard defines pathogenic microorganisms that cause infections less frequently than those covered by CLSI M02, M07, and M100 as Infrequently Isolated or Fastidious Bacteria and specifies antimicrobial susceptibility testing methods. Our study investigated the epidemiology and antimicrobial susceptibility testing data of Infrequently Isolated or Fastidious Bacteria strains isolated from blood specimens in 70 hospitals in Guangdong Province between 2017 and 2021. We defined testing methods other than those specified in CLSI M45 A3 as "Non-Standardized." The proportion of standardized antimicrobial susceptibility testing for penicillin increased significantly (Corynebacterium spp. 17.4% vs. 50.0% p < 0.05; Micrococcus spp. 50.0% vs. 77.8% p < 0.05; Abiotrophia spp. and Granulicatella spp. 21.4% vs. 90.9% p < 0.001), while for cefotaxime (Corynebacterium spp. 0.0% vs. 45.2% p < 0.05; Abiotrophia spp. and Granulicatella spp. 0.0% vs. 14.3% p = 0.515) and vancomycin increased finitely. Non-standardized methods were used for all other antimicrobials. Due to limitations in the economic and medical environment, some clinical laboratories are unable to fully comply with CLSI M45 A3 standard. We recommend that CLSI should add breakpoints for disk diffusion method to improve the standardization of antimicrobial susceptibility testing.

Synergistic interactions of essential oil components with antibiotics against multidrug-resistant Corynebacterium striatum

AIM

In this study, it was aimed to examine the antibacterial activity of the essential oil components (EOCs), carvacrol (CAR), cinnamaldehyde (CIN), thymol (TH), alpha pinene (α-PN), eucalyptol (EU), limonene (LIM), and the antibiotics, linezolid (LZD), vancomycin (VAN), gentamicin (GEN), ciprofloxacin (CIP), clindamycin (CLN), and penicillin (PEN) against 50 multidrug resistant Corynebacterium striatum strains, and the synergistic interactions of CAR and CIN with the antibiotics against 10 randomly selected Coryne. striatum strains to explore synergistic interactions to determine if their combined use could enhance antibiotic activity and potentially reduce resistance.

METHODS AND RESULTS

The activity of the EOCs and the antibiotics against Coryne. striatum strains isolated from clinical specimens, was examined by broth microdilution method. The synergistic interactions of the EOCs with the antibiotics against 10 randomly selected Coryne. striatum strains were determined by checkerboard method. EOCs, CIN, and CAR and antibiotics, LZD, VAN, GEN, CIP, and CLN were detected to have antibacterial activity against Coryne. striatum strains alone and either synergistic interactions were observed in combinations of the antibiotics with EOCs.

CONCLUSIONS

All Coryne. striatum strains were determined to be susceptible to VAN and LZD and resistant to GEN, PEN, CIP, and CLN. Synergistic interactions were observed in all combinations of antibiotics tested with CAR and CIN.

Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates

Introduction

Over the past decade, Corynebacterium striatum (C. striatum), an emerging multidrug-resistant (MDR) pathogen, has significantly challenged healthcare settings, especially those involving individuals with weakened immune systems. The rise of these superbugs necessitates innovative solutions.

Methods

This study aimed to isolate and characterize bacteriophages targeting MDR-C. striatum. Utilizing 54 MDR-C. striatum isolates from a local hospital as target strains, samples were collected from restroom puddles for phage screening. Dot Plaque and Double-layer plate Assays were employed for screening.

Results

A novel temperate bacteriophage, named CSP1, was identified through a series of procedures, including purification, genome extraction, sequencing, and one-step growth curves. CSP1 possesses a 39,752 base pair circular double-stranded DNA genome with HK97-like structural proteins and potential for site-specific recombination. It represents a new species within the unclassified Caudoviricetes class, as supported by transmission electron microscopy, genomic evolutionary analysis, and collinearity studies. Notably, CSP1 infected and lysed 21 clinical MDR-C. striatum isolates, demonstrating a wide host range. The phage remained stable in conditions ranging from -40 to 55°C, pH 4 to 12, and in 0.9% NaCl buffer, showing no cytotoxicity.

Discussion

The identification of CSP1 as the first phage targeting clinical C. striatum strains opens new possibilities in bacteriophage therapy research, and the development of diagnostic and therapeutic tools against pathogenic bacteria.

The urogenital microbiome in chronic kidney disease patients on peritoneal dialysis

INTRODUCTION AND OBJECTIVES

Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters.

MATERIALS AND METHODS

Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Correlations with the patients' clinical data and inflammatory profile were performed.

RESULTS

CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14.

CONCLUSIONS

Our results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.

Native mitral valve endocarditis due to Corynebacterium striatum, an uncommon pathogen

Corynebacterium striatum, a commensal gram-positive rod, is an emerging cause of human disease in individuals with multiple comorbidities and in immunocompromised patient populations. New microbiologic laboratory tests including molecular diagnostics with greater sensitivity to detect pathogens facilitate appropriate clinical diagnosis and treatment to decrease patient morbidity and mortality. Here we report a case of community-acquired C. striatum infective endocarditis of a native mitral valve in a patient with multiple comorbidities.

Infective Endocarditis Caused by Corynebacterium striatum: Navigating Challenges and Treatment Strategies in an Emerging Threat

Corynebacterium striatum is a type of bacteria normally found in the environment and is considered a benign microbe on the human body surface. However, it can induce severe medical conditions, including bacteremia, infective endocarditis, osteomyelitis, and infections, in other organs. This case study focuses on a 56-year-old male patient with multiple comorbidities who presented with an ischemic stroke. Several days after the insertion of a right internal jugular line, the patient developed fever and tachycardia. Blood cultures revealed the presence of Corynebacterium striatum, a Gram-positive bacilli. Transesophageal echocardiography confirmed the diagnosis of complicated infective endocarditis (IE) with mitral valve vegetation and moderate mitral regurgitation. Prompt treatment with appropriate antibiotics, including linezolid and later vancomycin, led to the patient's improvement and eventual discharge in good condition. This case highlights the importance of early recognition, aggressive management, and accurate diagnosis in cases of IE caused by Corynebacterium striatum. Proper antibiotic selection is crucial, considering the emerging antibiotic resistance patterns associated with this pathogen. By addressing these aspects, patient outcomes can be improved, and potential complications such as IE can be prevented.

Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

Introduction: Genome-scale metabolic models (GEMs) are organism-specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. However, the validity of predictions for bacterial proliferation in in vitro settings is hardly investigated. Methods: The present work combines in silico and in vitro approaches to create and curate strain-specific genome-scale metabolic models of Corynebacterium striatum. Results: We introduce five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and were validated by laboratory experiments. For the curation of those models, the software infrastructure refineGEMs was developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Discussion: Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available from https://github.com/draeger-lab/refinegems.

A Rare Case of Aggressive Infective Endocarditis Due to Corynebacterium striatum

Corynebacterium striatum is considered a rare pathogen in infective endocarditis (IE). C. striatum is a Gram-positive facultative anaerobic bacterium found in the environment and human flora. It is part of the microbiota of the skin and nasal mucosa of humans and has been increasingly reported as the etiologic agent of community-acquired and nosocomial diseases. A 91-year-old female patient was admitted to our clinic with complaints of increased fatigue for a week. Transthoracic echocardiography revealed a labile, echogenic appearance on the mitral valve that may be consistent with infective endocarditis, causing mitral regurgitation. Transesophageal echocardiography (TEE) confirmed this finding on the same day. In three-dimensional (3D) TEE, there was an oval mass of 1.9 cm × 1.1 cm at the level of the P2 scallop of the posterior mitral leaflet, and 1.0 cm of mobile vegetation was observed on it. Three serial blood cultures from peripheral vessels identified C. striatum. Antibiotic treatment of the patient was started with daptomycin 1 × 750 mg and meropenem 3 × 1 g. The cardiology team advised the patient to undergo early surgery, but the patient declined, and the case was followed up medically. On the 10th follow-up day, the patient had a speech disorder. Cerebral computed tomographic angiography showed an appearance compatible with a septic embolism in the left main cerebral artery. The patient's condition worsened throughout follow-ups, and she died on day 12. The purpose of presenting this case is to emphasize the importance of Corynebacterium species, which is a cause of rare native valve infectious endocarditis, and to show the difficulties in its treatment.

Phylogenetic analyses of antimicrobial resistant Corynebacterium striatum strains isolated from a nosocomial outbreak in a tertiary hospital in China

Corynebacterium striatum is an emerging, multidrug-resistant pathogen that frequently causes nosocomial infections worldwide. This study aimed to investigate phylogenetic relationship and presence of genes responsible for antimicrobial resistance among C. striatum strains associated with an outbreak at the Shanxi Bethune Hospital, China, in 2021. Fecal samples were collected from 65 patients with C. striatum infection at Shanxi Bethune Hospital between February 12, 2021 and April 12, 2021. C. striatum isolates were identified by 16S rRNA and rpoB gene sequencing. E-test strips were used to examine the antimicrobial susceptibility of the isolates. Whole-genome sequencing and bioinformatics analysis were employed to assess the genomic features and identify antimicrobial resistance genes of the isolates. Crystal violet staining was conducted to determine the ability of biofilm formation of each isolate. A total of 64 C. striatum isolates were identified and categorized into 4 clades based on single nucleotide polymorphisms. All isolates were resistant to penicillin, meropenem, ceftriaxone, and ciprofloxacin but susceptible to vancomycin and linezolid. Most isolates were also resistant to tetracycline, clindamycin, and erythromycin, with susceptibility rates of 10.77, 4.62, and 7.69%, respectively. Genomic analysis revealed 14 antimicrobial resistance genes in the isolates, including tetW, ermX, and sul1. Crystal violet staining showed that all isolates formed biofilms on the abiotic surface. Four clades of multidrug-resistant C. striatum spread in our hospitals possibly due to the acquisition of antimicrobial resistance genes.

Corynebacterium guaraldiae sp. nov.: a new species of Corynebacterium from human infections

Non-diphtheria Corynebacterium species (NDC) belonging to the human skin and mucosa microbiota are frequently neglected as contaminants. However, reports of human infections by Corynebacterium spp. have increased considerably in recent years. In this study, a group of six NDC isolates of urine (n = 5) and sebaceous cyst (n = 1) from two South American countries were identified at genus level or misidentified based on API® Coryne and genetic/molecular analyses. The 16S rRNA (99.09-99.56%) and rpoB (96.18-97.14%) gene sequence similarities of the isolates were higher when compared with Corynebacterium aurimucosum DSM 44532 T. Multilocus sequence analysis (MLSA) indicated that these six NDC isolates compose a distinctive phylogenetic clade. Genome-based taxonomic analysis with the whole-genome sequences was able to separate these six isolates from other known Corynebacterium type strains. Average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between closely related type strains and the six isolates were considerably lower than the currently recommended threshold values for species circumscription. Phylogenetic and genomic taxonomy analyses indicated these microorganisms as a novel Corynebacterium species, for which we formally propose the name Corynebacterium guaraldiae sp. nov. with isolate 13T (= CBAS 827T = CCBH 35012T) as type strain.

Prescription of Rifampicin for Staphylococcus aureus Infections Increased the Incidence of Corynebacterium striatum with Decreased Susceptibility to Rifampicin in a Hungarian Clinical Center

Several reports have suggested a role for Corynebacterium striatum as an opportunistic pathogen. The authors have conducted a retrospective study at the Clinical Center of the University of Szeged, Hungary, between 2012 and 2021 that revealed significantly increased rifampicin resistance in this species. This work aimed to investigate the reasons behind this phenomenon. The data were collected corresponding to the period between 1 January 2012 and 31 December 2021 at the Department of Medical Microbiology, University of Szeged. To characterize the resistance trends, the antibiotic resistance index was calculated for each antibiotic in use. Fourteen strains with different resistance patterns were further analyzed with Fourier-transform infrared spectroscopy using the IR Biotyper^®. The decline in C. striatum sensitivity to rifampicin seen during the COVID-19 pandemic may have been attributable to the use of Rifadin^® to treat concomitant Staphylococcus aureus infections. The fact that the IR Biotyper^® typing method revealed that the rifampicin-resistant C. striatum strains were closely related supports this hypothesis. The IR Biotyper^® infrared spectroscopy proved to be a modern and fast method to support effective antimicrobial stewardship programs.

