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.

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.

806. Uncluttering Case Clusters: Use of Rapid Sequencing to Exclude Transmission Events

Background Newly identified multi-drug resistant organisms (MDRO) isolated from hospitalized patients with shared epidemiological characteristics can either represent transmission events or independent, unrelated acquisitions. Whole genome sequencing (WGS) can improve the efficiency of investigations triggered by MDRO cases with apparent epidemiological linkages by early exclusion of clonality. We report an implementation of WGS to investigate a cluster of methicillin-resistant Staphylococcus aureus (MRSA) and a cluster of carbapenem-resistant Enterobacterales (CRE) inpatient nosocomial infections. Methods Study participants included five Neonatal ICU (NICU) patients with nosocomial MRSA isolates recovered between June and August 2020, and two Respiratory Acute Care Unit (RACU) patients with nosocomial CRE infections in October 2020. Routine unit surveillance activities and characterization using standard epidemiologic criteria identified the isolates as nosocomial to their respective unit. The isolates then underwent WGS and single nucleotide polymorphism (SNP)-based relatedness analysis. Results The MRSA cluster included five neonates with either clinical or surveillance isolates. WGS identified one of the five isolates as methicillin susceptible S. aureus due to the absence of the mecA or mecC resistance gene, despite growth on chromogenic MRSA screening agar. WGS revealed each of the five isolates as belonging to a distinct multi locus sequence type (MLST) group with thousands of SNP differences between samples. The CRE cluster included two patients with Klebsiella pneumoniae isolated from clinical cultures within five days of each other with identical antimicrobial susceptibility profiles. WGS of the two isolates revealed that they belonged to different MLSTs and had tens of thousands of differing SNPs. WGS results suggest that a nosocomial transmission linking these infections was highly unlikely. For both investigations, WGS returned results within thirty-six hours of sample receipt. Figure 1. Corynebacterium striatum Respiratory Cultures January 2020-February 2021 Panel showing single nucleotide polymorphism (SNP) differences between isolates for respective clusters. Conclusion Apparent transmission events can be resource intensive to investigate and manage. The application of rapid WGS allowed for early discontinuation of cluster investigations and conservation of resources. Disclosures Virginia M. Pierce, MD, UpToDate, Inc. (Other Financial or Material Support, Author) Mohamad Sater, PhD, Day Zero Diagnostics (Employee, Shareholder) Miriam Huntley, PhD, Day Zero Diagnostics (Employee, Shareholder) Ian Herriott, BS, Day Zero Diagnostics (Employee, Shareholder) Tim Farrell, MS, Day Zero Diagnostics, Inc. (Employee, Shareholder) David C. Rosenberg, MD, Cepheid Diagnostics (Consultant)Day Zero Diagnostics (Consultant)SeLux Diagnostics (Consultant) Erica S. Shenoy, MD, PhD, Vertex Pharmaceuticals (Individual(s) Involved: Self): I gave a single lecture in 3/2020 for which I received financial compensation, Other Financial or Material Support