Identification and Characterization of Corynaridin, a Novel Linaridin from Corynebacterium lactis

Genome analysis of Corynebacterium lactis revealed a bacteriocin gene cluster encoding a putative bacteriocin of the linaridin family of ribosomally synthesized and posttranslationally modified peptides (RiPPs). The locus harbors typical linaridin modification enzymes but lacks genes for a decarboxylase and methyltransferase, which is unusual for type B linaridins. Supernatants of Corynebacterium lactis RW3-42 showed antimicrobial activity against Corynebacterium glutamicum. Deletion of the precursor gene crdA clearly linked the antimicrobial activity of the producer strain to the identified gene cluster. Following purification, we observed potent activity of the peptide against Actinobacteria, mainly other members of the genus Corynebacterium, including the pathogenic species Corynebacterium striatum and Corynebacterium amycolatum. Also, low activity against some Firmicutes was observed, but there was no activity against Gram-negative species. The peptide is resilient towards heat but sensitive to proteolytic degradation by trypsin and proteinase K. Analysis by mass spectrometry indicates that corynaridin is processed by cleaving off the leader sequence at a conserved motif and posttranslationally modified by dehydration of all threonine and serin residues, resulting in a monoisotopic mass of 3,961.19 Da. Notably, time-kill kinetics and experiments using live biosensors to monitor membrane integrity suggest bactericidal activity that does not involve formation of pores in the cytoplasmic membrane. As Corynebacterium species are ubiquitous in nature and include important commensals and pathogens of mammalian organisms, secretion of bacteriocins by species of this genus could be a hitherto neglected trait with high relevance for intra- and interspecies competition and infection. IMPORTANCE Bacteriocins are antimicrobial peptides produced by bacteria to fend off competitors in ecological niches and are considered to be important factors influencing the composition of microbial communities. However, bacteriocin production by bacteria of the genus Corynebacterium has been a hitherto neglected trait, although its species are ubiquitous in nature and make up large parts of the microbiome of humans and animals. In this study, we describe and characterize a novel linaridin family bacteriocin from Corynebacterium lactis and show its narrow-spectrum activity, mainly against other actinobacteria. Moreover, we were able to extend the limited knowledge on linaridin bioactivity in general and for the first time describe the bactericidal activity of such a bacteriocin. Interestingly, the peptide, which was named corynaridin, appears bactericidal, but without formation of pores in the bacterial membrane.

Expanding the Bacterial Diversity of the Female Urinary Microbiome: Description of Eight New Corynebacterium Species

The genus Corynebacterium is frequently found in the female urinary microbiome (FUM). In-depth characterization of Corynebacterium at the species level has been barely exploited. During ongoing FUM research studies, eight strains (c8Ua_144^T, c8Ua_172^T, c8Ua_174^T, c8Ua_181^T, c9Ua_112^T, c19Ua_109^T, c19Ua_121^T, and c21Ua_68^T) isolated from urine samples of healthy women or diagnosed with overactive bladder could not be allocated to any valid Corynebacterium species. In this work, we aimed to characterize these strains based on a polyphasic approach. The strains were Gram stain positive, rod to coccoid shaped, nonmotile, catalase positive, and oxidase negative. Phylogenetic analysis based on 16S rRNA and rpoB gene sequences indicated that all strains belonged to the genus Corynebacterium. The average nucleotide identity and digital DNA-DNA hybridization values among the genomes of the above eight strains and closely related type strains of the Corynebacterium genus were <95 (74.1%-93.9%) and <70% (22.2%-56.5%), respectively. Mycolic acids were identified in all strains. MK-8(H2) and/or MK-9(H2) were identified as the major menaquinones. The polar lipids' pattern mostly consisted of diphosphatidylglycerol, phosphatidylglycerol, and glycophospholipids. The major fatty acid was C_18:1ω9c. Corynebacterium lehmanniae (c8Ua_144^T = DSM 113405^T = CCP 74^T), Corynebacterium meitnerae (c8Ua_172^T = DSM 113406^T = CCP 75^T), Corynebacterium evansiae (c8Ua_174^T = DSM 113407^T = CCP 76^T), Corynebacterium curieae (c8Ua_181^T = DSM 113408^T = CCP 77^T), Corynebacterium macclintockiae (c9Ua_112^T = DSM 113409^T = CCP 78^T), Corynebacterium hesseae (c19Ua_109^T = DSM 113410^T= CCP 79^T), Corynebacterium marquesiae (c19Ua_121^T = DSM 113411^T = CCP 80^T), and Corynebacterium yonathiae (c21Ua_68^T = DSM 113412^T = CCP 81^T) are proposed. This study evidenced that commonly used methodologies on FUM research presented limited resolution for discriminating Corynebacterium at the species level. Future research studying the biological mechanisms of the new Corynebacterium species here described may shed light on their possible beneficial role for healthy FUM.

'Targeting' the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets

Bacterial biofilms, often as multispecies communities, are recalcitrant to conventional antibiotics, making the treatment of biofilm infections a challenge. There is a push towards developing novel anti-biofilm approaches, such as antimicrobial peptides (AMPs), with activity against specific biofilm targets. In previous work, we developed Biofilm-AMP, a structural and functional repository of AMPs for biofilm studies (B-AMP v1.0) with more than 5000 structural models of AMPs and a vast library of AMP annotations to existing biofilm literature. In this study, we present an upgraded version of B-AMP, with a focus on existing and novel bacterial biofilm targets. B-AMP v2.0 hosts a curated collection of 2502 biofilm protein targets across 473 bacterial species, with structural protein models and functional annotations from PDB, UniProt, and PubMed databases. The biofilm targets can be searched for using the name of the source organism, and function and type of protein, and results include designated Target IDs (unique to B-AMP v2.0), UniProt IDs, 3D predicted protein structures, PDBQT files, pre-defined protein functions, and relevant scientific literature. To present an example of the combined applicability of both, the AMP and biofilm target libraries in the repository, we present two case studies. In the first case study, we expand an in silico pipeline to evaluate AMPs against a single biofilm target in the multidrug resistant, bacterial pathogen Corynebacterium striatum, using 3D protein-peptide docking models from previous work and Molecular Dynamics simulations (~1.2µs). In the second case study, we build an in silico pipeline to identify candidate AMPs (using AMPs with both anti-Gram positive and anti-Gram negative activity) against two biofilm targets with a common functional annotation in Pseudomonas aeruginosa and Staphylococcus aureus, widely-encountered bacterial co-pathogens. With its enhanced structural and functional capabilities, B-AMP v2.0 serves as a comprehensive resource for AMP investigations related to biofilm studies. B-AMP v2.0 is freely available at https://b-amp.karishmakaushiklab.com and will be regularly updated with structural models of AMPs and biofilm targets, as well as 3D protein-peptide interaction models for key biofilm-forming pathogens.

The microbiota in eosinophilic esophagitis: A systematic review

Eosinophilic esophagitis (EoE) is an atopic disease of the esophagus that has shown a significant increase in incidence and prevalence in the last 20 years. The etiology of EoE is unclear, and few studies explore the esophageal microbiota in EoE. The local microbiome has been implicated in the pathogenesis of several allergic and inflammatory diseases, such as asthma and eczema. In this study, we performed a systematic review to evaluate differences in the microbiota profile of patients with EoE compared with controls. MEDLINE, Embase, Cochrane Library, Scopus, and CINAHL (Cumulative Index to Nursing and Allied Health Literature) databases were searched to identify studies investigating the microbiota composition in EoE. Three reviewers screened the articles for eligibility and quality. Seven articles underwent full-text review, and a narrative synthesis was undertaken. The microbiota of the mouth and esophagus are correlated. Patients with active EoE present increased esophageal microbial load and increased abundance in particular species, such as Haemophilus and Aggregatibacter. On the other hand, EoE patients present a decrease in Firmicutes. High microbial load and abundance of Haemophilus are observed in EoE patients, but little evidence exists to demonstrate their influence on inflammation and disease. Understanding microbial signatures in EoE might contribute to the development of novel therapeutic strategies.

Corynebacterium striatum-Got Worse by a Pandemic?

The role of Corynebacterium striatum has been demonstrated in different nosocomial infections. An increasing number of publications have demonstrated its virulence in the respiratory tract, especially in the immunosuppressed patient population. The number of these patients has increased significantly during the COVID-19 pandemic. For this reason, we aimed to investigate the prevalence and antimicrobial resistance pattern of this species between 2012 and 2021 at the Clinical Center of the University of Szeged, Hungary. Altogether, 498 positive samples were included from 312 patients during the study period. On the isolates, 4529 antibiotic susceptibility tests were performed. Our data revealed that the prevalence of C. striatum increased during the COVID-19 pandemic, the rise occurred in respiratory, blood culture, and superficial samples. During the study period, the rifampicin resistance significantly increased, but others have also changed dynamically, including linezolid. The species occurred with diverse and changing co-pathogens in the COVID-19 era. However, the increasing rifampicin and linezolid resistance of C. striatum was probably not due to the most commonly isolated co-pathogens. Based on resistance predictions, vancomycin is likely to remain the only effective agent currently in use by 2030.

Corynebacterium striatum Bacteremia during SARS-CoV2 Infection: Case Report, Literature Review, and Clinical Considerations

Bacterial infections, especially those in hospital settings, represent a major complication of COVID-19 patients, complicating management and worsening clinical outcomes. Corynebacterium striatum is a non-diphtheric actinobacterium that has been reported as being the causative agent of several different infections, affecting both immunocompetent and immunocompromised patients. Recently, C. striatum has been recognized as a nosocomial pathogen that is responsible for severe infection in critical patients, as well as in fragile and immunocompromised subjects. C. striatum has been described as the etiological agent of bacteremia, central line infections, and endocarditis. We report a case of a 91-year-old woman who was hospitalized due to SARS-CoV-2 infection, who developed C. striatum bacteremia and died despite antimicrobial therapy and clinical efforts. Furthermore, we discuss C. striatum diagnosis and treatment based on evidence from the scientific literature.

Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of Genus Brevundimonas and Description of Brevundimonas pishanensis sp. nov

The genus Brevundimonas consists of Gram-negative bacteria widely distributed in environment and can cause human infections. However, the genomic characteristics and pathogenicity of Brevundimonas remain poorly studied. Here, the whole-genome features of 24 Brevundimonas type strains were described. Brevundimonas spp. had relatively small genomes (3.13 ± 0.29 Mb) within the family Caulobacteraceae but high G+C contents (67.01 ± 2.19 mol%). Two-dimensional hierarchical clustering divided those genomes into 5 major clades, in which clades II and V contained nine and five species, respectively. Interestingly, phylogenetic analysis showed a one-to-one match between core and accessory genomes, which suggested coevolution of species within the genus Brevundimonas. The unique genes were annotated to biological functions like catalytic activity, signaling and cellular processes, multisubstance metabolism, etc. The majority of Brevundimonas spp. harbored virulence-associated genes icl, tufA, kdsA, htpB, and acpXL, which encoded isocitrate lyase, elongation factor, 2-dehydro-3-deoxyphosphooctonate aldolase, heat shock protein, and acyl carrier protein, respectively. In addition, genomic islands (GIs) and phages/prophages were identified within the Brevundimonas genus. Importantly, a novel Brevundimonas species was identified from the feces of a patient (suffering from diarrhea) by the analyses of biochemical characteristics, phylogenetic tree of 16S rRNA gene, multilocus sequence analysis (MLSA) sequences, and genomic data. The name Brevundimonas pishanensis sp. nov. was proposed, with type strain CHPC 1.3453 (= GDMCC 1.2503^T= KCTC 82824^T). Brevundimonas spp. also showed obvious slow growth compared with that of Escherichia coli. Our study reveals insights into genomic characteristics and potential virulence-associated genes of Brevundimonas spp., and provides a basis for further intensive study of the pathogenicity of Brevundimonas.