802. Corynebacterium striatum Outbreak Among Ventilated COVID-19 Patients in an Acute Care Hospital – California, 2021

Background Corynebacterium striatum (CS), a common human commensal colonizing the skin and nasopharynx, has been associated with nosocomial infections in immunocompromised and chronically ill patients. During the winter 2020-2021 COVID-19 surge, a 420-bed California hospital reported a marked increase in CS respiratory cultures among ventilated COVID-19 patients. We conducted a public health investigation to assess and mitigate nosocomial transmission and contributing infection prevention and control (IPC) practices. Methods A case was defined as a patient with CS in respiratory cultures from January 1, 2020 - February 28, 2021. We reviewed clinical characteristics on a subset of cases in 2021 and IPC practices in affected hospital locations. CS respiratory isolates collected on different dates and locations were assessed for relatedness by whole genome sequencing (WGS) on MiSeq. Results Eighty-three cases were identified, including 75 among COVID-19 patients (Figure 1). Among 62 patients identified in 2021, all were ventilated; 58 also had COVID-19, including 4 cases identified on point prevalence survey (PPS). The median time from admission to CS culture was 19 days (range, 0-60). Patients were critically ill; often it was unclear whether CS cultures represented colonization or infection. During the COVID-19 surge, two hospital wings (7W and 7S) were converted to negative-pressure COVID-19 units. Staff donned and doffed personal protective equipment in anterooms outside the units; extended use of gowns was practiced, and lapses in glove changes and hand hygiene (HH) between patients likely occurred. In response to the CS outbreak, patients were placed in Contact precautions and cohorted. Staff were re-educated on IPC for COVID-19 patients. Gowns were changed between CS patients. Subsequent PPS were negative. Two CS clusters were identified by WGS: cluster 1 (5 cases) in unit 7W, and cluster 2 (2 cases) in unit 7S (Figure 2). Figure 1. Corynebacterium striatum Respiratory Cultures January 2020-February 2021 Figure 2. Phylogenetic Tree Corynebacterium striatum Isolates Conclusion A surge in patients, extended use of gowns and lapses in core IPC practices including HH and environmental cleaning and disinfection during the winter 2020-2021 COVID-19 surge likely contributed to this CS outbreak. WGS provides supportive evidence for nosocomial CS transmission among critically ill COVID-19 patients. Disclosures All Authors: No reported disclosures

Wide spread and diversity of mutation in the gyrA gene of quinolone-resistant Corynebacterium striatum strains isolated from three tertiary hospitals in China

Background Corynebacterium striatum was confirmed to be an important opportunistic pathogen, which could lead to multiple-site infections and presented high prevalence of multidrug resistance, particularly to quinolone antibiotics. This study aimed to investigate the mechanism underlying resistance to quinolones and the epidemiological features of 410 quinolone-resistant C. striatum clinical strains isolated from three tertiary hospitals in China. Methods A total of 410 C. striatum clinical strains were isolated from different clinical samples of patients admitted to three tertiary teaching hospitals in China. Antibiotic susceptibility testing was performed using the microdilution broth method and pulsed-field gel electrophoresis (PFGE) was used for genotyping. Gene sequencing was used to identify possible mutations in the quinolone resistance-determining regions (QRDRs) of gyrA. Results In total, 410 C. striatum isolates were sensitive to vancomycin, linezolid, and daptomycin but resistant to ciprofloxacin. Depending on the antibiotic susceptibility testing results of 12 antimicrobial agents, the 410 C. striatum strains were classified into 12 resistant biotypes; of these, the three biotypes R1, R2, and R3 were dominant and accounted for 47.3% (194/410), 21.0% (86/410), and 23.2% (95/410) of the resistant biotypes, respectively. Mutations in the QRDRs ofgyrA were detected in all quinolone-resistant C. striatum isolates, and 97.3% of the isolates (399/410) showed double mutations in codons 87 and 91 of the QRDRs of gyrA. Ser-87 to Phe-87 and Asp-91 to Ala-91 double mutation in C. striatum was the most prevalent and accounted for 72.2% (296/410) of all mutations. Four new mutations in gyrA were identified in this study; these included Ser-87 to Tyr-87 and Asp-91 to Ala-91 (double mutation, 101 isolates); Ser-87 to Val-87 and Asp-91 toGly-91 (double mutation, one isolate); Ser-87 to Val-87 and Asp-91 to Ala-91 (double mutation, one isolate); and Ser-87 to Ile-87 (single mutation, one isolate). The minimum inhibitory concentration of ciprofloxacin for isolates with double (96.5%; 385/399) and single (72.7%; 8/11) mutations was high (≥ 32 µg/mL). Based on the PFGE typing results, 101 randomly selected C. striatum strains were classified into 50 genotypes (T01-T50), including the three multidrug-resistant epidemic clones T02, T06, and T28; these accounted for 14.9% (15/101), 5.9% (6/101), and 11.9% (12/101) of all genotypes, respectively. The multidrug-resistant T02 clone was identified in hospitals A and C and persisted from 2016 to 2018. Three outbreaks resulting from the T02, T06, and T28 clones were observed among intensive care unit (ICU) patients in hospital C between April and May 2019. Conclusions Quinolone-resistant C. striatum isolates showed a high prevalence of multidrug resistance. Point mutations in the QRDRs of gyrA conferred quinolone resistance to C. striatum, and several mutations in gyrA were newly found in this study. The great clonal diversity, high-level quinolone resistance and increased prevalence among patients susceptible to C. striatum isolates deserve more attention in the future. Moreover, more thorough investigation of the relationship between quinolone exposure and resistance evolution in C. striatum is necessary.