IMPORTANCEBrevundimonas spp., a group of bacteria from the family Caulobacteraceae, is associated with nosocomial infections, deserve widespread attention. Our study elucidated genes potentially associated with the pathogenicity of the Brevundimonas genus. We also described some new characteristics of Brevundimonas spp., such as small chromosome size, high G+C content, and slow-growth phenotypes, which made the Brevundimonas genus a good model organism for in-depth studies of growth rate traits. Apart from the comparative analysis of the genomic features of the Brevundimonas genus, we also reported a novel Brevundimonas species, Brevundimonas pishanensis, from the feces of a patient with diarrhea. Our study promotes the understanding of the pathogenicity characteristics of Brevundimonas species bacteria.

The challenge of antibiotic selection in prosthetic joint infections due to Corynebacterium striatum: a case report

Background

Corynebacterium striatum is a gram-positive facultative anaerobe found in the environment and human flora that has historically been considered a contaminant. More recently, Corynebacterium striatum has been implicated in human infections, including respiratory infections, endocarditis, and bone and joint infections, particularly those involving hardware or implanted devices.

Case presentation

A 65-year-old man presented for washout of his left total knee arthroplasty following a revision 20 days prior. The patient underwent debridement of his left total knee and revision of the left total femur arthroplasty. Daptomycin was initiated empirically due to a previous rash from vancomycin. Operative tissue cultures grew Staphylococcus haemolyticus, Staphylococcus epidermidis and Corynebacterium striatum. Given concern for daptomycin resistance and the reliability of vancomycin susceptibility, daptomycin was discontinued and vancomycin initiated following a graded challenge. Within a few days, the patient developed a diffuse, blanching, erythematous, maculopapular rash and daptomycin was restarted. Over the next 72 h, his rash progressed and he met criteria for drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome. Daptomycin was stopped and oral linezolid initiated; rash improved. C. striatum returned with susceptibility to gentamicin, linezolid, vancomycin and daptomycin. Due to concern for adverse effects on long-term linezolid, daptomycin was restarted and was tolerated for 20 days, at which point purulent drainage from incision increased. The patient underwent another arthroplasty revision and washout. Operative cultures from this surgery were again positive for C. striatum. Repeat C. striatum susceptibilities revealed resistance to daptomycin but retained susceptibility to linezolid. Daptomycin was again changed to linezolid. He completed six weeks of linezolid followed by linezolid 600 mg daily for suppression and ultimately opted for disarticulation.

Conclusions

C. striatum has historically been regarded as a contaminant, particularly when grown in tissue culture in the setting of prosthetic joint infection. Based on the available literature and susceptibility patterns, the most appropriate first-line therapy is vancomycin or linezolid. Treatment with daptomycin should be avoided, even when isolates appear susceptible, due to the risk of development of high-level resistance (MIC > 256 µg/mL) and clinical failure.

ISPD peritonitis guideline recommendations: 2022 update on prevention and treatment

Peritoneal dialysis (PD)-associated peritonitis is a serious complication of PD and prevention and treatment of such is important in reducing patient morbidity and mortality. The ISPD 2022 updated recommendations have revised and clarified definitions for refractory peritonitis, relapsing peritonitis, peritonitis-associated catheter removal, PD-associated haemodialysis transfer, peritonitis-associated death and peritonitis-associated hospitalisation. New peritonitis categories and outcomes including pre-PD peritonitis, enteric peritonitis, catheter-related peritonitis and medical cure are defined. The new targets recommended for overall peritonitis rate should be no more than 0.40 episodes per year at risk and the percentage of patients free of peritonitis per unit time should be targeted at >80% per year. Revised recommendations regarding management of contamination of PD systems, antibiotic prophylaxis for invasive procedures and PD training and reassessment are included. New recommendations regarding management of modifiable peritonitis risk factors like domestic pets, hypokalaemia and histamine-2 receptor antagonists are highlighted. Updated recommendations regarding empirical antibiotic selection and dosage of antibiotics and also treatment of peritonitis due to specific microorganisms are made with new recommendation regarding adjunctive oral N-acetylcysteine therapy for mitigating aminoglycoside ototoxicity. Areas for future research in prevention and treatment of PD-related peritonitis are suggested.

Corynebacterium striatum thrombophlebitis: a nosocomial multidrug-resistant disease?

Introduction

Corynebacterium striatum is a non-Diphteriae commensal bacterium with a wide range of pathogenicity. The identification of multidrug-resistant (MDR) C. striatum is concerning because drug susceptibility testing is not usually performed in microbiology laboratories. There is no consensus yet on the treatment of septic thrombophlebitis in this situation.

Case report

We report here the first case of a quinquagenarian patient with a history of AIDS and fungic endocarditis, who was diagnosed with a nosocomial thrombophlebitis in the right jugular vein caused by C. striatum. Bitherapy with daptomycin for 12 days and linezolid for 23 days was combined with a therapeutic anticoagulant. The follow-up included weekly cervical ultrasound controls. The efficiency of the treatment and the stability of the lesions allowed us to alleviate the medication with a prophylactic dose of anticoagulant. The patient was discharged from hospital and showed no signs of recurrence after 12 months.

Conclusion

The lack of consensus relative to the management of septic thrombophlebitis precludes the validation of a specific treatment for the condition. Our results suggest that a combination that includes removal of the medical device is needed. A total of 6 weeks of antibiotherapy should be applied, starting with 2 weeks of vancomycin or a combination of antibiotitherapy with daptomycin in order to reduce the bacterial load and avoid resistance. Six weeks of anticoagulation therapy is effective.

Corynebacterium striatum cardiac device-related endocarditis: A case report

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Diagnosis of cardiac device-related endocarditis may be complex.

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Corynebacterium striatum has been increasingly associated with severe infections.

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Antimicrobial treatment is difficult, especially in the presence of resistance.

Corynebacterium striatum is an emerging Gram-positive bacillus associated with invasive infection in both immunocompetent and immunocompromised patients, especially associated with medical devices. Its ability to form biofilms has been demonstrated and it has been occasionally associated with cardiac device-related infective endocarditis with few cases described in literature. We report a case of C. striatum cardiac device-related infective endocarditis of complex management.

Time to positivity of Corynebacterium in blood culture: Characteristics and diagnostic performance

The presence of Corynebacterium in blood samples can indicate true bacteremia or contamination, thus complicating the diagnosis of true bacteremia. We aimed to evaluate the usefulness of time to positivity (TTP) in diagnosing true bacteremia and contamination in cases where Corynebacterium was isolated from blood samples. We compared the TTP of the true-bacteremia group (n = 77) with that of the contamination group (n = 88). For the true-bacteremia cases that had only one set of positive blood cultures (n = 14), considering clinical and bacteriological data, additional cultures were performed on blood or other specimens. The same Corynebacterium spp. as in blood were isolated from these specimens. Receiver operating characteristic curves were generated, and the sensitivity and specificity of TTP were calculated for diagnosing true bacteremia. The median TTP of the true-bacteremia group (26.8 h) was shorter than that of the contamination group (43.3 h) (P < 0.0001). When considering TTP ≤ 25.0 h as true bacteremia, the sensitivity and specificity were 44.2% and 95.5%, respectively. Moreover, when considering TTP ≤ 69.4 h as true bacteremia, the sensitivity and specificity were 96.1% and 20.5%, respectively. Among the true-bacteremia groups with one set of positive blood cultures (n = 14), no case exhibited a TTP > 69.4 h. Only three cases showed TTP ≤ 25.0 h in the true-bacteremia group with one set of positive blood cultures. TTP > 69.4 h is likely to indicate contamination and may be useful to exclude true bacteremia in cases with one set of positive blood cultures. Meanwhile, diagnosing true bacteremia using the threshold of TTP 25.0 h would be difficult. Therefore, the clinical and bacteriological data are important for diagnosing bacteremia, especially in cases with TTP ≤ 69.4 h.

AMPing Up the Search: A Structural and Functional Repository of Antimicrobial Peptides for Biofilm Studies, and a Case Study of Its Application to Corynebacterium striatum, an Emerging Pathogen

Antimicrobial peptides (AMPs) have been recognized for their ability to target processes important for biofilm formation. Given the vast array of AMPs, identifying potential anti-biofilm candidates remains a significant challenge, and prompts the need for preliminary in silico investigations prior to extensive in vitro and in vivo studies. We have developed Biofilm-AMP (B-AMP), a curated 3D structural and functional repository of AMPs relevant to biofilm studies. In its current version, B-AMP contains predicted 3D structural models of 5544 AMPs (from the DRAMP database) developed using a suite of molecular modeling tools. The repository supports a user-friendly search, using source, name, DRAMP ID, and PepID (unique to B-AMP). Further, AMPs are annotated to existing biofilm literature, consisting of a vast library of over 10,000 articles, enhancing the functional capabilities of B-AMP. To provide an example of the usability of B-AMP, we use the sortase C biofilm target of the emerging pathogen Corynebacterium striatum as a case study. For this, 100 structural AMP models from B-AMP were subject to in silico protein-peptide molecular docking against the catalytic site residues of the C. striatum sortase C protein. Based on docking scores and interacting residues, we suggest a preference scale using which candidate AMPs could be taken up for further in silico, in vitro and in vivo testing. The 3D protein-peptide interaction models and preference scale are available in B-AMP. B-AMP is a comprehensive structural and functional repository of AMPs, and will serve as a starting point for future studies exploring AMPs for biofilm studies. B-AMP is freely available to the community at https://b-amp.karishmakaushiklab.com and will be regularly updated with AMP structures, interaction models with potential biofilm targets, and annotations to biofilm literature.

Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS

Background

Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS).

Methods

A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis.

Results

A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL_B and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL_B and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples.

Conclusion

High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL_B and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.

Internal-Fixation Hardware Infection With Corynebacterium jeikeium

Corynebacterium is a rare cause of prosthetic joint infections (PJIs) and infection after fracture fixation (IAFF). We present a case of a patient who developed Corynebacterium jeikeium-associated IAFF three weeks after his fracture fixation. Due to its slow-growing nature, surgical cultures remained negative after 72 hours and grew only on day 5. We highlight that physicians should have Corynebacterium-associated infection in their differential in such cases, especially when the cultures remain negative after 72 hours. We also review the literature of PJI and implant-associated infection with C. jeikeium and discuss the antibiotic resistance patterns and some microbiological considerations associated with C. jeikeium.

Corynebacterium striatum Cardiac Device-Related Infective Endocarditis: The First Case Report in a Patient With a Cardiac Resynchronization Therapy Defibrillator Device and Review of the Literature

Corynebacterium striatum (C. striatum) is a skin commensal agent, rarely described as a cause of infective endocarditis. We describe a case of a 48-year-old man, with multiple comorbidities with cardiac resynchronization therapy defibrillator (CRT-D) device implanted 1 year before. A cardiac device-related infective endocarditis (CDRIE) due to C. striatum, with vegetations in the tricuspid valve adjacent to the electrode lead and concomitant lumbar spondylodiscitis were diagnosed. The patient was treated initially with a 6-week course of vancomycin with sterile blood cultures and reduction of inflammatory parameters. Surgery was refused at this stage. Six weeks later, he was readmitted due to C. striatum bacteriemia recurrence, with vegetations adhering to the electrode wire, being treated with daptomycin 10mg/kg body weight, after presenting renal toxicity to vancomycin. CRT-D device was removed with implantation of epicardial cardiac resynchronization therapy pacemaker (CRT-P). To our knowledge, this might be the first description of C. striatum CDRIE in a patient with a CRT-D. In the five cases described in the literature of CDRIE by this agent, early removal of the pacemaker was performed with good results. In this case, the device was removed only after failure of medical treatment alone.

Treat Me Well or Will Resist: Uptake of Mobile Genetic Elements Determine the Resistome of Corynebacterium striatum

Corynebacterium striatum, a bacterium that is part of the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and in-hospital and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. However, there are no studies about the genomic determinants related to antimicrobial resistance in C. striatum. This review updates global information related to antimicrobial resistance found in C. striatum and highlights the essential genomic aspects in its persistence and dissemination. The resistome of C. striatum comprises chromosomal and acquired elements. Resistance to fluoroquinolones and daptomycin are due to mutations in chromosomal genes. Conversely, resistance to macrolides, tetracyclines, phenicols, beta-lactams, and aminoglycosides are associated with mobile genomic elements such as plasmids and transposons. The presence and diversity of insertion sequences suggest an essential role in the expression of antimicrobial resistance genes (ARGs) in genomic rearrangements and their potential to transfer these elements to other pathogens. The present study underlines that the resistome of C. striatum is dynamic; it is in evident expansion and could be acting as a reservoir for ARGs.