Culturomics Approach to Identify Diabetic Foot Infection Bacteria

The main goal of the study was to evaluate the usefulness of the culturomics approach in the reflection of diabetic foot infections (DFIs) microbial compositions in Poland. Superficial swab samples of 16 diabetic foot infection patients (Provincial Polyclinical Hospital in Toruń, Poland) were subjected to culturing using 10 different types of media followed by the identification via the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Biotyper platform. Identified 204 bacterial isolates representing 18 different species—mostly Enterococcus faecalis (63%) and Staphylococcus aureus (44%). Most of the infections (81%) demonstrated a polymicrobial character. Great differences in the species coverage, the number of isolated Gram-positive and Gram-negative bacteria, and the efficiency of the microbial composition reflection between the investigated media were revealed. The use of commonly recommended blood agar allowed to reveal only 53% of the entire microbial composition of the diabetic foot infection samples, which considerably improved when the chromagar orientation and vancomycin-resistant enterococi agar were applied. In general, efficiency increased in the following order: selective < universal < enriched < differential media. Performed analysis also revealed the impact of the culture media composition on the molecular profiles of some bacterial species, such as Corynebacterium striatum, Proteus mirabilis or Morganella morganii that contributed to the differences in the identification quality. Our results indicated that the culturomics approach can significantly improve the accuracy of the reflection of the diabetic foot infections microbial compositions as long as an appropriate media set is selected. The chromagar orientation and vancomycin-resistant enterococi agar media which were used for the first time to study diabetic foot infection microbial profiles demonstrate the highest utility in the culturomics approach and should be included in further studies directed to find a faster and more reliable diabetic foot infection diagnostic tool.

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.

Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

Background: Accurate identification of primary pathogens in foot infections remains challenging due to the diverse microbiome. Conventional culture may show false-positive or false-negative growth, leading to ineffective postoperative antibiotic treatment. Next-generation sequencing (NGS) has been explored as an alternative to standard culture in orthopedic infections. NGS is highly sensitive and can detect an entire bacterial genome along with genes conferring antibiotic resistance in a given sample. We investigated the potential use of NGS for accurate identification and quantification of microbes in infected diabetic foot ulcer (DFU). We hypothesize that NGS will aid identification of dominant pathogen and provide a more complete profile of microorganisms in infected DFUs compared to the standard culture method. Methods: Data were prospectively collected from 30 infected DFU patients who underwent operative treatment by a fellowship-trained orthopedic foot and ankle surgeon from October 2018 to September 2019. The average age of the patient was 60.4 years. Operative procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-the-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Concordance between the standard culture and NGS was assessed. Results: In 29 of 30 patients, pathogens were identified by both NGS and culture, with a concordance rate of 70%. In standard culture, Staphylococcus aureus (58.6%) was the most common pathogen, followed by coagulase-negative Staphylococcus (24.1%), Corynebacterium striatum (17.2%), and Enterococcus faecalis (17.2%). In NGS, Finegoldia magna (44.8%) was the most common microorganism followed by S. aureus (41.4%), and Anaerococcus vaginalis (24.1%). On average, NGS revealed 5.1 (range, 1-11) pathogens in a given sample, whereas culture revealed 2.6 (range, 1-6) pathogens. Conclusion: NGS is an emerging molecular diagnostic method of microbial identification in orthopedic infection. It frequently provides different profiles of microorganisms along with antibiotic-resistant gene information compared to conventional culture in polymicrobial foot infection. Clinical use of NGS for management of foot and ankle infections warrants further investigation. Level of Evidence: Level II, diagnostic study.