Biofilm Formation and Antimicrobial Susceptibility of Non-Diphtheria Corynebacterium Strains Isolated from Blood Cultures: First Report from Turkey

Objective

Non-diphtheriae Corynebacterium strains have been recognized as important pathogens after decades of confusion regarding their microbiological classification and clinical significance. The aim of this study was to identify non-diphtheriae Corynebacterium strains and the prevalence of biofilm formation and antimicrobial resistance.

Method

In total, 126 non-diphtheriae Corynebacterium strains were isolated from blood cultures of inpatients with bacteremia in our hospital between January 2015 and January 2020. Blood cultures were analyzed with the Bactec-9120 system. Strains were identified using MALDI-TOF MS (Bruker Daltonics, Germany). Antimicrobial susceptibilities were determined using the Kirby-Bauer disk diffusion method on a Mueller-Hinton agar and evaluated according to EUCAST standards. Biofilm formation was assessed with the Congo Red Agar method.

Results

Corynebacterium striatum and Corynebacterium matruchotii were the most prevalent with 29 and 26 isolates, respectively. Biofilm production was detected in 62.06% (18/29) of C. striatum, in 53.8% (14/26) of C. matruchotii, in 50% (9/18) of Corynebacterium afermentans, 50% (6/12) of Corynebacterium amycolatum, and in 46% (7/15) of Corynebacterium jeikeium strains. Among the five most prevalent strains, we found a high biofilm rate of 54%. The resistance rates to penicillin, clindamycin, ciprofloxacin, rifampicin, tetracycline, and gentamicin were 91.2%, 87.3%, 79.3%, 56.3%, 45.2%, and 39.6%, respectively. All 126 strains were susceptible to vancomycin and linezolid.

Conclusion

Non-diphtheriae Corynebacterium strains isolated from blood cultures of hospitalized patients with bacteremia may have multidrug resistance and the ability to produce biofilm. These results emphasize the importance of identifying strains and determining their antimicrobial susceptibility and biofilm production potential.

Antimicrobial treatment of Corynebacterium striatum invasive infections: a systematic review

The aim of this study was to establish an evidence-based guideline for the antibiotic treatment of Corynebacterium striatum infections. Several electronic databases were systematically searched for clinical trials, observational studies or individual cases on patients of any age and gender with systemic inflammatory response syndrome, harboring C. striatum isolated from body fluids or tissues in which it is not normally present. C. striatum had to be identified as the only causative agent of the invasive infection, and its isolation from blood, body fluids or tissues had to be confirmed by one of the more advanced diagnostic methods (biochemical methods, mass spectrometry and/or gene sequencing). This systematic review included 42 studies that analyzed 85 individual cases with various invasive infections caused by C. striatum. More than one isolate of C. striatum exhibited 100% susceptibility to vancomycin, linezolid, teicoplanin, piperacillin-tazobactam, amoxicillin-clavulanate and cefuroxime. On the other hand, some strains of this bacterium showed a high degree of resistance to fluoroquinolones, to the majority majority of β-lactams, aminoglycosides, macrolides, lincosamides and cotrimoxazole. Despite the antibiotic treatment, fatal outcomes were reported in almost 20% of the patients included in this study. Gene sequencing methods should be the gold standard for the identification of C. striatum, while MALDI-TOF and the Vitek system can be used as alternative methods. Vancomycin should be used as the antibiotic of choice for the treatment of C. striatum infections, in monotherapy or in combination with piperacillin-tazobactam. Alternatively, linezolid, teicoplanin or daptomycin may be used in severe infections, while amoxicillin-clavulanate may be used to treat mild infections caused by C. striatum.

Clinical characteristics of Corynebacterium simulans

Corynebacterium simulans was first reported in 2000. Its characteristics such as isolation frequency, specimen types, and antimicrobial susceptibilities are poorly understood, because identification is difficult using conventional methods. We performed a retrospective observational study of 13 and 317 strains of C. simulans and C. striatum, respectively, isolated from consecutive patients at Nagoya University Hospital from January 2017 to December 2018. We analyzed patients' backgrounds, types of specimens, and antimicrobial susceptibilities. Antimicrobial susceptibilities were compared with those of C. striatum. The frequencies of isolation of C. simulans and C. striatum were 3.9% and 96%, respectively. C. simulans was not detected in specimens associated with mucous membranes, such as sputum and secretions from the craniocervical region, which were frequent for C. striatum. C. simulans was mainly detected in the skin (61.5%). All C. simulans isolates were susceptible to anti-MRSA drugs, as well as to numerous other antibiotics, including those that are orally administered. For example, C. simulans was significantly more susceptible to penicillin G, ceftriaxone, and ciprofloxacin than C. striatum (respective susceptibilities: 66.7% vs 5.4%, 50.0% vs 4.0%, 66.7% vs 5.9%). There was no significant difference between meropenem and erythromycin, although susceptibility to each was relatively high (100.0% vs 31.7%, 50.0% vs 11.9%). C. simulans was susceptible to numerous orally administered antibiotics and more susceptible to antimicrobial drugs than C. striatum. C. simulans was detected less frequently than C. striatum and was infrequently detected in specimens associated with mucous membranes. These characteristics will aid the selection of optimal antimicrobial therapies.

Evaluating the Rapid Emergence of Daptomycin Resistance in Corynebacterium: a Multicenter Study

Members of the genus Corynebacterium are increasingly recognized as pathobionts and can be very resistant to antimicrobial agents. Previous studies have demonstrated that Corynebacterium striatum can rapidly develop high-level daptomycin resistance (HLDR) (MIC, ≥256 μg/ml). Here, we conducted a multicenter study to assay for this in vitro phenotype in diverse Corynebacterium species. Corynebacterium clinical isolates (n = 157) from four medical centers were evaluated. MIC values to daptomycin, vancomycin, and telavancin were determined before and after overnight exposure to daptomycin to identify isolates able to rapidly develop daptomycin nonsusceptibility. To investigate assay reproducibility, 18 isolates were evaluated at three study sites. In addition, the stability of daptomycin nonsusceptibility was tested using repeated subculture without selective pressure. The impact of different medium brands was also investigated. Daptomycin nonsusceptibility emerged in 12 of 23 species evaluated in this study (C. afermentans, C. amycolatum, C. aurimucosum, C. bovis, C. jeikeium, C. macginleyi, C. pseudodiphtheriticum, C. resistens, C. simulans, C. striatum, C. tuberculostearicum, and C. ulcerans) and was detected in 50 of 157 (31.8%) isolates tested. All isolates displayed low (susceptible) MIC values to vancomycin and telavancin before and after daptomycin exposure. Repeated subculture demonstrated that 2 of 9 isolates (22.2%) exhibiting HLDR reverted to a susceptible phenotype. Of 30 isolates tested on three medium brands, 13 (43.3%) had differences in daptomycin MIC values between brands. Multiple Corynebacterium species can rapidly develop daptomycin nonsusceptibility, including HLDR, after a short daptomycin exposure period.

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.

Alteration of Gut Microbiota After Antibiotic Exposure in Finishing Swine

Subclinical doses of antimicrobials are commonly used in the swine industry to control infectious diseases and growth performance. Accumulating evidence suggests that swine administered with antibiotics are susceptible to disease development due to disruption of the beneficial gut microbial community, which is associated with host immune regulation, nutrient digestion, and colonization resistance against pathogens. In this study, we found that finishing swine administered with lincomycin showed gut dysbiosis and increased diarrhea incidence compared with control swine. 16S rRNA amplicon sequencing was used to analyze the gut microbiota in finishing swine administered with lincomycin. The relative abundance of detrimental microbes, such as species of Clostridium, Aerococcus, Escherichia-Shigella, and Corynebacterium was increased in the feces of lincomycin-administered finishing swine, but that of bacteria associated with fiber degradation, such as species of Treponema, Succinivibrio, Fibrobacter, and Cellulosilyticum was decreased. Moreover, administration of lincomycin significantly increased the enrichment of metabolic pathways related to pathogenicity and deficiency of polysaccharide degradation. These results suggest that lincomycin treatment could cause severe disruption of the commensal microbiota in finishing swine.

Infective Endocarditis Due to Corynebacterium Species: Clinical Features and Antibiotic Resistance

Background

Corynebacterium species are often dismissed as contaminants in blood cultures, but they can also cause infective endocarditis (IE), which is a severe condition. Antibiotic resistance of corynebacteria is increasing making treatment challenging. Reports on IE caused by Corynebacterium species are scarce and more knowledge is needed.

Methods

Cases of IE caused by Corynebacterium species were identified through the Swedish Registry of Infective Endocarditis. Isolates were collected for species redetermination by matrix-assisted laser desorption ionization-time of flight and for antibiotic susceptibility testing using Etests.

Results

Thirty episodes of IE due to Corynebacterium species were identified between 2008 and 2017. The median age of patients was 71 years (interquartile range, 60–76) and 77% were male. Corynebacterium striatum (n = 11) was the most common IE causing pathogen followed by Corynebacterium jeikeium (n = 5). Surgery was performed in 50% and in-hospital mortality rate was 13%. Patients with IE caused by Corynebacterium species were significantly more likely to have prosthetic valve endocarditis (70%), compared with patients with IE due to Staphylococcus aureus or non-beta-hemolytic streptococci (14% and 26%, respectively) (P < .0001). Vancomycin was active towards all Corynebacterium isolates, whereas resistance towards penicillin G was common.

Conclusions

Corynebacterium species cause IE, where prosthetic valves are mainly affected and surgery is often performed. Corynebacterium striatum is an important causative agent of IE within the genus. Antibiotic resistance of corynebacteria is relatively common but resistance towards vancomycin could not be detected in vitro.

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.

Corynebacterium striatum meningitis combined with suspected brain and lung abscesses: a case report and review

Background

Intracranial infections with Corynebacterium striatum (C. striatum) have been described sporadically in the literature over the last two decades. However, C. striatum meningitis combined with multiple abscesses has not been published before.

Case presentation

In this report, we describe the clinical and imaging findings in a 54-year-old woman with meningitis caused by C. striatum and combined with suspected brain and lung abscesses. This patient who underwent multiple fractures and a recent cut presented with headache and paraphasia. C. striatum was isolated in cerebrospinal fluid and supposedly transmitted from the skin purulent wound through blood. The patient was treated with intravenous vancomycin and had a transient improvement, but died finally. Multiple abscesses, especially in the brain, could be a reason to explain her conditions were deteriorating rapidly.

Conclusions

Note that C. striatum can cause life-threatening infections. Early identification and diagnosis, early administration of antibiotics to which the bacterium is susceptible, and treatment of complications will be beneficial in patients with C. striatum-related infection.

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.

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.

Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods

Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often are resistant to antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates are low, ca. 1-2 %, the overall increase in the sheer number of joint replacement surgeries results in an increase in patients at risk.Aims. This study investigates the consensus of microbial species comprising PJI ecology, which is currently lacking.Methodology. In this study, PJI populations from seven patients were analysed using combined culturing and whole-genome shotgun sequencing (WGSS) to establish population profiles and compare WGSS and culture methods for detection and identification of the PJI microbiome.Results. WGSS detected strains when culture did not, notably dormant, culture-resistant and rare microbes. The CosmosID algorithm was used to predict micro-organisms present in the PJI and discriminate contaminants. However, culturing indicated the presence of microbes falling below the WGSS algorithm threshold. In these instances, microbes cultured are believed to be minor species. The two strategies were combined to build a population profile.Conclusions. Variability between and among PJIs showed that most infections were distinct and unique. Comparative analysis of populations revealed PJIs to form clusters that were related to, but separate from, vaginal, skin and gut microbiomes. Fungi and protists were detected by WGSS, but the role of fungi is just beginning to be understood and for protists it is unknown. These micro-organisms and their novel and strain-specific microbial interactions remain to be determined in current clinical tests.